A5052055509- Cancer-related molecular mechanisms research
- Polyomavirus and related diseases
- Bacteriophages and microbial interactions
- Plant Virus Research Studies
- RNA modifications and cancer
- Prostate Cancer Treatment and Research
- Renal cell carcinoma treatment
- Cancer, Lipids, and Metabolism
- Cancer Genomics and Diagnostics
- Renal and related cancers
- Epigenetics and DNA Methylation
- Ferroptosis and cancer prognosis
- RNA Research and Splicing
- Antenna Design and Analysis
- MicroRNA in disease regulation
- Hippo pathway signaling and YAP/TAZ
- RNA regulation and disease
- Glioma Diagnosis and Treatment
- Circular RNAs in diseases
- Cancer-related Molecular Pathways
- Analytical Chemistry and Sensors
- Cancer-related gene regulation
- Genomics and Phylogenetic Studies
- AI in cancer detection
- Neuroblastoma Research and Treatments
Indian Institute of Technology Dharwad
2018-2024
Michigan Center for Translational Pathology
2015-2023
Roche (Switzerland)
2022
University of Michigan–Ann Arbor
2015-2021
University of Luxembourg
2021
Michigan Medicine
2017-2018
Indian Institute of Science Bangalore
2011-2016
Michigan United
2016
National Institute of Mental Health and Neurosciences
2014
All India Institute of Medical Sciences
2011-2014
Precision therapy for lung cancer will require comprehensive genomic testing to identify actionable targets as well ascertain disease prognosis. RNA-seq is a robust platform that meets these requirements, but microarray-derived prognostic signatures are not optimal data. Thus, we undertook the first analysis of adenocarcinoma data and generated signature. Lung clinical from The Cancer Genome Atlas (TCGA) were divided chronologically into training (n = 255) validation 157) cohorts. In cohort,...
Abstract Mucinous tubular and spindle cell carcinoma (MTSCC) is a relatively rare subtype of renal (RCC) with distinctive morphologic cytogenetic features. Here, we carry out whole-exome transcriptome sequencing multi-institutional cohort MTSCC (n = 22). We demonstrate the presence either biallelic loss Hippo pathway tumor suppressor genes (TSG) and/or evidence alteration in 85% samples. PTPN14 (31%) NF2 (22%) were most commonly implicated genes, whereas other such as SAV1 HIPK2 also...
Abstract Glioblastoma (GBM) is the most common, malignant adult primary tumor with dismal patient survival, yet molecular determinants of survival are poorly characterized. Global methylation profile GBM samples (our cohort; n = 44) using high-resolution microarrays was carried out. Cox regression analysis identified a 9-gene signature that predicted in patients. A risk-score derived from univariate our and The Cancer Genome Atlas (TCGA) cohort. Multivariate risk score as an independent...
Abstract Motivation: Discovery of novel splicing from RNA sequence data remains a critical and exciting focus transcriptomics, but reduced alignment power impedes expression quantification splice junctions. Results: Here, we profile performance characteristics two-pass alignment, which separates junction discovery quantification. Per sample, across variety transcriptome sequencing datasets, improved at least 94% simulated junctions, provided as much 1.7-fold deeper median read depth over...
Rapid advances in the discovery of long noncoding RNAs (lncRNAs) have identified lineage- and cancer-specific biomarkers that may be relevant clinical management prostate cancer (PCa). Here we assembled analyzed a large RNA-seq dataset, from 585 patient samples, including benign tissue both localized metastatic PCa to discover validate differentially expressed genes associated with disease aggressiveness. We performed Sample Set Enrichment Analysis (SSEA) low versus high Gleason score...
Non-small Cell Lung Cancer (NSCLC) is a heterogeneous disease with poor prognosis. Identifying novel subtypes in cancer can help classify patients similar molecular and clinical phenotypes. This work proposes an end-to-end pipeline for subgroup identification NSCLC. Here, we used machine learning (ML) based approach to compress the multi-omics NSCLC data lower dimensional space. subjected consensus K-means clustering identify five clusters (C1-C5). Survival analysis of resulting revealed...
Colorectal cancer (CRC) is the third most common in world, and second leading cause of deaths US. Although, anti-EGFR therapy commonly prescribed for CRC, patients harboring mutations KRAS or BRAF show poor treatment response, indicating an ardent demand new therapeutic targets discovery. SPINK1 (serine peptidase inhibitor, Kazal type 1) overexpression has been identified many cancers including colon, lung, breast prostate. Our study demonstrates functional significance CRC progression...
// Lihui Wang 1, 2 , Yanli He 2, 3 Weijun Liu 4 Shengbin Bai 5 Lei Xiao Jie Zhang 6 Saravana M. Dhanasekaran 7 Zhuwen Shanker Kalyana-Sundaram O. Alejandro Balbin Sudhanshu Shukla Yi Lu 1 Jules Lin Rishindra Reddy Philip W. Carrott Jr William R. Lynch Andrew C. Chang Arul Chinnaiyan David G. Beer Jian Guoan Chen Guangxi Medical University, Nanning, China Section of Thoracic Surgery, Department University Michigan, Ann Arbor, United States America Guangzhou Chinese Medicine, Guangzhou, The...
Advanced prostate cancer initially responds to androgen deprivation therapy (ADT), but the disease inevitably recurs as castration-resistant (CRPC). Although CRPC abiraterone and enzalutamide, invariably becomes nonresponsive these agents. Novel approaches are required circumvent resistance pathways extend survival, mechanisms underlying remain poorly defined. Our group previously showed histone lysine-N-methyltransferase EZH2 be overexpressed in quantitatively associated with progression...
One way of early diagnosis cancer is by detecting the biomarkers that get introduced into easily accessible body fluids. We report development portable and rapid electronic biosensors for quantitative detection two secretive biomarkers-Carcinoembryonic antigen (CEA) Cytokeratin fragment 19 (CYFRA 21-1). The reduced graphene oxide (rGO)/ melamine (MEL)/antibodies/ bovine serum albumin (BSA) based devices were tested 1 pg/mL to 800 ng/mL CEA CYFRA 21-1. responses sensors ranged from 7.14 59.1%...
Mitoribosomes play a pivotal role in cellular energy metabolism by synthesizing proteins involved oxidative phosphorylation (OXPHOS) system. Dysregulation of mitoribosomes has been linked to Cancer, yet there have no studies demonstrating the genetics and epigenetic landscape mitoribosomal (MRPs). In this study, we conducted comprehensive analysis expression, copy number variations, mutations, data from TCGA NSCLC patients elucidate genetic mechanism regulating MRPs NSCLC. Consequently,...
Background Recent research on glioblastoma (GBM) has focused deducing gene signatures predicting prognosis. The present study evaluated the mRNA expression of selected genes and correlated with outcome to arrive at a prognostic signature. Methods Patients GBM (n = 123) were prospectively recruited, treated uniform protocol followed up. Expression 175 in tissue was determined using qRT-PCR. A supervised principal component analysis by derivation signature performed. Independent validation...
Several studies on molecular profiling of oligodendrogliomas (OGs) in adults have shown a distinctive genetic pattern characterized by combined deletions chromosome arms 1p and 19q, O6-methylguanine-methyltransferase (MGMT) methylation, isocitrate dehydrogenase 1 (IDH1) mutation, which potential diagnostic, prognostic, even therapeutic relevance. OGs pediatric young adult patients are rare been poorly biological basis, it remains uncertain whether markers with prognostic significance also...
Kidney Renal Clear Cell Carcinoma (KIRC) is a significant cause of cancer-related deaths. Here, we aim to identify the LncRNAs associated with immune system and characterise their clinical utility in KIRC. A total 504 patients' data was used from TCGA-GDC. In silico correlation analysis identified 143 immune-related genes (r > 0.7, P < 0.05). K-means consensus method clustered KIRC samples three clusters, namely cluster C1, C2, C3 based on expression LncRNAs. Kaplan-Meier showed that...
The most common and aggressive form of primary brain tumor in adults is glioblastoma (GBM).From the global DNA methylation profiling study, previously published from our laboratory, we identified Guanine Nucleotide binding-protein Gamma subunit 4 (GNG4) to be one hyper methylated down regulated genes GBM.GBM derived cell lines showed reduced GNG4 transcript levels, which could reversed by inhibitor treatment.Bisulphite sequencing confirmed status tissue GBM lines.Overexpression was found...
Renal cell carcinoma (RCC) associated with neuroblastoma (NB) was included as a distinct entity in the 2004 World Health Organization classification of kidney tumors. A spectrum RCC subtypes has been reported NB survivors. We herein describe series 8 RCCs diagnosed 7 patients history NB. Microscopic evaluation, immunohistochemical staining for PAX8, cathepsin K, and succinate dehydrogenase subunit B (SDHB), fluorescence situ hybridization (FISH) TFE3 TFEB were performed. Four morphologic...
Purpose: Merkel cell carcinoma (MCC) is a highly aggressive neuroendocrine tumor of the skin. polyomavirus (MCPyV) plays an oncogenic role in majority MCCs. Detection MCPyV MCCs has diagnostic utility and prognostic potential. We investigated whether RNAscope, RNA situ hybridization (ISH) assay for detection transcripts tissues, useful detection.Experimental Design: applied RNAscope probe targeting T antigen on tissue microarrays (TMA) whole-tissue sections encompassing 87 from 75 patients,...
Pediatric glioblastoma multiforme (GBM) is rare, and there a single study, seminal discovery showing association of histone H3.3 isocitrate dehydrogenase (IDH)1 mutation with DNA methylation signature. The present study aims to validate these findings in an independent cohort pediatric GBM, compare it adult evaluate the involvement important functionally altered pathways. Genome-wide profiling 21 GBM cases was done compared data (GSE22867). We performed gene analysis IDH1 H3 family 3A...