482 results on '"Thomas, Reuben"'
Search Results
2. Long COVID manifests with T cell dysregulation, inflammation and an uncoordinated adaptive immune response to SARS-CoV-2.
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Yin, Kailin, Luo, Xiaoyu, Thomas, Reuben, Shin, Min-Gyoung, Neidleman, Jason, Andrew, Alicer, Young, Kyrlia, Ma, Tongcui, Hoh, Rebecca, Anglin, Khamal, Argueta, Urania, Lopez, Monica, Valdivieso, Daisy, Asare, Kofi, Deveau, Tyler-Marie, Munter, Sadie, Ibrahim, Rania, Ständker, Ludger, Lu, Scott, Goldberg, Sarah, Lee, Sulggi, Lynch, Kara, Kelly, J, Roan, Nadia, Münch, Jan, Deeks, Steven, Martin, Jeffrey, Henrich, Timothy, Peluso, Michael, and Huang, Beatrice
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Female ,Male ,Humans ,SARS-CoV-2 ,Post-Acute COVID-19 Syndrome ,CD8-Positive T-Lymphocytes ,COVID-19 ,Immunity ,Humoral ,Antibodies ,Viral ,Inflammation - Abstract
Long COVID (LC) occurs after at least 10% of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, yet its etiology remains poorly understood. We used omic assays and serology to deeply characterize the global and SARS-CoV-2-specific immunity in the blood of individuals with clear LC and non-LC clinical trajectories, 8 months postinfection. We found that LC individuals exhibited systemic inflammation and immune dysregulation. This was evidenced by global differences in T cell subset distribution implying ongoing immune responses, as well as by sex-specific perturbations in cytolytic subsets. LC individuals displayed increased frequencies of CD4+ T cells poised to migrate to inflamed tissues and exhausted SARS-CoV-2-specific CD8+ T cells, higher levels of SARS-CoV-2 antibodies and a mis-coordination between their SARS-CoV-2-specific T and B cell responses. Our analysis suggested an improper crosstalk between the cellular and humoral adaptive immunity in LC, which can lead to immune dysregulation, inflammation and clinical symptoms associated with this debilitating condition.
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- 2024
3. The APOE-R136S mutation protects against APOE4-driven Tau pathology, neurodegeneration and neuroinflammation.
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Nelson, Maxine, Liu, Peng, Agrawal, Ayushi, Yip, Oscar, Blumenfeld, Jessica, Traglia, Michela, Kim, Min, Koutsodendris, Nicole, Rao, Antara, Grone, Brian, Hao, Yanxia, Yoon, Seo, Xu, Qin, De Leon, Samuel, Choenyi, Tenzing, Thomas, Reuben, Lopera, Francisco, Quiroz, Yakeel, Arboleda-Velasquez, Joseph, Reiman, Eric, Mahley, Robert, and Huang, Yadong
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Animals ,Humans ,Mice ,Alzheimer Disease ,Apolipoprotein E3 ,Apolipoprotein E4 ,Mutation ,Neuroinflammatory Diseases ,Tauopathies - Abstract
Apolipoprotein E4 (APOE4) is the strongest genetic risk factor for late-onset Alzheimers disease (LOAD), leading to earlier age of clinical onset and exacerbating pathologies. There is a critical need to identify protective targets. Recently, a rare APOE variant, APOE3-R136S (Christchurch), was found to protect against early-onset AD in a PSEN1-E280A carrier. In this study, we sought to determine if the R136S mutation also protects against APOE4-driven effects in LOAD. We generated tauopathy mouse and human iPSC-derived neuron models carrying human APOE4 with the homozygous or heterozygous R136S mutation. We found that the homozygous R136S mutation rescued APOE4-driven Tau pathology, neurodegeneration and neuroinflammation. The heterozygous R136S mutation partially protected against APOE4-driven neurodegeneration and neuroinflammation but not Tau pathology. Single-nucleus RNA sequencing revealed that the APOE4-R136S mutation increased disease-protective and diminished disease-associated cell populations in a gene dose-dependent manner. Thus, the APOE-R136S mutation protects against APOE4-driven AD pathologies, providing a target for therapeutic development against AD.
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- 2023
4. Population Size, Network Density, and the Emergence of Inherited Inequality
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Thomas, Reuben J. and Mark, Noah P.
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- 2013
5. Increased parvovirus B19 seropositivity in healthy blood donors in India
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Kumari, Swati, Kuruvilla Thomas, Reuben, Sruthi, S., Barani, Ramya, Sangvi, S., Krishnamoorthy, R., and Srikanth, Padma
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- 2024
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6. Fecal calgranulin as a potential screening tool to differentiate inflammatory bowel disease from irritable bowel syndrome
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Kumar, Santhosh E., Jaleel, Rajeeb, Varghese, Tintu, Praharaj, Ira, Benny, Stephan, Chowdhury, Sudipta D., Thomas, Reuben, Simon, Ebby, Joseph, A. J., and Dutta, Amit Kumar
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- 2024
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7. Neuronal APOE4 removal protects against tau-mediated gliosis, neurodegeneration and myelin deficits
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Koutsodendris, Nicole, Blumenfeld, Jessica, Agrawal, Ayushi, Traglia, Michela, Grone, Brian, Zilberter, Misha, Yip, Oscar, Rao, Antara, Nelson, Maxine R, Hao, Yanxia, Thomas, Reuben, Yoon, Seo Yeon, Arriola, Patrick, and Huang, Yadong
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Biomedical and Clinical Sciences ,Clinical Sciences ,Neurodegenerative ,Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) ,Brain Disorders ,Aging ,Neurosciences ,Acquired Cognitive Impairment ,Genetics ,Alzheimer's Disease ,Dementia ,Aetiology ,2.1 Biological and endogenous factors ,Neurological ,Mice ,Animals ,Apolipoprotein E4 ,Neurodegenerative Diseases ,Myelin Sheath ,Gliosis ,Tauopathies ,Neurons ,Clinical sciences - Abstract
Apolipoprotein E4 (APOE4) is the strongest known genetic risk factor for late-onset Alzheimer's disease (AD). Conditions of stress or injury induce APOE expression within neurons, but the role of neuronal APOE4 in AD pathogenesis is still unclear. Here we report the characterization of neuronal APOE4 effects on AD-related pathologies in an APOE4-expressing tauopathy mouse model. The selective genetic removal of APOE4 from neurons led to a significant reduction in tau pathology, gliosis, neurodegeneration, neuronal hyperexcitability and myelin deficits. Single-nucleus RNA-sequencing revealed that the removal of neuronal APOE4 greatly diminished neurodegenerative disease-associated subpopulations of neurons, oligodendrocytes, astrocytes and microglia whose accumulation correlated to the severity of tau pathology, neurodegeneration and myelin deficits. Thus, neuronal APOE4 plays a central role in promoting the development of major AD pathologies and its removal can mitigate the progressive cellular and tissue alterations occurring in this model of APOE4-driven tauopathy.
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- 2023
8. Single-cell multimodal analyses reveal epigenomic and transcriptomic basis for birth defects in maternal diabetes
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Nishino, Tomohiro, Ranade, Sanjeev S., Pelonero, Angelo, van Soldt, Benjamin J., Ye, Lin, Alexanian, Michael, Koback, Frances, Huang, Yu, Wallace, Langley Grace, Sadagopan, Nandhini, Lam, Adrienne, Zholudeva, Lyandysha V., Li, Feiya, Padmanabhan, Arun, Thomas, Reuben, van Bemmel, Joke G., Gifford, Casey A., Costa, Mauro W., and Srivastava, Deepak
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- 2023
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9. Deep immunophenotyping reveals endometriosis is marked by dysregulation of the mononuclear phagocytic system in endometrium and peripheral blood
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Vallvé-Juanico, Júlia, George, Ashley F, Sen, Sushmita, Thomas, Reuben, Shin, Min-Gyoung, Kushnoor, Divyashree, Vásquez, Joshua J, Vo, Kim Chi, Irwin, Juan C, Roan, Nadia R, Combes, Alexis J, and Giudice, Linda C
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Reproductive Medicine ,Biomedical and Clinical Sciences ,Endometriosis ,Contraception/Reproduction ,Pain Research ,Clinical Research ,Underpinning research ,2.1 Biological and endogenous factors ,1.1 Normal biological development and functioning ,Aetiology ,Inflammatory and immune system ,Reproductive health and childbirth ,Case-Control Studies ,Endometrium ,Female ,Humans ,Immunophenotyping ,Inflammation ,Macrophages ,Monocytes ,Mononuclear phagocytes ,SIRP alpha ,Innate immune ,CyTOF ,Biomarker ,SIRPα ,Medical and Health Sciences ,General & Internal Medicine ,Biomedical and clinical sciences ,Health sciences - Abstract
BackgroundEndometriosis is a chronic, estrogen-dependent disorder where inflammation contributes to disease-associated symptoms of pelvic pain and infertility. Immune dysfunction includes insufficient immune lesion clearance, a pro-inflammatory endometrial environment, and systemic inflammation. Comprehensive understanding of endometriosis immune pathophysiology in different hormonal milieu and disease severity has been hampered by limited direct characterization of immune populations in endometrium, blood, and lesions. Simultaneous deep phenotyping at single-cell resolution of complex tissues has transformed our understanding of the immune system and its role in many diseases. Herein, we report mass cytometry and high dimensional analyses to study immune cell phenotypes, abundance, activation states, and functions in endometrium and blood of women with and without endometriosis in different cycle phases and disease stages.MethodsA case-control study was designed. Endometrial biopsies and blood (n = 60 total) were obtained from women with (n = 20, n = 17, respectively) and without (n = 14, n = 9) endometriosis in the proliferative and secretory cycle phases of the menstrual cycle. Two mass cytometry panels were designed: one broad panel and one specific for mononuclear phagocytic cells (MPC), and all samples were multiplexed to characterize both endometrium and blood immune composition at unprecedented resolution. We combined supervised and unsupervised analyses to finely define the immune cell subsets with an emphasis on MPC. Then, association between cell types, protein expression, disease status, and cycle phase were performed.ResultsThe broad panel highlighted a significant modification of MPC in endometriosis; thus, they were studied in detail with an MPC-focused panel. Endometrial CD91+ macrophages overexpressed SIRPα (phagocytosis inhibitor) and CD64 (associated with inflammation) in endometriosis, and they were more abundant in mild versus severe disease. In blood, classical and intermediate monocytes were less abundant in endometriosis, whereas plasmacytoid dendritic cells and non-classical monocytes were more abundant. Non-classical monocytes were higher in severe versus mild disease.ConclusionsA greater inflammatory phenotype and decreased phagocytic capacity of endometrial macrophages in endometriosis are consistent with defective clearance of endometrial cells shed during menses and in tissue homeostasis, with implications in endometriosis pathogenesis and pathophysiology. Different proportions of monocytes and plasmacytoid dendritic cells in blood from endometriosis suggest systemically aberrant functionality of the myeloid system opening new venues for the study of biomarkers and therapies for endometriosis.
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- 2022
10. Transcription Factor GATA4 Regulates Cell Type-Specific Splicing Through Direct Interaction With RNA in Human Induced Pluripotent Stem Cell-Derived Cardiac Progenitors.
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Zhu, Lili, Gonzalez-Teran, Barbara, Ang, Yen-Sin, Thomas, Reuben, Stone, Nicole, Liu, Lei, Zhou, Ping, Zhu, Chenchen, Ruan, Hongmei, Huang, Yu, Jin, Shibo, Pelonero, Angelo, Koback, Frances, Padmanabhan, Arun, Sadagopan, Nandhini, Hsu, Austin, Costa, Mauro, Gifford, Casey, van Bemmel, Joke, Hüttenhain, Ruth, Conklin, Bruce, Black, Brian, Bruneau, Benoit, Steinmetz, Lars, Krogan, Nevan, Pollard, Katherine, Srivastava, Deepak, Vedantham, Vasanth, and Choudhary, Krishna
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GATA4 transcription factor ,RNA splicing ,RNA-binding motifs ,induced pluripotent stem cells ,myocytes ,cardiac ,Alternative Splicing ,Animals ,GATA4 Transcription Factor ,Heart ,Humans ,Induced Pluripotent Stem Cells ,Mice ,Myocytes ,Cardiac ,RNA - Abstract
BACKGROUND: GATA4 (GATA-binding protein 4), a zinc finger-containing, DNA-binding transcription factor, is essential for normal cardiac development and homeostasis in mice and humans, and mutations in this gene have been reported in human heart defects. Defects in alternative splicing are associated with many heart diseases, yet relatively little is known about how cell type- or cell state-specific alternative splicing is achieved in the heart. Here, we show that GATA4 regulates cell type-specific splicing through direct interaction with RNA and the spliceosome in human induced pluripotent stem cell-derived cardiac progenitors. METHODS: We leveraged a combination of unbiased approaches including affinity purification of GATA4 and mass spectrometry, enhanced cross-linking with immunoprecipitation, electrophoretic mobility shift assays, in vitro splicing assays, and unbiased transcriptomic analysis to uncover GATA4s novel function as a splicing regulator in human induced pluripotent stem cell-derived cardiac progenitors. RESULTS: We found that GATA4 interacts with many members of the spliceosome complex in human induced pluripotent stem cell-derived cardiac progenitors. Enhanced cross-linking with immunoprecipitation demonstrated that GATA4 also directly binds to a large number of mRNAs through defined RNA motifs in a sequence-specific manner. In vitro splicing assays indicated that GATA4 regulates alternative splicing through direct RNA binding, resulting in functionally distinct protein products. Correspondingly, knockdown of GATA4 in human induced pluripotent stem cell-derived cardiac progenitors resulted in differential alternative splicing of genes involved in cytoskeleton organization and calcium ion import, with functional consequences associated with the protein isoforms. CONCLUSIONS: This study shows that in addition to its well described transcriptional function, GATA4 interacts with members of the spliceosome complex and regulates cell type-specific alternative splicing via sequence-specific interactions with RNA. Several genes that have splicing regulated by GATA4 have functional consequences and many are associated with dilated cardiomyopathy, suggesting a novel role for GATA4 in achieving the necessary cardiac proteome in normal and stress-responsive conditions.
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- 2022
11. Differential Etv2 threshold requirement for endothelial and erythropoietic development
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Sinha, Tanvi, van Bueren, Kelly Lammerts, Dickel, Diane E, Zlatanova, Ivana, Thomas, Reuben, Lizama, Carlos O, Xu, Shan-Mei, Zovein, Ann C, Ikegami, Kohta, Moskowitz, Ivan P, Pollard, Katherine S, Pennacchio, Len A, and Black, Brian L
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Biochemistry and Cell Biology ,Biological Sciences ,Stem Cell Research ,Stem Cell Research - Nonembryonic - Non-Human ,Genetics ,Endothelium ,Gene Regulatory Networks ,Transcription Factors ,CP: Developmental biology ,CP: Molecular biology ,Etv2 ,GRN ,Tal1 ,endothelial development ,erythropoiesis ,gene regulatory network ,hematopoiesis ,transcriptional regulation ,yolk sac ,Medical Physiology ,Biological sciences - Abstract
Endothelial and erythropoietic lineages arise from a common developmental progenitor. Etv2 is a master transcriptional regulator required for the development of both lineages. However, the mechanisms through which Etv2 initiates the gene-regulatory networks (GRNs) for endothelial and erythropoietic specification and how the two GRNs diverge downstream of Etv2 remain incompletely understood. Here, by analyzing a hypomorphic Etv2 mutant, we demonstrate different threshold requirements for initiation of the downstream GRNs for endothelial and erythropoietic development. We show that Etv2 functions directly in a coherent feedforward transcriptional network for vascular endothelial development, and a low level of Etv2 expression is sufficient to induce and sustain the endothelial GRN. In contrast, Etv2 induces the erythropoietic GRN indirectly via activation of Tal1, which requires a significantly higher threshold of Etv2 to initiate and sustain erythropoietic development. These results provide important mechanistic insight into the divergence of the endothelial and erythropoietic lineages.
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- 2022
12. Transient Cell Cycle Induction in Cardiomyocytes to Treat Subacute Ischemic Heart Failure
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Abouleisa, Riham RE, Salama, Abou Bakr M, Ou, Qinghui, Tang, Xian-Liang, Solanki, Mitesh, Guo, Yiru, Nong, Yibing, McNally, Lindsey, Lorkiewicz, Pawel K, Kassem, Kamal M, Ahern, Brooke M, Choudhary, Krishna, Thomas, Reuben, Huang, Yu, Juhardeen, Hamzah R, Siddique, Aisha, Ifthikar, Zainab, Hammad, Sally K, Elbaz, Ayman S, Ivey, Kathryn N, Conklin, Daniel J, Satin, Jonathan, Hill, Bradford G, Srivastava, Deepak, Bolli, Roberto, and Mohamed, Tamer MA
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Cardiovascular ,Heart Disease ,Regenerative Medicine ,Heart Disease - Coronary Heart Disease ,Genetics ,Animals ,Cell Cycle ,Heart Failure ,Humans ,Induced Pluripotent Stem Cells ,Mice ,Myocardial Infarction ,Myocytes ,Cardiac ,Rats ,Stroke Volume ,Swine ,Ventricular Function ,Left ,cardiomyopathies ,cell cycle ,genetic therapy ,heart failure ,metabolism ,sarcomeres ,Cardiorespiratory Medicine and Haematology ,Clinical Sciences ,Public Health and Health Services ,Cardiovascular System & Hematology - Abstract
BackgroundThe regenerative capacity of the heart after myocardial infarction is limited. Our previous study showed that ectopic introduction of 4 cell cycle factors (4F; CDK1 [cyclin-dependent kinase 1], CDK4 [cyclin-dependent kinase 4], CCNB [cyclin B1], and CCND [cyclin D1]) promotes cardiomyocyte proliferation in 15% to 20% of infected cardiomyocytes in vitro and in vivo and improves cardiac function after myocardial infarction in mice.MethodsUsing temporal single-cell RNA sequencing, we aimed to identify the necessary reprogramming stages during the forced cardiomyocyte proliferation with 4F on a single cell basis. Using rat and pig models of ischemic heart failure, we aimed to start the first preclinical testing to introduce 4F gene therapy as a candidate for the treatment of ischemia-induced heart failure.ResultsTemporal bulk and single-cell RNA sequencing and further biochemical validations of mature human induced pluripotent stem cell-derived cardiomyocytes treated with either LacZ or 4F adenoviruses revealed full cell cycle reprogramming in 15% of the cardiomyocyte population at 48 hours after infection with 4F, which was associated mainly with sarcomere disassembly and metabolic reprogramming (n=3/time point/group). Transient overexpression of 4F, specifically in cardiomyocytes, was achieved using a polycistronic nonintegrating lentivirus (NIL) encoding 4F; each is driven by a TNNT2 (cardiac troponin T isoform 2) promoter (TNNT2-4Fpolycistronic-NIL). TNNT2-4Fpolycistronic-NIL or control virus was injected intramyocardially 1 week after myocardial infarction in rats (n=10/group) or pigs (n=6-7/group). Four weeks after injection, TNNT2-4Fpolycistronic-NIL-treated animals showed significant improvement in left ventricular ejection fraction and scar size compared with the control virus-treated animals. At 4 months after treatment, rats that received TNNT2-4Fpolycistronic-NIL still showed a sustained improvement in cardiac function and no obvious development of cardiac arrhythmias or systemic tumorigenesis (n=10/group).ConclusionsThis study provides mechanistic insights into the process of forced cardiomyocyte proliferation and advances the clinical feasibility of this approach by minimizing the oncogenic potential of the cell cycle factors owing to the use of a novel transient and cardiomyocyte-specific viral construct.
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- 2022
13. Transcription factor protein interactomes reveal genetic determinants in heart disease
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Gonzalez-Teran, Barbara, Pittman, Maureen, Felix, Franco, Thomas, Reuben, Richmond-Buccola, Desmond, Hüttenhain, Ruth, Choudhary, Krishna, Moroni, Elisabetta, Costa, Mauro W, Huang, Yu, Padmanabhan, Arun, Alexanian, Michael, Lee, Clara Youngna, Maven, Bonnie EJ, Samse-Knapp, Kaitlen, Morton, Sarah U, McGregor, Michael, Gifford, Casey A, Seidman, JG, Seidman, Christine E, Gelb, Bruce D, Colombo, Giorgio, Conklin, Bruce R, Black, Brian L, Bruneau, Benoit G, Krogan, Nevan J, Pollard, Katherine S, and Srivastava, Deepak
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Biological Sciences ,Bioinformatics and Computational Biology ,Biomedical and Clinical Sciences ,Genetics ,Cardiovascular Medicine and Haematology ,Clinical Sciences ,Stem Cell Research ,Biotechnology ,Heart Disease - Coronary Heart Disease ,Pediatric ,Cardiovascular ,Heart Disease ,Congenital Structural Anomalies ,Stem Cell Research - Embryonic - Human ,Aetiology ,2.1 Biological and endogenous factors ,Animals ,GATA4 Transcription Factor ,Heart Defects ,Congenital ,Mice ,Mutation ,Nuclear Proteins ,Oxidoreductases ,Proteomics ,T-Box Domain Proteins ,Transcription Factors ,GATA4 ,GLYR1 ,NPAC ,TBX5 ,congenital heart disease ,de novo variants ,disease variants ,genetics ,protein interactome networks ,Medical and Health Sciences ,Developmental Biology ,Biological sciences ,Biomedical and clinical sciences - Abstract
Congenital heart disease (CHD) is present in 1% of live births, yet identification of causal mutations remains challenging. We hypothesized that genetic determinants for CHDs may lie in the protein interactomes of transcription factors whose mutations cause CHDs. Defining the interactomes of two transcription factors haplo-insufficient in CHD, GATA4 and TBX5, within human cardiac progenitors, and integrating the results with nearly 9,000 exomes from proband-parent trios revealed an enrichment of de novo missense variants associated with CHD within the interactomes. Scoring variants of interactome members based on residue, gene, and proband features identified likely CHD-causing genes, including the epigenetic reader GLYR1. GLYR1 and GATA4 widely co-occupied and co-activated cardiac developmental genes, and the identified GLYR1 missense variant disrupted interaction with GATA4, impairing in vitro and in vivo function in mice. This integrative proteomic and genetic approach provides a framework for prioritizing and interrogating genetic variants in heart disease.
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- 2022
14. Brahma safeguards canalization of cardiac mesoderm differentiation
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Hota, Swetansu K, Rao, Kavitha S, Blair, Andrew P, Khalilimeybodi, Ali, Hu, Kevin M, Thomas, Reuben, So, Kevin, Kameswaran, Vasumathi, Xu, Jiewei, Polacco, Benjamin J, Desai, Ravi V, Chatterjee, Nilanjana, Hsu, Austin, Muncie, Jonathon M, Blotnick, Aaron M, Winchester, Sarah AB, Weinberger, Leor S, Hüttenhain, Ruth, Kathiriya, Irfan S, Krogan, Nevan J, Saucerman, Jeffrey J, and Bruneau, Benoit G
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Biochemistry and Cell Biology ,Biomedical and Clinical Sciences ,Biological Sciences ,Genetics ,Cardiovascular ,Stem Cell Research - Embryonic - Non-Human ,Heart Disease ,Pediatric ,Stem Cell Research ,1.1 Normal biological development and functioning ,Animals ,Bone Morphogenetic Protein 4 ,Cell Differentiation ,Cell Lineage ,Chromatin ,Chromatin Assembly and Disassembly ,DNA Helicases ,Embryo ,Mammalian ,Epigenesis ,Genetic ,Female ,Gene Expression Regulation ,Male ,Mesoderm ,Mice ,Myocardium ,Myocytes ,Cardiac ,Neurogenesis ,Neurons ,Nuclear Proteins ,Octamer Transcription Factor-6 ,Phenotype ,Repressor Proteins ,Stem Cells ,Time Factors ,Transcription Factors ,General Science & Technology - Abstract
Differentiation proceeds along a continuum of increasingly fate-restricted intermediates, referred to as canalization1,2. Canalization is essential for stabilizing cell fate, but the mechanisms that underlie robust canalization are unclear. Here we show that the BRG1/BRM-associated factor (BAF) chromatin-remodelling complex ATPase gene Brm safeguards cell identity during directed cardiogenesis of mouse embryonic stem cells. Despite the establishment of a well-differentiated precardiac mesoderm, Brm-/- cells predominantly became neural precursors, violating germ layer assignment. Trajectory inference showed a sudden acquisition of a non-mesodermal identity in Brm-/- cells. Mechanistically, the loss of Brm prevented de novo accessibility of primed cardiac enhancers while increasing the expression of neurogenic factor POU3F1, preventing the binding of the neural suppressor REST and shifting the composition of BRG1 complexes. The identity switch caused by the Brm mutation was overcome by increasing BMP4 levels during mesoderm induction. Mathematical modelling supports these observations and demonstrates that Brm deletion affects cell fate trajectory by modifying saddle-node bifurcations2. In the mouse embryo, Brm deletion exacerbated mesoderm-deleted Brg1-mutant phenotypes, severely compromising cardiogenesis, and reveals an in vivo role for Brm. Our results show that Brm is a compensable safeguard of the fidelity of mesoderm chromatin states, and support a model in which developmental canalization is not a rigid irreversible path, but a highly plastic trajectory.
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- 2022
15. Answer ALS, a large-scale resource for sporadic and familial ALS combining clinical and multi-omics data from induced pluripotent cell lines
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Baxi, Emily G, Thompson, Terri, Li, Jonathan, Kaye, Julia A, Lim, Ryan G, Wu, Jie, Ramamoorthy, Divya, Lima, Leandro, Vaibhav, Vineet, Matlock, Andrea, Frank, Aaron, Coyne, Alyssa N, Landin, Barry, Ornelas, Loren, Mosmiller, Elizabeth, Thrower, Sara, Farr, S Michelle, Panther, Lindsey, Gomez, Emilda, Galvez, Erick, Perez, Daniel, Meepe, Imara, Lei, Susan, Mandefro, Berhan, Trost, Hannah, Pinedo, Louis, Banuelos, Maria G, Liu, Chunyan, Moran, Ruby, Garcia, Veronica, Workman, Michael, Ho, Richie, Wyman, Stacia, Roggenbuck, Jennifer, Harms, Matthew B, Stocksdale, Jennifer, Miramontes, Ricardo, Wang, Keona, Venkatraman, Vidya, Holewenski, Ronald, Sundararaman, Niveda, Pandey, Rakhi, Manalo, Danica-Mae, Donde, Aneesh, Huynh, Nhan, Adam, Miriam, Wassie, Brook T, Vertudes, Edward, Amirani, Naufa, Raja, Krishna, Thomas, Reuben, Hayes, Lindsey, Lenail, Alex, Cerezo, Aianna, Luppino, Sarah, Farrar, Alanna, Pothier, Lindsay, Prina, Carolyn, Morgan, Todd, Jamil, Arish, Heintzman, Sarah, Jockel-Balsarotti, Jennifer, Karanja, Elizabeth, Markway, Jesse, McCallum, Molly, Joslin, Ben, Alibazoglu, Deniz, Kolb, Stephen, Ajroud-Driss, Senda, Baloh, Robert, Heitzman, Daragh, Miller, Tim, Glass, Jonathan D, Patel-Murray, Natasha Leanna, Yu, Hong, Sinani, Ervin, Vigneswaran, Prasha, Sherman, Alexander V, Ahmad, Omar, Roy, Promit, Beavers, Jay C, Zeiler, Steven, Krakauer, John W, Agurto, Carla, Cecchi, Guillermo, Bellard, Mary, Raghav, Yogindra, Sachs, Karen, Ehrenberger, Tobias, Bruce, Elizabeth, Cudkowicz, Merit E, Maragakis, Nicholas, Norel, Raquel, Van Eyk, Jennifer E, Finkbeiner, Steven, Berry, James, Sareen, Dhruv, Thompson, Leslie M, Fraenkel, Ernest, and Svendsen, Clive N
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Stem Cell Research ,Rare Diseases ,Stem Cell Research - Induced Pluripotent Stem Cell ,ALS ,Clinical Research ,Neurodegenerative ,Genetics ,Neurosciences ,Human Genome ,Stem Cell Research - Induced Pluripotent Stem Cell - Human ,Brain Disorders ,Neurological ,Generic health relevance ,Good Health and Well Being ,Amyotrophic Lateral Sclerosis ,Cell Line ,Humans ,Induced Pluripotent Stem Cells ,Motor Neurons ,Psychology ,Cognitive Sciences ,Neurology & Neurosurgery - Abstract
Answer ALS is a biological and clinical resource of patient-derived, induced pluripotent stem (iPS) cell lines, multi-omic data derived from iPS neurons and longitudinal clinical and smartphone data from over 1,000 patients with ALS. This resource provides population-level biological and clinical data that may be employed to identify clinical-molecular-biochemical subtypes of amyotrophic lateral sclerosis (ALS). A unique smartphone-based system was employed to collect deep clinical data, including fine motor activity, speech, breathing and linguistics/cognition. The iPS spinal neurons were blood derived from each patient and these cells underwent multi-omic analytics including whole-genome sequencing, RNA transcriptomics, ATAC-sequencing and proteomics. The intent of these data is for the generation of integrated clinical and biological signatures using bioinformatics, statistics and computational biology to establish patterns that may lead to a better understanding of the underlying mechanisms of disease, including subgroup identification. A web portal for open-source sharing of all data was developed for widespread community-based data analytics.
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- 2022
16. Deep Phenotypic Analysis of Blood and Lymphoid T and NK Cells From HIV+ Controllers and ART-Suppressed Individuals
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George, Ashley F, Luo, Xiaoyu, Neidleman, Jason, Hoh, Rebecca, Vohra, Poonam, Thomas, Reuben, Shin, Min-Gyoung, Lee, Madeline J, Blish, Catherine A, Deeks, Steven G, Greene, Warner C, Lee, Sulggi A, and Roan, Nadia R
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Medical Microbiology ,Biomedical and Clinical Sciences ,Immunology ,HIV/AIDS ,Infectious Diseases ,Aetiology ,2.1 Biological and endogenous factors ,Infection ,Good Health and Well Being ,Adult ,Aged ,Anti-Retroviral Agents ,CD4-Positive T-Lymphocytes ,CD8-Positive T-Lymphocytes ,Female ,HIV Infections ,HIV-1 ,Humans ,Killer Cells ,Natural ,Leukocytes ,Lymphocytes ,Male ,Middle Aged ,Phenotype ,Sustained Virologic Response ,HIV ,lymph node ,T cells ,NK cells ,CXCR5 ,controllers ,CyTOF ,mass cytometry ,CyTOF/mass cytometry ,Biochemistry and cell biology ,Genetics - Abstract
T and natural killer (NK) cells are effector cells with key roles in anti-HIV immunity, including in lymphoid tissues, the major site of HIV persistence. However, little is known about the features of these effector cells from people living with HIV (PLWH), particularly from those who initiated antiretroviral therapy (ART) during acute infection. Our study design was to use 42-parameter CyTOF to conduct deep phenotyping of paired blood- and lymph node (LN)-derived T and NK cells from three groups of HIV+ aviremic individuals: elite controllers (N = 5), and ART-suppressed individuals who had started therapy during chronic (N = 6) vs. acute infection (N = 8), the latter of which is associated with better outcomes. We found that acute-treated individuals are enriched for specific subsets of T and NK cells, including blood-derived CD56-CD16+ NK cells previously associated with HIV control, and LN-derived CD4+ T follicular helper cells with heightened expansion potential. An in-depth comparison of the features of the cells from blood vs. LNs of individuals from our cohort revealed that T cells from blood were more activated than those from LNs. By contrast, LNs were enriched for follicle-homing CXCR5+ CD8+ T cells, which expressed increased levels of inhibitory receptors and markers of survival and proliferation as compared to their CXCR5- counterparts. In addition, a subset of memory-like CD56brightTCF1+ NK cells was enriched in LNs relative to blood. These results together suggest unique T and NK cell features in acute-treated individuals, and highlight the importance of examining effector cells not only in blood but also the lymphoid tissue compartment, where the reservoir mostly persists, and where these cells take on distinct phenotypic features.
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- 2022
17. Abstract 11332: Integration of Protein Interactome Networks with Congenital Heart Disease Variants Reveals Candidate Disease Genes
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Teran, Barbara Gonzalez, Pittman, Maureen, Thomas, Reuben, Felix, Franco, Richmond-Buccola, Desmond, Choudhary, Krishna, Moroni, Elisabetta, Giorgio, Colombo, Padmanabhan, Arun, Costa, Mauro, Huang, Yu, Alexanian, Michael, Lee, Clara, Cole, Bonie, Samse-Knapp, Kaitlen, McGregor, Michael, Gifford, Casey, Huttenhain, Ruth, Gelb, Bruce, Conklin, Bruce, Black, Brian L, Bruneau, Benoit, Krogan, Nevan, Pollard, Katherine, and Srivastava, Deepak
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Biotechnology ,Cardiovascular ,Stem Cell Research ,Stem Cell Research - Embryonic - Human ,Heart Disease ,Genetics ,Congenital Structural Anomalies ,Pediatric ,Human Genome ,2.1 Biological and endogenous factors ,Aetiology ,Good Health and Well Being ,Cardiorespiratory Medicine and Haematology ,Clinical Sciences ,Public Health and Health Services ,Cardiovascular System & Hematology - Abstract
Congenital heart disease (CHD) is present in 1% of live births, yet despite large-scale genomic sequencing efforts, identification of causal mutations remains a challenge. We hypothesized that genetic determinants for CHDs may lie in the protein interactomes of GATA4 and TBX5, two transcription factors whose mutation cause CHDs. Defining the GATA4 or TBX5 interactomes in human cardiac progenitors via affinity purification-mass spectrometry and integrating the results with genetic data from the Pediatric Cardiac Genomic Consortium revealed an enrichment of de novo variants associated with CHD. A consolidative score that prioritized interactome members based on variant, gene, and proband features identified likely CHD-causing genes, including the epigenetic reader GLYR1. GLYR1 and GATA4 widely co-occupied and co-activated cardiac developmental genes, and the GLYR1 missense variant identified disrupted interaction with GATA4 and impaired transcriptional co-regulation in cardiomyocyte differentiation in vitro and cardiogenesis in vivo. This integrative proteomic and genetic approach provides a framework for prioritizing and interrogating the contribution of genetic variants in disease.
- Published
- 2021
18. Integration of Protein Interactome Networks With Congenital Heart Disease Variants Reveals Candidate Disease Genes
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Gonzalez-Teran, Barbara, Pittman, Maureen, Felix, Franco, Richmond-Buccola, Desmond, Thomas, Reuben, Choudhary, Krishna, Moroni, Elisabetta, Colombo, Giorgio, Alexanian, Michael, Cole, Bonnie, Samse-Knapp, Kaitlen, McGregor, Michael, Gifford, Casey A, Huttenhain, Ruth, Gelb, Bruce D, Conklin, Bruce, Black, Brian L, Bruneau, Benoit G, Krogan, Nevan J, Pollard, Katherine S, and Srivastava, Deepak
- Published
- 2021
19. BMP receptor blockade overcomes extrinsic inhibition of remyelination and restores neurovascular homeostasis
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Petersen, Mark A, Tognatta, Reshmi, Meyer-Franke, Anke, Bushong, Eric A, Mendiola, Andrew S, Yan, Zhaoqi, Muthusamy, Abinaya, Merlini, Mario, Meza-Acevedo, Rosa, Cabriga, Belinda, Zhou, Yungui, Thomas, Reuben, Ryu, Jae Kyu, Lassmann, Hans, Ellisman, Mark H, and Akassoglou, Katerina
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Brain Disorders ,Multiple Sclerosis ,Autoimmune Disease ,Neurosciences ,Stem Cell Research - Nonembryonic - Non-Human ,Stem Cell Research ,Neurodegenerative ,Development of treatments and therapeutic interventions ,5.1 Pharmaceuticals ,Neurological ,Cardiovascular ,Animals ,Blood-Brain Barrier ,Bone Morphogenetic Protein Receptors ,Bone Morphogenetic Proteins ,Cell Differentiation ,Homeostasis ,Mice ,Mice ,Transgenic ,Myelin Sheath ,Oligodendrocyte Precursor Cells ,Oligodendroglia ,Pyrazoles ,Pyrimidines ,Quinolines ,Remyelination ,Spinal Cord ,multiple sclerosis ,blood-brain barrier ,promyelinating drugs ,neuroinflammation ,RNA sequencing ,Medical and Health Sciences ,Psychology and Cognitive Sciences ,Neurology & Neurosurgery - Abstract
Extrinsic inhibitors at sites of blood-brain barrier disruption and neurovascular damage contribute to remyelination failure in neurological diseases. However, therapies to overcome the extrinsic inhibition of remyelination are not widely available and the dynamics of glial progenitor niche remodelling at sites of neurovascular dysfunction are largely unknown. By integrating in vivo two-photon imaging co-registered with electron microscopy and transcriptomics in chronic neuroinflammatory lesions, we found that oligodendrocyte precursor cells clustered perivascularly at sites of limited remyelination with deposition of fibrinogen, a blood coagulation factor abundantly deposited in multiple sclerosis lesions. By developing a screen (OPC-X-screen) to identify compounds that promote remyelination in the presence of extrinsic inhibitors, we showed that known promyelinating drugs did not rescue the extrinsic inhibition of remyelination by fibrinogen. In contrast, bone morphogenetic protein type I receptor blockade rescued the inhibitory fibrinogen effects and restored a promyelinating progenitor niche by promoting myelinating oligodendrocytes, while suppressing astrocyte cell fate, with potent therapeutic effects in chronic models of multiple sclerosis. Thus, abortive oligodendrocyte precursor cell differentiation by fibrinogen is refractory to known promyelinating compounds, suggesting that blockade of the bone morphogenetic protein signalling pathway may enhance remyelinating efficacy by overcoming extrinsic inhibition in neuroinflammatory lesions with vascular damage.
- Published
- 2021
20. Phenotypic Differences between the Alzheimer's Disease-Related hAPP-J20 Model and Heterozygous Zbtb20 Knock-Out Mice.
- Author
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Gulbranson, Daniel R, Ho, Kaitlyn, Yu, Gui-Qiu, Yu, Xinxing, Das, Melanie, Shao, Eric, Kim, Daniel, Zhang, Weiping J, Choudhary, Krishna, Thomas, Reuben, and Mucke, Lennart
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Animals ,Mice ,Transgenic ,Mice ,Knockout ,Mice ,Alzheimer Disease ,Disease Models ,Animal ,Amyloid beta-Protein Precursor ,Transcription Factors ,Phenotype ,Amyloid beta-Peptides ,Alzheimer’s disease ,Zbtb20 ,amyloid precursor protein ,behavior ,epilepsy ,mouse model ,Genetics ,Aging ,Dementia ,Acquired Cognitive Impairment ,Alzheimer's Disease ,Neurosciences ,Biotechnology ,Brain Disorders ,Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) ,Neurodegenerative ,2.1 Biological and endogenous factors ,Neurological - Abstract
Diverse gene products contribute to the pathogenesis of Alzheimer's disease (AD). Experimental models have helped elucidate their mechanisms and impact on brain functions. Human amyloid precursor protein (hAPP) transgenic mice from line J20 (hAPP-J20 mice) are widely used to simulate key aspects of AD. However, they also carry an insertional mutation in noncoding sequence of one Zbtb20 allele, a gene involved in neural development. We demonstrate that heterozygous hAPP-J20 mice have reduced Zbtb20 expression in some AD-relevant brain regions, but not others, and that Zbtb20 levels are higher in hAPP-J20 mice than heterozygous Zbtb20 knock-out (Zbtb20 +/-) mice. Whereas hAPP-J20 mice have premature mortality, severe deficits in learning and memory, other behavioral alterations, and prominent nonconvulsive epileptiform activity, Zbtb20 +/- mice do not. Thus, the insertional mutation in hAPP-J20 mice does not ablate the affected Zbtb20 allele and is unlikely to account for the AD-like phenotype of this model.
- Published
- 2021
21. Phenotypic differences between the Alzheimer’s disease-related hAPP-J20 model and heterozygous Zbtb20 knockout mice
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Gulbranson, Daniel R, Ho, Kaitlyn, Yu, Gui-Qiu, Yu, Xinxing, Das, Melanie, Shao, Eric, Kim, Daniel, Zhang, Weiping J, Choudhary, Krishna, Thomas, Reuben, and Mucke, Lennart
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Biological Psychology ,Biomedical and Clinical Sciences ,Psychology ,Genetics ,Neurodegenerative ,Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) ,Acquired Cognitive Impairment ,Brain Disorders ,Alzheimer's Disease ,Biotechnology ,Aging ,Dementia ,Neurosciences ,2.1 Biological and endogenous factors ,Aetiology ,Neurological ,Good Health and Well Being ,Alzheimer Disease ,Amyloid beta-Peptides ,Amyloid beta-Protein Precursor ,Animals ,Disease Models ,Animal ,Mice ,Mice ,Knockout ,Mice ,Transgenic ,Phenotype ,Transcription Factors ,Alzheimer’s disease ,Zbtb20 ,amyloid precursor protein ,behavior ,epilepsy ,mouse model - Abstract
Diverse gene products contribute to the pathogenesis of Alzheimer's disease (AD). Experimental models have helped elucidate their mechanisms and impact on brain functions. Human amyloid precursor protein (hAPP) transgenic mice from line J20 (hAPP-J20 mice) are widely used to simulate key aspects of AD. However, they also carry an insertional mutation in noncoding sequence of one Zbtb20 allele, a gene involved in neural development. We demonstrate that heterozygous hAPP-J20 mice have reduced Zbtb20 expression in some AD-relevant brain regions, but not others, and that Zbtb20 levels are higher in hAPP-J20 mice than heterozygous Zbtb20 knock-out (Zbtb20+/-) mice. Whereas hAPP-J20 mice have premature mortality, severe deficits in learning and memory, other behavioral alterations, and prominent nonconvulsive epileptiform activity, Zbtb20+/- mice do not. Thus, the insertional mutation in hAPP-J20 mice does not ablate the affected Zbtb20 allele and is unlikely to account for the AD-like phenotype of this model.
- Published
- 2021
22. APOE4-promoted gliosis and degeneration in tauopathy are ameliorated by pharmacological inhibition of HMGB1 release
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Koutsodendris, Nicole, Blumenfeld, Jessica, Agrawal, Ayushi, Traglia, Michela, Yip, Oscar, Rao, Antara, Kim, Min Joo, Nelson, Maxine R., Wang, Yung-Hua, Grone, Brian, Hao, Yanxia, Thomas, Reuben, Zilberter, Misha, Yoon, Seo Yeon, Arriola, Patrick, and Huang, Yadong
- Published
- 2023
- Full Text
- View/download PDF
23. Modeling Human TBX5 Haploinsufficiency Predicts Regulatory Networks for Congenital Heart Disease.
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Kathiriya, Irfan S, Rao, Kavitha S, Iacono, Giovanni, Devine, W Patrick, Blair, Andrew P, Hota, Swetansu K, Lai, Michael H, Garay, Bayardo I, Thomas, Reuben, Gong, Henry Z, Wasson, Lauren K, Goyal, Piyush, Sukonnik, Tatyana, Hu, Kevin M, Akgun, Gunes A, Bernard, Laure D, Akerberg, Brynn N, Gu, Fei, Li, Kai, Speir, Matthew L, Haeussler, Maximilian, Pu, William T, Stuart, Joshua M, Seidman, Christine E, Seidman, JG, Heyn, Holger, and Bruneau, Benoit G
- Subjects
Heart Ventricles ,Myocytes ,Cardiac ,Animals ,Humans ,Mice ,Heart Defects ,Congenital ,T-Box Domain Proteins ,Cell Differentiation ,Transcription ,Genetic ,Body Patterning ,Gene Dosage ,Mutation ,Models ,Biological ,Gene Regulatory Networks ,Haploinsufficiency ,MEF2 Transcription Factors ,cardiomyocyte differentiation ,congenital heart disease ,disease modeling ,gene dosage ,gene regulation ,gene regulatory networks ,haploinsufficiency ,human induced pluripotent stem cells ,single cell transcriptomics ,transcription factor ,Heart Disease - Coronary Heart Disease ,Cardiovascular ,Genetics ,Human Genome ,Stem Cell Research ,Heart Disease ,Congenital Structural Anomalies ,Pediatric ,1.1 Normal biological development and functioning ,Aetiology ,2.1 Biological and endogenous factors ,Underpinning research ,Biological Sciences ,Medical and Health Sciences ,Developmental Biology - Abstract
Haploinsufficiency of transcriptional regulators causes human congenital heart disease (CHD); however, the underlying CHD gene regulatory network (GRN) imbalances are unknown. Here, we define transcriptional consequences of reduced dosage of the CHD transcription factor, TBX5, in individual cells during cardiomyocyte differentiation from human induced pluripotent stem cells (iPSCs). We discovered highly sensitive dysregulation of TBX5-dependent pathways-including lineage decisions and genes associated with heart development, cardiomyocyte function, and CHD genetics-in discrete subpopulations of cardiomyocytes. Spatial transcriptomic mapping revealed chamber-restricted expression for many TBX5-sensitive transcripts. GRN analysis indicated that cardiac network stability, including vulnerable CHD-linked nodes, is sensitive to TBX5 dosage. A GRN-predicted genetic interaction between Tbx5 and Mef2c, manifesting as ventricular septation defects, was validated in mice. These results demonstrate exquisite and diverse sensitivity to TBX5 dosage in heterogeneous subsets of iPSC-derived cardiomyocytes and predicts candidate GRNs for human CHDs, with implications for quantitative transcriptional regulation in disease.
- Published
- 2021
24. Microglial Gi-dependent dynamics regulate brain network hyperexcitability
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Merlini, Mario, Rafalski, Victoria A, Ma, Keran, Kim, Keun-Young, Bushong, Eric A, Rios Coronado, Pamela E, Yan, Zhaoqi, Mendiola, Andrew S, Sozmen, Elif G, Ryu, Jae Kyu, Haberl, Matthias G, Madany, Matthew, Sampson, Daniel Naranjo, Petersen, Mark A, Bardehle, Sophia, Tognatta, Reshmi, Dean, Terry, Acevedo, Rosa Meza, Cabriga, Belinda, Thomas, Reuben, Coughlin, Shaun R, Ellisman, Mark H, Palop, Jorge J, and Akassoglou, Katerina
- Subjects
Neurosciences ,Neurodegenerative ,Epilepsy ,Brain Disorders ,Prevention ,2.1 Biological and endogenous factors ,Aetiology ,Neurological ,Animals ,Calcium Signaling ,Cell Movement ,Convulsants ,Electroencephalography ,G-Protein-Coupled Receptor Kinase 1 ,Immunologic Surveillance ,Mice ,Microglia ,Nerve Net ,Nervous System Diseases ,Nervous System Physiological Phenomena ,Pilocarpine ,Seizures ,Signal Transduction ,rho GTP-Binding Proteins ,Psychology ,Cognitive Sciences ,Neurology & Neurosurgery - Abstract
Microglial surveillance is a key feature of brain physiology and disease. Here, we found that Gi-dependent microglial dynamics prevent neuronal network hyperexcitability. By generating MgPTX mice to genetically inhibit Gi in microglia, we show that sustained reduction of microglia brain surveillance and directed process motility induced spontaneous seizures and increased hypersynchrony after physiologically evoked neuronal activity in awake adult mice. Thus, Gi-dependent microglia dynamics may prevent hyperexcitability in neurological diseases.
- Published
- 2021
25. Integration of Protein Interactome Networks with Congenital Heart Disease Variants Reveals Candidate Disease Genes
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Teran, Barbara Gonzalez, Pittman, Maureen, Thomas, Reuben, Felix, Franco, Richmond-Buccola, Desmond, Choudhary, Krishna, Moroni, Elisabetta, Giorgio, Colombo, Padmanabhan, Arun, Costa, Mauro, Huang, Yu, Alexanian, Michael, Lee, Clara, Cole, Bonie, Samse-Knapp, Kaitlen, McGregor, Michael, Gifford, Casey, Huttenhain, Ruth, Gelb, Bruce, and Conklin, Bruce
- Subjects
Cardiorespiratory Medicine and Haematology ,Clinical Sciences ,Public Health and Health Services ,Cardiovascular System & Hematology - Published
- 2021
26. Phenotypic analysis of the unstimulated in vivo HIV CD4 T cell reservoir.
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Neidleman, Jason, Luo, Xiaoyu, Frouard, Julie, Xie, Guorui, Hsiao, Feng, Ma, Tongcui, Morcilla, Vincent, Lee, Ashley, Telwatte, Sushama, Thomas, Reuben, Tamaki, Whitney, Wheeler, Benjamin, Hoh, Rebecca, Somsouk, Ma, Vohra, Poonam, Milush, Jeffrey, James, Katherine Sholtis, Archin, Nancie M, Hunt, Peter W, Deeks, Steven G, Yukl, Steven A, Palmer, Sarah, Greene, Warner C, and Roan, Nadia R
- Subjects
CD4-Positive T-Lymphocytes ,Humans ,Proviruses ,HIV-1 ,HIV Infections ,Cell Separation ,Immunophenotyping ,Virus Latency ,Mass Spectrometry ,CyTOF ,HIV ,clonal expansion ,human ,infectious disease ,microbiology ,replication-competent reservoir ,tissues ,virus ,Biochemistry and Cell Biology - Abstract
The latent reservoir is a major barrier to HIV cure. As latently infected cells cannot be phenotyped directly, the features of the in vivo reservoir have remained elusive. Here, we describe a method that leverages high-dimensional phenotyping using CyTOF to trace latently infected cells reactivated ex vivo to their original pre-activation states. Our results suggest that, contrary to common assumptions, the reservoir is not randomly distributed among cell subsets, and is remarkably conserved between individuals. However, reservoir composition differs between tissues and blood, as do cells successfully reactivated by different latency reversing agents. By selecting 8-10 of our 39 original CyTOF markers, we were able to isolate highly purified populations of unstimulated in vivo latent cells. These purified populations were highly enriched for replication-competent and intact provirus, transcribed HIV, and displayed clonal expansion. The ability to isolate unstimulated latent cells from infected individuals enables previously impossible studies on HIV persistence.
- Published
- 2020
27. A Chromatin Accessibility Atlas of the Developing Human Telencephalon
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Markenscoff-Papadimitriou, Eirene, Whalen, Sean, Przytycki, Pawel, Thomas, Reuben, Binyameen, Fadya, Nowakowski, Tomasz J, Kriegstein, Arnold R, Sanders, Stephan J, State, Matthew W, Pollard, Katherine S, and Rubenstein, John L
- Subjects
Neurosciences ,Genetics ,Brain Disorders ,Mental Health ,Underpinning research ,1.1 Normal biological development and functioning ,Animals ,Autistic Disorder ,Cell Line ,Chromatin ,Chromatin Immunoprecipitation Sequencing ,Enhancer Elements ,Genetic ,Euchromatin ,GABA Plasma Membrane Transport Proteins ,Gene Expression Regulation ,Developmental ,Gene Ontology ,Genetic Predisposition to Disease ,Gestational Age ,Humans ,Mice ,Mice ,Transgenic ,Nucleotide Motifs ,Point Mutation ,Prefrontal Cortex ,Repressor Proteins ,Spatio-Temporal Analysis ,Telencephalon ,Transcription Factors ,ATAC-seq ,autism ,chromatin ,enhancers ,gene regulation ,machine learning ,neurodevelopment ,neuropsychiatric disorders ,Biological Sciences ,Medical and Health Sciences ,Developmental Biology - Abstract
To discover regulatory elements driving the specificity of gene expression in different cell types and regions of the developing human brain, we generated an atlas of open chromatin from nine dissected regions of the mid-gestation human telencephalon, as well as microdissected upper and deep layers of the prefrontal cortex. We identified a subset of open chromatin regions (OCRs), termed predicted regulatory elements (pREs), that are likely to function as developmental brain enhancers. pREs showed temporal, regional, and laminar differences in chromatin accessibility and were correlated with gene expression differences across regions and gestational ages. We identified two functional de novo variants in a pRE for autism risk gene SLC6A1, and using CRISPRa, demonstrated that this pRE regulates SCL6A1. Additionally, mouse transgenic experiments validated enhancer activity for pREs proximal to FEZF2 and BCL11A. Thus, this atlas serves as a resource for decoding neurodevelopmental gene regulation in health and disease.
- Published
- 2020
28. Transcriptional profiling and therapeutic targeting of oxidative stress in neuroinflammation
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Mendiola, Andrew S, Ryu, Jae Kyu, Bardehle, Sophia, Meyer-Franke, Anke, Ang, Kenny Kean-Hooi, Wilson, Chris, Baeten, Kim M, Hanspers, Kristina, Merlini, Mario, Thomas, Sean, Petersen, Mark A, Williams, Alexander, Thomas, Reuben, Rafalski, Victoria A, Meza-Acevedo, Rosa, Tognatta, Reshmi, Yan, Zhaoqi, Pfaff, Samuel J, Machado, Michael R, Bedard, Catherine, Rios Coronado, Pamela E, Jiang, Xiqian, Wang, Jin, Pleiss, Michael A, Green, Ari J, Zamvil, Scott S, Pico, Alexander R, Bruneau, Benoit G, Arkin, Michelle R, and Akassoglou, Katerina
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Biomedical and Clinical Sciences ,Immunology ,Neurodegenerative ,Genetics ,Human Genome ,Neurosciences ,Biotechnology ,Brain Disorders ,5.1 Pharmaceuticals ,Development of treatments and therapeutic interventions ,2.1 Biological and endogenous factors ,Aetiology ,Neurological ,Animals ,Antioxidants ,Disease Models ,Animal ,Encephalomyelitis ,Autoimmune ,Experimental ,Female ,Gene Expression Profiling ,Gene Regulatory Networks ,High-Throughput Screening Assays ,Humans ,Immunity ,Innate ,Isoxazoles ,Mice ,Mice ,Inbred C57BL ,Mice ,Mutant Strains ,Microglia ,Multiple Sclerosis ,Neurogenic Inflammation ,Oxidative Stress ,Sequence Analysis ,RNA ,Single-Cell Analysis ,Biochemistry and cell biology - Abstract
Oxidative stress is a central part of innate immune-induced neurodegeneration. However, the transcriptomic landscape of central nervous system (CNS) innate immune cells contributing to oxidative stress is unknown, and therapies to target their neurotoxic functions are not widely available. Here, we provide the oxidative stress innate immune cell atlas in neuroinflammatory disease and report the discovery of new druggable pathways. Transcriptional profiling of oxidative stress-producing CNS innate immune cells identified a core oxidative stress gene signature coupled to coagulation and glutathione-pathway genes shared between a microglia cluster and infiltrating macrophages. Tox-seq followed by a microglia high-throughput screen and oxidative stress gene network analysis identified the glutathione-regulating compound acivicin, with potent therapeutic effects that decrease oxidative stress and axonal damage in chronic and relapsing multiple sclerosis models. Thus, oxidative stress transcriptomics identified neurotoxic CNS innate immune populations and may enable discovery of selective neuroprotective strategies.
- Published
- 2020
29. Differential Effects of the Hormonal and Copper Intrauterine Device on the Endometrial Transcriptome.
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Smith-McCune, Karen, Thomas, Reuben, Averbach, Sarah, Seidman, Dominika, Takeda, Margaret, Houshdaran, Sahar, and Giudice, Linda C
- Abstract
The contraceptive effectiveness of intrauterine devices (IUDs) has been attributed in part to a foreign body reaction in the endometrium. We performed this study to better understand mechanisms of action of contraceptives of by studying their effects on endometrial and cervical transcriptomes. We collected endometrial and cervical biopsies from women using the levonorgestrel-releasing intrauterine system (LNG-IUS, n = 11), copper intrauterine device (cu-IUD, n = 13) or levonorgestrel-containing combined oral contraceptives (COC, n = 12), and from women not using contraceptives (control group, n = 11). Transcriptional profiling was performed with Affymetrix arrays, Principal Component Analysis and the bioconductor package limma. In endometrial samples from cu-IUD users, there were no genes with statistically significant differential expression compared to controls. In LNG-IUS users, 2509 genes were differentially expressed and mapped predominantly onto immune and inflammatory pathways. The cervical samples showed no statistically significant differential gene expression compared to controls. Hormonal and copper IUDs have significantly different effects on the endometrial transcriptome, with the LNG-IUS transcriptome showing pronounced inflammation and immune activation compared to controls whereas the cu-IUD transcriptome was indistinguishable from luteal phase endometrium. These findings argue against a foreign body reaction as a common mechanism of action of IUDs.
- Published
- 2020
30. ML and GIS-Based Approaches to Flood Prediction: A Comparative Study
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Tewari, Abha, Kshemkalyani, Varad, Kukreja, Heer, Menon, Pratheek, Thomas, Reuben, Kacprzyk, Janusz, Series Editor, Gomide, Fernando, Advisory Editor, Kaynak, Okyay, Advisory Editor, Liu, Derong, Advisory Editor, Pedrycz, Witold, Advisory Editor, Polycarpou, Marios M., Advisory Editor, Rudas, Imre J., Advisory Editor, Wang, Jun, Advisory Editor, Tavares, João Manuel R. S., editor, Dutta, Paramartha, editor, Dutta, Soumi, editor, and Samanta, Debabrata, editor
- Published
- 2022
- Full Text
- View/download PDF
31. A Chromatin Accessibility Atlas of the Developing Human Telencephalon
- Author
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Markenscoff-Papadimitriou, Eirene, Whalen, Sean, Przytycki, Pawel, Thomas, Reuben, Binyameen, Fadya, Nowakowski, Tomasz J, Sanders, Stephan J, State, Matthew W, Pollard, Katherine S, and Rubenstein, John L
- Subjects
Neurosciences ,Stem Cell Research ,Genetics ,Pediatric ,Autism ,Brain Disorders ,Human Genome ,Mental Health ,Intellectual and Developmental Disabilities (IDD) ,Underpinning research ,1.1 Normal biological development and functioning ,Neurological - Abstract
Abstract Gene expression differs between cell types and regions within complex tissues such as the developing brain. To discover regulatory elements underlying this specificity, we generated genome-wide maps of chromatin accessibility in eleven anatomically-defined regions of the developing human telencephalon, including upper and deep layers of the prefrontal cortex. We predicted a subset of open chromatin regions (18%) that are most likely to be active enhancers, many of which are dynamic with 26% differing between early and late mid-gestation and 28% present in only one brain region. These region-specific predicted regulatory elements (pREs) are enriched proximal to genes with expression differences across regions and developmental stages and harbor distinct sequence motifs that suggest potential upstream regulators of regional and temporal transcription. We leverage this atlas to identify regulators of genes associated with autism spectrum disorder (ASD) including an enhancer of BCL11A , validated in mouse, and two functional de novo mutations in individuals with ASD in an enhancer of SLC6A1 , validated in neuroblastoma cells. These applications demonstrate the utility of this atlas for decoding neurodevelopmental gene regulation in health and disease. Summary To discover regulatory elements driving the specificity of gene expression in different cell types and regions of the developing human brain, we generated an atlas of open chromatin from eleven dissected regions of the mid-gestation human telencephalon, including upper and deep layers of the prefrontal cortex. We identified a subset of open chromatin regions (OCRs), termed predicted regulatory elements (pREs), that are likely to function as developmental brain enhancers. pREs showed regional differences in chromatin accessibility, including many specific to one brain region, and were correlated with gene expression differences across the same regions and gestational ages. pREs allowed us to map neurodevelopmental disorder risk genes to developing telencephalic regions, and we identified three functional de novo noncoding variants in pREs that alter enhancer function. In addition, transgenic experiments in mouse validated enhancer activity for a pRE proximal to BCL11A , showing how this atlas serves as a resource for decoding neurodevelopmental gene regulation in health and disease.
- Published
- 2019
32. Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis
- Author
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Hota, Swetansu K, Johnson, Jeffrey R, Verschueren, Erik, Thomas, Reuben, Blotnick, Aaron M, Zhu, Yiwen, Sun, Xin, Pennacchio, Len A, Krogan, Nevan J, and Bruneau, Benoit G
- Subjects
Biological Sciences ,Biomedical and Clinical Sciences ,Genetics ,Cardiovascular ,Heart Disease ,1.1 Normal biological development and functioning ,Animals ,Cell Differentiation ,Chromatin ,Chromatin Assembly and Disassembly ,DNA Helicases ,Gene Expression Regulation ,Developmental ,Genome ,Heart ,Mice ,Multiprotein Complexes ,Myocytes ,Cardiac ,Nuclear Proteins ,Organogenesis ,Protein Binding ,Protein Subunits ,Time Factors ,Transcription Factors ,Differentiation ,Gene regulation ,Medical and Health Sciences ,Biological sciences ,Biomedical and clinical sciences ,Health sciences - Abstract
Chromatin remodeling complexes instruct cellular differentiation and lineage specific transcription. The BRG1/BRM-associated factor (BAF) complexes are important for several aspects of differentiation. We show that the catalytic subunit gene Brg1 has a specific role in cardiac precursors (CPs) to initiate cardiac gene expression programs and repress non-cardiac expression. Using immunopurification with mass spectrometry, we have determined the dynamic composition of BAF complexes during mammalian cardiac differentiation, identifying several cell-type specific subunits. We focused on the CP- and cardiomyocyte (CM)-enriched subunits BAF60c (SMARCD3) and BAF170 (SMARCC2). Baf60c and Baf170 co-regulate gene expression with Brg1 in CPs, and in CMs their loss results in broadly deregulated cardiac gene expression. BRG1, BAF60c and BAF170 modulate chromatin accessibility, to promote accessibility at activated genes while closing chromatin at repressed genes. BAF60c and BAF170 are required for proper BAF complex composition, and BAF170 loss leads to retention of BRG1 at CP-specific sites. Thus, dynamic interdependent BAF complex subunit assembly modulates chromatin states and thereby participates in directing temporal gene expression programs in cardiogenesis.
- Published
- 2019
33. Zoom & WhatsApp digital information and communication technologies (ICTs) enhance community engaged research with women immigrants from Mexico
- Author
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Mendivil-Aguayo, Pachely, primary, Rivera, Megan, additional, Armendariz, Daniela, additional, Perez Rodriguez, Daniel, additional, Vasquez, Camille, additional, Regino, Lidia, additional, Tellez, Maria, additional, Perez, Jackie, additional, Medina, Dulce, additional, Sandoval, Virginia, additional, Murray-Krezan, Cristina, additional, Aragon, Alejandro, additional, Thomas, Reuben J., additional, Bearer, Elaine L., additional, and Page-Reeves, Janet, additional
- Published
- 2024
- Full Text
- View/download PDF
34. Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics during Cardiac Reprogramming
- Author
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Stone, Nicole R, Gifford, Casey A, Thomas, Reuben, Pratt, Karishma JB, Samse-Knapp, Kaitlen, Mohamed, Tamer MA, Radzinsky, Ethan M, Schricker, Amelia, Ye, Lin, Yu, Pengzhi, van Bemmel, Joke G, Ivey, Kathryn N, Pollard, Katherine S, and Srivastava, Deepak
- Subjects
Biochemistry and Cell Biology ,Biomedical and Clinical Sciences ,Biological Sciences ,Genetics ,Heart Disease ,Human Genome ,Cardiovascular ,Animals ,Cell Differentiation ,Cell Lineage ,Cells ,Cultured ,Cellular Reprogramming ,Chromatin Assembly and Disassembly ,Epigenesis ,Genetic ,GATA4 Transcription Factor ,MEF2 Transcription Factors ,Machine Learning ,Mice ,Myocytes ,Cardiac ,Protein Binding ,T-Box Domain Proteins ,Transcriptional Activation ,ATAC-seq ,ChIP-seq ,cardiac fibroblast ,cardiomyocyte ,reprogramming ,single-cell RNA-seq ,transcription factor ,Medical and Health Sciences ,Developmental Biology ,Biological sciences ,Biomedical and clinical sciences - Abstract
Ectopic expression of combinations of transcription factors (TFs) can drive direct lineage conversion, thereby reprogramming a somatic cell's identity. To determine the molecular mechanisms by which Gata4, Mef2c, and Tbx5 (GMT) induce conversion from a cardiac fibroblast toward an induced cardiomyocyte, we performed comprehensive transcriptomic, DNA-occupancy, and epigenomic interrogation throughout the reprogramming process. Integration of these datasets identified new TFs involved in cardiac reprogramming and revealed context-specific roles for GMT, including the ability of Mef2c and Tbx5 to independently promote chromatin remodeling at previously inaccessible sites. We also find evidence for cooperative facilitation and refinement of each TF's binding profile in a combinatorial setting. A reporter assay employing newly defined regulatory elements confirmed that binding of a single TF can be sufficient for gene activation, suggesting that co-binding events do not necessarily reflect synergy. These results shed light on fundamental mechanisms by which combinations of TFs direct lineage conversion.
- Published
- 2019
35. A shift in circulating rotaviral genotypes among hospitalized neonates
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Reju, Sudhabharathi, Srikanth, Padma, Selvarajan, Sribal, Thomas, Reuben Kuruvilla, Barani, Ramya, Amboiram, Prakash, Palani, Gunasekaran, and Kang, Gagandeep
- Published
- 2022
- Full Text
- View/download PDF
36. Identification of gene expression predictors of occupational benzene exposure
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Schiffman, Courtney, McHale, Cliona M, Hubbard, Alan E, Zhang, Luoping, Thomas, Reuben, Vermeulen, Roel, Li, Guilan, Shen, Min, Rappaport, Stephen M, Yin, Songnian, Lan, Qing, Smith, Martyn T, and Rothman, Nathaniel
- Subjects
Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Prevention ,Aetiology ,2.1 Biological and endogenous factors ,Adult ,Area Under Curve ,Benzene ,Biomarkers ,Coenzyme A Ligases ,Eosinophil Major Basic Protein ,Female ,Gene Expression ,Humans ,Immunity ,Innate ,Lectins ,C-Type ,Leukocytes ,Male ,NF-kappa B p50 Subunit ,Occupational Exposure ,Oligonucleotide Array Sequence Analysis ,Proteoglycans ,RNA ,Messenger ,ROC Curve ,Receptors ,Cell Surface ,Sequence Analysis ,RNA ,Young Adult ,General Science & Technology - Abstract
BackgroundPreviously, using microarrays and mRNA-Sequencing (mRNA-Seq) we found that occupational exposure to a range of benzene levels perturbed gene expression in peripheral blood mononuclear cells.ObjectivesIn the current study, we sought to identify gene expression biomarkers predictive of benzene exposure below 1 part per million (ppm), the occupational standard in the U.S.MethodsFirst, we used the nCounter platform to validate altered expression of 30 genes in 33 unexposed controls and 57 subjects exposed to benzene (0.7, p0.9 (p
- Published
- 2018
37. Phosphorylation of tau at Y18, but not tau-fyn binding, is required for tau to modulate NMDA receptor-dependent excitotoxicity in primary neuronal culture
- Author
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Miyamoto, Takashi, Stein, Liana, Thomas, Reuben, Djukic, Biljana, Taneja, Praveen, Knox, Joseph, Vossel, Keith, and Mucke, Lennart
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Biochemistry and Cell Biology ,Biomedical and Clinical Sciences ,Biological Sciences ,Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) ,Brain Disorders ,Aging ,Neurodegenerative ,Neurosciences ,Alzheimer's Disease ,Acquired Cognitive Impairment ,Dementia ,Genetics ,2.1 Biological and endogenous factors ,Development of treatments and therapeutic interventions ,5.2 Cellular and gene therapies ,Aetiology ,Neurological ,Animals ,Cells ,Cultured ,Excitatory Amino Acid Agents ,Hippocampus ,Mice ,Mice ,Inbred C57BL ,Mice ,Knockout ,Neurons ,Phosphorylation ,Proto-Oncogene Proteins c-fyn ,Receptors ,N-Methyl-D-Aspartate ,tau Proteins ,Calcium ,Excitotoxicity ,Fyn ,NMDARs ,Tau ,Y18 ,Clinical Sciences ,Neurology & Neurosurgery ,Biochemistry and cell biology - Abstract
BackgroundHyperexcitability of neuronal networks can lead to excessive release of the excitatory neurotransmitter glutamate, which in turn can cause neuronal damage by overactivating NMDA-type glutamate receptors and related signaling pathways. This process (excitotoxicity) has been implicated in the pathogenesis of many neurological conditions, ranging from childhood epilepsies to stroke and neurodegenerative disorders such as Alzheimer's disease (AD). Reducing neuronal levels of the microtubule-associated protein tau counteracts network hyperexcitability of diverse causes, but whether this strategy can also diminish downstream excitotoxicity is less clear.MethodsWe established a cell-based assay to quantify excitotoxicity in primary cultures of mouse hippocampal neurons and investigated the role of tau in exicitotoxicity by modulating neuronal tau expression through genetic ablation or transduction with lentiviral vectors expressing anti-tau shRNA or constructs encoding wildtype versus mutant mouse tau.ResultsWe demonstrate that shRNA-mediated knockdown of tau reduces glutamate-induced, NMDA receptor-dependent Ca2+ influx and neurotoxicity in neurons from wildtype mice. Conversely, expression of wildtype mouse tau enhances Ca2+ influx and excitotoxicity in tau-deficient (Mapt -/-) neurons. Reconstituting tau expression in Mapt -/- neurons with mutant forms of tau reveals that the tau-related enhancement of Ca2+ influx and excitotoxicity depend on the phosphorylation of tau at tyrosine 18 (pY18), which is mediated by the tyrosine kinase Fyn. These effects are most evident at pathologically elevated concentrations of glutamate, do not involve GluN2B-containing NMDA receptors, and do not require binding of Fyn to tau's major interacting PxxP motif or of tau to microtubules.ConclusionsAlthough tau has been implicated in diverse neurological diseases, its most pathogenic forms remain to be defined. Our study suggests that reducing the formation or level of pY18-tau can counteract excitotoxicity by diminishing NMDA receptor-dependent Ca2+ influx.
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- 2017
38. A disrupted compartment boundary underlies abnormal cardiac patterning and congenital heart defects
- Author
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Kathiriya, Irfan S., primary, Dominguez, Martin H., additional, Rao, Kavitha S., additional, Muncie-Vasic, Jonathon M., additional, Devine, W. Patrick, additional, Hu, Kevin M., additional, Hota, Swetansu K., additional, Garay, Bayardo I., additional, Quintero, Diego, additional, Goyal, Piyush, additional, Matthews, Megan N., additional, Thomas, Reuben, additional, Sukonnik, Tatyana, additional, Perez, Dario Miguel-, additional, Winchester, Sarah, additional, Brower, Emily F., additional, Forjaz, André, additional, Wu, Pei-Hsun, additional, Wirtz, Denis, additional, Kiemen, Ashley L., additional, and Bruneau, Benoit G., additional
- Published
- 2024
- Full Text
- View/download PDF
39. Sources of Friendship and Structurally Induced Homophily across the Life Course
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Thomas, Reuben J.
- Published
- 2019
40. Abstract 14797: Single Cell Multi-Modal Analyses Reveal Epigenomic and Transcriptomic Basis Underlying Cardiac Defects in Maternal Diabetes
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Nishino, Tomohiro, Ranade, Sanjeev, Angelo, Pelonero, van Soldt, Benjamin J, Ye, Lin, Alexanian, Michael, Koback, Frances, Huang, Yu, Sadagopan, Nandhini, Padmanabhan, Arun, Thomas, Reuben, van Bemmel, Joke, Gifford, Casey, Costa, Mauro, and Srivastava, Deepak
- Published
- 2022
- Full Text
- View/download PDF
41. T2-based area-at-risk and edema are influenced by ischemic duration in acute myocardial infarction
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Thomas, Reuben, Thai, Kevin, Barry, Jennifer, Wright, Graham A., Strauss, Bradley H., and Ghugre, Nilesh R.
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- 2021
- Full Text
- View/download PDF
42. BAF chromatin remodeling complex subunit diversity promotes temporally distinct gene expression programs in cardiogenesis
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Hota, Swetansu K, Johnson, Jeffrey R, Verschueren, Erik, Thomas, Reuben, Blotnick, Aaron M, Zhu, Yiwen, Sun, Xin, Pennacchio, Len A, Krogan, Nevan J, and Bruneau, Benoit G
- Subjects
Genetics ,Cardiovascular ,Heart Disease ,2.1 Biological and endogenous factors - Abstract
AbstractChromatin remodeling complexes instruct cellular differentiation and lineage specific transcription. The BRG1/BRM associated factor (BAF) complexes are important for several aspects of differentiation. We show that the catalytic subunit Brg1 has a specific role in cardiac precursors (CPs) to initiate cardiac gene expression programs and repress non-cardiac expression. Using immunoprecipitation with mass spectrometry (IP-MS), we determined the dynamic composition of BAF complexes during mammalian cardiac differentiation, and identified BAF60c (SMARCD3) and BAF170 (SMARCC2) as subunits enriched in CPs and cardiomyocytes (CM). Baf60c and Baf170 co-regulate gene expression with Brg1 in CPs, but in CMs control different gene expression programs, although still promoting a cardiac-specific gene set. BRG1, BAF60, and BAF170 all modulate chromatin accessibility, to either promote accessibility at activated genes, while closing up chromatin at repressed genes. BAF60c and BAF170 are required for proper BAF complex composition and stoichiometry, and promote BRG1 occupancy in CM. Additionally, BAF170 facilitates expulsion of BRG1-containing complexes in the transition from CP to CM. Thus, dynamic interdependent BAF complex subunit assembly modulates chromatin states and thereby directs temporal gene expression programs in cardiogenesis.Significance statementBRG1/BRM associated factors (BAF) form multi-subunit protein complexes that reorganize chromatin and regulate transcription. Specific BAF complex subunits have important roles during cell differentiation and development. We systematically identify BAF subunit composition and find temporal enrichment of subunits during cardiomyocyte differentiation. We find the catalytic subunit BRG1 has important contributions in initiating gene expression programs in cardiac progenitors along with cardiac-enriched subunits BAF60c and BAF170. Both these proteins regulated BAF subunit composition and chromatin accessibility and prevent expression of non-cardiac developmental genes during precursor to cardiomyocyte differentiation. Mechanistically, we find BAF170 destabilizes the BRG1 complex and expels BRG1 from cardiomyocyte-specific genes. Thus, our data shows synergies between diverse BAF subunits in facilitating temporal gene expression programs during cardiogenesis.
- Published
- 2017
43. Features that define the best ChIP-seq peak calling algorithms
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Thomas, Reuben, Thomas, Sean, Holloway, Alisha K, and Pollard, Katherine S
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Genetics ,Generic health relevance ,Algorithms ,Binding Sites ,Chromatin Immunoprecipitation ,High-Throughput Nucleotide Sequencing ,Histones ,Oligonucleotide Array Sequence Analysis ,Sequence Analysis ,DNA ,Transcription Factors ,ChIP-seq ,peak caller ,benchmark ,Biochemistry and Cell Biology ,Computation Theory and Mathematics ,Other Information and Computing Sciences ,Bioinformatics - Abstract
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is an important tool for studying gene regulatory proteins, such as transcription factors and histones. Peak calling is one of the first steps in the analysis of these data. Peak calling consists of two sub-problems: identifying candidate peaks and testing candidate peaks for statistical significance. We surveyed 30 methods and identified 12 features of the two sub-problems that distinguish methods from each other. We picked six methods GEM, MACS2, MUSIC, BCP, Threshold-based method (TM) and ZINBA] that span this feature space and used a combination of 300 simulated ChIP-seq data sets, 3 real data sets and mathematical analyses to identify features of methods that allow some to perform better than the others. We prove that methods that explicitly combine the signals from ChIP and input samples are less powerful than methods that do not. Methods that use windows of different sizes are more powerful than the ones that do not. For statistical testing of candidate peaks, methods that use a Poisson test to rank their candidate peaks are more powerful than those that use a Binomial test. BCP and MACS2 have the best operating characteristics on simulated transcription factor binding data. GEM has the highest fraction of the top 500 peaks containing the binding motif of the immunoprecipitated factor, with 50% of its peaks within 10 base pairs of a motif. BCP and MUSIC perform best on histone data. These findings provide guidance and rationale for selecting the best peak caller for a given application.
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- 2017
44. Cooperative activation of cardiac transcription through myocardin bridging of paired MEF2 sites.
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Anderson, Courtney M, Hu, Jianxin, Thomas, Reuben, Gainous, T Blair, Celona, Barbara, Sinha, Tanvi, Dickel, Diane E, Heidt, Analeah B, Xu, Shan-Mei, Bruneau, Benoit G, Pollard, Katherine S, Pennacchio, Len A, and Black, Brian L
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Myocardium ,Animals ,Mice ,Transgenic ,Trans-Activators ,Nuclear Proteins ,Transcription ,Genetic ,Enhancer Elements ,Genetic ,AMP-Activated Protein Kinases ,Protein Multimerization ,MEF2 Transcription Factors ,AMPK ,MEF2 ,Mouse ,Myocardin ,Prkaa2 ,Transcription ,Biological Sciences ,Medical and Health Sciences - Abstract
Enhancers frequently contain multiple binding sites for the same transcription factor. These homotypic binding sites often exhibit synergy, whereby the transcriptional output from two or more binding sites is greater than the sum of the contributions of the individual binding sites alone. Although this phenomenon is frequently observed, the mechanistic basis for homotypic binding site synergy is poorly understood. Here, we identify a bona fide cardiac-specific Prkaa2 enhancer that is synergistically activated by homotypic MEF2 binding sites. We show that two MEF2 sites in the enhancer function cooperatively due to bridging of the MEF2C-bound sites by the SAP domain-containing co-activator protein myocardin, and we show that paired sites buffer the enhancer from integration site-dependent effects on transcription in vivo Paired MEF2 sites are prevalent in cardiac enhancers, suggesting that this might be a common mechanism underlying synergy in the control of cardiac gene expression in vivo.
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- 2017
45. ML and GIS-Based Approaches to Flood Prediction: A Comparative Study
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Tewari, Abha, primary, Kshemkalyani, Varad, additional, Kukreja, Heer, additional, Menon, Pratheek, additional, and Thomas, Reuben, additional
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- 2021
- Full Text
- View/download PDF
46. A foundational atlas of autism protein interactions reveals molecular convergence
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Wang, Belinda, primary, Vartak, Rasika, additional, Zaltsman, Yefim, additional, Naing, Zun Zar Chi, additional, Hennick, Kelsey M., additional, Polacco, Benjamin J., additional, Bashir, Ali, additional, Eckhardt, Manon, additional, Bouhaddou, Mehdi, additional, Xu, Jiewei, additional, Sun, Nawei, additional, Lasser, Micaela C., additional, Zhou, Yuan, additional, McKetney, Justin, additional, Guiley, Keelan Z., additional, Chan, Una, additional, Kaye, Julia A., additional, Chadha, Nishant, additional, Cakir, Merve, additional, Gordon, Martin, additional, Khare, Prachi, additional, Drake, Sam, additional, Drury, Vanessa, additional, Burke, David F., additional, Gonzalez, Silvano, additional, Alkhairy, Sahar, additional, Thomas, Reuben, additional, Lam, Stephanie, additional, Morris, Montana, additional, Bader, Ethel, additional, Seyler, Meghan, additional, Baum, Tierney, additional, Krasnoff, Rebecca, additional, Wang, Sheng, additional, Pham, Presley, additional, Arbalaez, Juan, additional, Pratt, Dexter, additional, Chag, Shivali, additional, Mahmood, Nadir, additional, Rolland, Thomas, additional, Bourgeron, Thomas, additional, Finkbeiner, Steven, additional, Swaney, Danielle L., additional, Bandyopadhay, Sourav, additional, Ideker, Trey, additional, Beltrao, Pedro, additional, Willsey, Helen Rankin, additional, Obernier, Kirsten, additional, Nowakowski, Tomasz J., additional, Hüttenhain, Ruth, additional, State, Matthew W., additional, Willsey, A. Jeremy, additional, and Krogan, Nevan J., additional
- Published
- 2023
- Full Text
- View/download PDF
47. Disintermediating your friends : How online dating in the United States displaces other ways of meeting
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Rosenfeld, Michael J., Thomas, Reuben J., and Hausen, Sonia
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- 2019
48. Joining Young, Voting Young: The Effects of Youth Voluntary Associations on Early Adult Voting. CIRCLE Working Paper #73
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CIRCLE (The Center for Information and Research on Civic Learning and Engagement), Thomas, Reuben J., and McFarland, Daniel A.
- Abstract
Adolescent voluntary associations are particularly well positioned in the life course to encourage voting as youth become full citizens. Extracurriculars socialize students into voting by habituating them to civic engagement and by connecting them to politically engaged cultures. We establish this argument by testing the effects of high school extracurriculars on voting and the formation of political ideology in young adulthood, using two nationally representative longitudinal datasets and propensity score matching. We find that participation in general promotes voting, though some activities (notably, some sports) decrease it. Specific activities that encourage voting often have no political content, and their effects are not explained by the voting rates of peers in these groups. One of the biggest and most robust effects is for the performing arts: participation in high school performing arts is related to a higher rate of voting in early adulthood. Furthermore, some activities affect political ideology and party membership in adulthood, illustrating socialization into distinct political cultures. The overall pattern is that religious attendance and a few sports steer students to the conservative end of the political spectrum and into the Republican party, while academic clubs, drama clubs, and honor society steer students towards the liberal end and/or into the Democratic party. Schools can create environments that encourage extracurricular involvement through funding and policy. But they can also discourage extracurriculars through neglect. These results demonstrate that which activities thrive and which shrink will have an impact on future voting behaviors of young adults. (Contains 7 tables.)
- Published
- 2010
49. Improving Power to Detect Changes in Blood miRNA Expression by Accounting for Sources of Variability in Experimental Designs
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Daniels, Sarah I, Sillé, Fenna CM, Goldbaum, Audrey, Yee, Brenda, Key, Ellen F, Zhang, Luoping, Smith, Martyn T, and Thomas, Reuben
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Biomedical and Clinical Sciences ,Clinical Sciences ,Genetics ,Biotechnology ,Detection ,screening and diagnosis ,4.1 Discovery and preclinical testing of markers and technologies ,Healthy Volunteers ,Humans ,MicroRNAs ,Research Design ,Medical and Health Sciences ,Epidemiology ,Biomedical and clinical sciences ,Health sciences - Abstract
BackgroundBlood miRNAs are a new promising area of disease research, but variability in miRNA measurements may limit detection of true-positive findings. Here, we measured sources of miRNA variability and determine whether repeated measures can improve power to detect fold-change differences between comparison groups.MethodsBlood from healthy volunteers (N = 12) was collected at three time points. The miRNAs were extracted by a method predetermined to give the highest miRNA yield. Nine different miRNAs were quantified using different qPCR assays and analyzed using mixed models to identify sources of variability. A larger number of miRNAs from a publicly available blood miRNA microarray dataset with repeated measures were used for a bootstrapping procedure to investigate effects of repeated measures on power to detect fold changes in miRNA expression for a theoretical case-control study.ResultsTechnical variability in qPCR replicates was identified as a significant source of variability (P < 0.05) for all nine miRNAs tested. Variability was larger in the TaqMan qPCR assays (SD = 0.15-0.61) versus the qScript qPCR assays (SD = 0.08-0.14). Inter- and intraindividual and extraction variability also contributed significantly for two miRNAs. The bootstrapping procedure demonstrated that repeated measures (20%-50% of N) increased detection of a 2-fold change for approximately 10% to 45% more miRNAs.ConclusionStatistical power to detect small fold changes in blood miRNAs can be improved by accounting for sources of variability using repeated measures and choosing appropriate methods to minimize variability in miRNA quantification.ImpactThis study demonstrates the importance of including repeated measures in experimental designs for blood miRNA research. See all the articles in this CEBP Focus section, "Biomarkers, Biospecimens, and New Technologies in Molecular Epidemiology."
- Published
- 2014
50. Characterization of changes in gene expression and biochemical pathways at low levels of benzene exposure.
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Thomas, Reuben, Hubbard, Alan, McHale, Cliona, Zhang, Luoping, Rappaport, Stephen, Lan, Qing, Rothman, Nathaniel, Vermeulen, Roel, Guyton, Kathryn, Jinot, Jennifer, Sonawane, Babasaheb, and Smith, Martyn T.
- Subjects
Air Pollutants ,Occupational ,Benzene ,Blood Cell Count ,Cluster Analysis ,Female ,Gene Expression Profiling ,Gene Expression Regulation ,Humans ,Leukemia ,Myeloid ,Acute ,Male ,Metabolic Networks and Pathways ,Occupational Exposure - Abstract
Benzene, a ubiquitous environmental pollutant, causes acute myeloid leukemia (AML). Recently, through transcriptome profiling of peripheral blood mononuclear cells (PBMC), we reported dose-dependent effects of benzene exposure on gene expression and biochemical pathways in 83 workers exposed across four airborne concentration ranges (from 10 ppm) compared with 42 subjects with non-workplace ambient exposure levels. Here, we further characterize these dose-dependent effects with continuous benzene exposure in all 125 study subjects. We estimated air benzene exposure levels in the 42 environmentally-exposed subjects from their unmetabolized urinary benzene levels. We used a novel non-parametric, data-adaptive model selection method to estimate the change with dose in the expression of each gene. We describe non-parametric approaches to model pathway responses and used these to estimate the dose responses of the AML pathway and 4 other pathways of interest. The response patterns of majority of genes as captured by mean estimates of the first and second principal components of the dose-response for the five pathways and the profiles of 6 AML pathway response-representative genes (identified by clustering) exhibited similar apparent supra-linear responses. Responses at or below 0.1 ppm benzene were observed for altered expression of AML pathway genes and CYP2E1. Together, these data show that benzene alters disease-relevant pathways and genes in a dose-dependent manner, with effects apparent at doses as low as 100 ppb in air. Studies with extensive exposure assessment of subjects exposed in the low-dose range between 10 ppb and 1 ppm are needed to confirm these findings.
- Published
- 2014
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