A5049047003- Biochemical and Molecular Research
- Adenosine and Purinergic Signaling
- Folate and B Vitamins Research
- RNA modifications and cancer
- Epigenetics and DNA Methylation
- interferon and immune responses
- Cancer-related Molecular Pathways
- Viral Infections and Vectors
- Mitochondrial Function and Pathology
- Cancer Immunotherapy and Biomarkers
- DNA Repair Mechanisms
- Telomeres, Telomerase, and Senescence
- RNA Research and Splicing
- Nanoparticles: synthesis and applications
- Viral gastroenteritis research and epidemiology
- Cytomegalovirus and herpesvirus research
- Viral Infections and Outbreaks Research
- Monoclonal and Polyclonal Antibodies Research
- Cancer, Hypoxia, and Metabolism
- Parvovirus B19 Infection Studies
- Phagocytosis and Immune Regulation
- Trace Elements in Health
- Advanced biosensing and bioanalysis techniques
- Molecular Biology Techniques and Applications
- Amino Acid Enzymes and Metabolism
UPMC Hillman Cancer Center
2022-2025
University of Pittsburgh
2023-2024
Washington University in St. Louis
2020-2022
Abstract Homologous recombination (HR) deficiency enhances sensitivity to DNA damaging agents commonly used treat cancer. In HR-proficient cancers, metabolic mechanisms driving response or resistance remain unclear. Here we identified that depletion of alpha-ketoglutarate (αKG) sensitizes cells by regulation histone acetylation. αKG is required for the activity αKG-dependent dioxygenases (αKGDDs), and prior work has shown changes in αKGDD affect demethylases. Using a targeted CRISPR knockout...
Background: Identifying cells engaged in fundamental cellular processes, such as proliferation or living/death statuses, is pivotal across numerous research fields. However, prevailing methods relying on molecular biomarkers are constrained by high costs, limited specificity, protracted sample preparation, and reliance fluorescence imaging. Methods: Based morphology phase contrast images, we developed a deep-learning model named Detector of Mitosis, Apoptosis, Interphase, Necrosis,...
ABSTRACT Approximately 50% of cancers exhibit decreased CDKN2A expression ( Low ), which is linked to immune checkpoint blockade (ICB) resistance. While traditionally recognized as a tumor suppressor and cell cycle regulator, we have previously put forth new paradigm demonstrating its role in intracellular metabolic reprogramming. Whether the derangement due loss alters metabolites within microenvironment (TME) how that affects compartment ICB response has never been investigated. Here found...
Abstract p16 is a tumor suppressor encoded by the CDKN2A gene whose expression lost in approximately 50% of all human cancers. In its canonical role, inhibits G1–S-phase cell cycle progression through suppression cyclin-dependent kinases. Interestingly, also has roles metabolic reprogramming, and we previously published that loss promotes nucleotide synthesis via pentose phosphate pathway. However, broader impact p16/CDKN2A on other pathways potential therapeutic targets remains unexplored....
Significance The human respiratory syncytial virus (RSV) is a significant cause of lower tract infections in the young and elderly substantial burden to global health. Currently, there are no specific effective treatments for RSV infections. Here we report first X-ray crystal structure nonstructural protein 2 (NS2), which revealed unique fold. combined biochemical structural analyses NS2 identified region that binds inhibits ubiquitination an inactive form RIG-I MDA5, preventing downstream...
Summary Nucleocapsid protein (N) is the most abundant viral encoded by SARS-CoV-2, causative agent of COVID-19. N plays key roles at different steps in replication cycle and used as a serological marker infection. Here we characterize biochemical properties SARS-CoV-2 N. We define domains important for oligomerization RNA binding that are associated with spherical droplet formation suggest accessibility assembly may be regulated phosphorylation. also map interface using hydrogen-deuterium...
Macropinocytosis is a nonspecific endocytic process that may enhance cancer cell survival under nutrient-poor conditions. Ataxia-Telangiectasia mutated (ATM) tumor suppressor has been previously shown to play role in cellular metabolic reprogramming. We report the suppression of ATM increases macropinocytosis promote Combined inhibition and suppressed proliferation induced death both vitro vivo. Supplementation ATM-inhibited cells with amino acids, branched-chain acids (BCAAs) particular,...
ABSTRACT DNA damage and cellular metabolism exhibit a complex interplay characterized by bidirectional feedback mechanisms. Key mediators of the response metabolic regulation include Ataxia Telangiectasia Rad3-related protein (ATR) mechanistic Target Rapamycin Complex 1 (mTORC1), respectively. Previous studies have established ATR as regulatory upstream factor mTORC1 during replication stress; however, precise mechanisms which is activated in this context remain poorly defined. Additionally,...
Nucleocapsid proteins are essential for SARS-CoV-2 life cycle. Here, we describe protocols to gather domain-specific insights about properties of nucleocapsids. These assays include dynamic light scattering characterize oligomerization, fluorescence polarization quantify RNA binding, hydrogen-deuterium exchange mass spectrometry map binding regions, negative-stain electron microscopy visualize oligomeric species, interferon reporter assay evaluate signaling modulation, and a serology reveal...
<div>Abstract<p>p16 is a tumor suppressor encoded by the <i>CDKN2A</i> gene whose expression lost in approximately 50% of all human cancers. In its canonical role, p16 inhibits G<sub>1</sub>–S-phase cell cycle progression through suppression cyclin-dependent kinases. Interestingly, also has roles metabolic reprogramming, and we previously published that loss promotes nucleotide synthesis via pentose phosphate pathway. However, broader impact...
<p>Multiple CRISPR KO screens identify nucleotide metabolism genes that are selectively depleted in p16/<i>CDKN2A</i><sup>low</sup> cells. <b>A,</b> Schematic of our screens. p16/<i>Cdkn2a</i> wildtype cells were infected with lentiviruses expressing shGFP control (shCont), shp16 (human), or sh<i>Cdkn2a</i> (mouse). Human and mouse isogenic cell pairs nucleotide-focused whole metabolism-focused gRNA libraries, respectively, at...
<p>p16/<i>CDKN2A</i><sup>low</sup> cells are more sensitive to inhibitors of nucleotide metabolism. <b>A,</b> Table used in <i>in vitro</i> cell line studies. 1C metabolism = one carbon <b>B,</b> SKMEL28 human melanoma were infected with lentivirus expressing a shRNA targeting p16 (shp16). shGFP was as control (shCont). Cells treated the indicated and proliferation assessed by crystal violet staining....
<p>Multiple CRISPR KO screens identify nucleotide metabolism genes that are selectively depleted in p16/<i>CDKN2A</i><sup>low</sup> cells. <b>A,</b> Schematic of our screens. p16/<i>Cdkn2a</i> wildtype cells were infected with lentiviruses expressing shGFP control (shCont), shp16 (human), or sh<i>Cdkn2a</i> (mouse). Human and mouse isogenic cell pairs nucleotide-focused whole metabolism-focused gRNA libraries, respectively, at...
<p>p16/<i>CDKN2A</i><sup>low</sup> cells are more sensitive to inhibitors of nucleotide metabolism. <b>A,</b> Table used in <i>in vitro</i> cell line studies. 1C metabolism = one carbon <b>B,</b> SKMEL28 human melanoma were infected with lentivirus expressing a shRNA targeting p16 (shp16). shGFP was as control (shCont). Cells treated the indicated and proliferation assessed by crystal violet staining....
<p>p16/<i>CDKN2A</i> negatively correlates with multiple nucleotide metabolism genes, proteins, and metabolites. <b>A–D,</b> SKMEL28 human melanoma cells were infected lentivirus expressing a shRNA targeting p16 (shp16). shGFP was used as control (shCont). <b>A,</b> Expression of the 128 gene signature from RNA-seq. Raw data can be found in <a href="#SMT6" target="_blank">Supplementary Table S6</a>. <b>B,</b> Polysome...
<div>Abstract<p>p16 is a tumor suppressor encoded by the <i>CDKN2A</i> gene whose expression lost in approximately 50% of all human cancers. In its canonical role, p16 inhibits G<sub>1</sub>–S-phase cell cycle progression through suppression cyclin-dependent kinases. Interestingly, also has roles metabolic reprogramming, and we previously published that loss promotes nucleotide synthesis via pentose phosphate pathway. However, broader impact...
<p>p16/<i>CDKN2A</i> negatively correlates with multiple nucleotide metabolism genes, proteins, and metabolites. <b>A–D,</b> SKMEL28 human melanoma cells were infected lentivirus expressing a shRNA targeting p16 (shp16). shGFP was used as control (shCont). <b>A,</b> Expression of the 128 gene signature from RNA-seq. Raw data can be found in <a href="#SMT6" target="_blank">Supplementary Table S6</a>. <b>B,</b> Polysome...
<p>shp16 tumors are more sensitive to the antifolate methotrexate. <b>A</b> and <b>B,</b> SKMEL28 human melanoma cells were infected with lentivirus expressing a shRNA targeting GFP (shCont) or p16 (shp16). A total of 10<sup>7</sup> subcutaneously implanted into athymic nude mice. Mice treated vehicle controls methotrexate (MTX). Individual tumor growth curves in shp16 (<b>A</b>) shCont (<b>B</b>). Shown rates ± SE. Linear...
<p>Knockdown or knockout of Cdkn2a in mouse melanoma cell lines increases sensitivity to multiple anti-folates but not de novo pyrimidine synthesis; Knockdown RB1 does recapitulate the anti-folate response exhibited by shp16 cells. Related Figure 3.</p>
<p>31 common genes identified in screens and publicly available data</p>
<p>31 common genes identified in screens and publicly available data</p>
<p>CRISPR KO library containing 128 genes comprising the nucleotide metabolism signature</p>