A5112864725- Genetic factors in colorectal cancer
- Cancer Genomics and Diagnostics
- Molecular Biology Techniques and Applications
- Cancer-related molecular mechanisms research
- Cancer Cells and Metastasis
- Single-cell and spatial transcriptomics
- Genomics and Chromatin Dynamics
- RNA modifications and cancer
- RNA Research and Splicing
- DNA Repair Mechanisms
- Colorectal Cancer Surgical Treatments
- Exercise and Physiological Responses
- Adipose Tissue and Metabolism
- Immune cells in cancer
- Cancer Immunotherapy and Biomarkers
- Circadian rhythm and melatonin
- Epigenetics and DNA Methylation
- Genetics and Physical Performance
- Colorectal Cancer Treatments and Studies
- Gene expression and cancer classification
- Nutrition, Genetics, and Disease
- IL-33, ST2, and ILC Pathways
- Cancer, Lipids, and Metabolism
- Inflammatory mediators and NSAID effects
- Advanced Electron Microscopy Techniques and Applications
Stanford Medicine
2021-2025
Stanford University
2021-2024
Guardant (United States)
2024
Palo Alto University
2023
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 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...
Abstract Regular exercise promotes whole-body health and prevents disease, yet the underlying molecular mechanisms throughout a whole organism are incompletely understood. Here, Molecular Transducers of Physical Activity Consortium (MoTrPAC) profiled temporal transcriptome, proteome, metabolome, lipidome, phosphoproteome, acetylproteome, ubiquitylproteome, epigenome, immunome in blood, plasma, 18 solid tissues Rattus norvegicus over 8 weeks endurance training. The resulting data compendium...
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...
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 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....
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...
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 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 Aberrant shifts in DNA methylation have long been regarded as an early biomarker for cancer onset and progression. However, it is unclear when aberrance starts how interacts with other epigenomic modifications. To address changes occur interact during the transformation from normal healthy colon tissue to malignant colorectal (CRC), we collected 51 samples 15 familial adenomatous polyposis (FAP) non-FAP patients. We generated 30-70x of whole-genome enzymatic sequencing (WGEM-seq)...
Abstract Although 3D genome architecture can be essential for gene regulation, the biological implications of long-range chromatin interactions in disease remain elusive. In this study, we traced early evolution and malignant transformation colorectal cancer by generating high-resolution conformation maps 33 colon samples spanning different stages neoplastic growth from polyps Familial Adenomatous Polyposis (FAP) patients. Our analysis reveals a substantial progressive loss genome-wide...
<title>Abstract</title> Although 3D genome architecture is essential for long-range gene regulation, the significance of distal regulatory chromatin contacts challenged by recent findings low correlation between contact propensity and expression. To better understand role interactions elements during early transformation from healthy colon to colorectal cancer, here we performed high resolution conformation capture 33 samples including non-neoplastic mucosa, adenomatous polyps...
10x single-cell multiome nuclei isolation and library preparation protocol for HuBMAP colon project.