Topic Editors

Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Science, Zhejiang University, Hangzhou 310058, China
Dr. Linghui Qian
Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Cancer Center, Zhejiang University, Hangzhou 310058, China
College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China

Biomarker Development and Application

Abstract submission deadline
closed (31 October 2023)
Manuscript submission deadline
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Topic Information

Dear Colleagues,

Biomarkers are critical to the precise disease diagnosis, rational design of medical therapeutics, drug discovery and development, etc. For biomarkers to assume their rightful role, information related to the mechanism of disease progression, strategies for therapeutic intervention, requirements for biomarker selection and validation, and validation and application of biomarker assay methods are needed. This Special Issue aims to give an overview of the latest advances in biomarker detection and application. Potential topics include but are not limited to:

  • biomarker selection and validation
  • biomarker assay
  • biomarker validation and application

Dr. Sheng Cai
Dr. Linghui Qian
Prof. Dr. Su Zeng
Prof. Dr. Xin Su
Topic Editors

Keywords

  • biomarker selection
  • biomarker assay
  • biomarker application

Participating Journals

Journal Name Impact Factor CiteScore Launched Year First Decision (median) APC
Biomedicines
biomedicines
4.7 3.7 2013 15.4 Days CHF 2600
Cancers
cancers
5.2 7.4 2009 17.9 Days CHF 2900
Diagnostics
diagnostics
3.6 3.6 2011 20.7 Days CHF 2600
Journal of Clinical Medicine
jcm
3.9 5.4 2012 17.9 Days CHF 2600
Metabolites
metabolites
4.1 5.3 2011 13.2 Days CHF 2700

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Published Papers (48 papers)

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10 pages, 1618 KiB  
Article
In-Vitro Effects of Perfluorooctanoic Acid on Human Sperm Function: What Are the Clinical Consequences?
by Angela Alamo, Sandro La Vignera, Laura M. Mogioì, Andrea Crafa, Federica Barbagallo, Rossella Cannarella, Antonio Aversa, Aldo E. Calogero and Rosita A. Condorelli
J. Clin. Med. 2024, 13(8), 2201; https://doi.org/10.3390/jcm13082201 - 11 Apr 2024
Viewed by 160
Abstract
Background: Lifestyle and environmental pollution harm male fertility. Perfluoroalkyl substances (PFAS) are bio-accumulates in the environment as well as in several human tissues, and one of the most common PFAS is perfluorooctanoic acid (PFOA). Therefore, this study aimed to evaluate the in [...] Read more.
Background: Lifestyle and environmental pollution harm male fertility. Perfluoroalkyl substances (PFAS) are bio-accumulates in the environment as well as in several human tissues, and one of the most common PFAS is perfluorooctanoic acid (PFOA). Therefore, this study aimed to evaluate the in vitro effects of PFOA with hydrophobic and waterproofing properties on motility and bio-functional sperm parameters. Methods: To accomplish this, 50 healthy men with normozoospermia and not exposed to high doses of PFAS were enrolled. Their spermatozoa were incubated for 3 h with increasing concentrations of PFOA (0, 0.01, 0.1, and 1 mM) to evaluate its effects. In particular, we evaluated the effects of PFOA on total and progressive sperm motility and, by flow cytometry, on the following bio-functional sperm parameters: degree of chromatin compactness, viability, early and late apoptosis, mitochondrial membrane potential, the degree of lipoperoxidation, and concentrations of mitochondrial superoxide anion. Results: The results showed that PFOA decreased both total and progressive sperm motility, impaired chromatin compactness, and increased sperm lipid peroxidation and mitochondrial superoxide anion levels. Conclusions: This study showed that PFOA alters several sperm parameters and thus it may play a negative role in male fertility. Full article
(This article belongs to the Topic Biomarker Development and Application)
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12 pages, 3852 KiB  
Article
Glioblastoma and Internal Carotid Artery Calcium Score: A Possible Novel Prognostic Partnership?
by Francesco Pasqualetti, Michela Gabelloni, Lorenzo Faggioni, Giovanni Donato Aquaro, Fabrizio De Vietro, Vincenzo Mendola, Nicola Spina, Jessica Frey, Nicola Montemurro, Martina Cantarella, Mario Caccese, Giovanni Gadducci, Noemi Giannini, Silvia Valenti, Riccardo Morganti, Tamara Ius, Maria Caffo, Giuseppe Vergaro, Mirco Cosottini, Antonio Giuseppe Naccarato, Giuseppe Lombardi, Guido Bocci, Emanuele Neri and Fabiola Paiaradd Show full author list remove Hide full author list
J. Clin. Med. 2024, 13(5), 1512; https://doi.org/10.3390/jcm13051512 - 06 Mar 2024
Viewed by 462
Abstract
Purpose: Clinical evidence suggests an association between comorbidities and outcome in patients with glioblastoma (GBM). We hypothesised that the internal carotid artery (ICA) calcium score could represent a promising prognostic biomarker in a competing risk analysis in patients diagnosed with GBM. Methods: We [...] Read more.
Purpose: Clinical evidence suggests an association between comorbidities and outcome in patients with glioblastoma (GBM). We hypothesised that the internal carotid artery (ICA) calcium score could represent a promising prognostic biomarker in a competing risk analysis in patients diagnosed with GBM. Methods: We validated the use of the ICA calcium score as a surrogate marker of the coronary calcium score in 32 patients with lung cancer. Subsequently, we assessed the impact of the ICA calcium score on overall survival in GBM patients treated with radio-chemotherapy. Results: We analysed 50 GBM patients. At the univariate analysis, methyl-guanine-methyltransferase gene (MGMT) promoter methylation (p = 0.048), gross total tumour resection (p = 0.017), and calcium score (p = 0.011) were significant prognostic predictors in patients with GBM. These three variables also maintained statistical significance in the multivariate analysis. Conclusions: the ICA calcium score could be a promising prognostic biomarker in GBM patients. Full article
(This article belongs to the Topic Biomarker Development and Application)
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13 pages, 1859 KiB  
Article
Fibroblast Activation Protein (FAP)-Mediated Cleavage of Type III Collagen Reveals Serum Biomarker Potential in Non-Small Cell Lung Cancer and Spondyloarthritis
by Rasmus S. Pedersen, Jeppe Thorlacius-Ussing, Maria G. Raimondo, Lasse L. Langholm, Georg Schett, Andreas Ramming, Morten Karsdal and Nicholas Willumsen
Biomedicines 2024, 12(3), 545; https://doi.org/10.3390/biomedicines12030545 - 29 Feb 2024
Viewed by 788
Abstract
Fibroblast activation protein (FAP) is a known promoter of tumor development and is associated with poor clinical outcome for various cancer types. Being specifically expressed in pathological conditions including multiple types of fibrosis and cancers, FAP is an optimal target for diagnostics and [...] Read more.
Fibroblast activation protein (FAP) is a known promoter of tumor development and is associated with poor clinical outcome for various cancer types. Being specifically expressed in pathological conditions including multiple types of fibrosis and cancers, FAP is an optimal target for diagnostics and treatment. Treatment strategies utilizing the unique proteolytic activity of FAP are emerging, thus emphasizing the importance of biomarkers to directly assess FAP activity. FAP is a type II transmembrane serine protease that has been shown to cleave collagens and other ECM components. In this study, we developed an ELISA assay (C3F) targeting a circulating type III collagen fragment derived from FAP cleavage to reflect FAP activity. We demonstrated that C3F was specific to the neoepitope of the cleavage site and that the fragment was generated through FAP cleavage of type III collagen. We measured C3F in serum from a cohort of patients with non-small cell lung cancer (NSCLC) (n = 109) matched to healthy subjects (n = 42) and a cohort of patients with spondyloarthritis (SpA) (n = 17) matched to healthy subjects (n = 19). We found that C3F was significantly elevated in patients with NSCLC and in patients with SpA compared to healthy controls (p < 0.0001 and p = 0.0015, respectively). These findings suggest that C3F is a promising non-invasive biomarker reflecting FAP activity, which may aid in understanding tumor heterogeneity and potentially FAP-targeted therapies. Full article
(This article belongs to the Topic Biomarker Development and Application)
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14 pages, 2460 KiB  
Article
Diagnostic and Prognostic Performance of Metabolic Signatures in Pancreatic Ductal Adenocarcinoma: The Clinical Application of Quantitative NextGen Mass Spectrometry
by Paulo D’Amora, Ismael D. C. G. Silva, Steven S. Evans, Adam J. Nagourney, Katharine A. Kirby, Brett Herrmann, Daniela Cavalheiro, Federico R. Francisco, Paula J. Bernard and Robert A. Nagourney
Metabolites 2024, 14(3), 148; https://doi.org/10.3390/metabo14030148 - 29 Feb 2024
Viewed by 3225
Abstract
With 64,050 new diagnoses and 50,550 deaths in the US in 2023, pancreatic ductal adenocarcinoma (PDAC) is among the most lethal of all human malignancies. Early detection and improved prognostication remain critical unmet needs. We applied next-generation metabolomics, using quantitative tandem mass spectrometry [...] Read more.
With 64,050 new diagnoses and 50,550 deaths in the US in 2023, pancreatic ductal adenocarcinoma (PDAC) is among the most lethal of all human malignancies. Early detection and improved prognostication remain critical unmet needs. We applied next-generation metabolomics, using quantitative tandem mass spectrometry on plasma, to develop biochemical signatures that identify PDAC. We first compared plasma from 10 PDAC patients to 169 samples from healthy controls. Using metabolomic algorithms and machine learning, we identified ratios that incorporate amino acids, biogenic amines, lysophosphatidylcholines, phosphatidylcholines and acylcarnitines that distinguished PDAC from normal controls. A confirmatory analysis then applied the algorithms to 30 PDACs compared with 60 age- and sex-matched controls. Metabolic signatures were then analyzed to compare survival, measured in months, from date of diagnosis to date of death that identified metabolite ratios that stratified PDACs into distinct survival groups. The results suggest that metabolic signatures could provide PDAC diagnoses earlier than tumor markers or radiographic measures and offer insights into disease severity that could allow more judicious use of therapy by stratifying patients into metabolic-risk subgroups. Full article
(This article belongs to the Topic Biomarker Development and Application)
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10 pages, 243 KiB  
Article
ABO Blood Groups, RhD Factor and Their Association with Subclinical Atherosclerosis Assessed by Carotid Ultrasonography
by Malin Mickelsson, Kim Ekblom, Kristina Stefansson, Per Liv, Emma Nyman, Anders Själander, Ulf Näslund and Johan Hultdin
J. Clin. Med. 2024, 13(5), 1333; https://doi.org/10.3390/jcm13051333 - 27 Feb 2024
Viewed by 491
Abstract
Background: The ABO blood group system has previously been associated with cardiovascular disease (CVD), where non-O blood group individuals have shown an increased risk. Studies assessing early atherosclerotic disease while also including RhD are few. We aimed to determine whether the ABO and [...] Read more.
Background: The ABO blood group system has previously been associated with cardiovascular disease (CVD), where non-O blood group individuals have shown an increased risk. Studies assessing early atherosclerotic disease while also including RhD are few. We aimed to determine whether the ABO and RhD blood groups are associated with subclinical atherosclerosis in a healthy population. Methods: We included 3532 participants from the VIPVIZA trial with available carotid ultrasonography results to assess subclinical disease. Information about blood groups was obtained from the SCANDAT-3 database, where 85% of VIPVIZA participants were registered. Results: RhD− individuals aged 40 years showed increased carotid intima–media thickness (B 1.09 CI 95% 1.03; 1.14) compared to RhD+ individuals. For ABO, there were no differences in ultrasonography results when assessing the whole study population. However, 60-year-old individuals with heredity for CVD and a non-O blood group had decreased odds for carotid plaques (OR 0.54 CI 95% 0.33; 0.88). Conclusions: RhD blood group is associated with subclinical atherosclerosis in younger individuals, indicating a role as a mediator in the atherosclerotic process. In addition, a non-O blood group was associated with decreased subclinical atherosclerosis in individuals aged 60 and with heredity (corresponding to the group with the highest atherosclerotic burden). Full article
(This article belongs to the Topic Biomarker Development and Application)
23 pages, 16062 KiB  
Article
The Predictive Value of 8-Hydroxy-Deoxyguanosine (8-OHdG) Serum Concentrations in Irradiated Non-Small Cell Lung Carcinoma (NSCLC) Patients
by Kyriakos Orfanakos, Constantinos E. Alifieris, Emmanouil K. Verigos, Maria V. Deligiorgi, Kosmas E. Verigos, Mihalis I. Panayiotidis, Michail Nikolaou and Dimitrios T. Trafalis
Biomedicines 2024, 12(1), 134; https://doi.org/10.3390/biomedicines12010134 - 09 Jan 2024
Viewed by 856
Abstract
Ionizing radiation is strongly linked to direct or indirect DNA damage, as with the production of reactive oxygen species (ROS), which in turn produce DNA damage products, such as 8-hydroxy-2-deoxyguanosine (8-OHdG). In this study, we aimed to investigate the formation of 8-OHdG after [...] Read more.
Ionizing radiation is strongly linked to direct or indirect DNA damage, as with the production of reactive oxygen species (ROS), which in turn produce DNA damage products, such as 8-hydroxy-2-deoxyguanosine (8-OHdG). In this study, we aimed to investigate the formation of 8-OHdG after irradiation in patients with non-small cell cancer (NSCLC) and its use as a biomarker. Sixteen patients with squamous and thirty-six patients with non-squamous pathology were included. An enzyme-linked-immunosorbent assay (ELISA) was performed before and after radiation. A dose-dependent relationship was confirmed: 8-OHdG plasma concentrations, increased in the total of NSCLC patients and specifically with a linear correlation in non-squamous pathology; in squamous histology, after an initial increase, a significant decrease followed after 20 Gy dose of irradiation. The pretreatment total irradiated tumor volume (cm3) was positively correlated with 8-OHdG levels in patients with squamous histology. When plotting the 8-OHdG plasma concentration at a 10 Gy irradiation dose to the baseline, the AUC was 0.873 (95% CI 0.614–0.984), p < 0.0001, with an associated criterion value of >1378 as a cutoff (sensitivity 72.7%, specificity 100%). When normalizing this ratio to BSA, the associated criterion cutoff value was >708 (sensitivity of 100%, specificity 80%). Lastly, 8-OHdG levels were closely related with the development of radiation-induced toxicities. Full article
(This article belongs to the Topic Biomarker Development and Application)
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12 pages, 2771 KiB  
Article
1H NMR Serum Metabolomic Change of Trimethylamine N-oxide (TMAO) Is Associated with Alcoholic Liver Disease Progression
by Junsang Oh, Jayoung Kim, Sanghak Lee, Gyubin Park, Kei-Anne Garcia Baritugo, Ki Jun Han, Sangheun Lee and Gi-Ho Sung
Metabolites 2024, 14(1), 39; https://doi.org/10.3390/metabo14010039 - 08 Jan 2024
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Abstract
Without early detection and treatment, chronic and excessive alcohol consumption can lead to the development of alcoholic liver disease (ALD). With this in mind, we exploit the recent concept of the liver–gut axis and analyze the serum profile of ALD patients for identification [...] Read more.
Without early detection and treatment, chronic and excessive alcohol consumption can lead to the development of alcoholic liver disease (ALD). With this in mind, we exploit the recent concept of the liver–gut axis and analyze the serum profile of ALD patients for identification of microbiome-derived metabolites that can be used as diagnostic biomarkers for onset of ALD. 1H-NMR was used to analyze serum metabolites of 38 ALD patients that were grouped according to their Child–Turcotte–Pugh scores (CTP): class A (CTP-A; 19), class B(CTP-B; 10), and class C (CTP-C; 9). A partial least squares-discriminant analysis (PLS-DA) and a variable importance of projection (VIP) score were used to identify significant metabolites. A receiver operating characteristic (ROC) curve and correlation heatmap were used to evaluate the predictability of identified metabolites as ALD biomarkers. Among 42 identified metabolites, 6 were significantly correlated to exacerbation of ALD. As ALD progressed in CTP-C, the levels of trimethylamine N-oxide (TMAO), malate, tyrosine, and 2-hydroxyisovalerate increased, while isobutyrate and isocitrate decreased. Out of six metabolites, elevated levels of TMAO and its precursors (carnitine, betaine, choline) were associated with severity of ALD. This indicates that TMAO can be used as an effective biomarker for the diagnosis of ALD progression. Full article
(This article belongs to the Topic Biomarker Development and Application)
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21 pages, 872 KiB  
Systematic Review
The Impact of Biomarkers on the Early Detection of Acute Mesenteric Ischemia
by Aleksandar Zafirovski, Marija Zafirovska, Dimitrij Kuhelj and Tadeja Pintar
Biomedicines 2024, 12(1), 85; https://doi.org/10.3390/biomedicines12010085 - 29 Dec 2023
Viewed by 877
Abstract
Background: acute mesenteric ischemia (AMI) is a life-threatening condition that is caused by inadequate blood flow through the mesenteric vessel and is related to high mortality rates due to systemic complications. This study aims to systematically review the available literature concerning the major [...] Read more.
Background: acute mesenteric ischemia (AMI) is a life-threatening condition that is caused by inadequate blood flow through the mesenteric vessel and is related to high mortality rates due to systemic complications. This study aims to systematically review the available literature concerning the major findings of possible biomarkers for early detection of acute mesenteric ischemia in the human population. Methods: studies that measured the performance of biomarkers during acute mesenteric ischemia were identified with the search of PubMed, Embase, Medline, and Cochrane library. Results: from a total of 654 articles, 46 articles examining 14 different biomarkers were filtered, falling within our inclusion criteria. Intestinal fatty acid-binding protein (I-FABP) was the most commonly researched biomarker regarding AMI, with sensitivity ranging from 61.5% to 100% and specificity ranging from 40% to 100%. The second most commonly researched biomarker was D-dimer, with a sensitivity of 60–100% and a specificity of 18–85.71%. L-lactate had a sensitivity of 36.6–90.91% and a specificity of 64.29–96%. Several parameters within the blood count were examined as potential markers for AMI, including NLR, PLR, MPV, RDW, DNI, and IG. Citrulline, interleukin 6 (IL-6), and procalcitonin (PCT) were the least-researched biomarkers. Conclusion: different biomarkers showed different accuracies in detecting AMI. I-FABP and D-dimer have been the most researched and shown to be valuable in the diagnosis of AMI, whereas L-lactate could be used as an additional tool. Ischemia-modified albumin (IMA), alpha glutathione S-transferase (αGST), interleukin 6 (IL-6), and citrulline showed potential use in their respective studies. However, further research needs to be done on larger sample sizes and with controls to reduce bias. Several studies showed that neutrophil–lymphocyte ratio (NLR), platelet–lymphocyte ratio (PLR), mean platelet volume (MPV), red-cell distribution width (RDW), delta neutrophil index (DNI), and immature granulocytes (IGs) might be useful, as well at the same time be widely distributed and affordable in combination with other markers presenting higher specificity and sensitivity. Full article
(This article belongs to the Topic Biomarker Development and Application)
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18 pages, 4469 KiB  
Article
The Detection of Primary Sclerosing Cholangitis Using Volatile Metabolites in Fecal Headspace and Exhaled Breath
by Robert van Vorstenbosch, Kim van Munster, Danielle Pachen, Alex Mommers, Georgios Stavropoulos, Frederik-Jan van Schooten, Cyriel Ponsioen and Agnieszka Smolinska
Metabolites 2024, 14(1), 23; https://doi.org/10.3390/metabo14010023 - 29 Dec 2023
Viewed by 966
Abstract
Up to 5% of inflammatory bowel disease patients may at some point develop primary sclerosing cholangitis (PSC). PSC is a rare liver disease that ultimately results in liver damage, cirrhosis and liver failure. It typically remains subclinical until irreversible damage has been inflicted. [...] Read more.
Up to 5% of inflammatory bowel disease patients may at some point develop primary sclerosing cholangitis (PSC). PSC is a rare liver disease that ultimately results in liver damage, cirrhosis and liver failure. It typically remains subclinical until irreversible damage has been inflicted. Hence, it is crucial to screen IBD patients for PSC, but its early detection is challenging, and the disease’s etiology is not well understood. This current study aimed at the early detection of PSC in an IBD population using Volatile Organic Compounds in fecal headspace and exhaled breath. To this aim, fecal material and exhaled breath were collected from 73 patients (n = 16 PSC/IBD; n = 8 PSC; n = 49 IBD), and their volatile profile were analyzed using Gas Chromatography–Mass Spectrometry. Using the most discriminatory features, PSC detection resulted in areas under the ROC curve (AUCs) of 0.83 and 0.84 based on fecal headspace and exhaled breath, respectively. Upon data fusion, the predictive performance increased to AUC 0.92. The observed features in the fecal headspace relate to detrimental microbial dysbiosis and exogenous exposure. Future research should aim for the early detection of PSC in a prospective study design. Full article
(This article belongs to the Topic Biomarker Development and Application)
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14 pages, 4539 KiB  
Article
Blood-Based Biomarkers Reflecting Protease 3 and MMP-12 Catalyzed Elastin Degradation as Potential Noninvasive Surrogate Markers of Endoscopic and Clinical Disease in Inflammatory Bowel Disease
by Martin Pehrsson, Viktor Domislovic, Marta Sorokina Alexdottir, Marko Brinar, Morten Asser Karsdal, Ana Barisic, Zeljko Krznaric and Joachim Høg Mortensen
J. Clin. Med. 2024, 13(1), 21; https://doi.org/10.3390/jcm13010021 - 19 Dec 2023
Viewed by 662
Abstract
Chronic inflammation in inflammatory bowel disease (IBD) triggers significant extracellular matrix remodeling, including elastin remodeling, leading to severe clinical complications. Novel methods to assess intestinal tissue destruction may act as surrogate markers of endoscopic disease activity, relieving patients of invasive endoscopy. We explored [...] Read more.
Chronic inflammation in inflammatory bowel disease (IBD) triggers significant extracellular matrix remodeling, including elastin remodeling, leading to severe clinical complications. Novel methods to assess intestinal tissue destruction may act as surrogate markers of endoscopic disease activity, relieving patients of invasive endoscopy. We explored the noninvasive blood-based biomarkers ELP-3 and ELM-12, measuring elastin degradation in IBD. In a study involving 104 Crohn’s disease (CD), 39 ulcerative colitis (UC), and 29 healthy donors, we assessed these biomarkers’ association with endoscopic and clinical disease activity using ELISA. Patients were evaluated based on the SES-CD and CDAI for CD patients and modified MES and partial Mayo for UC patients. ELP-3 and ELM-12 were elevated in patients with IBD. Discerning CD patients in endoscopic remission and mild from moderate to severe, ELP-3 provided an AUC of 0.69 and ELM-12 an AUC of 0.73. The ELP-3 biomarker was associated with UC patients and provided the highest diagnostic power of 0.87 for remission vs. active clinical disease. The data suggest an association of ELP-3 with active CD and ELM-12 with endoscopic remission in CD patients. Additionally, ELP-3 could identify UC patients with active clinical disease from patients in remission. The noninvasive biomarkers ELP-3 and ELM-12 could be potential surrogate biomarkers of elastin degradation and endoscopic and clinical disease markers. Full article
(This article belongs to the Topic Biomarker Development and Application)
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18 pages, 1681 KiB  
Article
The Challenge to Stabilize, Extract and Analyze Urinary Cell-Free DNA (ucfDNA) during Clinical Routine
by Ivonne Nel, Carolin Münch, Saikal Shamkeeva, Mitja L. Heinemann, Berend Isermann and Bahriye Aktas
Diagnostics 2023, 13(24), 3670; https://doi.org/10.3390/diagnostics13243670 - 14 Dec 2023
Viewed by 899
Abstract
Background: The “Liquid Biopsy” has become a powerful tool for cancer research during the last decade. Circulating cell-free DNA (cfDNA) that originates from tumors has emerged as one of the most promising analytes. In contrast to plasma-derived cfDNA, only a few studies have [...] Read more.
Background: The “Liquid Biopsy” has become a powerful tool for cancer research during the last decade. Circulating cell-free DNA (cfDNA) that originates from tumors has emerged as one of the most promising analytes. In contrast to plasma-derived cfDNA, only a few studies have investigated urinary cfDNA. One reason might be rapid degradation and hence inadequate concentrations for downstream analysis. In this study, we examined the stability of cfDNA in urine using different methods of preservation under various storage conditions. Methodology: To mimic patient samples, a pool of healthy male and female urine donors was spiked with a synthetic cfDNA reference standard (fragment size 170 bp) containing the T790M mutation in the EGFR gene. Spiked samples were preserved with three different buffers and with no buffer over four different storage periods (0 h; 4 h; 12 h; 24 h) at room temperature vs. 4 °C. The preservatives used were Urinary Analyte Stabilizer (UAS, Novosanis, Wijnegem, Belgium), Urine Conditioning Buffer (UCB, Zymo, Freiburg, Germany) and a self-prepared buffer called “AlloU”. CfDNA was extracted using the QIAamp MinElute ccfDNA Mini Kit (Qiagen, Hilden, Germany). CfDNA concentration was measured using the Qubit™ 4 fluorometer (Thermo Fisher Scientific, Waltham, MA, USA). Droplet digital PCR (ddPCR) was used for detection and quantification of the T790M mutation. Results: Almost no spiked cfDNA was recoverable from samples with no preservation buffer and the T790M variant was not detectable in these samples. These findings indicate that cfDNA was degraded below the detection limit by urinary nucleases. Stabilizing buffers showed varying efficiency in preventing this degradation. The most effective stabilizing buffer under all storage conditions was the UAS, enabling adequate recovery of the T790M variant using ddPCR. Conclusion: From a technical point of view, stabilizing buffers and adequate storage conditions are a prerequisite for translation of urinary cfDNA diagnostics into clinical routine. Full article
(This article belongs to the Topic Biomarker Development and Application)
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14 pages, 645 KiB  
Article
Butyrylcarnitine Elevation in Newborn Screening: Reducing False Positives and Distinguishing between Two Rare Diseases through the Evaluation of New Ratios
by MariaAnna Messina, Alessia Arena, Riccardo Iacobacci, Luisa La Spina, Concetta Meli, Federica Raudino and Martino Ruggieri
Biomedicines 2023, 11(12), 3247; https://doi.org/10.3390/biomedicines11123247 - 07 Dec 2023
Viewed by 657
Abstract
One of the main challenges of newborn screening programs, which screen for inherited metabolic disorders, is cutting down on false positives (FPs) in order to avoid family stresses, additional analyses, and unnecessary costs. False positives are partly caused by an insubstantial number of [...] Read more.
One of the main challenges of newborn screening programs, which screen for inherited metabolic disorders, is cutting down on false positives (FPs) in order to avoid family stresses, additional analyses, and unnecessary costs. False positives are partly caused by an insubstantial number of robust biomarkers in evaluations. Another challenge is how to distinguish between diseases which share the same primary marker and for which secondary biomarkers are just as highly desirable. Focusing on pathologies that involve butyrylcarnitine (C4) elevation, such as short-chain acylCoA dehydrogenase deficiency (SCADD) and isobutyrylCoA dehydrogenase deficiency (IBDD), we investigated the acylcarnitine profile of 121 newborns with a C4 increase to discover secondary markers to achieve two goals: reduce the FP rate and discriminate between the two rare diseases. Analyses were carried out using tandem mass spectrometry with whole blood samples spotted on filter paper. Seven new biomarkers (C4/C0, C4/C5, C4/C5DC\C6OH, C4/C6, C4/C8, C4/C14:1, C4/C16:1) were identified using a non-parametric ANOVA analysis. Then, the corresponding cut-off values were found and applied to the screening program. The seven new ratios were shown to be robust (p < 0.001 and p < 0.01, 0.0937 < ε2 < 0.231) in discriminating between FP and IBDD patients, FP and SCADD patients, or SCADD and IBDD patients. Our results suggest that the new ratios are optimal indicators for identifying true positives, distinguishing between two rare diseases that share the same primary biomarker, improving the predictive positive value (PPV) and reducing the false positive rate (FPR). Full article
(This article belongs to the Topic Biomarker Development and Application)
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16 pages, 3087 KiB  
Article
Technical Report: A Comprehensive Comparison between Different Quantification Versions of Nightingale Health’s 1H-NMR Metabolomics Platform
by Daniele Bizzarri, Marcel J. T. Reinders, Marian Beekman, P. Eline Slagboom, Erik B. van den Akker and on behalf of the BbmriNl
Metabolites 2023, 13(12), 1181; https://doi.org/10.3390/metabo13121181 - 30 Nov 2023
Viewed by 1030
Abstract
1H-NMR metabolomics data is increasingly used to track health and disease. Nightingale Health, a major supplier of 1H-NMR metabolomics, has recently updated the quantification strategy to further align with clinical standards. Such updates, however, might influence backward replicability, particularly affecting studies [...] Read more.
1H-NMR metabolomics data is increasingly used to track health and disease. Nightingale Health, a major supplier of 1H-NMR metabolomics, has recently updated the quantification strategy to further align with clinical standards. Such updates, however, might influence backward replicability, particularly affecting studies with repeated measures. Using data from BBMRI-NL consortium (~28,000 samples from 28 cohorts), we compared Nightingale data, originally released in 2014 and 2016, with a re-quantified version released in 2020, of which both versions were based on the same NMR spectra. Apart from two discontinued and twenty-three new analytes, we generally observe a high concordance between quantification versions with 73 out of 222 (33%) analytes showing a mean ρ > 0.9 across all cohorts. Conversely, five analytes consistently showed lower Spearman’s correlations (ρ < 0.7) between versions, namely acetoacetate, LDL-L, saturated fatty acids, S-HDL-C, and sphingomyelins. Furthermore, previously trained multi-analyte scores, such as MetaboAge or MetaboHealth, might be particularly sensitive to platform changes. Whereas MetaboHealth replicated well, the MetaboAge score had to be retrained due to use of discontinued analytes. Notably, both scores in the re-quantified data recapitulated mortality associations observed previously. Concluding, we urge caution in utilizing different platform versions to avoid mixing analytes, having different units, or simply being discontinued. Full article
(This article belongs to the Topic Biomarker Development and Application)
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26 pages, 1604 KiB  
Review
Recent Advances in Surface Plasmon Resonance (SPR) Technology for Detecting Ovarian Cancer Biomarkers
by Vikneswary Ravi Kumar, Nirmala Chandralega Kampan, Nor Haslinda Abd Aziz, Chew Kah Teik, Mohamad Nasir Shafiee and P. Susthitha Menon
Cancers 2023, 15(23), 5607; https://doi.org/10.3390/cancers15235607 - 27 Nov 2023
Viewed by 1222
Abstract
Epithelial Ovarian Cancer (EOC) is a leading cause of cancer-related deaths among women, mainly due to a lack of early detection and screening methods. Advanced immunoassay techniques, such as Luminex and proximity extension assay (PEA) technology, show promise in improving EOC detection by [...] Read more.
Epithelial Ovarian Cancer (EOC) is a leading cause of cancer-related deaths among women, mainly due to a lack of early detection and screening methods. Advanced immunoassay techniques, such as Luminex and proximity extension assay (PEA) technology, show promise in improving EOC detection by utilizing highly sensitive and specific multiplex panels to detect multiple combinations of biomarkers. However, these advanced immunoassay techniques have certain limitations, especially in validating the performance characteristics such as specificity, sensitivity, limit of detection (LOD), and dynamic range for each EOC biomarker within the panel. Implementing multiplexing in point-of-care (POC) biosensors can enhance EOC biomarker detection, with Surface Plasmon Resonance (SPR) being a versatile option among optical biosensors. There is no study on multiplex SPR biosensors specifically tailored for diagnosing EOC. Recent studies have shown promising results in the single detection of EOC biomarkers using SPR, with LOD for cancer antigen 125 (CA125) at 0.01 U/mL−1 and human epididymis protein 4 (HE4) at 1pM. This study proposes a potential roadmap for scientists and engineers in academia and industry to develop a cost effective yet highly efficient SPR biosensor platform for detecting EOC. Full article
(This article belongs to the Topic Biomarker Development and Application)
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14 pages, 3969 KiB  
Article
Identification of Novel Biomarkers for Early Diagnosis of Atherosclerosis Using High-Resolution Metabolomics
by Syed Wasim Sardar, Jeonghun Nam, Tae Eun Kim, Hyunil Kim and Youngja H. Park
Metabolites 2023, 13(11), 1160; https://doi.org/10.3390/metabo13111160 - 18 Nov 2023
Cited by 2 | Viewed by 1460
Abstract
Atherosclerosis (AS) is a metabolic disorder and the pre-stage of several cardiovascular diseases, including myocardial infarction, stroke, and angina pectoris. Early detection of AS can provide the opportunity for effective management and better clinical results, along with the prevention of further progression of [...] Read more.
Atherosclerosis (AS) is a metabolic disorder and the pre-stage of several cardiovascular diseases, including myocardial infarction, stroke, and angina pectoris. Early detection of AS can provide the opportunity for effective management and better clinical results, along with the prevention of further progression of the disease. In the current study, an untargeted and targeted metabolomic approach was used to identify possible metabolic signatures that have altered levels in AS patients. A total of 200 serum samples from individuals with AS and normal were analyzed via liquid chromatography–high-resolution mass spectrometry. Univariate and multivariate analysis approaches were used to identify differential metabolites. A group of metabolites associated with bile acids, amino acids, steroid hormones, and purine metabolism were identified that are capable of distinguishing AS-risk sera from normal. Further, the targeted metabolomics approach confirmed that six metabolites, namely taurocholic acid, cholic acid, cortisol, hypoxanthine, trimethylamine N-oxide (TMAO), and isoleucine, were found to be significantly upregulated, while the concentrations of glycoursodeoxycholic acid, glycocholic acid, testosterone, leucine, methionine, phenylalanine, tyrosine, and valine were found to be significantly downregulated in the AS-risk sera. The receiver operating characteristic curves of three metabolites, including cortisol, hypoxanthine, and isoleucine, showed high sensitivity and specificity. Taken together, these findings suggest cortisol, hypoxanthine, and isoleucine as novel biomarkers for the early and non-invasive detection of AS. Thus, this study provides new insights for further investigations into the prevention and management of AS. Full article
(This article belongs to the Topic Biomarker Development and Application)
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19 pages, 860 KiB  
Systematic Review
The Role of Mucin Expression in the Diagnosis of Oesophago-Gastric Cancer: A Systematic Literature Review
by Nikhil Manish Patel, Georgios Geropoulos, Pranav Harshad Patel, Ricky Harminder Bhogal, Kevin Joseph Harrington, Aran Singanayagam and Sacheen Kumar
Cancers 2023, 15(21), 5252; https://doi.org/10.3390/cancers15215252 - 01 Nov 2023
Viewed by 1252
Abstract
Survival in oesophago-gastric cancer (OGC) is poor due to early diagnostic challenges. Non-invasive risk stratification may identify susceptible patients with pre-malignant or benign disease. Following diagnostic confirmation with endoscopic biopsy, early OGC may be treated sooner. Mucins are transmembrane glycoproteins implicated in OGC [...] Read more.
Survival in oesophago-gastric cancer (OGC) is poor due to early diagnostic challenges. Non-invasive risk stratification may identify susceptible patients with pre-malignant or benign disease. Following diagnostic confirmation with endoscopic biopsy, early OGC may be treated sooner. Mucins are transmembrane glycoproteins implicated in OGC with potential use as biomarkers of malignant transformation. This systematic review defines the role of mucins in OGC diagnosis. A literature search of MEDLINE, Web of Science, Embase and Cochrane databases was performed following PRISMA protocols for studies published January 1960–December 2022. Demographic data and data on mucin sampling and analysis methods were extracted. The review included 124 studies (n = 11,386 patients). Gastric adenocarcinoma (GAc) was the commonest OG malignancy (n = 101) followed by oesophageal adenocarcinoma (OAc, n = 24) and squamous cell carcinoma (OSqCc, n = 10). Mucins MUC1, MUC2, MUC5AC and MUC6 were the most frequently implicated. High MUC1 expression correlated with poorer prognosis and metastases in OSqCc. MUC2 expression decreases during progression from healthy mucosa to OAc, causing reduced protection from gastric acid. MUC5AC was upregulated, and MUC6 downregulated in GAc. Mucin expression varies in OGC; changes may be epigenetic or mutational. Profiling upper GI mucin expression in OGC, with pre-malignant, benign and healthy controls may identify potential early diagnostic biomarkers. Full article
(This article belongs to the Topic Biomarker Development and Application)
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19 pages, 6033 KiB  
Article
Biomarker Discovery for Hepatocellular Carcinoma in Patients with Liver Cirrhosis Using Untargeted Metabolomics and Lipidomics Studies
by Md Mamunur Rashid, Rency S. Varghese, Yuansong Ding and Habtom W. Ressom
Metabolites 2023, 13(10), 1047; https://doi.org/10.3390/metabo13101047 - 02 Oct 2023
Viewed by 1251
Abstract
Hepatocellular carcinoma (HCC), the most prevalent form of liver cancer, is the third leading cause of mortality globally. Patients with HCC have a poor prognosis due to the fact that the emergence of symptoms typically occurs at a late stage of the disease. [...] Read more.
Hepatocellular carcinoma (HCC), the most prevalent form of liver cancer, is the third leading cause of mortality globally. Patients with HCC have a poor prognosis due to the fact that the emergence of symptoms typically occurs at a late stage of the disease. In addition, conventional biomarkers perform suboptimally when identifying HCC in its early stages, heightening the need for the identification of new and more effective biomarkers. Using metabolomics and lipidomics approaches, this study aims to identify serum biomarkers for identification of HCC in patients with liver cirrhosis (LC). Serum samples from 20 HCC cases and 20 patients with LC were analyzed using ultra-high-performance liquid chromatography-Q Exactive mass spectrometry (UHPLC-Q-Exactive-MS). Metabolites and lipids that are significantly altered between HCC cases and patients with LC were identified. These include organic acids, amino acids, TCA cycle intermediates, fatty acids, bile acids, glycerophospholipids, sphingolipids, and glycerolipids. The most significant variability was observed in the concentrations of bile acids, fatty acids, and glycerophospholipids. In the context of HCC cases, there was a notable increase in the levels of phosphatidylethanolamine and triglycerides, but the levels of fatty acids and phosphatidylcholine exhibited a substantial decrease. In addition, it was observed that all of the identified metabolites exhibited a superior area under the receiver operating characteristic (ROC) curve in comparison to alpha-fetoprotein (AFP). The pathway analysis of these metabolites revealed fatty acid, lipid, and energy metabolism as the most impacted pathways. Putative biomarkers identified in this study will be validated in future studies via targeted quantification. Full article
(This article belongs to the Topic Biomarker Development and Application)
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17 pages, 4367 KiB  
Article
Insights on the Organ-Dependent, Molecular Sexual Dimorphism in the Zebra Mussel, Dreissena polymorpha, Revealed by Ultra-High-Performance Liquid Chromatography–Tandem Mass Spectrometry Metabolomics
by Emilie Lance, Lucas Sartor, Pierre Foucault, Alain Geffard and Benjamin Marie
Metabolites 2023, 13(10), 1046; https://doi.org/10.3390/metabo13101046 - 01 Oct 2023
Viewed by 873
Abstract
The zebra mussel, Dreissena polymorpha, is extensively used as a sentinel species for biosurveys of environmental contaminants in freshwater ecosystems and for ecotoxicological studies. However, its metabolome remains poorly understood, particularly in light of the potential molecular sexual dimorphism between its different [...] Read more.
The zebra mussel, Dreissena polymorpha, is extensively used as a sentinel species for biosurveys of environmental contaminants in freshwater ecosystems and for ecotoxicological studies. However, its metabolome remains poorly understood, particularly in light of the potential molecular sexual dimorphism between its different tissues. From an ecotoxicological point of view, inter-sex and inter-organ differences in the metabolome suggest variability in responsiveness, which can influence the analysis and interpretation of data, particularly in the case where males and females would be analyzed indifferently. This study aimed to assess the extent to which the molecular fingerprints of functionally diverse tissues like the digestive glands, gonads, gills, and mantle of D. polymorpha can reveal tissue-specific molecular sexual dimorphism. We employed a non-targeted metabolomic approach using liquid chromatography high-resolution mass spectrometry and revealed a significant sexual molecular dimorphism in the gonads, and to a lesser extent in the digestive glands, of D. polymorpha. Our results highlight the critical need to consider inter-sex differences in the metabolome of D. polymorpha to avoid confounding factors, particularly when investigating environmental effects on molecular regulation in the gonads, and to a lesser extent in the digestive glands. Full article
(This article belongs to the Topic Biomarker Development and Application)
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12 pages, 2186 KiB  
Article
Method Comparison and Clinical Performance of Breast Cancer Tumor Markers on Novel Multiplex Immunoassay and Automatized LOCI Technology Platforms
by Lars Schröder, Michael R. Mallmann, Christian M. Domroese, Natalie Wefers, Ramona Dolscheid-Pommerich, Birgit Stoffel-Wagner, Inga Trulson, Kai Vahldiek, Frank Klawonn and Stefan Holdenrieder
Diagnostics 2023, 13(19), 3101; https://doi.org/10.3390/diagnostics13193101 - 30 Sep 2023
Viewed by 888
Abstract
Tumor marker determinations are valuable tools for the guidance of breast cancer patients during the course of disease. They are assessed on diverse analytical platforms that may be associated with differences according to the methods applied and the clinical performance. To investigate the [...] Read more.
Tumor marker determinations are valuable tools for the guidance of breast cancer patients during the course of disease. They are assessed on diverse analytical platforms that may be associated with differences according to the methods applied and the clinical performance. To investigate the method dependency and clinical significance of breast cancer protein tumor markers, CEA, CA 15-3, CA 125, CA 19-9 and AFP were measured in a total of 154 biobanked samples from 77 patients with breast cancer, 10 with DCIS, 31 with benign breast diseases and 36 healthy controls using a Millipore multiplex biomarker panel (MP) and an automized version of the routinely used Vista LOCI technology. The markers were compared between methods and investigated for diagnostic performance. CEA, CA 15-3 and AFP showed good correlations between both platforms with correlation coefficients of R = 0.85, 0.85 and 0.92, respectively, in all samples, but similarly also in the various subgroups. CA 125 and CA 19-9 showed only moderate correlations (R = 0.71 and 0.56, respectively). Absolute values were significantly higher for CEA, CA 15-3, CA 125 and AFP in the Vista LOCI as compared with the MP method and vice versa for CA 19-9. The diagnostic performance for discrimination of breast cancer from healthy controls was similar for both methods with AUCs in ROC curves for CEA (MP 0.81, 95% CI 0.72–0.91; LOCI 0.81; 95% CI 0.72–0.91) and CA-15-3 (MP 0.75, 95% CI 0.65–0.86; LOCI 0.67, 95% CI 0.54–0.79). Similar results were obtained for the comparison of breast cancer with benign breast diseases regarding CEA (AUC MP 0.62, 95% CI 0.51–0.73; LOCI 0.64, 95% CI 0.53–0.74) and CA-15-3 (MP 0.70, 95% CI 0.6–0.81; LOCI 0.66, 95% CI 0.54–0.77). Both platforms show moderate to good method comparability for tumor markers with similar clinical performance. However, absolute levels in individual patients should be interpreted with care. Full article
(This article belongs to the Topic Biomarker Development and Application)
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11 pages, 848 KiB  
Article
Increased Prevalence of Autoimmune Gastritis in Patients with a Gastric Precancerous Lesion
by Xiaopei Guo, Marco W. J. Schreurs, Fleur E. Marijnissen, Michiel C. Mommersteeg, Stella A. V. Nieuwenburg, Michail Doukas, Nicole S. Erler, Lisette G. Capelle, Marco J. Bruno, Maikel P. Peppelenbosch, Manon C. W. Spaander and Gwenny M. Fuhler
J. Clin. Med. 2023, 12(19), 6152; https://doi.org/10.3390/jcm12196152 - 23 Sep 2023
Cited by 1 | Viewed by 1150
Abstract
Background: Autoimmune gastritis (AIG), characterized with the presence of anti-parietal-cell antibodies (APCA), is a risk factor for gastric cancer. However, AIG may go underdiagnosed, especially in the case of H. pylori infection and the presence of gastric precancerous lesions (GPL), due to [...] Read more.
Background: Autoimmune gastritis (AIG), characterized with the presence of anti-parietal-cell antibodies (APCA), is a risk factor for gastric cancer. However, AIG may go underdiagnosed, especially in the case of H. pylori infection and the presence of gastric precancerous lesions (GPL), due to the ambiguous pathology and delayed symptom onset. Aim: Investigate the prevalence and characteristics of AIG in GPL patients. Methods: Prevalence of AIG was determined with the presence of APCA in patients with GPL (n = 256) and the control group (n = 70). Pathological characteristics and levels of gastrin 17 (G17), pepsinogen (PG) I and II and anti-Helicobacter pylori IgG were assessed in GPL cases, and the severity of intestinal metaplasia and gastric atrophy was scored by expert pathologists. Results: APCA positivity was observed in 18% of cases vs. 7% of controls (p = 0.033). Only 3/256 patients were previously diagnosed with AIG. The presence of APCA was associated with corpus-limited and extended GPL. A receiver operating curve analysis demonstrated that the G17 and PGI/II ratio could identify APCA-positive patients within GPL cases (AUC: 0.884). Conclusions: The prevalence of AIG is higher in patients with GPL but goes undiagnosed. Using G17 and PG I/II as diagnostic markers can help to identify patients with AIG and improve surveillance programs for patients with GPL. Full article
(This article belongs to the Topic Biomarker Development and Application)
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39 pages, 947 KiB  
Review
Interpretations of the Role of Plasma Albumin in Prognostic Indices: A Literature Review
by Kim Oren Gradel
J. Clin. Med. 2023, 12(19), 6132; https://doi.org/10.3390/jcm12196132 - 22 Sep 2023
Cited by 1 | Viewed by 1034
Abstract
This review assesses how publications interpret factors that influence the serum or plasma albumin (PA) level in prognostic indices, focusing on inflammation and nutrition. On PubMed, a search for “albumin AND prognosis” yielded 23,919 results. From these records, prognostic indices were retrieved, and [...] Read more.
This review assesses how publications interpret factors that influence the serum or plasma albumin (PA) level in prognostic indices, focusing on inflammation and nutrition. On PubMed, a search for “albumin AND prognosis” yielded 23,919 results. From these records, prognostic indices were retrieved, and their names were used as search strings on PubMed. Indices found in 10 or more original research articles were included. The same search strings, restricted to “Review” or “Systematic review”, retrieved yielded on the indices. The data comprised the 10 latest original research articles and up to 10 of the latest reviews. Thirty indices had 294 original research articles (6 covering two indices) and 131 reviews, most of which were from recent years. A total of 106 articles related the PA level to inflammation, and 136 related the PA level to nutrition. For the reviews, the equivalent numbers were 54 and 65. In conclusion, more publications mention the PA level as a marker of nutrition rather than inflammation. This is in contrast to several general reviews on albumin and nutritional guidelines, which state that the PA level is a marker of inflammation but not nutrition. Hypoalbuminemia should prompt clinicians to focus on the inflammatory aspects in their patients. Full article
(This article belongs to the Topic Biomarker Development and Application)
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12 pages, 1772 KiB  
Article
The Usefulness of the Ratio of Antigen–Autoantibody Immune Complexes to Their Free Antigens in the Diagnosis of Non-Small Cell Lung Cancer
by Heyjin Kim, Jin Kyung Lee, Ae-Chin Oh, Hye-Ryoun Kim and Young Jun Hong
Diagnostics 2023, 13(18), 2999; https://doi.org/10.3390/diagnostics13182999 - 20 Sep 2023
Viewed by 804
Abstract
Autoantibodies against specific lung cancer-associated antigens have been suggested for the performance of lung cancer diagnosis. This study aimed to evaluate the diagnostic performance of the antigen–autoantibody immune complex (AIC) against its free antigens for CYFRA21-1, ProGRP, neutrophil gelatinase-associated lipocalin (NGAL), and neuron-specific [...] Read more.
Autoantibodies against specific lung cancer-associated antigens have been suggested for the performance of lung cancer diagnosis. This study aimed to evaluate the diagnostic performance of the antigen–autoantibody immune complex (AIC) against its free antigens for CYFRA21-1, ProGRP, neutrophil gelatinase-associated lipocalin (NGAL), and neuron-specific enolase (NSE) in non-small cell lung cancer (NSCLC). In total, 85 patients with NSCLC and 120 healthy controls (HCs) were examined using a 9-guanine DNA chip method. The ratios of AICs to their antigens and the combinations of ratios consisting of two to four markers were calculated. The levels of AICs for CYFRA21-1, ProGRP, NGAL, and NSE were higher than those for their free antigens in all participants. The levels of each free antigens distinguished patients with NSCLC from the HCs. The ratios of the AIC to its antigen and seven combinations of two to four ratios were significantly higher in patients with NSCLC than in the HCs. Excellent diagnostic performance was observed for all combination ratios (C4-1), with 85.9% sensitivity and 86.7% specificity at a 3.51 cut-off. Higher sensitivity was observed in the early stages (0–I) and adenocarcinoma than in stages II–IV and other pathological types. Combining all ratios of AICs and their antigens for all four markers was useful when diagnosing NSCLC. Full article
(This article belongs to the Topic Biomarker Development and Application)
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20 pages, 15475 KiB  
Article
Development and Validation of the Oxidative Stress Related lncRNAs for Prognosis in Esophageal Squamous Cell Carcinoma
by Xuan Zheng, Wei Liu, Yingze Zhu, Wenyue Kong, Xin Su, Lanxiang Huang, Yishuang Cui and Guogui Sun
Cancers 2023, 15(17), 4399; https://doi.org/10.3390/cancers15174399 - 02 Sep 2023
Viewed by 1144
Abstract
Esophageal squamous cell cancer (ESCC) is an aggressive disease associated with a poor prognosis. Long non-coding RNAs (lncRNAs) and oxidative stress play crucial roles in tumor progression. We aimed to identify an oxidative stress-related lncRNA signature that could predict the prognosis in ESCC. [...] Read more.
Esophageal squamous cell cancer (ESCC) is an aggressive disease associated with a poor prognosis. Long non-coding RNAs (lncRNAs) and oxidative stress play crucial roles in tumor progression. We aimed to identify an oxidative stress-related lncRNA signature that could predict the prognosis in ESCC. In the GSE53625 dataset, we identified 332 differentially expressed lncRNAs (DElncRNAs) between ESCC and control samples, out of which 174 were oxidative stress-related DElncRNAs. Subsequently, seven oxidative stress-related DElncRNAs (CCR5AS, LINC01749, PCDH9-AS1, TMEM220-AS1, KCNMA1-AS1, SNHG1, LINC01672) were selected based on univariate and LASSO Cox to build a prognostic risk model, and their expression was detected by RT-qPCR. The model exhibited an excellent ability for the prediction of overall survival (OS) and other clinicopathological traits using Kaplan–Meier (K-M) survival curves, receiver operating characteristic (ROC) curves, and the Wilcoxon test. Additionally, analysis of infiltrated immune cells and immune checkpoints indicated differences in immune status between the two risk groups. Finally, the in vitro experiments showed that PCDH9-AS1 overexpression inhibited proliferation ability and promoted apoptosis and oxidative stress levels in ESCC cells. In conclusion, our study demonstrated that a novel oxidative stress-related DElncRNA prognostic model performed favorably in predicting ESCC patient prognosis and benefits personalized clinical applications. Full article
(This article belongs to the Topic Biomarker Development and Application)
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47 pages, 2234 KiB  
Review
Revisiting Circulating Extracellular Matrix Fragments as Disease Markers in Myelofibrosis and Related Neoplasms
by Hans Carl Hasselbalch, Peter Junker, Vibe Skov, Lasse Kjær, Trine A. Knudsen, Morten Kranker Larsen, Morten Orebo Holmström, Mads Hald Andersen, Christina Jensen, Morten A. Karsdal and Nicholas Willumsen
Cancers 2023, 15(17), 4323; https://doi.org/10.3390/cancers15174323 - 29 Aug 2023
Cited by 2 | Viewed by 2600
Abstract
Philadelphia chromosome-negative chronic myeloproliferative neoplasms (MPNs) arise due to acquired somatic driver mutations in stem cells and develop over 10–30 years from the earliest cancer stages (essential thrombocythemia, polycythemia vera) towards the advanced myelofibrosis stage with bone marrow failure. The JAK2V617F mutation is [...] Read more.
Philadelphia chromosome-negative chronic myeloproliferative neoplasms (MPNs) arise due to acquired somatic driver mutations in stem cells and develop over 10–30 years from the earliest cancer stages (essential thrombocythemia, polycythemia vera) towards the advanced myelofibrosis stage with bone marrow failure. The JAK2V617F mutation is the most prevalent driver mutation. Chronic inflammation is considered to be a major pathogenetic player, both as a trigger of MPN development and as a driver of disease progression. Chronic inflammation in MPNs is characterized by persistent connective tissue remodeling, which leads to organ dysfunction and ultimately, organ failure, due to excessive accumulation of extracellular matrix (ECM). Considering that MPNs are acquired clonal stem cell diseases developing in an inflammatory microenvironment in which the hematopoietic cell populations are progressively replaced by stromal proliferation—“a wound that never heals”—we herein aim to provide a comprehensive review of previous promising research in the field of circulating ECM fragments in the diagnosis, treatment and monitoring of MPNs. We address the rationales and highlight new perspectives for the use of circulating ECM protein fragments as biologically plausible, noninvasive disease markers in the management of MPNs. Full article
(This article belongs to the Topic Biomarker Development and Application)
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16 pages, 440 KiB  
Systematic Review
Effectiveness of Treatments That Alter Metabolomics in Cancer Patients—A Systematic Review
by Santiago Navarro Ledesma, Dina Hamed-Hamed, Ana González-Muñoz and Leo Pruimboom
Cancers 2023, 15(17), 4297; https://doi.org/10.3390/cancers15174297 - 28 Aug 2023
Cited by 2 | Viewed by 2168
Abstract
Introduction: Cancer is the leading cause of death worldwide, with the most frequent being breast cancer in women, prostate cancer in men and colon cancer in both sexes. The use of metabolomics to find new biomarkers can provide knowledge about possible interventions based [...] Read more.
Introduction: Cancer is the leading cause of death worldwide, with the most frequent being breast cancer in women, prostate cancer in men and colon cancer in both sexes. The use of metabolomics to find new biomarkers can provide knowledge about possible interventions based on the presence of oncometabolites in different cancer types. Objectives: The primary purpose of this review is to analyze the characteristic metabolome of three of the most frequent cancer types. We further want to identify the existence and success rate of metabolomics-based intervention in patients suffering from those cancer types. Our conclusions are based on the analysis of the methodological quality of the studies. Methods: We searched for studies that investigated the metabolomic characteristics in patients suffering from breast cancer, prostate cancer or colon cancer in clinical trials. The data were analyzed, as well as the effects of specific interventions based on identified metabolomics and one or more oncometabolites. The used databases were PubMed, Virtual Health Library, Web of Science, EBSCO and Cochrane Library. Only nine studies met the selection criteria. Study bias was analyzed using the Cochrane risk of bias tool. This systematic review protocol was registered at the International Prospective Register of Systematic Reviews (PROSPERO: CRD42023401474). Results: Only nine studies about clinical trials were included in this review and show a moderate quality of evidence. Metabolomics-based interventions related with disease outcome were conflictive with no or small changes in the metabolic characteristics of the different cancer types. Conclusions: This systematic review shows some interesting results related with metabolomics-based interventions and their effects on changes in certain cancer oncometabolites. The small number of studies we identified which fulfilled our inclusion criteria in this systematic review does not allow us to draw definitive conclusions. Nevertheless, some results can be considered as promising although further research is needed. That research must focus not only on the presence of possible oncometabolites but also on possible metabolomics-based interventions and their influence on the outcome in patients suffering from breast cancer, prostate cancer or colon cancer. Full article
(This article belongs to the Topic Biomarker Development and Application)
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12 pages, 2893 KiB  
Article
Does the Necrotic Portion of Metastatic Lymphadenopathy from Squamous Cell Carcinoma Still Have Tumoral Oncologic Information? Differential Diagnosis of Benign Necrotic Lymphadenopathy Using microRNA
by Eun Shin, Seung Hoon Han, Il-Seok Park, Jee Hye Wee, Joong Seob Lee and Heejin Kim
Biomedicines 2023, 11(9), 2407; https://doi.org/10.3390/biomedicines11092407 - 28 Aug 2023
Viewed by 3772
Abstract
Neck necrotic lymph nodes commonly correspond to metastasis or benign inflammatory conditions such as Kikuchi disease and tuberculosis. Ultrasound-guided biopsy can be used for differential diagnosis, but results may be unclear. Therefore, this study aimed to identify target microRNAs (miRNAs) and genes for [...] Read more.
Neck necrotic lymph nodes commonly correspond to metastasis or benign inflammatory conditions such as Kikuchi disease and tuberculosis. Ultrasound-guided biopsy can be used for differential diagnosis, but results may be unclear. Therefore, this study aimed to identify target microRNAs (miRNAs) and genes for the differential diagnosis of inflammatory and malignant necrotic lymph nodes. We selected six inflammatory lymphadenitis formalin-fixed paraffin-embedded (FFPE) samples that showed internal necrosis and five cancer necrotic FFPE samples. Tissue microarray (TMA) was performed to separate the necrotic and cancerous portions. Total RNA was extracted from six pairs of separated inflammatory necrosis, five pairs of cancer necrosis, and cancer portions. Differentially expressed miRNAs were analyzed by comparing inflammatory necrosis, cancer, and cancer necrosis. Seventeen miRNAs were upregulated in cancer necrosis compared to inflammatory necrosis, and two miRNAs (hsa-miR-155-5p and hsa-miR-146b-5p) showed lower expression in cancer necrotic cells. Nineteen miRNAs that were differentially expressed between inflammatory and cancer necrosis were analyzed for target gene expression; these transcripts demonstrated a clear relationship with cancer. The differentially expressed miRNAs in inflammatory and tumor necrosis were associated with cancer-related pathways. These preliminary results might help in the differential diagnosis of cervical metastatic necrotic lymphadenopathy and avoiding unnecessary excisional biopsies. Full article
(This article belongs to the Topic Biomarker Development and Application)
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15 pages, 6806 KiB  
Article
Elevated UTI Biomarkers in Symptomatic Patients with Urine Microbial Densities of 10,000 CFU/mL Indicate a Lower Threshold for Diagnosing UTIs
by Laura K. S. Parnell, Natalie Luke, Mohit Mathur, Richard A. Festa, Emery Haley, Jimin Wang, Yan Jiang, Lori Anderson and David Baunoch
Diagnostics 2023, 13(16), 2688; https://doi.org/10.3390/diagnostics13162688 - 16 Aug 2023
Cited by 5 | Viewed by 1411
Abstract
The literature lacks consensus on the minimum microbial density required for diagnosing urinary tract infections (UTIs). This study categorized the microbial densities of urine specimens from symptomatic UTI patients aged ≥ 60 years and correlated them with detected levels of the immune response [...] Read more.
The literature lacks consensus on the minimum microbial density required for diagnosing urinary tract infections (UTIs). This study categorized the microbial densities of urine specimens from symptomatic UTI patients aged ≥ 60 years and correlated them with detected levels of the immune response biomarkers neutrophil gelatinase-associated lipocalin (NGAL), interleukin-8 (IL-8), and interleukin-1-beta (IL-1β). The objective was to identify the microbial densities associated with significant elevation of these biomarkers in order to determine an optimal threshold for diagnosing symptomatic UTIs. Biobanked midstream voided urine samples were analyzed for microbial identification and quantification using standard urine culture (SUC) and multiplex-polymerase chain reaction (M-PCR) testing, while NGAL, IL-8, and IL-1β levels were measured via enzyme-linked immunosorbent assay (ELISA). NGAL, IL-8, and IL-1β levels were all significantly elevated at microbial densities ≥ 10,000 cells/mL when measured via M-PCR (p < 0.0069) or equivalent colony-forming units (CFUs)/mL via SUC (p < 0.0104) compared to samples with no detectable microbes. With both PCR and SUC, a consensus of two or more elevated biomarkers correlated well with microbial densities > 10,000 cells/mL or CFU/mL, respectively. The association between ≥10,000 cells and CFU per mL with elevated biomarkers in symptomatic patients suggests that this lower threshold may be more suitable than 100,000 CFU/mL for diagnosing UTIs. Full article
(This article belongs to the Topic Biomarker Development and Application)
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10 pages, 1248 KiB  
Article
Analysis of Urinary Glycosaminoglycans to Predict Outcome in COVID-19 and Community-Acquired Pneumonia—A Proof-of-Concept Study
by Alexandros Rovas, Julia Katharina Neumann, Carolin Christina Drost, Richard Vollenberg, Gerold Thölking, Manfred Fobker, Martin Witzenrath, Philipp Kümpers, AGAMOTTO Study Group and CAPNETZ Study Group
J. Clin. Med. 2023, 12(16), 5269; https://doi.org/10.3390/jcm12165269 - 13 Aug 2023
Viewed by 903
Abstract
Although coronavirus disease 2019 (COVID-19) is considered a systemic disease associated with vascular inflammation and eventual destruction of the protective endothelial glycocalyx (eGC), biomarkers of eGC damage are not yet available in the clinic. The most prominent components of eGC are sulphated glycosaminoglycans [...] Read more.
Although coronavirus disease 2019 (COVID-19) is considered a systemic disease associated with vascular inflammation and eventual destruction of the protective endothelial glycocalyx (eGC), biomarkers of eGC damage are not yet available in the clinic. The most prominent components of eGC are sulphated glycosaminoglycans (sGAGs) attached to core proteoglycans. We hypothesised that the amount of sGAG fragments shed in urine (as a surrogate for systemic eGC damage) would correlate with disease severity and outcome. Total urinary sGAG concentration was measured using an in-house optimised 1,9-dimethylmethylene blue (DMMB) assay, which is highly accurate and insensitive to interferences. The median urinary sGAG concentration was significantly higher in 67 hospitalised patients with COVID-19 compared to 72 hospitalised patients with community-acquired pneumonia (CAP). In both groups, urinary sGAG concentrations predicted a combined endpoint (including intubation and death) with an area under the receiver operator characteristic curve of 0.72 (95% CI 0.55–0.88, p = 0.01) and 0.70 (95% CI 0.57–0.83, p = 0.007), respectively. In conclusion, the inexpensive and easy-to-perform DMMB assay provides a surrogate parameter for eGC damage that may be useful for risk stratification of patients with COVID-19 and CAP. Full article
(This article belongs to the Topic Biomarker Development and Application)
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9 pages, 857 KiB  
Article
Evaluation of CIN2/3 Lesion Regression in GynTect® DNA Methylation-Marker-Negative Patients in a Longitudinal Study
by Heike Hoyer, Claudia Stolte, Gerd Böhmer, Monika Hampl, Ingke Hagemann, Elisabeth Maier, Agnieszka Denecke, Christine Hirchenhain, Jan Patzke, Matthias Jentschke, Axel Gerick, Tabitha Heller, Juliane Hippe, Kristina Wunsch, Martina Schmitz and Matthias Dürst
Cancers 2023, 15(15), 3951; https://doi.org/10.3390/cancers15153951 - 03 Aug 2023
Viewed by 960
Abstract
Cervical intraepithelial neoplasia (CIN) grade 2/3 has a high spontaneous regression rate, especially among women ≤29 years of age. To reduce overtreatment, reliable prognostic biomarkers would be helpful. The main aim of this study was to analyze the negative predictive value of the [...] Read more.
Cervical intraepithelial neoplasia (CIN) grade 2/3 has a high spontaneous regression rate, especially among women ≤29 years of age. To reduce overtreatment, reliable prognostic biomarkers would be helpful. The main aim of this study was to analyze the negative predictive value of the methylation marker panel GynTect® for lesion regression. In this prospective, multicenter, longitudinal observational proof-of-concept study, women aged ≤29 years with histologically confirmed CIN2 (n = 24) or CIN3 (n = 36) were closely monitored without treatment for up to 24 or 12 months, respectively. The outcome was either regression, persistence, or progression of the lesion. For each patient, a single baseline sample (V0) for cytology, hrHPV detection and methylation analysis was taken. In a primary analysis, the negative predictive value (NPV) of a GynTect®-negative test result at V0 for regression was determined. We tested the null hypothesis NPV ≤ 70% against the alternative hypothesis NPV ≥ 90%. Twelve of the eighteen GynTect®-negative CIN2 patients showed regression (NPV = 67%, 90% CI 44–85%, p = 0.53). Of the 27 GynTect®-negative CIN3 lesions, 15 regressed (NPV = 56%, 90% CI 38–72%, p = 0.92). Although the majority of GynTect®-negative lesions regressed, the postulated NPV of ≥90% was not observed. Thus, the clinical relevance for an implementation of the GynTect® assay for patients undergoing watchful waiting remains questionable. Further studies with longer observation periods should be undertaken. Full article
(This article belongs to the Topic Biomarker Development and Application)
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12 pages, 1831 KiB  
Article
Optical Coherence Tomography: Focus on the Pathology of Macula in Scleritis Patients
by Lilla Smeller, Edit Toth-Molnar and Nicolette Sohar
J. Clin. Med. 2023, 12(14), 4825; https://doi.org/10.3390/jcm12144825 - 21 Jul 2023
Viewed by 747
Abstract
Optical coherence tomography (OCT) is a non-invasive imaging technique for high-resolution, cross-sectional tissue imaging of the eye. During the past two and a half decades, OCT has become an essential tool in ophthalmology. It is a painless method for examining details of ocular [...] Read more.
Optical coherence tomography (OCT) is a non-invasive imaging technique for high-resolution, cross-sectional tissue imaging of the eye. During the past two and a half decades, OCT has become an essential tool in ophthalmology. It is a painless method for examining details of ocular structures in vivo with high resolution that has revolutionized patient care following and treating scleritis patients. Methods: Twenty-four patients diagnosed with scleritis were selected for this study. All of the patients went through basic ophthalmological examinations, such as visual acuity testing (VA), intraocular pressure measurement (IOP), slit lamp examination, ophthalmoscopic examination, and OCT. OCT examinations were taken by SD-OCT Spectralis OCT system (Heidelberg Engineering, Heidelberg, Germany). Results: Twenty-seven eyes of 24 patients (7 males and 17 females) were included in this study, who were diagnosed with scleritis. OCT examinations showed epiretinal membrane (ERM) in three patients (12%), cystoid macular edema (CME) (three cases, 12%), diffuse macular edema (DME) (one case, 4%), and serous retinal detachment (SRD) (one case, 4%). Conclusions: OCT proved to be a valuable, non-invasive method for detecting macular pathology in patients with scleritis. Despite the best treatment regimen applied, macular involvement resulting in reduced visual acuity (VA) can develop, which we could detect with OCT since macular edema (ME) is the leading cause of decreased vision due to the damaged outer blood–retina barrier (BRB) in inflammation. OCT investigation is a highly important method for early detection of ocular complications in scleritis in order to prevent blindness. Full article
(This article belongs to the Topic Biomarker Development and Application)
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17 pages, 6326 KiB  
Article
Cell-Free DNA Extracted from CSF for the Molecular Diagnosis of Pediatric Embryonal Brain Tumors
by Mathieu Chicard, Yasmine Iddir, Julien Masliah Planchon, Valérie Combaret, Valéry Attignon, Alexandra Saint-Charles, Didier Frappaz, Cécile Faure-Conter, Kévin Beccaria, Pascale Varlet, Birgit Geoerger, Sylvain Baulande, Gaelle Pierron, Yassine Bouchoucha, François Doz, Olivier Delattre, Joshua J. Waterfall, Franck Bourdeaut and Gudrun Schleiermacher
Cancers 2023, 15(13), 3532; https://doi.org/10.3390/cancers15133532 - 07 Jul 2023
Viewed by 1421
Abstract
Background: Liquid biopsies are revolutionary tools used to detect tumor-specific genetic alterations in body fluids, including the use of cell-free DNA (cfDNA) for molecular diagnosis in cancer patients. In brain tumors, cerebrospinal fluid (CSF) cfDNA might be more informative than plasma cfDNA. Here, [...] Read more.
Background: Liquid biopsies are revolutionary tools used to detect tumor-specific genetic alterations in body fluids, including the use of cell-free DNA (cfDNA) for molecular diagnosis in cancer patients. In brain tumors, cerebrospinal fluid (CSF) cfDNA might be more informative than plasma cfDNA. Here, we assess the use of CSF cfDNA in pediatric embryonal brain tumors (EBT) for molecular diagnosis. Methods: The CSF cfDNA of pediatric patients with medulloblastoma (n = 18), ATRT (n = 3), ETMR (n = 1), CNS NB FOXR2 (n = 2) and pediatric EBT NOS (n = 1) (mean cfDNA concentration 48 ng/mL; range 4–442 ng/mL) and matched tumor genomic DNA were sequenced by WES and/or a targeted sequencing approach to determine single-nucleotide variations (SNVs) and copy number alterations (CNA). A specific capture covering transcription start sites (TSS) of genes of interest was also used for nucleosome footprinting in CSF cfDNA. Results: 15/25 CSF cfDNA samples yielded informative results, with informative CNA and SNVs in 11 and 15 cases, respectively. For cases with paired tumor and CSF cfDNA WES (n = 15), a mean of 83 (range 1–160) shared SNVs were observed, including SNVs in classical medulloblastoma genes such as SMO and KMT2D. Interestingly, tumor-specific SNVs (mean 18; range 1–62) or CSF-specific SNVs (mean 5; range 0–25) were also observed, suggesting clonal heterogeneity. The TSS panel resulted in differential coverage profiles across all 112 studied genes in 7 cases, indicating distinct promoter accessibility. Conclusion: CSF cfDNA sequencing yielded informative results in 60% (15/25) of all cases, with informative results in 83% (15/18) of all cases analyzed by WES. These results pave the way for the implementation of these novel approaches for molecular diagnosis and minimal residual disease monitoring. Full article
(This article belongs to the Topic Biomarker Development and Application)
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13 pages, 2384 KiB  
Review
Atomic Force Microscopy Methods to Measure Tumor Mechanical Properties
by Julian Najera, Matthew R. Rosenberger and Meenal Datta
Cancers 2023, 15(13), 3285; https://doi.org/10.3390/cancers15133285 - 22 Jun 2023
Cited by 3 | Viewed by 1979
Abstract
Atomic force microscopy (AFM) is a popular tool for evaluating the mechanical properties of biological materials (cells and tissues) at high resolution. This technique has become particularly attractive to cancer researchers seeking to bridge the gap between mechanobiology and cancer initiation, progression, and [...] Read more.
Atomic force microscopy (AFM) is a popular tool for evaluating the mechanical properties of biological materials (cells and tissues) at high resolution. This technique has become particularly attractive to cancer researchers seeking to bridge the gap between mechanobiology and cancer initiation, progression, and treatment resistance. The majority of AFM studies thus far have been extensively focused on the nanomechanical characterization of cells. However, these approaches fail to capture the complex and heterogeneous nature of a tumor and its host organ. Over the past decade, efforts have been made to characterize the mechanical properties of tumors and tumor-bearing tissues using AFM. This has led to novel insights regarding cancer mechanopathology at the tissue scale. In this Review, we first explain the principles of AFM nanoindentation for the general study of tissue mechanics. We next discuss key considerations when using this technique and preparing tissue samples for analysis. We then examine AFM application in characterizing the mechanical properties of cancer tissues. Finally, we provide an outlook on AFM in the field of cancer mechanobiology and its application in the clinic. Full article
(This article belongs to the Topic Biomarker Development and Application)
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11 pages, 960 KiB  
Article
Acute Prosthetic Joint Infections with Poor Outcome Caused by Staphylococcus Aureus Strains Producing the Panton–Valentine Leukocidin
by Martina Maritati, Marco Manfrini, Maria Rosa Iaquinta, Alessandro Trentini, Silva Seraceni, Matteo Guarino, Anna Costanzini, Roberto De Giorgio, Gustavo Alberto Zanoli, Alessandro Borghi, Elisa Mazzoni, Giuseppe De Rito and Carlo Contini
Biomedicines 2023, 11(6), 1767; https://doi.org/10.3390/biomedicines11061767 - 20 Jun 2023
Viewed by 808
Abstract
The aim of this study was to investigate whether the presence of Staphylococcus aureus (SA) producing the Panton–Valentine leukocidin (PVL) affects the outcome of Prosthetic Joint Infection (PJI). Patients with acute and chronic PJI sustained by SA were prospectively enrolled at the orthopedic [...] Read more.
The aim of this study was to investigate whether the presence of Staphylococcus aureus (SA) producing the Panton–Valentine leukocidin (PVL) affects the outcome of Prosthetic Joint Infection (PJI). Patients with acute and chronic PJI sustained by SA were prospectively enrolled at the orthopedic unit of “Casa di Cura Santa Maria Maddalena”, from January 2019 to October 2021. PJI diagnosis was reached according to the diagnostic criteria of the International Consensus Meeting on PJI of Philadelphia. Synovial fluid obtained via joint aspirations was collected in order to isolate SA. The detection of PVL was performed via real-time quantitative PCR (RT-qPCR). The outcome assessment was performed using the criteria of the Delphi-based International Multidisciplinary Consensus. Twelve cases of PJI caused by SA were included. Nine (75%) cases were acute PJI treated using debridement, antibiotic and implant retention (DAIR); the remaining three (25%) were chronic PJI treated using two-stage (n = 2) and one-stage revision (n = 1), respectively. The SA strains that tested positive for PVL genes were 5/12 (41.6%,). Treatment failure was documented in three cases of acute PJI treated using DAIR, all supported by SA–PVL strains (p < 0.045). The remaining two cases were chronic PJI treated with a revision arthroplasty (one and two stage, respectively), with a 100% eradication rate in a medium follow-up of 24 months. Although a small case series, our study showed a 100% failure rate in acute PJI, probably caused by SA PVL-producing strains treated conservatively (p < 0.04). In this setting, toxin research should guide radical surgical treatment and targeted antibiotic therapy. Full article
(This article belongs to the Topic Biomarker Development and Application)
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10 pages, 1694 KiB  
Article
Novel Metabolomic Approach for Identifying Pathology-Specific Biomarkers in Rare Diseases: A Case Study in Oculopharyngeal Muscular Dystrophy (OPMD)
by Pradeep Harish, Alberto Malerba, Rosemarie H. M. J. M. Kroon, Milad Shademan, Baziel van Engelan, Vered Raz, Linda Popplewell and Stuart G. Snowden
Metabolites 2023, 13(6), 769; https://doi.org/10.3390/metabo13060769 - 19 Jun 2023
Cited by 1 | Viewed by 988
Abstract
The identification of metabolomic biomarkers relies on the analysis of large cohorts of patients compared to healthy controls followed by the validation of markers in an independent sample set. Indeed, circulating biomarkers should be causally linked to pathology to ensure that changes in [...] Read more.
The identification of metabolomic biomarkers relies on the analysis of large cohorts of patients compared to healthy controls followed by the validation of markers in an independent sample set. Indeed, circulating biomarkers should be causally linked to pathology to ensure that changes in the marker precede changes in the disease. However, this approach becomes unfeasible in rare diseases due to the paucity of samples, necessitating the development of new methods for biomarker identification. The present study describes a novel approach that combines samples from both mouse models and human patients to identify biomarkers of OPMD. We initially identified a pathology-specific metabolic fingerprint in murine dystrophic muscle. This metabolic fingerprint was then translated into (paired) murine serum samples and then to human plasma samples. This study identified a panel of nine candidate biomarkers that could predict muscle pathology with a sensitivity of 74.3% and specificity of 100% in a random forest model. These findings demonstrate that the proposed approach can identify biomarkers with good predictive performance and a higher degree of confidence in their relevance to pathology than markers identified in a small cohort of human samples alone. Therefore, this approach has a high potential utility for identifying circulating biomarkers in rare diseases. Full article
(This article belongs to the Topic Biomarker Development and Application)
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16 pages, 3109 KiB  
Article
Serum β-Defensin 2, A Novel Biomarker for the Diagnosis of Acute Infections
by John G. Routsias, Dionysia Marinou, Maria Mavrouli, Athanasios Tsakris and Vassiliki Pitiriga
Diagnostics 2023, 13(11), 1885; https://doi.org/10.3390/diagnostics13111885 - 28 May 2023
Cited by 3 | Viewed by 1124
Abstract
Background: Defensins are natural antimicrobial peptides that the human body secretes to protect itself from an infection. Thus, they are ideal molecules to serve as biomarkers for infection. This study was conducted to evaluate the levels of human β-defensins in patients with inflammation. [...] Read more.
Background: Defensins are natural antimicrobial peptides that the human body secretes to protect itself from an infection. Thus, they are ideal molecules to serve as biomarkers for infection. This study was conducted to evaluate the levels of human β-defensins in patients with inflammation. Methods: CRP, hBD2 and procalcitonin were measured in 423 sera of 114 patients with inflammation and healthy individuals using nephelometry and commercial ELISA assays. Results: Levels of hBD2 in the serum of patients with an infection were markedly elevated compared to those of hBD2 in patients with inflammation of non-infectious etiology (p < 0.0001, t = 10.17) and healthy individuals. ROC analysis demonstrated that hBD2 showed the highest detection performance for infection (AUC 0.897; p < 0.001) followed by PCT (AUC 0.576; p = ns) and CRP (AUC 0.517; p = ns). In addition, analysis of hBD2 and CRP in patients’ sera collected at different time points showed that hBD2 levels could help differentiate inflammation of infectious and non-infectious etiology during the first 5 days of hospitalization, while CRP levels could not. Conclusions: hBD2 has the potential to serve as a diagnostic biomarker for infection. In addition, the levels of hBD2 may reflect the efficacy of antibiotic treatment. Full article
(This article belongs to the Topic Biomarker Development and Application)
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16 pages, 2750 KiB  
Review
Lot-to-Lot Variance in Immunoassays—Causes, Consequences, and Solutions
by Yunyun Luo, Martin Pehrsson, Lasse Langholm, Morten Karsdal, Anne-Christine Bay-Jensen and Shu Sun
Diagnostics 2023, 13(11), 1835; https://doi.org/10.3390/diagnostics13111835 - 24 May 2023
Cited by 2 | Viewed by 2150
Abstract
Immunoassays, which have gained popularity in clinical practice and modern biomedical research, play an increasingly important role in quantifying various analytes in biological samples. Despite their high sensitivity and specificity, as well as their ability to analyze multiple samples in a single run, [...] Read more.
Immunoassays, which have gained popularity in clinical practice and modern biomedical research, play an increasingly important role in quantifying various analytes in biological samples. Despite their high sensitivity and specificity, as well as their ability to analyze multiple samples in a single run, immunoassays are plagued by the problem of lot-to-lot variance (LTLV). LTLV negatively affects assay accuracy, precision, and specificity, leading to considerable uncertainty in reported results. Therefore, maintaining consistency in technical performance over time presents a challenge in reproducing immunoassays. In this article, we share our two-decade-long experience and delve into the reasons for and locations of LTLV, as well as explore methods to mitigate its effects. Our investigation identifies potential contributing factors, including quality fluctuation in critical raw materials and deviations in manufacturing processes. These findings offer valuable insights to developers and researchers working with immunoassays, emphasizing the importance of considering lot-to-lot variance in assay development and application. Full article
(This article belongs to the Topic Biomarker Development and Application)
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13 pages, 1857 KiB  
Review
Biomarkers to Be Used for Decision of Treatment of Hypogonadal Men with or without Insulin Resistance
by Lello Zolla
Metabolites 2023, 13(6), 681; https://doi.org/10.3390/metabo13060681 - 23 May 2023
Viewed by 981
Abstract
Male hypogonadism is a result of low testosterone levels, but patients could be insulin-sensitive (IS) or insulin-resistant (IR), showing different impaired metabolic pathways. Thus, testosterone coadministration, which is commonly used to reestablish testosterone levels in hypogonadism, must take into account whether or not [...] Read more.
Male hypogonadism is a result of low testosterone levels, but patients could be insulin-sensitive (IS) or insulin-resistant (IR), showing different impaired metabolic pathways. Thus, testosterone coadministration, which is commonly used to reestablish testosterone levels in hypogonadism, must take into account whether or not insulin is still active. By comparing metabolic cycles recorded in IS and IR plasma before and after testosterone therapy (TRT), it is possible to know what metabolic pathways can be reactivated in the two different groups upon testosterone recovery, and it is possible to understand if antagonism or synergy exists between these two hormones. IS hypogonadism uses glycolysis, while IR hypogonadism activates gluconeogenesis through the degradation of branched-chain amino acids (BCAAs). Upon administration of testosterone, acceptable improvements are observed in IS patients, wherein many metabolic pathways are restored, while in IR patients, a reprogramming of metabolic cycles is observed. However, in both subgroups, lactate and acetyl-CoA increases significantly. In IS patients, lactate is used through the glucose–lactate cycle to produce energy, while in IR patients, both lactate and acetyl-CoA are metabolized into ketone bodies, which are used to produce energy. Thus, in IR patients, an ancestral molecular mechanism is activated to produce energy, mimicking insulin effects. Regarding lipids, in both groups, the utilization of fatty acids for energy (β-oxidation) is blocked, even after TRT; free fatty acids (FFAs) increase in the blood in IS patients, while they are incorporated into triglycerides in those with IR. In both subgroups of hypogonadism, supplementation of useful chemicals is recommended during and after TRT when metabolites are not restored; they are listed in this review. Full article
(This article belongs to the Topic Biomarker Development and Application)
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12 pages, 3714 KiB  
Article
Clofazimine-Mediated, Age-Related Changes in Skeletal Muscle Mitochondrial Metabolites
by Jennifer Diaz-Espinosa, Kathleen A. Stringer and Gus R. Rosania
Metabolites 2023, 13(5), 671; https://doi.org/10.3390/metabo13050671 - 19 May 2023
Cited by 1 | Viewed by 1058
Abstract
Mitochondrial health declines with age, and older patients can demonstrate dysfunction in mitochondrial-rich tissues, such as cardiac and skeletal muscle. Aged mitochondria may make older adults more susceptible to adverse drug reactions (ADRs). We assessed mitochondrial metabolic function by measuring two metabolites, l-carnitine [...] Read more.
Mitochondrial health declines with age, and older patients can demonstrate dysfunction in mitochondrial-rich tissues, such as cardiac and skeletal muscle. Aged mitochondria may make older adults more susceptible to adverse drug reactions (ADRs). We assessed mitochondrial metabolic function by measuring two metabolites, l-carnitine and acetylcarnitine, to determine their effectiveness as candidate clinical biomarkers for age-related, drug-induced alterations in mitochondrial metabolism. To study age- and medication-related changes in mitochondrial metabolism, we administered the FDA-approved mitochondriotropic drug, clofazimine (CFZ), or vehicle for 8 weeks to young (4-week-old) and old (61-week-old) male C57BL/6J mice. At the end of treatment, whole blood and cardiac and skeletal muscle were analyzed for l-carnitine, acetylcarnitine, and CFZ levels; muscle function was measured via a treadmill test. No differences were found in blood or cardiac carnitine levels of CFZ-treated mice, but CFZ-treated mice displayed lost body mass and alterations in endurance and levels of skeletal muscle mitochondrial metabolites. These findings demonstrate the age-related susceptibility of the skeletal muscle to mitochondria drug toxicity. Since drug-induced alterations in mitochondrial metabolism in skeletal muscle were not reflected in the blood by l-carnitine or acetylcarnitine levels, drug-induced catabolism and changes in muscle function appear more relevant to stratifying individuals at increased risk for ADRs. Full article
(This article belongs to the Topic Biomarker Development and Application)
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27 pages, 4387 KiB  
Article
Development and Validation of Blood-Based Predictive Biomarkers for Response to PD-1/PD-L1 Checkpoint Inhibitors: Evidence of a Universal Systemic Core of 3D Immunogenetic Profiling across Multiple Oncological Indications
by Ewan Hunter, Matthew Salter, Ryan Powell, Ann Dring, Tarun Naithani, Maria Eleni Chatziioannou, Abel Gebregzabhar, Mutaz Issa, Jayne Green, Serene Ng, Chun Ren Lim, Cheah Soon Keat, Ang Tick Suan, Rakesh Raman, Ho Kean Fatt, Fabian Lee Wei Luen, Heba Alshaker, Dmitri Pchejetski, Dave Blum, Thomas Guiel, Robert Heaton, Jr., Jedd Levine and Alexandre Akoulitchevadd Show full author list remove Hide full author list
Cancers 2023, 15(10), 2696; https://doi.org/10.3390/cancers15102696 - 10 May 2023
Cited by 3 | Viewed by 3555
Abstract
Background: Unprecedented advantages in cancer treatment with immune checkpoint inhibitors (ICIs) remain limited to only a subset of patients. Systemic analyses of the regulatory 3D genome architecture linked to individual epigenetic and immunogenetic controls associated with tumour immune evasion mechanisms and immune checkpoint [...] Read more.
Background: Unprecedented advantages in cancer treatment with immune checkpoint inhibitors (ICIs) remain limited to only a subset of patients. Systemic analyses of the regulatory 3D genome architecture linked to individual epigenetic and immunogenetic controls associated with tumour immune evasion mechanisms and immune checkpoint pathways reveal a highly prevalent molecular profile predictive of response to PD-1/PD-L1 ICIs. A clinical blood test based on a set of eight (8) 3D genomic biomarkers has been developed and validated on the basis of an observational trial to predict response to ICI therapy. Methods: The predictive eight biomarker set is derived from prospective observational clinical trials, representing 280 treatments with Pembrolizumab, Atezolizumab, Durvalumab, Nivolumab, and Avelumab in a broad range of indications: melanoma, lung, hepatocellular, renal, breast, bladder, colon, head and neck, bone, brain, lymphoma, prostate, vulvar, and cervical cancers. Results: The 3D genomic eight biomarker panel for response to immune checkpoint therapy achieved a high accuracy of 85%, sensitivity of 93%, and specificity of 82%. Conclusions: This study demonstrates that a 3D genomic approach can be used to develop a predictive clinical assay for response to PD-1/PD-L1 checkpoint inhibition in cancer patients. Full article
(This article belongs to the Topic Biomarker Development and Application)
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11 pages, 3739 KiB  
Article
Cerebral Glutamate Alterations Using Chemical Exchange Saturation Transfer Imaging in a Rat Model of Lipopolysaccharide-Induced Sepsis
by Do-Wan Lee, Jae-Im Kwon, Hwon Heo, Chul-Woong Woo, Na Hee Yu, Kyung Won Kim and Dong-Cheol Woo
Metabolites 2023, 13(5), 636; https://doi.org/10.3390/metabo13050636 - 08 May 2023
Cited by 3 | Viewed by 1199
Abstract
Glutamate-weighted chemical exchange saturation transfer (GluCEST) is a useful imaging tool to detect glutamate signal alterations caused by neuroinflammation. This study aimed to visualize and quantitatively evaluate hippocampal glutamate alterations in a rat model of sepsis-induced brain injury using GluCEST and proton magnetic [...] Read more.
Glutamate-weighted chemical exchange saturation transfer (GluCEST) is a useful imaging tool to detect glutamate signal alterations caused by neuroinflammation. This study aimed to visualize and quantitatively evaluate hippocampal glutamate alterations in a rat model of sepsis-induced brain injury using GluCEST and proton magnetic resonance spectroscopy (1H-MRS). Twenty-one Sprague Dawley rats were divided into three groups (sepsis-induced groups (SEP05, n = 7 and SEP10, n = 7) and controls (n = 7)). Sepsis was induced through a single intraperitoneal injection of lipopolysaccharide (LPS) at a dose of 5 mg/kg (SEP05) or 10 mg/kg (SEP10). GluCEST values and 1H-MRS concentrations in the hippocampal region were quantified using conventional magnetization transfer ratio asymmetry and a water scaling method, respectively. In addition, we examined immunohistochemical and immunofluorescence staining to observe the immune response and activity in the hippocampal region after LPS exposure. The GluCEST and 1H-MRS results showed that GluCEST values and glutamate concentrations were significantly higher in sepsis-induced rats than those in controls as the LPS dose increased. GluCEST imaging may be a helpful technique for defining biomarkers to estimate glutamate-related metabolism in sepsis-associated diseases. Full article
(This article belongs to the Topic Biomarker Development and Application)
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15 pages, 494 KiB  
Article
Plasma and Urinary Biomarkers Improve Prediction of Mortality through 1 Year in Intensive Care Patients: An Analysis from FROG-ICU
by Beth A. Davison, Christopher Edwards, Gad Cotter, Antoine Kimmoun, Étienne Gayat, Agnieszka Latosinska, Harald Mischak, Koji Takagi, Benjamin Deniau, Adrien Picod and Alexandre Mebazaa
J. Clin. Med. 2023, 12(9), 3311; https://doi.org/10.3390/jcm12093311 - 06 May 2023
Viewed by 1102
Abstract
Background: This study aimed to assess the value of blood and urine biomarkers in addition to routine clinical variables in risk stratification of patients admitted to ICU. Methods: Multivariable prognostic models were developed in this post hoc analysis of the French and EuRopean [...] Read more.
Background: This study aimed to assess the value of blood and urine biomarkers in addition to routine clinical variables in risk stratification of patients admitted to ICU. Methods: Multivariable prognostic models were developed in this post hoc analysis of the French and EuRopean Outcome ReGistry in Intensive Care Units study, a prospective observational study of patients admitted to ICUs. The study included 2087 patients consecutively admitted to the ICU who required invasive mechanical ventilation or a vasoactive agent for more than 24 h. The main outcome measures were in-ICU, in-hospital, and 1 year mortality. Results: Models including only SAPS II or APACHE II scores had c-indexes for in-hospital and 1 year mortality of 0.64 and 0.65, and 0.63 and 0.61, respectively. The c-indexes for a model including age and estimated glomerular filtration rate were higher at 0.69 and 0.67, respectively. Models utilizing available clinical variables increased the c-index for in-hospital and 1 year mortality to 0.80 and 0.76, respectively. The addition of biomarkers and urine proteomic markers increased c-indexes to 0.83 and 0.78. Conclusions: The commonly used scores for risk stratification in ICU patients did not perform well in this study. Models including clinical variables and biomarkers had significantly higher predictive values. Full article
(This article belongs to the Topic Biomarker Development and Application)
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15 pages, 1107 KiB  
Article
Identification of Serum Metabolites as Prognostic Biomarkers Following Spinal Cord Injury: A Pilot Study
by Elani A. Bykowski, Jamie N. Petersson, Sean Dukelow, Chester Ho, Chantel T. Debert, Tony Montina and Gerlinde A. S. Metz
Metabolites 2023, 13(5), 605; https://doi.org/10.3390/metabo13050605 - 28 Apr 2023
Cited by 3 | Viewed by 1656
Abstract
The assessment, management, and prognostication of spinal cord injury (SCI) mainly rely upon observer-based ordinal scales measures. 1H nuclear magnetic resonance (NMR) spectroscopy provides an effective approach for the discovery of objective biomarkers from biofluids. These biomarkers have the potential to aid [...] Read more.
The assessment, management, and prognostication of spinal cord injury (SCI) mainly rely upon observer-based ordinal scales measures. 1H nuclear magnetic resonance (NMR) spectroscopy provides an effective approach for the discovery of objective biomarkers from biofluids. These biomarkers have the potential to aid in understanding recovery following SCI. This proof-of-principle study determined: (a) If temporal changes in blood metabolites reflect the extent of recovery following SCI; (b) whether changes in blood-derived metabolites serve as prognostic indicators of patient outcomes based on the spinal cord independence measure (SCIM); and (c) whether metabolic pathways involved in recovery processes may provide insights into mechanisms that mediate neural damage and repair. Morning blood samples were collected from male complete and incomplete SCI patients (n = 7) following injury and at 6 months post-injury. Multivariate analyses were used to identify changes in serum metabolic profiles and were correlated to clinical outcomes. Specifically, acetyl phosphate, 1,3,7-trimethyluric acid, 1,9-dimethyluric acid, and acetic acid significantly related to SCIM scores. These preliminary findings suggest that specific metabolites may serve as proxy measures of the SCI phenotype and prognostic markers of recovery. Thus, serum metabolite analysis combined with machine learning holds promise in understanding the physiology of SCI and aiding in prognosticating outcomes following injury. Full article
(This article belongs to the Topic Biomarker Development and Application)
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12 pages, 1523 KiB  
Brief Report
Human Archaeological Dentin as Source of Polar and Less Polar Metabolites for Untargeted Metabolomic Research: The Case of Yersinia pestis
by Diego Armando Badillo-Sanchez, Donald J. L. Jones, Sarah A. Inskip and Christiana L. Scheib
Metabolites 2023, 13(5), 588; https://doi.org/10.3390/metabo13050588 - 24 Apr 2023
Viewed by 1267
Abstract
Metabolomic approaches, such as in clinical applications of living individuals, have shown potential use for solving questions regarding the past when applied to archaeological material. Here, we study for the first time the potential of this Omic approach as applied to metabolites extracted [...] Read more.
Metabolomic approaches, such as in clinical applications of living individuals, have shown potential use for solving questions regarding the past when applied to archaeological material. Here, we study for the first time the potential of this Omic approach as applied to metabolites extracted from archaeological human dentin. Dentin obtained from micro sampling the dental pulp of teeth of victims and non-victims of Yersinia pestis (plague) from a 6th century Cambridgeshire site are used to evaluate the potential use of such unique material for untargeted metabolomic studies on disease state through liquid chromatography hyphenated to high-resolution mass spectrometry (LC-HRMS). Results show that small molecules of both likely endogenous and exogenous sources are preserved for a range of polar and less polar/apolar metabolites in archaeological dentin; however, untargeted metabolomic profiles show no clear differentiation between healthy and infected individuals in the small sample analysed (n = 20). This study discusses the potential of dentin as a source of small molecules for metabolomic assays and highlights: (1) the need for follow up research to optimise sampling protocols, (2) the requirements of studies with larger sample numbers and (3) the necessity of more databases to amplify the positive results achievable with this Omic technique in the archaeological sciences. Full article
(This article belongs to the Topic Biomarker Development and Application)
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9 pages, 1026 KiB  
Brief Report
Long-Term Outcomes of Nasopharyngeal Carcinoma by Epstein–Barr Virus Status in the Chinese Population: A Multicenter Investigation
by Yudi Xiong, Mengting Yuan, Zhigang Liu, Jing Huang, Jianping Bi, Guoliang Pi, Ying Li, Yanping Li, Hanping He, Vivek Verma, Suqing Tian and Guang Han
J. Clin. Med. 2023, 12(8), 3005; https://doi.org/10.3390/jcm12083005 - 20 Apr 2023
Viewed by 982
Abstract
Background: Because the vast majority of nasopharyngeal carcinoma (NPC) in Chinese patients is a direct result of Epstein–Barr virus (EBV) infection, there is a dearth of data for EBV-negative patients in this population. This multicenter study sought to examine the clinical characteristics of [...] Read more.
Background: Because the vast majority of nasopharyngeal carcinoma (NPC) in Chinese patients is a direct result of Epstein–Barr virus (EBV) infection, there is a dearth of data for EBV-negative patients in this population. This multicenter study sought to examine the clinical characteristics of EBV-negative patients and compare long-term outcomes with a propensity-matched (1:1.5) EBV-positive cohort. Methods: NPC patients with known EBV status from four hospitals were collated (2013–2021). A logistic regression model was conducted to evaluate the relationship between patient characteristics and EBV status. The Kaplan–Meier method and Cox regression analysis were used to analyze survival data. Results: This study analyzed 48 (40%) EBV-negative and 72 (60%) EBV-positive patients. The median follow-up time was 63.5 months. Most EBV-negative NPC patients (77.1%) were diagnosed in advanced stages with a higher rate (87.5%) of positive lymph node disease, and no significant prognostic factors were discerned in this subpopulation. The EBV-negative disease was more associated with the keratinizing subtype (18.8% vs. 1.4%, p < 0.05). Compared to EBV-negative NPC patients, EBV-positive NPC patients were more likely to develop a local recurrence (9.7% vs. 0%, p = 0.026). There was no statistical difference in mortality (EBV-negative vs. EBV- positive, 8.3% vs. 4.2%, p = 0.34) during the follow-up period. Although the median PFS and median OS were not reached, the 3-year PFS rate was 68.8% vs. 70.8% (EBV-negative vs. EBV-positive, p = 0.06), the 3-year OS rate was 70.8% vs. 76.4% (EBV-negative vs. EBV-positive, p = 0.464), the 5-year PFS rate was 56.3% vs. 50% (EBV-negative vs. EBV-positive, p = 0.451), and the 5-year OS rate was 56.3% vs. 58.3% (EBV-negative vs. EBV-positive, p = 0.051), respectively. These data show that EBV-positive NPC patients seem to have a tendency to gain better survival compared with EBV-negative NPC patients. Conclusions: Most of the EBV-negative patients were in the middle and late stages at the time of diagnosis and were more associated with the keratinizing subtype. EBV status may be associated with prognosis in NPC. EBV positivity seems to be associated with better survival in NPC patients. Still, due to the small cohort of patients and the short observation period for a number of patients, further work is required to corroborate these conclusions. Full article
(This article belongs to the Topic Biomarker Development and Application)
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12 pages, 3117 KiB  
Article
Biophysical Changes of Leukocyte Activation (and NETosis) in the Cellular Host Response to Sepsis
by Matt G. Sorrells, Yurim Seo, Melia Magnen, Bliss Broussard, Roya Sheybani, Ajay M. Shah, Hollis R. O’Neal, Henry T. K. Tse, Jr., Mark R. Looney and Dino Di Carlo
Diagnostics 2023, 13(8), 1435; https://doi.org/10.3390/diagnostics13081435 - 16 Apr 2023
Cited by 3 | Viewed by 3165
Abstract
Sepsis, the leading cause of mortality in hospitals, currently lacks effective early diagnostics. A new cellular host response test, the IntelliSep test, may provide an indicator of the immune dysregulation characterizing sepsis. The objective of this study was to examine the correlation between [...] Read more.
Sepsis, the leading cause of mortality in hospitals, currently lacks effective early diagnostics. A new cellular host response test, the IntelliSep test, may provide an indicator of the immune dysregulation characterizing sepsis. The objective of this study was to examine the correlation between the measurements performed using this test and biological markers and processes associated with sepsis. Phorbol myristate acetate (PMA), an agonist of neutrophils known to induce neutrophil extracellular trap (NET) formation, was added to whole blood of healthy volunteers at concentrations of 0, 200, and 400 nM and then evaluated using the IntelliSep test. Separately, plasma from a cohort of subjects was segregated into Control and Diseased populations and tested for levels of NET components (citrullinated histone (cit-H3) DNA and neutrophil elastase (NE) DNA) using customized ELISA assays and correlated with ISI scores from the same patient samples. Significant increases in IntelliSep Index (ISI) scores were observed with increasing concentrations of PMA in healthy blood (0 and 200: p < 10−10; 0 and 400: p < 10−10). Linear correlation was observed between the ISI and quantities of NE DNA and Cit-H3 DNA in patient samples. Together these experiments demonstrate that the IntelliSep test is associated with the biological processes of leukocyte activation and NETosis and may indicate changes consistent with sepsis. Full article
(This article belongs to the Topic Biomarker Development and Application)
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14 pages, 4861 KiB  
Article
EZH2 and POU2F3 Can Aid in the Distinction of Thymic Carcinoma from Thymoma
by Julia R. Naso, Julie A. Vrana, Justin W. Koepplin, Julian R. Molina and Anja C. Roden
Cancers 2023, 15(8), 2274; https://doi.org/10.3390/cancers15082274 - 13 Apr 2023
Cited by 4 | Viewed by 1237
Abstract
Thymic carcinoma is an aggressive malignancy that can be challenging to distinguish from thymoma using histomorphology. We assessed two emerging markers for these entities, EZH2 and POU2F3, and compared them with conventional immunostains. Whole slide sections of 37 thymic carcinomas, 23 type A [...] Read more.
Thymic carcinoma is an aggressive malignancy that can be challenging to distinguish from thymoma using histomorphology. We assessed two emerging markers for these entities, EZH2 and POU2F3, and compared them with conventional immunostains. Whole slide sections of 37 thymic carcinomas, 23 type A thymomas, 13 type B3 thymomas, and 8 micronodular thymomas with lymphoid stroma (MNTLS) were immunostained for EZH2, POU2F3, CD117, CD5, TdT, BAP1, and MTAP. POU2F3 (≥10% hotspot staining), CD117, and CD5 showed 100% specificity for thymic carcinoma versus thymoma with 51%, 86%, and 35% sensitivity, respectively, for thymic carcinoma. All POU2F3 positive cases were also positive for CD117. All thymic carcinomas showed >10% EZH2 staining. EZH2 (≥80% staining) had a sensitivity of 81% for thymic carcinoma and a specificity of 100% for thymic carcinoma versus type A thymoma and MNTLS but had poor specificity (46%) for thymic carcinoma versus B3 thymoma. Adding EZH2 to a panel of CD117, TdT, BAP1, and MTAP increased cases with informative results from 67/81 (83%) to 77/81 (95%). Overall, absent EZH2 staining may be useful for excluding thymic carcinoma, diffuse EZH2 staining may help to exclude type A thymoma and MNTLS, and ≥10% POU2F3 staining has excellent specificity for thymic carcinoma versus thymoma. Full article
(This article belongs to the Topic Biomarker Development and Application)
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18 pages, 3778 KiB  
Article
A Dual Biomarker TK1 Protein and CA125 or HE4-Based Algorithm as a Better Diagnostic Tool than ROMA Index in Early Detection of Ovarian Cancer
by Diana Cviič, Kiran Jagarlamudi, Leon Meglič, Erik Škof, Andrej Zore, David Lukanović, Staffan Eriksson and Joško Osredkar
Cancers 2023, 15(5), 1593; https://doi.org/10.3390/cancers15051593 - 03 Mar 2023
Cited by 4 | Viewed by 2233
Abstract
Background: The early detection of ovarian cancer is presently not effective, and it is crucial to establish biomarkers for the early diagnosis of ovarian cancer to improve the survival of patients. Materials and methods: The aim of this study was to investigate the [...] Read more.
Background: The early detection of ovarian cancer is presently not effective, and it is crucial to establish biomarkers for the early diagnosis of ovarian cancer to improve the survival of patients. Materials and methods: The aim of this study was to investigate the role of thymidine kinase 1 (TK1) in combination with CA 125 or HE4 to serve as a potential diagnostic biomarkers for ovarian cancer. In this study, a set of 198 serum samples consisting of 134 ovarian tumor patients and 64 healthy age-matched controls were analyzed. The TK1 protein levels in serum samples were determined using the AroCell TK 210 ELISA. Results: A combination of TK1 protein with CA 125 or HE4 showed better performance than either of them alone in the differentiation of early stage ovarian cancer from the healthy control group, but also a significantly better performance than the ROMA index. However, this was not observed using a TK1 activity test in combination with the other markers. Furthermore, the combination of TK1 protein and CA 125 or HE4 could differentiate early stage disease (stage I, II) more efficiently from advanced-stage (stage III, IV) disease (p < 0.0001). Conclusions: The combination of TK1 protein with CA 125 or HE4 increased the potential of detecting ovarian cancer at early stages. Full article
(This article belongs to the Topic Biomarker Development and Application)
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10 pages, 971 KiB  
Article
Glucose-6-Phosphate Dehydrogenase Activity in Milk May Serve as a Non-Invasive Metabolic Biomarker of Energy Balance in Postpartum Dairy Cows
by Ayelet Hod, Jayasimha Rayalu Daddam, Gitit Kra, Hadar Kamer, Yuri Portnick, Uzi Moallem and Maya Zachut
Metabolites 2023, 13(2), 312; https://doi.org/10.3390/metabo13020312 - 20 Feb 2023
Viewed by 1403
Abstract
Negative energy balance (EB) postpartum is associated with adverse outcomes in dairy cows; therefore, non-invasive biomarkers to measure EB are of particular interest. We determined whether specific metabolites, oxidative stress indicators, enzyme activity, and fatty acid (FA) profiles in milk can serve as [...] Read more.
Negative energy balance (EB) postpartum is associated with adverse outcomes in dairy cows; therefore, non-invasive biomarkers to measure EB are of particular interest. We determined whether specific metabolites, oxidative stress indicators, enzyme activity, and fatty acid (FA) profiles in milk can serve as indicators of negative EB. Forty-two multiparous Holstein dairy cows were divided at calving into 2 groups: one was milked 3 times daily and the other, twice a day for the first 30 d in milk (DIM). Cows were classified retrospectively as being in either negative EB (NEB, n = 19; the mean EB during the first 21 DIM were less than the overall median of −2.8 Mcal/d), or in positive EB (PEB, n = 21; the mean EB was ≥−2.8 Mcal/d). The daily milk yield, feed intake, and body weight were recorded individually. Blood samples were analyzed for metabolites and stress biomarkers. Milk samples were taken twice weekly from 5 to 45 DIM to analyze the milk solids, the FA profile, glucose, glucose-6-P (G6P), G6P-dehydrogenase (G6PDH) activity, malic and lactic acids, malondialdehyde (MDA), and oxygen radical antioxidant capacity (ORAC). The NEB cows produced 10.5% more milk, and consumed 7.6% less dry matter than the PEB cows. The plasma glucose concentration was greater and β-hydroxybutyrate was lower in the PEB vs. the NEB cows. The average concentrations of milk glucose, G6P, malic and lactic acids, and MDA did not differ between groups; however, the G6PDH activity was higher and ORAC tended to be higher in the milk of NEB vs. the PEB cows. The correlation between milk G6PDH activity and EB was significant (r = −0.39). The percentages of oleic acid and total unsaturated FA in milk were higher for the NEB vs. the PEB cows. These findings indicate that G6PDH activity in milk is associated with NEB and that it can serve as a non-invasive candidate biomarker of NEB in postpartum cows, that should be validated in future studies. Full article
(This article belongs to the Topic Biomarker Development and Application)
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