A5042011803- Cancer Genomics and Diagnostics
- Single-cell and spatial transcriptomics
- Cancer Immunotherapy and Biomarkers
- Pancreatic and Hepatic Oncology Research
- Cancer Cells and Metastasis
- Prostate Cancer Treatment and Research
- Epigenetics and DNA Methylation
- Molecular Biology Techniques and Applications
- Viral-associated cancers and disorders
- Cytomegalovirus and herpesvirus research
- Radiomics and Machine Learning in Medical Imaging
- Genomic variations and chromosomal abnormalities
- Herpesvirus Infections and Treatments
- Gene expression and cancer classification
- AI in cancer detection
- Immune cells in cancer
- RNA modifications and cancer
- Genetic factors in colorectal cancer
- Genetics, Bioinformatics, and Biomedical Research
- Immune responses and vaccinations
- Phagocytosis and Immune Regulation
- Cardiovascular Disease and Adiposity
- Prostate Cancer Diagnosis and Treatment
- PARP inhibition in cancer therapy
- Cancer-related molecular mechanisms research
The University of Texas MD Anderson Cancer Center
2016-2025
The University of Texas Southwestern Medical Center
2011-2015
Southwestern Medical Center
2013
Metastasis is a complex biological process that has been difficult to delineate in human colorectal cancer (CRC) patients. A major obstacle understanding metastatic lineages the extensive intra-tumor heterogeneity at primary and tumor sites. To address this problem, we developed highly multiplexed single-cell DNA sequencing approach trace of two CRC patients with matched liver metastases. Single-cell copy number or mutational profiling was performed, addition bulk exome targeted...
Abstract Single cell RNA sequencing has emerged as a powerful tool for resolving transcriptional diversity in tumors, but is limited by throughput, cost and the ability to process archival frozen tissue samples. Here we develop high-throughput 3′ single-nucleus approach that combines nanogrid technology, automated imaging, selection sequence up ~1800 single nuclei parallel. We compare transcriptomes of 485 424 cells breast cancer line, which shows high concordance (93.34%) gene levels...
Ductal carcinoma in situ (DCIS) is the most common form of preinvasive breast cancer and, despite treatment, a small fraction (5-10%) DCIS patients develop subsequent invasive disease. A fundamental biologic question whether disease arises from tumor cells initial or represents new unrelated To address this question, we performed genomic analyses on lesion and paired recurrent tumors 95 together with single-cell DNA sequencing subset cases. Our data show that 75% cases recurrence was...
Pancreatic ductal adenocarcinoma (PDAC) has few effective treatments. Immunotherapy, an attractive alternative strategy, remains challenging with the lack of knowledge on tumor-infiltrating lymphocyte (TIL) landscape in PDAC. To generate a reference T-cell subpopulations, we profiled 80,000 T cells from 57 PDAC samples, 22 uninvolved/normal and cultured TIL using single-cell transcriptomic receptor analysis. These data revealed 20 cell states heterogeneous distributions populations. The CD8+...
Intra-tumor heterogeneity (ITH) of human tumors is important for tumor progression, treatment response, and drug resistance. However, the spatial distribution ITH remains incompletely understood. Here, we present analysis in lung adenocarcinomas from 147 patients using multi-region mass spectrometry >5,000 regions, single-cell copy number sequencing ∼2,000 single cells, cyclic immunofluorescence >10 million cells. We identified two distinct patterns among tumors, termed clustered random...
Abstract Treatment decisions in metastatic castration-resistant prostate cancer (mCRPC) are mostly guided by clinical variables, but efforts to molecularly monitor the disease remain hampered challenges acquiring tumor tissue repeatedly. Here, we simultaneously profiled genome copy number and exome longitudinal plasma circulating DNA (ctDNA) acquired before, during, upon progression serial treatments with androgen signaling inhibitors (ASI) taxane chemotherapy from 60 mCRPC patients (2-10...
Abstract Purpose: Aggressive variant prostate cancer (AVPC) represents a clinical subset distinguished by therapy resistance and poor prognosis, linked to combined losses of the tumor suppressor genes (TSG) PTEN, RB1, TP53. Circulating cells (CTC) provide minimally invasive opportunity for identification molecular characterization AVPC. We aimed evaluate incidence significance compound (2+)TSG genomic instability in CTC, expand set biomarkers relevant Experimental Design: Genomic analysis...
Abstract Ductal carcinoma in situ (DCIS) harbors genomic copy number changes reflecting early events advancing invasive breast cancer, and specific cell states related to cancer initiation progression. DNA methylation is a covalent modification cytosines with type specificity, stable archival samples, provides most of the specificity multiple noninvasive pan-cancer screens. However, creation single-cell methylomes technically challenging analysis immature, leaving state level interpretation...
Single-cell DNA sequencing (scDNA-seq) methods are powerful tools for profiling mutations in cancer cells; however, most genomic regions sequenced single cells non-informative. To overcome this issue, we developed a multi-patient-targeted (MPT) scDNA-seq method. MPT involves first performing bulk exome across cohort of patients to identify somatic mutations, which then pooled together develop custom targeted panel high-throughput using microfluidics platform. We applied profile 330 23,500...
The adult human breast comprises an intricate network of epithelial ducts and lobules that are embedded in connective adipose tissue. While previous studies have mainly focused on the system, many non-epithelial cell types remain understudied. Here, we constructed a comprehensive Human Breast Cell Atlas (HBCA) at single-cell spatial resolution. Our transcriptomics data profiled 535,941 cells from 62 women, 120,024 nuclei 20 identifying 11 major 53 states. These revealed abundant pericyte,...
The Kaposi's sarcoma associated herpesvirus (KSHV) is an oncogenic virus that causes sarcoma, primary effusion lymphoma (PEL), and some forms of multicentric Castleman's disease. KSHV ORF57 protein a conserved posttranscriptional regulator gene expression essential for replication. multifunctional, but most its activities are directly linked to ability bind RNA. We globally identified host RNAs bound by during lytic reactivation in PEL cells using high-throughput sequencing RNA isolated...