A5025530956- Cancer Genomics and Diagnostics
- Cancer Immunotherapy and Biomarkers
- Cancer Cells and Metastasis
- Genomics and Chromatin Dynamics
- Genomics and Phylogenetic Studies
- Single-cell and spatial transcriptomics
- Epigenetics and DNA Methylation
- Chromosomal and Genetic Variations
- Bioinformatics and Genomic Networks
- Microbial infections and disease research
- Ferroptosis and cancer prognosis
- HER2/EGFR in Cancer Research
- Cancer-related molecular mechanisms research
- RNA Research and Splicing
- Genomics and Rare Diseases
- Immunotherapy and Immune Responses
- Breast Cancer Treatment Studies
- RNA modifications and cancer
- Bacteriophages and microbial interactions
- Genomic variations and chromosomal abnormalities
University of North Carolina at Chapel Hill
2022-2025
Washington University in St. Louis
2019-2021
University of California, Los Angeles
2020-2021
Abstract The AURORA US Metastasis Project was established with the goal to identify molecular features associated metastasis. We assayed 55 females metastatic breast cancer (51 primary cancers and 102 metastases) by RNA sequencing, tumor/germline DNA exome low-pass whole-genome sequencing global methylation microarrays. Expression subtype changes were observed in ~30% of samples coincident clonality shifts, especially involving HER2. Downregulation estrogen receptor (ER)-mediated cell–cell...
Abstract Early-stage and metastatic breast cancers (MBC) can exhibit genomic heterogeneity, even within the same individual. Response to therapy in cancer patients with multiple metastases also be heterogeneous, different degrees of responsiveness drug(s) across sites, termed “mixed response,” patient. Whether this treatment response variability is influenced by factors such as intrinsic tumor characteristics lesions and/or microenvironment unknown. Through analysis from patient, assayed 6...
Abstract Triple-negative breast cancer (TNBC) is an aggressive and heterogeneous disease that remains challenging to target with traditional therapies predict risk. We provide a comprehensive characterization of 238 stage II-III TNBC tumors paired RNA DNA sequencing data from the CALGB 40603 (Alliance) clinical trial, along 448 three additional datasets. identify mutations associated RNA-based subtypes, specific TP53 missense compatible potential neoantigen activity, consistently highly...
Abstract Breast cancer is a heterogeneous malignancy where precision medicine approaches have informed treatment decisions; currently, these decisions are largely driven by IHC subtyping based on the expression of targetable receptor proteins (ER, PR, and HER2). Between clinical subtypes, immune cell infiltration its prognostic impact vary considerably. Tumor-infiltrating lymphocytes (TILs) most common in triple-negative breast cancers associated with improved patient prognosis. In contrast,...
More than half of non-small cell lung cancer (NSCLC) patients present with metastatic disease at initial diagnosis an estimated five-year survival rate ~5%. Despite advances in understanding primary oncogenesis remains poorly characterized. Recent studies demonstrate important roles long non-coding RNAs (lncRNAs) tumor physiology and as prognostic markers. Therefore, we the first transcriptome analysis to identify lncRNAs altered adenocarcinoma leading discovery characterization lncRNA...
SUMMARY Annotation of the cis -regulatory elements that drive transcriptional dysregulation in cancer cells is critical to improving our understanding tumor biology. Herein, we present a compendium matched chromatin accessibility (scATAC-seq) and transcriptome (scRNA-seq) profiles at single-cell resolution from human breast tumors healthy mammary tissues processed immediately following surgical resection. We identify most likely cell-of-origin for luminal basal then introduce novel...
Abstract ConsHMM is a method recently introduced to annotate genomes into conservation states, which are defined based on the combinatorial and spatial patterns of species align match reference genome in multi-species DNA sequence alignment. Previously, was only applied single for one Here, we apply produce 22 additional annotations covering human seven other organisms variety alignments. Additionally, extend generate allele-specific annotations, use state every possible single-nucleotide...
Abstract In Triple-Negative Breast Cancer (TNBC) patients, adaptive immune system activity in the tumor microenvironment is associated with improved prognosis. However, tumors can evolve to evade detection, likely leading worse patient outcomes. Multi-omic data of paired primary and metastatic breast demonstrate that TNBC metastases frequently lose expression genes involved major histocompatibility complex class I (MHC-I) antigen presentation, a key pathway for activation (PMID: 36585450)....
Abstract ConsHMM is a method recently introduced to annotate genomes into conservation states, which are defined based on the combinatorial and spatial patterns of species align match reference genome in multi-species DNA sequence alignment. Previously, was only applied single for one Here we apply produce 22 additional annotations covering human seven other organisms variety alignments. Additionally, have extended generate allele specific annotations, used state every possible nucleotide...
We present here the complete genomes of two Streptomyces bacteriophages, Satis and JustBecause. Both phages were isolated directly from soil samples collected in St. Louis, MO, with an unusual prolate head morphology large genome lengths over 180 kb.