Chandra Sekhar Pedamallu
A5031720013- RNA Interference and Gene Delivery
- Acute Myeloid Leukemia Research
- Mesenchymal stem cell research
- Epigenetics and DNA Methylation
- Fibroblast Growth Factor Research
- Medical Imaging and Pathology Studies
- Cancer Research and Treatments
- Virus-based gene therapy research
- Interstitial Lung Diseases and Idiopathic Pulmonary Fibrosis
- MicroRNA in disease regulation
- RNA modifications and cancer
- Cancer Genomics and Diagnostics
- Genomics and Chromatin Dynamics
- Eosinophilic Disorders and Syndromes
- Metastasis and carcinoma case studies
- Veterinary Oncology Research
- Bioinformatics and Genomic Networks
- Glioma Diagnosis and Treatment
- Genomics and Phylogenetic Studies
- Pancreatic function and diabetes
- Gut microbiota and health
- RNA Research and Splicing
- Lung Cancer Treatments and Mutations
- Vascular Tumors and Angiosarcomas
- RNA and protein synthesis mechanisms
Excell Research (United States)
2025
Dana-Farber Cancer Institute
2013-2024
Broad Institute
2011-2024
Harvard University
2014-2024
Excel Life Sciences (India)
2024
Sanofi (United States)
2024
Massachusetts Institute of Technology
2011-2021
Brigham and Women's Hospital
2021
University of Alabama at Birmingham
2021
Harvard University Press
2014-2015
Gastric cancer is a leading cause of deaths, but analysis its molecular and clinical characteristics has been complicated by histological aetiological heterogeneity. Here we describe comprehensive evaluation 295 primary gastric adenocarcinomas as part The Cancer Genome Atlas (TCGA) project. We propose classification dividing into four subtypes: tumours positive for Epstein–Barr virus, which display recurrent PIK3CA mutations, extreme DNA hypermethylation, amplification JAK2, CD274 (also...
We performed an extensive immunogenomic analysis of more than 10,000 tumors comprising 33 diverse cancer types by utilizing data compiled TCGA. Across types, we identified six immune subtypes—wound healing, IFN-γ dominant, inflammatory, lymphocyte depleted, immunologically quiet, and TGF-β dominant—characterized differences in macrophage or signatures, Th1:Th2 cell ratio, extent intratumoral heterogeneity, aneuploidy, neoantigen load, overall proliferation, expression immunomodulatory genes,...
The Cancer Genome Atlas profiled 279 head and neck squamous cell carcinomas (HNSCCs) to provide a comprehensive landscape of somatic genomic alterations. Here we show that human-papillomavirus-associated tumours are dominated by helical domain mutations the oncogene PIK3CA, novel alterations involving loss TRAF3, amplification cycle gene E2F1. Smoking-related HNSCCs demonstrate near universal loss-of-function TP53 CDKN2A inactivation with frequent copy number including 3q26/28 11q13/22. A...
Urothelial carcinoma of the bladder is a common malignancy that causes approximately 150,000 deaths per year worldwide. So far, no molecularly targeted agents have been approved for treatment disease. As part The Cancer Genome Atlas project, we report here an integrated analysis 131 urothelial carcinomas to provide comprehensive landscape molecular alterations. There were statistically significant recurrent mutations in 32 genes, including multiple genes involved cell-cycle regulation,...
The tumor microenvironment of colorectal carcinoma is a complex community genomically altered cancer cells, nonneoplastic and diverse collection microorganisms. Each these components may contribute to carcinogenesis; however, the role microbiota least well understood. We have characterized composition in using whole genome sequences from nine tumor/normal pairs. Fusobacterium were enriched carcinomas, confirmed by quantitative PCR 16S rDNA sequence analysis 95 carcinoma/normal DNA pairs,...
Bacteria go the distance in cancer The bacterial species Fusobacterium nucleatum is associated with a subset of human colorectal cancers, but its role tumorigenesis unclear. Studying patient samples, Bullman et al. found that F. and certain co-occurring bacteria were present not only primary tumors also distant metastases. Preliminary evidence suggests bacterium localized primarily within metastatic cells rather than stroma. Antibiotic treatment mice carrying xenografts –positive slowed...
Significance A significant proportion of head and neck cancer is driven by human papillomavirus (HPV) infection, the expression viral oncogenes involved in development these tumors. However, role HPV integration primary tumors beyond increasing oncoproteins not understood. Here, we describe how impacts host genome amplification disruption tumor suppressors as well driving inter- intrachromosomal rearrangements. Tumors that do have integrants display distinct gene profiles DNA methylation...
Highlights•SCCs show chromosome or methylation alterations affecting multiple related genes•These regulate squamous stemness, differentiation, growth, survival, and inflammation•Copy-quiet SCCs have hypermethylated (FANCF, TET1) mutated (CASP8, MAPK-RAS) genes•Potential targets include ΔNp63, WEE1, IAPs, PI3K-mTOR/MAPK, immune responsesSummaryThis integrated, multiplatform PanCancer Atlas study co-mapped identified distinguishing molecular features of cell carcinomas (SCCs) from five sites...
Genetic screens in cancer cell lines inform gene function and drug discovery. More comprehensive screen datasets with multi-omics data are needed to enhance opportunities functionally map genetic vulnerabilities. Here, we construct a second-generation of dependencies by annotating 930 multi-omic analyze relationships between molecular markers derived from CRISPR-Cas9 screens. We identify dependency-associated expression beyond driver genes, observe many addiction driven gain rather than...
Purpose Lung squamous cell carcinoma (SCC) is the second most prevalent type of lung cancer. Currently, no targeted therapeutics are approved for treatment this cancer, largely because a lack systematic understanding molecular pathogenesis disease. To identify therapeutic targets and perform comparative analyses SCC, we probed somatic genome alterations SCC by using samples from Korean patients. Patients Methods We performed whole-exome sequencing DNA 104 patients matched normal DNA. In...
The transcription factor SOX2 is an essential regulator of pluripotent stem cells and promotes development maintenance squamous epithelia. We previously reported that oncogene subject to highly recurrent genomic amplification in cell carcinomas (SCCs). Here, we have further characterized the function SCC. Using ChIP-seq analysis, compared SOX2-regulated gene profiles multiple SCC lines ES determined binds distinct loci SCCs. In SCCs, preferentially interacts with p63, as opposed OCT4, which...
Cardiomyopathy syndrome (CMS) is a severe disease affecting large farmed Atlantic salmon. Mortality often appears without prior clinical signs, typically shortly to slaughter. We recently reported the finding and complete genomic sequence of novel piscine reovirus (PRV), which associated with another cardiac in salmon; heart skeletal muscle inflammation (HSMI). In present work we have studied whether PRV or other infectious agents may be involved etiology CMS.Using high throughput sequencing...
Abstract Summary We present an updated version of our computational pipeline, PathSeq, for the discovery and identification microbial sequences in genomic transcriptomic libraries from eukaryotic hosts. This pipeline is available Genome Analysis Toolkit (GATK) as a suite configurable tools that can report composition DNA or RNA short-read sequencing samples identify unknown downstream assembly novel organisms. GATK PathSeq enables sample analysis minutes at low cost. In addition, these are...
Here we report the complete genome sequence of Teredinibacter turnerae T7901. T. is a marine gamma proteobacterium that occurs as an intracellular endosymbiont in gills wood-boring bivalves family Teredinidae (shipworms). This species sole cultivated member endosymbiotic consortium thought to provide host with enzymes, including cellulases and nitrogenase, critical for digestion wood supplementation host's nitrogen-deficient diet. closely related free-living polysaccharide degrading...
Background: Inteins are protein maturation machines that enable technologies for regulating enzymes and semisynthesis.Results: Robust splicing was achieved with novel genetically selected exteins.Conclusion: In contrast to commonly held perceptions, the natural extein not fastest substrate.Significance: Natural precursors balance extein- intein-selective pressures. Specificity studies provide a predictive rubric identifying new intein insertion sites.Inteins naturally occurring intervening...
Hemangiosarcoma and angiosarcoma are soft-tissue sarcomas of blood vessel-forming cells in dogs humans, respectively. These vasoformative aggressive highly metastatic, with disorganized, irregular blood-filled vascular spaces. Our objective was to define molecular programs which support the niche that enables progression canine hemangiosarcoma human angiosarcoma. Dog-in-mouse xenografts recapitulated angiogenic morphology characteristics primary tumors. Blood vessels tumors were complex they...
Significance Non-small cell lung cancers (NSCLCs) harboring mutations in the epidermal growth factor receptor ( EGFR ) gene are often singularly reliant on activity for tumor survival, but genetic basis this dependence is not fully understood. In study, we have performed a screen to identify spectrum of kinase genes whose overexpression can overcome NSCLC cells’ reliance EGFR. Using both unbiased and targeted approaches, demonstrate that these commonly bypass through reactivation downstream...
Protein-protein interactions are crucially important for cellular processes. Knowledge of these improves the understanding cell cycle, metabolism, signaling, transport, and secretion. Information about can hint at molecular causes diseases, provide clues new therapeutic approaches. Several (usually expensive time consuming) experimental methods probe protein - interactions. Data sets, derived from such experiments make development prediction feasible, creation protein-protein interaction...
Cervical cancer tumors with undetectable HPV (HPVU) have been underappreciated in clinical decision making. In this study, two independent CC datasets were used to characterize the largest cohort of HPVU date (HPVU = 35, HPV+ 430). Genomic and transcriptome tumor profiles patient survival outcomes compared between tumors. vitro analyses done determine efficacy selective CDK4/6 inhibitor palbociclib on cell lines. Patients had worse progression-free overall patients. TP53, ARID1A, PTEN,...