A5005886858- Molecular Biology Techniques and Applications
- Cancer Genomics and Diagnostics
- Single-cell and spatial transcriptomics
- Cancer Cells and Metastasis
- Pancreatic and Hepatic Oncology Research
- Prostate Cancer Treatment and Research
- Phagocytosis and Immune Regulation
- Epigenetics and DNA Methylation
- Cancer Research and Treatments
- Melanoma and MAPK Pathways
- Cell Image Analysis Techniques
- Pancreatic function and diabetes
- Endoplasmic Reticulum Stress and Disease
- Nitric Oxide and Endothelin Effects
- Renal and related cancers
- Gene expression and cancer classification
- Receptor Mechanisms and Signaling
- Renin-Angiotensin System Studies
- Advanced Proteomics Techniques and Applications
- Cell Adhesion Molecules Research
- Advanced Biosensing Techniques and Applications
10X Genomics (United States)
2021-2024
Stony Brook University
2012-2019
Cold Spring Harbor Laboratory
2016-2018
The majority of patients with pancreatic ductal adenocarcinoma (PDA) develop metastatic disease after resection their primary tumor. We found that livers from and mice PDA harbor single disseminated cancer cells (DCCs) lacking expression cytokeratin 19 (CK19) major histocompatibility complex class I (MHCI). created a mouse model to determine how these DCCs develop. Intraportal injection immunogenic into preimmunized seeded only single, nonreplicating were CK19- MHCI- exhibited an endoplasmic...
Single-cell RNA-seq's (scRNA-seq) unprecedented cellular resolution at a genome-wide scale enables us to address questions about heterogeneity that are inaccessible using methods average over bulk tissue extracts. However, scRNA-seq data sets also present additional challenges such as high transcript dropout rates, stochastic transcription events, and complex population substructures. Here, we s ingle-cell RNA-seq nalysis k lustering e valuation (SAKE), robust method for analysis provides...
Many lines of evidence have indicated that both genetic and non-genetic determinants can contribute to intra-tumor heterogeneity influence cancer outcomes. Among the best described sub-population cells generated by mechanisms are characterized a CD44+/CD24− cell surface marker profile. Here, we report human genetically highly unstable because intrinsic defects in their DNA-repair capabilities. In fact, cells, constitutive activation TGF-beta axis was necessary sufficient reduce expression...
<h3>Background</h3> The tumor microenvironment (TME) is composed of highly heterogeneous cell types that dynamically interact with each other. To more precisely distinguish and characterize cellular diversity disease states within tissues, technologies single-cell resolution are required. Visium HD Spatial Gene Expression assay (Visium HD) a high-resolution spatial technology utilizes whole-transcriptome probe panel, resolving data at the scale intact tissue sections. This offers...
Abstract Single-cell RNA-Seq’s (scRNA-Seq) unprecedented cellular resolution at a genome wide scale enables us to address questions about heterogeneity that are inaccessible using methods average over bulk tissue extracts. However, scRNA-Seq datasets also present additional challenges such as high transcript dropout rates, stochastic transcription events, and complex population substructures. Here, we SAKE (Single-cell RNA-Seq Analysis Klustering Evaluation): robust method for analysis...
The tumor microenvironment (TME) is composed of highly heterogeneous structures and cell types that dynamically influence communicate with each other. constant interaction between a its plays critical role in how the cancer develops, progresses, responds to therapies. Traditionally, Hematoxylin Eosin (H&E) immunohistochemistry staining have been used annotate characterize tissues associated pathologies. Recent single analyte approaches spatially interrogate targeted or transcriptome-wide...
Background Despite years of studies and effort, the best strategies for treating prostate cancer minimizing complications treatment remain unanswered questions. This gap in knowledge is partially due to inability dissect complex heterogeneous tumor microenvironment (TME) immune compartment. Spatially resolved molecular profiling sections will enhance our understanding these complexities; However, it has been particularly challenging do spatial formalin-fixed paraffin-embedded (FFPE) tissues...
Abstract Patients who have had their primary pancreatic ductal adenocarcinoma (PDA) surgically resected often develop metastatic disease, exemplifying the problem of latent metastases. Livers from patients and mice with PDA contained single, disseminated cancer cells (DCCs) an unusual phenotype being cytokeratin-19 (CK19) - MHC class I (MHCI) . We created a mouse model to determine how DCCs develop, relationship latency, role immunity. Intra-portal injection immunogenic into pre-immunized...
Despite years of studies and effort, the best strategies for treating prostate cancer minimizing complications treatment remain unanswered questions. This gap in knowledge is partially due to inability dissect complex heterogeneous tumor microenvironment (TME) immune compartment. Spatially resolved molecular profiling sections will enhance our understanding these complexities; However, it has been particularly challenging do spatial formalin-fixed paraffin-embedded (FFPE) tissues RNA...
Abstract Despite years of prostate cancer-related research, balancing the risk treatment-derived complications with tumor progression remains a challenge. The inability to dissect heterogeneous microenvironments (TME) and immune compartments partly contribute this knowledge gap. Spatially resolved molecular profiling can enhance our understanding these complexities bring us closer personalized treatment; however, deploying such methods in oncology workflows is challenging as prevalent tissue...
Abstract The tumor microenvironment (TME) is composed of highly heterogeneous structures and cell types that dynamically influence communicate with each other. constant interaction between a its plays critical role in how the cancer develops, progresses, responds to therapies. Traditionally, Hematoxylin Eosin (H&E) staining has been used annotate characterize tissues associated pathologies. Recent single analyte approaches spatially interrogate targeted or transcriptome-wide expression...
Background The tumor microenvironment (TME) is composed of highly heterogeneous extracellular structures and cell types such as endothelial cells, immune fibroblasts that dynamically influence communicate with each other. constant interaction between a its plays critical role in cancer development progression can significantly affect tumor’s response to therapy capacity for multi-drug resistance. High resolution analyses gene protein expression spatial context provide deeper insights into...