Vishaka Gopalan
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View article: TMIC-77. Identification of Clinically Relevant Cell State Interactions in the Tumor Microenvironment of IDH-Mut Glioma
TMIC-77. Identification of Clinically Relevant Cell State Interactions in the Tumor Microenvironment of IDH-Mut Glioma Open
Tumor progression is driven not only by the complex milieu of transcriptional cell states of distinct lineages that populate the tumor microenvironment (TME) but also by the interactions these states forge with one another. Systematically …
View article: Predicting gene expression changes upon epigenomic drug treatment
Predicting gene expression changes upon epigenomic drug treatment Open
Background Tumors are characterized by global changes in epigenetic modifications such as DNA methylation and histone modifications that are functionally linked to tumor progression. Accordingly, several drugs targeting the epigenome have …
View article: Characterizing the pan-cancer role of exosomal miRNAs in metastasis across cancers
Characterizing the pan-cancer role of exosomal miRNAs in metastasis across cancers Open
Exosomal microRNAs (exomiRs) play a critical role in intercellular communication, especially in cancer, where they regulate key cellular processes like proliferation, angiogenesis, and metastasis, highlighting their significance as potenti…
View article: Notch1 sets the molecular clock for T cell development
Notch1 sets the molecular clock for T cell development Open
Notch1 signaling is instructive for T cell development, but how this single factor orchestrates commitment remains unclear. Here, by integrating multi-omics platforms, we identified 46 transcription factors (TF) that are directly regulated…
View article: IMMUNE AND MOLECULAR CORRELATES OF RESPONSE TO IMMUNOTHERAPY REVEALED BY BRAIN-METASTATIC MELANOMA MODELS
IMMUNE AND MOLECULAR CORRELATES OF RESPONSE TO IMMUNOTHERAPY REVEALED BY BRAIN-METASTATIC MELANOMA MODELS Open
SUMMARY Despite the promising results of immune checkpoint blockade (ICB) therapy, outcomes for patients with brain metastasis (BrM) remain poor. Identifying resistance mechanisms has been hindered by limited access to patient samples and …
View article: Characterizing the role of exosomal miRNAs in metastasis
Characterizing the role of exosomal miRNAs in metastasis Open
Background Exosomal microRNAs (exomiRs), transported via exosomes, play a pivotal role in intercellular communication. In cancer, exomiRs influence tumor progression by regulating key cellular processes such as proliferation, angiogenesis,…
View article: Resistance Signatures Manifested in Early Drug Response in Cancer and Across Species
Resistance Signatures Manifested in Early Drug Response in Cancer and Across Species Open
Therapeutic resistance is a major cause of cancer treatment failure, with increasing evidence suggesting a non-genetic basis. This non-genetic resistance is often due to drug-resistant transcriptional cell states, either induced by treatme…
View article: Network-based approach elucidates critical genes in BRCA subtypes and chemotherapy response in triple negative breast cancer
Network-based approach elucidates critical genes in BRCA subtypes and chemotherapy response in triple negative breast cancer Open
View article: Predicting gene expression changes upon epigenomic drug treatment
Predicting gene expression changes upon epigenomic drug treatment Open
Background Tumors are characterized by global changes in epigenetic modifications such as DNA methylation and histone modifications that are functionally linked to tumor progression. Accordingly, several drugs targeting the epigenome have…
View article: PARP14 inhibition restores PD-1 immune checkpoint inhibitor response following IFNγ-driven acquired resistance in preclinical cancer models
PARP14 inhibition restores PD-1 immune checkpoint inhibitor response following IFNγ-driven acquired resistance in preclinical cancer models Open
View article: PARP14 inhibition restores PD-1 immune checkpoint inhibitor response following IFNγ-driven acquired resistance in preclinical cancer models
PARP14 inhibition restores PD-1 immune checkpoint inhibitor response following IFNγ-driven acquired resistance in preclinical cancer models Open
Resistance mechanisms to immune checkpoint blockade therapy (ICBT) limit its response duration and magnitude. Paradoxically, Interferon γ (IFNγ), a key cytokine for cellular immunity, can promote ICBT resistance. Using syngeneic mouse tumo…
View article: Predicting gene expression changes upon epigenomic drug treatment
Predicting gene expression changes upon epigenomic drug treatment Open
Background: Tumors are characterized by global changes in epigenetic modifications such as DNA methylation and histone modifications that are functionally linked to tumor progression. Accordingly, several drugs targeting the epigenome ha…
View article: Predicting gene expression changes upon epigenomic drug treatment
Predicting gene expression changes upon epigenomic drug treatment Open
Background Tumors are characterized by global changes in epigenetic changes such as DNA methylation and histone modifications that are functionally linked to tumor progression. Accordingly, several drugs targeting the epigenome have been p…
View article: Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models
Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models Open
Recent studies exploring the impact of methylation in tumor evolution suggest that while the methylation status of many of the CpG sites are preserved across distinct lineages, others are altered as the cancer progresses. Since changes in …
View article: Noncoding RNA circuitry in melanoma onset, plasticity, and therapeutic response
Noncoding RNA circuitry in melanoma onset, plasticity, and therapeutic response Open
View article: Network-based approach elucidates critical genes in BRCA subtypes and chemotherapy response in Triple Negative Breast Cancer
Network-based approach elucidates critical genes in BRCA subtypes and chemotherapy response in Triple Negative Breast Cancer Open
Breast cancers exhibit substantial transcriptional heterogeneity, posing a significant challenge to the prediction of treatment response and prognostication of outcomes. Especially, translation of TNBC subtypes to the clinic remains a work…
View article: Protocol for using single-cell sequencing to study the heterogeneity of NF1 nerve sheath tumors from clinical biospecimens
Protocol for using single-cell sequencing to study the heterogeneity of NF1 nerve sheath tumors from clinical biospecimens Open
Single-cell sequencing is a powerful technology to understand the heterogeneity of clinical biospecimens. Here, we present a protocol for obtaining single-cell suspension from neurofibromatosis type 1-associated nerve sheath tumors for tra…
View article: Melanoma clonal subline analysis uncovers heterogeneity-driven immunotherapy resistance mechanisms
Melanoma clonal subline analysis uncovers heterogeneity-driven immunotherapy resistance mechanisms Open
Intratumoral heterogeneity (ITH) can promote cancer progression and treatment failure, but the complexity of the regulatory programs and contextual factors involved complicates its study. To understand the specific contribution of ITH to i…
View article: Towards a Synthesis of the Non-Genetic and Genetic Views of Cancer in Understanding Pancreatic Ductal Adenocarcinoma Initiation and Prevention
Towards a Synthesis of the Non-Genetic and Genetic Views of Cancer in Understanding Pancreatic Ductal Adenocarcinoma Initiation and Prevention Open
While much of the research in oncogenesis and cancer therapy has focused on mutations in key cancer driver genes, more recent work suggests a complementary non-genetic paradigm. This paradigm focuses on how transcriptional and phenotypic h…
View article: Table S3 from A Transcriptionally Distinct Subpopulation of Healthy Acinar Cells Exhibit Features of Pancreatic Progenitors and PDAC
Table S3 from A Transcriptionally Distinct Subpopulation of Healthy Acinar Cells Exhibit Features of Pancreatic Progenitors and PDAC Open
Differentially expressed genes in the edge acinar state compared to the non-edge acinar state.
View article: Supplementary Material from A Transcriptionally Distinct Subpopulation of Healthy Acinar Cells Exhibit Features of Pancreatic Progenitors and PDAC
Supplementary Material from A Transcriptionally Distinct Subpopulation of Healthy Acinar Cells Exhibit Features of Pancreatic Progenitors and PDAC Open
Contains Supplementary Sections S1-S4 and Supplementary Figures S1-S3.
View article: Data from A Transcriptionally Distinct Subpopulation of Healthy Acinar Cells Exhibit Features of Pancreatic Progenitors and PDAC
Data from A Transcriptionally Distinct Subpopulation of Healthy Acinar Cells Exhibit Features of Pancreatic Progenitors and PDAC Open
Pancreatic ductal adenocarcinoma (PDAC) tumors can originate either from acinar or ductal cells in the adult pancreas. We re-analyze multiple pancreas and PDAC single-cell RNA-seq datasets and find a subset of nonmalignant acinar cells, wh…
View article: Data from A Transcriptionally Distinct Subpopulation of Healthy Acinar Cells Exhibit Features of Pancreatic Progenitors and PDAC
Data from A Transcriptionally Distinct Subpopulation of Healthy Acinar Cells Exhibit Features of Pancreatic Progenitors and PDAC Open
Pancreatic ductal adenocarcinoma (PDAC) tumors can originate either from acinar or ductal cells in the adult pancreas. We re-analyze multiple pancreas and PDAC single-cell RNA-seq datasets and find a subset of nonmalignant acinar cells, wh…
View article: Supplementary Material from A Transcriptionally Distinct Subpopulation of Healthy Acinar Cells Exhibit Features of Pancreatic Progenitors and PDAC
Supplementary Material from A Transcriptionally Distinct Subpopulation of Healthy Acinar Cells Exhibit Features of Pancreatic Progenitors and PDAC Open
Contains Supplementary Sections S1-S4 and Supplementary Figures S1-S3.
View article: Table S1 from A Transcriptionally Distinct Subpopulation of Healthy Acinar Cells Exhibit Features of Pancreatic Progenitors and PDAC
Table S1 from A Transcriptionally Distinct Subpopulation of Healthy Acinar Cells Exhibit Features of Pancreatic Progenitors and PDAC Open
Enrichment of Hallmark oncogenic pathways in the non-edge acinar to edge acinar transition.
View article: Table S1 from A Transcriptionally Distinct Subpopulation of Healthy Acinar Cells Exhibit Features of Pancreatic Progenitors and PDAC
Table S1 from A Transcriptionally Distinct Subpopulation of Healthy Acinar Cells Exhibit Features of Pancreatic Progenitors and PDAC Open
Enrichment of Hallmark oncogenic pathways in the non-edge acinar to edge acinar transition.
View article: Table S2 from A Transcriptionally Distinct Subpopulation of Healthy Acinar Cells Exhibit Features of Pancreatic Progenitors and PDAC
Table S2 from A Transcriptionally Distinct Subpopulation of Healthy Acinar Cells Exhibit Features of Pancreatic Progenitors and PDAC Open
Transcription factor regulon activities in the non-edge acinar to edge acinar transition.
View article: Table S3 from A Transcriptionally Distinct Subpopulation of Healthy Acinar Cells Exhibit Features of Pancreatic Progenitors and PDAC
Table S3 from A Transcriptionally Distinct Subpopulation of Healthy Acinar Cells Exhibit Features of Pancreatic Progenitors and PDAC Open
Differentially expressed genes in the edge acinar state compared to the non-edge acinar state.
View article: Table S2 from A Transcriptionally Distinct Subpopulation of Healthy Acinar Cells Exhibit Features of Pancreatic Progenitors and PDAC
Table S2 from A Transcriptionally Distinct Subpopulation of Healthy Acinar Cells Exhibit Features of Pancreatic Progenitors and PDAC Open
Transcription factor regulon activities in the non-edge acinar to edge acinar transition.
View article: Network-Based Approach Elucidates Critical Genes in BRCA Subtypes and Chemotherapy Response in Triple Negative Breast Cancer
Network-Based Approach Elucidates Critical Genes in BRCA Subtypes and Chemotherapy Response in Triple Negative Breast Cancer Open