A5014840923- Single-cell and spatial transcriptomics
- Cancer Genomics and Diagnostics
- Dermatology and Skin Diseases
- Skin Protection and Aging
- CAR-T cell therapy research
- Molecular Biology Techniques and Applications
- Cutaneous Melanoma Detection and Management
- Nonmelanoma Skin Cancer Studies
- IL-33, ST2, and ILC Pathways
- T-cell and B-cell Immunology
- Immunotherapy and Immune Responses
- Food Allergy and Anaphylaxis Research
- Epigenetics and DNA Methylation
- Cell Image Analysis Techniques
- CRISPR and Genetic Engineering
- Genomics and Chromatin Dynamics
- Allergic Rhinitis and Sensitization
- Evolution and Genetic Dynamics
- Melanoma and MAPK Pathways
- PI3K/AKT/mTOR signaling in cancer
- Cancer-related Molecular Pathways
- RNA modifications and cancer
- Interstitial Lung Diseases and Idiopathic Pulmonary Fibrosis
- Psoriasis: Treatment and Pathogenesis
- Infectious Diseases and Mycology
Icahn School of Medicine at Mount Sinai
2022-2025
Stanford University
2016-2025
Stem Cell Institute
2022-2024
Centers for Disease Control and Prevention
2024
ORCID
2021
Stanford Medicine
2016
Memorial Sloan Kettering Cancer Center
2015
Wake Forest University
2013
Galderma (United States)
2013
To define the cellular composition and architecture of cutaneous squamous cell carcinoma (cSCC), we combined single-cell RNA sequencing with spatial transcriptomics multiplexed ion beam imaging from a series human cSCCs matched normal skin. cSCC exhibited four tumor subpopulations, three recapitulating epidermal states, tumor-specific keratinocyte (TSK) population unique to cancer, which localized fibrovascular niche. Integration data mapped ligand-receptor networks specific types, revealing...
Abstract Defining the transition from benign to malignant tissue is fundamental improving early diagnosis of cancer 1 . Here we use a systematic approach study spatial genome integrity in situ and describe previously unidentified clonal relationships. We used spatially resolved transcriptomics 2 infer copy number variations >120,000 regions across multiple organs, tissues. demonstrate that genome-wide variation reveals distinct patterns within tumours nearby using an organ-wide focused on...
Abstract Quantitative criteria to identify proteins as RNA-binding (RBPs) are presently lacking, define RBP target RNAs. Here, we develop an ultraviolet (UV) cross-linking immunoprecipitation (CLIP)-sequencing method, easyCLIP. easyCLIP provides absolute cross-link rates, well increased simplicity, efficiency, and capacity visualize RNA libraries during sequencing library preparation. Measurement of >200 independent experiments across >35 identifies rate threshold that distinguishes...
Itch is a common symptom that can greatly diminish quality of life. Histamine potent endogenous pruritogen, and while antihistamines are often the first-line treatment for itch, in conditions like chronic spontaneous urticaria (CSU), many patients remain symptomatic receiving maximal doses. Mechanisms drive resistance to poorly defined.
Spatial transcriptomic technologies, such as the Visium platform, measure gene expression in different regions of tissues. Here, we describe new software, STmut, to visualize somatic point mutations, allelic imbalance, and copy number alterations data. STmut is tested on fresh-frozen data, formalin-fixed paraffin-embedded (FFPE) tumors with without matching DNA sequencing Copy inferred all conditions, but chemistry FFPE platform does not permit analyses single nucleotide variants. Taken...
Sarcoidosis is an inflammatory disease characterized by immune cell–rich granulomas that form in multiple organs. In this issue of the JCI, Sati and colleagues used scRNA-seq spatial transcriptomics skin samples from patients with sarcoidosis non-sarcoidosis granulomatous to identify upregulation a stromal-immune CXCL12/CXCR4 axis accumulation type 1 innate lymphoid cells (ILC1s) sarcoidosis. The ILC1s blood was specific not observed other diseases. authors mouse model lung granuloma show...
Glucose is a universal energy currency for living organisms, however, its non-energetic functions in processes such as differentiation are undefined. In epidermis, differentiating cells exhibit dynamic changes gene expression 1–4 driven by specific transcription factors (TFs) 5–9 . The interplay between TFs and biomolecules that also change this process not understood. Metabolomic analyses revealed increased intracellular glucose accompanies of epidermal keratinocytes. This elevation...
Abstract Defining the transition from benign to malignant tissue is fundamental improve early diagnosis of cancer. Here, we provide an unsupervised approach study spatial genome integrity in situ gain molecular insight into clonal relationships. We employed spatially resolved transcriptomics infer copy number variations >120 000 regions across multiple organs, and tissues. demonstrate that genome-wide variation reveals distinct patterns within tumours nearby tissue. Our results suggest a...
Summary Here we present Perturb-ATAC, a method which combines multiplexed CRISPR interference or knockout with genome-wide chromatin accessibility profiling in single cells, based on the simultaneous detection of guide RNAs and open sites by assay transposase-accessible sequencing (ATAC-seq). We applied Perturb-ATAC to transcription factors (TFs), chromatin-modifying factors, noncoding (ncRNAs) ∼4,300 encompassing more than 63 unique genotype-phenotype relationships. human B lymphocytes...
Objective. To examine trends in melanoma visits the ambulatory care setting. Methods. Data from National Ambulatory Medical Care Survey (NAMCS) 1979 to 2010 were used analyze visit characteristics including number of visits, age and gender patients, physician specialty. These data compared US Census population estimates during same time period. Results. The overall rate increased (P < 0.0001) at an apparently higher than increase over this time. patients with approximately double (0.47 year...
Abstract Tools to visualize genetic alterations within tissues remain underdeveloped despite the growth of spatial transcriptomic technologies, which measure gene expression in different regions tissues. Since can be detected RNA-sequencing data, we explored feasibility observing somatic transcriptomics data. Extracting information from data would illuminate distribution clones and allow for correlations with regional changes support genotype-phenotype studies. Recent work demonstrates that...
ABSTRACT Ocular syphilis is a serious complication of Treponema pallidum infection that can occur at any stage and affect eye structure. It remains unknown if certain T. strains are associated with ocular infections; therefore, we performed genotyping whole genome sequencing (WGS) to characterize from patients syphilis. Seventy-five or non-ocular specimens 55 in 14 states within the United States were collected between February 2016 November 2020. Sufficient DNA was available nine for three...