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In Vivo (Athens, Greece) 2024Gliomas are highly heterogeneous malignancies originating from diverse cell types within the brain. Although their precise etiology is frequently unknown, risk factors,...
BACKGROUND/AIM
Gliomas are highly heterogeneous malignancies originating from diverse cell types within the brain. Although their precise etiology is frequently unknown, risk factors, such as chemical exposure, radiation, and specific uncommon genetic disorders have been identified. Diagnosis typically entails imaging tests, such as magnetic resonance imaging and computed tomography, complemented by a biopsy for confirmation, which may be further validated through genetic testing.
CASE REPORT
Next-generation sequencing technology revealed germline co-deletion deletion of cyclin-dependent kinase inhibitor 2 A and B genes (CDKN2A and CDKN2B) in a patient diagnosed with pleomorphic xanthoastrocytoma based on the tumor's molecular characteristics. Following this result, we performed focused genetic analysis with use of multiplex ligation-dependent probe amplification technology for the mother that revealed the same co-deletion. Moreover, due to the father's neuroendocrine pancreatic cancer, application of the NGS technology detected a pathogenic variant in the BRCA1-interacting helicase 1 (BRIP1) gene. Comprehensive multi-gene testing conducted within the familial context, marked by a varied spectrum of cancer type, revealed a constellation of genetic predispositions.
CONCLUSION
This case study underscores the critical importance of molecular testing for tumor characterization and highlights the pivotal role of genetic testing in facilitating early intervention and screening for at-risk family members. Furthermore, the identification of germline co-deletions in cancer lays the foundation for the development of targeted therapeutic strategies aimed at restoring normal cellular regulation and improving patient management.
Topics: Humans; Cyclin-Dependent Kinase Inhibitor p16; Astrocytoma; Cyclin-Dependent Kinase Inhibitor p15; Germ-Line Mutation; High-Throughput Nucleotide Sequencing; Genetic Predisposition to Disease; Male; Female; Adult; Brain Neoplasms; Pedigree; Magnetic Resonance Imaging; Gene Deletion
PubMed: 38936911
DOI: 10.21873/invivo.13617 -
In Vivo (Athens, Greece) 2024Bladder cancer (BC) is the most prevalent malignant tumor in the urinary tract, classified mainly into muscle-invasive BC (MIBC) and non-MIBC (NMIBC). Recent studies...
BACKGROUND/AIM
Bladder cancer (BC) is the most prevalent malignant tumor in the urinary tract, classified mainly into muscle-invasive BC (MIBC) and non-MIBC (NMIBC). Recent studies highlight the important role of changes in transcriptome activity in carcinogenesis, aiding in the identification of additional differentially regulated candidate genes, improving our understanding of the molecular basis of gene regulation in BC. This study aimed to evaluate the transcriptome of MIBC patients compared with normal subjects.
MATERIALS AND METHODS
mRNA sequencing was conducted using the Illumina NovaSeq 6000 Dx system in a case series comprising 11 subjects with MIBC and 19 healthy controls matched for age and sex. For functional analysis, the pathfindR package was utilized to comprehensively identify pathways enriched in omics data within active subnetworks.
RESULTS
Our results demonstrated the presence of differentiated pathways, including spliceosome activity, oxidative phosphorylation, and chemical carcinogenesis due to reactive oxygen species, in MIBC patients compared with controls.
CONCLUSION
The identification of novel molecular pathways in MIBC patients could prove useful in defining cancer predisposition factors and exploring potential therapeutic options.
Topics: Humans; Urinary Bladder Neoplasms; Male; Female; Gene Expression Profiling; Transcriptome; Middle Aged; Aged; Gene Expression Regulation, Neoplastic; Neoplasm Invasiveness; Case-Control Studies; Biomarkers, Tumor; Gene Regulatory Networks; High-Throughput Nucleotide Sequencing; Computational Biology
PubMed: 38936905
DOI: 10.21873/invivo.13615 -
HLA Jun 2024Twenty-five years ago, in 1998, the HLA Informatics Group of the Anthony Nolan Research Institute released the IMGT/HLA Database. Since this time, this online resource... (Review)
Review
Twenty-five years ago, in 1998, the HLA Informatics Group of the Anthony Nolan Research Institute released the IMGT/HLA Database. Since this time, this online resource has acted as the repository for the numerous variant sequences of HLA alleles named by the WHO Nomenclature Committee for Factors of the HLA System. The IPD-IMGT/HLA Database has provided a stable, highly accessible, user-friendly repository for this work. During this time, the technology underlying HLA typing has undergone significant changes. Next generation sequencing (NGS) has superseded previous methodologies of HLA typing and can generate large amounts of high-resolution sequencing data. This has resulted in a drastic increase in the number and complexity of sequences submitted to the database. The challenge for the IPD-IMGT/HLA Database has been to maintain the highest standards of curation, while supporting the core set of tools and functionality to our users with increased numbers of submissions and sequences. Traditional methods of accessing and presenting data have been challenged and new methods utilising new computing technologies have had to be developed to keep pace and support a shifting user demographic.
Topics: Humans; HLA Antigens; Databases, Genetic; Histocompatibility Testing; High-Throughput Nucleotide Sequencing; Alleles; Software; History, 21st Century; History, 20th Century; Computational Biology
PubMed: 38936817
DOI: 10.1111/tan.15549 -
JCO Precision Oncology Jun 2024There is limited information about the clinical utility of targeted next-generation sequencing (NGS) panel testing to inform decision making for patients with advanced...
PURPOSE
There is limited information about the clinical utility of targeted next-generation sequencing (NGS) panel testing to inform decision making for patients with advanced solid tumors. The Ontario-wide Cancer Targeted Nucleic Acid Evaluation (OCTANE) is a prospective study that enrolled more than 4,500 patients with solid tumor for NGS panel testing. We performed a retrospective survey of medical oncologists to evaluate the impact of NGS testing on treatment decisions.
METHODS
Patients and treating oncologists were identified at the Princess Margaret Cancer Center between 2016 and 2021. Tumor-only sequencing was performed using a gene panel of either 555 or 161 cancer genes. Oncologists were asked to review testing results and complete a survey indicating whether NGS testing affected treatment decisions. The primary outcome of this study was rate of treatment change on the basis of mutation results. Patient, test, and physician factors were evaluated for association with treatment changes using univariate analyses and a mixed-effects model.
RESULTS
Of the 582 surveys sent, 394 (67.7%) were completed. We found that 188 (47.7%) patients had testing results classified as actionable by the oncologist and 62 (15.7%) patients were matched to treatment, of whom 37 (60%) were enrolled in a clinical trial, 13 (21%) received an approved drug, four (6%) were prescribed off-label therapy, and eight (13%) avoided ineffective treatment. Patient, test, and physician characteristics were not significantly associated with treatment change. There was no difference in overall survival between patients who received matched treatment versus those who did not ( = .55, median survival not reached).
CONCLUSION
OCTANE testing led to a change in drug treatment in 15.7% of patients, supporting the clinical utility of NGS panel testing for patients with advanced solid tumors.
Topics: Humans; Neoplasms; High-Throughput Nucleotide Sequencing; Male; Female; Middle Aged; Tertiary Care Centers; Retrospective Studies; Aged; Clinical Decision-Making; Adult; Ontario; Prospective Studies
PubMed: 38935894
DOI: 10.1200/PO.24.00092 -
PloS One 2024Tuberculosis is a serious life-threatening disease among the top global health challenges and rapid and effective diagnostic biomarkers are vital for early diagnosis...
BACKGROUND
Tuberculosis is a serious life-threatening disease among the top global health challenges and rapid and effective diagnostic biomarkers are vital for early diagnosis especially given the increasing prevalence of multidrug resistance.
METHODS
Two human whole blood microarray datasets, GSE42826 and GSE42830 were retrieved from publicly available gene expression omnibus (GEO) database. Deregulated genes (DEGs) were identified using GEO2R online tool and Gene Ontology (GO), protein-protein interaction (PPI) network analysis was performed using Metascape and STRING databases. Significant genes (n = 8) were identified using T-test/ANOVA and Molecular Complex Detection (MCODE) score ≥10, which was validated in GSE34608 dataset. The diagnostic potential of three biomarkers was assessed using Area Under Curve (AUC) of Receiver Operating Characteristic (ROC) plot. The transcriptional levels of these genes were also examined in a separate dataset GSE31348, to monitor the patterns of variation during tuberculosis treatment.
RESULTS
A total of 62 common DEGs (57 upregulated, 7 downregulated genes) were identified in two discovery datasets. GO functions and pathway enrichment analysis shed light on the functional roles of these DEGs in immune response and type-II interferon signaling. The genes in Module-1 (n = 18) were linked to innate immune response, interferon-gamma signaling. The common genes (n = 8) were validated in GSE34608 dataset, that corroborates the results obtained from discovery sets. The gene expression levels demonstrated responsiveness to Mtb infection during anti-TB therapy in GSE31348 dataset. In GSE34608 dataset, the expression levels of three specific genes, GBP5, IFITM3, and EPSTI1, emerged as potential diagnostic makers. In combination, these genes scored remarkable diagnostic performance with 100% sensitivity and 89% specificity, resulting in an impressive Area Under Curve (AUC) of 0.958. However, GBP5 alone showed the highest AUC of 0.986 with 100% sensitivity and 89% specificity.
CONCLUSIONS
The study presents valuable insights into the critical gene network perturbed during tuberculosis. These genes are determinants for assessing the effectiveness of an anti-TB response and distinguishing between active TB and healthy individuals. GBP5, IFITM3 and EPSTI1 emerged as candidate core genes in TB and holds potential as novel molecular targets for the development of interventions in the treatment of TB.
Topics: Humans; Tuberculosis; Protein Interaction Maps; RNA-Seq; Computational Biology; Gene Expression Profiling; ROC Curve; Gene Regulatory Networks; Databases, Genetic; Biomarkers; Gene Ontology
PubMed: 38935691
DOI: 10.1371/journal.pone.0305582 -
Briefings in Bioinformatics May 2024In the past decade, single-cell RNA sequencing (scRNA-seq) has emerged as a pivotal method for transcriptomic profiling in biomedical research. Precise cell-type...
MOTIVATION
In the past decade, single-cell RNA sequencing (scRNA-seq) has emerged as a pivotal method for transcriptomic profiling in biomedical research. Precise cell-type identification is crucial for subsequent analysis of single-cell data. And the integration and refinement of annotated data are essential for building comprehensive databases. However, prevailing annotation techniques often overlook the hierarchical organization of cell types, resulting in inconsistent annotations. Meanwhile, most existing integration approaches fail to integrate datasets with different annotation depths and none of them can enhance the labels of outdated data with lower annotation resolutions using more intricately annotated datasets or novel biological findings.
RESULTS
Here, we introduce scPLAN, a hierarchical computational framework designed for scRNA-seq data analysis. scPLAN excels in annotating unlabeled scRNA-seq data using a reference dataset structured along a hierarchical cell-type tree. It identifies potential novel cell types in a systematic, layer-by-layer manner. Additionally, scPLAN effectively integrates annotated scRNA-seq datasets with varying levels of annotation depth, ensuring consistent refinement of cell-type labels across datasets with lower resolutions. Through extensive annotation and novel cell detection experiments, scPLAN has demonstrated its efficacy. Two case studies have been conducted to showcase how scPLAN integrates datasets with diverse cell-type label resolutions and refine their cell-type labels.
AVAILABILITY
https://github.com/michaelGuo1204/scPLAN.
Topics: Single-Cell Analysis; Gene Expression Profiling; Computational Biology; Humans; Software; Transcriptome; Sequence Analysis, RNA; RNA-Seq; Molecular Sequence Annotation
PubMed: 38935069
DOI: 10.1093/bib/bbae305 -
HLA Jun 2024The novel HLA-DRB1*03:215 allele, first described in a potential bone marrow donor from Brazil.
The novel HLA-DRB1*03:215 allele, first described in a potential bone marrow donor from Brazil.
Topics: Humans; HLA-DRB1 Chains; Alleles; Histocompatibility Testing; Exons; Sequence Analysis, DNA; Tissue Donors; Brazil; High-Throughput Nucleotide Sequencing
PubMed: 38934049
DOI: 10.1111/tan.15588 -
F1000Research 2023The risk of recurrence after nephrectomy for primary clear cell renal cell carcinoma (ccRCC) is estimated in daily practice solely based on clinical criteria. The aim of...
BACKGROUND
The risk of recurrence after nephrectomy for primary clear cell renal cell carcinoma (ccRCC) is estimated in daily practice solely based on clinical criteria. The aim of this study was to assess the prognostic relevance of common somatic mutations with respect to tumor aggressiveness and outcomes of ccRCC patients after definitive treatment.
METHODS
Primary tumors from 37 patients with ccRCC who underwent radical nephrectomy were analyzed for presence of somatic mutations using a 15-gene targeted next-generation sequencing (NGS) panel. Associations to histopathologic characteristics and outcomes were investigated in the study cohort (n=37) and validated in The Cancer Genome Atlas (TCGA) ccRCC cohort (n=451).
RESULTS
was the most frequently mutated gene (51%), followed by (27%), (13%), (13%), (5%), (5%), (5%), and (3%). One-third of patients did not have any somatic mutations within the 15-gene panel. The vast majority of tumors harboring no mutations at all or VHL-only mutations (51%) were more frequently of smaller size (pT1-2) and earlier stage (I/II), whereas presence of any other gene mutations in various combinations with or without was enriched in larger (pT3) and higher stage tumors (III) (p=0.02). No recurrences were noted in patients with unmutated tumors or -only mutations as opposed to three relapses in patients with non- somatic mutations (p=0.06). Presence of somatic mutations in , or genes in 451 TCGA ccRCC patients was associated with a significantly shorter disease-free survival (DFS) compared to those with unaltered tumors (q=0.01).
CONCLUSIONS
Preliminary findings from this ongoing study support the prognostic value of non- mutations including , and in primary ccRCC tumors as surrogates of earlier recurrence and potential selection for adjuvant immune checkpoint inhibition.
Topics: Humans; Carcinoma, Renal Cell; Male; Female; Kidney Neoplasms; Middle Aged; Mutation; Aged; Immune Checkpoint Inhibitors; Ubiquitin Thiolesterase; Neoplasm Recurrence, Local; Tumor Suppressor Proteins; Ataxia Telangiectasia Mutated Proteins; Von Hippel-Lindau Tumor Suppressor Protein; Prognosis; Histone-Lysine N-Methyltransferase; Adult; Transcription Factors; Aged, 80 and over; Nuclear Proteins; High-Throughput Nucleotide Sequencing; DNA-Binding Proteins; Histone Demethylases
PubMed: 38933491
DOI: 10.12688/f1000research.136087.2 -
Sheng Wu Yi Xue Gong Cheng Xue Za Zhi =... Jun 2024The rapid development of high-throughput chromatin conformation capture (Hi-C) technology provides rich genomic interaction data between chromosomal loci for chromatin...
The rapid development of high-throughput chromatin conformation capture (Hi-C) technology provides rich genomic interaction data between chromosomal loci for chromatin structure analysis. However, existing methods for identifying topologically associated domains (TADs) based on Hi-C data suffer from low accuracy and sensitivity to parameters. In this context, a TAD identification method based on spatial density clustering was designed and implemented in this paper. The method preprocessed the raw Hi-C data to obtain normalized Hi-C contact matrix data. Then, it computed the distance matrix between loci, generated a reachability graph based on the core distance and reachability distance of loci, and extracted clustering clusters. Finally, it extracted TAD boundaries based on clustering results. This method could identify TAD structures with higher coherence, and TAD boundaries were enriched with more ChIP-seq factors. Experimental results demonstrate that our method has advantages such as higher accuracy and practical significance in TAD identification.
Topics: Chromatin; Cluster Analysis; Algorithms; Humans; Chromatin Immunoprecipitation Sequencing
PubMed: 38932542
DOI: 10.7507/1001-5515.202311059 -
Journal of Medical Virology Jun 2024Integration of the human papillomavirus (HPV) genome into the cellular genome is a key event that leads to constitutive expression of viral oncoprotein E6/E7 and drives...
Integration of the human papillomavirus (HPV) genome into the cellular genome is a key event that leads to constitutive expression of viral oncoprotein E6/E7 and drives the progression of cervical cancer. However, HPV integration patterns differ on a case-by-case basis among related malignancies. Next-generation sequencing technologies still face challenges for interrogating HPV integration sites. In this study, utilizing Nanopore long-read sequencing, we identified 452 and 108 potential integration sites from the cervical cancer cell lines (CaSki and HeLa) and five tissue samples, respectively. Based on long Nanopore chimeric reads, we were able to analyze the methylation status of the HPV long control region (LCR), which controls oncogene E6/E7 expression, and to identify transcriptionally-active integrants among the numerous integrants. As a proof of concept, we identified an active HPV integrant in between RUNX2 and CLIC5 on chromosome 6 in the CaSki cell line, which was supported by ATAC-seq, H3K27Ac ChIP-seq, and RNA-seq analysis. Knockout of the active HPV integrant, by the CRISPR/Cas9 system, dramatically crippled cell proliferation and induced cell senescence. In conclusion, identifying transcriptionally-active HPV integrants with Nanopore sequencing can provide viable targets for gene therapy against HPV-associated cancers.
Topics: Humans; Uterine Cervical Neoplasms; Female; Nanopore Sequencing; Virus Integration; Genetic Therapy; Papillomavirus Infections; Cell Line, Tumor; HeLa Cells; Oncogene Proteins, Viral; High-Throughput Nucleotide Sequencing; Papillomaviridae; Human Papillomavirus Viruses
PubMed: 38932482
DOI: 10.1002/jmv.29769