1
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Francis JS, Nguyen Q, Markov V, Leone P. Over-expression of N-acetylaspartate synthase exacerbates pathological energetic deficit and accelerates cognitive decline in the 5xFAD mouse. J Neurochem 2024; 168:69-82. [PMID: 38178803 DOI: 10.1111/jnc.16044] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/06/2024]
Abstract
N-acetylaspartate (NAA) is an abundant central nervous system amino acid derivative that is tightly coupled to mitochondria and energy metabolism in neurons. A reduced NAA signature is a prominent early pathological biomarker in multiple neurodegenerative diseases and becomes progressively more pronounced as disease advances. Because NAA synthesis requires aspartate drawn directly from mitochondria, we argued that this process is in direct competition with oxidative phosphorylation for substrate and that sustained high levels of NAA synthesis would be incompatible with pathological energy crisis. We show here that over-expression of the rate-limiting NAA synthetic enzyme in the hippocampus of the 5x familial Alzheimer's disease (5xFAD) mouse results in an exaggerated pathological ATP deficit and accelerated cognitive decline. Over-expression of NAA synthase did not increase amyloid burden or result in cell loss but did significantly deplete mitochondrial aspartate and impair the ability of mitochondria to oxidize glutamate for adenosine triphosphate (ATP) synthesis. These results define NAA as a sink for energetic substrate and suggest initial pathological reductions in NAA are part of a response to energetic crisis designed to preserve substrate bioavailability for mitochondrial ATP synthesis.
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Affiliation(s)
- Jeremy S Francis
- Cell & Gene Therapy Center, Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, New Jersey, USA
| | - Quy Nguyen
- Cell & Gene Therapy Center, Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, New Jersey, USA
| | - Vladimir Markov
- Cell & Gene Therapy Center, Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, New Jersey, USA
| | - Paola Leone
- Cell & Gene Therapy Center, Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, New Jersey, USA
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2
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Han E, Nabity SA, Dasgupta-Tsinikas S, Guevara RE, Moore M, Kadakia A, Henry H, Cilnis M, Buhain S, Chitnis A, Chakrabarty M, Ky A, Nguyen Q, Low J, Jain S, Higashi J, Barry PM, Flood J. Tuberculosis Diagnostic Delays and Treatment Outcomes among Patients with COVID-19, California, USA, 2020. Emerg Infect Dis 2024; 30:136-140. [PMID: 38147063 PMCID: PMC10756354 DOI: 10.3201/eid3001.230924] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023] Open
Abstract
We assessed tuberculosis (TB) diagnostic delays among patients with TB and COVID-19 in California, USA. Among 58 persons, 43% experienced TB diagnostic delays, and a high proportion (83%) required hospitalization for TB. Even when viral respiratory pathogens circulate widely, timely TB diagnostic workup for at-risk persons remains critical for reducing TB-related illness.
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Affiliation(s)
| | | | - Shom Dasgupta-Tsinikas
- California Department of Public Health, Richmond, California, USA (E. Han, S.A. Nabity, H. Henry, M. Cilnis, S. Jain, P.M. Barry, J. Flood)
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (S.A. Nabity, M. Moore)
- Los Angeles County Department of Public Health, Los Angeles, California, USA (S. Dasgupta-Tsinikas, R.E. Guevara, J. Higashi)
- San Diego County Health and Human Services Agency, San Diego, California, USA (M. Moore, A. Kadakia)
- Alameda County Public Health Department, San Leandro, California, USA (S. Buhain, A. Chitnis)
- Sacramento County Health Services, Sacramento, California, USA (M. Chakrabarty)
- Santa Clara County Public Health Department, San Jose, California, USA (A. Ky)
- Orange County Health Care Agency, Santa Ana, California, USA (Q. Nguyen, J. Low)
| | - Ramon E. Guevara
- California Department of Public Health, Richmond, California, USA (E. Han, S.A. Nabity, H. Henry, M. Cilnis, S. Jain, P.M. Barry, J. Flood)
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (S.A. Nabity, M. Moore)
- Los Angeles County Department of Public Health, Los Angeles, California, USA (S. Dasgupta-Tsinikas, R.E. Guevara, J. Higashi)
- San Diego County Health and Human Services Agency, San Diego, California, USA (M. Moore, A. Kadakia)
- Alameda County Public Health Department, San Leandro, California, USA (S. Buhain, A. Chitnis)
- Sacramento County Health Services, Sacramento, California, USA (M. Chakrabarty)
- Santa Clara County Public Health Department, San Jose, California, USA (A. Ky)
- Orange County Health Care Agency, Santa Ana, California, USA (Q. Nguyen, J. Low)
| | - Marisa Moore
- California Department of Public Health, Richmond, California, USA (E. Han, S.A. Nabity, H. Henry, M. Cilnis, S. Jain, P.M. Barry, J. Flood)
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (S.A. Nabity, M. Moore)
- Los Angeles County Department of Public Health, Los Angeles, California, USA (S. Dasgupta-Tsinikas, R.E. Guevara, J. Higashi)
- San Diego County Health and Human Services Agency, San Diego, California, USA (M. Moore, A. Kadakia)
- Alameda County Public Health Department, San Leandro, California, USA (S. Buhain, A. Chitnis)
- Sacramento County Health Services, Sacramento, California, USA (M. Chakrabarty)
- Santa Clara County Public Health Department, San Jose, California, USA (A. Ky)
- Orange County Health Care Agency, Santa Ana, California, USA (Q. Nguyen, J. Low)
| | - Ankita Kadakia
- California Department of Public Health, Richmond, California, USA (E. Han, S.A. Nabity, H. Henry, M. Cilnis, S. Jain, P.M. Barry, J. Flood)
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (S.A. Nabity, M. Moore)
- Los Angeles County Department of Public Health, Los Angeles, California, USA (S. Dasgupta-Tsinikas, R.E. Guevara, J. Higashi)
- San Diego County Health and Human Services Agency, San Diego, California, USA (M. Moore, A. Kadakia)
- Alameda County Public Health Department, San Leandro, California, USA (S. Buhain, A. Chitnis)
- Sacramento County Health Services, Sacramento, California, USA (M. Chakrabarty)
- Santa Clara County Public Health Department, San Jose, California, USA (A. Ky)
- Orange County Health Care Agency, Santa Ana, California, USA (Q. Nguyen, J. Low)
| | - Hannah Henry
- California Department of Public Health, Richmond, California, USA (E. Han, S.A. Nabity, H. Henry, M. Cilnis, S. Jain, P.M. Barry, J. Flood)
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (S.A. Nabity, M. Moore)
- Los Angeles County Department of Public Health, Los Angeles, California, USA (S. Dasgupta-Tsinikas, R.E. Guevara, J. Higashi)
- San Diego County Health and Human Services Agency, San Diego, California, USA (M. Moore, A. Kadakia)
- Alameda County Public Health Department, San Leandro, California, USA (S. Buhain, A. Chitnis)
- Sacramento County Health Services, Sacramento, California, USA (M. Chakrabarty)
- Santa Clara County Public Health Department, San Jose, California, USA (A. Ky)
- Orange County Health Care Agency, Santa Ana, California, USA (Q. Nguyen, J. Low)
| | - Martin Cilnis
- California Department of Public Health, Richmond, California, USA (E. Han, S.A. Nabity, H. Henry, M. Cilnis, S. Jain, P.M. Barry, J. Flood)
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (S.A. Nabity, M. Moore)
- Los Angeles County Department of Public Health, Los Angeles, California, USA (S. Dasgupta-Tsinikas, R.E. Guevara, J. Higashi)
- San Diego County Health and Human Services Agency, San Diego, California, USA (M. Moore, A. Kadakia)
- Alameda County Public Health Department, San Leandro, California, USA (S. Buhain, A. Chitnis)
- Sacramento County Health Services, Sacramento, California, USA (M. Chakrabarty)
- Santa Clara County Public Health Department, San Jose, California, USA (A. Ky)
- Orange County Health Care Agency, Santa Ana, California, USA (Q. Nguyen, J. Low)
| | - Sonal Buhain
- California Department of Public Health, Richmond, California, USA (E. Han, S.A. Nabity, H. Henry, M. Cilnis, S. Jain, P.M. Barry, J. Flood)
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (S.A. Nabity, M. Moore)
- Los Angeles County Department of Public Health, Los Angeles, California, USA (S. Dasgupta-Tsinikas, R.E. Guevara, J. Higashi)
- San Diego County Health and Human Services Agency, San Diego, California, USA (M. Moore, A. Kadakia)
- Alameda County Public Health Department, San Leandro, California, USA (S. Buhain, A. Chitnis)
- Sacramento County Health Services, Sacramento, California, USA (M. Chakrabarty)
- Santa Clara County Public Health Department, San Jose, California, USA (A. Ky)
- Orange County Health Care Agency, Santa Ana, California, USA (Q. Nguyen, J. Low)
| | - Amit Chitnis
- California Department of Public Health, Richmond, California, USA (E. Han, S.A. Nabity, H. Henry, M. Cilnis, S. Jain, P.M. Barry, J. Flood)
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (S.A. Nabity, M. Moore)
- Los Angeles County Department of Public Health, Los Angeles, California, USA (S. Dasgupta-Tsinikas, R.E. Guevara, J. Higashi)
- San Diego County Health and Human Services Agency, San Diego, California, USA (M. Moore, A. Kadakia)
- Alameda County Public Health Department, San Leandro, California, USA (S. Buhain, A. Chitnis)
- Sacramento County Health Services, Sacramento, California, USA (M. Chakrabarty)
- Santa Clara County Public Health Department, San Jose, California, USA (A. Ky)
- Orange County Health Care Agency, Santa Ana, California, USA (Q. Nguyen, J. Low)
| | - Melony Chakrabarty
- California Department of Public Health, Richmond, California, USA (E. Han, S.A. Nabity, H. Henry, M. Cilnis, S. Jain, P.M. Barry, J. Flood)
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (S.A. Nabity, M. Moore)
- Los Angeles County Department of Public Health, Los Angeles, California, USA (S. Dasgupta-Tsinikas, R.E. Guevara, J. Higashi)
- San Diego County Health and Human Services Agency, San Diego, California, USA (M. Moore, A. Kadakia)
- Alameda County Public Health Department, San Leandro, California, USA (S. Buhain, A. Chitnis)
- Sacramento County Health Services, Sacramento, California, USA (M. Chakrabarty)
- Santa Clara County Public Health Department, San Jose, California, USA (A. Ky)
- Orange County Health Care Agency, Santa Ana, California, USA (Q. Nguyen, J. Low)
| | - Ann Ky
- California Department of Public Health, Richmond, California, USA (E. Han, S.A. Nabity, H. Henry, M. Cilnis, S. Jain, P.M. Barry, J. Flood)
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (S.A. Nabity, M. Moore)
- Los Angeles County Department of Public Health, Los Angeles, California, USA (S. Dasgupta-Tsinikas, R.E. Guevara, J. Higashi)
- San Diego County Health and Human Services Agency, San Diego, California, USA (M. Moore, A. Kadakia)
- Alameda County Public Health Department, San Leandro, California, USA (S. Buhain, A. Chitnis)
- Sacramento County Health Services, Sacramento, California, USA (M. Chakrabarty)
- Santa Clara County Public Health Department, San Jose, California, USA (A. Ky)
- Orange County Health Care Agency, Santa Ana, California, USA (Q. Nguyen, J. Low)
| | - Quy Nguyen
- California Department of Public Health, Richmond, California, USA (E. Han, S.A. Nabity, H. Henry, M. Cilnis, S. Jain, P.M. Barry, J. Flood)
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (S.A. Nabity, M. Moore)
- Los Angeles County Department of Public Health, Los Angeles, California, USA (S. Dasgupta-Tsinikas, R.E. Guevara, J. Higashi)
- San Diego County Health and Human Services Agency, San Diego, California, USA (M. Moore, A. Kadakia)
- Alameda County Public Health Department, San Leandro, California, USA (S. Buhain, A. Chitnis)
- Sacramento County Health Services, Sacramento, California, USA (M. Chakrabarty)
- Santa Clara County Public Health Department, San Jose, California, USA (A. Ky)
- Orange County Health Care Agency, Santa Ana, California, USA (Q. Nguyen, J. Low)
| | - Julie Low
- California Department of Public Health, Richmond, California, USA (E. Han, S.A. Nabity, H. Henry, M. Cilnis, S. Jain, P.M. Barry, J. Flood)
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (S.A. Nabity, M. Moore)
- Los Angeles County Department of Public Health, Los Angeles, California, USA (S. Dasgupta-Tsinikas, R.E. Guevara, J. Higashi)
- San Diego County Health and Human Services Agency, San Diego, California, USA (M. Moore, A. Kadakia)
- Alameda County Public Health Department, San Leandro, California, USA (S. Buhain, A. Chitnis)
- Sacramento County Health Services, Sacramento, California, USA (M. Chakrabarty)
- Santa Clara County Public Health Department, San Jose, California, USA (A. Ky)
- Orange County Health Care Agency, Santa Ana, California, USA (Q. Nguyen, J. Low)
| | - Seema Jain
- California Department of Public Health, Richmond, California, USA (E. Han, S.A. Nabity, H. Henry, M. Cilnis, S. Jain, P.M. Barry, J. Flood)
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (S.A. Nabity, M. Moore)
- Los Angeles County Department of Public Health, Los Angeles, California, USA (S. Dasgupta-Tsinikas, R.E. Guevara, J. Higashi)
- San Diego County Health and Human Services Agency, San Diego, California, USA (M. Moore, A. Kadakia)
- Alameda County Public Health Department, San Leandro, California, USA (S. Buhain, A. Chitnis)
- Sacramento County Health Services, Sacramento, California, USA (M. Chakrabarty)
- Santa Clara County Public Health Department, San Jose, California, USA (A. Ky)
- Orange County Health Care Agency, Santa Ana, California, USA (Q. Nguyen, J. Low)
| | - Julie Higashi
- California Department of Public Health, Richmond, California, USA (E. Han, S.A. Nabity, H. Henry, M. Cilnis, S. Jain, P.M. Barry, J. Flood)
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (S.A. Nabity, M. Moore)
- Los Angeles County Department of Public Health, Los Angeles, California, USA (S. Dasgupta-Tsinikas, R.E. Guevara, J. Higashi)
- San Diego County Health and Human Services Agency, San Diego, California, USA (M. Moore, A. Kadakia)
- Alameda County Public Health Department, San Leandro, California, USA (S. Buhain, A. Chitnis)
- Sacramento County Health Services, Sacramento, California, USA (M. Chakrabarty)
- Santa Clara County Public Health Department, San Jose, California, USA (A. Ky)
- Orange County Health Care Agency, Santa Ana, California, USA (Q. Nguyen, J. Low)
| | - Pennan M. Barry
- California Department of Public Health, Richmond, California, USA (E. Han, S.A. Nabity, H. Henry, M. Cilnis, S. Jain, P.M. Barry, J. Flood)
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (S.A. Nabity, M. Moore)
- Los Angeles County Department of Public Health, Los Angeles, California, USA (S. Dasgupta-Tsinikas, R.E. Guevara, J. Higashi)
- San Diego County Health and Human Services Agency, San Diego, California, USA (M. Moore, A. Kadakia)
- Alameda County Public Health Department, San Leandro, California, USA (S. Buhain, A. Chitnis)
- Sacramento County Health Services, Sacramento, California, USA (M. Chakrabarty)
- Santa Clara County Public Health Department, San Jose, California, USA (A. Ky)
- Orange County Health Care Agency, Santa Ana, California, USA (Q. Nguyen, J. Low)
| | - Jennifer Flood
- California Department of Public Health, Richmond, California, USA (E. Han, S.A. Nabity, H. Henry, M. Cilnis, S. Jain, P.M. Barry, J. Flood)
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (S.A. Nabity, M. Moore)
- Los Angeles County Department of Public Health, Los Angeles, California, USA (S. Dasgupta-Tsinikas, R.E. Guevara, J. Higashi)
- San Diego County Health and Human Services Agency, San Diego, California, USA (M. Moore, A. Kadakia)
- Alameda County Public Health Department, San Leandro, California, USA (S. Buhain, A. Chitnis)
- Sacramento County Health Services, Sacramento, California, USA (M. Chakrabarty)
- Santa Clara County Public Health Department, San Jose, California, USA (A. Ky)
- Orange County Health Care Agency, Santa Ana, California, USA (Q. Nguyen, J. Low)
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3
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Das BK, Kannan A, Velasco GJ, Kunika MD, Lambrecht N, Nguyen Q, Zhao H, Wu J, Gao L. Single-cell dissection of Merkel cell carcinoma heterogeneity unveils transcriptomic plasticity and therapeutic vulnerabilities. Cell Rep Med 2023; 4:101101. [PMID: 37421947 PMCID: PMC10394170 DOI: 10.1016/j.xcrm.2023.101101] [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: 12/07/2022] [Revised: 03/23/2023] [Accepted: 06/13/2023] [Indexed: 07/10/2023]
Abstract
Merkel cell carcinoma (MCC), a rare but aggressive skin cancer, remains a challenge in the era of precision medicine. Immune checkpoint inhibitors (ICIs), the only approved therapy for advanced MCC, are impeded by high primary and acquired resistance. Hence, we dissect transcriptomic heterogeneity at single-cell resolution in a panel of patient tumors, revealing phenotypic plasticity in a subset of treatment-naive MCC. The tumor cells in a "mesenchymal-like" state are endowed with an inflamed phenotype that portends a better ICI response. This observation is also validated in the largest whole transcriptomic dataset available from MCC patient tumors. In contrast, ICI-resistant tumors predominantly express neuroepithelial markers in a well-differentiated state with "immune-cold" landscape. Importantly, a subtle shift to "mesenchymal-like" state reverts copanlisib resistance in primary MCC cells, highlighting potential strategies in patient stratification for therapeutics to harness tumor cell plasticity, augment treatment efficacy, and avert resistance.
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Affiliation(s)
- Bhaba K Das
- Southern California Institute for Research and Education, Long Beach, CA 90822, USA
| | - Aarthi Kannan
- Southern California Institute for Research and Education, Long Beach, CA 90822, USA; Department of Dermatology, University of California-Irvine, Irvine, CA 92697, USA
| | - Graham J Velasco
- Pathology Department, Tibor Rubin VA Medical Center, VA Long Beach Healthcare System, Long Beach, CA 90822, USA
| | - Mikaela D Kunika
- Southern California Institute for Research and Education, Long Beach, CA 90822, USA
| | - Nils Lambrecht
- Pathology Department, Tibor Rubin VA Medical Center, VA Long Beach Healthcare System, Long Beach, CA 90822, USA
| | - Quy Nguyen
- Genomics Research and Technology Hub, Department of Biological Chemistry, University of California-Irvine, Irvine, CA 92697, USA
| | - Haibo Zhao
- Southern California Institute for Research and Education, Long Beach, CA 90822, USA
| | - Jie Wu
- Genomics Research and Technology Hub, Department of Biological Chemistry, University of California-Irvine, Irvine, CA 92697, USA
| | - Ling Gao
- Southern California Institute for Research and Education, Long Beach, CA 90822, USA; Department of Dermatology, University of California-Irvine, Irvine, CA 92697, USA; Dermatology Section, Tibor Rubin VA Medical Center, VA Long Beach Healthcare System, Long Beach, CA 90822, USA.
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4
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Coulis G, Jaime D, Guerrero-Juarez C, Kastenschmidt JM, Farahat PK, Nguyen Q, Pervolarakis N, McLinden K, Thurlow L, Movahedi S, Hughes BS, Duarte J, Sorn A, Montoya E, Mozaffar I, Dragan M, Othy S, Joshi T, Hans CP, Kimonis V, MacLean AL, Nie Q, Wallace LM, Harper SQ, Mozaffar T, Hogarth MW, Bhattacharya S, Jaiswal JK, Golann DR, Su Q, Kessenbrock K, Stec M, Spencer MJ, Zamudio JR, Villalta SA. Single-cell and spatial transcriptomics identify a macrophage population associated with skeletal muscle fibrosis. Sci Adv 2023; 9:eadd9984. [PMID: 37418531 PMCID: PMC10328414 DOI: 10.1126/sciadv.add9984] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 06/05/2023] [Indexed: 07/09/2023]
Abstract
Macrophages are essential for skeletal muscle homeostasis, but how their dysregulation contributes to the development of fibrosis in muscle disease remains unclear. Here, we used single-cell transcriptomics to determine the molecular attributes of dystrophic and healthy muscle macrophages. We identified six clusters and unexpectedly found that none corresponded to traditional definitions of M1 or M2 macrophages. Rather, the predominant macrophage signature in dystrophic muscle was characterized by high expression of fibrotic factors, galectin-3 (gal-3) and osteopontin (Spp1). Spatial transcriptomics, computational inferences of intercellular communication, and in vitro assays indicated that macrophage-derived Spp1 regulates stromal progenitor differentiation. Gal-3+ macrophages were chronically activated in dystrophic muscle, and adoptive transfer assays showed that the gal-3+ phenotype was the dominant molecular program induced within the dystrophic milieu. Gal-3+ macrophages were also elevated in multiple human myopathies. These studies advance our understanding of macrophages in muscular dystrophy by defining their transcriptional programs and reveal Spp1 as a major regulator of macrophage and stromal progenitor interactions.
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Affiliation(s)
- Gerald Coulis
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, USA
- Institute for Immunology, University of California Irvine, Irvine, CA, USA
| | - Diego Jaime
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, USA
- Institute for Immunology, University of California Irvine, Irvine, CA, USA
| | | | - Jenna M. Kastenschmidt
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, USA
- Institute for Immunology, University of California Irvine, Irvine, CA, USA
| | - Philip K. Farahat
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, USA
- Institute for Immunology, University of California Irvine, Irvine, CA, USA
| | - Quy Nguyen
- Department of Biological Chemistry, University of California Irvine, Irvine, CA USA
| | | | - Katherine McLinden
- Department of Molecular Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Lauren Thurlow
- Department of Molecular Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Saba Movahedi
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, USA
| | - Brandon S. Hughes
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, USA
| | - Jorge Duarte
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, USA
| | - Andrew Sorn
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, USA
| | - Elizabeth Montoya
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, USA
| | - Izza Mozaffar
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, USA
| | - Morgan Dragan
- Department of Biological Chemistry, University of California Irvine, Irvine, CA USA
| | - Shivashankar Othy
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, USA
- Institute for Immunology, University of California Irvine, Irvine, CA, USA
| | - Trupti Joshi
- Department of Health Management and Informatics, University of Missouri, Columbia, MO, USA
| | - Chetan P. Hans
- Department of Cardiovascular Medicine, University of Missouri, Columbia, MO USA
| | - Virginia Kimonis
- Department of Pediatrics, University of California Irvine, Irvine, CA, USA
| | - Adam L. MacLean
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Qing Nie
- Department of Mathematics, Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA
| | - Lindsay M. Wallace
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, USA
| | - Scott Q. Harper
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Tahseen Mozaffar
- Department of Neurology, University of California Irvine, Irvine, CA, USA
- Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, CA, USA
| | - Marshall W. Hogarth
- Children’s National Hospital, Research Center for Genetic Medicine, Washington, DC, USA
| | - Surajit Bhattacharya
- Children’s National Hospital, Research Center for Genetic Medicine, Washington, DC, USA
| | - Jyoti K. Jaiswal
- Children’s National Hospital, Research Center for Genetic Medicine, Washington, DC, USA
| | | | - Qi Su
- Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Kai Kessenbrock
- Department of Biological Chemistry, University of California Irvine, Irvine, CA USA
| | - Michael Stec
- Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Melissa J. Spencer
- Department of Neurology, University of California Los Angeles, Los Angeles, CA, USA
| | - Jesse R. Zamudio
- Department of Molecular Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - S. Armando Villalta
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, USA
- Institute for Immunology, University of California Irvine, Irvine, CA, USA
- Department of Neurology, University of California Irvine, Irvine, CA, USA
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5
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Sato S, Hishida T, Kinouchi K, Hatanaka F, Li Y, Nguyen Q, Chen Y, Wang PH, Kessenbrock K, Li W, Izpisua Belmonte JC, Sassone-Corsi P. The circadian clock CRY1 regulates pluripotent stem cell identity and somatic cell reprogramming. Cell Rep 2023; 42:112590. [PMID: 37261952 DOI: 10.1016/j.celrep.2023.112590] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 03/28/2023] [Accepted: 05/16/2023] [Indexed: 06/03/2023] Open
Abstract
Distinct metabolic conditions rewire circadian-clock-controlled signaling pathways leading to the de novo construction of signal transduction networks. However, it remains unclear whether metabolic hallmarks unique to pluripotent stem cells (PSCs) are connected to clock functions. Reprogramming somatic cells to a pluripotent state, here we highlighted non-canonical functions of the circadian repressor CRY1 specific to PSCs. Metabolic reprogramming, including AMPK inactivation and SREBP1 activation, was coupled with the accumulation of CRY1 in PSCs. Functional assays verified that CRY1 is required for the maintenance of self-renewal capacity, colony organization, and metabolic signatures. Genome-wide occupancy of CRY1 identified CRY1-regulatory genes enriched in development and differentiation in PSCs, albeit not somatic cells. Last, cells lacking CRY1 exhibit differential gene expression profiles during induced PSC (iPSC) reprogramming, resulting in impaired iPSC reprogramming efficiency. Collectively, these results suggest the functional implication of CRY1 in pluripotent reprogramming and ontogenesis, thereby dictating PSC identity.
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Affiliation(s)
- Shogo Sato
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA; Center for Biological Clocks Research, Department of Biology, Texas A&M University, College Station, TX, USA.
| | - Tomoaki Hishida
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA; Laboratory of Biological Chemistry, School of Pharmaceutical Sciences, Wakayama Medical University, Wakayama, Japan
| | - Kenichiro Kinouchi
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Fumiaki Hatanaka
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA; Altos Labs, San Diego, CA, USA
| | - Yumei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Quy Nguyen
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Yumay Chen
- UC Irvine Diabetes Center, Sue and Bill Gross Stem Cell Research Center, Department of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Ping H Wang
- UC Irvine Diabetes Center, Sue and Bill Gross Stem Cell Research Center, Department of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Kai Kessenbrock
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Juan Carlos Izpisua Belmonte
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA; Altos Labs, San Diego, CA, USA.
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
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Coulis G, Jaime D, Guerrero-Juarez C, Kastenschmidt JM, Farahat PK, Nguyen Q, Pervolarakis N, McLinden K, Thurlow L, Movahedi S, Duarte J, Sorn A, Montoya E, Mozaffar I, Dragan M, Othy S, Joshi T, Hans CP, Kimonis V, MacLean AL, Nie Q, Wallace LM, Harper SQ, Mozaffar T, Hogarth MW, Bhattacharya S, Jaiswal JK, Golann DR, Su Q, Kessenbrock K, Stec M, Spencer MJ, Zamudio JR, Villalta SA. Single-cell and spatial transcriptomics identify a macrophage population associated with skeletal muscle fibrosis. bioRxiv 2023:2023.04.18.537253. [PMID: 37131694 PMCID: PMC10153153 DOI: 10.1101/2023.04.18.537253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The monocytic/macrophage system is essential for skeletal muscle homeostasis, but its dysregulation contributes to the pathogenesis of muscle degenerative disorders. Despite our increasing knowledge of the role of macrophages in degenerative disease, it still remains unclear how macrophages contribute to muscle fibrosis. Here, we used single-cell transcriptomics to determine the molecular attributes of dystrophic and healthy muscle macrophages. We identified six novel clusters. Unexpectedly, none corresponded to traditional definitions of M1 or M2 macrophage activation. Rather, the predominant macrophage signature in dystrophic muscle was characterized by high expression of fibrotic factors, galectin-3 and spp1. Spatial transcriptomics and computational inferences of intercellular communication indicated that spp1 regulates stromal progenitor and macrophage interactions during muscular dystrophy. Galectin-3 + macrophages were chronically activated in dystrophic muscle and adoptive transfer assays showed that the galectin-3 + phenotype was the dominant molecular program induced within the dystrophic milieu. Histological examination of human muscle biopsies revealed that galectin-3 + macrophages were also elevated in multiple myopathies. These studies advance our understanding of macrophages in muscular dystrophy by defining the transcriptional programs induced in muscle macrophages, and reveal spp1 as a major regulator of macrophage and stromal progenitor interactions.
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Affiliation(s)
- Gerald Coulis
- Department of Physiology and Biophysics, University of California Irvine, USA
- Institute for Immunology, University of California Irvine, USA
| | - Diego Jaime
- Department of Physiology and Biophysics, University of California Irvine, USA
- Institute for Immunology, University of California Irvine, USA
| | - Christian Guerrero-Juarez
- Department of Mathematics, University of California Irvine, USA
- Department of Developmental and Cell Biology, University of California Irvine, USA
| | - Jenna M. Kastenschmidt
- Department of Physiology and Biophysics, University of California Irvine, USA
- Institute for Immunology, University of California Irvine, USA
| | - Philip K. Farahat
- Department of Physiology and Biophysics, University of California Irvine, USA
- Institute for Immunology, University of California Irvine, USA
| | - Quy Nguyen
- Department of Biological Chemistry, University of California Irvine, USA
| | | | - Katherine McLinden
- Department of Molecular Cell and Developmental Biology, University of California Los Angeles, USA
| | - Lauren Thurlow
- Department of Molecular Cell and Developmental Biology, University of California Los Angeles, USA
| | - Saba Movahedi
- Department of Physiology and Biophysics, University of California Irvine, USA
| | - Jorge Duarte
- Department of Physiology and Biophysics, University of California Irvine, USA
| | - Andrew Sorn
- Department of Physiology and Biophysics, University of California Irvine, USA
| | - Elizabeth Montoya
- Department of Physiology and Biophysics, University of California Irvine, USA
| | - Izza Mozaffar
- Department of Physiology and Biophysics, University of California Irvine, USA
| | - Morgan Dragan
- Department of Molecular Cell and Developmental Biology, University of California Los Angeles, USA
| | - Shivashankar Othy
- Department of Physiology and Biophysics, University of California Irvine, USA
- Institute for Immunology, University of California Irvine, USA
| | - Trupti Joshi
- Department of Health Management and Informatics, University of Missouri, Columbia, USA
| | - Chetan P. Hans
- Department of Cardiovascular Medicine, University of Missouri, Columbia, USA
| | | | - Adam L. MacLean
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA
| | - Qing Nie
- Department of Mathematics, University of California Irvine, USA
- Department of Developmental and Cell Biology, University of California Irvine, USA
| | - Lindsay M. Wallace
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital
| | - Scott Q. Harper
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital
| | - Tahseen Mozaffar
- Department of Neurology, University of California Irvine, USA
- Department of Pathology and Laboratory Medicine, University of California Irvine, USA
| | - Marshall W. Hogarth
- Children’s National Hospital, Research Center for Genetic Medicine, Washington, DC, USA
| | - Surajit Bhattacharya
- Children’s National Hospital, Research Center for Genetic Medicine, Washington, DC, USA
| | - Jyoti K. Jaiswal
- Children’s National Hospital, Research Center for Genetic Medicine, Washington, DC, USA
| | | | - Qi Su
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | - Kai Kessenbrock
- Department of Biological Chemistry, University of California Irvine, USA
| | - Michael Stec
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | | | - Jesse R. Zamudio
- Department of Molecular Cell and Developmental Biology, University of California Los Angeles, USA
| | - S. Armando Villalta
- Department of Physiology and Biophysics, University of California Irvine, USA
- Institute for Immunology, University of California Irvine, USA
- Department of Neurology, University of California Irvine, USA
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Lemon N, Taylor L, Rech M, Nguyen Q, Matthews G, Smith P, Dronzek V, Lew G, Lovett S. 378 A Higher D-Dimer Threshold Can be Used to Predict Pulmonary Embolism in COVID-19 Patients Presenting to the Emergency Department. Ann Emerg Med 2022. [PMCID: PMC9519197 DOI: 10.1016/j.annemergmed.2022.08.405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Dinh V, Nguyen H, Nguyen H, Pham H, Nguyen Q. Sperm retrieval in infertile men with non-obstructive azoospermia using microdissection testicular sperm extraction. Reprod Biomed Online 2022. [DOI: 10.1016/j.rbmo.2022.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Nguyen Q, Wybrow M, Burstein F, Taylor D, Enticott J. Understanding the impacts of health information systems on patient flow management: A systematic review across several decades of research. PLoS One 2022; 17:e0274493. [PMID: 36094946 PMCID: PMC9467348 DOI: 10.1371/journal.pone.0274493] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/28/2022] [Indexed: 11/18/2022] Open
Abstract
Background Patient flow describes the progression of patients along a pathway of care such as the journey from hospital inpatient admission to discharge. Poor patient flow has detrimental effects on health outcomes, patient satisfaction and hospital revenue. There has been an increasing adoption of health information systems (HISs) in various healthcare settings to address patient flow issues, yet there remains limited evidence of their overall impacts. Objective To systematically review evidence on the impacts of HISs on patient flow management including what HISs have been used, their application scope, features, and what aspects of patient flow are affected by the HIS adoption. Methods A systematic search for English-language, peer-review literature indexed in MEDLINE and EMBASE, CINAHL, INSPEC, and ACM Digital Library from the earliest date available to February 2022 was conducted. Two authors independently scanned the search results for eligible publications, and reporting followed the PRISMA guidelines. Eligibility criteria included studies that reported impacts of HIS on patient flow outcomes. Information on the study design, type of HIS, key features and impacts was extracted and analysed using an analytical framework which was based on domain-expert opinions and literature review. Results Overall, 5996 titles were identified, with 44 eligible studies, across 17 types of HIS. 22 studies (50%) focused on patient flow in the department level such as emergency department while 18 studies (41%) focused on hospital-wide level and four studies (9%) investigated network-wide HIS. Process outcomes with time-related measures such as ‘length of stay’ and ‘waiting time’ were investigated in most of the studies. In addition, HISs were found to address flow problems by identifying blockages, streamlining care processes and improving care coordination. Conclusion HIS affected various aspects of patient flow at different levels of care; however, how and why they delivered the impacts require further research.
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Affiliation(s)
- Quy Nguyen
- Department of Human-Centred Computing, Faculty of Information Technology, Monash University, Melbourne, Australia
- * E-mail:
| | - Michael Wybrow
- Department of Human-Centred Computing, Faculty of Information Technology, Monash University, Melbourne, Australia
| | - Frada Burstein
- Department of Human-Centred Computing, Faculty of Information Technology, Monash University, Melbourne, Australia
| | - David Taylor
- Office of Research and Ethics, Eastern Health, Melbourne, Australia
| | - Joanne Enticott
- Monash Centre for Health Research and Implementation, Monash University, Melbourne, Australia
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Chan T, Neill B, Murga A, Sojka K, Thakrar S, Nguyen Q, Felten C, Blaustein J, Falconer D, Marquez T, Wakamiya K, Hsu S, Houston D, Hertle N, Tabuena-Frolli S, Borgert M, Smith S, Oroudjev E. 1235P Analytical performance of PD-L1 IHC 28-8 pharmDx in gastric, gastroesophageal junction (GEJ), and esophageal carcinoma evaluated using combined positive score (CPS). Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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Tran M, Yoon S, Teoh M, Andersen S, Lam PY, Purdue BW, Raghubar A, Hanson SJ, Devitt K, Jones K, Walters S, Monkman J, Kulasinghe A, Tuong ZK, Soyer HP, Frazer IH, Nguyen Q. A robust experimental and computational analysis framework at multiple resolutions, modalities and coverages. Front Immunol 2022; 13:911873. [PMID: 35967449 PMCID: PMC9373800 DOI: 10.3389/fimmu.2022.911873] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 07/05/2022] [Indexed: 11/16/2022] Open
Abstract
The ability to study cancer-immune cell communication across the whole tumor section without tissue dissociation is needed, especially for cancer immunotherapy development, which requires understanding of molecular mechanisms and discovery of more druggable targets. In this work, we assembled and evaluated an integrated experimental framework and analytical process to enable genome-wide scale discovery of ligand-receptors potentially used for cellular crosstalks, followed by targeted validation. We assessed the complementarity of four different technologies: single-cell RNA sequencing and Spatial transcriptomic (measuring over >20,000 genes), RNA In Situ Hybridization (RNAscope, measuring 4-12 genes) and Opal Polaris multiplex protein staining (4-9 proteins). To utilize the multimodal data, we implemented existing methods and also developed STRISH (Spatial TRanscriptomic In Situ Hybridization), a computational method that can automatically scan across the whole tissue section for local expression of gene (e.g. RNAscope data) and/or protein markers (e.g. Polaris data) to recapitulate an interaction landscape across the whole tissue. We evaluated the approach to discover and validate cell-cell interaction in situ through in-depth analysis of two types of cancer, basal cell carcinoma and squamous cell carcinoma, which account for over 70% of cancer cases. We showed that inference of cell-cell interactions using scRNA-seq data can misdetect or detect false positive interactions. Spatial transcriptomics still suffers from misdetecting lowly expressed ligand-receptor interactions, but reduces false discovery. RNAscope and Polaris are sensitive methods for defining the location of potential ligand receptor interactions, and the STRISH program can determine the probability that local gene co-expression reflects true cell-cell interaction. We expect that the approach described here will be widely applied to discover and validate ligand receptor interaction in different types of solid cancer tumors.
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Affiliation(s)
- M. Tran
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - S. Yoon
- Genome Innovation Hub, The University of Queensland, Brisbane, QLD, Australia
| | - M. Teoh
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - S. Andersen
- Genome Innovation Hub, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience (IMB) Sequencing Facility, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - PY. Lam
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - B. W. Purdue
- Genome Innovation Hub, The University of Queensland, Brisbane, QLD, Australia
| | - A. Raghubar
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - SJ. Hanson
- School of Medical Science, Menzies Health Institute, Griffith University, Gold Coast, QLD, Australia
| | - K. Devitt
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - K. Jones
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - S. Walters
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - J. Monkman
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - A. Kulasinghe
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - ZK. Tuong
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council (MRC)-Laboratory of Molecular Biology, Brisbane, United Kingdom
- Cellular Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - HP. Soyer
- The University of Queensland Diamantina Institute, Dermatology Research Center, The University of Queensland, Brisbane, QLD, Australia
| | - I. H. Frazer
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Q. Nguyen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- *Correspondence: Q. Nguyen,
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Bhatti P, Jung J, Adenaw N, Swehla B, Kalaria A, Nguyen Q. Abstract No. 318 Fluoroscopy-guided versus CT-guided bone marrow aspiration and biopsies: comparison of patient radiation exposure, biopsy yield and cost. J Vasc Interv Radiol 2022. [DOI: 10.1016/j.jvir.2022.03.399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Bardin T, Ducrot YM, Nguyen Q, Letavernier E, Ea HK, Touzain F, Do DM, Corot J, Barguil Y, Biron A, Richette P, Collet C. POS1165 ASSOCIATION OF LDHD RARE VARIANTS WITH EARLY-ONSET GOUT IN TWO FAMILIES WITH AN ADDITIONAL ASSOCIATION OF RHBG VARIANT IN ONE. Ann Rheum Dis 2022. [DOI: 10.1136/annrheumdis-2022-eular.3016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BackgroundElevated lactate is known to favor urine urate reabsorption by the URAT1 urate/anion exchanger. Autosomal recessive gout caused by pathogenic variant in the LDHD gene encoding for D-lactate deshydrogenase has been recently identified in a large consanguineous Bedouin-Israeli kindred (1).ObjectivesWe report here on two families in whom early-onset gout was linked to other variants leading to deficient D-LDH enzymes.MethodsStudies of the two families were approved by appropriate Ethics committees. Whole exome sequencing (WES) was used to identify the genetic cause of familial gout. Dosages of D-lactate were performed on immediately frozen serum and urine samples by ELISA, using a D-lactate colorimetric assay kit (Abcam ab83429).ResultsFamily 1 was Melanesian, living in the Lifou island of New Caledonia. The two index patients were two sisters who developed gout at the age of 13 and 16 years respectively. When seen at the ages of 25 and 27 years, they both had severe gout with frequent polyarticular flares, and multiple tophi and destructive arthropathies in the earliest age of onset one. WES, performed on the 2 affected sisters, their non-consanguine parents, and an unaffected brother, showed that the 2 affected sisters carried homozygous rare variant in DLDH gene (NM_153486.3: c.206 C>T; rs1035398551). This variant was at heterozygote level in both parents and absent in the unaffected brother. It was considered as probably damaging according to in silico prediction software. No association with any other gene was found.The c.206C>T variant in LDHD was searched by Sanger sequencing method in 13 other extended family members. One 23 year-old brother of the two diseased sisters with atypical MTP flares, high uricemia and double contours at US examination of his MTPs, carried the c.206 C>T variant at the homozygous level. Three other heterozygous patients were found; two of whom were male with late-onset gout, the third one being a non-menopausal female with no gout. No variant carrier was found in the other 9 genotyped family members. The 3 homozygous patients for the c.206 C>T variant had very high hyperuricemia (range 738-834 was searched by Sanger sequencing method in 13 other extended family members. One 23 year-old brother of the two diseased sisters with atypical MTP flares, high uricemia and double contours at US examination of had very low or no D-lactate in plasma and urine. L-lactate blood and urine levels were normal in all subjects.Family 2 was Vietnamese, living in a remote area of central Vietnam. The two affected children suffered from an extremely severe, destructive gout, which started at the age of 21 years in a daughter and at the age of 9 in her youngest brother, who had developed for the last 3 years, dysarthria, night shakes, memory loss, urine incontinence and an inability to read and count and died at the age of 34, a few months after being seen by us. WES was performed in the two probands, their father and mother (who denied consanguinity), and an unaffected brother. An undescribed variant in LDHD (NM_153486.3: c.1363dupG) was identified in homozygous level in the 2 juvenile gout patients and at the heterozygous level in their 2 parents and unaffected brother. This variant led to a frameshift followed by a stop codon p.(AlaGly432fsTer58). In addition, the two juvenile gout patients were homozygous for an undescribed frameshift (NR_046115.1: c.1064dup) variant of the RHBG gene encoding for a Rhesus Blood Group family ammonium transporter. The two parents carried the heterozygous variant which was not identified in the non-gout brother.ConclusionWe report on 2 families in whom autosomal recessive juvenile gout was due to rare or undescribed, damaging LDHD gene variants. In addition, we observed in the Vietnamese family, an additional non-described frameshift homozygous variant in RHBG, the pathophysiological role of which deserves to be investigated.References[1]Drabkin M et al. Hyperuricemia and gout caused by missense mutation in D-lactate dehydrogenase. J Clin Invest. 2019;129:5163-5168Disclosure of InterestsThomas Bardin Consultant of: leo Pharma, Yves-Marie Ducrot: None declared, Quang Nguyen: None declared, Emmanuel Letavernier: None declared, Hang-Korng Ea: None declared, Frederic Touzain: None declared, Duc Minh Do: None declared, Julien Corot: None declared, Yan Barguil: None declared, Antoine Biron: None declared, Pascal Richette: None declared, Corinne Collet: None declared
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Nguyen Q, Bui Van Q, Nguyen Duy K, Nguyen Huu T, Cao Dac T, Nguyen Thi V. The prevalence and combination of gonorrhea and chlamydia in patients with urethritis and treatment outcome. J Sex Med 2022. [DOI: 10.1016/j.jsxm.2022.03.525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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15
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Nguyen Q, Van HD. Assessment of the results of treatment erectile dysfunction in diabetic patients by tadalafil 20mg once every there days. J Sex Med 2022. [DOI: 10.1016/j.jsxm.2022.03.429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Rivera J, Schechtman K, Glassman R, Mart M, Nguyen Q. Investigating SARS-CoV-2 Test Positivity Calculations Across US Jurisdictions. Int J Infect Dis 2022. [PMCID: PMC8884747 DOI: 10.1016/j.ijid.2021.12.270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Purpose Throughout the COVID-19 pandemic, many US epidemiologists and policymakers turned to an indicator called test positivity, or the percent of tests coming back positive for SARS-CoV-2, to contextualize COVID-19 case counts with testing volume. But the nation's patchworked health data infrastructure, composed of 56 systems managed by each state and territory, complicated efforts to calculate the metric in a comparable way across US jurisdictions. We set out to map jurisdictional reporting differences in test positivity and investigate whether they interfered with its effectiveness and comparability as an indicator. Understanding these differences is important because jurisdictional test positivity informed consequential policy and individuals’ understanding of risk in their communities. Methods & Materials We surveyed the health department websites of all US states and territories to examine how these jurisdictions were presenting test positivity on COVID-19 dashboards. When details about definitions were unavailable on jurisdictional websites, we reached out to jurisdictional public health officials for clarification. We also scored jurisdictions' presentations against best practices we identified for calculating the metric. Results Among the 48 states and territories posting test positivity values, we observed no consensus on how to calculate the metric—jurisdictions used different units, test types, averaging techniques, and dating schemes. By looking at data for jurisdictions that posted multiple test positivity metrics, we observed that these definitional differences could result in variations from 31% to 300%. Only four states were following all ten of the best practices for reporting test positivity. Conclusion The sheer number of ways states and territories define test positivity is alarming, given how much the indicator influenced US COVID-19 policy. Based on our survey, we believe the confidence of regulators in the precision and national comparability of test positivity is misplaced: The metric's value reflects state and territorial reporting decisions as much as actual viral prevalence. These findings underscore the need to invest in centralized public health infrastructure and create national reporting standards to improve unity of state reporting.
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Schechtman K, Rivera J, Nguyen Q, Glassman R, Mart M. Evaluating the Quality of Federal SARS-CoV-2 Diagnostic Testing Data. Int J Infect Dis 2022. [PMCID: PMC8884835 DOI: 10.1016/j.ijid.2021.12.071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Purpose In April 2020, the US Department of Health and Human Services (HHS) and the US Centers for Disease Control and Prevention established the COVID-19 Electronic Laboratory Reporting program (CELR) to collect data on SARS-CoV-2 laboratory tests. Over the course of the following year, the federal government, partnering with the Association for Public Health Laboratories, onboarded every state to submit laboratory results to this system—the first of its kind in the US. We set out to evaluate the quality of data collected by CELR. Methods & Materials We compared jurisdiction-level data collected through CELR and published by HHS to the testing data published by jurisdictions on their health department webpages. Because jurisdictions define their testing data differently, we anticipated some differences from federal testing data. However, jurisdictions also tend to prioritize their dashboard reporting—since it is what is used for policy decisions like reopening—so we hypothesized that differences from federal data absent a definitional explanation could point to problems with federal data. Where we found differences between jurisdictional and federal data, we conducted interviews with public health officials to understand their cause. Results Of the 56 states and territories, as of April 2021 (the first month when all states were onboarded to CELR), 38 had federal total data that diverges from state data by more than 5%. Of those states, the differences of 27 could not be explained by definitional factors. Based on our interviews, we identified three problems: non-electronic reporting streams, out-of-date surveillance systems, and deduplication of laboratory data. Conclusion The federal testing dataset displays major unresolved quality problems, and because states present testing data so differently, state-published data forms a poor alternative to federal datasets. The federal government, which is uniquely positioned to provide testing data on infectious diseases, must work to improve the quality of laboratory data submissions by states. To support better national laboratory data, the United States should invest in updating state and laboratory data surveillance infrastructure—including updates to state surveillance systems and laboratory system updates to eliminate outdated reporting methods like faxes—and in creating more national laboratory data infrastructure.
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Han Y, Villarreal-Ponce A, Gutierrez G, Nguyen Q, Sun P, Wu T, Sui B, Berx G, Brabletz T, Kessenbrock K, Zeng YA, Watanabe K, Dai X. Coordinate control of basal epithelial cell fate and stem cell maintenance by core EMT transcription factor Zeb1. Cell Rep 2022; 38:110240. [PMID: 35021086 PMCID: PMC9894649 DOI: 10.1016/j.celrep.2021.110240] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [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: 06/05/2021] [Revised: 09/30/2021] [Accepted: 12/16/2021] [Indexed: 02/04/2023] Open
Abstract
Maintenance of undifferentiated, long-lived, and often quiescent stem cells in the basal compartment is important for homeostasis and regeneration of multiple epithelial tissues, but the molecular mechanisms that coordinately control basal cell fate and stem cell quiescence are elusive. Here, we report an epithelium-intrinsic requirement for Zeb1, a core transcriptional inducer of epithelial-to-mesenchymal transition, for mammary epithelial ductal side branching and for basal cell regenerative capacity. Our findings uncover an evolutionarily conserved role of Zeb1 in promoting basal cell fate over luminal differentiation. We show that Zeb1 loss results in increased basal cell proliferation at the expense of quiescence and self-renewal. Moreover, Zeb1 cooperates with YAP to activate Axin2 expression, and inhibition of Wnt signaling partially restores stem cell function to Zeb1-deficient basal cells. Thus, Zeb1 is a transcriptional regulator that maintains both basal cell fate and stem cell quiescence, and it functions in part through suppressing Wnt signaling.
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Affiliation(s)
- Yingying Han
- Department of Biological Chemistry, School of Medicine, D250 Med Sci I, University of California, Irvine, Irvine, CA 92697-1700, USA,These authors contributed equally
| | - Alvaro Villarreal-Ponce
- Department of Biological Chemistry, School of Medicine, D250 Med Sci I, University of California, Irvine, Irvine, CA 92697-1700, USA,These authors contributed equally
| | - Guadalupe Gutierrez
- Department of Biological Chemistry, School of Medicine, D250 Med Sci I, University of California, Irvine, Irvine, CA 92697-1700, USA
| | - Quy Nguyen
- Department of Biological Chemistry, School of Medicine, D250 Med Sci I, University of California, Irvine, Irvine, CA 92697-1700, USA
| | - Peng Sun
- Department of Biological Chemistry, School of Medicine, D250 Med Sci I, University of California, Irvine, Irvine, CA 92697-1700, USA
| | - Ting Wu
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-yang Road, Shanghai 200031, China
| | - Benjamin Sui
- Department of Biological Chemistry, School of Medicine, D250 Med Sci I, University of California, Irvine, Irvine, CA 92697-1700, USA
| | - Geert Berx
- Molecular and Cellular Oncology Lab, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, 9052 Zwijnaarde, Belgium,Cancer Research Institute Ghent, Ghent, Belgium
| | - Thomas Brabletz
- Department of Experimental Medicine, Nikolaus-Fiebiger-Center for Molecular Medicine I, University, Erlangen-Nuernberg Glueckstr. 6, 91054 Erlangen, Germany
| | - Kai Kessenbrock
- Department of Biological Chemistry, School of Medicine, D250 Med Sci I, University of California, Irvine, Irvine, CA 92697-1700, USA
| | - Yi Arial Zeng
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-yang Road, Shanghai 200031, China
| | - Kazuhide Watanabe
- Department of Biological Chemistry, School of Medicine, D250 Med Sci I, University of California, Irvine, Irvine, CA 92697-1700, USA,RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Xing Dai
- Department of Biological Chemistry, School of Medicine, D250 Med Sci I, University of California, Irvine, Irvine, CA 92697-1700, USA,Lead contact,Correspondence:
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19
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Selvakumar D, Clayton Z, Prowse A, Dingwall S, George J, Shah H, Paterson H, Jeyaprakesh P, Wu Z, Campbell T, Kotake Y, Turnbull S, Nguyen Q, Grieve S, Palpant N, Pathan F, Kizana E, Kumar S, Gray P, Chong J. Cellular Heterogeneity of Pluripotent Stem Cell Derived Cardiomyocyte Grafts is Mechanistically Linked to Treatable Arrhythmias. Heart Lung Circ 2022. [DOI: 10.1016/j.hlc.2022.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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20
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White A, Nguyen Q, Hong Y, Moon M, Wang S, Wang W. RAPID DEPLOYMENT VALVES ARE ADVANTAGEOUS IN THE REDO SETTING: COHORT STUDY. Can J Cardiol 2021. [DOI: 10.1016/j.cjca.2021.07.190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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21
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Das BK, Kannan A, Nguyen Q, Gogoi J, Zhao H, Gao L. Selective Inhibition of Aurora Kinase A by AK-01/LY3295668 Attenuates MCC Tumor Growth by Inducing MCC Cell Cycle Arrest and Apoptosis. Cancers (Basel) 2021; 13:cancers13153708. [PMID: 34359608 PMCID: PMC8345130 DOI: 10.3390/cancers13153708] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/17/2021] [Accepted: 07/20/2021] [Indexed: 12/31/2022] Open
Abstract
Merkel cell carcinoma (MCC) is an often-lethal skin cancer with increasing incidence and limited treatment options. Although immune checkpoint inhibitors (ICI) have become the standard of care in advanced MCC, 50% of all MCC patients are ineligible for ICIs, and amongst those treated, many patients develop resistance. There is no therapeutic alternative for these patients, highlighting the urgent clinical need for alternative therapeutic strategies. Using patient-derived genetic insights and data generated in our lab, we identified aurora kinase as a promising therapeutic target for MCC. In this study, we examined the efficacy of the recently developed and highly selective AURKA inhibitor, AK-01 (LY3295668), in six patient-derived MCC cell lines and two MCC cell-line-derived xenograft mouse models. We found that AK-01 potently suppresses MCC survival through apoptosis and cell cycle arrest, particularly in MCPyV-negative MCC cells without RB expression. Despite the challenge posed by its short in vivo durability upon discontinuation, the swift and substantial tumor suppression with low toxicity makes AK-01 a strong potential candidate for MCC management, particularly in combination with existing regimens.
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Affiliation(s)
- Bhaba K. Das
- Southern California Institute for Research and Education, Long Beach, CA 90822, USA; (B.K.D.); (J.G.); (H.Z.)
- Veterans Affairs Long Beach Healthcare System, Long Beach, CA 90822, USA;
| | - Aarthi Kannan
- Veterans Affairs Long Beach Healthcare System, Long Beach, CA 90822, USA;
- Department of Dermatology, University of California, Irvine, CA 92697, USA
| | - Quy Nguyen
- Genomics High Throughput Sequencing Facility, Department of Biological Chemistry, University of California, Irvine, CA 92697, USA;
| | - Jyoti Gogoi
- Southern California Institute for Research and Education, Long Beach, CA 90822, USA; (B.K.D.); (J.G.); (H.Z.)
| | - Haibo Zhao
- Southern California Institute for Research and Education, Long Beach, CA 90822, USA; (B.K.D.); (J.G.); (H.Z.)
- Veterans Affairs Long Beach Healthcare System, Long Beach, CA 90822, USA;
| | - Ling Gao
- Southern California Institute for Research and Education, Long Beach, CA 90822, USA; (B.K.D.); (J.G.); (H.Z.)
- Veterans Affairs Long Beach Healthcare System, Long Beach, CA 90822, USA;
- Department of Dermatology, University of California, Irvine, CA 92697, USA
- Correspondence:
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22
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Sun P, Vu R, Dragan M, Haensel D, Gutierrez G, Nguyen Q, Greenberg E, Chen Z, Wu J, Atwood S, Pearlman E, Shi Y, Han W, Kessenbrock K, Dai X. OVOL1 Regulates Psoriasis-Like Skin Inflammation and Epidermal Hyperplasia. J Invest Dermatol 2021; 141:1542-1552. [PMID: 33333123 PMCID: PMC8532526 DOI: 10.1016/j.jid.2020.10.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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] [Received: 06/17/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 12/21/2022]
Abstract
Psoriasis is a common inflammatory skin disease characterized by aberrant inflammation and epidermal hyperplasia. Molecular mechanisms that regulate psoriasis-like skin inflammation remain to be fully understood. Here, we show that the expression of Ovol1 (encoding ovo-like 1 transcription factor) is upregulated in psoriatic skin, and its deletion results in aggravated psoriasis-like skin symptoms following stimulation with imiquimod. Using bulk and single-cell RNA sequencing, we identify molecular changes in the epidermal, fibroblast, and immune cells of Ovol1-deficient skin that reflect an altered course of epidermal differentiation and enhanced inflammatory responses. Furthermore, we provide evidence for excessive full-length IL-1α signaling in the microenvironment of imiquimod-treated Ovol1-deficient skin that functionally contributes to immune cell infiltration and epidermal hyperplasia. Collectively, our study uncovers a protective role for OVOL1 in curtailing psoriasis-like inflammation and the associated skin pathology.
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Affiliation(s)
- Peng Sun
- Department of Biological Chemistry, University of California, Irvine, California, USA
| | - Remy Vu
- Department of Biological Chemistry, University of California, Irvine, California, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, California, USA
| | - Morgan Dragan
- Department of Biological Chemistry, University of California, Irvine, California, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, California, USA
| | - Daniel Haensel
- Department of Biological Chemistry, University of California, Irvine, California, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, California, USA
| | - Guadalupe Gutierrez
- Department of Biological Chemistry, University of California, Irvine, California, USA
| | - Quy Nguyen
- Department of Biological Chemistry, University of California, Irvine, California, USA
| | - Elyse Greenberg
- Department of Biological Chemistry, University of California, Irvine, California, USA
| | - Zeyu Chen
- Department of Biological Chemistry, University of California, Irvine, California, USA; Department of Dermatology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China; Institute of Psoriasis, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Jie Wu
- Department of Biological Chemistry, University of California, Irvine, California, USA
| | - Scott Atwood
- Department of Developmental and Cell Biology, University of California, Irvine, California, USA
| | - Eric Pearlman
- Department of Ophthalmology and Department of Physiology and Biophysics, University of California, Irvine, California, USA
| | - Yuling Shi
- Institute of Psoriasis, Tongji University School of Medicine, Shanghai, People's Republic of China; Department of Dermatology, Shanghai Skin Disease Hospital, Tongji University School of Medicine, People's Republic of China
| | - Wei Han
- Laboratory of Regeneromics, School of Pharmacy, Shanghai Jiaotong University, Shanghai, People's Republic of China
| | - Kai Kessenbrock
- Department of Biological Chemistry, University of California, Irvine, California, USA
| | - Xing Dai
- Department of Biological Chemistry, University of California, Irvine, California, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, California, USA.
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23
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Haensel D, Jin S, Sun P, Cinco R, Dragan M, Nguyen Q, Cang Z, Gong Y, Vu R, MacLean AL, Kessenbrock K, Gratton E, Nie Q, Dai X. Defining Epidermal Basal Cell States during Skin Homeostasis and Wound Healing Using Single-Cell Transcriptomics. Cell Rep 2021; 30:3932-3947.e6. [PMID: 32187560 PMCID: PMC7218802 DOI: 10.1016/j.celrep.2020.02.091] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [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: 09/14/2019] [Revised: 01/07/2020] [Accepted: 02/25/2020] [Indexed: 01/17/2023] Open
Abstract
Our knowledge of transcriptional heterogeneities in epithelial stem and progenitor cell compartments is limited. Epidermal basal cells sustain cutaneous tissue maintenance and drive wound healing. Previous studies have probed basal cell heterogeneity in stem and progenitor potential, but a comprehensive dissection of basal cell dynamics during differentiation is lacking. Using single-cell RNA sequencing coupled with RNAScope and fluorescence lifetime imaging, we identify three non-proliferative and one proliferative basal cell state in homeostatic skin that differ in metabolic preference and become spatially partitioned during wound re-epithelialization. Pseudotemporal trajectory and RNA velocity analyses predict a quasi-linear differentiation hierarchy where basal cells progress from Col17a1Hi/Trp63Hi state to early-response state, proliferate at the juncture of these two states, or become growth arrested before differentiating into spinous cells. Wound healing induces plasticity manifested by dynamic basal-spinous interconversions at multiple basal transcriptional states. Our study provides a systematic view of epidermal cellular dynamics, supporting a revised “hierarchical-lineage” model of homeostasis. Haensel et al. performed a comprehensive dissection of the cellular makeup of skin during homeostasis and wound healing and the molecular heterogeneity and cellular dynamics within its stem-cell-containing epidermal basal layer. Their work provides insights and stimulates further investigation into the mechanism of skin maintenance and repair.
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Affiliation(s)
- Daniel Haensel
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697, USA
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA 92627, USA
- These authors contributed equally
| | - Suoqin Jin
- Department of Mathematics, University of California, Irvine, CA 92697, USA
- These authors contributed equally
| | - Peng Sun
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697, USA
| | - Rachel Cinco
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA
| | - Morgan Dragan
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697, USA
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA 92627, USA
| | - Quy Nguyen
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697, USA
| | - Zixuan Cang
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA 92627, USA
- Department of Mathematics, University of California, Irvine, CA 92697, USA
| | - Yanwen Gong
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA
| | - Remy Vu
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697, USA
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA 92627, USA
| | - Adam L. MacLean
- Department of Mathematics, University of California, Irvine, CA 92697, USA
| | - Kai Kessenbrock
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697, USA
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA
| | - Qing Nie
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA 92627, USA
- Department of Mathematics, University of California, Irvine, CA 92697, USA
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
- Correspondence: (Q.N.), (X.D.)
| | - Xing Dai
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697, USA
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA 92627, USA
- Lead Contact
- Correspondence: (Q.N.), (X.D.)
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24
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Alshetaiwi H, Pervolarakis N, McIntyre LL, Ma D, Nguyen Q, Rath JA, Nee K, Hernandez G, Evans K, Torosian L, Silva A, Walsh C, Kessenbrock K. Defining the emergence of myeloid-derived suppressor cells in breast cancer using single-cell transcriptomics. Sci Immunol 2020; 5:5/44/eaay6017. [PMID: 32086381 PMCID: PMC7219211 DOI: 10.1126/sciimmunol.aay6017] [Citation(s) in RCA: 247] [Impact Index Per Article: 61.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 01/23/2020] [Indexed: 12/26/2022]
Abstract
Myeloid-derived suppressor cells (MDSCs) are innate immune cells that acquire the capacity to suppress adaptive immune responses during cancer. It remains elusive how MDSCs differ from their normal myeloid counterparts, which limits our ability to specifically detect and therapeutically target MDSCs during cancer. Here, we sought to determine the molecular features of breast cancer-associated MDSCs using the widely studied mouse model based on the mouse mammary tumor virus (MMTV) promoter-driven expression of the polyomavirus middle T oncoprotein (MMTV-PyMT). To identify MDSCs in an unbiased manner, we used single-cell RNA sequencing to compare MDSC-containing splenic myeloid cells from breast tumor-bearing mice with wild-type controls. Our computational analysis of 14,646 single-cell transcriptomes revealed that MDSCs emerge through an aberrant neutrophil maturation trajectory in the spleen that confers them an immunosuppressive cell state. We establish the MDSC-specific gene signature and identify CD84 as a surface marker for improved detection and enrichment of MDSCs in breast cancers.
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Affiliation(s)
- Hamad Alshetaiwi
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA.,Department of Pathology, University of Hail, Hail 2440, Saudi Arabia
| | - Nicholas Pervolarakis
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | - Laura Lynn McIntyre
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Dennis Ma
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Quy Nguyen
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Jan Akara Rath
- Ludwig Institute for Cancer Research, University of Lausanne, Epalinges 1066, Switzerland
| | - Kevin Nee
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Grace Hernandez
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA
| | - Katrina Evans
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA
| | - Leona Torosian
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Anushka Silva
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Craig Walsh
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Kai Kessenbrock
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA.
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25
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Wang K, Youngson E, Nikhanj A, Nguyen Q, Qi A, Thomas J, McAlister F, Oudit G. Differential trajectories in LVEF predicts divergent clinical outcomes in HFrEF patients. Eur Heart J 2020. [DOI: 10.1093/ehjci/ehaa946.0929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Recovery or improvement in LVEF is observed in many HFrEF patients following optimal medical management and device therapies, but whether this reflects true myocardial recovery remains controversial and the significance of LVEF decompensation in relation to clinical outcomes is unclear.
Purpose
To elucidate clinical characteristics and assess prognosis of HFrEF patients with differential trajectories in LVEF.
Methods
Heart failure (HF) patients were enrolled in a prospective Heart Function registry from outpatient cardiology clinics at an academic institution between Feb 2018 and Nov 2019. Retrospective analysis was conducted on 2D-echocardiography (echo) performed between Jan 2009 and Nov 2019. In total, 590 patients met the inclusion criteria with ≥2 repeated echo evaluations separated by ≥1 year. Patient demographics and clinical characteristics at enrollment were collected through review of medical records. Cardiovascular and HF specific admissions were captured using the corresponding ICD-10-CA codes. During a median follow-up of 5.9 years (IQR: 3.1 to 8.5 years) from the first echo date, clinical outcomes were assessed through composite mortality and hospitalizations endpoints.
Results
We identified 3 independent cohorts with 279 patients having permanently reduced LVEF (<40%, HFrEF), 236 patients with recovered LVEF (>40% on serial evaluations, HFrecEF) and 75 patients with subsequent decompensation in LVEF (>40%, then <40%, HFdecEF) following initial recovery. Use of ACE inhibitors or ARBs (94% vs. 99% vs. 91%) and beta blockers (88% vs. 87% vs. 87%) at baseline echo was similar amongst HFrEF, HFrecEF and HFdecEF cohorts respectively. HFrecEF cohort had higher usage of MRA (55% vs. 65% vs. 44%, p=0.002) and diuretics (74% vs. 80% vs. 65%, p=0.026). HFdecEF cohort was characterized by a predominance of males (80% vs. 69% vs. 80%, p=0.01), and more patients with ischemic etiology (41% vs. 28% vs. 60%, p<0.001) compared with the HFrecEF cohort and resembled more closely to demographics of the HFrEF cohort. Median LVEF at baseline echo was similar across the cohorts. However, HFdecEF cohort had lower LV end-diastolic diameter (p<0.001), LV end-systolic diameter (p<0.001) and LV mass (p=0.01) compared with the HFrEF cohort sharing similarities with the HFrecEF cohort on baseline echo, suggesting lesser extent of adverse cardiac remodeling in both HFrecEF and HFdecEF cohorts initially. Over a median 5.9 years follow-up, HFdecEF and HFrEF patients had a significantly higher risk (compared to those with HFrecEF) of composite all-cause mortality with all-cause (80% vs. 75% vs. 57%, p=0.004), cardiovascular (48% vs. 50% vs. 29%, p=0.001) and HF hospitalizations (31% vs. 32% vs. 16%, p=0.004).
Conclusion
HFrEF patients who never recover their LVEF and patients with decompensation in LVEF following initial recovery represent a clinically higher risk group than patients who remained recovered during follow-up.
Funding Acknowledgement
Type of funding source: Foundation. Main funding source(s): University of Alberta Hospital Foundation, Canadian Institutes of Health Research
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Affiliation(s)
- K Wang
- Mazankowski Alberta Heart Institute, Edmonton, Canada
| | | | - A Nikhanj
- Mazankowski Alberta Heart Institute, Edmonton, Canada
| | - Q Nguyen
- Mazankowski Alberta Heart Institute, Edmonton, Canada
| | - A Qi
- Mazankowski Alberta Heart Institute, Edmonton, Canada
| | - J Thomas
- Mazankowski Alberta Heart Institute, Edmonton, Canada
| | - F McAlister
- Mazankowski Alberta Heart Institute, Edmonton, Canada
| | - G.Y Oudit
- Mazankowski Alberta Heart Institute, Edmonton, Canada
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26
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Zhang H, Jamieson K, Grenier J, Nikhanj A, Tang J, Nguyen Q, Wang S, Thompson R, Seubert J, Oudit G. Myocardial iron depletion exacerbates end-stage heart failure by promoting adverse remodeling and worsening mitochondrial function. Eur Heart J 2020. [DOI: 10.1093/ehjci/ehaa946.1144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Heart failure (HF) is highly associated with systemic iron deficiency (ID) yet its association with myocardial iron depletion (MID) remains barely unveiled. Similarly, it has been unclear whether and how MID deteriorates the progression to advanced HF. Furthermore, neither the underlying pathophysiology nor the negative impact of unmet iron availability to the failing heart, at the molecular level, is elucidated.
Purpose
We aim to integrate clinical information and experimental data from human explanted heart tissues: 1) to establish the defining criterion of MID in advanced HF population; 2) to recapitulate the pathophysiological role MID plays in the progression of HF; and 3) to identify novel HF molecular signatures or potential cures to correct MID status underestimated in the failing hearts.
Methods
Adult failing hearts (N=143), including dilated (n=76) and ischemic (n=67) cardiomyopathies, and non-failing control hearts (NFC, N=46) were collected per Human Explanted Heart Program. Iron levels were measured directly from both ventricles, which were re-evaluated by cardiac magnetic resonance imaging (CMR) mapping sequences (e.g. T1, T2*, etc.). Mitochondrial metabolic, reactive oxygen species (ROS) and ROS-scavenging profiles were assessed spectrophotometrically. Tissue remodeling and ultrastructure characteristics were captured by confocal and electron microscopies respectively. Meanwhile, the patients' clinical profiles were integrated into the analysis of molecular regulatory mechanism.
Results
Myocardial iron content in LV was significantly lower in HF versus NFC [121.4 (88.1–150.3) vs. 137.4 (109.2–165.9) μg/g dry weight, p<0.05], while both RVs showed no difference. With a cutoff of 86.1 μg/g iron level in LV, it screened ∼23% HF patients with MID (HF-MID). Compared with non-MID HF patients, depleted iron store weakly correlated with systemic hemoglobin concentration (r=−0.27, p=0.13) but highly with T2* and magnetic susceptibility proving CMR as an exceptional surrogate for non-invasive diagnosis. And it was noted that MID independently predicted ominous endpoints as NYHA grade increased and LV dysfunctions worsened (all p<0.05). Cardiac respiratory chain enzymatic activities from complex I to V (except for COX III) were further suppressed in the iron-deficient failing hearts, indicating altered myocardial metabolism and excessive ROS production. Moreover, the whole anti-ROS defense were severely impaired, consistent with remarkably inverse tissue remodeling and ultrastructure disintegrity in HF-MID. Mechanistically, two iron-regulatory proteins (IRP-1/2) and following iron trafficking pathways were inactivated possibly determine the restricted iron availability to advanced failing hearts.
Conclusions
MID worsens HF progression primarily mediated by mitochondrial dysfunction and collapsed oxidative protection in LV, independently predicting an inferior prognosis. CMR demonstrates clinical potential to monitor MID.
Funding Acknowledgement
Type of funding source: Public grant(s) – National budget only. Main funding source(s): Canadian Institutes for Health Research (CIHR); Heart & Stroke Foundation (HSF)
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Affiliation(s)
- H Zhang
- University of Alberta, Division of Cardiology, Department of Medicine, Edmonton, Canada
| | - K.L Jamieson
- University of Alberta, Department of Pharmacology, Edmonton, Canada
| | - J Grenier
- University of Alberta, Department of Biomedical Engineering, Edmonton, Canada
| | - A Nikhanj
- University of Alberta, Division of Cardiology, Department of Medicine, Edmonton, Canada
| | - J Tang
- University of Alberta, Division of Cardiology, Department of Medicine, Edmonton, Canada
| | - Q Nguyen
- University of Alberta, Division of Cardiology, Department of Medicine, Edmonton, Canada
| | - S Wang
- Mazankowski Alberta Heart Institute, Edmonton, Canada
| | - R.B Thompson
- University of Alberta, Department of Biomedical Engineering, Edmonton, Canada
| | - J.M Seubert
- University of Alberta, Department of Pharmacology, Edmonton, Canada
| | - G.Y Oudit
- University of Alberta, Division of Cardiology, Department of Medicine, Edmonton, Canada
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27
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Gunnarsdottir O, Kim Y, Reichart D, Nguyen Q, Zhang H, Nikhanj A, Pereira A, Gorham J, Depalma S, Seidman J, Oudit G, Seidman C. Discovery and analyses of pathogenic variants in explanted hearts from primary cardiomyopathy patients. Eur Heart J 2020. [DOI: 10.1093/ehjci/ehaa946.2097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Dilated cardiomyopathy (DCM) and hypertrophic cardiomyopathy (HCM) are disorders of the myocardium that affect the structure and function of the heart.
Purpose
The primary aim of this study was to discover damaging genetic variants in myocardial tissue from patients with DCM or HCM, who underwent heart transplantation.
Methods
Whole exome sequencing was performed on myocardial tissue from 103 explanted hearts with diagnosis of cardiomyopathy; 80 DCM and 13 HCM. Sanger sequencing was performed to confirm the loss-of-function variants in genes known to be linked to cardiomyopathy. RNA sequencing was conducted to confirm copy number variation deletions detected in the cohort. Burden analysis was performed by comparing the frequency of variants found in the study cohort to the frequency in the population database gnomAD.
Results
Rare (minor allele frequency <1.0E-04) loss-of-function variants, deleterious missense variants, or copy number variation deletions, collectively described as damaging variants, were identified in cardiomyopathy genes in 42 of all 93 samples (45.2%). Damaging variants were identified in 37 of 80 DCM samples (46.3%) and 5 of 13 HCM samples (38.4%). The mean read depth for normal and variant allele were comparable. All the 28 loss-of-function variants in cardiomyopathy genes found in the cardiomyopathy cases were confirmed by Sanger sequencing. Two copy number variation deletions both in titin (TTN) were also detected and confirmed. Burden analyses showed that the genes TTN and lamin A/C (LMNA) had a higher frequency of loss-of function variants in the DCM cohort (17.5% and 3.75%, respectively) compared to the reference population with genome-wide significance (p=3.45E-22 and 4.34E-07, respectively). Furthermore, our analysis showed that deleterious missense variants in osteoclast-stimulating factor 1 (OSTF1), which previously has not been associated with cardiomyopathy, was highly enriched in the DCM cohort compared to the reference population (p=2.10E-06).
Conclusions
The frequency of damaging variants that are likely pathogenic (46.3%) is higher in DCM cases in this cohort compared to previous studies. These data indicate that patients with end-stage DCM are more likely to have a genetic cause for their disease. As read depth of variant and normal alleles were, these are likely germline and not mosaic variants, and can enable cascade testing in family members. Moreover, our study demonstrates that CNVs in TTN that alter the reading frame can cause DCM.
Funding Acknowledgement
Type of funding source: None
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Affiliation(s)
| | - Y Kim
- Harvard Medical School, Boston, United States of America
| | - D Reichart
- Harvard Medical School, Boston, United States of America
| | - Q Nguyen
- University of Alberta, Edmonton, Canada
| | - H Zhang
- University of Alberta, Edmonton, Canada
| | - A Nikhanj
- University of Alberta, Edmonton, Canada
| | - A.C Pereira
- Harvard Medical School, Boston, United States of America
| | - J Gorham
- Harvard Medical School, Boston, United States of America
| | - S.R Depalma
- Harvard Medical School, Boston, United States of America
| | - J.G Seidman
- Harvard Medical School, Boston, United States of America
| | - G Oudit
- University of Alberta, Edmonton, Canada
| | - C.E Seidman
- Harvard Medical School, Boston, United States of America
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28
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Maruyama R, Lim K, Nguyen Q, Tsoumpra M, Takeda S, Aoki Y, Yokota T. DMD – ANIMAL MODELS & PRECLINICAL TREATMENT. Neuromuscul Disord 2020. [DOI: 10.1016/j.nmd.2020.08.215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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29
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Nguyen Q, Coghlan K, Nagendran J, MacArthur R, Lam W. FACTORS ASSOCIATED WITH EARLY EXTUBATION AFTER CARDIAC SURGERY: A RETROSPECTIVE STUDY. Can J Cardiol 2020. [DOI: 10.1016/j.cjca.2020.07.189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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30
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Abstract
High quality Ge doping of GaN is demonstrated using primarily thermal neutrons for the first time. In this study, GaN was doped with Ge to concentrations from 1016 Ge atoms/cm3 to 1018 Ge atoms/cm3. The doping concentrations were measured using gamma-ray spectroscopy and confirmed using SIMS analysis. The data from SIMS analysis also show consistent Ge doping concentration throughout the depth of the GaN wafers. After irradiation, the GaN was annealed in a nitrogen environment at 950 °C for 30 min. The neutron doping process turns out to produce spatially uniform doping throughout the whole volume of the GaN substrate.
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Affiliation(s)
- R Barber
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, 65201, USA
| | - Q Nguyen
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, 65201, USA
| | - J Brockman
- University of Missouri Research Reactor, University of Missouri, Columbia, MO, 65201, USA
| | - J Gahl
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, 65201, USA.,University of Missouri Research Reactor, University of Missouri, Columbia, MO, 65201, USA
| | - J Kwon
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, 65201, USA.
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31
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Kumar T, Nguyen Q, Nee K, Bai S, Hu M, Sei E, Wood A, Wiley J, Chen H, Contreras A, Teshome M, Chen K, Lim B, Lawson D, Navin N, Kessenbrock K. Abstract 5702: A spatially resolved single cell atlas of the human breast. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-5702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The human breast consists of lobules connected to an intricate network of ducts that are surrounded by fatty tissues, designed to produce and transport milk to nourish offspring. Histopathology has identified 10 major cell types based on morphological features but have provided limited information on cell states - the transcriptional programs of cell types that reflect different biological functions. In this study we have generated an unbiased ‘cell atlas' of the normal human breast to define the cell types and cell states using single cell RNA sequencing and spatial transcriptomics methods. We performed 3' microdroplet based single cell and nuclei RNA sequencing of 248,687 stromal cells and 89,301 nuclei from 24 women with pathologically normal breast tissues that were collected from mastectomies and reduction mammoplasties. Unbiased expression analysis identified four major cell types: adipocytes, epithelial cells (luminal and basal), fibroblasts and endothelial cells and defined their transcriptional programs. Additionally, 8 minor cell types were identified in the breast, including macrophages, T-cells, natural killer cells, mast cells, pericytes, apocrine cells, neurons and smooth muscle cells. Our data revealed hundreds of novel markers of these cell types and defined their transcriptional programs and cell states. Most cell types had multiple transcriptional programs including luminal epithelial cells (hormone receptor positive and secretory), basal epithelial cells (myoepithelial or basal), endothelial cells (E1, E2, E3), myeloid cells, T-cells and fibroblasts (F1-F4) and provided insight into developmental lineages. We further delineated the spatial organization of these cell types and cell states within the tissue architecture using spatial transcriptomics assay. The breast cell atlas data provides an invaluable normal reference for the research community to understand how normal cell types are reprogrammed in diseases such as breast cancer.
Citation Format: Tapsi Kumar, Quy Nguyen, Kevin Nee, Shanshan Bai, Min Hu, Emi Sei, Anita Wood, Jie Wiley, Hui Chen, Alejandro Contreras, Mediget Teshome, Ken Chen, Bora Lim, Devon Lawson, Nicholas Navin, Kai Kessenbrock. A spatially resolved single cell atlas of the human breast [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5702.
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Affiliation(s)
- Tapsi Kumar
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Quy Nguyen
- 2University of California, Irvine, Irvine, CA
| | - Kevin Nee
- 2University of California, Irvine, Irvine, CA
| | - Shanshan Bai
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Min Hu
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Emi Sei
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Anita Wood
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jie Wiley
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Hui Chen
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Mediget Teshome
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ken Chen
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Bora Lim
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Nicholas Navin
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
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32
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COULIS G, Kastenschmidt J, Mannaa A, Nguyen Q, Pervolarakis N, Duarte J, Emami M, Yang C, Kessenbrock K, VILLALTA A. Regulatory T cells suppress novel skeletal muscle macrophages identified by single-cell RNA sequencing. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.145.41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Duchenne muscular dystrophy (DMD) is a lethal X-linked disorder that results from mutations in the dystrophin gene causing necrosis, inflammation and ultimately fibrosis. In DMD, muscle macrophages are multifaceted effector immune cells that regulate multiple pathogenic processes, including myofiber injury, inflammation and fibrosis, but also promote regeneration. Previously, we demonstrated that regulatory T cells (Tregs) ameliorated the severity of muscular dystrophy by regulating M1-like and M2-like macrophage activation, and more recently, a subset of undefined macrophages. Herein, we used single-cell RNA sequencing (scRNAseq) approaches to define the phenotypic complexity and transcriptional profile of muscle macrophages in healthy and dystrophic muscle. A T-distributed Stochastic Neighbor Embedding (t-SNE) analysis of gene expression data revealed that muscle macrophages clustered into six novel populations defined by unique transcriptional programs. We observed that a population expressing high levels of galectin-3 was absent in wildtype and dystrophic muscle before the onset of disease, but was increased at the onset of acute pathology and further expanded when Tregs were depleted in the mdx mouse model of DMD. In light of emerging evidence in the literature suggesting a role for galectin-3 and Tregs in fibrosis, we performed in vivo functional assays to underscore the role of the Treg-Macrophages axis in the control of fibrosis in DMD. Our data support a new paradigm, in which unique transcriptional programs define novel macrophage populations likely adapted to the diseased muscle milieu, and suggest that therapies focused on augmenting Tregs function in dystrophic muscle may be beneficial to treat fibrosis.
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Affiliation(s)
- Gerald COULIS
- 1Department of Physiology and Biophysics, University of California Irvine
| | | | - Ali Mannaa
- 1Department of Physiology and Biophysics, University of California Irvine
| | - Quy Nguyen
- 2Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697
| | - Nicholas Pervolarakis
- 2Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697
| | - Jorge Duarte
- 1Department of Physiology and Biophysics, University of California Irvine
| | - Melissa Emami
- 1Department of Physiology and Biophysics, University of California Irvine
| | - Catherine Yang
- 1Department of Physiology and Biophysics, University of California Irvine
| | - Kai Kessenbrock
- 2Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697
| | - Armando VILLALTA
- 1Department of Physiology and Biophysics, University of California Irvine
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Doost A, Rangel A, Nguyen Q, Morahan G, Arnolda L. 139 Micro-CT Scan With Virtual Dissection of Left Ventricle a Non-destructive, Reproducible, Alternative to Dissection and Weighing for Left Ventricular Size. Heart Lung Circ 2020. [DOI: 10.1016/j.hlc.2020.09.146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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34
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Nguyen Q, Wang B, Chen-Song D, Nikhanj A, Mirhosseini M, Cujec B, Ezekowitz J, DeKock I, Oudit G. SUPPORTIVE CARE IN HEART FAILURE: ESTABLISHING A NEW INTEGRATIVE CARE INITIATIVE. Can J Cardiol 2019. [DOI: 10.1016/j.cjca.2019.07.589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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35
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Jain P, Boso G, Langer S, Soonthornvacharin S, De Jesus PD, Nguyen Q, Olivieri KC, Portillo AJ, Yoh SM, Pache L, Chanda SK. Large-Scale Arrayed Analysis of Protein Degradation Reveals Cellular Targets for HIV-1 Vpu. Cell Rep 2019; 22:2493-2503. [PMID: 29490283 DOI: 10.1016/j.celrep.2018.01.091] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 11/05/2016] [Revised: 11/03/2017] [Accepted: 01/30/2018] [Indexed: 11/28/2022] Open
Abstract
Accessory proteins of lentiviruses, such as HIV-1, target cellular restriction factors to enhance viral replication. Systematic analyses of proteins that are targeted for degradation by HIV-1 accessory proteins may provide a better understanding of viral immune evasion strategies. Here, we describe a high-throughput platform developed to study cellular protein stability in a highly parallelized matrix format. We used this approach to identify cellular targets of the HIV-1 accessory protein Vpu through arrayed coexpression with 433 interferon-stimulated genes, followed by differential fluorescent labeling and automated image analysis. Among the previously unreported Vpu targets identified by this approach, we find that the E2 ligase mediating ISG15 conjugation, UBE2L6, and the transmembrane protein PLP2 are targeted by Vpu during HIV-1 infection to facilitate late-stage replication. This study provides a framework for the systematic and high-throughput evaluation of protein stability and establishes a more comprehensive portrait of cellular Vpu targets.
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Affiliation(s)
- Prashant Jain
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Guney Boso
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Simon Langer
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Stephen Soonthornvacharin
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Paul D De Jesus
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Quy Nguyen
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Kevin C Olivieri
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Alex J Portillo
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sunnie M Yoh
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Lars Pache
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.
| | - Sumit K Chanda
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.
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36
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Ho C, Trinh T, Nguyen A, Nguyen Q, Ercan A, Kavvas ML. Reconstruction and evaluation of changes in hydrologic conditions over a transboundary region by a regional climate model coupled with a physically-based hydrology model: Application to Thao river watershed. Sci Total Environ 2019; 668:768-779. [PMID: 30865907 DOI: 10.1016/j.scitotenv.2019.02.368] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/04/2019] [Accepted: 02/24/2019] [Indexed: 06/09/2023]
Abstract
The differences among countries in terms of physical features, governmental policies, priorities in short- and long-term water resources management may lead to conflicts in managing and sharing of water resources over the transboundary regions. Due to no formal data sharing agreement between countries, there has been usually no data availability at transboundary regions. In this study, a methodology, in which a physically-based hydrology model was coupled with a regional climate model, is proposed to reconstruct and evaluate hydrologic conditions over transboundary regions. For the case study, Thao river watershed (TRW), within Vietnam and China, was selected. The Watershed Environmental Hydrology (WEHY) model was implemented based on topography, soil, and land use/cover information which was retrieved from global satellite data resources. The watershed model-WEHY was first validated over the TRW, and then was used to reconstruct historical hydrologic conditions during 1950-2007. The results of this study suggest no significant trend in the annual streamflow over the target watershed. In addition, there is a time shift in the wet season between the upstream sector in China and the downstream sector in Vietnam over the TRW. The annual flow contribution from the upstream sector in China to the outlet of TRW is estimated to be around 66%, and the remaining 34% contribution comes from the downstream sector in Vietnam territory. Last but not the least, the annual flow as a function of return period varies not only with the return period but also as a function of the time window, reflecting the effect of the changing regime on the streamflows at the TRW. The evolution of the flow frequency through time is an evidence of the ongoing non-stationarity in the hydrologic conditions over TRW.
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Affiliation(s)
- C Ho
- The Key Laboratory of River and Coastal Engineering, Viet Nam.
| | - T Trinh
- Faculty of Hydrology and Water Resources, Thuy loi University, Viet Nam; Hydrologic Research Laboratory, Dept. of Civil and Environmental Engineering, Univ. of California, Davis, CA, United States of America.
| | - A Nguyen
- Hydrologic Research Laboratory, Dept. of Civil and Environmental Engineering, Univ. of California, Davis, CA, United States of America.
| | - Q Nguyen
- The Key Laboratory of River and Coastal Engineering, Viet Nam
| | - A Ercan
- J. Amorocho Hydraulics Laboratory, Dept. of Civil and Environmental Engineering, Univ. of California, Davis, CA, United States of America.
| | - M L Kavvas
- Hydrologic Research Laboratory, Dept. of Civil and Environmental Engineering, Univ. of California, Davis, CA, United States of America.
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37
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Keighley C, Chen SCA, Marriott D, Pope A, Chapman B, Kennedy K, Bak N, Underwood N, Wilson HL, McDonald K, Darvall J, Halliday C, Kidd S, Nguyen Q, Hajkowicz K, Sorrell TC, Van Hal S, Slavin MA. Candidaemia and a risk predictive model for overall mortality: a prospective multicentre study. BMC Infect Dis 2019; 19:445. [PMID: 31113382 PMCID: PMC6528341 DOI: 10.1186/s12879-019-4065-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 05/02/2019] [Indexed: 01/21/2023] Open
Abstract
Background Candidaemia is associated with high mortality. Variables associated with mortality have been published previously, but not developed into a risk predictive model for mortality. We sought to describe the current epidemiology of candidaemia in Australia, analyse predictors of 30-day all-cause mortality, and develop and validate a mortality risk predictive model. Methods Adults with candidaemia were studied prospectively over 12 months at eight institutions. Clinical and laboratory variables at time of blood culture-positivity were subject to multivariate analysis for association with 30-day all-cause mortality. A predictive score for mortality was examined by area under receiver operator characteristic curves and a historical data set was used for validation. Results The median age of 133 patients with candidaemia was 62 years; 76 (57%) were male and 57 (43%) were female. Co-morbidities included underlying haematologic malignancy (n = 20; 15%), and solid organ malignancy in (n = 25; 19%); 55 (41%) were in an intensive care unit (ICU). Non-albicans Candida spp. accounted for 61% of cases (81/133). All-cause 30-day mortality was 31%. A gastrointestinal or unknown source was associated with higher overall mortality than an intravascular or urologic source (p < 0.01). A risk predictive score based on age > 65 years, ICU admission, chronic organ dysfunction, preceding surgery within 30 days, haematological malignancy, source of candidaemia and antibiotic therapy for ≥10 days stratified patients into < 20% or ≥ 20% predicted mortality. The model retained accuracy when validated against a historical dataset (n = 741). Conclusions Mortality in patients with candidaemia remains high. A simple mortality risk predictive score stratifying patients with candidaemia into < 20% and ≥ 20% 30-day mortality is presented. This model uses information available at time of candidaemia diagnosis is easy to incorporate into decision support systems. Further validation of this model is warranted. Electronic supplementary material The online version of this article (10.1186/s12879-019-4065-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- C Keighley
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR, New South Wales Health Pathology, Westmead Hospital, Darcy Rd, 3rd Level, ICPMR Building, Westmead, Sydney, New South Wales, 2145, Australia. .,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia. .,Department of Infectious Diseases, Westmead Hospital, Westmead, Sydney, NSW, Australia.
| | - S C-A Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR, New South Wales Health Pathology, Westmead Hospital, Darcy Rd, 3rd Level, ICPMR Building, Westmead, Sydney, New South Wales, 2145, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Department of Infectious Diseases, Westmead Hospital, Westmead, Sydney, NSW, Australia
| | - D Marriott
- Department of Microbiology and Infectious Diseases, St. Vincent's Hospital, Sydney, NSW, Australia
| | - A Pope
- Eastern Health Clinical School, Monash University, Melbourne, Victoria, Australia.,School of Mathematics and Statistics, University of NSW, Sydney, NSW, Australia
| | - B Chapman
- Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - K Kennedy
- Department of Infectious Diseases and Microbiology, Canberra Hospital, Australian National University Medical School, Canberra, ACT, Australia
| | - N Bak
- Department of Infectious Diseases, Royal Adelaide Hospital, Adelaide, SA, Australia
| | - N Underwood
- Infection Management Services, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - H L Wilson
- Department of Infectious Diseases and Microbiology, Canberra Hospital, Australian National University Medical School, Canberra, ACT, Australia
| | - K McDonald
- Department of Microbiology and Infectious Diseases, St. Vincent's Hospital, Sydney, NSW, Australia
| | - J Darvall
- Department of Intensive Care, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - C Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR, New South Wales Health Pathology, Westmead Hospital, Darcy Rd, 3rd Level, ICPMR Building, Westmead, Sydney, New South Wales, 2145, Australia
| | - S Kidd
- National Mycology Reference Centre, SA Pathology, Adelaide, SA, Australia
| | - Q Nguyen
- National Centre for Clinical Excellence on Emerging Drugs of Concern (NCCRED), National Drug and Alcohol Research Centre (NDARC), University of New South Wales, Sydney, Australia
| | - K Hajkowicz
- Department of Infectious Diseases, Royal Brisbane and Women's Hospital, School of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - T C Sorrell
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Department of Infectious Diseases, Westmead Hospital, Westmead, Sydney, NSW, Australia.,Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - S Van Hal
- Department of Infectious Diseases and Microbiology, New South Wales Health Pathology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - M A Slavin
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, National Centre for Infections in Cancer, Melbourne, VIC, Australia
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38
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Alshetaiwi H, Pervolarakis N, McIntyre LL, Ma D, Nguyen Q, Nee K, Rath J, Evans K, Torosian L, Silva A, Walsh C, Kessenbrock K. Single cell RNA sequencing reveals distinct gene expression signatures of myeloidderived suppressor cells in breast cancer. The Journal of Immunology 2019. [DOI: 10.4049/jimmunol.202.supp.135.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Myeloid-derived suppressor cells (MDSCs) are a heterogeneous population of immature myeloid cells with potent immune suppressive activity. MDSCs regulate anti-tumor immunity by suppressing T cell proliferation. MDSCs can be further classified into granulocytic MDSCs (G-MDSCs) and monocytic MDSC (M-MDSCs). However, there is a lack of MDSC-specific markers since MDSCs, normal neutrophil granulocytes, and monocytes are defined by the same flow cytometry markers (CD11b+Gr1+). We used a breast cancer mouse model (MMTV-PyMT) to define cellular and molecular properties of MDSCs in single cell resolution. To test the capacity of MDSCs to inhibit immune responses, CD11b+Gr1+ cells from PyMT and wild type (WT) mice were sorted by fluorescence-activated cell sorting (FACS) from bone marrow, lung, and spleen, and then subjected to a T cell activation assay in co-culture with T cells. We found that predominantly spleen-derived CD11b+Gr1+ cells from PyMT significantly suppressed CD4 and CD8 T cell proliferation, while CD11b+Gr1+cells from bone marrow and lung showed no effect on T cell proliferation. Thus, we focused on spleen-derived CD11b+Gr1+ cells and utilized single cell RNA sequencing (scRNAseq) to compare breast cancer derived MDSCs to the respective cell populations harvested from normal, and non-tumor bearing hosts. Our computational analysis of 14,646 single cell transcriptomes revealed a separate G-MDSCs cluster from normal neutrophils and a M-MDSCs cluster from normal monocytes and a distinct gene expression signature for the entire MDSCs population. Our studies provide crucial insights into the biology of MDSCs, which may ultimately form the basis for novel marker and therapeutic avenues to improve cancer immunotherapy.
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Affiliation(s)
- Hamad Alshetaiwi
- 1Univ. of California, Irvine, Sch. of Med
- 2Chao Family Comprehensive Cancer Center
- 3Institute for Immunology
| | - Nicholas Pervolarakis
- 1Univ. of California, Irvine, Sch. of Med
- 2Chao Family Comprehensive Cancer Center
- 4Center for Complex Biological Systems
| | | | - Dennis Ma
- 1Univ. of California, Irvine, Sch. of Med
- 2Chao Family Comprehensive Cancer Center
| | - Quy Nguyen
- 1Univ. of California, Irvine, Sch. of Med
- 2Chao Family Comprehensive Cancer Center
| | - Kevin Nee
- 1Univ. of California, Irvine, Sch. of Med
- 2Chao Family Comprehensive Cancer Center
| | - Jan Rath
- 1Univ. of California, Irvine, Sch. of Med
| | - Katrina Evans
- 1Univ. of California, Irvine, Sch. of Med
- 2Chao Family Comprehensive Cancer Center
| | - Leona Torosian
- 6Univ. of California, Irvine, Sch. of Health and Pharmaceutical Sci
| | - Anushka Silva
- 6Univ. of California, Irvine, Sch. of Health and Pharmaceutical Sci
| | - Craig Walsh
- 3Institute for Immunology
- 5Univ. of California, Irvine, Sch. of Bio
| | - Kai Kessenbrock
- 1Univ. of California, Irvine, Sch. of Med
- 2Chao Family Comprehensive Cancer Center
- 3Institute for Immunology
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39
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Greilach SA, McIntyre LL, Hasselmann J, Othy S, Nguyen Q, Kessenbrock K, Cahalan MD, Blurton-Jones M, Lane T, Walsh CM. Human neural stem cells induce central nervous system specific regulatory T cells from the ex Treg pool and promote repair in models of multiple sclerosis. The Journal of Immunology 2019. [DOI: 10.4049/jimmunol.202.supp.193.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Multiple Sclerosis (MS) is a chronic inflammatory autoimmune disease affecting the central nervous system (CNS) and for which there is no cure. Current treatments focus on suppression of the immune system but fail to repair the resulting damage to the CNS. Neural stem cell (NSC) transplantation is a promising therapeutic strategy for treating neurodegenerative diseases through cell replacement and repair however it is unclear how these cells would mediate repair in MS. We report that human NSCs promote CNS specific T regulatory cells (Tregs) which activate endogenous repair pathways and promote remyelination in a murine model of MS. We observed remyelination, decreased inflammation and an increase in (CNS)-infiltrating CD4+CD25+FoxP3+ Tregs in EAE mice receiving an intra-spinal transplant of NSCs. Recovery was not a result of cell replacement, as NSCs underwent xenograft rejection, and was Treg dependent, as ablation of Tregs abrogated histopathological improvement. RAG2−/−2D2 (R2D2) mice, which bear a TCR repertoire restricted to myelin oligodendrocyte glycoprotein (MOG) and neurofilament, lack CD25+FoxP3+ Tregs under homeostatic conditions; however, upon exposure to MOG, R2D2 mice developed CD25+FoxP3+ Tregs in cervical lymph nodes and the spinal cord. hNSCs also promoted Tregs in vitro in co-cultures with wild type B6 and R2D2 splenocytes, but not with RAG2−/− OT-II+ splenocytes. Additionally, hNSC-Tregs also appear to derive from the exTreg pool suggesting both antigen specific expansion and antigen dependent maintenance of FOXP3 in CNS-specific Tregs. hNSC Tregs also have a unique expression profile and express transglutimase-2 which is implicated in oligodendrocyte dependent repair in the CNS.
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Affiliation(s)
- Scott A Greilach
- 1Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697
| | - Laura L. McIntyre
- 1Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697
| | - Jonathan Hasselmann
- 2Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, 92697
| | - Shivashankar Othy
- 3Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, 92697
| | - Quy Nguyen
- 4Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697
- 5Department of Biological Chemistry, University of California, Irvine, Irvine
| | - Kai Kessenbrock
- 4Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697
| | - Michael D Cahalan
- 3Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, 92697
| | - Mathew Blurton-Jones
- 2Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, 92697
| | - Thomas Lane
- 6Department of Pathology, University of Utah, School of Medicine, Salt Lake City, UT, 84132
- 7Department of Pathology, University of Utah, School of Medicine, Salt Lake City, UT
| | - Craig M Walsh
- 1Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697
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Htoo J, Ho T, Dao T, Carpena M, Le N, Vu C, Nguyen Q. 187 Optimal standardized ileal digestible lysine and methionine + cysteine to lysine ratio for 30. J Anim Sci 2018. [DOI: 10.1093/jas/sky404.665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- J Htoo
- Evonik Nutrition & Care GmbH, No.4, Rodenbacher Chaussee,63457, Hanau, Germany, Hanau-Wolfgang,Hessen, Germany
| | - T Ho
- College of Agriculture and Forestry - Hue University,Vietnam, Hue, Vietnam
| | - T Dao
- Institute of Animal Husbandry,Hanoi, Vietnam, Hue, Vietnam
| | - M Carpena
- Evonik (SEA) Pte Ltd,Singapore, Singapore, Philippines
| | - N Le
- College of Agriculture and Forestry - Hue University,Vietnam, Hue, Vietnam
| | - C Vu
- Institute of Animal Husbandry,Hanoi, Vietnam, Hue, Vietnam
| | - Q Nguyen
- College of Agriculture and Forestry - Hue University,Vietnam, Hue, Vietnam
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41
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Nguyen Q, Peters E, Wassef A, Desmarais P, Remillard-Labrosse D, Tremblay-Gravel M. THE EVOLUTION OF AGE AND WOMEN REPRESENTATION IN THE MOST CITED RANDOMIZED TRIALS OF CARDIOLOGY OF THE LAST 20 YEARS. Innov Aging 2018. [DOI: 10.1093/geroni/igy023.2616] [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: 11/13/2022] Open
Affiliation(s)
| | | | | | - P Desmarais
- Centre Hospitalier de l’Université de Montréal
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Evans K, Nguyen Q, Blake K, Lawson D. Abstract 5197: Single-cell analysis of the brain metastatic microenvironment in breast cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-5197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Breast cancer brain metastasis affects 10-20% of patients, and there are no effective treatments. Activated infiltrating microglia and astrocytes are a major component of metastatic breast tumors in the brain, but it is not known whether these cells are involved in the promotion or rejection of breast cancer cells. To characterize the brain metastatic microenvironment, we used an FACS-based approach to capture pure and viable microglia and astrocytes from normal and metastatic mouse brains for single-cell mRNA sequencing analysis. Using this approach, we have captured more than 10,000 microglia and astrocytes from normal and metastatic brains. Applying our analysis pipelines to this data revealed distinct pathways and markers associated with microglia and astrocytes in metastatic brains. Future work will aim to identify spatial locations and function of specific microglia and astrocyte subpopulations in the metastatic brain.
Citation Format: Katrina Evans, Quy Nguyen, Kerrigan Blake, Devon Lawson. Single-cell analysis of the brain metastatic microenvironment in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5197.
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Affiliation(s)
| | - Quy Nguyen
- University of California Irvine, Irvine, CA
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43
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McIntyre LL, Plaisted WC, Nguyen Q, Kessenbrock K, Lane T, Walsh CM. Emergence of T Regulatory Cells Following Neural Precursor Cell Transplantation in Mouse Models of Multiple Sclerosis. The Journal of Immunology 2018. [DOI: 10.4049/jimmunol.200.supp.101.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Multiple Sclerosis (MS) is a chronic, autoimmune disease of the central nervous system for which there is no cure. Defects in neurological function are a result of demyelination and axonal loss caused by infiltrating immune cells. Transplantation of neural precursor cells (NPCs) is a promising therapeutic strategy to treat neurological diseases. However, studies evaluating NPC transplantation often employ a syngeneic donor or immune suppressed subjects. Therefore, it is important to consider how transplanted cells elicit an immune response. We report that human neural precursor cells (hNPCs) induce antigen specific Tregs which influence endogenous repair pathways to promote remyelination in murine models of MS. We observed remyelination and decreased neuroinflammation in mice receiving an intra-spinal transplant of syngeneic NPCs, which replaced damaged cells. Alternatively, mice receiving transplants of xenogeneic human NPCs displayed remyelination, a decrease in neuroinflammation, and an increase in CD4+CD25+FoxP3+ Tregs. Recovery was not a result of direct cell replacement as hNPCs underwent xenograft rejection. Importantly, ablation of Tregs abrogated histopathological improvement. Furthermore, hNPCs promoted generation of Tregs in vitro. These findings support an emerging role for Tregs in promoting tissue regeneration, distinct from immune modulation.
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44
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Minwell G, Buethe J, Liddell R, Nguyen Q, Reynolds D, Brock M, Frangakis C, Georgiades C. Abstract No. 591 Percutaneous ethanol sympatholysis for treatment of primary craniofacial hyperhidrosis. J Vasc Interv Radiol 2018. [DOI: 10.1016/j.jvir.2018.01.636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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45
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Bouvier C, Macagno N, Nguyen Q, Loundou A, Jiguet-Jiglaire C, Gentet JC, Jouve JL, Rochwerger A, Mattei JC, Bouvard D, Salas S. Prognostic value of the Hippo pathway transcriptional coactivators YAP/TAZ and β1-integrin in conventional osteosarcoma. Oncotarget 2018; 7:64702-64710. [PMID: 27608849 PMCID: PMC5323109 DOI: 10.18632/oncotarget.11876] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [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: 05/23/2016] [Accepted: 08/01/2016] [Indexed: 11/25/2022] Open
Abstract
Introduction Currently, very few studies are available concerning the mammalian Hippo pathway in bone sarcomas. YAP/TAZ transcription co-activators are key downstream effectors of this pathway and may also have oncogenic properties. Additionally, recent in-vitro experiments showed that expression of β1-integrin promoted metastasis in osteosarcomas. This study investigated the expression of YAP/TAZ and β1-integrin in human osteosarcomas. Materials and methods We performed automated immunohistochemistry on tissue-microarrays (TMA) in which 69 conventional osteosarcomas biopsies performed prior to chemotherapy were embedded. Cellular localization and semi-quantitative analysis of each immunostain was performed using Immunoreactive Score (IRS) and correlated to clinico-pathological data. Results Cytoplasmic expression of β1-integrin was noted in 54/59 osteosarcomas (92%), with 33/59 cases (56%) displaying membranous staining. YAP/TAZ was expressed in 27/45 osteosarcomas (60%), with 14 cases (31%) showing cytoplasmic expression while 13 other cases (28%) displayed nuclear expression. No link was found between YAP/TAZ or β1-integrin expression and response to chemotherapy. In univariate analysis, YAP/TAZ immunoreactive score was pejoratively correlated with overall survival (p = 0.01). Expression of β1-integrin on cell membrane was also pejorative for OS (p = 0.045). In multivariate analysis, YAP/TAZ nuclear expression was an independent prognostic factor for PFS (p = 0.035). Conclusion this study indicates that β1-integrin and YAP/TAZ proteins are linked to prognosis and therefore could be therapeutic targets in conventional osteosarcomas.
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Affiliation(s)
- Corinne Bouvier
- Aix-Marseille University (AMU), Faculty of Medecine, CRO2, UMR 911 (Equipe IV), Marseille, France.,Department of Pathology, APHM, Timone Hospital, Marseille, France
| | - Nicolas Macagno
- Aix-Marseille University (AMU), Faculty of Medecine, CRO2, UMR 911 (Equipe IV), Marseille, France.,Department of Pathology, APHM, Timone Hospital, Marseille, France
| | - Quy Nguyen
- Aix-Marseille University (AMU), Faculty of Medecine, CRO2, UMR 911 (Equipe IV), Marseille, France
| | - Anderson Loundou
- Department of Public Health, Aix-Marseille University (AMU), Faculty of Medecine, EA 3270 Research Unit, Marseille, France.,Department of Research and Innovation, APHM, Timone Hospital, Support Unit for Clinical Research and Economic Evaluation, Marseille, France
| | - Carine Jiguet-Jiglaire
- Aix-Marseille University (AMU), Faculty of Medecine, CRO2, UMR 911 (Equipe IV), Marseille, France
| | - Jean-Claude Gentet
- Department of Pediatric Oncology, APHM, Timone Hospital, Marseille, France
| | - Jean-Luc Jouve
- Department of Pediatric Orthopaedic Surgery, APHM, Timone Hospital, Marseille, France
| | | | - Jean-Camille Mattei
- Aix-Marseille University (AMU), Faculty of Medecine, CRO2, UMR 911 (Equipe IV), Marseille, France.,Department of Adult Orthopaedic Surgery, APHM, Nord Hospital, Marseille, France
| | | | - Sébastien Salas
- Aix-Marseille University (AMU), Faculty of Medecine, CRO2, UMR 911 (Equipe IV), Marseille, France.,Department of Pathology, APHM, Timone Hospital, Marseille, France
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Ito TK, Lu C, Khan J, Nguyen Q, Huang HZ, Kim D, Phillips JJ, Tan J, Lee Y, Nguyen T, Khessib S, Lim N, Mekvanich S, Oh J, Pineda VV, Wang W, Bitto A, An JY, Morton JF, Setou M, Ladiges WC, Kaeberlein M. Corrigendum: Hepatic S6K1 Partially Regulates Lifespan of Mice with Mitochondrial Complex I Deficiency. Front Genet 2017; 8:221. [PMID: 29285026 PMCID: PMC5744015 DOI: 10.3389/fgene.2017.00221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 12/06/2017] [Indexed: 11/13/2022] Open
Affiliation(s)
- Takashi K Ito
- Department of Pathology, University of Washington, Seattle, WA, United States.,Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan.,International Mass Imaging Center, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Chenhao Lu
- Department of Pathology, University of Washington, Seattle, WA, United States
| | - Jacob Khan
- Department of Pathology, University of Washington, Seattle, WA, United States
| | - Quy Nguyen
- Department of Pathology, University of Washington, Seattle, WA, United States
| | - Heather Z Huang
- Department of Pathology, University of Washington, Seattle, WA, United States
| | - Dayae Kim
- Department of Pathology, University of Washington, Seattle, WA, United States
| | - James J Phillips
- Department of Pathology, University of Washington, Seattle, WA, United States
| | - Jo Tan
- Department of Pathology, University of Washington, Seattle, WA, United States
| | - Yenna Lee
- Department of Pathology, University of Washington, Seattle, WA, United States
| | - Tuyet Nguyen
- Department of Pathology, University of Washington, Seattle, WA, United States
| | - Samy Khessib
- Department of Pathology, University of Washington, Seattle, WA, United States
| | - Natalie Lim
- Department of Pathology, University of Washington, Seattle, WA, United States
| | - Surapat Mekvanich
- Department of Pathology, University of Washington, Seattle, WA, United States
| | - Joshua Oh
- Department of Pathology, University of Washington, Seattle, WA, United States
| | - Victor V Pineda
- Department of Pathology, University of Washington, Seattle, WA, United States
| | - Weirong Wang
- Department of Pathology, University of Washington, Seattle, WA, United States.,Research Institute of Atherosclerotic Disease, Xi'an Jiaotong University Cardiovascular Research Center, Xi'an, China.,Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Alessandro Bitto
- Department of Pathology, University of Washington, Seattle, WA, United States
| | - Jonathan Y An
- Department of Pathology, University of Washington, Seattle, WA, United States
| | - John F Morton
- Department of Comparative Medicine, University of Washington, Seattle, WA, United States
| | - Mitsutoshi Setou
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan.,International Mass Imaging Center, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Warren C Ladiges
- Department of Comparative Medicine, University of Washington, Seattle, WA, United States
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, WA, United States
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Ito TK, Lu C, Khan J, Nguyen Q, Huang HZ, Kim D, Phillips J, Tan J, Lee Y, Nguyen T, Khessib S, Lim N, Mekvanich S, Oh J, Pineda VV, Wang W, Bitto A, An JY, Morton JF, Setou M, Ladiges WC, Kaeberlein M. Hepatic S6K1 Partially Regulates Lifespan of Mice with Mitochondrial Complex I Deficiency. Front Genet 2017; 8:113. [PMID: 28919908 PMCID: PMC5585733 DOI: 10.3389/fgene.2017.00113] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [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: 06/26/2017] [Accepted: 08/16/2017] [Indexed: 01/09/2023] Open
Abstract
The inactivation of ribosomal protein S6 kinase 1 (S6K1) recapitulates aspects of caloric restriction and mTORC1 inhibition to achieve prolonged longevity in invertebrate and mouse models. In addition to delaying normative aging, inhibition of mTORC1 extends the shortened lifespan of yeast, fly, and mouse models with severe mitochondrial disease. Here we tested whether disruption of S6K1 can recapitulate the beneficial effects of mTORC1 inhibition in the Ndufs4 knockout (NKO) mouse model of Leigh Syndrome caused by Complex I deficiency. These NKO mice develop profound neurodegeneration resulting in brain lesions and death around 50–60 days of age. Our results show that liver-specific, as well as whole body, S6K1 deletion modestly prolongs survival and delays onset of neurological symptoms in NKO mice. In contrast, we observed no survival benefit in NKO mice specifically disrupted for S6K1 in neurons or adipocytes. Body weight was reduced in WT mice upon disruption of S6K1 in adipocytes or whole body, but not altered when S6K1 was disrupted only in neurons or liver. Taken together, these data indicate that decreased S6K1 activity in liver is sufficient to delay the neurological and survival defects caused by deficiency of Complex I and suggest that mTOR signaling can modulate mitochondrial disease and metabolism via cell non-autonomous mechanisms.
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Affiliation(s)
- Takashi K Ito
- Department of Pathology, University of WashingtonSeattle, WA, United States.,Department of Cellular and Molecular Anatomy, Hamamatsu University School of MedicineHamamatsu, Japan.,International Mass Imaging Center, Hamamatsu University School of MedicineHamamatsu, Japan
| | - Chenhao Lu
- Department of Pathology, University of WashingtonSeattle, WA, United States
| | - Jacob Khan
- Department of Pathology, University of WashingtonSeattle, WA, United States
| | - Quy Nguyen
- Department of Pathology, University of WashingtonSeattle, WA, United States
| | - Heather Z Huang
- Department of Pathology, University of WashingtonSeattle, WA, United States
| | - Dayae Kim
- Department of Pathology, University of WashingtonSeattle, WA, United States
| | - James Phillips
- Department of Pathology, University of WashingtonSeattle, WA, United States
| | - Jo Tan
- Department of Pathology, University of WashingtonSeattle, WA, United States
| | - Yenna Lee
- Department of Pathology, University of WashingtonSeattle, WA, United States
| | - Tuyet Nguyen
- Department of Pathology, University of WashingtonSeattle, WA, United States
| | - Samy Khessib
- Department of Pathology, University of WashingtonSeattle, WA, United States
| | - Natalie Lim
- Department of Pathology, University of WashingtonSeattle, WA, United States
| | - Surapat Mekvanich
- Department of Pathology, University of WashingtonSeattle, WA, United States
| | - Joshua Oh
- Department of Pathology, University of WashingtonSeattle, WA, United States
| | - Victor V Pineda
- Department of Pathology, University of WashingtonSeattle, WA, United States
| | - Weirong Wang
- Department of Pathology, University of WashingtonSeattle, WA, United States.,Research Institute of Atherosclerotic Disease, Xi'an Jiaotong University Cardiovascular Research CenterXi'an, China.,Laboratory Animal Center, Xi'an Jiaotong University Health Science CenterXi'an, China
| | - Alessandro Bitto
- Department of Pathology, University of WashingtonSeattle, WA, United States
| | - Jonathan Y An
- Department of Pathology, University of WashingtonSeattle, WA, United States
| | - John F Morton
- Department of Comparative Medicine, University of WashingtonSeattle, WA, United States
| | - Mitsutoshi Setou
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of MedicineHamamatsu, Japan.,International Mass Imaging Center, Hamamatsu University School of MedicineHamamatsu, Japan
| | - Warren C Ladiges
- Department of Comparative Medicine, University of WashingtonSeattle, WA, United States
| | - Matt Kaeberlein
- Department of Pathology, University of WashingtonSeattle, WA, United States
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Nguyen Q, Wu C, Odden M, Kim D. MULTIMORBIDITY PATTERNS PROVIDE ADDED PROGNOSTIC INFORMATION BEYOND FRAILTY STATUS IN OLDER ADULTS. Innov Aging 2017. [DOI: 10.1093/geroni/igx004.945] [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: 11/15/2022] Open
Affiliation(s)
- Q. Nguyen
- University of Montreal, Montreal, Quebec, Canada,
| | - C. Wu
- Oregon State University, Corvallis, Oregon
| | - M. Odden
- Oregon State University, Corvallis, Oregon
| | - D. Kim
- Brigham and Women’s Hospital, Boston, Massachusetts,
- Beth Israel Deaconess Medical Center, Boston, Massachusetts,
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Holliday EB, Kuban DA, Levy LB, Bolukbasi Y, Master P, Choi S, Nguyen Q, McGuire SE, Mahmood U, Frank SJ, Hoffman KE. Select men benefit from androgen deprivation therapy delivered with salvage radiation therapy after prostatectomy. Prostate Cancer Prostatic Dis 2017; 20:389-394. [PMID: 28462945 DOI: 10.1038/pcan.2017.24] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 03/07/2017] [Accepted: 03/13/2017] [Indexed: 11/09/2022]
Abstract
BACKGROUND Which men benefit most from adding androgen deprivation therapy (ADT) to salvage radiation therapy (SRT) after prostatectomy has not clearly been defined; therefore, we evaluated the impact of ADT to SRT on failure-free survival (FFS) in men with a rising or persistent PSA after prostatectomy. METHODS We identified 332 men who received SRT after prostatectomy from 1987 to 2010. Recursive partitioning analysis (RPA) identified favorable, intermediate and unfavorable groups based on the risk of failure after SRT alone. Kaplan-Meier and log-rank tests compared FFS with and without ADT. RESULTS Forty-three percent received SRT alone and 57% received SRT with ADT (median 6.6 months (interquartile range (IQR) 5.8-18.1) ADT). Median SRT dose was 70 Gy (IQR 70-70), and median follow-up after SRT was 6.7 years (IQR 4.5-10.8). On Cox's proportional hazard regression, ADT improved FFS (adjusted hazard ratio 0.60, 95% confidence interval: 0.42-0.86; P=0.006). RPA classified unfavorable disease as negative surgical margins (SMs) and preradiation PSA of ⩾0.5 ng ml-1. Favorable disease had neither adverse factor, and intermediate disease had one adverse factor. The addition of ADT to SRT improved 5-year FFS for men with unfavorable disease (70.3% vs 23.4%; P<0.001) and intermediate disease (69.8% vs 48.0%; P=0.003), but not for men with favorable disease (81.2% vs 78.0%; P=0.971). CONCLUSIONS The addition of ADT to SRT appears to improve FFS for men with a preradiation PSA of ⩾0.5 ng ml-1 or with negative SM at prostatectomy. Men with involved surgical margins and PSA <0.5 ng ml-1 appear to be at a lower risk of failure after SRT alone and may not derive as much benefit from the administration of ADT with SRT. These results are hypothesis-generating only, and further prospective data are required to see if ADT can safely be omitted in this select group of men.
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Affiliation(s)
- E B Holliday
- Department of Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - D A Kuban
- Department of Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - L B Levy
- Department of Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - P Master
- Department of Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - S Choi
- Department of Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Q Nguyen
- Department of Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - S E McGuire
- Department of Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - U Mahmood
- Department of Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - S J Frank
- Department of Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - K E Hoffman
- Department of Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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50
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Soonthornvacharin S, Rodriguez-Frandsen A, Zhou Y, Galvez F, Huffmaster NJ, Tripathi S, Balasubramaniam VRMT, Inoue A, de Castro E, Moulton H, Stein DA, Sánchez-Aparicio MT, De Jesus PD, Nguyen Q, König R, Krogan NJ, García-Sastre A, Yoh SM, Chanda SK. Systems-based analysis of RIG-I-dependent signalling identifies KHSRP as an inhibitor of RIG-I receptor activation. Nat Microbiol 2017; 2:17022. [PMID: 28248290 PMCID: PMC5338947 DOI: 10.1038/nmicrobiol.2017.22] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 01/23/2017] [Indexed: 01/05/2023]
Abstract
Retinoic acid-inducible gene I (RIG-I) receptor recognizes 5'-triphosphorylated RNA and triggers a signalling cascade that results in the induction of type-I interferon (IFN)-dependent responses. Its precise regulation represents a pivotal balance between antiviral defences and autoimmunity. To elucidate the cellular cofactors that regulate RIG-I signalling, we performed two global RNA interference analyses to identify both positive and negative regulatory nodes operating on the signalling pathway during virus infection. These factors were integrated with experimentally and computationally derived interactome data to build a RIG-I protein interaction network. Our analysis revealed diverse cellular processes, including the unfolded protein response, Wnt signalling and RNA metabolism, as critical cellular components governing innate responses to non-self RNA species. Importantly, we identified K-Homology Splicing Regulatory Protein (KHSRP) as a negative regulator of this pathway. We find that KHSRP associates with the regulatory domain of RIG-I to maintain the receptor in an inactive state and attenuate its sensing of viral RNA (vRNA). Consistent with increased RIG-I antiviral signalling in the absence of KHSRP, viral replication is reduced when KHSRP expression is knocked down both in vitro and in vivo. Taken together, these data indicate that KHSRP functions as a checkpoint regulator of the innate immune response to pathogen challenge.
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Affiliation(s)
- Stephen Soonthornvacharin
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA
- The San Diego Center for Systems Biology (SDCSB), La Jolla, California 92093, USA
- Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Ariel Rodriguez-Frandsen
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA
- The San Diego Center for Systems Biology (SDCSB), La Jolla, California 92093, USA
| | - Yingyao Zhou
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, USA
| | - Felipe Galvez
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA
- The San Diego Center for Systems Biology (SDCSB), La Jolla, California 92093, USA
| | - Nicholas J Huffmaster
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA
- The San Diego Center for Systems Biology (SDCSB), La Jolla, California 92093, USA
| | - Shashank Tripathi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, New York 10029, USA
- Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, New York 10029, USA
| | - Vinod R M T Balasubramaniam
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, New York 10029, USA
- Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, New York 10029, USA
| | - Atsushi Inoue
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Elisa de Castro
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, New York 10029, USA
- Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, New York 10029, USA
| | - Hong Moulton
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University Corvallis, 450 SW 30th Street, Oregon 97331, USA
| | - David A Stein
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University Corvallis, 450 SW 30th Street, Oregon 97331, USA
| | - María Teresa Sánchez-Aparicio
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, New York 10029, USA
- Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, New York 10029, USA
| | - Paul D De Jesus
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA
- The San Diego Center for Systems Biology (SDCSB), La Jolla, California 92093, USA
| | - Quy Nguyen
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA
- The San Diego Center for Systems Biology (SDCSB), La Jolla, California 92093, USA
| | - Renate König
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA
- Host-Pathogen-Interactions, Paul-Ehrlich-Institute, German Center for Infection Research (DZIF), Paul-Ehrlich-Straße 51-59, 63225 Langen, Germany
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, 1700 4th Street, Byers Hall 308D, Box 2530, San Francisco, California 94158, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, New York 10029, USA
- Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, New York 10029, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, New York 10029, USA
| | - Sunnie M Yoh
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA
- The San Diego Center for Systems Biology (SDCSB), La Jolla, California 92093, USA
| | - Sumit K Chanda
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA
- The San Diego Center for Systems Biology (SDCSB), La Jolla, California 92093, USA
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