A5040965653- Cancer Genomics and Diagnostics
- Radiomics and Machine Learning in Medical Imaging
- Cancer Research and Treatments
- Nanoplatforms for cancer theranostics
- interferon and immune responses
- Nanoparticle-Based Drug Delivery
- Chemical Reactions and Isotopes
- Immune cells in cancer
- Cell Image Analysis Techniques
- Computational Drug Discovery Methods
- Biosimilars and Bioanalytical Methods
- Single-cell and spatial transcriptomics
- Advanced Biosensing Techniques and Applications
- Cancer, Hypoxia, and Metabolism
- DNA and Nucleic Acid Chemistry
- Cancer Immunotherapy and Biomarkers
- DNA Repair Mechanisms
- Monoclonal and Polyclonal Antibodies Research
- Ferroptosis and cancer prognosis
- Cytokine Signaling Pathways and Interactions
- Pancreatic and Hepatic Oncology Research
- RNA modifications and cancer
- Immunotherapy and Immune Responses
- Medical Imaging Techniques and Applications
- Tuberculosis Research and Epidemiology
Nanostring Technologies (United States)
2021-2025
Henry Ford Health System
2024-2025
Wayne State University
2024
Bruker (United States)
2024
Seattle University
2023
National Institute of Diabetes and Digestive and Kidney Diseases
2012-2021
National Institutes of Health
2012-2018
Fred Hutch Cancer Center
2015-2017
Environmental Molecular Sciences Laboratory
2015
Johns Hopkins University
2012-2014
Abstract Characterizing the transcriptome of individual cells is fundamental to understanding complex biological systems. We describe a droplet-based system that enables 3′ mRNA counting tens thousands single per sample. Cell encapsulation, up 8 samples at time, takes place in ∼6 min, with ∼50% cell capture efficiency. To demonstrate system’s technical performance, we collected data from ∼250k across 29 samples. validated sensitivity and its ability detect rare populations using lines...
DNA polymerase ζ (Pol ζ) is a eukaryotic B-family that specializes in translesion synthesis and essential for normal embryogenesis. At minimum, Pol consists of catalytic subunit Rev3 an accessory Rev7. Mammalian contains >3,000 residues twice as large the yeast homolog. To date, no vertebrate has been purified biochemical characterization. Here we report purification series human deletion constructs expressed HEK293 cells identification minimally catalytically active variant. With tagged...
ABSTRACT Characterizing the transcriptome of individual cells is fundamental to understanding complex biological systems. We describe a droplet-based system that enables 3′ mRNA counting up tens thousands single per sample. Cell encapsulation in droplets takes place ∼6 minutes, with ∼50% cell capture efficiency, 8 samples at time. The speed and efficiency allow processing precious while minimizing stress cells. To demonstrate system′s technical performance its applications, we collected data...
Cisplatin (cis-diamminedichloroplatinum) and related compounds cause DNA damage are widely used as anticancer agents. Chemoresistance to cisplatin treatment is due in part translesion synthesis by human polymerase η (hPol η). Here, we report crystal structures of hPol complexed with intrastrand cisplatin-1,2–cross-linked DNA, representing four consecutive steps synthesis. In contrast the generally enlarged nondiscriminating active site Y-family polymerases like Dpo4, Pol specialized for...
Abstract The Spatial Molecular Imaging platform (CosMx TM SMI, NanoString Technologies, Seattle, WA) utilizes high-plex in-situ imaging chemistry for both RNA and protein detection. This automated instrument provides 1000’s of plex, at high sensitivity (1 to 2 copies/cell), very low error rate (0.0092 false calls/cell) background (∼0.04 counts/cell). system generates three-dimensional super-resolution localization analytes ∼2 million cells per sample, four samples run. Cell segmentation is...
Abstract Background The molecular underpinnings of organ dysfunction in severe COVID-19 and its potential long-term sequelae are under intense investigation. To shed light on these the context liver function, we perform single-nucleus RNA-seq spatial transcriptomic profiling livers from 17 decedents. Results We identify hepatocytes positive for SARS-CoV-2 RNA with an expression phenotype resembling infected lung epithelial cells, a central role pro-fibrotic TGFβ signaling cell–cell...
Somatic hypermutation is programmed base substitutions in the variable regions of Ig genes for high-affinity antibody generation. Two motifs, RGYW and WA (R, purine; Y, pyrimidine; W, A or T), have been found to be somatic hotspots. Overwhelming evidence suggests that DNA polymerase η (Pol η) responsible converting motif WG by misincorporating dGTP opposite templating T. To elucidate molecular mechanism, crystal structures kinetics human Pol substituting dATP four sequence contexts, TA, AA,...
Next-generation sequencing (NGS) technologies have transformed genomic research and the potential to revolutionize clinical medicine. However, background error rates of instruments limitations in targeted read coverage precluded detection rare DNA sequence variants by NGS. Here we describe a method, termed CypherSeq, which combines double-stranded barcoding correction rolling circle amplification (RCA)-based target enrichment vastly improve NGS-based variant detection. The CypherSeq...
Abstract Accurate cell typing is fundamental to analysis of spatial single-cell transcriptomics, but legacy scRNA-seq algorithms can underperform in this new type data. We have developed a algorithm, Insitutype, designed for statistical and computational efficiency transcriptomics Insitutype based on likelihood model that weighs the evidence from every expression value, extracting all information available each cell’s profile. This underlies Bayes classifier supervised typing, an...
Significance In this work we investigated the ability of phenanthriplatin, a novel, potent monofunctional platinum anticancer agent, to inhibit DNA replication. Biochemical assays using site-specifically platinated probes revealed phenanthriplatin lesions block replication by all polymerases tested except for Pol η, which exhibited inefficient but high-fidelity lesion bypass. Crystallographic studies η stalled at different stages translesion synthesis past phenanthriplatin-platinated...
Significance To determine if there is a general base in the DNA synthesis reaction that deprotonates nucleophile, we systematically removed potential hydrogen-bond acceptors of 3′-OH primer strand. We then characterized activity human Pol η by kinetic, structural, and molecular dynamics simulation analyses. found no single or combined perturbations eliminate catalysis. Moreover, removal two proton mutating conserved S113 to Ala addition 2′-F end rescued defects S113A mutation alone. Our...
Cancer drug development is currently limited by a paradigm of preclinical evaluation that does not adequately recapitulate the complexity intact human tumor microenvironment (TME). To overcome this, we combined trackable intratumor microdosing (CIVO) with spatial biology readouts to directly assess effects in patient tumors situ.In first-of-its-kind phase 0 clinical trial, explored an investigational stage SUMOylation-activating enzyme (SAE) inhibitor, subasumstat (TAK-981) 12 patients head...
ABSTRACT Cells live and interact in three-dimensional (3D) cellular neighborhoods. However, histology spatial omics methods mostly focus on 2D tissue sections. Here we present a 3D atlas of routine clinical sample, an aggressive human lung carcinoma, by combining situ quantification 960 cancer-related genes across ∼340,000 cells with measurements tissue-mechanical components. neighborhoods subdivided the tumor microenvironment into tumor, stromal, immune multicellular niches. Interestingly,...
Tumors are complex ecosystems composed of malignant and non-malignant cells embedded in a dynamic extracellular matrix (ECM). In the tumor microenvironment, molecular phenotypes controlled by cell-cell ECM interactions 3D cellular neighborhoods (CNs). While their inhibition can impede progression, routine profiling fails to capture interactions. Single-cell spatial transcriptomics (ST) maps receptor-ligand but usually remains limited 2D tissue sections lacks readouts. Here, we integrate ST...
Abstract The three-dimensional X-ray crystal structure of the ‘rare cutting’ type II restriction endonuclease SgrAI bound to cognate DNA is presented. forms a dimer one duplex DNA. Two Ca2+ bind in enzyme active site, with ion at interface between protein and DNA, second distal from These sites are differentially occupied by Mn2+, strong binding protein–DNA interface, but only partial occupancy site. remains uncleaved structures crystals grown presence either divalent cation. similar those...
Abstract Background Immunotherapy has improved survival for patients with advanced clear cell renal carcinoma (ccRCC), but resistance to therapy develops in most patients. We use cellular-resolution spatial transcriptomics immunotherapy naïve and exposed primary ccRCC tumors better understand resistance. Results Spatial molecular imaging of tumor adjacent stroma samples from 21 suggests that viable following harbor more stromal CD8 + T cells neutrophils than tumors. YES1 is significantly...
In combination with cell intrinsic properties, interactions in the tumor microenvironment modulate therapeutic response. We leveraged high-plex single-cell spatial transcriptomics to dissect remodeling of multicellular neighborhoods and cell-cell human pancreatic cancer associated specific malignant subtypes neoadjuvant chemotherapy/radiotherapy. developed Spatially Constrained Optimal Transport Interaction Analysis (SCOTIA), an optimal transport model a cost function that includes both...
Oxidatively induced DNA lesions 8,5′-cyclopurine-2′-deoxynucleosides (cdPus) are prevalent and cytotoxic by impeding replication transcription. Both the 5′ R - S -diastereomers of cdPu can be removed nucleotide excision repair; however, -cdPu is more resistant to repair than counterpart. Here, we report crystal structures human polymerase (Pol) η bypassing -8,5′-cyclo-2′-deoxyadenosine (cdA) in insertion following two extension steps. The cdA-containing vary response protein environment....
Latency remains a major obstacle to finding cure for HIV despite the availability of antiretroviral therapy. Due virus dormancy, limited biomarkers are available identify latent HIV-infected cells. Profiling individual cells is needed explore potential latency and study mechanisms persistence that maintain reservoir.