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Guo K, Yombo DJK, Wang Z, Navaeiseddighi Z, Xu J, Schmit T, Ahamad N, Tripathi J, De Kumar B, Mathur R, Hur J, Sun J, Olszewski MA, Khan N. The chemokine receptor CXCR3 promotes CD8 + T cell-dependent lung pathology during influenza pathogenesis. Sci Adv 2024; 10:eadj1120. [PMID: 38170765 PMCID: PMC10776024 DOI: 10.1126/sciadv.adj1120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024]
Abstract
The dual role of CD8+ T cells in influenza control and lung pathology is increasingly appreciated. To explore whether protective and pathological functions can be linked to specific subsets, we dissected CD8+ T responses in influenza-infected murine lungs. Our single-cell RNA-sequencing (scRNA-seq) analysis revealed notable diversity in CD8+ T subpopulations during peak viral load and infection-resolved state. While enrichment of a Cxcr3hi CD8+ T effector subset was associated with a more robust cytotoxic response, both CD8+ T effector and central memory exhibited equally potent effector potential. The scRNA-seq analysis identified unique regulons regulating the cytotoxic response in CD8+ T cells. The late-stage CD8+ T blockade in influenza-cleared lungs or continuous CXCR3 blockade mitigated lung injury without affecting viral clearance. Furthermore, adoptive transfer of wild-type CD8+ T cells exacerbated influenza lung pathology in Cxcr3-/- mice. Collectively, our data imply that CXCR3 interception could have a therapeutic effect in preventing influenza-linked lung injury.
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Affiliation(s)
- Kai Guo
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dan J. K. Yombo
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Zhihan Wang
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | | | - Jintao Xu
- Research Service, Ann Arbor VA Health System, Department of Veterans Affairs Health System, Ann Arbor, MI 48109, USA
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Health System, Ann Arbor, MI 48109, USA
| | - Taylor Schmit
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Nassem Ahamad
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL 32610, USA
| | - Jitendra Tripathi
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Bony De Kumar
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Ramkumar Mathur
- Department of Geriatrics, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Junguk Hur
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Jie Sun
- Carter Immunology Center, University of Virginia, Charlottesville, VA 22908, USA
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA 22908, USA
| | - Michal A. Olszewski
- Research Service, Ann Arbor VA Health System, Department of Veterans Affairs Health System, Ann Arbor, MI 48109, USA
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Health System, Ann Arbor, MI 48109, USA
| | - Nadeem Khan
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL 32610, USA
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2
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Dastidar SG, De Kumar B, Lauckner B, Parrello D, Perley D, Vlasenok M, Tyagi A, Koney NKK, Abbas A, Nechaev S. Transcriptional responses of cancer cells to heat shock-inducing stimuli involve amplification of robust HSF1 binding. Nat Commun 2023; 14:7420. [PMID: 37973875 PMCID: PMC10654513 DOI: 10.1038/s41467-023-43157-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
Responses of cells to stimuli are increasingly discovered to involve the binding of sequence-specific transcription factors outside of known target genes. We wanted to determine to what extent the genome-wide binding and function of a transcription factor are shaped by the cell type versus the stimulus. To do so, we induced the Heat Shock Response pathway in two different cancer cell lines with two different stimuli and related the binding of its master regulator HSF1 to nascent RNA and chromatin accessibility. Here, we show that HSF1 binding patterns retain their identity between basal conditions and under different magnitudes of activation, so that common HSF1 binding is globally associated with distinct transcription outcomes. HSF1-induced increase in DNA accessibility was modest in scale, but occurred predominantly at remote genomic sites. Apart from regulating transcription at existing elements including promoters and enhancers, HSF1 binding amplified during responses to stimuli may engage inactive chromatin.
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Affiliation(s)
- Sayantani Ghosh Dastidar
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA
- Illumina, Inc., San Diego, CA, 92122, USA
| | - Bony De Kumar
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA
- Yale Center for Genome Analysis, Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Bo Lauckner
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA
| | - Damien Parrello
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA
| | - Danielle Perley
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA
- Canadian Centre for Computational Genomics, McGill Genome Centre, Montreal, QC, H3A0G1, Canada
| | - Maria Vlasenok
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
| | - Antariksh Tyagi
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA
- Yale Center for Genome Analysis, Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Nii Koney-Kwaku Koney
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA
- University of Ghana Medical School, University of Ghana, Accra, Ghana
| | - Ata Abbas
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Sergei Nechaev
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA.
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3
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Sun Z, Zhang Z, Banu K, Gibson IW, Colvin RB, Yi Z, Zhang W, De Kumar B, Reghuvaran A, Pell J, Manes TD, Djamali A, Gallon L, O’Connell PJ, He JC, Pober JS, Heeger PS, Menon MC. Multiscale genetic architecture of donor-recipient differences reveals intronic LIMS1 mismatches associated with kidney transplant survival. J Clin Invest 2023; 133:e170420. [PMID: 37676733 PMCID: PMC10617779 DOI: 10.1172/jci170420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 09/06/2023] [Indexed: 09/09/2023] Open
Abstract
Donor-recipient (D-R) mismatches outside of human leukocyte antigens (HLAs) contribute to kidney allograft loss, but the mechanisms remain unclear, specifically for intronic mismatches. We quantified non-HLA mismatches at variant-, gene-, and genome-wide scales from single nucleotide polymorphism (SNP) data of D-Rs from 2 well-phenotyped transplant cohorts: Genomics of Chronic Allograft Rejection (GoCAR; n = 385) and Clinical Trials in Organ Transplantation-01/17 (CTOT-01/17; n = 146). Unbiased gene-level screening in GoCAR uncovered the LIMS1 locus as the top-ranked gene where D-R mismatches associated with death-censored graft loss (DCGL). A previously unreported, intronic, LIMS1 haplotype of 30 SNPs independently associated with DCGL in both cohorts. Haplotype mismatches showed a dosage effect, and minor-allele introduction to major-allele-carrying recipients showed greater hazard of DCGL. The LIMS1 haplotype and the previously reported LIMS1 SNP rs893403 are expression quantitative trait loci (eQTL) in immune cells for GCC2 (not LIMS1), which encodes a protein involved in mannose-6-phosphase receptor (M6PR) recycling. Peripheral blood and T cell transcriptome analyses associated the GCC2 gene and LIMS1 SNPs with the TGF-β1/SMAD pathway, suggesting a regulatory effect. In vitro GCC2 modulation impacted M6PR-dependent regulation of active TGF-β1 and downstream signaling in T cells. Together, our data link LIMS1 locus D-R mismatches to DCGL via GCC2 eQTLs that modulate TGF-β1-dependent effects on T cells.
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Affiliation(s)
- Zeguo Sun
- Division of Nephrology, Department of Medicine
| | - Zhongyang Zhang
- Department of Genetics and Genomic Science, and
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Khadija Banu
- Department of Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Ian W. Gibson
- Max Rady college of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Zhengzi Yi
- Division of Nephrology, Department of Medicine
| | | | - Bony De Kumar
- Yale Center for Genomics, New Haven, Connecticut, USA
| | - Anand Reghuvaran
- Department of Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - John Pell
- Department of Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Thomas D. Manes
- Department of Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Lorenzo Gallon
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Philip J. O’Connell
- The Westmead Institute for Medical Research, University of Sydney, New South Wales, Australia
| | | | - Jordan S. Pober
- Department of Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Madhav C. Menon
- Department of Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
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4
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Afzal Z, Lange JJ, Nolte C, McKinney S, Wood C, Paulson A, De Kumar B, Unruh J, Slaughter BD, Krumlauf R. Shared retinoic acid responsive enhancers coordinately regulate nascent transcription of Hoxb coding and non-coding RNAs in the developing mouse neural tube. Development 2023; 150:dev201259. [PMID: 37102683 PMCID: PMC10233718 DOI: 10.1242/dev.201259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 04/19/2023] [Indexed: 04/28/2023]
Abstract
Signaling pathways regulate the patterns of Hox gene expression that underlie their functions in the specification of axial identity. Little is known about the properties of cis-regulatory elements and underlying transcriptional mechanisms that integrate graded signaling inputs to coordinately control Hox expression. Here, we optimized a single molecule fluorescent in situ hybridization (smFISH) technique with probes spanning introns to evaluate how three shared retinoic acid response element (RARE)-dependent enhancers in the Hoxb cluster regulate patterns of nascent transcription in vivo at the level of single cells in wild-type and mutant embryos. We predominately detect nascent transcription of only a single Hoxb gene in each cell, with no evidence for simultaneous co-transcriptional coupling of all or specific subsets of genes. Single and/or compound RARE mutations indicate that each enhancer differentially impacts global and local patterns of nascent transcription, suggesting that selectivity and competitive interactions between these enhancers is important to robustly maintain the proper levels and patterns of nascent Hoxb transcription. This implies that rapid and dynamic regulatory interactions potentiate transcription of genes through combined inputs from these enhancers in coordinating the retinoic acid response.
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Affiliation(s)
- Zainab Afzal
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Anatomy and Cell Biology Department, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Jeffrey J. Lange
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Christof Nolte
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Sean McKinney
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Christopher Wood
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Ariel Paulson
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jay Unruh
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Anatomy and Cell Biology Department, Kansas University Medical Center, Kansas City, KS 66160, USA
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5
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Pramio DT, Vieceli FM, Varella-Branco E, Goes CP, Kobayashi GS, da Silva Pelegrina DV, de Moraes BC, El Allam A, De Kumar B, Jara G, Farfel JM, Bennett DA, Kundu S, Viapiano MS, Reis EM, de Oliveira PSL, Dos Santos E Passos-Bueno MR, Rothlin CV, Ghosh S, Schechtman D. DNA methylation of the promoter region at the CREB1 binding site is a mechanism for the epigenetic regulation of brain-specific PKMζ. Biochim Biophys Acta Gene Regul Mech 2023; 1866:194909. [PMID: 36682583 PMCID: PMC10037092 DOI: 10.1016/j.bbagrm.2023.194909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 01/05/2023] [Accepted: 01/13/2023] [Indexed: 01/21/2023]
Abstract
Protein kinase M zeta, PKMζ, is a brain enriched kinase with a well characterized role in Long-Term Potentiation (LTP), the activity-dependent strengthening of synapses involved in long-term memory formation. However, little is known about the molecular mechanisms that maintain the tissue specificity of this kinase. Here, we characterized the epigenetic factors, mainly DNA methylation, regulating PKMζ expression in the human brain. The PRKCZ gene has an upstream promoter regulating Protein kinase C ζ (PKCζ), and an internal promoter driving PKMζ expression. A demethylated region, including a canonical CREB binding site, situated at the internal promoter was only observed in human CNS tissues. The induction of site-specific hypermethylation of this region resulted in decreased CREB1 binding and downregulation of PKMζ expression. Noteworthy, CREB binding sites were absent in the upstream promoter of PRKCZ locus, suggesting a specific mechanism for regulating PKMζ expression. These observations were validated using a system of human neuronal differentiation from induced pluripotent stem cells (iPSCs). CREB1 binding at the internal promoter was detected only in differentiated neurons, where PKMζ is expressed. The same epigenetic mechanism in the context of CREB binding site was identified in other genes involved in neuronal differentiation and LTP. Additionally, aberrant DNA hypermethylation at the internal promoter was observed in cases of Alzheimer's disease, correlating with decreased expression of PKMζ in patient brains. Altogether, we present a conserved epigenetic mechanism regulating PKMζ expression and other genes enhanced in the CNS with possible implications in neuronal differentiation and Alzheimer's disease.
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Affiliation(s)
| | | | | | - Carolina Purcell Goes
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, SP, Brazil; Laboratory of Neuromodulation of Experimental Pain, Department of Anatomy, Institute of Biomedical Sciences, University of Sao Paulo, SP, Brazil
| | | | | | | | - Aicha El Allam
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | | | - Gabriel Jara
- Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian National Biosciences Laboratory (LNBio) Campinas, SP, Brazil
| | - José Marcelo Farfel
- Traumatology and Orthopedy Department, Faculdade de Medicina, Universidade de São Paulo, SP, Brazil; Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Health Sciences Program, Instituto de Assistência Medica ao Servidor Público do Estado (IAMSPE), SP, Brazil
| | - David Alan Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Somanath Kundu
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Mariano S Viapiano
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Eduardo Moraes Reis
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, SP, Brazil
| | - Paulo Sergio Lopes de Oliveira
- Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian National Biosciences Laboratory (LNBio) Campinas, SP, Brazil
| | | | - Carla V Rothlin
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA; Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | - Sourav Ghosh
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA; Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA.
| | - Deborah Schechtman
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, SP, Brazil.
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6
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Chhoda A, Sharma A, Sailo B, Tang H, Ruzgar N, Tan WY, Ying L, Khatri R, Narayanan A, Mane S, De Kumar B, Wood LD, Iacobuzio-Donahue C, Wolfgang CL, Kunstman JW, Salem RR, Farrell JJ, Ahuja N. Utility of promoter hypermethylation in malignant risk stratification of intraductal papillary mucinous neoplasms. Clin Epigenetics 2023; 15:28. [PMID: 36803844 PMCID: PMC9942382 DOI: 10.1186/s13148-023-01429-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 01/14/2023] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND Intraductal papillary mucinous neoplasms (IPMNs), a type of cystic pancreatic cancer (PC) precursors, are increasingly identified on cross-sectional imaging and present a significant diagnostic challenge. While surgical resection of IPMN-related advanced neoplasia, i.e., IPMN-related high-grade dysplasia or PC, is an essential early PC detection strategy, resection is not recommended for IPMN-low-grade dysplasia (LGD) due to minimal risk of carcinogenesis, and significant procedural risks. Based on their promising results in prior validation studies targeting early detection of classical PC, DNA hypermethylation-based markers may serve as a biomarker for malignant risk stratification of IPMNs. This study investigates our DNA methylation-based PC biomarker panel (ADAMTS1, BNC1, and CACNA1G genes) in differentiating IPMN-advanced neoplasia from IPMN-LGDs. METHODS Our previously described genome-wide pharmaco-epigenetic method identified multiple genes as potential targets for PC detection. The combination was further optimized and validated for early detection of classical PC in previous case-control studies. These promising genes were evaluated among micro-dissected IPMN tissue (IPMN-LGD: 35, IPMN-advanced neoplasia: 35) through Methylation-Specific PCR. The discriminant capacity of individual and combination of genes were delineated through Receiver Operating Characteristics curve analysis. RESULTS As compared to IPMN-LGDs, IPMN-advanced neoplasia had higher hypermethylation frequency of candidate genes: ADAMTS1 (60% vs. 14%), BNC1 (66% vs. 3%), and CACGNA1G (25% vs. 0%). We observed Area Under Curve (AUC) values of 0.73 for ADAMTS1, 0.81 for BNC1, and 0.63 for CACNA1G genes. The combination of the BNC1/ CACNA1G genes resulted in an AUC of 0.84, sensitivity of 71%, and specificity of 97%. Combining the methylation status of the BNC1/CACNA1G genes, blood-based CA19-9, and IPMN lesion size enhanced the AUC to 0.92. CONCLUSION DNA-methylation based biomarkers have shown a high diagnostic specificity and moderate sensitivity for differentiating IPMN-advanced neoplasia from LGDs. Addition of specific methylation targets can improve the accuracy of the methylation biomarker panel and enable the development of noninvasive IPMN stratification biomarkers.
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Affiliation(s)
- Ankit Chhoda
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, USA
| | - Anup Sharma
- Department of Surgery, Yale School of Medicine, New Haven, USA
| | - Bethsebie Sailo
- Department of Surgery, Yale School of Medicine, New Haven, USA
| | - Haoyu Tang
- Yale Systems Biology Institute, Yale University, New Haven, USA
| | - Nensi Ruzgar
- Department of Surgery, Yale School of Medicine, New Haven, USA
| | - Wan Ying Tan
- Department of Surgery, Yale School of Medicine, New Haven, USA
| | - Lee Ying
- Department of Surgery, Yale School of Medicine, New Haven, USA
| | - Rishabh Khatri
- Department of Internal Medicine, Temple University Hospital, Philadelphia, USA
| | | | | | | | - Laura D Wood
- Department of Pathology, Johns Hopkins University, Baltimore, USA
| | | | | | - John W Kunstman
- Department of Surgery, Yale School of Medicine, New Haven, USA
| | - Ronald R Salem
- Department of Surgery, Yale School of Medicine, New Haven, USA
| | - James J Farrell
- Section of Digestive Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, USA.
| | - Nita Ahuja
- Department of Surgery, Yale School of Medicine, New Haven, USA.
- Section of Digestive Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, USA.
- Department of Pathology, Yale School of Medicine, New Haven, USA.
- Department of Biological and Biomedical Sciences, Yale School of Medicine, New Haven, USA.
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7
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Filardi BA, Monteiro VS, Schwartzmann PV, do Prado Martins V, Zucca LER, Baiocchi GC, Malik AA, Silva J, Hahn AM, Chen NFG, Pham K, Pérez-Then E, Miric M, Brache V, Cochon L, Larocca RA, Mendez RDR, Bardini Silveira D, Pinto AR, Croda J, Yildirim I, Omer SB, Ko AI, Vermund SH, Grubaugh ND, Iwasaki A, Lucas C, Vogels CBF, Breban M, Koch TR, Chaguza C, Tikhonova I, Castaldi C, Mane S, De Kumar B, Ferguson D, Kerantzas N, Peaper D, Landry ML, Schulz W. Age-dependent impairment in antibody responses elicited by a homologous CoronaVac booster dose. Sci Transl Med 2023; 15:eade6023. [PMID: 36791210 DOI: 10.1126/scitranslmed.ade6023] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
The emergence of the SARS-CoV-2 Omicron sublineages resulted in increased transmission rates and reduced protection from vaccines. To counteract these effects, multiple booster strategies were used in different countries, although data comparing their efficiency in improving protective immunity remain sparse, especially among vulnerable populations, including older adults. The inactivated CoronaVac vaccine was among the most widely distributed vaccine worldwide and was essential in the early control of SARS-CoV-2-related hospitalizations and deaths. However, it is not well understood whether homologous versus heterologous booster doses in those fully vaccinated with CoronaVac induce distinct humoral responses or whether these responses vary across age groups. We analyzed plasma antibody responses from CoronaVac-vaccinated younger or older individuals who received a homologous CoronaVac or heterologous BNT162b2 or ChAdOx1 booster vaccine. All three evaluated boosters resulted in increased virus-specific IgG titers 28 days after the booster dose. However, we found that both IgG titers against SARS-CoV-2 Spike or RBD and neutralization titers against Omicron sublineages were substantially reduced in participants who received homologous CoronaVac compared with the heterologous BNT162b2 or ChAdOx1 booster. This effect was specifically prominent in recipients >50 years of age. In this group, the CoronaVac booster induced low virus-specific IgG titers and failed to elevate neutralization titers against any Omicron sublineage. Our results point to the notable inefficiency of CoronaVac immunization and boosting in mounting protective antiviral humoral immunity, particularly among older adults, during the Omicron wave. These observations also point to benefits of heterologous regimens in high-risk populations fully vaccinated with CoronaVac.
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Affiliation(s)
- Bruno Andraus Filardi
- Instituto do Cancer Brasil - Unidade de Ribeirão Preto, São Paulo, São Paulo, Brazil.,Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, São Paulo, São Paulo, Brazil
| | | | - Pedro Vellosa Schwartzmann
- Intensive Cardiac Unit, Hospital Unimed Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil.,Advanced Research Center - CAPED, Centro Médico Ribeirão Shopping, Ribeirão Preto, São Paulo, Brazil
| | | | | | - Gabriela Crispim Baiocchi
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Amyn A Malik
- Yale Institute for Global Health, Yale University, New Haven, CT, USA.,Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Julio Silva
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Nicholas F G Chen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Kien Pham
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Eddy Pérez-Then
- Ministry of Health, Santo Domingo, Dominican Republic.,Two Oceans in Health, Santo Domingo, Dominican Republic
| | - Marija Miric
- Two Oceans in Health, Santo Domingo, Dominican Republic
| | - Vivian Brache
- Profamilia, Biomedical Research Department, Santo Domingo, Dominican Republic
| | - Leila Cochon
- Intensive Cardiac Unit, Hospital Unimed Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Rafael A Larocca
- Center of Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | | | - Douglas Bardini Silveira
- Laboratório de Imunologia Aplicada, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Aguinaldo Roberto Pinto
- Laboratório de Imunologia Aplicada, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Julio Croda
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.,Oswaldo Cruz Foundation Mato Grosso do Sul, Campo Grande, Brazil.,Federal University of Mato Grosso do Sul, Campo Grande, Brazil
| | - Inci Yildirim
- Yale Institute for Global Health, Yale University, New Haven, CT, USA.,Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.,Department of Pediatric, Section of Infectious Diseases and Global Health, Yale University School of Medicine, New Haven, CT, USA
| | - Saad B Omer
- Yale Institute for Global Health, Yale University, New Haven, CT, USA.,Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA.,Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Albert I Ko
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA.,Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.,Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, BA, Brazil
| | - Sten H Vermund
- Department of Pediatric, Section of Infectious Diseases and Global Health, Yale University School of Medicine, New Haven, CT, USA.,Yale School of Public Health, New Haven, CT, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.,Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.,Center for Infection and Immunity, Yale University, New Haven, CT, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Carolina Lucas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.,Center for Infection and Immunity, Yale University, New Haven, CT, USA
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8
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Chaguza C, Coppi A, Earnest R, Ferguson D, Kerantzas N, Warner F, Young HP, Breban MI, Billig K, Koch RT, Pham K, Kalinich CC, Ott IM, Fauver JR, Hahn AM, Tikhonova IR, Castaldi C, De Kumar B, Pettker CM, Warren JL, Weinberger DM, Landry ML, Peaper DR, Schulz W, Vogels CBF, Grubaugh ND. Rapid emergence of SARS-CoV-2 Omicron variant is associated with an infection advantage over Delta in vaccinated persons. Med 2022; 3:325-334.e4. [PMID: 35399324 PMCID: PMC8983481 DOI: 10.1016/j.medj.2022.03.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 03/25/2021] [Accepted: 03/29/2022] [Indexed: 11/30/2022]
Abstract
Background The SARS-CoV-2 Omicron variant became a global concern due to its rapid spread and displacement of the dominant Delta variant. We hypothesized that part of Omicron's rapid rise was based on its increased ability to cause infections in persons that are vaccinated compared to Delta. Methods We analyzed nasal swab PCR tests for samples collected between December 12 and 16, 2021, in Connecticut when the proportion of Delta and Omicron variants was relatively equal. We used the spike gene target failure (SGTF) to classify probable Delta and Omicron infections. We fitted an exponential curve to the estimated infections to determine the doubling times for each variant. We compared the test positivity rates for each variant by vaccination status, number of doses, and vaccine manufacturer. Generalized linear models were used to assess factors associated with odds of infection with each variant among persons testing positive for SARS-CoV-2. Findings For infections with high virus copies (Ct < 30) among vaccinated persons, we found higher odds that they were infected with Omicron compared to Delta, and that the odds increased with increased number of vaccine doses. Compared to unvaccinated persons, we found significant reduction in Delta positivity rates after two (43.4%-49.1%) and three vaccine doses (81.1%), while we only found a significant reduction in Omicron positivity rates after three doses (62.3%). Conclusion The rapid rise in Omicron infections was likely driven by Omicron's escape from vaccine-induced immunity. Funding This work was supported by the Centers for Disease Control and Prevention (CDC).
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Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Andreas Coppi
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Rebecca Earnest
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - David Ferguson
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Nicholas Kerantzas
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Frederick Warner
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - H Patrick Young
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Kendall Billig
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Robert Tobias Koch
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Kien Pham
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Chaney C Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Isabel M Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Joseph R Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Irina R Tikhonova
- Yale Center for Genome Analysis, Yale University, New Haven, CT, USA
| | | | - Bony De Kumar
- Yale Center for Genome Analysis, Yale University, New Haven, CT, USA
| | - Christian M Pettker
- Quality and Safety, Yale New Haven Health, New Haven, CT, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Joshua L Warren
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Daniel M Weinberger
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Marie L Landry
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Section of Infectious Diseases, Department of Medicine, Yale School of Medicine, New Haven, CT, USA
- Clinical Virology Laboratory, Yale New Haven Hospital, New Haven, CT, USA
| | - David R Peaper
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Wade Schulz
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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9
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Chaguza C, Coppi A, Earnest R, Ferguson D, Kerantzas N, Warner F, Young HP, Breban MI, Billig K, Koch RT, Pham K, Kalinich CC, Ott IM, Fauver JR, Hahn AM, Tikhonova IR, Castaldi C, De Kumar B, Pettker CM, Warren JL, Weinberger DM, Landry ML, Peaper DR, Schulz W, Vogels CBF, Grubaugh ND. Rapid emergence of SARS-CoV-2 Omicron variant is associated with an infection advantage over Delta in vaccinated persons. Med 2022; 3:325-334.e4. [PMID: 35399324 DOI: 10.1101/2022.01.22.22269660] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 03/25/2021] [Accepted: 03/29/2022] [Indexed: 05/22/2023]
Abstract
BACKGROUND The SARS-CoV-2 Omicron variant became a global concern due to its rapid spread and displacement of the dominant Delta variant. We hypothesized that part of Omicron's rapid rise was based on its increased ability to cause infections in persons that are vaccinated compared to Delta. METHODS We analyzed nasal swab PCR tests for samples collected between December 12 and 16, 2021, in Connecticut when the proportion of Delta and Omicron variants was relatively equal. We used the spike gene target failure (SGTF) to classify probable Delta and Omicron infections. We fitted an exponential curve to the estimated infections to determine the doubling times for each variant. We compared the test positivity rates for each variant by vaccination status, number of doses, and vaccine manufacturer. Generalized linear models were used to assess factors associated with odds of infection with each variant among persons testing positive for SARS-CoV-2. FINDINGS For infections with high virus copies (Ct < 30) among vaccinated persons, we found higher odds that they were infected with Omicron compared to Delta, and that the odds increased with increased number of vaccine doses. Compared to unvaccinated persons, we found significant reduction in Delta positivity rates after two (43.4%-49.1%) and three vaccine doses (81.1%), while we only found a significant reduction in Omicron positivity rates after three doses (62.3%). CONCLUSION The rapid rise in Omicron infections was likely driven by Omicron's escape from vaccine-induced immunity. FUNDING This work was supported by the Centers for Disease Control and Prevention (CDC).
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Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Andreas Coppi
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Rebecca Earnest
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - David Ferguson
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Nicholas Kerantzas
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Frederick Warner
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - H Patrick Young
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Kendall Billig
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Robert Tobias Koch
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Kien Pham
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Chaney C Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Isabel M Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Joseph R Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Irina R Tikhonova
- Yale Center for Genome Analysis, Yale University, New Haven, CT, USA
| | | | - Bony De Kumar
- Yale Center for Genome Analysis, Yale University, New Haven, CT, USA
| | - Christian M Pettker
- Quality and Safety, Yale New Haven Health, New Haven, CT, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Joshua L Warren
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Daniel M Weinberger
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Marie L Landry
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Section of Infectious Diseases, Department of Medicine, Yale School of Medicine, New Haven, CT, USA
- Clinical Virology Laboratory, Yale New Haven Hospital, New Haven, CT, USA
| | - David R Peaper
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Wade Schulz
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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Earnest R, Uddin R, Matluk N, Renzette N, Turbett SE, Siddle KJ, Loreth C, Adams G, Tomkins-Tinch CH, Petrone ME, Rothman JE, Breban MI, Koch RT, Billig K, Fauver JR, Vogels CBF, Bilguvar K, De Kumar B, Landry ML, Peaper DR, Kelly K, Omerza G, Grieser H, Meak S, Martha J, Dewey HB, Kales S, Berenzy D, Carpenter-Azevedo K, King E, Huard RC, Novitsky V, Howison M, Darpolor J, Manne A, Kantor R, Smole SC, Brown CM, Fink T, Lang AS, Gallagher GR, Pitzer VE, Sabeti PC, Gabriel S, MacInnis BL, Tewhey R, Adams MD, Park DJ, Lemieux JE, Grubaugh ND. Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA. Cell Rep Med 2022; 3:100583. [PMID: 35480627 PMCID: PMC8913280 DOI: 10.1016/j.xcrm.2022.100583] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/30/2021] [Accepted: 03/01/2022] [Indexed: 12/11/2022]
Abstract
The SARS-CoV-2 Delta variant rose to dominance in mid-2021, likely propelled by an estimated 40%-80% increased transmissibility over Alpha. To investigate if this ostensible difference in transmissibility is uniform across populations, we partner with public health programs from all six states in New England in the United States. We compare logistic growth rates during each variant's respective emergence period, finding that Delta emerged 1.37-2.63 times faster than Alpha (range across states). We compute variant-specific effective reproductive numbers, estimating that Delta is 63%-167% more transmissible than Alpha (range across states). Finally, we estimate that Delta infections generate on average 6.2 (95% CI 3.1-10.9) times more viral RNA copies per milliliter than Alpha infections during their respective emergence. Overall, our evidence suggests that Delta's enhanced transmissibility can be attributed to its innate ability to increase infectiousness, but its epidemiological dynamics may vary depending on underlying population attributes and sequencing data availability.
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Affiliation(s)
- Rebecca Earnest
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA.
| | - Rockib Uddin
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nicholas Matluk
- Maine Center for Disease Control and Prevention, Augusta, ME 04333, USA; Health and Environmental Testing Laboratory, Augusta, ME 04333, USA
| | - Nicholas Renzette
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Sarah E Turbett
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | | | - Gordon Adams
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Mary E Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Jessica E Rothman
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Robert Tobias Koch
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Kendall Billig
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Joseph R Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Kaya Bilguvar
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA; Departments of Neurosurgery and Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Medical Genetics, Acibadem University School of Medicine, Istanbul, Turkey
| | - Bony De Kumar
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA
| | - Marie L Landry
- Departments of Laboratory Medicine and Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - David R Peaper
- Departments of Laboratory Medicine and Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Kevin Kelly
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Greg Omerza
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Heather Grieser
- Maine Center for Disease Control and Prevention, Augusta, ME 04333, USA; Health and Environmental Testing Laboratory, Augusta, ME 04333, USA
| | - Sim Meak
- Maine Center for Disease Control and Prevention, Augusta, ME 04333, USA; Health and Environmental Testing Laboratory, Augusta, ME 04333, USA
| | - John Martha
- Maine Center for Disease Control and Prevention, Augusta, ME 04333, USA; Health and Environmental Testing Laboratory, Augusta, ME 04333, USA
| | | | - Susan Kales
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | | | | | - Ewa King
- Rhode Island Department of Health, State Health Laboratories, Providence, RI 02904, USA
| | - Richard C Huard
- Rhode Island Department of Health, State Health Laboratories, Providence, RI 02904, USA
| | - Vlad Novitsky
- Division of Infectious Diseases, Brown University Alpert Medical School, Providence, RI 02906, USA
| | - Mark Howison
- Research Improving People's Lives, Providence, RI 02903, USA
| | - Josephine Darpolor
- Division of Infectious Diseases, Brown University Alpert Medical School, Providence, RI 02906, USA
| | - Akarsh Manne
- Division of Infectious Diseases, Brown University Alpert Medical School, Providence, RI 02906, USA
| | - Rami Kantor
- Division of Infectious Diseases, Brown University Alpert Medical School, Providence, RI 02906, USA
| | - Sandra C Smole
- Massachusetts Department of Public Health, Boston, MA 02130, USA
| | | | - Timelia Fink
- Massachusetts Department of Public Health, Boston, MA 02130, USA
| | - Andrew S Lang
- Massachusetts Department of Public Health, Boston, MA 02130, USA
| | - Glen R Gallagher
- Massachusetts Department of Public Health, Boston, MA 02130, USA
| | - Virginia E Pitzer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Stacey Gabriel
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Ryan Tewhey
- Department of Medical Genetics, Acibadem University School of Medicine, Istanbul, Turkey; Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA 02111, USA; Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469, USA
| | - Mark D Adams
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Daniel J Park
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jacob E Lemieux
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06510, USA.
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11
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Parker HJ, De Kumar B, Pushel I, Bronner ME, Krumlauf R. Analysis of lamprey meis genes reveals that conserved inputs from Hox, Meis and Pbx proteins control their expression in the hindbrain and neural tube. Dev Biol 2021; 479:61-76. [PMID: 34310923 DOI: 10.1016/j.ydbio.2021.07.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 06/10/2021] [Accepted: 07/22/2021] [Indexed: 11/23/2022]
Abstract
Meis genes are known to play important roles in the hindbrain and neural crest cells of jawed vertebrates. To explore the roles of Meis genes in head development during evolution of vertebrates, we have identified four meis genes in the sea lamprey genome and characterized their patterns of expression and regulation, with a focus on the hindbrain and pharynx. Each of the lamprey meis genes displays temporally and spatially dynamic patterns of expression, some of which are coupled to rhombomeric domains in the developing hindbrain and select pharyngeal arches. Studies of Meis loci in mouse and zebrafish have identified enhancers that are bound by Hox and TALE (Meis and Pbx) proteins, implicating these factors in the direct regulation of Meis expression. We examined the lamprey meis loci and identified a series of cis-elements conserved between lamprey and jawed vertebrate meis genes. In transgenic reporter assays we demonstrated that these elements act as neural enhancers in lamprey embryos, directing reporter expression in appropriate domains when compared to expression of their associated endogenous meis gene. Sequence alignments reveal that these conserved elements are in similar relative positions of the meis loci and contain a series of consensus binding motifs for Hox and TALE proteins. This suggests that ancient Hox and TALE-responsive enhancers regulated expression of ancestral vertebrate meis genes in segmental domains in the hindbrain and have been retained in the meis loci during vertebrate evolution. The presence of conserved Meis, Pbx and Hox binding sites in these lamprey enhancers links Hox and TALE factors to regulation of lamprey meis genes in the developing hindbrain, indicating a deep ancestry for these regulatory interactions prior to the divergence of jawed and jawless vertebrates.
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Affiliation(s)
- Hugo J Parker
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Irina Pushel
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA; Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, KS, 66160, USA.
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12
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Earnest R, Uddin R, Matluk N, Renzette N, Siddle KJ, Loreth C, Adams G, Tomkins-Tinch CH, Petrone ME, Rothman JE, Breban MI, Koch RT, Billig K, Fauver JR, Vogels CB, Turbett S, Bilguvar K, De Kumar B, Landry ML, Peaper DR, Kelly K, Omerza G, Grieser H, Meak S, Martha J, Dewey HH, Kales S, Berenzy D, Carpenter-Azevedo K, King E, Huard RC, Smole SC, Brown CM, Fink T, Lang AS, Gallagher GR, Sabeti PC, Gabriel S, MacInnis BL, Tewhey R, Adams MD, Park DJ, Lemieux JE, Grubaugh ND. Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA. medRxiv 2021:2021.10.06.21264641. [PMID: 34642698 PMCID: PMC8509091 DOI: 10.1101/2021.10.06.21264641] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant quickly rose to dominance in mid-2021, displacing other variants, including Alpha. Studies using data from the United Kingdom and India estimated that Delta was 40-80% more transmissible than Alpha, allowing Delta to become the globally dominant variant. However, it was unclear if the ostensible difference in relative transmissibility was due mostly to innate properties of Delta's infectiousness or differences in the study populations. To investigate, we formed a partnership with SARS-CoV-2 genomic surveillance programs from all six New England US states. By comparing logistic growth rates, we found that Delta emerged 37-163% faster than Alpha in early 2021 (37% Massachusetts, 75% New Hampshire, 95% Maine, 98% Rhode Island, 151% Connecticut, and 163% Vermont). We next computed variant-specific effective reproductive numbers and estimated that Delta was 58-120% more transmissible than Alpha across New England (58% New Hampshire, 68% Massachusetts, 76% Connecticut, 85% Rhode Island, 98% Maine, and 120% Vermont). Finally, using RT-PCR data, we estimated that Delta infections generate on average ∼6 times more viral RNA copies per mL than Alpha infections. Overall, our evidence indicates that Delta's enhanced transmissibility could be attributed to its innate ability to increase infectiousness, but its epidemiological dynamics may vary depending on the underlying immunity and behavior of distinct populations.
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Affiliation(s)
- Rebecca Earnest
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Rockib Uddin
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nicholas Matluk
- Maine Center for Disease Control and Prevention, Augusta, ME 04333
- Health and Environmental Testing Laboratory, Augusta, ME 04333
| | - Nicholas Renzette
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | | | | | - Gordon Adams
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Mary E. Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Jessica E. Rothman
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Robert Tobias Koch
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Kendall Billig
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Joseph R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Chantal B.F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Sarah Turbett
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kaya Bilguvar
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA
- Departments of Neurosurgery and Genetics, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Medical Genetics, Acibadem University School of Medicine, Istanbul, Turkey
| | - Bony De Kumar
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA
| | - Marie L. Landry
- Departments of Laboratory Medicine and Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - David R. Peaper
- Departments of Laboratory Medicine and Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Kevin Kelly
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Greg Omerza
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Heather Grieser
- Maine Center for Disease Control and Prevention, Augusta, ME 04333
- Health and Environmental Testing Laboratory, Augusta, ME 04333
| | - Sim Meak
- Maine Center for Disease Control and Prevention, Augusta, ME 04333
- Health and Environmental Testing Laboratory, Augusta, ME 04333
| | - John Martha
- Maine Center for Disease Control and Prevention, Augusta, ME 04333
- Health and Environmental Testing Laboratory, Augusta, ME 04333
| | | | - Susan Kales
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | | | | | - Ewa King
- Rhode Island Department of Health, State Health Laboratories, Providence, RI 02904, USA
| | - Richard C. Huard
- Rhode Island Department of Health, State Health Laboratories, Providence, RI 02904, USA
| | - Sandra C. Smole
- Massachusetts Department of Public Health, Boston MA 02130, USA
| | | | - Timelia Fink
- Massachusetts Department of Public Health, Boston MA 02130, USA
| | - Andrew S. Lang
- Massachusetts Department of Public Health, Boston MA 02130, USA
| | | | | | - Stacey Gabriel
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Ryan Tewhey
- Department of Medical Genetics, Acibadem University School of Medicine, Istanbul, Turkey
- Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA 02111, USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469, USA
| | - Mark D. Adams
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Daniel J. Park
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jacob E. Lemieux
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06510, USA
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13
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Ansari KI, Bhan A, Saotome M, Tyagi A, De Kumar B, Chen C, Takaku M, Jandial R. Autocrine GM-CSF signaling contributes to growth of HER2+ breast leptomeningeal carcinomatosis. Cancer Res 2021; 81:4723-4735. [PMID: 34247146 DOI: 10.1158/0008-5472.can-21-0259] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 05/29/2021] [Accepted: 07/08/2021] [Indexed: 11/16/2022]
Abstract
Leptomeningeal carcinomatosis (LC) occurs when tumor cells spread to the cerebrospinal fluid-containing leptomeninges surrounding the brain and spinal cord. LC is an ominous complication of cancer with a dire prognosis. Although any malignancy can spread to the leptomeninges, breast cancer, particularly the HER2+ subtype, is its most common origin. HER2+ breast LC (HER2+ LC) remains incurable, with few treatment options, and the molecular mechanisms underlying proliferation of HER2+ breast cancer cells in the acellular, protein, and cytokine-poor leptomeningeal environment remain elusive. Therefore, we sought to characterize signaling pathways that drive HER2+ LC development as well as those that restrict its growth to leptomeninges. Primary HER2+ LC patient-derived ("Lepto") cell lines in co-culture with various central nervous system (CNS) cell types revealed that oligodendrocyte progenitor cells (OPC), the largest population of dividing cells in the CNS, inhibited HER2+ LC growth in vitro and in vivo, thereby limiting the spread of HER2+ LC beyond the leptomeninges. Cytokine array-based analyses identified Lepto cell-secreted granulocyte-macrophage colony-stimulating factor (GM-CSF) as an oncogenic autocrine driver of HER2+ LC growth. Liquid chromatography-tandem mass spectrometry-based analyses revealed that the OPC-derived protein TPP1 proteolytically degrades GM-CSF, decreasing GM-CSF signaling and leading to suppression of HER2+ LC growth and limiting its spread. Lastly, intrathecal delivery of neutralizing anti-GM-CSF antibodies and a pan-Aurora kinase inhibitor (CCT137690) synergistically inhibited GM-CSF and suppressed activity of GM-CSF effectors, reducing HER2+ LC growth in vivo. Thus, OPC suppress GM-CSF-driven growth of HER2+ LC in the leptomeningeal environment, providing a potential targetable axis.
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14
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Singh NP, De Kumar B, Paulson A, Parrish ME, Zhang Y, Florens L, Conaway JW, Si K, Krumlauf R. A six-amino-acid motif is a major determinant in functional evolution of HOX1 proteins. Genes Dev 2020; 34:1680-1696. [PMID: 33184220 PMCID: PMC7706710 DOI: 10.1101/gad.342329.120] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/09/2020] [Indexed: 01/19/2023]
Abstract
Gene duplication and divergence is a major driver in the emergence of evolutionary novelties. How variations in amino acid sequences lead to loss of ancestral activity and functional diversification of proteins is poorly understood. We used cross-species functional analysis of Drosophila Labial and its mouse HOX1 orthologs (HOXA1, HOXB1, and HOXD1) as a paradigm to address this issue. Mouse HOX1 proteins display low (30%) sequence similarity with Drosophila Labial. However, substituting endogenous Labial with the mouse proteins revealed that HOXA1 has retained essential ancestral functions of Labial, while HOXB1 and HOXD1 have diverged. Genome-wide analysis demonstrated similar DNA-binding patterns of HOXA1 and Labial in mouse cells, while HOXB1 binds to distinct targets. Compared with HOXB1, HOXA1 shows an enrichment in co-occupancy with PBX proteins on target sites and exists in the same complex with PBX on chromatin. Functional analysis of HOXA1-HOXB1 chimeric proteins uncovered a novel six-amino-acid C-terminal motif (CTM) flanking the homeodomain that serves as a major determinant of ancestral activity. In vitro DNA-binding experiments and structural prediction show that CTM provides an important domain for interaction of HOXA1 proteins with PBX. Our findings show that small changes outside of highly conserved DNA-binding regions can lead to profound changes in protein function.
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Affiliation(s)
| | - Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Ariel Paulson
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Mark E Parrish
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Ying Zhang
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Joan W Conaway
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA.,Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, Kansas 66160, USA
| | - Kausik Si
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA.,Department of Molecular and Integrative Physiology, Kansas University Medical Center, Kansas City, Kansas 66160, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA.,Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, Kansas 66160, USA
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15
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Takaku M, Grimm SA, De Kumar B, Bennett BD, Wade PA. Cancer-specific mutation of GATA3 disrupts the transcriptional regulatory network governed by Estrogen Receptor alpha, FOXA1 and GATA3. Nucleic Acids Res 2020; 48:4756-4768. [PMID: 32232341 DOI: 10.1093/nar/gkaa179] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 02/27/2020] [Accepted: 03/11/2020] [Indexed: 11/15/2022] Open
Abstract
Estrogen receptors (ER) are activated by the steroid hormone 17β-estradiol. Estrogen receptor alpha (ER-α) forms a regulatory network in mammary epithelial cells and in breast cancer with the transcription factors FOXA1 and GATA3. GATA3 is one of the most frequently mutated genes in breast cancer and is capable of specifying chromatin localization of FOXA1 and ER-α. How GATA3 mutations found in breast cancer impact genomic localization of ER-α and the transcriptional network downstream of ER-α and FOXA1 remains unclear. Here, we investigate the function of a recurrent patient-derived GATA3 mutation (R330fs) on this regulatory network. Genomic analysis indicates that the R330fs mutant can disrupt localization of ER-α and FOXA1. Loci co-bound by all three factors are enriched for genes integral to mammary gland development as well as epithelial cell biology. This gene set is differentially regulated in GATA3 mutant cells in culture and in tumors bearing similar mutations in vivo. The altered distribution of ER-α and FOXA1 in GATA3-mutant cells is associated with altered chromatin architecture, which leads to differential gene expression. These results suggest an active role for GATA3 zinc finger 2 mutants in ER-α positive breast tumors.
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Affiliation(s)
- Motoki Takaku
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA.,Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Sara A Grimm
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Bony De Kumar
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA
| | - Brian D Bennett
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Paul A Wade
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
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16
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Rodriquez M, Shetty M, Black E, Kretschmar M, Perley D, De Kumar B, Henry LK. Analysis of DNA Methylation Changes in Mice Mediated by Early‐life Exposure to the Antidepressant S‐citalopram. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.06398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Meghan Rodriquez
- University of North Dakota School of Medicine and Health Sciences
| | - Madhur Shetty
- University of North Dakota School of Medicine and Health Sciences
| | - Elizabeth Black
- University of North Dakota School of Medicine and Health Sciences
| | | | - Danielle Perley
- University of North Dakota School of Medicine and Health Sciences
| | - Bony De Kumar
- University of North Dakota School of Medicine and Health Sciences
| | - L. Keith Henry
- University of North Dakota School of Medicine and Health Sciences
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17
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Qian P, De Kumar B, He XC, Nolte C, Gogol M, Ahn Y, Chen S, Li Z, Xu H, Perry JM, Hu D, Tao F, Zhao M, Han Y, Hall K, Peak A, Paulson A, Zhao C, Venkatraman A, Box A, Perera A, Haug JS, Parmely T, Li H, Krumlauf R, Li L. Retinoid-Sensitive Epigenetic Regulation of the Hoxb Cluster Maintains Normal Hematopoiesis and Inhibits Leukemogenesis. Cell Stem Cell 2019; 22:740-754.e7. [PMID: 29727682 DOI: 10.1016/j.stem.2018.04.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 09/15/2017] [Accepted: 04/13/2018] [Indexed: 12/16/2022]
Abstract
Hox genes modulate the properties of hematopoietic stem cells (HSCs) and reacquired Hox expression in progenitors contributes to leukemogenesis. Here, our transcriptome and DNA methylome analyses revealed that Hoxb cluster and retinoid signaling genes are predominantly enriched in LT-HSCs, and this coordinate regulation of Hoxb expression is mediated by a retinoid-dependent cis-regulatory element, distal element RARE (DERARE). Deletion of the DERARE reduced Hoxb expression, resulting in changes to many downstream signaling pathways (e.g., non-canonical Wnt signaling) and loss of HSC self-renewal and reconstitution capacity. DNA methyltransferases mediate DNA methylation on the DERARE, leading to reduced Hoxb cluster expression. Acute myeloid leukemia patients with DNMT3A mutations exhibit DERARE hypomethylation, elevated HOXB expression, and adverse outcomes. CRISPR-Cas9-mediated specific DNA methylation at DERARE attenuated HOXB expression and alleviated leukemogenesis. Collectively, these findings demonstrate pivotal roles for retinoid signaling and the DERARE in maintaining HSCs and preventing leukemogenesis by coordinate regulation of Hoxb genes.
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Affiliation(s)
- Pengxu Qian
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Xi C He
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Christof Nolte
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Madelaine Gogol
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Youngwook Ahn
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Shiyuan Chen
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Zhenrui Li
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Hanzhang Xu
- Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - John M Perry
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Deqing Hu
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Tianjin Medical University School of Basic Medicine, Tian Jin 300070, China
| | - Fang Tao
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Meng Zhao
- Key Laboratory of Stem Cells and Tissue Engineering, Sun Yat-Sen University, Ministry of Education, Guangzhou, Guangdong 510080, China
| | - Yingli Han
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Kate Hall
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Allison Peak
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Ariel Paulson
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Chongbei Zhao
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Andrew Box
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Anoja Perera
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jeffrey S Haug
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Tari Parmely
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Hua Li
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Linheng Li
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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18
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Nolte C, De Kumar B, Krumlauf R. Hox genes: Downstream "effectors" of retinoic acid signaling in vertebrate embryogenesis. Genesis 2019; 57:e23306. [PMID: 31111645 DOI: 10.1002/dvg.23306] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 12/31/2022]
Abstract
One of the major regulatory challenges of animal development is to precisely coordinate in space and time the formation, specification, and patterning of cells that underlie elaboration of the basic body plan. How does the vertebrate plan for the nervous and hematopoietic systems, heart, limbs, digestive, and reproductive organs derive from seemingly similar population of cells? These systems are initially established and patterned along the anteroposterior axis (AP) by opposing signaling gradients that lead to the activation of gene regulatory networks involved in axial specification, including the Hox genes. The retinoid signaling pathway is one of the key signaling gradients coupled to the establishment of axial patterning. The nested domains of Hox gene expression, which provide a combinatorial code for axial patterning, arise in part through a differential response to retinoic acid (RA) diffusing from anabolic centers established within the embryo during development. Hence, Hox genes are important direct effectors of retinoid signaling in embryogenesis. This review focuses on describing current knowledge on the complex mechanisms and regulatory processes, which govern the response of Hox genes to RA in several tissue contexts including the nervous system during vertebrate development.
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Affiliation(s)
- Christof Nolte
- Stowers Institute for Medical Research, Kansas City, Missouri
| | - Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, Missouri
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, Missouri.,Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, Kansas
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19
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De Kumar B, Parker HJ, Paulson A, Parrish ME, Pushel I, Singh NP, Zhang Y, Slaughter BD, Unruh JR, Florens L, Zeitlinger J, Krumlauf R. HOXA1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on HOXA1 targets. Genome Res 2017; 27:1501-1512. [PMID: 28784834 PMCID: PMC5580710 DOI: 10.1101/gr.219386.116] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 07/24/2017] [Indexed: 01/02/2023]
Abstract
Hoxa1 has diverse functional roles in differentiation and development. We identify and characterize properties of regions bound by HOXA1 on a genome-wide basis in differentiating mouse ES cells. HOXA1-bound regions are enriched for clusters of consensus binding motifs for HOX, PBX, and MEIS, and many display co-occupancy of PBX and MEIS. PBX and MEIS are members of the TALE family and genome-wide analysis of multiple TALE members (PBX, MEIS, TGIF, PREP1, and PREP2) shows that nearly all HOXA1 targets display occupancy of one or more TALE members. The combinatorial binding patterns of TALE proteins define distinct classes of HOXA1 targets, which may create functional diversity. Transgenic reporter assays in zebrafish confirm enhancer activities for many HOXA1-bound regions and the importance of HOX-PBX and TGIF motifs for their regulation. Proteomic analyses show that HOXA1 physically interacts on chromatin with PBX, MEIS, and PREP family members, but not with TGIF, suggesting that TGIF may have an independent input into HOXA1-bound regions. Therefore, TALE proteins appear to represent a wide repertoire of HOX cofactors, which may coregulate enhancers through distinct mechanisms. We also discover extensive auto- and cross-regulatory interactions among the Hoxa1 and TALE genes, indicating that the specificity of HOXA1 during development may be regulated though a complex cross-regulatory network of HOXA1 and TALE proteins. This study provides new insight into a regulatory network involving combinatorial interactions between HOXA1 and TALE proteins.
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Affiliation(s)
- Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Hugo J Parker
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Ariel Paulson
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Mark E Parrish
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Irina Pushel
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | | | - Ying Zhang
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Brian D Slaughter
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA.,Department of Pathology
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA.,Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, Kansas 66160, USA
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20
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Abstract
The clustered Hox genes play fundamental roles in regulation of axial patterning and elaboration of the basic body plan in animal development. There are common features in the organization and regulatory landscape of Hox clusters associated with their highly conserved functional roles. The presence of transcribed noncoding sequences embedded within the vertebrate Hox clusters is providing insight into a new layer of regulatory information associated with Hox genes.
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Affiliation(s)
- Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, KS 66160, USA
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21
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De Kumar B, Parrish ME, Slaughter BD, Unruh JR, Gogol M, Seidel C, Paulson A, Li H, Gaudenz K, Peak A, McDowell W, Fleharty B, Ahn Y, Lin C, Smith E, Shilatifard A, Krumlauf R. Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cells. Genome Res 2015; 25:1229-43. [PMID: 26025802 PMCID: PMC4510006 DOI: 10.1101/gr.184978.114] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 05/28/2015] [Indexed: 11/24/2022]
Abstract
The clustered Hox genes, which are highly conserved across metazoans, encode homeodomain-containing transcription factors that provide a blueprint for segmental identity along the body axis. Recent studies have underscored that in addition to encoding Hox genes, the homeotic clusters contain key noncoding RNA genes that play a central role in development. In this study, we have taken advantage of genome-wide approaches to provide a detailed analysis of retinoic acid (RA)-induced transcriptional and epigenetic changes within the homeotic clusters of mouse embryonic stem cells. Although there is a general colinear response, our analyses suggest a lack of strict colinearity for several genes in the HoxA and HoxB clusters. We have identified transcribed novel noncoding RNAs (ncRNAs) and their cis-regulatory elements that function in response to RA and demonstrated that the expression of these ncRNAs from both strands represent some of the most rapidly induced transcripts in ES cells. Finally, we have provided dynamic analyses of chromatin modifications for the coding and noncoding genes expressed upon activation and suggest that active transcription can occur in the presence of chromatin modifications and machineries associated with repressed transcription state over the clusters. Overall, our data provide a resource for a better understanding of the dynamic nature of the coding and noncoding transcripts and their associated chromatin marks in the regulation of homeotic gene transcription during development.
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Affiliation(s)
- Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Mark E Parrish
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Brian D Slaughter
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Madelaine Gogol
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Christopher Seidel
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Ariel Paulson
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Hua Li
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Karin Gaudenz
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Allison Peak
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - William McDowell
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Brian Fleharty
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Youngwook Ahn
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Chengqi Lin
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Edwin Smith
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Ali Shilatifard
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA; Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, Kansas 66160, USA
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22
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Parrish M, Ahn Y, Nolte C, De Kumar B, Krumlauf R. Hox complex analysis through BAC recombineering. Methods Mol Biol 2014; 1196:59-87. [PMID: 25151158 DOI: 10.1007/978-1-4939-1242-1_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
BAC transgenesis in mice has proved to be useful in exploring the regulatory mechanisms and functions of the Hox complexes. The large constructs used may include most of the relevant components of the cis-regulatory landscape. Manipulations can be accomplished without compromising the integrity of the endogenous complex which reduces the likelihood of producing confounding phenotypic abnormalities. The development of recombineering tools has been critical in providing the means necessary to make many types of precise and varied manipulations of these large constructs. Here, we will discuss the methodologies necessary to manipulate Hox complex BACs, generation of transgenic animals bearing these constructs and the utilization of these resources to address fundamental aspects of Hox biology.
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Affiliation(s)
- Mark Parrish
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
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23
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Yurieva M, De Kumar B, Krumlauf R. Insights from transcriptional profiling the mouse hindbrain: Novel feedback between retinoids and Hox genes. FASEB J 2013. [DOI: 10.1096/fasebj.27.1_supplement.966.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Marina Yurieva
- Krumlauf labStowers Institute for Medical ResearchKansas cityMO
| | - Bony De Kumar
- Krumlauf labStowers Institute for Medical ResearchKansas cityMO
| | - Robb Krumlauf
- Krumlauf labStowers Institute for Medical ResearchKansas cityMO
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24
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Gaertner B, Johnston J, Chen K, Wallaschek N, Paulson A, Garruss AS, Gaudenz K, De Kumar B, Krumlauf R, Zeitlinger J. Poised RNA polymerase II changes over developmental time and prepares genes for future expression. Cell Rep 2012; 2:1670-83. [PMID: 23260668 DOI: 10.1016/j.celrep.2012.11.024] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 09/29/2012] [Accepted: 11/27/2012] [Indexed: 01/20/2023] Open
Abstract
Poised RNA polymerase II (Pol II) is predominantly found at developmental control genes and is thought to allow their rapid and synchronous induction in response to extracellular signals. How the recruitment of poised RNA Pol II is regulated during development is not known. By isolating muscle tissue from Drosophila embryos at five stages of differentiation, we show that the recruitment of poised Pol II occurs at many genes de novo and this makes them permissive for future gene expression. A comparison with other tissues shows that these changes are stage specific and not tissue specific. In contrast, Polycomb group repression is tissue specific, and in combination with Pol II (the balanced state) marks genes with highly dynamic expression. This suggests that poised Pol II is temporally regulated and is held in check in a tissue-specific fashion. We compare our data with findings in mammalian embryonic stem cells and discuss a framework for predicting developmental programs on the basis of the chromatin state.
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Affiliation(s)
- Bjoern Gaertner
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
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25
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Lin C, Garrett AS, De Kumar B, Smith ER, Gogol M, Seidel C, Krumlauf R, Shilatifard A. Dynamic transcriptional events in embryonic stem cells mediated by the super elongation complex (SEC). Genes Dev 2011; 25:1486-98. [PMID: 21764852 DOI: 10.1101/gad.2059211] [Citation(s) in RCA: 149] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Transcriptional regulation of developmentally controlled genes is at the heart of differentiation and organogenesis. In this study, we performed global genomic analyses in murine embryonic stem (ES) cells and in human cells in response to activation signals. We identified an essential role for the ELL (eleven-nineteen lysine-rich leukemia gene)/P-TEFb (positive transcription elongation factor)-containing super elongation complex (SEC) in the regulation of gene expression, including several genes bearing paused RNA polymerase II (Pol II). Paused Pol II has been proposed to be associated with loci that respond rapidly to environmental stimuli. However, our studies in ES cells also identified a requirement for SEC at genes without paused Pol II, which also respond dynamically to differentiation signals. Our findings suggest that SEC is a major class of active P-TEFb-containing complexes required for transcriptional activation in response to environmental cues such as differentiation signals.
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Affiliation(s)
- Chengqi Lin
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
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Munz Y, Kumar BD, Moorthy K, Bann S, Darzi A. Laparoscopic virtual reality and box trainers: is one superior to the other? Surg Endosc 2004; 18:485-94. [PMID: 14752633 DOI: 10.1007/s00464-003-9043-7] [Citation(s) in RCA: 180] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2003] [Accepted: 09/02/2003] [Indexed: 12/22/2022]
Abstract
BACKGROUND Virtual reality (VR) simulators now have the potential to replace traditional methods of laparoscopic training. The aim of this study was to compare the VR simulator with the classical box trainer and determine whether one has advantages over the other. METHODS Twenty four novices were tested to determine their baseline laparoscopic skills and then randomized into the following three group: LapSim, box trainer, and no training (control). After 3 weekly training sessions lasting 30-min each, all subjects were reassessed. Assessment included motion analysis and error scores. Nonparametric tests were applied, and p < 0.05 was deemed significant. RESULTS Both trained groups made significant improvements in all parameters measured ( p < 0.05). Compared to the controls, the box trainer group performed significantly better on most of the parameters, whereas the LapSim group performed significantly better on some parameters. There were no significant differences between the LapSim and box trainer groups. CONCLUSIONS LapSim is effective in teaching skills that are transferable to a real laparoscopic task. However, there appear to be no substantial advantages of one system over the other.
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Affiliation(s)
- Y Munz
- Department of Surgical Oncology and Technology, Imperial College of Science, Technology, and Medicine, St. Mary's Hospital, QEQM Wing, London W2 1NY, England, United Kingdom.
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Affiliation(s)
- B D Kumar
- Department of Surgical Oncology and Techology, Imperial College of Science Technology and Medicine, St Marry's Hospital, London, UK
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Krishnaswamy K, Kumar BD. Lead toxicity. Indian Pediatr 1998; 35:209-16. [PMID: 9707873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Affiliation(s)
- B D Kumar
- Food and Drug Toxicology Research Centre National Institute of Nutrition, Jamai Osmania, Hyderabad, India
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Abstract
Automotive use of leaded gasoline continues to be an important source of occupational exposure to lead in India and other countries. The present study assessed the renal function and markers of early renal damage of 22 mechanics at three automobile garages. Urinary N-acetyl-3-D-glucosaminidase activity and beta-2-microglobulin levels were significantly increased in auto garage mechanics with blood leads of 30-69 micrograms/dL. A significant correlation was observed between blood lead levels and urinary N-acetyl-3-D-glucosaminidase activity but not with urine beta-2-microglobulin levels. A marginal impairment in creatinine clearance was not statistically significant. Urinary N-acetyl-3-D-glucosaminidase activity offers a sensitive monitor of blood lead and renal tubular injury.
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Affiliation(s)
- B D Kumar
- Food and Drug Toxicology Research Centre, National Institute of Nutrition, Jamai Osmania, Hyderabad, India
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Kumar BD, Prasad CE, Krishnaswamy K. Detection of rifampicin-induced nephrotoxicity by N-acetyl-3-D-glucosaminidase activity. J Trop Med Hyg 1992; 95:424-7. [PMID: 1460703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The objective of the present study was to assess renal damage, if any, by non-invasive technique, viz NAG activity in urine and GFR in patients on continuous and intermittent rifampicin therapy. Eighty-four tuberculosis patients for cross-sectional study and six subjects for longitudinal study on antitubercular therapy and ten patients on withdrawal of rifampicin participated in the investigation; 13 leprosy patients intermittently treated with rifampicin were also included. Twenty-seven normal subjects served as controls. Rifampicin on continuous use resulted in a progressive increase in enzymuria with no change in GFR. An additive toxic effect was obvious in patients receiving streptomycin; when the treatment was withdrawn the urinary NAG activity stabilized within 15-21 days. However, patients receiving rifampicin intermittently did not show any evidence of renal damage. The results suggest that there is a need for monitoring renal damage, particularly on antitubercular therapy, when nephrotoxic agents are administered together.
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Affiliation(s)
- B D Kumar
- Food and Drug Toxicology Research Centre, National Institute of Nutrition, Hyderabad, India
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Abstract
An attempt has been made to quantitate drug consumption in a conurbation. The prescribing habits of physicians, self medication rate and therapeutic classes of drugs purchased have been evaluated. The study indicates that some of the prevailing practices in the area are unhealthy. The high self medication rate, faulty prescribing habits of physicians and liberal dispensing methods of pharmacist need to be viewed with concern. The wide gap between the precepts and practices prevailing among practitioners, the use of potent medicines without proper medical advice and the uninhibited sale of scheduled drugs over the pharmacy counter require careful consideration. If such unhealthy trends persist iatrogenic problems may surface in the near future. The physician, pharmacist and the public need to cooperate to create the proper pattern of drug usage.
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