A5001309501- Cancer Genomics and Diagnostics
- Prostate Cancer Treatment and Research
- Genomics and Chromatin Dynamics
- Epigenetics and DNA Methylation
- Single-cell and spatial transcriptomics
- Pluripotent Stem Cells Research
- CRISPR and Genetic Engineering
- HIV Research and Treatment
- Developmental Biology and Gene Regulation
- Protein Degradation and Inhibitors
- HIV/AIDS drug development and treatment
- Molecular Biology Techniques and Applications
- RNA modifications and cancer
- CAR-T cell therapy research
- Advanced biosensing and bioanalysis techniques
- Genetic factors in colorectal cancer
- Neurogenesis and neuroplasticity mechanisms
- Ubiquitin and proteasome pathways
- Radiomics and Machine Learning in Medical Imaging
- Renal cell carcinoma treatment
- Acute Myeloid Leukemia Research
- Cancer, Lipids, and Metabolism
- Gene expression and cancer classification
- Peptidase Inhibition and Analysis
- MicroRNA in disease regulation
Fred Hutch Cancer Center
2018-2025
Cape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa
2020-2025
Van Andel Institute
2024-2025
Cancer Research Center
2019-2022
University of Michigan–Ann Arbor
2014-2020
Howard Hughes Medical Institute
2019
Office of Basic Energy Sciences
2019
Abstract Chromatin profiling at locus resolution uncovers gene regulatory features that define cell types and developmental trajectories, but it remains challenging to map compare different chromatin-associated proteins in the same sample. Here we describe Multiple Target Identification by Tagmentation (MulTI-Tag), an antibody barcoding approach for multiple chromatin simultaneously single cells. We optimized MulTI-Tag retain high sensitivity specificity, demonstrate detection of up three...
Abstract Acute myeloid and lymphoid leukemias often harbor chromosomal translocations involving the KMT2A gene, encoding lysine methyltransferase (also known as mixed-lineage leukemia-1), produce in-frame fusions of to other chromatin-regulatory proteins. Here we map fusion-specific targets across genome for diverse oncofusion proteins in cell lines patient samples. By modifying CUT&Tag chromatin profiling full automation, identify common tumor-subtype-specific sites aberrant regulation...
Abstract Cleavage Under Targets and Tagmentation (CUT&Tag) is an antibody-directed transposase tethering strategy for in situ chromatin profiling small samples single cells. We describe a modified CUT&Tag protocol using mixture of antibody to the initiation form RNA polymerase II (Pol2 Serine-5 phosphate) repressive Polycomb domains (H3K27me3) followed by computational signal deconvolution produce high-resolution maps both active regulomes The ability seamlessly map promoters,...
Despite expressing stem cell self-renewal factors, intermediate progenitor cells possess restricted developmental potential, which allows them to give rise exclusively differentiated progeny rather than progeny. Failure restrict the potential can allow revert into aberrant that might contribute tumorigenesis. Insight stable restriction of in could improve our understanding development and growth tumors, but mechanisms involved remain largely unknown. Intermediate neural progenitors (INPs),...
Our understanding of eukaryotic gene regulation is limited by the complexity protein-DNA interactions that comprise chromatin landscape and inefficient methods for characterizing these interactions. We recently introduced CUT&RUN, an antibody-targeted nuclease cleavage method profiles DNA-binding proteins, histones chromatin-modifying proteins in situ with exceptional sensitivity resolution.Here, we describe automated CUT&RUN platform apply it to characterize landscapes human cells. find...
Lysine 27-to-methionine (K27M) mutations in the H3.1 or H3.3 histone genes are characteristic of pediatric diffuse midline gliomas (DMGs). These oncohistone dominantly inhibit H3K27 trimethylation and silencing, but it is unknown how type affects gliomagenesis. We show that genomic distributions oncohistones human patient-derived DMG cells consistent with DNAreplication-coupled deposition predominant replication-independent H3.3. Although reduced for both types, H3.3K27M-bearing retain some...
Advanced prostate cancers comprise distinct phenotypes, but tumor classification remains clinically challenging. Here, we harnessed circulating DNA (ctDNA) to study phenotypes by ascertaining nucleosome positioning patterns associated with transcription regulation. We sequenced plasma ctDNA whole genomes from patient-derived xenografts representing a spectrum of androgen receptor active (ARPC) and neuroendocrine (NEPC) cancers. Nucleosome transcriptional activity were reflected in at regions...
Transcriptional silencing of latent HIV-1 proviruses entails complex and overlapping mechanisms that pose a major barrier to in vivo elimination HIV-1. We developed new latency CRISPR screening strategy, called Latency HIV-CRISPR which uses the packaging guideRNA-encoding lentiviral vector genomes into supernatant budding virions as direct readout factors involved maintenance latency. custom guideRNA library targeting epigenetic regulatory genes paired screen with without reversal...
Although MAX is regarded as an obligate dimerization partner for MYC, its function in normal development and neoplasia poorly defined. We show that B-cell-specific deletion of Max has a modest effect on B-cell but completely abrogates Eµ- Myc- driven lymphomagenesis. While loss affects only few hundred genes B cells, it leads to the global down-regulation Myc -activated premalignant cells. balance between MYC–MAX MNT–MAX interactions cells shifts toward MYC-driven transcriptional program....
Prostate cancer (PC) is driven by androgen receptor (AR) activity, a master regulator of prostate development and homeostasis. Frontline therapies for metastatic PC deprive the AR activating ligands testosterone (T) dihydrotestosterone (DHT) limiting their biosynthesis or blocking binding. Notably, signaling dichotomous, inducing growth at lower activity levels, while suppressing higher levels. Recent clinical studies have exploited this effect administration supraphysiological...
Abstract The dynamic three-dimensional (3D) organization of the human genome (the “4D Nucleome”) is closely linked to function. Here, we integrate a wide variety genomic data generated by 4D Nucleome Project provide detailed view 3D in widely used embryonic stem cells (H1-hESCs) and immortalized fibroblasts (HFFc6). We extensive benchmarking mapping assays these diverse datasets annotate spatial features across scales. reveal rich complexity chromatin domains their sub-nuclear positions,...
The latent HIV reservoir is a major barrier to cure. Combining latency reversal agents (LRAs) with differing mechanisms of action such as AZD5582, non-canonical NF-kB activator, and I-BET151, bromodomain inhibitor appealing towards inducing HIV-1 reactivation. However, even this LRA combination needs improvement it inefficient at activating proviruses in cells from people living (PLWH). We performed CRISPR screen conjunction AZD5582 & I-BET151 identified member the Integrator complex...
Abstract For more than a century, formalin-fixed paraffin-embedded (FFPE) sample preparation has been the preferred method for long-term preservation of biological material. However, use FFPE samples epigenomic studies difficult because chromatin damage from long exposure to high concentrations formaldehyde. Previously, we introduced Cleavage Under Targeted Accessible Chromatin (CUTAC), an antibody-targeted accessibility mapping protocol based on CUT&Tag. Here show that simple...
The mechanisms that maintain the functional heterogeneity of stem cells, which generates diverse differentiated cell types required for organogenesis, are not understood. In this study, we report Trithorax (Trx) actively maintains neural cells (neuroblasts) in developing Drosophila larval brain. trx mutant type II neuroblasts gradually adopt a I neuroblast identity, losing competence to generate intermediate progenitors (INPs) and directly generating cells. Trx regulates identity part by...
Abstract Chromosomal translocations involving the mixed-lineage leukemia (MLL ) locus generate potent oncogenic fusion proteins (oncoproteins) that disrupt regulation of developmental gene expression. By profiling oncoprotein-target sites 36 broadly representative MLL -rearranged samples, including three samples underwent a lymphoid-to-myeloid lineage-switching event in response to therapy, we find genomic enrichment oncoprotein is highly variable between and subject dynamic regulation. At...
Stem cells that indirectly generate differentiated through intermediate progenitors drives vertebrate brain evolution. Due to a lack of lineage information, how stem cell functionality, including the competency progenitors, becomes extinguished during progenitor commitment remains unclear. Type II neuroblasts in fly larval brains divide asymmetrically neuroblast and progeny commits an (INP) identity. We identified Tailless (Tll) as master regulator type functional identity, INPs. Successive...