A5061902626- Cancer Genomics and Diagnostics
- Prostate Cancer Treatment and Research
- Genetic factors in colorectal cancer
- Molecular Biology Techniques and Applications
- Cancer Cells and Metastasis
- Medical Imaging Techniques and Applications
- AI in cancer detection
- Single-cell and spatial transcriptomics
- Cancer-related molecular mechanisms research
- Colorectal Cancer Screening and Detection
- Epigenetics and DNA Methylation
- RNA modifications and cancer
- Colorectal Cancer Surgical Treatments
- Pulsars and Gravitational Waves Research
- Cancer, Lipids, and Metabolism
- Mathematical Biology Tumor Growth
- Radiopharmaceutical Chemistry and Applications
- Animal and Plant Science Education
- Genomics and Chromatin Dynamics
- Astronomy and Astrophysical Research
- Climate Change Communication and Perception
- Inflammatory mediators and NSAID effects
- Cancer Immunotherapy and Biomarkers
- Astrophysical Phenomena and Observations
- Gamma-ray bursts and supernovae
Stanford Medicine
2021-2025
Stanford University
2021-2024
Palo Alto University
2024
Amgen (United States)
2024
Thermo Fisher Scientific (United States)
2021-2023
23andMe (United States)
2023
Stratford University
2022
The University of Texas Health Science Center at San Antonio
2014-2019
The University of Texas Health Science Center at Houston
2018-2019
Mays Cancer Center at UT Health San Antonio
2019
To chart cell composition and state changes that occur during the transformation of healthy colon to precancerous adenomas colorectal cancer (CRC), we generated single-cell chromatin accessibility profiles transcriptomes from 1,000 10,000 cells per sample for 48 polyps, 27 normal tissues 6 CRCs collected patients with or without germline APC mutations. A large fraction polyp CRC exhibit a stem-like phenotype, define continuum epigenetic transcriptional occurring in these as they progress...
Abstract The intestine is a complex organ that promotes digestion, extracts nutrients, participates in immune surveillance, maintains critical symbiotic relationships with microbiota and affects overall health 1 . intesting has length of over nine metres, along which there are differences structure function 2 localization individual cell types, type development trajectories detailed transcriptional programs probably drive these function. Here, to better understand differences, we evaluated...
Abstract Increasing evidence suggests the presence of minor cell subpopulations in prostate cancer that are androgen independent and poised for selection as dominant clones after deprivation therapy. In this study, we investigated phenomenon by stratifying based on transcriptome profiling 144 single LNCaP cells treated or untreated with cell-cycle synchronization. Model-based clustering 397 differentially expressed genes identified eight potential cells, revealing a previously unappreciable...
Abstract Although three-dimensional (3D) genome architecture is crucial for gene regulation, its role in disease remains elusive. We traced the evolution and malignant transformation of colorectal cancer (CRC) by generating high-resolution chromatin conformation maps 33 colon samples spanning different stages early neoplastic growth persons with familial adenomatous polyposis (FAP). Our analysis revealed a substantial progressive loss genome-wide cis-regulatory connectivity at malignancy...
Identifying prostate cancer-driving transcription factors (TFs) in addition to the androgen receptor promises improve our ability effectively diagnose and treat this disease. We employed an integrative genomics analysis of master TFs CREB1 FoxA1 androgen-dependent cancer (ADPC) castration-resistant (CRPC) cell lines, primary tissues circulating tumor cells (CTCs) investigate their role defining gene expression profiles. Combining genome-wide binding site profiles we define as a critical...
BACKGROUND Emerging evidence shows that nanomechanical phenotypes of circulating tumor cells (CTC) could become potential biomarkers for metastatic castration resistant prostate cancer (mCRPC). METHODS To determine the CTCs we applied atomic force microscopy (AFM) employing PeakForce quantitative (QNM) imaging. We assessed biophysical parameters (elasticity, deformation, and adhesion) 130 isolated from blood samples five sensitive (CS) 12 (CRPCa) patients. RESULTS found CRPCa patients are...
Altered DNA methylation in CpG islands of gene promoters has been implicated prostate cancer (PCa) progression and can be used to predict disease outcome. In this study, we determine whether changes androgen biosynthesis pathway (ABP)-related genes patients' plasma cell-free (cfDNA) serve as prognostic markers for biochemical recurrence (BCR).Methyl-binding domain capture sequencing (MBDCap-seq) was identify differentially methylated regions (DMRs) primary tumors patients who subsequently...
Abstract The Human BioMolecular Atlas Program (HuBMAP) aims to compile a Reference (HRA) for the healthy adult body at cellular level. Functional tissue units (FTUs), relevant HRA construction, are of pathobiological significance. Manual segmentation FTUs does not scale; highly accurate and performant, open-source machine-learning algorithms needed. We designed hosted Kaggle competition that focused on development such 1200 teams from 60 countries participated. present outcomes an expanded...
Familial adenomatous polyposis (FAP) is a genetic disease causing hundreds of premalignant polyps in affected persons and an ideal model to study transitions early precancer states colorectal cancer (CRC). We performed deep multiomic profiling 93 samples, including normal mucosa, benign dysplastic polyps, from six with FAP. Transcriptomic, proteomic, metabolomic lipidomic analyses revealed dynamic choreography thousands molecular cellular events that occur during precancerous toward...
Abstract The colon is a complex organ that promotes digestion, extracts nutrients, participates in immune surveillance, maintains critical symbiotic relationships with microbiota, and affects overall health. To better understand its organization, functions, regulation at single cell level, we performed CODEX multiplexed imaging, as well nuclear RNA open chromatin assays across eight different intestinal sites of four donors. Through systematic analyses find compositions differ dramatically...
Advanced prostate cancer is a very heterogeneous disease reflecting in diverse regulations of oncogenic signaling pathways. Aberrant spatial dynamics epidermal growth factor receptor (EGFR) promote their dimerization and clustering, leading to constitutive activation oncogenesis. The EphB2 Src pathways are associated with the reorganization cytoskeleton malignancy, but roles regulating EGFR scarcely reported. Using single-particle tracking techniques, we found that highly phosphorylated...
ABSTRACT To chart cell composition and state changes that occur during the transformation of healthy colon to precancerous adenomas colorectal cancer (CRC), we generated 451,886 single-cell chromatin accessibility profiles 208,557 transcriptomes from 48 polyps, 27 normal tissues, 6 CRCs collected patients with without germline APC mutations. A large fraction polyp CRC cells exhibit a stem-like phenotype, define continuum epigenetic transcriptional occurring in these as they progress CRC....
Stanford FAP Colectomy SOP Due to the time and temperature sensitive nature of tissue collection, we must be fully prepared with all supplies for procedure that persons involved in collection process are assigned a particular role. Here, have provided detailed guidelines on exactly how navigate through colectomy. Purpose: To establish on: 1)Preparation colectomy procedures at hospitals (e.g. supplies, gross room set up) 2)Responsibilities different roles ensure during runs smoothly...
Abstract Aberrant shifts in DNA methylation have long been regarded as an early marker for cancer onset and progression. To chart changes that occur during the transformation from normal healthy colon tissue to malignant colorectal (CRC), we collected over 50 samples 15 familial adenomatous polyposis (FAP) non-FAP patients, generated 30-70x whole-genome sequencing (WGMS) runs via novel Ultima Genomics ultra high-throughput platform. We observed process, gene promoters distal regulatory...
Abstract Familial adenomatous polyposis (FAP) patients develop hundreds of premalignant polyps that progress to colorectal cancer due a germline mutation in the APC tumor suppressor. Polyps from FAP uniquely facilitate interrogation continuum malignant transformation histologically normal mucosa benign and dysplastic eventual adenocarcinomas. As part Human Tumor Atlas Network (HTAN), we performed multi-omic profiling, including whole genome sequencing, on 135 samples six across pre-malignant...
Abstract The widely accepted paradigm that cancer initiation is a monoclonal event has not been definitively resolved. This largely due to the limitations of experimental systems study initiation, transient step in tumorigenesis. Individuals with familial adenomatous polyposis (FAP) possess germline APC mutation, leading hundreds colonic polyps adolescence and an eventual 100% lifetime risk colorectal cancer. As such, total colectomies are performed once polyp burden becomes unmanageable...
Abstract The widely accepted paradigm that cancer initiation is a monoclonal event has not been definitively resolved. In sporadic cancers this due to the requirement for longitudinal sampling study occult process, which occurs over years decades. Individuals with familial adenomatous polyposis (FAP) possess germline APC mutation, leading hundreds of colonic polyps in adolescence and 100% lifetime risk colorectal cancer. Resected colons from FAP patients contain normal mucosa, benign...
Colorectal cancer (CRC) is the third leading cause of mortality in United States. Familial adenomatous polyposis (FAP) a hereditary syndrome that raises risk developing CRC, with total colectomy as only effective prevention. Even though FAP rare (0.5% all CRC cases), this disease model well suited for studying early stages malignant transformation patients form many polyps reflective pre-cancer states. In order to spatially profile and analyze tumor microenvironment, we have performed...
Abstract The Human BioMolecular Atlas Program aims to compile a reference atlas for the healthy human adult body at cellular level. Functional tissue units (FTU, e.g., renal glomeruli and colonic crypts) are of pathobiological significance relevant modeling understanding disease progression. Yet, annotation FTUs is time consuming expensive when done manually existing algorithms achieve low accuracy do not generalize well. This paper compares five winning from “Hacking Kidney” Kaggle...
<ns4:p>Science outreach improves science literacy among the public and communication skills of scientists. However, despite array well-documented benefits, robust efforts are often absent from communities which stand to benefit most these initiatives. Here, we introduce “Science Fiesta,” a graduate student-led initiative utilizes cultural traditions South Texas as vehicle establish self-sustaining interactions between scientists their local community. Event assessment surveys indicated that...
Abstract Familial adenomatous polyposis (FAP) is a genetic disease causing hundreds of premalignant polyps in affected patients, leading to colorectal cancer (CRC), and an ideal model study early transition CRC. We performed deep multi-omic profiling 135 normal mucosal, benign dysplastic adenocarcinoma samples from 6 FAP patients who consented broad data sharing. Whole genome sequencing indicates that spatially separated the same donor harbor numerous mutations common, but evolve...
Abstract Approximately 30% of prostate cancer (PCa) patients who receive androgen-deprivation therapy experience disease progression, including bone metastasis, in 18-36 months. Clinical diagnosis this castration resistance is primarily based on a continuous rise serum PSA levels during therapy. However, the underlying progression predates clinical onset by many The challenge to distinguish indolent vs aggressive for better management. During malignant circulating tumor cells (CTC) shed from...