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J. Mol. Pathol., Volume 5, Issue 1 (March 2024) – 9 articles

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20 pages, 3136 KiB  
Article
Regulation of a Metabolic Gene Signature in Response to Respiratory Viruses and Type I Interferon Signaling
by Chilakamarti V. Ramana
J. Mol. Pathol. 2024, 5(1), 133-152; https://doi.org/10.3390/jmp5010009 - 07 Mar 2024
Viewed by 575
Abstract
Respiratory viruses are the causative agents responsible for seasonal epidemics and occasional pandemic outbreaks and are a leading cause of death worldwide. Type I interferon (IFNα/β) signaling in the lung epithelial cells plays a major role in the innate immunity to respiratory viruses. [...] Read more.
Respiratory viruses are the causative agents responsible for seasonal epidemics and occasional pandemic outbreaks and are a leading cause of death worldwide. Type I interferon (IFNα/β) signaling in the lung epithelial cells plays a major role in the innate immunity to respiratory viruses. Gene signatures are a set of differentially expressed genes in a particular disease or condition and are used to diagnose, monitor, and predict disease progression. These signatures can be used to identify regulatory modules and gene regulatory networks (GRNs) in mammalian signal transduction pathways. Considerable progress has been made in the identification of type I interferon-regulated gene signatures in the host response to respiratory viruses, including antiviral, immunomodulatory, apoptosis, and transcription factor signatures. Respiratory virus infections and host defenses require a dramatic change in the metabolic flux of macromolecules involved in nucleotide, lipid, and protein metabolism. The profiling of IFN-stimulated metabolic genes induced in the host response to several respiratory viruses led to the identification of a common gene signature in human lung epithelial cells and in the lungs of mouse models of respiratory virus infection. The regulation of the metabolic gene signature was correlated with the induction of IFN-beta (IFN-β) and IFN-inducible transcription factors at the RNA level in lung epithelial cells. Furthermore, the gene signature was also detected in response to bacterial lipopolysaccharide-induced acute lung injury. A protein interaction network analysis revealed that metabolic enzymes interact with IFN-regulated transcription factors and members of the unfolded protein response (UPR) to form a module and potentially regulate type I interferon signaling, constituting a feedback loop. In addition, components of the metabolic gene expression signature were differentially regulated in the lung tissues of COVID-19 patients compared with healthy controls. These results suggest that the metabolic gene signature is a potential therapeutic target for the treatment of respiratory virus infections and inflammatory diseases. Full article
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14 pages, 959 KiB  
Review
The Role of IRF8 Polymorphisms in Systemic Sclerosis Development and Pathogenesis
by Anna Mennella, Giuseppe Ocone, Katia Stefanantoni and Loredana Frasca
J. Mol. Pathol. 2024, 5(1), 120-132; https://doi.org/10.3390/jmp5010008 - 02 Mar 2024
Viewed by 503
Abstract
Systemic sclerosis (SSc) is a rare autoimmune disease whose molecular mechanisms are not yet fully understood. There is no definitive cure, and the main causes of death are pulmonary fibrosis and pulmonary arterial hypertension. Here, we focus on the interferon regulators factor 8 [...] Read more.
Systemic sclerosis (SSc) is a rare autoimmune disease whose molecular mechanisms are not yet fully understood. There is no definitive cure, and the main causes of death are pulmonary fibrosis and pulmonary arterial hypertension. Here, we focus on the interferon regulators factor 8 (IRF8), a factor involved in the type I interferon (IFN-I) signature, which is present in about half of SSc patients. Variants of this factor may play a role in autoimmunity, but little is known regarding the role of IRF8 in SSc pathogenesis. We carried out a literature search to address the association between the IRF8 factor and SSc susceptibility and clinical manifestations. The current studies appear to confirm a possible association between the alteration of the gene for IRF8 and SSc susceptibility. A link between IRF8 mutations and expression of a pro-fibrotic phenotype at the cellular level also emerges. Additional investigations are needed to confirm the role of IRF8 in SSc. However, IRF8 is worth consideration as a possible new disease marker of fibrosis in SSc patients. Full article
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24 pages, 2906 KiB  
Review
Oxidative Stress and ROS Link Diabetes and Cancer
by Homer S. Black
J. Mol. Pathol. 2024, 5(1), 96-119; https://doi.org/10.3390/jmp5010007 - 01 Mar 2024
Viewed by 1178
Abstract
Type 2 diabetes mellitus (T2DM) accounts for one-sixth of deaths globally, whereas cancer is the second leading cause of death in the U.S. T2DM is a known risk factor for many cancers. Reactive oxygen species (ROS)-altered metabolic and signaling pathways link T2DM to [...] Read more.
Type 2 diabetes mellitus (T2DM) accounts for one-sixth of deaths globally, whereas cancer is the second leading cause of death in the U.S. T2DM is a known risk factor for many cancers. Reactive oxygen species (ROS)-altered metabolic and signaling pathways link T2DM to cancer. These reprogrammed metabolic and signaling pathways contribute to diabetic complications, impact the redox balance (oxidative stress), and have differential roles in the early and late stages of cancer. A respiratory chain that is highly reduced (as under hyperglycemic conditions) or if reduced cofactors accumulate, ROS are greatly elevated. ROS may cause mutations in mitochondrial DNA (mtDNA) that result in further ROS elevations. The amplification of ROS results in the activation of PKC, an overarching signaling pathway that activates MAPK with a subsequent regulation in several factors that result in pathophysiological manifestations of T2DM and cancer. An upregulation in PKC leads to a deregulation in NF-kß, which regulates the PKB/P13/Akt pathway and orchestrates the cell survival, growth, proliferation, and glucose metabolism manifested in cancer. It also affects Insulin Receptor Substrate (IRS-1), decreasing insulin-stimulated glucose transport and glucose uptake, disrupting subsequent cell signaling pathways contributing to the development of T2DM. Dyslipidemia is a hallmark of T2DM and cancer. ROS-induced lipid peroxidation leads to systemic inflammation, producing inflammatory prostaglandins, cytokines, and chemokines that result in tumor proliferation, rapid tumor growth, and modulation of immunity. The dual role of ROS in the early and late stages of cancer makes antioxidant therapy precarious and may be responsible for controversial results. A system that delivers an antioxidant directly to mitochondria may be useful in inhibiting the formation of ROS early during the pre-diabetic stage, whereas antioxidant therapy must be halted in later stages to retard metastasis. Full article
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15 pages, 4749 KiB  
Article
Comparing Classifications from Multiple Variant Annotation Software Solutions Using Real-World Next Generation Sequencing Data from Oncology Testing
by Roy Khalife, Tara M. Love, Lara Sucheston-Campbell, Michael J. Clark, Helle Sorensen, Shuba Krishna and Anthony Magliocco
J. Mol. Pathol. 2024, 5(1), 81-95; https://doi.org/10.3390/jmp5010006 - 01 Mar 2024
Viewed by 1034
Abstract
Variant annotation is an important step in deciphering the functional impact of genomic variants and their association with diseases. In this study, we analyzed 80 pan-cancer cases that underwent comprehensive genomic testing and compared the auto-classified variant tiers among four globally-available software solutions [...] Read more.
Variant annotation is an important step in deciphering the functional impact of genomic variants and their association with diseases. In this study, we analyzed 80 pan-cancer cases that underwent comprehensive genomic testing and compared the auto-classified variant tiers among four globally-available software solutions for variant interpretation from Roche, SOPHiA GENETICS, QIAGEN, and Genoox. The results revealed striking differences in tier classifications, which are believed to be a result of several factors, including subjectivity in the AMP/ASCO/CAP guidelines, threshold settings for variant allele frequencies and population allele frequencies, as well as variation in disease ontologies. Although the software tools described here provide a time-saving and repeatable process for interpretation of genomic data, it is crucial to understand the nuances and various settings for these solutions, as they can strongly influence variant tier classifications and downstream management. Full article
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15 pages, 10897 KiB  
Article
Delving into the Role of Receptor-like Tyrosine Kinase (RYK) in Cancer: In Silico Insights into Its Diagnostic and Prognostic Utility
by Jessica Alejandra Zapata-García, Luis Felipe Jave-Suárez and Adriana Aguilar-Lemarroy
J. Mol. Pathol. 2024, 5(1), 66-80; https://doi.org/10.3390/jmp5010005 - 06 Feb 2024
Viewed by 680
Abstract
The RYK gene encodes a receptor-like tyrosine kinase crucial for several biological processes, including development, tissue homeostasis, and cancer. This study utilized data from the Cancer Genome Atlas Project (TCGA) to evaluate RYK expression at both mRNA and protein levels in various cancers, [...] Read more.
The RYK gene encodes a receptor-like tyrosine kinase crucial for several biological processes, including development, tissue homeostasis, and cancer. This study utilized data from the Cancer Genome Atlas Project (TCGA) to evaluate RYK expression at both mRNA and protein levels in various cancers, determine its prognostic significance, and explore its involvement in cancer-related signaling pathways. Elevated levels of RYK mRNA were identified in cholangiocarcinoma (CHOL), pancreatic adenocarcinoma (PAAD), glioblastoma multiforme (GBM), lung squamous cell carcinoma (LUSC), brain lower grade glioma (LGG), head and neck squamous cell carcinoma (HNSC), liver hepatocellular carcinoma (LICH), esophageal carcinoma (ESCA), and colon adenocarcinoma (COAD), while RYK protein levels were observed to be increased in colon adenocarcinoma (COAD), GBM, LICH, cervical and endocervical adenocarcinoma (CESC), and breast invasive carcinoma (BRCA). Additionally, RYK overexpression correlated with poorer prognosis in several cancers, including PAAD, LICH, BRCA, ESCA, COAD, and CESC. Furthermore, RYK showed a positive correlation with the upregulation of multiple receptors and coreceptors in the WNT signaling pathway in various types of cancer. In terms of cancer-related signaling pathways, RYK was found to potentially interact with DNA damage, TSC/mTOR, PI3K/AKT, EMT, RTK, RAS/MAPK, ER hormone, AR hormone, and the cell cycle. This study provides new and previously unreported insights into the role of RYK in cancer biology. Full article
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21 pages, 3826 KiB  
Article
A Novel Single-Tube Next Generation Sequencing Assay for B-Cell Receptor Clonality Testing
by Landon Pastushok, Shrutii Sarda, Karen Mochoruk, Wayne Hill, Loni T. Pickle, Michelle Toro, Carolina Gonzalez, Stephanie Ostresh, Timothy J. Looney, Chenchen Yang, Julie Stakiw, Mark J. Bosch, Hadi Goubran, C. Ronald Geyer, Geoffrey M. Lowman and John F. DeCoteau
J. Mol. Pathol. 2024, 5(1), 45-65; https://doi.org/10.3390/jmp5010004 - 02 Feb 2024
Viewed by 989
Abstract
B-cell neoplasms possess clonal B-cell receptor rearrangements (BCR clonotype lineages) that can be identified by sequencing the B-cell repertoire for use in diagnostics, risk stratification, and high-sensitivity monitoring. BCR somatic hypermutation (SHM) can result in clonality detection failure from point mutations in PCR [...] Read more.
B-cell neoplasms possess clonal B-cell receptor rearrangements (BCR clonotype lineages) that can be identified by sequencing the B-cell repertoire for use in diagnostics, risk stratification, and high-sensitivity monitoring. BCR somatic hypermutation (SHM) can result in clonality detection failure from point mutations in PCR primer binding regions, often necessitating splitting samples into multiple reactions which increases test costs, turnaround times, and sample requirements. We evaluated the Oncomine BCR Pan-Clonality Assay, a novel single-tube PCR reaction that simultaneously amplifies all BCR loci for next-generation DNA sequencing, using neoplastic B-cell lines and clinical research samples from multiple myeloma (MM) patients, a plasma cell neoplasm associated with high SHM levels. The assay showed a linear detection range down to 1 ng of clonal DNA input, sensitivity to 10−6 in a polyclonal background, and high reproducibility. Clonotype lineages were identified in 42/45 (93%) MM samples. Ion Reporter software packaged with the assay permitted straightforward identification of MM subgroups. As expected, SHM was identified in 94% of MM cases, but several unexpected subgroups were identified including biased IGHV3-11 or IGHV4-34 usage in 20% of MM samples, and two cases with very low levels of SHM. Evidence of intraclonal diversity/ongoing SHM was identified in 18% of samples, suggesting a possible germinal center origin for some MM cases. The single-tube Oncomine BCR Pan-Clonality assay efficiently detects BCR clonotype lineages at rates comparable to existing multiple reaction assays and permits their characterization for cell of origin studies and lymphoma classification. Full article
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17 pages, 2948 KiB  
Article
AI-Enhanced Blood Cell Recognition and Analysis: Advancing Traditional Microscopy with the Web-Based Platform IKOSA
by Manuel Campos-Medina, Aiden Blumer, Patrick Kraus-Füreder, Michael Mayrhofer-Reinhartshuber, Philipp Kainz and Johannes A. Schmid
J. Mol. Pathol. 2024, 5(1), 28-44; https://doi.org/10.3390/jmp5010003 - 25 Jan 2024
Viewed by 1157
Abstract
Microscopy of stained blood smears is still a ubiquitous technique in pathology. It is often used in addition to automated electronic counters or flow cytometers to evaluate leukocytes and their morphologies in a rather simple manner and has low requirements for resources and [...] Read more.
Microscopy of stained blood smears is still a ubiquitous technique in pathology. It is often used in addition to automated electronic counters or flow cytometers to evaluate leukocytes and their morphologies in a rather simple manner and has low requirements for resources and equipment. However, despite the constant advances in microscopy, computer science, and pathology, it still usually follows the traditional approach of manual assessment by humans. We aimed to extend this technique using AI-based automated cell recognition methods while maintaining its technical simplicity. Using the web platform IKOSA, we developed an AI-based workflow to segment and identify all blood cells in DAPI-Giemsa co-stained blood smears. Thereby, we could automatically detect and classify neutrophils (young and segmented), lymphocytes, eosinophils, and monocytes, in addition to erythrocytes and platelets, in contrast to previously published algorithms, which usually focus on only one type of blood cell. Furthermore, our method delivers quantitative measurements, unattainable by the classical method or formerly published AI techniques, and it provides more sophisticated analyses based on entropy or gray-level co-occurrence matrices (GLCMs), which have the potential to monitor changes in internal cellular structures associated with disease states or responses to treatment. We conclude that AI-based automated blood cell evaluation has the potential to facilitate and improve routine diagnostics by adding quantitative shape and structure parameters to simple leukocyte counts of classical analysis. Full article
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17 pages, 10013 KiB  
Article
Human Metastatic Melanoma Cell Lines Panel for In Vitro and In Vivo Investigations
by Ekaterina N. Kosobokova, Nadezhda A. Kalinina, Ksenia M. Konoplina, Anastasiia A. Malchenkova, Alexandra E. Evdokimova, Marina V. Piniugina, Irina I. Khan, Ilya A. Kislyak, Anna A. Basharina, Anna N. Grishanina, Anna A. Rudakova, Pavel O. Varaksa, Maria A. Baryshnikova, Vadim S. Pokrovsky, Tatiana A. Bogush and Vyacheslav S. Kosorukov
J. Mol. Pathol. 2024, 5(1), 11-27; https://doi.org/10.3390/jmp5010002 - 08 Jan 2024
Viewed by 754
Abstract
The melanoma origin of cell lines obtained from the axillary lymph node (mel Kas, mel Pet, and mel Lap from patients with a verified diagnosis) was confirmed by the detection of the Melan A melanocyte marker expression. A hyperdiploid (2n+) for the mel [...] Read more.
The melanoma origin of cell lines obtained from the axillary lymph node (mel Kas, mel Pet, and mel Lap from patients with a verified diagnosis) was confirmed by the detection of the Melan A melanocyte marker expression. A hyperdiploid (2n+) for the mel Kas line; near-diploid (2n), and in some cells near-tertaploid (4n), and even hypo-octaploid (8n) set (172–179 chromosomes) in the mel Pet cell line; and a hypotetraploid (4n−) for the mel Lap line were detected by karyotypic analysis. All three cell lines are tumorigenic; however, mel Pet demonstrates tumor growth in Balb/c nude mice only in the presence of matrigel. All three lines showed a high expression of TUBB3 and PD-L1 markers, while ERa was low (minimum for mel Pet). Significant differences in the expression level were shown for the Cyt molecular marker. In the transplantation of cells to Balb/c nude mice, a stable expression level is observed only for TUBB3. For the rest of the markers, a decrease in their expression level of varying degrees was noted when the cells were growing in solid tumors in vivo. Mutations were detected in oncogenes (BRAF, EZH2, KIT, KRAS, NRAS, ROS1) and tumor suppressor genes (CDKN2A, FAT4, KMT2C, LRP1B, PTEN, PTPRB, TP53). The detailed characterization of the cell lines makes them valuable for various scientific and regulatory experiments, particularly those involving preclinical data on antiproliferative drugs for malignant melanoma or investigations into melanoma cell properties and progression. Full article
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10 pages, 1142 KiB  
Article
Novel Approach to Proficiency Testing Highlights Key Practice Variations in Cancer Biomarker Delivery
by Kassandra R. Bisson, Jennifer R. Won, Andrea Beharry, Michael D. Carter, Shaan Dudani, John G. Garratt, Jonathan M. Loree, Stephanie Snow, Stephen Yip and Brandon S. Sheffield
J. Mol. Pathol. 2024, 5(1), 1-10; https://doi.org/10.3390/jmp5010001 - 05 Jan 2024
Viewed by 1623
Abstract
Biomarkers are fundamental to modern oncology practice, forming a close link to pathology practice. Pathology results must be accurate, timely, comprehensive, and comprehendible. External proficiency testing is a key tool in maintaining biomarker quality. Here, we demonstrate the feasibility and utility of a [...] Read more.
Biomarkers are fundamental to modern oncology practice, forming a close link to pathology practice. Pathology results must be accurate, timely, comprehensive, and comprehendible. External proficiency testing is a key tool in maintaining biomarker quality. Here, we demonstrate the feasibility and utility of a novel end-to-end proficiency testing exercise exploring accuracy, turnaround time, and communication. Challenge specimens were made using resected colon cancer tissue, each paired with a fictional clinical vignette, and distributed to participants who were asked to provide all molecular testing required and return a final report for each case upon completion. Reports were redistributed to an assessor team including medical oncologists, each of whom was asked to recommend a systemic therapy based on each lab’s biomarker report. Participants were graded based on their ability to guide oncologists to the correct treatment. Eight laboratories participated. Three laboratories were found to have suboptimal results, two leading oncologists to incorrect therapeutic prescriptions, and one withdrawn. Turnaround time ranged from 6 to 86 days (median 24). Substantial qualitative reporting differences were identified. This study demonstrates the feasibility of end-to-end proficiency testing. The approach provides considerable value beyond analytic accuracy, including specimen management, turnaround time, and communication of results. Results suggest that reporting differences may lead to treatment disparities. This style of quality assurance will help reinforce good practices critical to the delivery of precision cancer care. Full article
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