A5025510640- Immune Cell Function and Interaction
- CRISPR and Genetic Engineering
- Cellular Mechanics and Interactions
- T-cell and B-cell Immunology
- Cancer Genomics and Diagnostics
- Cancer Cells and Metastasis
- Wnt/β-catenin signaling in development and cancer
- Single-cell and spatial transcriptomics
- CAR-T cell therapy research
- Genomics and Chromatin Dynamics
- Monoclonal and Polyclonal Antibodies Research
- Advanced biosensing and bioanalysis techniques
- Hippo pathway signaling and YAP/TAZ
- Cancer-related molecular mechanisms research
- Immune cells in cancer
- Chromosomal and Genetic Variations
- 3D Printing in Biomedical Research
- Cell Adhesion Molecules Research
- Protein Degradation and Inhibitors
- Molecular Biology Techniques and Applications
- RNA Research and Splicing
- Advanced Fluorescence Microscopy Techniques
- RNA and protein synthesis mechanisms
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- RNA modifications and cancer
Stanford University
2015-2025
University Dermatology
2025
Dynamic Imaging (United Kingdom)
2020-2022
Palo Alto University
2015-2020
Stanford Cancer Institute
2017-2019
Franciscan University of Steubenville
2019
Bay Area Medical Center
2015
University of Illinois Urbana-Champaign
2008-2014
Oregon Health & Science University
2013
University of California, Berkeley
2013
Journal Article Human breast cancer invasion and aggression correlates with ECM stiffening immune cell infiltration Get access I. Acerbi, Acerbi Center for Bioengineering, Tissue Regeneration, Department of Surgery, UCSF, San Francisco, CA, USA. Fax: +1-415-476-3985; Tel: +1-415-476-3826 Search other works by this author on: Oxford Academic Google Scholar L. Cassereau, Cassereau Dean, Dean Q. Shi, Shi Bay Area Physical Sciences Oncology Center, USADepartment Stanford University, Palo Alto,...
Cell surface receptors integrate chemical and mechanical cues to regulate a wide range of biological processes. Integrin complexes are the mechanotransducers between extracellular matrix actomyosin cytoskeleton. By analogy, cadherin may function as mechanosensors at cell–cell junctions, but this capacity cadherins has not been directly demonstrated. Furthermore, molecular composition link E-cadherin actin, which is needed sustain such function, unresolved. In study, we describe...
SARS-CoV-2 is the cause of a pandemic with growing global mortality. Using comprehensive identification RNA-binding proteins by mass spectrometry (ChIRP-MS), we identified 309 host that bind RNA during active infection. Integration this data ChIRP-MS from three other viruses defined viral specificity RNA-host protein interactions. Targeted CRISPR screens revealed majority functional protect virus-induced cell death, and comparative across seven shared SARS-specific antiviral factors....
The long non-coding RNA (lncRNA) XIST establishes X chromosome inactivation (XCI) in female cells early development and thereafter is thought to be largely dispensable. Here, we show continually required adult human B silence a subset of X-linked immune genes such as TLR7. XIST-dependent lack promoter DNA methylation require continual histone deacetylation. RNA-directed proteomics CRISPRi screen reveal distinctive somatic cell-type-specific complexes identify TRIM28 that mediates Pol II...
Abstract Oncogene amplification on extrachromosomal DNA (ecDNA) is a common event, driving aggressive tumor growth, drug resistance and shorter survival. Currently, the impact of nonchromosomal oncogene inheritance—random identity by descent—is poorly understood. Also unclear ecDNA somatic variation selection. Here integrating theoretical models random segregation, unbiased image analysis, CRISPR-based tagging with live-cell imaging CRISPR-C, we demonstrate that inheritance results in...
Significance Tissue mechanics are important in differentiation and development but also diseases like breast cancer. Most cancers start mammary acini, which basic anatomical units of the gland. We found a model system that acini can coordinate their disorganization toward malignant phenotype through long-range mechanical interactions. When two or more contractile sufficiently close together, they interact via collagen lines form between them due to acinar contractility nonlinearity...
Women with dense breasts have an increased lifetime risk of malignancy that has been attributed to a higher epithelial density. Quantitative proteomics, collagen analysis, and mechanical measurements in normal tissue revealed stroma the high-density breast contains more oriented, fibrillar is stiffer correlates cell microRNA (miR) profiling identified miR-203 as matrix stiffness-repressed transcript downregulated by density reduced epithelium women high mammographic Culture studies...
Cells communicate with each other via receptor-ligand interactions. Here, we describe lentiviral-mediated cell entry by engineered interaction (ENTER) to display ligand proteins, deliver payloads, and record receptor specificity. We optimize ENTER decode interactions between T (TCR)-MHC peptides, antibody-antigen, pairs. A viral presentation strategy allows capture B any antigen. engineer genetic payloads antigen-specific or cells selectively modulate cellular behavior in mixed populations....
Abstract CRISPR perturbation methods are limited in their ability to study non-coding elements and genetic interactions. In this study, we developed a system for bidirectional epigenetic editing, called CRISPRai, which apply activating (CRISPRa) repressive (CRISPRi) perturbations two loci simultaneously the same cell. We CRISPRai Perturb-seq by coupling dual gRNA detection with single-cell RNA sequencing, enabling of pooled mixed population. applied platform interaction between hematopoietic...
Abstract Yes-associated protein 1 (YAP) is a transcriptional regulator with critical roles in mechanotransduction, organ size control, and regeneration. Here, using advanced tools for real-time visualization of native YAP target gene transcription dynamics, we show that cycle fast exodus nuclear to the cytoplasm followed by reentry nucleus (“localization-resets”) activates genes. These “resets” are induced calcium signaling, modulation actomyosin contractility, or mitosis. Using...
Naturally occurring cases of monogenic type 1 diabetes (T1D) help establish direct mechanisms driving this complex autoimmune disease. A recently identified de novo germline gain-of-function (GOF) mutation in the transcriptional regulator STAT3 was found to cause neonatal T1D. We engineered a novel knock-in mouse incorporating highly diabetogenic human (K392R) and that these mice recapitulated phenotype. Paired single-cell TCR RNA sequencing revealed STAT3-GOF drives proliferation clonal...
HOTAIR is a 2.2-kb long noncoding RNA (lncRNA) whose dysregulation has been linked to oncogenesis, defects in pattern formation during early development, and irregularities the process of epithelial-to-mesenchymal transition (EMT). However, oncogenic transformation determined by vivo its impact on chromatin dynamics are incompletely understood. Here, we generate transgenic mouse model with doxycycline-inducible expression human context MMTV-PyMT breast cancer-prone background systematically...
The Xist lncRNA mediates X chromosome inactivation (XCI). Here we show that Spen, an Xist-binding repressor protein essential for XCI , binds to ancient retroviral RNA, performing a surveillance role recruit chromatin silencing machinery these parasitic loci. Spen loss activates subset of endogenous (ERV) elements in mouse embryonic stem cells, with gain accessibility, active histone modifications, and ERV RNA transcription. directly RNAs structural similarity the A-repeat Xist, region...
Differential binding between cadherin subtypes is widely believed to mediate cell sorting during embryogenesis. However, a fundamental unanswered question whether dictated by the biophysical properties of bonds, or broader, cadherin-dependent differences in intercellular adhesion membrane tension. This report describes atomic force microscope measurements strengths and dissociation rates homophilic heterophilic (CAD) bonds. Measurements conducted with chicken N-CAD, canine E-CAD, Xenopus...
This study investigates the relationship between classical cadherin binding affinities and mechanotransduction through cadherin-mediated adhesions. The mechanical properties of cadherin-dependent intercellular junctions are generally attributed to differences in subtypes that contribute cohesive energies cells. However, cell mechanics may also regulate contacts. Here, micropipette measurements quantified two-dimensional cadherins at surface, two complementary assessed ligand-dependent At...
Abstract The Satb1 genome organizer regulates multiple cellular and developmental processes. It is not yet clear how selects different sets of targets throughout the genome. Here we have used live-cell single molecule imaging deep sequencing to assess determinants binding-site selectivity. We found that preferentially nucleosome-dense regions can directly bind consensus motifs within nucleosomes. Some genomic harbor multiple, regularly spaced binding (typical separation ~1 turn DNA helix)...
Abstract Four out of five patients with autoimmune diseases are women. The XIST ribonucleoprotein (RNP) complex, comprising the female-specific long noncoding RNA and over 100 associated proteins, may drive several that disproportionately affect women, who have elevated levels autoantibodies against RNP. However, structural distribution, potential origin, clinical significance RNP remained unexplored. Here, we find is autoantigens six female-biased conditions. Mapping autoantibody targets to...