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Articles 1 - 30 of 335
Full-Text Articles in Medicine and Health Sciences
Stat5 Induces Androgen Receptor (Ar) Gene Transcription In Prostate Cancer And Offers A Druggable Pathway To Target Ar Signaling, Cristina Maranto, Lavannya Sabharwal, Vindhya Udhane, Samuel P. Pitzen, Braedan Mccluskey, Songyan Qi, Christine O'Connor, Savita Devi, Scott Johnson, Kenneth Jacobsohn, Anjishnu Banerjee, Kenneth A. Iczkowski, Liang Wang, Scott M. Dehm, Marja T. Nevalainen
Stat5 Induces Androgen Receptor (Ar) Gene Transcription In Prostate Cancer And Offers A Druggable Pathway To Target Ar Signaling, Cristina Maranto, Lavannya Sabharwal, Vindhya Udhane, Samuel P. Pitzen, Braedan Mccluskey, Songyan Qi, Christine O'Connor, Savita Devi, Scott Johnson, Kenneth Jacobsohn, Anjishnu Banerjee, Kenneth A. Iczkowski, Liang Wang, Scott M. Dehm, Marja T. Nevalainen
Department of Pharmacology, Physiology, and Cancer Biology Faculty Papers
Androgen receptor (AR) drives prostate cancer (PC) growth and progression, and targeting AR signaling is the mainstay of pharmacological therapies for PC. Resistance develops relatively fast as a result of refueled AR activity. A major gap in the field is the lack of understanding of targetable mechanisms that induce persistent AR expression in castrate-resistant PC (CRPC). This study uncovers an unexpected function of active Stat5 signaling, a known promoter of PC growth and clinical progression, as a potent inducer of AR gene transcription. Stat5 suppression inhibited AR gene transcription in preclinical PC models and reduced the levels of wild-type, mutated, …
Star Allele Search: A Pharmacogenetic Annotation Database And User-Friendly Search Tool Of Publicly Available 1000 Genomes Project Biospecimens., N Gharani, G Calendo, D Kusic, Josef Madzo, Laua Scheinfeldt
Star Allele Search: A Pharmacogenetic Annotation Database And User-Friendly Search Tool Of Publicly Available 1000 Genomes Project Biospecimens., N Gharani, G Calendo, D Kusic, Josef Madzo, Laua Scheinfeldt
Cooper Medical School of Rowan University Faculty Scholarship
Here we describe a new public pharmacogenetic (PGx) annotation database of a large (n = 3,202) and diverse biospecimen collection of 1000 Genomes Project cell lines and DNAs. The database is searchable with a user friendly, web-based tool ( www.coriell.org/StarAllele/Search ). This resource leverages existing whole genome sequencing data and PharmVar annotations to characterize *alleles for each biospecimen in the collection. This new tool is designed to facilitate in vitro functional characterization of *allele haplotypes and diplotypes as well as support clinical PGx assay development, validation, and implementation.
Factors Associated With Blood Mercury Concentrations And Their Interactions With Three Glutathione S-Transferase Genes (Gstt1, Gstm1, And Gstp1): An Exposure Assessment Study Of Typically Developing Jamaican Children, Sheikh Farzana Zaman, Maureen Samms-Vaughan, Sepideh Saroukhani, Jan Bressler, Manouchehr Hessabi, Megan L Grove, Sydonnie Shakespeare Pellington, Katherine A Loveland, Mohammad H Rahbar
Factors Associated With Blood Mercury Concentrations And Their Interactions With Three Glutathione S-Transferase Genes (Gstt1, Gstm1, And Gstp1): An Exposure Assessment Study Of Typically Developing Jamaican Children, Sheikh Farzana Zaman, Maureen Samms-Vaughan, Sepideh Saroukhani, Jan Bressler, Manouchehr Hessabi, Megan L Grove, Sydonnie Shakespeare Pellington, Katherine A Loveland, Mohammad H Rahbar
Journal Articles
BACKGROUND: Jamaican soil is abundant in heavy metals including mercury (Hg). Due to availability and ease of access, fish is a traditional dietary component in Jamaica and a significant source of Hg exposure. Mercury is a xenobiotic and known neuro-toxicant that affects children's neurodevelopment. Human glutathione S-transferase (GST) genes, including GSTT1, GSTM1, and GSTP1, affect Hg conjugation and elimination mechanisms.
METHODS: In this exposure assessment study we used data from 375 typically developing (TD) 2-8-year-old Jamaican children to explore the association between environmental Hg exposure, GST genes, and their interaction effects on blood Hg concentrations (BHgCs). We used multivariable general …
Factors Associated With Blood Mercury Concentrations And Their Interactions With Three Glutathione S-Transferase Genes (Gstt1, Gstm1, And Gstp1): An Exposure Assessment Study Of Typically Developing Jamaican Children, Sheikh Farzana Zaman, Maureen Samms-Vaughan, Sepideh Saroukhani, Jan Bressler, Manouchehr Hessabi, Megan L Grove, Sydonnie Shakespeare Pellington, Katherine A Loveland, Mohammad H Rahbar
Factors Associated With Blood Mercury Concentrations And Their Interactions With Three Glutathione S-Transferase Genes (Gstt1, Gstm1, And Gstp1): An Exposure Assessment Study Of Typically Developing Jamaican Children, Sheikh Farzana Zaman, Maureen Samms-Vaughan, Sepideh Saroukhani, Jan Bressler, Manouchehr Hessabi, Megan L Grove, Sydonnie Shakespeare Pellington, Katherine A Loveland, Mohammad H Rahbar
Journal Articles
BACKGROUND: Jamaican soil is abundant in heavy metals including mercury (Hg). Due to availability and ease of access, fish is a traditional dietary component in Jamaica and a significant source of Hg exposure. Mercury is a xenobiotic and known neuro-toxicant that affects children's neurodevelopment. Human glutathione S-transferase (GST) genes, including GSTT1, GSTM1, and GSTP1, affect Hg conjugation and elimination mechanisms.
METHODS: In this exposure assessment study we used data from 375 typically developing (TD) 2-8-year-old Jamaican children to explore the association between environmental Hg exposure, GST genes, and their interaction effects on blood Hg concentrations (BHgCs). We used multivariable general …
Factors Associated With Blood Mercury Concentrations And Their Interactions With Three Glutathione S-Transferase Genes (Gstt1, Gstm1, And Gstp1): An Exposure Assessment Study Of Typically Developing Jamaican Children, Sheikh Farzana Zaman, Maureen Samms-Vaughan, Sepideh Saroukhani, Jan Bressler, Manouchehr Hessabi, Megan L Grove, Sydonnie Shakespeare Pellington, Katherine A Loveland, Mohammad H Rahbar
Factors Associated With Blood Mercury Concentrations And Their Interactions With Three Glutathione S-Transferase Genes (Gstt1, Gstm1, And Gstp1): An Exposure Assessment Study Of Typically Developing Jamaican Children, Sheikh Farzana Zaman, Maureen Samms-Vaughan, Sepideh Saroukhani, Jan Bressler, Manouchehr Hessabi, Megan L Grove, Sydonnie Shakespeare Pellington, Katherine A Loveland, Mohammad H Rahbar
Journal Articles
BACKGROUND: Jamaican soil is abundant in heavy metals including mercury (Hg). Due to availability and ease of access, fish is a traditional dietary component in Jamaica and a significant source of Hg exposure. Mercury is a xenobiotic and known neuro-toxicant that affects children's neurodevelopment. Human glutathione S-transferase (GST) genes, including GSTT1, GSTM1, and GSTP1, affect Hg conjugation and elimination mechanisms.
METHODS: In this exposure assessment study we used data from 375 typically developing (TD) 2-8-year-old Jamaican children to explore the association between environmental Hg exposure, GST genes, and their interaction effects on blood Hg concentrations (BHgCs). We used multivariable general …
Multi-Tissue Epigenetic Analysis Identifies Distinct Associations Underlying Insulin Resistance And Alzheimer's Disease At Cpt1a Locus, Chloé Sarnowski, Tianxiao Huan, Yiyi Ma, Roby Joehanes, Alexa Beiser, Charles S Decarli, Nancy L Heard-Costa, Daniel Levy, Honghuang Lin, Ching-Ti Liu, Chunyu Liu, James B Meigs, Claudia L Satizabal, Jose C Florez, Marie-France Hivert, Josée Dupuis, Philip L De Jager, David A Bennett, Sudha Seshadri, Alanna C Morrison
Multi-Tissue Epigenetic Analysis Identifies Distinct Associations Underlying Insulin Resistance And Alzheimer's Disease At Cpt1a Locus, Chloé Sarnowski, Tianxiao Huan, Yiyi Ma, Roby Joehanes, Alexa Beiser, Charles S Decarli, Nancy L Heard-Costa, Daniel Levy, Honghuang Lin, Ching-Ti Liu, Chunyu Liu, James B Meigs, Claudia L Satizabal, Jose C Florez, Marie-France Hivert, Josée Dupuis, Philip L De Jager, David A Bennett, Sudha Seshadri, Alanna C Morrison
Journal Articles
BACKGROUND: Insulin resistance (IR) is a major risk factor for Alzheimer's disease (AD) dementia. The mechanisms by which IR predisposes to AD are not well-understood. Epigenetic studies may help identify molecular signatures of IR associated with AD, thus improving our understanding of the biological and regulatory mechanisms linking IR and AD.
METHODS: We conducted an epigenome-wide association study of IR, quantified using the homeostatic model assessment of IR (HOMA-IR) and adjusted for body mass index, in 3,167 participants from the Framingham Heart Study (FHS) without type 2 diabetes at the time of blood draw used for methylation measurement. We identified …
Hypertrophic Cardiomyopathy Diagnosis And Treatment In High- And Low-Income Countries: A Narrative Review, Ernesto Calderon Martinez, Nancy Y. Ortiz-Garcia, Domenica A. Herrera Hernandez, David Arriaga Escamilla, Diana L. Diaz Mendoza, Diana Othon, Luz M. Ramirez, Jonathan Reyes-Rivera, Jinal Choudhari, George Michel
Hypertrophic Cardiomyopathy Diagnosis And Treatment In High- And Low-Income Countries: A Narrative Review, Ernesto Calderon Martinez, Nancy Y. Ortiz-Garcia, Domenica A. Herrera Hernandez, David Arriaga Escamilla, Diana L. Diaz Mendoza, Diana Othon, Luz M. Ramirez, Jonathan Reyes-Rivera, Jinal Choudhari, George Michel
School of Medicine Publications and Presentations
Hypertrophic cardiomyopathy (HCM) is a hereditary cardiac condition characterized by unexplained left ventricular hypertrophy without a hemodynamic cause. This condition is prevalent in the United States, resulting in various clinical manifestations, including diastolic dysfunction, left ventricular outflow obstruction, cardiac ischemia, and atrial fibrillation. HCM is associated with several genetic mutations, with sarcomeric mutations being the most common and contributing to a more complex disease course. Early diagnosis of HCM is essential for effective management, as late diagnosis often requires invasive treatments and creates a substantial financial burden. Disparities in HCM diagnosis and treatment exist between highincome and low-income countries. High-income …
The Effects Of Natural Epigenetic Therapies In 3d Ovarian Cancer And Patient-Derived Tumor Explants: New Avenues In Regulating The Cancer Secretome., Rebeca Kelly, Diego Aviles, Catriona Krisulevicz, Krystal Hunter, Lauren Krill, David Warshal, Olga Ostrovsky
The Effects Of Natural Epigenetic Therapies In 3d Ovarian Cancer And Patient-Derived Tumor Explants: New Avenues In Regulating The Cancer Secretome., Rebeca Kelly, Diego Aviles, Catriona Krisulevicz, Krystal Hunter, Lauren Krill, David Warshal, Olga Ostrovsky
Cooper Medical School of Rowan University Faculty Scholarship
High mortality rates in ovarian cancer have been linked to recurrence, metastasis, and chemoresistant disease, which are known to involve not only genetic changes but also epigenetic aberrations. In ovarian cancer, adipose-derived stem cells from the omentum (O-ASCs) play a crucial role in supporting the tumor and its tumorigenic microenvironment, further propagating epigenetic abnormalities and dissemination of the disease. Epigallocatechin gallate (EGCG), a DNA methyltransferase inhibitor derived from green tea, and Indole-3-carbinol (I3C), a histone deacetylase inhibitor from cruciferous vegetables, carry promising effects in reprograming aberrant epigenetic modifications in cancer. Therefore, we demonstrate the action of these diet-derived compounds in …
Structural Basis Of A Transcription Pre-Initiation Complex On A Divergent Promoter, Jose J Gorbea Colón, Leon Palao, Shin-Fu Chen, Hee Jong Kim, Laura Snyder, Yi-Wei Chang, Kuang-Lei Tsai, Kenji Murakami
Structural Basis Of A Transcription Pre-Initiation Complex On A Divergent Promoter, Jose J Gorbea Colón, Leon Palao, Shin-Fu Chen, Hee Jong Kim, Laura Snyder, Yi-Wei Chang, Kuang-Lei Tsai, Kenji Murakami
Journal Articles
Most eukaryotic promoter regions are divergently transcribed. As the RNA polymerase II pre-initiation complex (PIC) is intrinsically asymmetric and responsible for transcription in a single direction, it is unknown how divergent transcription arises. Here, the Saccharomyces cerevisiae Mediator complexed with a PIC (Med-PIC) was assembled on a divergent promoter and analyzed by cryoelectron microscopy. The structure reveals two distinct Med-PICs forming a dimer through the Mediator tail module, induced by a homodimeric activator protein localized near the dimerization interface. The tail dimer is associated with ∼80-bp upstream DNA, such that two flanking core promoter regions are positioned and oriented in …
Genomic Or Non-Genomic? A Question About The Pleiotropic Roles Of Vitamin D In Inflammatory-Based Diseases, Michael F. Holick, Luciana Mazzei, Sebastián García Menéndez, Virna Margarita Martín Giménez, Fatme Al Anouti, Walter Manucha
Genomic Or Non-Genomic? A Question About The Pleiotropic Roles Of Vitamin D In Inflammatory-Based Diseases, Michael F. Holick, Luciana Mazzei, Sebastián García Menéndez, Virna Margarita Martín Giménez, Fatme Al Anouti, Walter Manucha
All Works
Vitamin D (vit D) is widely known for its role in calcium metabolism and its importance for the bone system. However, various studies have revealed a myriad of extra-skeletal functions, including cell differentiation and proliferation, antibacterial, antioxidant, immunomodulatory, and anti-inflammatory properties in various cells and tissues. Vit D mediates its function via regulation of gene expression by binding to its receptor (VDR) which is expressed in almost all cells within the body. This review summarizes the pleiotropic effects of vit D, emphasizing its anti-inflammatory effect on different organ systems. It also provides a comprehensive overview of the genetic and epigenetic …
Systemic Interindividual Epigenetic Variation In Humans Is Associated With Transposable Elements And Under Strong Genetic Control, Chathura J Gunasekara, Harry Mackay, C Anthony Scott, Shaobo Li, Eleonora Laritsky, Maria S Baker, Sandra L Grimm, Goo Jun, Yumei Li, Rui Chen, Joseph L Wiemels, Cristian Coarfa, Robert A Waterland
Systemic Interindividual Epigenetic Variation In Humans Is Associated With Transposable Elements And Under Strong Genetic Control, Chathura J Gunasekara, Harry Mackay, C Anthony Scott, Shaobo Li, Eleonora Laritsky, Maria S Baker, Sandra L Grimm, Goo Jun, Yumei Li, Rui Chen, Joseph L Wiemels, Cristian Coarfa, Robert A Waterland
Journal Articles
BACKGROUND: Genetic variants can modulate phenotypic outcomes via epigenetic intermediates, for example at methylation quantitative trait loci (mQTL). We present the first large-scale assessment of mQTL at human genomic regions selected for interindividual variation in CpG methylation, which we call correlated regions of systemic interindividual variation (CoRSIVs). These can be assayed in blood DNA and do not reflect interindividual variation in cellular composition.
RESULTS: We use target-capture bisulfite sequencing to assess DNA methylation at 4086 CoRSIVs in multiple tissues from each of 188 donors in the NIH Gene-Tissue Expression (GTEx) program. At CoRSIVs, DNA methylation in peripheral blood correlates with …
Adding Gene Transcripts Into Genomic Prediction Improves Accuracy And Reveals Sampling Time Dependence., Bruno C Perez, Marco C A M Bink, Karen L. Svenson, Gary Churchill, Mario P L Calus
Adding Gene Transcripts Into Genomic Prediction Improves Accuracy And Reveals Sampling Time Dependence., Bruno C Perez, Marco C A M Bink, Karen L. Svenson, Gary Churchill, Mario P L Calus
Faculty Research 2022
Recent developments allowed generating multiple high-quality 'omics' data that could increase the predictive performance of genomic prediction for phenotypes and genetic merit in animals and plants. Here, we have assessed the performance of parametric and nonparametric models that leverage transcriptomics in genomic prediction for 13 complex traits recorded in 478 animals from an outbred mouse population. Parametric models were implemented using the best linear unbiased prediction, while nonparametric models were implemented using the gradient boosting machine algorithm. We also propose a new model named GTCBLUP that aims to remove between-omics-layer covariance from predictors, whereas its counterpart GTBLUP does not do …
[Rare-Disease Data Standards]., Peter N Robinson, Holm Graessner
[Rare-Disease Data Standards]., Peter N Robinson, Holm Graessner
Faculty Research 2022
The use of standardized data formats (data standards) in healthcare supports four main goals: (1) exchange of data, (2) integration of computer systems and tools, (3) data storage and archiving, and (4) support of federated databases. Standards are especially important for rare-disease research and clinical care.In this review, we introduce healthcare standards and present a selection of standards that are commonly used in the field of rare diseases. The Human Phenotype Ontology (HPO) is the most commonly used standard for annotating phenotypic abnormalities and supporting phenotype-driven analysis of diagnostic exome and genome sequencing. Numerous standards for diseases are available that …
Association Of Pediatric Buccal Epigenetic Age Acceleration With Adverse Neonatal Brain Growth And Neurodevelopmental Outcomes Among Children Born Very Preterm With A Neonatal Infection., Noha Gomaa, Chaini Konwar, Nicole Gladish, Stephanie H Au-Young, Ting Guo, Min Sheng, Sarah M Merrill, Edmond Kelly, Vann Chau, Helen M Branson, Linh G Ly, Emma G Duerden, Ruth E Grunau, Michael S Kobor, Steven P Miller
Association Of Pediatric Buccal Epigenetic Age Acceleration With Adverse Neonatal Brain Growth And Neurodevelopmental Outcomes Among Children Born Very Preterm With A Neonatal Infection., Noha Gomaa, Chaini Konwar, Nicole Gladish, Stephanie H Au-Young, Ting Guo, Min Sheng, Sarah M Merrill, Edmond Kelly, Vann Chau, Helen M Branson, Linh G Ly, Emma G Duerden, Ruth E Grunau, Michael S Kobor, Steven P Miller
Department of Medicine Publications
IMPORTANCE: Very preterm neonates (24-32 weeks' gestation) remain at a higher risk of morbidity and neurodevelopmental adversity throughout their lifespan. Because the extent of prematurity alone does not fully explain the risk of adverse neonatal brain growth or neurodevelopmental outcomes, there is a need for neonatal biomarkers to help estimate these risks in this population.
OBJECTIVES: To characterize the pediatric buccal epigenetic (PedBE) clock-a recently developed tool to measure biological aging-among very preterm neonates and to assess its association with the extent of prematurity, neonatal comorbidities, neonatal brain growth, and neurodevelopmental outcomes at 18 months of age.
DESIGN, SETTING, AND …
Epigenetic Activation Of The Flt3 Gene By Znf384 Fusion Confers A Therapeutic Susceptibility In Acute Lymphoblastic Leukemia., Xujie Zhao, Ping Wang, Jonathan D Diedrich, Brandon Smart, Noemi Reyes, Satoshi Yoshimura, Jingliao Zhang, Wentao Yang, Kelly Barnett, Beisi Xu, Zhenhua Li, Xin Huang, Jiyang Yu, Kristine Crews, Allen Eng Juh Yeoh, Marina Konopleva, Chia-Lin Wei, Ching-Hon Pui, Daniel Savic, Jun J Yang
Epigenetic Activation Of The Flt3 Gene By Znf384 Fusion Confers A Therapeutic Susceptibility In Acute Lymphoblastic Leukemia., Xujie Zhao, Ping Wang, Jonathan D Diedrich, Brandon Smart, Noemi Reyes, Satoshi Yoshimura, Jingliao Zhang, Wentao Yang, Kelly Barnett, Beisi Xu, Zhenhua Li, Xin Huang, Jiyang Yu, Kristine Crews, Allen Eng Juh Yeoh, Marina Konopleva, Chia-Lin Wei, Ching-Hon Pui, Daniel Savic, Jun J Yang
Faculty Research 2022
FLT3 is an attractive therapeutic target in acute lymphoblastic leukemia (ALL) but the mechanism for its activation in this cancer is incompletely understood. Profiling global gene expression in large ALL cohorts, we identify over-expression of FLT3 in ZNF384-rearranged ALL, consistently across cases harboring different fusion partners with ZNF384. Mechanistically, we discover an intergenic enhancer element at the FLT3 locus that is exclusively activated in ZNF384-rearranged ALL, with the enhancer-promoter looping directly mediated by the fusion protein. There is also a global enrichment of active enhancers within ZNF384 binding sites across the genome in ZNF384-rearranged ALL cells. Downregulation of ZNF384 blunts …
Integrative Analysis Of Clinical And Epigenetic Biomarkers Of Mortality, Tianxiao Huan, Steve Nguyen, Elena Colicino, Carolina Ochoa-Rosales, W David Hill, Jennifer A Brody, Mette Soerensen, Yan Zhang, Antoine Baldassari, Mohamed Ahmed Elhadad, Tanaka Toshiko, Yinan Zheng, Arce Domingo-Relloso, Dong Heon Lee, Jiantao Ma, Chen Yao, Chunyu Liu, Shih-Jen Hwang, Roby Joehanes, Myriam Fornage, Jan Bressler, Joyce B J Van Meurs, Birgit Debrabant, Jonas Mengel-From, Jacob Hjelmborg, Kaare Christensen, Pantel Vokonas, Joel Schwartz, Sina A Gahrib, Nona Sotoodehnia, Colleen M Sitlani, Sonja Kunze, Christian Gieger, Annette Peters, Melanie Waldenberger, Ian J Deary, Luigi Ferrucci, Yishu Qu, Philip Greenland, Donald M Lloyd-Jones, Lifang Hou, Stefania Bandinelli, Trudy Voortman, Brenner Hermann, Andrea Baccarelli, Eric Whitsel, James S Pankow, Daniel Levy
Integrative Analysis Of Clinical And Epigenetic Biomarkers Of Mortality, Tianxiao Huan, Steve Nguyen, Elena Colicino, Carolina Ochoa-Rosales, W David Hill, Jennifer A Brody, Mette Soerensen, Yan Zhang, Antoine Baldassari, Mohamed Ahmed Elhadad, Tanaka Toshiko, Yinan Zheng, Arce Domingo-Relloso, Dong Heon Lee, Jiantao Ma, Chen Yao, Chunyu Liu, Shih-Jen Hwang, Roby Joehanes, Myriam Fornage, Jan Bressler, Joyce B J Van Meurs, Birgit Debrabant, Jonas Mengel-From, Jacob Hjelmborg, Kaare Christensen, Pantel Vokonas, Joel Schwartz, Sina A Gahrib, Nona Sotoodehnia, Colleen M Sitlani, Sonja Kunze, Christian Gieger, Annette Peters, Melanie Waldenberger, Ian J Deary, Luigi Ferrucci, Yishu Qu, Philip Greenland, Donald M Lloyd-Jones, Lifang Hou, Stefania Bandinelli, Trudy Voortman, Brenner Hermann, Andrea Baccarelli, Eric Whitsel, James S Pankow, Daniel Levy
Journal Articles
DNA methylation (DNAm) has been reported to be associated with many diseases and with mortality. We hypothesized that the integration of DNAm with clinical risk factors would improve mortality prediction. We performed an epigenome-wide association study of whole blood DNAm in relation to mortality in 15 cohorts (n = 15,013). During a mean follow-up of 10 years, there were 4314 deaths from all causes including 1235 cardiovascular disease (CVD) deaths and 868 cancer deaths. Ancestry-stratified meta-analysis of all-cause mortality identified 163 CpGs in European ancestry (EA) and 17 in African ancestry (AA) participants at p < 1 × 10
Harmonizing Model Organism Data In The Alliance Of Genome Resources., Alliance Of Genome Resources Consortium, Anna V. Anagnostopoulos, Susan M. Bello, Judith A. Blake, Olin Blodgett, Carol J. Bult, Karen R. Christie, Mary E. Dolan, Paul Hale, James A. Kadin, Monica S. Mcandrews, Howie Motenko, David R. Shaw, Constance M. Smith, Cynthia L. Smith, Monika Tomczuk, Laurens G. Wilming
Harmonizing Model Organism Data In The Alliance Of Genome Resources., Alliance Of Genome Resources Consortium, Anna V. Anagnostopoulos, Susan M. Bello, Judith A. Blake, Olin Blodgett, Carol J. Bult, Karen R. Christie, Mary E. Dolan, Paul Hale, James A. Kadin, Monica S. Mcandrews, Howie Motenko, David R. Shaw, Constance M. Smith, Cynthia L. Smith, Monika Tomczuk, Laurens G. Wilming
Faculty Research 2022
The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of …
Mechanisms Of Mitochondrial Promoter Recognition In Humans And Other Mammalian Species, Angelica Zamudio-Ochoa, Yaroslav I Morozov, Azadeh Sarfallah, Michael Anikin, Dmitry Temiakov
Mechanisms Of Mitochondrial Promoter Recognition In Humans And Other Mammalian Species, Angelica Zamudio-Ochoa, Yaroslav I Morozov, Azadeh Sarfallah, Michael Anikin, Dmitry Temiakov
Department of Biochemistry and Molecular Biology Faculty Papers
Recognition of mammalian mitochondrial promoters requires the concerted action of mitochondrial RNA polymerase (mtRNAP) and transcription initiation factors TFAM and TFB2M. In this work, we found that transcript slippage results in heterogeneity of the human mitochondrial transcripts in vivo and in vitro. This allowed us to correctly interpret the RNAseq data, identify the bona fide transcription start sites (TSS), and assign mitochondrial promoters for > 50% of mammalian species and some other vertebrates. The divergent structure of the mammalian promoters reveals previously unappreciated aspects of mtDNA evolution. The correct assignment of TSS also enabled us to establish the precise register of …
Elucidating Mechanisms Of Genetic Cross-Disease Associations At The Procr Vascular Disease Locus, David Stacey, Lingyan Chen, Paulina J Stanczyk, Joanna M M Howson, Amy M Mason, Stephen Burgess, Stephen Macdonald, Jonathan Langdown, Harriett Mckinney, Kate Downes, Neda Farahi, James E Peters, Saonli Basu, James S Pankow, Weihong Tang, Nathan Pankratz, Maria Sabater-Lleal, Paul S De Vries, Nicholas L Smith, Amy D Gelinas, Daniel J Schneider, Nebojsa Janjic, Nilesh J Samani, Shu Ye, Charlotte Summers, Edwin R Chilvers, John Danesh, Dirk S Paul
Elucidating Mechanisms Of Genetic Cross-Disease Associations At The Procr Vascular Disease Locus, David Stacey, Lingyan Chen, Paulina J Stanczyk, Joanna M M Howson, Amy M Mason, Stephen Burgess, Stephen Macdonald, Jonathan Langdown, Harriett Mckinney, Kate Downes, Neda Farahi, James E Peters, Saonli Basu, James S Pankow, Weihong Tang, Nathan Pankratz, Maria Sabater-Lleal, Paul S De Vries, Nicholas L Smith, Amy D Gelinas, Daniel J Schneider, Nebojsa Janjic, Nilesh J Samani, Shu Ye, Charlotte Summers, Edwin R Chilvers, John Danesh, Dirk S Paul
Journal Articles
Many individual genetic risk loci have been associated with multiple common human diseases. However, the molecular basis of this pleiotropy often remains unclear. We present an integrative approach to reveal the molecular mechanism underlying the PROCR locus, associated with lower coronary artery disease (CAD) risk but higher venous thromboembolism (VTE) risk. We identify PROCR-p.Ser219Gly as the likely causal variant at the locus and protein C as a causal factor. Using genetic analyses, human recall-by-genotype and in vitro experimentation, we demonstrate that PROCR-219Gly increases plasma levels of (activated) protein C through endothelial protein C receptor (EPCR) ectodomain shedding in endothelial cells, …
Mouse Genome Informatics (Mgi): Latest News From Mgd And Gxd., Martin Ringwald, Joel E Richardson, Richard M. Baldarelli, Judith A. Blake, James A. Kadin, Cynthia Smith, Carol J Bult
Mouse Genome Informatics (Mgi): Latest News From Mgd And Gxd., Martin Ringwald, Joel E Richardson, Richard M. Baldarelli, Judith A. Blake, James A. Kadin, Cynthia Smith, Carol J Bult
Faculty Research 2022
The Mouse Genome Informatics (MGI) database system combines multiple expertly curated community data resources into a shared knowledge management ecosystem united by common metadata annotation standards. MGI's mission is to facilitate the use of the mouse as an experimental model for understanding the genetic and genomic basis of human health and disease. MGI is the authoritative source for mouse gene, allele, and strain nomenclature and is the primary source of mouse phenotype annotations, functional annotations, developmental gene expression information, and annotations of mouse models with human diseases. MGI maintains mouse anatomy and phenotype ontologies and contributes to the development of …
29 M 6 A-Rna Methylation (Epitranscriptomic) Regulators Are Regulated In 41 Diseases Including Atherosclerosis And Tumors Potentially Via Ros Regulation - 102 Transcriptomic Dataset Analyses, Ming Liu, Keman Xu, Fatma Saaoud, Ying Shao, Ruijing Zhang, Yifan Lu, Yu Sun, Charles Drummer Iv, Li Li, Sheng Wu, Satya P Kunapuli, Gerard J Criner, Jianxin Sun, Huimin Shan, Xiaohua Jiang, Hong Wang, Xiaofeng Yang
29 M 6 A-Rna Methylation (Epitranscriptomic) Regulators Are Regulated In 41 Diseases Including Atherosclerosis And Tumors Potentially Via Ros Regulation - 102 Transcriptomic Dataset Analyses, Ming Liu, Keman Xu, Fatma Saaoud, Ying Shao, Ruijing Zhang, Yifan Lu, Yu Sun, Charles Drummer Iv, Li Li, Sheng Wu, Satya P Kunapuli, Gerard J Criner, Jianxin Sun, Huimin Shan, Xiaohua Jiang, Hong Wang, Xiaofeng Yang
Center for Translational Medicine Faculty Papers
We performed a database mining on 102 transcriptomic datasets for the expressions of 29 m6A-RNA methylation (epitranscriptomic) regulators (m6A-RMRs) in 41 diseases and cancers and made significant findings: (1) a few m6A-RMRs were upregulated; and most m6A-RMRs were downregulated in sepsis, acute respiratory distress syndrome, shock, and trauma; (2) half of 29 m6A-RMRs were downregulated in atherosclerosis; (3) inflammatory bowel disease and rheumatoid arthritis modulated m6A-RMRs more than lupus and psoriasis; (4) some organ failures shared eight upregulated m6A-RMRs; end-stage renal failure (ESRF) downregulated 85% of m6A-RMRs; (5) Middle-East respiratory syndrome coronavirus infections modulated m6A-RMRs the most among viral infections; …
Genetic Interaction Between Mfrp And Adipor1 Mutations Affect Retinal Disease Phenotypes, Navdeep Gogna, Sonia Weatherly, Fuxin Zhao, Gayle B. Collin, Jai Pinkney, Lisa Stone, Juergen K. Naggert, Gregory W. Carter, Patsy M. Nishina
Genetic Interaction Between Mfrp And Adipor1 Mutations Affect Retinal Disease Phenotypes, Navdeep Gogna, Sonia Weatherly, Fuxin Zhao, Gayle B. Collin, Jai Pinkney, Lisa Stone, Juergen K. Naggert, Gregory W. Carter, Patsy M. Nishina
Faculty Research 2022
Adipor1tm1Dgen and Mfrprd6 mutant mice share similar eye disease characteristics. Previously, studies established a functional relationship of ADIPOR1 and MFRP proteins in maintaining retinal lipidome homeostasis and visual function. However, the independent and/or interactive contribution of both genes to similar disease phenotypes, including fundus spots, decreased axial length, and photoreceptor degeneration has yet to be examined. We performed a gene-interaction study where homozygous Adipor1tm1Dgen and Mfrprd6 mice were bred together and the resulting doubly heterozygous F1 offspring were intercrossed to produce 210 F2 progeny. Four-month-old mice from all nine genotypic combinations obtained in the F2 generation …
The Human Disease Ontology 2022 Update., Lynn M Schriml, James B Munro, Mike Schor, Dustin Olley, Carrie Mccracken, Victor Felix, J Allen Baron, Rebecca Jackson, Susan M. Bello, Cynthia Bearer, Richard Lichenstein, Katharine Bisordi, Nicole Campion Dialo, Michelle Giglio, Carol Greene
The Human Disease Ontology 2022 Update., Lynn M Schriml, James B Munro, Mike Schor, Dustin Olley, Carrie Mccracken, Victor Felix, J Allen Baron, Rebecca Jackson, Susan M. Bello, Cynthia Bearer, Richard Lichenstein, Katharine Bisordi, Nicole Campion Dialo, Michelle Giglio, Carol Greene
Faculty Research 2022
The Human Disease Ontology (DO) (www.disease-ontology.org) database, has significantly expanded the disease content and enhanced our userbase and website since the DO's 2018 Nucleic Acids Research DATABASE issue paper. Conservatively, based on available resource statistics, terms from the DO have been annotated to over 1.5 million biomedical data elements and citations, a 10× increase in the past 5 years. The DO, funded as a NHGRI Genomic Resource, plays a key role in disease knowledge organization, representation, and standardization, serving as a reference framework for multiscale biomedical data integration and analysis across thousands of clinical, biomedical and computational research projects and …
The 2021 Eurpean Alliance Of Associations For Rheumatology/American College Of Rheumatology Points To Consider For Diagnosis And Management Of Autoinflammatory Type I Interferonopathies: Candle/Praas, Savi And Ags, Kader Cetin Gedik, Lovro Lamot, Micol Romano, Erkan Demirkaya, David Piskin, Sofia Torreggiani, Laura A. Adang, Thais Armangue, Kathe Barchus, Devon R. Cordova, Yanick J. Crow, Russell C. Dale, Karen L. Durrant, Despina Eleftheriou, Elisa M. Fazzi, Marco Gattorno, Francesco Gavazzi, Eric P. Hanson, Min Ae Lee-Kirsch, Gina A. Montealegre Sanchez, Bénédicte Neven, Simona Orcesi, Seza Ozen, M. Cecilia Poli, Elliot Schumacher, Davide Tonduti, Katsiaryna Uss, Daniel Aletaha, Brian M. Feldman
The 2021 Eurpean Alliance Of Associations For Rheumatology/American College Of Rheumatology Points To Consider For Diagnosis And Management Of Autoinflammatory Type I Interferonopathies: Candle/Praas, Savi And Ags, Kader Cetin Gedik, Lovro Lamot, Micol Romano, Erkan Demirkaya, David Piskin, Sofia Torreggiani, Laura A. Adang, Thais Armangue, Kathe Barchus, Devon R. Cordova, Yanick J. Crow, Russell C. Dale, Karen L. Durrant, Despina Eleftheriou, Elisa M. Fazzi, Marco Gattorno, Francesco Gavazzi, Eric P. Hanson, Min Ae Lee-Kirsch, Gina A. Montealegre Sanchez, Bénédicte Neven, Simona Orcesi, Seza Ozen, M. Cecilia Poli, Elliot Schumacher, Davide Tonduti, Katsiaryna Uss, Daniel Aletaha, Brian M. Feldman
Paediatrics Publications
Objective: Autoinflammatory type I interferonopathies, chronic atypical neutrophilic dermatosis with lipodystrophy and elevated temperature/proteasome-associated autoinflammatory syndrome (CANDLE/PRAAS), stimulator of interferon genes (STING)-associated vasculopathy with onset in infancy (SAVI) and Aicardi-Goutières syndrome (AGS) are rare and clinically complex immunodysregulatory diseases. With emerging knowledge of genetic causes and targeted treatments, a Task Force was charged with the development of 'points to consider' to improve diagnosis, treatment and long-term monitoring of patients with these rare diseases. Methods: Members of a Task Force consisting of rheumatologists, neurologists, an immunologist, geneticists, patient advocates and an allied healthcare professional formulated research questions for a systematic literature …
Additive And Interactive Associations Of Environmental And Sociodemographic Factors With The Genotypes Of Three Glutathione S-Transferase Genes In Relation To The Blood Arsenic Concentrations Of Children In Jamaica, Mohammad H Rahbar, Maureen Samms-Vaughan, Yuansong Zhao, Sepideh Saroukhani, Sheikh F Zaman, Jan Bressler, Manouchehr Hessabi, Megan L Grove, Sydonnie Shakspeare-Pellington, Katherine A Loveland
Additive And Interactive Associations Of Environmental And Sociodemographic Factors With The Genotypes Of Three Glutathione S-Transferase Genes In Relation To The Blood Arsenic Concentrations Of Children In Jamaica, Mohammad H Rahbar, Maureen Samms-Vaughan, Yuansong Zhao, Sepideh Saroukhani, Sheikh F Zaman, Jan Bressler, Manouchehr Hessabi, Megan L Grove, Sydonnie Shakspeare-Pellington, Katherine A Loveland
Journal Articles
Arsenic (As) is a metalloid that has been classified as a xenobiotic with toxic effects on human beings, especially on children. Since the soil in Jamaica contains As, dietary intake is considered the main source of As exposure in Jamaicans. In addition, glutathione S-transferase (GST) genes, including
A Myc-Znf148-Id1/3 Regulatory Axis Modulating Cancer Stem Cell Traits In Aggressive Breast Cancer, Mijeong Kim, Manjot Singh, Bum-Kyu Lee, Moira Hibbs, Kirsty Richardson, Lesley Ellies, Larissa Wintle, Lisa M. Stuart, Jenny Y. Wang, Dominic C. Voon, Pilar Blancafort, Jianlong Wang, Jonghwan Kim, Peter J. Leedman, Andrew J. Woo
A Myc-Znf148-Id1/3 Regulatory Axis Modulating Cancer Stem Cell Traits In Aggressive Breast Cancer, Mijeong Kim, Manjot Singh, Bum-Kyu Lee, Moira Hibbs, Kirsty Richardson, Lesley Ellies, Larissa Wintle, Lisa M. Stuart, Jenny Y. Wang, Dominic C. Voon, Pilar Blancafort, Jianlong Wang, Jonghwan Kim, Peter J. Leedman, Andrew J. Woo
Research outputs 2022 to 2026
The MYC proto-oncogene (MYC) is one of the most frequently overexpressed genes in breast cancer that drives cancer stem cell-like traits, resulting in aggressive disease progression and poor prognosis. In this study, we identified zinc finger transcription factor 148 (ZNF148, also called Zfp148 and ZBP-89) as a direct target of MYC. ZNF148 suppressed cell proliferation and migration and was transcriptionally repressed by MYC in breast cancer. Depletion of ZNF148 by short hairpin RNA (shRNA) and CRISPR/Cas9 increased triple-negative breast cancer (TNBC) cell proliferation and migration. Global transcriptome and chromatin occupancy analyses of ZNF148 revealed a central role in inhibiting cancer …
Neuron-Specific Imp2 Overexpression By Synapsin Promoter-Driven Aav9: A Tool To Study Its Role In Axon Regeneration., Sarah Blizard, Danielle Park, Natalie O'Toole, Sheeva Norooz, Martin Dela Torre, Young Son, Adam Holstein, Scarlett Austin, Joshua Harman, Samantha Haraszti, Daved Fared, Mei Xu
Neuron-Specific Imp2 Overexpression By Synapsin Promoter-Driven Aav9: A Tool To Study Its Role In Axon Regeneration., Sarah Blizard, Danielle Park, Natalie O'Toole, Sheeva Norooz, Martin Dela Torre, Young Son, Adam Holstein, Scarlett Austin, Joshua Harman, Samantha Haraszti, Daved Fared, Mei Xu
PCOM Scholarly Papers
Insulin-like growth factor II mRNA-binding protein (IMP) 2 is one of the three homologues (IMP1-3) that belong to a conserved family of mRNA-binding proteins. Its alternative splice product is aberrantly expressed in human hepatocellular carcinoma, and it is therefore identified as HCC. Previous works have indicated that IMP1/ZBP1 (zipcode binding protein) is critical in axon guidance and regeneration by regulating localization and translation of specific mRNAs. However, the role of IMP2 in the nervous system is largely unknown. We used the synapsin promoter-driven adeno-associated viral (AAV) 9 constructs for transgene expression both in vitro and in vivo. These viral vectors …
The Pnpla3 Rs738409 Variant But Not Mboat7 Rs641738 Is A Risk Factor For Nonalcoholic Fatty Liver Disease In Obese U.S. Children Of Hispanic Ethnicity, Sana Mansoor, Anshu Maheshwari, Matthew D. Di Guglielmo, Katryn Furuya, Makala Wang, Erin Crowgey, Zarela Molle-Rios, Zhaoping He
The Pnpla3 Rs738409 Variant But Not Mboat7 Rs641738 Is A Risk Factor For Nonalcoholic Fatty Liver Disease In Obese U.S. Children Of Hispanic Ethnicity, Sana Mansoor, Anshu Maheshwari, Matthew D. Di Guglielmo, Katryn Furuya, Makala Wang, Erin Crowgey, Zarela Molle-Rios, Zhaoping He
Department of Pediatrics Faculty Papers
Purpose: The rs641738 C>T in membrane-bound O-acyltransferase domain-containing protein 7 (MBOAT7) is implicated, along with the rs738409 C>G polymorphism in patatin-like phospholipase domain-containing protein 3 (PNPLA3), in nonalcoholic fatty liver disease (NAFLD). The association of these polymorphisms and NAFLD are investigated in Hispanic children with obesity.
Methods: Obese children with and without NAFLD were enrolled at a pediatric tertiary care health system and genotyped for MBOAT7 rs641738 C>T and PNPLA3 rs738409 C>G. NAFLD was characterized by the ultrasonographic presence of hepatic steatosis along with persistently elevated liver enzymes. Genetic variants and demographic and biochemical data were …
Tet2 Controls The Responses Of Β Cells To Inflammation In Autoimmune Diabetes., Jinxiu Rui, Songyan Deng, Ana Luisa Perdigoto, Gerald Ponath, Romy Kursawe, Nathan Lawlor, Tomokazu Sumida, Maya Levine-Ritterman, Michael L. Stitzel, David Pitt, Jun Lu, Kevan C Herold
Tet2 Controls The Responses Of Β Cells To Inflammation In Autoimmune Diabetes., Jinxiu Rui, Songyan Deng, Ana Luisa Perdigoto, Gerald Ponath, Romy Kursawe, Nathan Lawlor, Tomokazu Sumida, Maya Levine-Ritterman, Michael L. Stitzel, David Pitt, Jun Lu, Kevan C Herold
Faculty Research 2021
β cells may participate and contribute to their own demise during Type 1 diabetes (T1D). Here we report a role of their expression of Tet2 in regulating immune killing. Tet2 is induced in murine and human β cells with inflammation but its expression is reduced in surviving β cells. Tet2-KO mice that receive WT bone marrow transplants develop insulitis but not diabetes and islet infiltrates do not eliminate β cells even though immune cells from the mice can transfer diabetes to NOD/scid recipients. Tet2-KO recipients are protected from transfer of disease by diabetogenic immune cells.Tet2-KO β cells show reduced expression …
Integrated Single-Cell Atlas Of Endothelial Cells Of The Human Lung, Jonas C Schupp, Taylor S Adams, Carlos Cosme, Micha Sam Brickman Raredon, Yifan Yuan, Norihito Omote, Sergio Poli, Maurizio Chioccioli, Kadi-Ann Rose, Edward P Manning, Maor Sauler, Giuseppe Deiuliis, Farida Ahangari, Nir Neumark, Arun C Habermann, Austin J Gutierrez, Linh T Bui, Robert Lafyatis, Richard W Pierce, Kerstin B Meyer, Martijn C Nawijn, Sarah A Teichmann, Nicholas E Banovich, Jonathan A Kropski, Laura E Niklason, Dana Pe'er, Xiting Yan, Robert J Homer, Ivan O Rosas, Naftali Kaminski
Integrated Single-Cell Atlas Of Endothelial Cells Of The Human Lung, Jonas C Schupp, Taylor S Adams, Carlos Cosme, Micha Sam Brickman Raredon, Yifan Yuan, Norihito Omote, Sergio Poli, Maurizio Chioccioli, Kadi-Ann Rose, Edward P Manning, Maor Sauler, Giuseppe Deiuliis, Farida Ahangari, Nir Neumark, Arun C Habermann, Austin J Gutierrez, Linh T Bui, Robert Lafyatis, Richard W Pierce, Kerstin B Meyer, Martijn C Nawijn, Sarah A Teichmann, Nicholas E Banovich, Jonathan A Kropski, Laura E Niklason, Dana Pe'er, Xiting Yan, Robert J Homer, Ivan O Rosas, Naftali Kaminski
Journal Articles
BACKGROUND: Cellular diversity of the lung endothelium has not been systematically characterized in humans. We provide a reference atlas of human lung endothelial cells (ECs) to facilitate a better understanding of the phenotypic diversity and composition of cells comprising the lung endothelium.
METHODS: We reprocessed human control single-cell RNA sequencing (scRNAseq) data from 6 datasets. EC populations were characterized through iterative clustering with subsequent differential expression analysis. Marker genes were validated by fluorescent microscopy and in situ hybridization. scRNAseq of primary lung ECs cultured in vitro was performed. The signaling network between different lung cell types was studied. For cross-species …