Veena Kochat
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View article: ATRX Loss Predicts Poor Outcomes and Reveals a Therapeutic Vulnerability to TEAD Inhibition in Soft Tissue Sarcomas
ATRX Loss Predicts Poor Outcomes and Reveals a Therapeutic Vulnerability to TEAD Inhibition in Soft Tissue Sarcomas Open
ATRX is one of the most frequently altered genes in sarcoma and encodes an ATP-dependent chromatin remodeler implicated in maintaining heterochromatin. However, ATRX alterations have not been leveraged for sarcoma treatment. We observed lo…
View article: Benchmarking Dimensionality Reduction Techniques for Spatial Transcriptomics
Benchmarking Dimensionality Reduction Techniques for Spatial Transcriptomics Open
We introduce a unified framework for evaluating dimensionality reduction techniques in spatial transcriptomics beyond standard PCA approaches. We benchmark six methods PCA, NMF, autoencoder, VAE, and two hybrid embeddings on a cholangiocar…
View article: Cancer-induced nerve injury promotes resistance to anti-PD-1 therapy
Cancer-induced nerve injury promotes resistance to anti-PD-1 therapy Open
View article: Reprogramming of Cellular Plasticity via ETS and MYC Core-regulatory Circuits During Response to MAPK Inhibition in BRAF-mutant Colorectal Cancer
Reprogramming of Cellular Plasticity via ETS and MYC Core-regulatory Circuits During Response to MAPK Inhibition in BRAF-mutant Colorectal Cancer Open
Background Aberrant enhancer dynamics play a critical role in the initiation and progression of colorectal cancer (CRC). BRAF V600E -mutated metastatic CRC may be a unique subtype, exhibiting a strong epigenetic phenotype. Interestingly, b…
View article: Spatial and multiomics analysis of human and mouse lung adenocarcinoma precursors reveals TIM-3 as a putative target for precancer interception
Spatial and multiomics analysis of human and mouse lung adenocarcinoma precursors reveals TIM-3 as a putative target for precancer interception Open
How tumor microenvironment shapes lung adenocarcinoma (LUAD) precancer evolution remains poorly understood. Spatial immune profiling of 114 human LUAD and LUAD precursors reveals a progressive increase of adaptive response and a relative d…
View article: Alternative polyadenylation regulates human urothelial cell differentiation
Alternative polyadenylation regulates human urothelial cell differentiation Open
The urothelium is stratified into progenitor basal cells, intermediate cells, and terminally differentiated umbrella cells. Proper renewal of umbrella cells is necessary for maintaining urinary tract barrier integrity. To investigate wheth…
View article: An iron-rich subset of macrophages promotes tumor growth through a Bach1-Ednrb axis
An iron-rich subset of macrophages promotes tumor growth through a Bach1-Ednrb axis Open
We define a subset of macrophages in the tumor microenvironment characterized by high intracellular iron and enrichment of heme and iron metabolism genes. These iron-rich tumor-associated macrophages (iTAMs) supported angiogenesis and immu…
View article: Spatial Biology Reveals Macrophage Dysfunction in Immunosuppressed Non-Melanoma Skin Cancer
Spatial Biology Reveals Macrophage Dysfunction in Immunosuppressed Non-Melanoma Skin Cancer Open
View article: High enhancer activity is an epigenetic feature of HPV negative atypical head and neck squamous cell carcinoma
High enhancer activity is an epigenetic feature of HPV negative atypical head and neck squamous cell carcinoma Open
Head and neck squamous cell carcinoma (HNSCC) is a heterogeneous disease with significant mortality and frequent recurrence. Prior efforts to transcriptionally classify HNSCC into groups of varying prognoses have identified four accepted m…
View article: High Enhancer Activity is an Epigenetic Feature of HPV Negative Atypical Head and Neck Squamous Cell Carcinoma
High Enhancer Activity is an Epigenetic Feature of HPV Negative Atypical Head and Neck Squamous Cell Carcinoma Open
Head and neck squamous cell carcinoma (HNSCC) is a heterogeneous disease with significant morbidity and mortality and frequent recurrence. Pre-NGS efforts to transcriptionally classify HNSCC into groups of varying prognosis have identified…
View article: New cellular models of undifferentiated pleomorphic sarcoma and malignant peripheral nerve sheath tumor
New cellular models of undifferentiated pleomorphic sarcoma and malignant peripheral nerve sheath tumor Open
Undifferentiated pleomorphic sarcoma (UPS) and malignant peripheral nerve sheath tumor (MPNST) are aggressive soft tissue sarcomas that do not respond well to current treatment modalities. The limited availability of UPS and MPNST cell lin…
View article: Mutations in the SWI/SNF complex induce a targetable dependence on oxidative phosphorylation in lung cancer
Mutations in the SWI/SNF complex induce a targetable dependence on oxidative phosphorylation in lung cancer Open
View article: JMJD3 aids in reprogramming of bone marrow progenitor cells to hepatic phenotype through epigenetic activation of hepatic transcription factors
JMJD3 aids in reprogramming of bone marrow progenitor cells to hepatic phenotype through epigenetic activation of hepatic transcription factors Open
The strictly regulated unidirectional differentiation program in some somatic stem/progenitor cells has been found to be modified in the ectopic site (tissue) undergoing regeneration. In these cases, the lineage barrier is crossed by eithe…
View article: Bone marrow stem cell therapy partially ameliorates pathological consequences in livers of mice expressing mutant human α1‐antitrypsin
Bone marrow stem cell therapy partially ameliorates pathological consequences in livers of mice expressing mutant human α1‐antitrypsin Open
Alpha‐1‐antitrypsin (AAT) deficiency (AATD) is a genetic disease, caused by mutation of the AAT gene. Accumulation of mutated AAT protein aggregates in hepatocytes leads to endoplasmic reticulum stress, resulting in impairment of liver fun…
View article: Molecular and Cellular Functions Distinguish Superior Therapeutic Efficiency of Bone Marrow CD45 Cells Over Mesenchymal Stem Cells in Liver Cirrhosis
Molecular and Cellular Functions Distinguish Superior Therapeutic Efficiency of Bone Marrow CD45 Cells Over Mesenchymal Stem Cells in Liver Cirrhosis Open
Liver fibrosis is strongly associated with chronic inflammation. As an alternative to conventional treatments for fibrosis, mesenchymal stem cells (MSCs) therapy is found to be attractive due to its immunomodulatory functions. However, low…
View article: Donor antigen-primed regulatory T cells permit liver regeneration and phenotype correction in hemophilia A mouse by allogeneic bone marrow stem cells
Donor antigen-primed regulatory T cells permit liver regeneration and phenotype correction in hemophilia A mouse by allogeneic bone marrow stem cells Open