A5068163504- Single-cell and spatial transcriptomics
- Cancer Genomics and Diagnostics
- Bioinformatics and Genomic Networks
- Molecular Biology Techniques and Applications
- Gene expression and cancer classification
- Breast Cancer Treatment Studies
- Immune cells in cancer
- CRISPR and Genetic Engineering
- Ferroptosis and cancer prognosis
- Metabolomics and Mass Spectrometry Studies
- Pluripotent Stem Cells Research
- Metabolism and Genetic Disorders
- Mitochondrial Function and Pathology
- Neurological Disease Mechanisms and Treatments
- Advanced biosensing and bioanalysis techniques
- Neuroinflammation and Neurodegeneration Mechanisms
- Meningioma and schwannoma management
- Cancer Cells and Metastasis
- Mechanisms of cancer metastasis
- Salivary Gland Tumors Diagnosis and Treatment
- Glioma Diagnosis and Treatment
- Congenital heart defects research
- Cancer-related molecular mechanisms research
- Biological Research and Disease Studies
- Chromatin Remodeling and Cancer
Beckman Research Institute
2024-2025
City of Hope
2024-2025
University of Southern California
2019-2023
10X Genomics (United States)
2020
Keck Hospital of USC
2019
Center for Genomic Science
2010
Triple-negative breast cancer (TNBC) is an aggressive disease that disproportionately affects African American (AA) women. Limited targeted therapeutic options exist for patients with TNBC. Here, we employ spatial transcriptomics to interrogate tissue from a racially diverse TNBC cohort comprehensively annotate the transcriptional states of spatially resolved cellular populations. A total 38,706 features 28 sections 14 were analyzed. Intratumoral analysis individual revealed heterogeneous...
The Foundational Data Initiative for Parkinson Disease (FOUNDIN-PD) is an international collaboration producing fundamental resources disease (PD). FOUNDIN-PD generated a multi-layered molecular dataset in cohort of induced pluripotent stem cell (iPSC) lines differentiated to dopaminergic (DA) neurons, major affected type PD. were derived from the Parkinson's Progression Markers study, which included participants with PD carrying monogenic variants, variants intermediate effects, and...
Abstract We performed shallow single-cell sequencing of genomic DNA across 1475 cells from a cell-line, COLO829, to resolve overall complexity and clonality. This melanoma tumor-line has been previously characterized by multiple technologies is benchmark for evaluating somatic alterations. In some these studies, COLO829 shown conflicting and/or indeterminate copy number and, thus, provides tool gaining insight. Following sequencing, we first identified at least four major sub-clones...
Deletions in the 16.6 kb mitochondrial genome have been implicated numerous disorders that often display muscular and/or neurological symptoms due to high-energy demands of these tissues. We describe a catalogue 4489 putative DNA (mtDNA) deletions, including their frequency and relative read rate, using combinatorial approach mitochondria-targeted PCR, next-generation sequencing, bioinformatics, post-hoc filtering, annotation, validation steps. Our bioinformatics pipeline uses MapSplice, an...
Abstract Ovarian cancer is one of the most lethal gynecologic malignancies, primarily due to its late-stage diagnosis and intrinsic tumor heterogeneity. Histologically, epithelial ovarian (EOC) accounts for approximately 70% cases exhibits distinct molecular clinical characteristics. High-grade serous (HGSOC), aggressive form EOC, stands out widespread genomic instability poor prognosis. Copy number variations (CNVs) play a critical role in heterogeneity, treatment resistance, disease...
Abstract Common mitochondrial DNA (mtDNA) deletions are large structural variants in the genome that accumulate metabolically active tissues with age and have been investigated various diseases. We applied Splice-Break2 pipeline (designed for high-throughput quantification of mtDNA deletions) to human RNA-Seq datasets describe methodological considerations evaluating common bulk, single-cell, spatial transcriptomics datasets. A robust evaluation 1570 samples from 14 studies showed: (i)...
Astrocytes play a pivotal role in central nervous system homeostasis and neuroinflammation. Despite advancements single-cell analyses, the heterogeneity of reactive astrocytes neurodegenerative diseases, particularly across species, remains understudied. Here, we present an integrated atlas 187,000 from mouse models Alzheimer's (AD) multiple sclerosis (MS) alongside 438,000 AD, MS, Parkinson's (PD) patients. Our analysis identified four distinct astrocyte clusters, including two...
<title>Abstract</title> Astrocytes play a pivotal role in central nervous system homeostasis and neuroinflammation. Despite advancements single-cell analyses, the heterogeneity of reactive astrocytes neurodegenerative diseases, particularly across species, remains understudied. Here, we present an integrated atlas 187,000 from mouse models Alzheimer's (AD) multiple sclerosis (MS) alongside 438,000 AD, MS, Parkinson's (PD) patients. Our analysis identified four distinct astrocyte clusters,...
Objective: Comprehensive molecular profiling of radioresistant and cystic vestibular schwannoma (VS) subtypes. Study Design: Our study utilized whole-exome sequencing (WES), RNA-sequencing (RNAseq), correlated clinical data from 12 samples (2 solid sporadic subtype, 8 with changes, 2 previously irradiated). Setting: Academic medical center. Patients: Patients diagnosed VS who required surgical treatment. Inclusion: Cystic tumors matched to age tumor volume, as control; Exclusion: NF-2...
Abstract Our previous work demonstrating enrichment of outflow tract (OFT) congenital heart disease (CHD) in children with cleft lip and/or palate (CL/P) suggests derangements common underlying developmental pathways. The current pilot study examines the genetics concomitant nonsyndromic CL/P and OFT CHD phenotype. Of 575 patients who underwent surgery at Children's Hospital Los Angeles, seven CHD, negative chromosomal microarray analysis, no recognizable syndromic association were recruited...
Abstract Background Glioblastoma exhibits aggressive growth and poor outcomes despite treatment, its marked variability renders therapeutic design prognostication challenging. The Oncology Research Information Exchange Network (ORIEN) database contains complementary clinical, genomic, transcriptomic profiling of 206 glioblastoma patients, providing opportunities to identify novel associations between molecular features clinical outcomes. Methods Survival analyses were performed using the...
Spatial transcriptomics (ST) represents a pivotal advancement in biomedical research, enabling the transcriptional profiling of cells within their morphological context and providing tool for understanding spatial heterogeneity cancer tissues. However, current analytical approaches, akin to single-cell analysis, largely depend on gene expression, underutilizing rich information inherent tissue. We present novel method integrating histopathological image data better capture biologically...
Abstract The FOUNdational Data INitiative for Parkinson’s Disease (FOUNDIN-PD) is an international collaboration producing fundamental resources disease (PD). FOUNDIN-PD generated a multi-layered molecular dataset in cohort of induced pluripotent stem cell (iPSC) lines differentiated to dopaminergic (DA) neurons, major affected type PD. were derived from the Progression Markers Initiative study including participants with PD carrying monogenic ( SNCA ) variants, variants intermediate effects...
ABSTRACT We performed shallow single-cell sequencing of genomic DNA across 1,475 cells from a well-studied cell-line, COLO829, to resolve overall tumor complexity and clonality. This melanoma tumor-line has been previously characterized by multiple technologies provides benchmark for evaluating somatic alterations, though exhibited conflicting indeterminate copy number states. identified at least four major sub-clones discriminant analysis principal components (DAPC) single cell data....
Abstract The mortality rate associated with ovarian cancer (OvCa) is disproportionately high in comparison to its incidence rate. This partly due the heterogeneous nature of disease, which reduces treatment efficacy and contributes rates relapse chemotherapy resistance. Most OvCa are epithelial origin can be classified into four main subtypes: serous, mucinous, endometrioid, clear cell. Of these, grade serous (HGSOC) deadliest. Epithelial carcinomas (EOC) typically exhibit widespread...
Abstract Background: Triple negative breast cancer (TNBC) is an aggressive subtype of that disproportionately affects African-American and black (AAB) women, who have higher rates incidence mortality. To understand this disparity, we must apply advanced molecular profiling to racially diverse cohorts. We propose the use spatial transcriptomics map whole transcriptome data several thousand coordinates within tissue sections, for comprehensive unbiased characterization TNBC tumors their...
Abstract Triple negative breast cancer (TNBC) is an aggressive and clinically challenging disease that disproportionately affects African-American (AA) women. Despite this well-known disparity, AA women have historically been underrepresented in large clinical genomic studies of TNBC. Furthermore, while a genetic association risk with African ancestry has established, the tumor biology TNBC not well characterized. We therefore sought to investigate contribution transcriptional substructure...
<div>Abstract<p>Triple-negative breast cancer (TNBC) is an aggressive disease that disproportionately affects African American (AA) women. Limited targeted therapeutic options exist for patients with TNBC. Here, we employ spatial transcriptomics to interrogate tissue from a racially diverse TNBC cohort comprehensively annotate the transcriptional states of spatially resolved cellular populations. A total 38,706 features 28 sections 14 were analyzed. Intratumoral analysis...
<p>Supplementary figures and figure legends</p>
<p>Case Demographics and Clinical Annotation</p>
<p>List of Expression Datasets used for Survival Analysis</p>
<p>Case Demographics and Clinical Annotation</p>
<p>List of Expression Datasets used for Survival Analysis</p>
<p>Supplementary figures and figure legends</p>