Research

16 pages, 1861 KiB

Open AccessArticle

Subpopulations of Circulating Cells with Morphological Features of Malignancy Are Preoperatively Detected and Have Differential Prognostic Significance in Non-Small Cell Lung Cancer

by Emanuela Fina, Davide Federico, Pierluigi Novellis, Elisa Dieci, Simona Monterisi, Federica Cioffi, Giuseppe Mangiameli, Giovanna Finocchiaro, Marco Alloisio and Giulia Veronesi

Cancers 2021, 13(17), 4488; https://doi.org/10.3390/cancers13174488 - 06 Sep 2021

Cited by 6 | Viewed by 3672

Abstract

Background: Non-small cell lung cancer (NSCLC) frequently presents when surgical intervention is no longer feasible. Despite local treatment with curative intent, patients might experience disease recurrence. In this context, accurate non-invasive biomarkers are urgently needed. We report the results of a pilot study [...] Read more.

Background: Non-small cell lung cancer (NSCLC) frequently presents when surgical intervention is no longer feasible. Despite local treatment with curative intent, patients might experience disease recurrence. In this context, accurate non-invasive biomarkers are urgently needed. We report the results of a pilot study on the diagnostic and prognostic role of circulating tumor cells (CTCs) in operable NSCLC. Methods: Blood samples collected from healthy volunteers (n = 10), nodule-negative high-risk individuals enrolled in a screening program (n = 7), and NSCLC patients (n = 74) before surgery were analyzed (4 mL) for the presence of cells with morphological features of malignancy enriched through the ISET^® technology. Results: CTC detection was 60% in patients, while no target cells were found in lung cancer-free donors. We identified single CTCs (sCTC, 46%) and clusters of CTCs and leukocytes (heterotypic clusters, hetCLU, 31%). The prevalence of sCTC (sCTC/4 mL ≥ 2) or the presence of hetCLU predicted the risk of disease recurrence within the cohort of early-stage (I–II, n = 52) or advanced stage cases (III–IVA, n = 22), respectively, while other tumor-related factors did not inform prognosis. Conclusions: Cancer cell hematogenous dissemination occurs frequently in patients with NSCLC without clinical evidence of distant metastases, laying the foundation for the application of cell-based tests in screening programs. CTC subpopulations are fine prognostic classifiers whose clinical validity should be further investigated in larger studies. Full article

(This article belongs to the Special Issue Cancer Biomarkers in Body Fluids)

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18 pages, 1699 KiB

Open AccessArticle

Serum HPV16 E7 Oncoprotein Is a Recurrence Marker of Oropharyngeal Squamous Cell Carcinomas

by Lucia Oton-Gonzalez, John Charles Rotondo, Carmen Lanzillotti, Elisa Mazzoni, Ilaria Bononi, Maria Rosa Iaquinta, Luca Cerritelli, Nicola Malagutti, Andrea Ciorba, Chiara Bianchini, Stefano Pelucchi, Mauro Tognon and Fernanda Martini

Cancers 2021, 13(13), 3370; https://doi.org/10.3390/cancers13133370 - 05 Jul 2021

Cited by 6 | Viewed by 2315

Abstract

Despite improved prognosis for many HPV-positive head and neck squamous cell carcinomas (HNSCCs), some cases are still marked by recurrence and metastasis. Our study aimed to identify novel biomarkers for patient stratification. Classical HPV markers: HPV-DNA, p16 and HPV mRNA expression were studied [...] Read more.

Despite improved prognosis for many HPV-positive head and neck squamous cell carcinomas (HNSCCs), some cases are still marked by recurrence and metastasis. Our study aimed to identify novel biomarkers for patient stratification. Classical HPV markers: HPV-DNA, p16 and HPV mRNA expression were studied in HNSCC (n = 67) and controls (n = 58) by qPCR. Subsequently, ELISA tests were used for HPV16 L1 antibody and HPV16 E7 oncoprotein detection in serum at diagnosis and follow-up. All markers were correlated to relapse-free survival (RFS) and overall survival (OS). HPV-DNA was found in HNSCCs (29.85%), HPV16-DNA in 95% of cases, HPV16 E7 mRNA was revealed in 93.75%. p16 was overexpressed in 75% of HPV-positive HNSCC compared to negative samples and controls (p < 0.001). Classical markers correlated with improved OS (p < 0.05). Serological studies showed similar proportions of HPV16 L1 antibodies in all HNSCCs (p > 0.05). Serum E7 oncoprotein was present in 30% HPV-positive patients at diagnosis (p > 0.05) and correlated to HNSCC HPV16 E7 mRNA (p < 0.01), whereas it was associated to worse RFS and OS, especially for oropharyngeal squamous cell carcinoma (OPSCC) (p < 0.01). Detection of circulating HPV16 E7 oncoprotein at diagnosis may be useful for stratifying and monitoring HPV-positive HNSCC patients for worse prognosis, providing clinicians a tool for selecting patients for treatment de-escalation. Full article

(This article belongs to the Special Issue Cancer Biomarkers in Body Fluids)

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24 pages, 4567 KiB

Open AccessArticle

Comprehensive Plasma Metabolomic Profile of Patients with Advanced Neuroendocrine Tumors (NETs). Diagnostic and Biological Relevance

by Beatriz Soldevilla, Angeles López-López, Alberto Lens-Pardo, Carlos Carretero-Puche, Angeles Lopez-Gonzalvez, Anna La Salvia, Beatriz Gil-Calderon, Maria C. Riesco-Martinez, Paula Espinosa-Olarte, Jacinto Sarmentero, Beatriz Rubio-Cuesta, Raúl Rincón, Coral Barbas and Rocio Garcia-Carbonero

Cancers 2021, 13(11), 2634; https://doi.org/10.3390/cancers13112634 - 27 May 2021

Cited by 8 | Viewed by 4132

Abstract

Purpose: High-throughput “-omic” technologies have enabled the detailed analysis of metabolic networks in several cancers, but NETs have not been explored to date. We aim to assess the metabolomic profile of NET patients to understand metabolic deregulation in these tumors and identify novel [...] Read more.

Purpose: High-throughput “-omic” technologies have enabled the detailed analysis of metabolic networks in several cancers, but NETs have not been explored to date. We aim to assess the metabolomic profile of NET patients to understand metabolic deregulation in these tumors and identify novel biomarkers with clinical potential. Methods: Plasma samples from 77 NETs and 68 controls were profiled by GC−MS, CE−MS and LC−MS untargeted metabolomics. OPLS-DA was performed to evaluate metabolomic differences. Related pathways were explored using Metaboanalyst 4.0. Finally, ROC and OPLS-DA analyses were performed to select metabolites with biomarker potential. Results: We identified 155 differential compounds between NETs and controls. We have detected an increase of bile acids, sugars, oxidized lipids and oxidized products from arachidonic acid and a decrease of carnitine levels in NETs. MPA/MSEA identified 32 enriched metabolic pathways in NETs related with the TCA cycle and amino acid metabolism. Finally, OPLS-DA and ROC analysis revealed 48 metabolites with diagnostic potential. Conclusions: This study provides, for the first time, a comprehensive metabolic profile of NET patients and identifies a distinctive metabolic signature in plasma of potential clinical use. A reduced set of metabolites of high diagnostic accuracy has been identified. Additionally, new enriched metabolic pathways annotated may open innovative avenues of clinical research. Full article

(This article belongs to the Special Issue Cancer Biomarkers in Body Fluids)

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22 pages, 10025 KiB

Open AccessArticle

Immune Monitoring in Melanoma and Urothelial Cancer Patients Treated with Anti-PD-1 Immunotherapy and SBRT Discloses Tumor Specific Immune Signatures

by Annabel Meireson, Simon J. Tavernier, Sofie Van Gassen, Nora Sundahl, Annelies Demeyer, Mathieu Spaas, Vibeke Kruse, Liesbeth Ferdinande, Jo Van Dorpe, Benjamin Hennart, Delphine Allorge, Filomeen Haerynck, Karel Decaestecker, Sylvie Rottey, Yvan Saeys, Piet Ost and Lieve Brochez

Cancers 2021, 13(11), 2630; https://doi.org/10.3390/cancers13112630 - 27 May 2021

Cited by 3 | Viewed by 2766

Abstract

(1) Background: Blockade of the PD-1/PD-L1 pathway has revolutionized the oncology field in the last decade. However, the proportion of patients experiencing a durable response is still limited. In the current study, we performed an extensive immune monitoring in patients with stage III/IV [...] Read more.

(1) Background: Blockade of the PD-1/PD-L1 pathway has revolutionized the oncology field in the last decade. However, the proportion of patients experiencing a durable response is still limited. In the current study, we performed an extensive immune monitoring in patients with stage III/IV melanoma and stage IV UC who received anti-PD-1 immunotherapy with SBRT. (2) Methods: In total 145 blood samples from 38 patients, collected at fixed time points before and during treatment, were phenotyped via high-parameter flow cytometry, luminex assay and UPLC-MS/MS. (3) Results: Baseline systemic immunity in melanoma and UC patients was different with a more prominent myeloid compartment and a higher neutrophil to lymphocyte ratio in UC. Proliferation (Ki67⁺) of CD8⁺ T-cells and of the PD-1⁺/PD-L1⁺ CD8⁺ subset at baseline correlated with progression free survival in melanoma. In contrast a higher frequency of PD-1/PD-L1 expressing non-proliferating (Ki67⁻) CD8⁺ and CD4⁺ T-cells before treatment was associated with worse outcome in melanoma. In UC, the expansion of Ki67⁺ CD8⁺ T-cells and of the PD-L1⁺ subset relative to tumor burden correlated with clinical outcome. (4) Conclusion: This study reveals a clearly different immune landscape in melanoma and UC at baseline, which may impact immunotherapy response. Signatures of proliferation in the CD8⁺ T-cell compartment prior to and early after anti-PD-1 initiation were positively correlated with clinical outcome in both cohorts. PD-1/PD-L1 expression on circulating immune cell subsets seems of clinical relevance in the melanoma cohort. Full article

(This article belongs to the Special Issue Cancer Biomarkers in Body Fluids)

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18 pages, 17385 KiB

Open AccessArticle

Immune Monitoring during Therapy Reveals Activitory and Regulatory Immune Responses in High-Risk Neuroblastoma

by Celina L. Szanto, Annelisa M. Cornel, Sara M. Tamminga, Eveline M. Delemarre, Coco C. H. de Koning, Denise A. M. H. van den Beemt, Ester Dunnebach, Michelle L. Tas, Miranda P. Dierselhuis, Lieve G. A. M. Tytgat, Max M. van Noesel, Kathelijne C. J. M. Kraal, Jaap-Jan Boelens, Alwin D. R. Huitema and Stefan Nierkens

Cancers 2021, 13(9), 2096; https://doi.org/10.3390/cancers13092096 - 26 Apr 2021

Cited by 10 | Viewed by 3192

Abstract

Despite intensive treatment, including consolidation immunotherapy (IT), prognosis of high-risk neuroblastoma (HR-NBL) is poor. Immune status of patients over the course of treatment, and thus immunological features potentially explaining therapy efficacy, are largely unknown. In this study, the dynamics of immune cell subsets [...] Read more.

Despite intensive treatment, including consolidation immunotherapy (IT), prognosis of high-risk neuroblastoma (HR-NBL) is poor. Immune status of patients over the course of treatment, and thus immunological features potentially explaining therapy efficacy, are largely unknown. In this study, the dynamics of immune cell subsets and their function were explored in 25 HR-NBL patients at diagnosis, during induction chemotherapy, before high-dose chemotherapy, and during IT. The dynamics of immune cells varied largely between patients. IL-2- and GM-CSF-containing IT cycles resulted in significant expansion of effector cells (NK-cells in IL-2 cycles, neutrophils and monocytes in GM-CSF cycles). Nonetheless, the cytotoxic phenotype of NK-cells was majorly disturbed at the start of IT, and both IL-2 and GM-CSF IT cycles induced preferential expansion of suppressive regulatory T-cells. Interestingly, proliferative capacity of purified patient T-cells was impaired at diagnosis as well as during therapy. This study indicates the presence of both immune-enhancing as well as regulatory responses in HR-NBL patients during (immuno)therapy. Especially the double-edged effects observed in IL-2-containing IT cycles are interesting, as this potentially explains the absence of clinical benefit of IL-2 addition to IT cycles. This suggests that there is a need to combine anti-GD2 with more specific immune-enhancing strategies to improve IT outcome in HR-NBL. Full article

(This article belongs to the Special Issue Cancer Biomarkers in Body Fluids)

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12 pages, 1061 KiB

Open AccessArticle

A Novel Two-Lipid Signature Is a Strong and Independent Prognostic Factor in Ovarian Cancer

by Liina Salminen, Elena Ioana Braicu, Mitja Lääperi, Antti Jylhä, Sinikka Oksa, Sakari Hietanen, Jalid Sehouli, Hagen Kulbe, Andreas du Bois, Sven Mahner, Philipp Harter, Olli Carpén, Kaisa Huhtinen, Johanna Hynninen and Mika Hilvo

Cancers 2021, 13(8), 1764; https://doi.org/10.3390/cancers13081764 - 07 Apr 2021

Cited by 5 | Viewed by 2618

Abstract

Epithelial ovarian cancer (EOC) generally responds well to oncological treatments, but the eventual development of a refractory disease is a major clinical problem. Presently, there are no prognostic blood-based biomarkers for the stratification of EOC patients at the time of diagnosis. We set [...] Read more.

Epithelial ovarian cancer (EOC) generally responds well to oncological treatments, but the eventual development of a refractory disease is a major clinical problem. Presently, there are no prognostic blood-based biomarkers for the stratification of EOC patients at the time of diagnosis. We set out to assess and validate the prognostic utility of a novel two-lipid signature, as the lipidome is known to be markedly aberrant in EOC patients. The study consisted of 499 women with histologically confirmed EOC that were prospectively recruited at the university hospitals in Turku (Finland) and Charité (Berlin, Germany). Lipidomic screening by tandem liquid chromatography–mass spectrometry (LC-MS/MS) was performed for all baseline serum samples of these patients, and additionally for 20 patients of the Turku cohort at various timepoints. A two-lipid signature, based on the ratio of the ceramide Cer(d18:1/18:0) and phosphatidylcholine PC(O-38:4), showed consistent prognostic performance in all investigated study cohorts. In the Turku cohort, the unadjusted hazard ratios (HRs) per standard deviation (SD) (95% confidence interval) were 1.79 (1.40, 2.29) for overall and 1.40 (1.14, 1.71) for progression-free survival. In a Charité cohort incorporating only stage III completely resected patients, the corresponding HRs were 1.59 (1.08, 2.35) and 1.53 (1.02, 2.30). In linear-mixed models predicting progression of the disease, the two-lipid signature showed higher performance (beta per SD increase 1.99 (1.38, 2.97)) than cancer antigen 125 (CA-125, 1.78 (1.13, 2.87)). The two-lipid signature was able to identify EOC patients with an especially poor prognosis at the time of diagnosis, and also showed promise for the detection of disease relapse. Full article

(This article belongs to the Special Issue Cancer Biomarkers in Body Fluids)

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14 pages, 5166 KiB

Open AccessArticle

Circulating Tumor DNA Reflects Uveal Melanoma Responses to Protein Kinase C Inhibition

by John J. Park, Russell J. Diefenbach, Natalie Byrne, Georgina V. Long, Richard A. Scolyer, Elin S. Gray, Matteo S. Carlino and Helen Rizos

Cancers 2021, 13(7), 1740; https://doi.org/10.3390/cancers13071740 - 06 Apr 2021

Cited by 17 | Viewed by 3359

Abstract

The prognosis for patients with UM is poor, and recent clinical trials have failed to prolong overall survival (OS) of these patients. Over 95% of UM harbor activating driver mutations, and this allows for the investigation of ctDNA. In this study, we investigated [...] Read more.

The prognosis for patients with UM is poor, and recent clinical trials have failed to prolong overall survival (OS) of these patients. Over 95% of UM harbor activating driver mutations, and this allows for the investigation of ctDNA. In this study, we investigated the value of ctDNA for adaptive clinical trial design in metastatic UM. Longitudinal plasma samples were analyzed for ctDNA in 17 metastatic UM patients treated with PKCi-based therapy in a phase 1 clinical trial setting. Plasma ctDNA was assessed using digital droplet PCR (ddPCR) and a custom melanoma gene panel for targeted next generation sequencing (NGS). Baseline ctDNA strongly correlated with baseline lactate dehydrogenase (LDH) (p < 0.001) and baseline disease burden (p = 0.002). Early during treatment (EDT) ctDNA accurately predicted patients with clinical benefit to PKCi using receiver operator characteristic (ROC) curves (AUC 0.84, [95% confidence interval 0.65–1.0, p = 0.026]). Longitudinal ctDNA assessment was informative for establishing clinical benefit and detecting disease progression with 7/8 (88%) of patients showing a rise in ctDNA and targeted NGS of ctDNA revealed putative resistance mechanisms prior to radiological progression. The inclusion of longitudinal ctDNA monitoring in metastatic UM can advance adaptive clinical trial design. Full article

(This article belongs to the Special Issue Cancer Biomarkers in Body Fluids)

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15 pages, 1756 KiB

Open AccessArticle

Somatic Mutation Profiling in the Liquid Biopsy and Clinical Analysis of Hereditary and Familial Pancreatic Cancer Cases Reveals KRAS Negativity and a Longer Overall Survival

by Julie Earl, Emma Barreto, María E. Castillo, Raquel Fuentes, Mercedes Rodríguez-Garrote, Reyes Ferreiro, Pablo Reguera, Gloria Muñoz, David Garcia-Seisdedos, Jorge Villalón López, Bruno Sainz, Jr., Nuria Malats and Alfredo Carrato

Cancers 2021, 13(7), 1612; https://doi.org/10.3390/cancers13071612 - 31 Mar 2021

Cited by 4 | Viewed by 2530 | Correction

Abstract

Pancreatic ductal adenocarcinoma (PDAC) presents many challenges in the clinic and there are many areas for improvement in diagnostics and patient management. The five-year survival rate is around 7.2% as the majority of patients present with advanced disease at diagnosis that is treatment [...] Read more.

Pancreatic ductal adenocarcinoma (PDAC) presents many challenges in the clinic and there are many areas for improvement in diagnostics and patient management. The five-year survival rate is around 7.2% as the majority of patients present with advanced disease at diagnosis that is treatment resistant. Approximately 10–15% of PDAC cases have a hereditary basis or Familial Pancreatic Cancer (FPC). Here we demonstrate the use of circulating free DNA (cfDNA) in plasma as a prognostic biomarker in PDAC. The levels of cfDNA correlated with disease status, disease stage, and overall survival. Furthermore, we show for the first time via BEAMing that the majority of hereditary or familial PDAC cases (around 84%) are negative for a KRAS somatic mutation. In addition, KRAS mutation negative cases harbor somatic mutations in potentially druggable genes such as KIT, PDGFR, MET, BRAF, and PIK3CA that could be exploited in the clinic. Finally, familial or hereditary cases have a longer overall survival compared to sporadic cases (10.2 vs. 21.7 months, respectively). Currently, all patients are treated the same in the clinic with cytotoxic agents, although here we demonstrate that there are different subtypes of tumors at the genetic level that could pave the way to personalized treatment. Full article

(This article belongs to the Special Issue Cancer Biomarkers in Body Fluids)

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14 pages, 1891 KiB

Open AccessArticle

Tracking the Progression of Triple Negative Mammary Tumors over Time by Chemometric Analysis of Urinary Volatile Organic Compounds

by Mark Woollam, Luqi Wang, Paul Grocki, Shengzhi Liu, Amanda P. Siegel, Maitri Kalra, John V. Goodpaster, Hiroki Yokota and Mangilal Agarwal

Cancers 2021, 13(6), 1462; https://doi.org/10.3390/cancers13061462 - 23 Mar 2021

Cited by 12 | Viewed by 2677

Abstract

Previous studies have shown that volatile organic compounds (VOCs) are potential biomarkers of breast cancer. An unanswered question is how urinary VOCs change over time as tumors progress. To explore this, BALB/c mice were injected with 4T1.2 triple negative murine tumor cells in [...] Read more.

Previous studies have shown that volatile organic compounds (VOCs) are potential biomarkers of breast cancer. An unanswered question is how urinary VOCs change over time as tumors progress. To explore this, BALB/c mice were injected with 4T1.2 triple negative murine tumor cells in the tibia. This typically causes tumor progression and osteolysis in 1–2 weeks. Samples were collected prior to tumor injection and from days 2–19. Samples were analyzed by headspace solid phase microextraction coupled to gas chromatography–mass spectrometry. Univariate analysis identified VOCs that were biomarkers for breast cancer; some of these varied significantly over time and others did not. Principal component analysis was used to distinguish Cancer (all Weeks) from Control and Cancer Week 1 from Cancer Week 3 with over 90% accuracy. Forward feature selection and linear discriminant analysis identified a unique panel that could identify tumor presence with 94% accuracy and distinguish progression (Cancer Week 1 from Cancer Week 3) with 97% accuracy. Principal component regression analysis also demonstrated that a VOC panel could predict number of days since tumor injection (R² = 0.71 and adjusted R² = 0.63). VOC biomarkers identified by these analyses were associated with metabolic pathways relevant to breast cancer. Full article

(This article belongs to the Special Issue Cancer Biomarkers in Body Fluids)

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20 pages, 2672 KiB

Open AccessArticle

Liquid Biopsy-Based Exo-oncomiRNAs Can Predict Prostate Cancer Aggressiveness

by Xavier Ruiz-Plazas, Antonio Altuna-Coy, Marta Alves-Santiago, José Vila-Barja, Joan Francesc García-Fontgivell, Salomé Martínez-González, José Segarra-Tomás and Matilde R. Chacón

Cancers 2021, 13(2), 250; https://doi.org/10.3390/cancers13020250 - 11 Jan 2021

Cited by 23 | Viewed by 3455

Abstract

Liquid biopsy-based biomarkers, including microRNAs packaged within extracellular vesicles, are promising tools for patient management. The cytokine tumor necrosis factor-like weak inducer of apoptosis (TWEAK) is related to PCa progression and is found in the semen of patients with PCa. TWEAK can induce [...] Read more.

Liquid biopsy-based biomarkers, including microRNAs packaged within extracellular vesicles, are promising tools for patient management. The cytokine tumor necrosis factor-like weak inducer of apoptosis (TWEAK) is related to PCa progression and is found in the semen of patients with PCa. TWEAK can induce the transfer of exo-oncomiRNAs from tumor cells to body fluids, and this process might have utility in non-invasive PCa prognosis. We investigated TWEAK-regulated exo-microRNAs in semen and in post-digital rectal examination urine from patients with different degrees of PCa aggressiveness. We first identified 14 exo-oncomiRNAs regulated by TWEAK in PCa cells in vitro, and subsequently validated those using liquid biopsies from 97 patients with PCa. Exo-oncomiR-221-3p, -222-3p and -31-5p were significantly higher in the semen of high-risk patients than in low-risk peers, whereas exo-oncomiR-193-3p and -423-5p were significantly lower in paired samples of post-digital rectal examination urine. A panel of semen biomarkers comprising exo-oncomiR-221-3p, -222-3p and TWEAK was designed that could correctly classify 87.5% of patients with aggressive PCa, with 85.7% specificity and 76.9% sensitivity with an area under the curve of 0.857. We additionally found that TWEAK modulated two exo-oncomiR-221-3p targets, TCF12 and NLK. Overall, we show that liquid biopsy detection of TWEAK-regulated exo-oncomiRNAs can improve PCa prognosis prediction. Full article

(This article belongs to the Special Issue Cancer Biomarkers in Body Fluids)

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22 pages, 4982 KiB

Open AccessArticle

Molecular Signature of Extracellular Vesicular Small Non-Coding RNAs Derived from Cerebrospinal Fluid of Leptomeningeal Metastasis Patients: Functional Implication of miR-21 and Other Small RNAs in Cancer Malignancy

by Kyue-Yim Lee, Yoona Seo, Ji Hye Im, Jiho Rhim, Woosun Baek, Sewon Kim, Ji-Woong Kwon, Byong Chul Yoo, Sang Hoon Shin, Heon Yoo, Jong Bae Park, Ho-Shin Gwak and Jong Heon Kim

Cancers 2021, 13(2), 209; https://doi.org/10.3390/cancers13020209 - 08 Jan 2021

Cited by 9 | Viewed by 3169

Abstract

Leptomeningeal metastasis (LM) is a fatal and rare complication of cancer in which the cancer spreads via the cerebrospinal fluid (CSF). At present, there is no definitive treatment or diagnosis for this deleterious disease. In this study, we systemically and quantitatively investigated biased [...] Read more.

Leptomeningeal metastasis (LM) is a fatal and rare complication of cancer in which the cancer spreads via the cerebrospinal fluid (CSF). At present, there is no definitive treatment or diagnosis for this deleterious disease. In this study, we systemically and quantitatively investigated biased expression of key small non-coding RNA (smRNA) subpopulations from LM CSF extracellular vesicles (EVs) via a unique smRNA sequencing method. The analyzed subpopulations included microRNA (miRNA), Piwi-interacting RNA (piRNA), Y RNA, small nuclear RNA (snRNA), small nucleolar RNAs (snoRNA), vault RNA (vtRNA), novel miRNA, etc. Here, among identified miRNAs, miR-21, which was already known to play an essential oncogenic role in tumorigenesis, was thoroughly investigated via systemic biochemical, miR-21 sensor, and physiological cell-based approaches, with the goal of confirming its functionality and potential as a biomarker for the pathogenesis and diagnosis of LM. We herein uncovered LM CSF extravesicular smRNAs that may be associated with LM-related complications and elucidated plausible pathways that may mechanistically contribute to LM progression. In sum, the analyzed smRNA subpopulations will be useful as targets for the development of therapeutic and diagnostic strategies for LM and LM-related complications. Full article

(This article belongs to the Special Issue Cancer Biomarkers in Body Fluids)

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14 pages, 548 KiB

Open AccessArticle

Plasma Nucleosomes in Primary Breast Cancer

by Michal Mego, Katarina Kalavska, Marian Karaba, Gabriel Minarik, Juraj Benca, Tatiana Sedlackova, Paulina Gronesova, Dana Cholujova, Daniel Pindak, Jozef Mardiak and Peter Celec

Cancers 2020, 12(9), 2587; https://doi.org/10.3390/cancers12092587 - 10 Sep 2020

Cited by 3 | Viewed by 2079

Abstract

When cells die, nucleosomes composed of DNA and histone proteins enter the extracellular space and end eventually in the circulation. In plasma, they might serve as a nonspecific marker of cell death, potentially useful for noninvasive monitoring of tumor dynamics. The aim of [...] Read more.

When cells die, nucleosomes composed of DNA and histone proteins enter the extracellular space and end eventually in the circulation. In plasma, they might serve as a nonspecific marker of cell death, potentially useful for noninvasive monitoring of tumor dynamics. The aim of this study was to analyze circulating nucleosomes in relation to patient/tumor characteristics and prognosis in primary breast cancer. This study included 92 patients with breast cancer treated with surgery for whom plasma isolated was available in the biobank. Plasma nucleosomes were detected in samples taken in the morning on the day of surgery using Cell Death Detection ELISA kit with anti-histone and anti-DNA antibodies. Circulating nucleosomes were positively associated with the systemic inflammatory index (SII), but not with other patient/tumor characteristics. Patients with high SII in comparison to low SII had higher circulating nucleosomes (by 59%, p = 0.02). Nucleosomes correlated with plasma plasminogen activator inhibitor-1, IL-15, IL-16, IL-18, and hepatocyte growth factor. Patients with lower nucleosomes had significantly better disease-free survival (HR = 0.46, p = 0.05). In a multivariate analysis, nucleosomes, hormone receptor status, HER2 status, lymph node involvement, and tumor grade were independent predictors of disease-free survival. Our data suggest that plasma nucleosomes in primary breast cancer are associated with systemic inflammation and might have a prognostic value. The underlying mechanisms require further studies. Full article

(This article belongs to the Special Issue Cancer Biomarkers in Body Fluids)

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Review

Jump to: Research, Other

21 pages, 3071 KiB

Open AccessReview

Biomarkers and Lung Cancer Early Detection: State of the Art

by Elisa Dama, Tommaso Colangelo, Emanuela Fina, Marco Cremonesi, Marinos Kallikourdis, Giulia Veronesi and Fabrizio Bianchi

Cancers 2021, 13(15), 3919; https://doi.org/10.3390/cancers13153919 - 03 Aug 2021

Cited by 31 | Viewed by 5685

Abstract

Lung cancer burden is increasing, with 2 million deaths/year worldwide. Current limitations in early detection impede lung cancer diagnosis when the disease is still localized and thus more curable by surgery or multimodality treatment. Liquid biopsy is emerging as an important tool for [...] Read more.

Lung cancer burden is increasing, with 2 million deaths/year worldwide. Current limitations in early detection impede lung cancer diagnosis when the disease is still localized and thus more curable by surgery or multimodality treatment. Liquid biopsy is emerging as an important tool for lung cancer early detection and for monitoring therapy response. Here, we reviewed recent advances in liquid biopsy for early diagnosis of lung cancer. We summarized DNA- or RNA-based biomarkers, proteins, autoantibodies circulating in the blood, as well as circulating tumor cells (CTCs), and compared the most promising studies in terms of biomarkers prediction performance. While we observed an overall good performance for the proposed biomarkers, we noticed some critical aspects which may complicate the successful translation of these biomarkers into the clinical setting. We, therefore, proposed a roadmap for successful development of lung cancer biomarkers during the discovery, prioritization, and clinical validation phase. The integration of innovative minimally invasive biomarkers in screening programs is highly demanded to augment lung cancer early detection. Full article

(This article belongs to the Special Issue Cancer Biomarkers in Body Fluids)

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29 pages, 1002 KiB

Open AccessReview

Prostate Cancer Liquid Biopsy Biomarkers’ Clinical Utility in Diagnosis and Prognosis

by Milena Matuszczak, Jack A. Schalken and Maciej Salagierski

Cancers 2021, 13(13), 3373; https://doi.org/10.3390/cancers13133373 - 05 Jul 2021

Cited by 31 | Viewed by 6104

Abstract

Prostate cancer (PCa) is the most common cancer in men worldwide. The current gold standard for diagnosing PCa relies on a transrectal ultrasound-guided systematic core needle biopsy indicated after detection changes in a digital rectal examination (DRE) and elevated prostate-specific antigen (PSA) level [...] Read more.

Prostate cancer (PCa) is the most common cancer in men worldwide. The current gold standard for diagnosing PCa relies on a transrectal ultrasound-guided systematic core needle biopsy indicated after detection changes in a digital rectal examination (DRE) and elevated prostate-specific antigen (PSA) level in the blood serum. PSA is a marker produced by prostate cells, not just cancer cells. Therefore, an elevated PSA level may be associated with other symptoms such as benign prostatic hyperplasia or inflammation of the prostate gland. Due to this marker’s low specificity, a common problem is overdiagnosis, which leads to unnecessary biopsies and overtreatment. This is associated with various treatment complications (such as bleeding or infection) and generates unnecessary costs. Therefore, there is no doubt that the improvement of the current procedure by applying effective, sensitive and specific markers is an urgent need. Several non-invasive, cost-effective, high-accuracy liquid biopsy diagnostic biomarkers such as Progensa PCA3, MyProstateScore ExoDx, SelectMDx, PHI, 4K, Stockholm3 and ConfirmMDx have been developed in recent years. This article compares current knowledge about them and their potential application in clinical practice. Full article

(This article belongs to the Special Issue Cancer Biomarkers in Body Fluids)

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24 pages, 1433 KiB

Open AccessReview

Cancer Epigenetic Biomarkers in Liquid Biopsy for High Incidence Malignancies

by Cora Palanca-Ballester, Aitor Rodriguez-Casanova, Susana Torres, Silvia Calabuig-Fariñas, Francisco Exposito, Diego Serrano, Esther Redin, Karmele Valencia, Eloisa Jantus-Lewintre, Angel Diaz-Lagares, Luis Montuenga, Juan Sandoval and Alfonso Calvo

Cancers 2021, 13(12), 3016; https://doi.org/10.3390/cancers13123016 - 16 Jun 2021

Cited by 39 | Viewed by 5799

Abstract

Early alterations in cancer include the deregulation of epigenetic events such as changes in DNA methylation and abnormal levels of non-coding (nc)RNAs. Although these changes can be identified in tumors, alternative sources of samples may offer advantages over tissue biopsies. Because tumors shed [...] Read more.

Early alterations in cancer include the deregulation of epigenetic events such as changes in DNA methylation and abnormal levels of non-coding (nc)RNAs. Although these changes can be identified in tumors, alternative sources of samples may offer advantages over tissue biopsies. Because tumors shed DNA, RNA, and proteins, biological fluids containing these molecules can accurately reflect alterations found in cancer cells, not only coming from the primary tumor, but also from metastasis and from the tumor microenvironment (TME). Depending on the type of cancer, biological fluids encompass blood, urine, cerebrospinal fluid, and saliva, among others. Such samples are named with the general term “liquid biopsy” (LB). With the advent of ultrasensitive technologies during the last decade, the identification of actionable genetic alterations (i.e., mutations) in LB is a common practice to decide whether or not targeted therapy should be applied. Likewise, the analysis of global or specific epigenetic alterations may also be important as biomarkers for diagnosis, prognosis, and even for cancer drug response. Several commercial kits that assess the DNA promoter methylation of single genes or gene sets are available, with some of them being tested as biomarkers for diagnosis in clinical trials. From the tumors with highest incidence, we can stress the relevance of DNA methylation changes in the following genes found in LB: SHOX2 (for lung cancer); RASSF1A, RARB2, and GSTP1 (for lung, breast, genitourinary and colon cancers); and SEPT9 (for colon cancer). Moreover, multi-cancer high-throughput methylation-based tests are now commercially available. Increased levels of the microRNA miR21 and several miRNA- and long ncRNA-signatures can also be indicative biomarkers in LB. Therefore, epigenetic biomarkers are attractive and may have a clinical value in cancer. Nonetheless, validation, standardization, and demonstration of an added value over the common clinical practice are issues needed to be addressed in the transfer of this knowledge from “bench to bedside”. Full article

(This article belongs to the Special Issue Cancer Biomarkers in Body Fluids)

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37 pages, 2153 KiB

Open AccessReview

Epigenomic and Metabolomic Integration Reveals Dynamic Metabolic Regulation in Bladder Cancer

by Alba Loras, Cristina Segovia and José Luis Ruiz-Cerdá

Cancers 2021, 13(11), 2719; https://doi.org/10.3390/cancers13112719 - 31 May 2021

Cited by 8 | Viewed by 3307

Abstract

Bladder cancer (BC) represents a clinical, social, and economic challenge due to tumor-intrinsic characteristics, limitations of diagnostic techniques and a lack of personalized treatments. In the last decade, the use of liquid biopsy has grown as a non-invasive approach to characterize tumors. Moreover, [...] Read more.

Bladder cancer (BC) represents a clinical, social, and economic challenge due to tumor-intrinsic characteristics, limitations of diagnostic techniques and a lack of personalized treatments. In the last decade, the use of liquid biopsy has grown as a non-invasive approach to characterize tumors. Moreover, the emergence of omics has increased our knowledge of cancer biology and identified critical BC biomarkers. The rewiring between epigenetics and metabolism has been closely linked to tumor phenotype. Chromatin remodelers interact with each other to control gene silencing in BC, but also with stress-inducible factors or oncogenic signaling cascades to regulate metabolic reprogramming towards glycolysis, the pentose phosphate pathway, and lipogenesis. Concurrently, one-carbon metabolism supplies methyl groups to histone and DNA methyltransferases, leading to the hypermethylation and silencing of suppressor genes in BC. Conversely, α-KG and acetyl-CoA enhance the activity of histone demethylases and acetyl transferases, increasing gene expression, while succinate and fumarate have an inhibitory role. This review is the first to analyze the interplay between epigenome, metabolome and cell signaling pathways in BC, and shows how their regulation contributes to tumor development and progression. Moreover, it summarizes non-invasive biomarkers that could be applied in clinical practice to improve diagnosis, monitoring, prognosis and the therapeutic options in BC. Full article

(This article belongs to the Special Issue Cancer Biomarkers in Body Fluids)

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15 pages, 273 KiB

Open AccessReview

Urine as a Source of Liquid Biopsy for Cancer

by Masanori Oshi, Vijayashree Murthy, Hideo Takahashi, Michelle Huyser, Maiko Okano, Yoshihisa Tokumaru, Omar M. Rashid, Ryusei Matsuyama, Itaru Endo and Kazuaki Takabe

Cancers 2021, 13(11), 2652; https://doi.org/10.3390/cancers13112652 - 28 May 2021

Cited by 48 | Viewed by 5836

Abstract

Tissue biopsy is the gold standard for diagnosis and morphological and immunohistochemical analyses to characterize cancer. However, tissue biopsy usually requires an invasive procedure, and it can be challenging depending on the condition of the patient and the location of the tumor. Even [...] Read more.

Tissue biopsy is the gold standard for diagnosis and morphological and immunohistochemical analyses to characterize cancer. However, tissue biopsy usually requires an invasive procedure, and it can be challenging depending on the condition of the patient and the location of the tumor. Even liquid biopsy analysis of body fluids such as blood, saliva, gastric juice, sweat, tears and cerebrospinal fluid may require invasive procedures to obtain samples. Liquid biopsy can be applied to circulating tumor cells (CTCs) or nucleic acids (NAs) in blood. Recently, urine has gained popularity due to its less invasive sampling, ability to easily repeat samples, and ability to follow tumor evolution in real-time, making it a powerful tool for diagnosis and treatment monitoring in cancer patients. With the development and advancements in extraction methods of urinary substances, urinary NAs have been found to be closely related to carcinogenesis, metastasis, and therapeutic response, not only in urological cancers but also in non-urological cancers. This review mainly highlights the components of urine liquid biopsy and their utility and limitations in oncology, especially in non-urological cancers. Full article

(This article belongs to the Special Issue Cancer Biomarkers in Body Fluids)

16 pages, 2228 KiB

Open AccessReview

Exosomes in Liquid Biopsy: The Nanometric World in the Pursuit of Precision Oncology

by Karmele Valencia and Luis M. Montuenga

Cancers 2021, 13(9), 2147; https://doi.org/10.3390/cancers13092147 - 29 Apr 2021

Cited by 31 | Viewed by 4208

Abstract

Among the different components that can be analyzed in liquid biopsy, the utility of exosomes is particularly promising because of their presence in all biological fluids and their potential for multicomponent analyses. Exosomes are extracellular vesicles with an average size of ~100 nm [...] Read more.

Among the different components that can be analyzed in liquid biopsy, the utility of exosomes is particularly promising because of their presence in all biological fluids and their potential for multicomponent analyses. Exosomes are extracellular vesicles with an average size of ~100 nm in diameter with an endosomal origin. All eukaryotic cells release exosomes as part of their active physiology. In an oncologic patient, up to 10% of all the circulating exosomes are estimated to be tumor-derived exosomes. Exosome content mirrors the features of its cell of origin in terms of DNA, RNA, lipids, metabolites, and cytosolic/cell-surface proteins. Due to their multifactorial content, exosomes constitute a unique tool to capture the complexity and enormous heterogeneity of cancer in a longitudinal manner. Due to molecular features such as high nucleic acid concentrations and elevated coverage of genomic driver gene sequences, exosomes will probably become the “gold standard” liquid biopsy analyte in the near future. Full article

(This article belongs to the Special Issue Cancer Biomarkers in Body Fluids)

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20 pages, 1172 KiB

Open AccessReview

Serum Exosomes and Their miRNA Load—A Potential Biomarker of Lung Cancer

by Mateusz Smolarz and Piotr Widlak

Cancers 2021, 13(6), 1373; https://doi.org/10.3390/cancers13061373 - 18 Mar 2021

Cited by 25 | Viewed by 3778

Abstract

Early detection of lung cancer in screening programs is a rational way to reduce mortality associated with this malignancy. Low-dose computed tomography, a diagnostic tool used in lung cancer screening, generates a relatively large number of false-positive results, and its complementation with molecular [...] Read more.

Early detection of lung cancer in screening programs is a rational way to reduce mortality associated with this malignancy. Low-dose computed tomography, a diagnostic tool used in lung cancer screening, generates a relatively large number of false-positive results, and its complementation with molecular biomarkers would greatly improve the effectiveness of such programs. Several biomarkers of lung cancer based on different components of blood, including miRNA signatures, were proposed. However, only a few of them have been positively validated in the context of early cancer detection yet, which imposes a constant need for new biomarker candidates. An emerging source of cancer biomarkers are exosomes and other types of extracellular vesicles circulating in body fluids. Hence, different molecular components of serum/plasma-derived exosomes were tested and showed different levels in lung cancer patients and healthy individuals. Several studies focused on the miRNA component of these vesicles. Proposed signatures of exosome miRNA had promising diagnostic value, though none of them have yet been clinically validated. These signatures involved a few dozen miRNA species overall, including a few species that recurred in different signatures. It is worth noting that all these miRNA species have cancer-related functions and have been associated with lung cancer progression. Moreover, a few of them, including known oncomirs miR-17, miR-19, miR-21, and miR-221, appeared in multiple miRNA signatures of lung cancer based on both the whole serum/plasma and serum/plasma-derived exosomes. Full article

(This article belongs to the Special Issue Cancer Biomarkers in Body Fluids)

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20 pages, 1589 KiB

Open AccessReview

The Roadmap of Colorectal Cancer Screening

by Enea Ferlizza, Rossella Solmi, Michela Sgarzi, Luigi Ricciardiello and Mattia Lauriola

Cancers 2021, 13(5), 1101; https://doi.org/10.3390/cancers13051101 - 04 Mar 2021

Cited by 29 | Viewed by 5221

Abstract

Colorectal cancer (CRC) is the third most common form of cancer in terms of incidence and the second in terms of mortality worldwide. CRC develops over several years, thus highlighting the importance of early diagnosis. National screening programs based on fecal occult blood [...] Read more.

Colorectal cancer (CRC) is the third most common form of cancer in terms of incidence and the second in terms of mortality worldwide. CRC develops over several years, thus highlighting the importance of early diagnosis. National screening programs based on fecal occult blood tests and subsequent colonoscopy have reduced the incidence and mortality, however improvements are needed since the participation rate remains low and the tests present a high number of false positive results. This review provides an overview of the CRC screening globally and the state of the art in approaches aimed at improving accuracy and participation in CRC screening, also considering the need for gender and age differentiation. New fecal tests and biomarkers such as DNA methylation, mutation or integrity, proteins and microRNAs are explored, including recent investigations into fecal microbiota. Liquid biopsy approaches, involving novel biomarkers and panels, such as circulating mRNA, micro- and long-non-coding RNA, DNA, proteins and extracellular vesicles are discussed. The approaches reported are based on quantitative PCR methods that could be easily applied to routine screening, or arrays and sequencing assays that should be better exploited to describe and identify candidate biomarkers in blood samples. Full article

(This article belongs to the Special Issue Cancer Biomarkers in Body Fluids)

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45 pages, 1738 KiB

Open AccessReview

Exosomes: Their Role in Pathogenesis, Diagnosis and Treatment of Diseases

by Houssam Aheget, Loubna Mazini, Francisco Martin, Boutaïna Belqat, Juan Antonio Marchal and Karim Benabdellah

Cancers 2021, 13(1), 84; https://doi.org/10.3390/cancers13010084 - 30 Dec 2020

Cited by 36 | Viewed by 4372

Abstract

Exosomes are lipid bilayer particles released from cells into their surrounding environment. These vesicles are mediators of near and long-distance intercellular communication and affect various aspects of cell biology. In addition to their biological function, they play an increasingly important role both in [...] Read more.

Exosomes are lipid bilayer particles released from cells into their surrounding environment. These vesicles are mediators of near and long-distance intercellular communication and affect various aspects of cell biology. In addition to their biological function, they play an increasingly important role both in diagnosis and as therapeutic agents. In this paper, we review recent literature related to the molecular composition of exosomes, paying special attention to their role in pathogenesis, along with their application as biomarkers and as therapeutic tools. In this context, we analyze the potential use of exosomes in biomedicine, as well as the limitations that preclude their wider application. Full article

(This article belongs to the Special Issue Cancer Biomarkers in Body Fluids)

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21 pages, 858 KiB

Open AccessReview

Position of Circulating Tumor Cells in the Clinical Routine in Prostate Cancer and Breast Cancer Patients

by Gerit Theil, Paolo Fornara and Joanna Bialek

Cancers 2020, 12(12), 3782; https://doi.org/10.3390/cancers12123782 - 15 Dec 2020

Cited by 7 | Viewed by 1943

Abstract

Prostate cancer and breast cancer are the most common cancers worldwide. Anti-tumor therapies are long and exhaustive for the patients. The real-time monitoring of the healing progression could be a useful tool to evaluate therapeutic response. Blood-based biosources like circulating tumor cells (CTCs) [...] Read more.

Prostate cancer and breast cancer are the most common cancers worldwide. Anti-tumor therapies are long and exhaustive for the patients. The real-time monitoring of the healing progression could be a useful tool to evaluate therapeutic response. Blood-based biosources like circulating tumor cells (CTCs) may offer this opportunity. Application of CTCs for the clinical diagnostics could improve the sequenced screening, provide additional valuable information of tumor dynamics, and help personalized management for the patients. In the past decade, CTCs as liquid biopsy (LB) has received tremendous attention. Many different isolation and characterization platforms are developed but the clinical validation is still missing. In this review, we focus on the clinical trials of circulating tumor cells that have the potential to monitor and stratify patients and lead to implementation into clinical practice. Full article

(This article belongs to the Special Issue Cancer Biomarkers in Body Fluids)

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2 pages, 865 KiB

Open AccessCorrection

Correction: Earl et al. Somatic Mutation Profiling in the Liquid Biopsy and Clinical Analysis of Hereditary and Familial Pancreatic Cancer Cases Reveals KRAS Negativity and a Longer Overall Survival. Cancers 2021, 13, 1612

by Julie Earl, Emma Barreto, María E. Castillo, Raquel Fuentes, Mercedes Rodríguez-Garrote, Reyes Ferreiro, Pablo Reguera, Gloria Muñoz, David Garcia-Seisdedos, Jorge Villalón López, Bruno Sainz, Jr., Nuria Malats and Alfredo Carrato

Cancers 2021, 13(15), 3687; https://doi.org/10.3390/cancers13153687 - 22 Jul 2021

Cited by 1 | Viewed by 1593

Abstract

The authors wish to make the following corrections to this paper [...] Full article

(This article belongs to the Special Issue Cancer Biomarkers in Body Fluids)

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9 pages, 1180 KiB

Open AccessCommentary

Rheumatoid Factor: A Novel Determiner in Cancer History

by Alessio Ugolini and Marianna Nuti

Cancers 2021, 13(4), 591; https://doi.org/10.3390/cancers13040591 - 03 Feb 2021

Cited by 7 | Viewed by 6000

Abstract

The possible interplay between autoimmunity and cancer is a topic that still needs to be deeply explored. Rheumatoid factors are autoantibodies that are able to bind the constant regions (Fc) of immunoglobulins class G (IgGs). In physiological conditions, their production is a transient [...] Read more.

The possible interplay between autoimmunity and cancer is a topic that still needs to be deeply explored. Rheumatoid factors are autoantibodies that are able to bind the constant regions (Fc) of immunoglobulins class G (IgGs). In physiological conditions, their production is a transient event aimed at contributing to the elimination of pathogens as well as limiting a redundant immune response by facilitating the clearance of antibodies and immune complexes. Their production can become persistent in case of different chronic infections or diseases, being for instance a fundamental marker for the diagnosis and prognosis of rheumatoid arthritis. Their presence is also associated with aging. Some studies highlighted how elevated levels of rheumatoid factors (RFs) in the blood of patients are correlated with an increased cancer risk, tumor recurrence, and load and with a reduced response to anti-tumor immunotherapies. In line with their physiological roles, RFs showed in different works the ability to impair in vitro anti-cancer immune responses and effector functions, suggesting their potential immunosuppressive activity in the context of tumor immunity. Thus, the aim of this review is to investigate the emerging role of RFs as determiners of cancer faith. Full article

(This article belongs to the Special Issue Cancer Biomarkers in Body Fluids)

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