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Roux AE, Yuan H, Podshivalova K, Hendrickson D, Kerr R, Kenyon C, Kelley D. Individual cell types in C. elegans age differently and activate distinct cell-protective responses. Cell Rep 2023; 42:112902. [PMID: 37531250 DOI: 10.1016/j.celrep.2023.112902] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 01/11/2023] [Revised: 05/17/2023] [Accepted: 07/14/2023] [Indexed: 08/04/2023] Open
Abstract
Aging is characterized by a global decline in physiological function. However, by constructing a complete single-cell gene expression atlas, we find that Caenorhabditis elegans aging is not random in nature but instead is characterized by coordinated changes in functionally related metabolic, proteostasis, and stress-response genes in a cell-type-specific fashion, with downregulation of energy metabolism being the only nearly universal change. Similarly, the rates at which cells age differ significantly between cell types. In some cell types, aging is characterized by an increase in cell-to-cell variance, whereas in others, variance actually decreases. Remarkably, multiple resilience-enhancing transcription factors known to extend lifespan are activated across many cell types with age; we discovered new longevity candidates, such as GEI-3, among these. Together, our findings suggest that cells do not age passively but instead react strongly, and individualistically, to events that occur during aging. This atlas can be queried through a public interface.
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Affiliation(s)
| | - Han Yuan
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA
| | | | | | - Rex Kerr
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA
| | - Cynthia Kenyon
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA.
| | - David Kelley
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA.
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2
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Buffenstein R, Amoroso V, Andziak B, Avdieiev S, Azpurua J, Barker AJ, Bennett NC, Brieño‐Enríquez MA, Bronner GN, Coen C, Delaney MA, Dengler‐Crish CM, Edrey YH, Faulkes CG, Frankel D, Friedlander G, Gibney PA, Gorbunova V, Hine C, Holmes MM, Jarvis JUM, Kawamura Y, Kutsukake N, Kenyon C, Khaled WT, Kikusui T, Kissil J, Lagestee S, Larson J, Lauer A, Lavrenchenko LA, Lee A, Levitt JB, Lewin GR, Lewis Hardell KN, Lin TD, Mason MJ, McCloskey D, McMahon M, Miura K, Mogi K, Narayan V, O'Connor TP, Okanoya K, O'Riain MJ, Park TJ, Place NJ, Podshivalova K, Pamenter ME, Pyott SJ, Reznick J, Ruby JG, Salmon AB, Santos‐Sacchi J, Sarko DK, Seluanov A, Shepard A, Smith M, Storey KB, Tian X, Vice EN, Viltard M, Watarai A, Wywial E, Yamakawa M, Zemlemerova ED, Zions M, Smith ESJ. The naked truth: a comprehensive clarification and classification of current 'myths' in naked mole-rat biology. Biol Rev Camb Philos Soc 2022; 97:115-140. [PMID: 34476892 PMCID: PMC9277573 DOI: 10.1111/brv.12791] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [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: 02/15/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 12/17/2022]
Abstract
The naked mole-rat (Heterocephalus glaber) has fascinated zoologists for at least half a century. It has also generated considerable biomedical interest not only because of its extraordinary longevity, but also because of unusual protective features (e.g. its tolerance of variable oxygen availability), which may be pertinent to several human disease states, including ischemia/reperfusion injury and neurodegeneration. A recent article entitled 'Surprisingly long survival of premature conclusions about naked mole-rat biology' described 28 'myths' which, those authors claimed, are a 'perpetuation of beautiful, but falsified, hypotheses' and impede our understanding of this enigmatic mammal. Here, we re-examine each of these 'myths' based on evidence published in the scientific literature. Following Braude et al., we argue that these 'myths' fall into four main categories: (i) 'myths' that would be better described as oversimplifications, some of which persist solely in the popular press; (ii) 'myths' that are based on incomplete understanding, where more evidence is clearly needed; (iii) 'myths' where the accumulation of evidence over the years has led to a revision in interpretation, but where there is no significant disagreement among scientists currently working in the field; (iv) 'myths' where there is a genuine difference in opinion among active researchers, based on alternative interpretations of the available evidence. The term 'myth' is particularly inappropriate when applied to competing, evidence-based hypotheses, which form part of the normal evolution of scientific knowledge. Here, we provide a comprehensive critical review of naked mole-rat biology and attempt to clarify some of these misconceptions.
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Affiliation(s)
| | - Vincent Amoroso
- Department of Biological SciencesUniversity of Illinois at ChicagoChicagoIL60607U.S.A.
| | - Blazej Andziak
- Graduate Center City University of New York365 Fifth AvenueNew YorkNY10016U.S.A.
| | | | - Jorge Azpurua
- Department of AnesthesiologyStony Brook University101 Nicolls RoadStony BrookNY11794U.S.A.
| | - Alison J. Barker
- Max Delbrück Center for Molecular MedicineRobert‐Rössle‐Str 10Berlin‐Buch13092Germany
| | - Nigel C. Bennett
- Mammal Research Institute, Department of Zoology and EntomologyUniversity of PretoriaPretoria0002South Africa
| | - Miguel A. Brieño‐Enríquez
- Department of Obstetrics, Gynecology & Reproductive MedicineMagee‐Womens Research Institute204 Craft AvenuePittsburghPA15213U.S.A.
| | - Gary N. Bronner
- Department Biological SciencesRondeboschCape Town7701South Africa
| | - Clive Coen
- Reproductive Neurobiology, Division of Women's HealthSchool of Medicine, King's College LondonWestminster Bridge RoadLondonSE1 7EHU.K.
| | - Martha A. Delaney
- Zoological Pathology ProgramUniversity of Illinois3505 Veterinary Medicine Basic Sciences Building, 2001 S Lincoln AvenueUrbanaIL6180U.S.A.
| | - Christine M. Dengler‐Crish
- Department of Pharmaceutical SciencesNortheast Ohio Medical University4209 State Route 44RootstownOH44272U.S.A.
| | - Yael H. Edrey
- Northwest Vista College3535 N. Ellison DriveSan AntonioTX78251U.S.A.
| | - Chris G. Faulkes
- School of Biological and Chemical SciencesQueen Mary University of LondonMile End RoadLondonE1 4NSU.K.
| | - Daniel Frankel
- School of EngineeringNewcastle UniversityMerz CourtNewcastle Upon TyneNE1 7RUU.K.
| | - Gerard Friedlander
- Université Paris DescartesFaculté de Médecine12 Rue de l'École de MédecineParis5006France
| | - Patrick A. Gibney
- Cornell University College of Veterinary MedicineIthacaNY14853U.S.A.
| | - Vera Gorbunova
- Departments of BiologyUniversity of Rochester402 Hutchison HallRochesterNY14627U.S.A.
| | - Christopher Hine
- Cleveland ClinicLerner Research Institute9500 Euclid AvenueClevelandOH44195U.S.A.
| | - Melissa M. Holmes
- Department of PsychologyUniversity of Toronto Mississauga3359 Mississauga Road NorthMississaugaONL5L 1C6Canada
| | | | - Yoshimi Kawamura
- Department of Aging and Longevity ResearchKumamoto University1‐1‐1 HonjoKumamoto860‐0811Japan
| | - Nobuyuki Kutsukake
- Department of Evolutionary Studies of BiosystemsThe Graduate University for Advanced StudiesHayama240‐0193Japan
| | - Cynthia Kenyon
- Calico Life Sciences LLC1170 Veterans BlvdSouth San FranciscoCA94080U.S.A.
| | - Walid T. Khaled
- The School of the Biological SciencesUniversity of CambridgeTennis Court RoadCambridgeCB2 1PDU.K.
| | - Takefumi Kikusui
- Companion Animal Research, School of Veterinary MedicineAzabu UniversitySagamihara252‐5201Japan
| | - Joseph Kissil
- Department of Cancer BiologyThe Scripps Research InstituteScripps FloridaJupiterFL33458U.S.A.
| | - Samantha Lagestee
- Department of Biological SciencesUniversity of Illinois at ChicagoChicagoIL60607U.S.A.
| | - John Larson
- Department of Biological SciencesUniversity of Illinois at ChicagoChicagoIL60607U.S.A.
| | - Amanda Lauer
- Department of OtolaryngologyJohns Hopkins School of MedicineBaltimoreMD21205U.S.A.
| | - Leonid A. Lavrenchenko
- A.N. Severtsov Institute of Ecology and EvolutionRussian Academy of SciencesLeninskii pr. 33Moscow119071Russia
| | - Angela Lee
- Graduate Center City University of New York365 Fifth AvenueNew YorkNY10016U.S.A.
| | - Jonathan B. Levitt
- Biology DepartmentThe City College of New York138th Street and Convent AvenueNew YorkNY10031U.S.A.
| | - Gary R. Lewin
- Max Delbrück Center for Molecular MedicineRobert‐Rössle‐Str 10Berlin‐Buch13092Germany
| | | | - TzuHua D. Lin
- Calico Life Sciences LLC1170 Veterans BlvdSouth San FranciscoCA94080U.S.A.
| | - Matthew J. Mason
- The School of the Biological SciencesUniversity of CambridgeTennis Court RoadCambridgeCB2 1PDU.K.
| | - Dan McCloskey
- College of Staten Island in the City University of New York2800 Victory BlvdStaten IslandNY10314U.S.A.
| | - Mary McMahon
- Calico Life Sciences LLC1170 Veterans BlvdSouth San FranciscoCA94080U.S.A.
| | - Kyoko Miura
- Department of Aging and Longevity ResearchKumamoto University1‐1‐1 HonjoKumamoto860‐0811Japan
| | - Kazutaka Mogi
- Companion Animal Research, School of Veterinary MedicineAzabu UniversitySagamihara252‐5201Japan
| | - Vikram Narayan
- Calico Life Sciences LLC1170 Veterans BlvdSouth San FranciscoCA94080U.S.A.
| | | | - Kazuo Okanoya
- Department of Life SciencesThe University of Tokyo7‐3‐1 HongoTokyo153‐8902Japan
| | | | - Thomas J. Park
- Department of Biological SciencesUniversity of Illinois at ChicagoChicagoIL60607U.S.A.
| | - Ned J. Place
- Cornell University College of Veterinary MedicineIthacaNY14853U.S.A.
| | - Katie Podshivalova
- Calico Life Sciences LLC1170 Veterans BlvdSouth San FranciscoCA94080U.S.A.
| | | | - Sonja J. Pyott
- Groningen Department of OtorhinolaryngologyUniversity Medical CenterPostbus 30.001GroningenRB9700The Netherlands
| | - Jane Reznick
- Cologne Excellence Cluster for Cellular Stress Responses in Aging‐Associated Diseases (CECAD)University Hospital CologneJoseph‐Stelzmann‐Street 26Cologne50931Germany
| | - J. Graham Ruby
- Calico Life Sciences LLC1170 Veterans BlvdSouth San FranciscoCA94080U.S.A.
| | - Adam B. Salmon
- Barshop Institute for Longevity and Aging StudiesUniversity of Texas Health Science Center4939 Charles Katz Dr.San AntonioTX78229U.S.A.
| | - Joseph Santos‐Sacchi
- Department of NeuroscienceYale University School of Medicine200 South Frontage Road, SHM C‐303New HavenCT06510U.S.A.
| | - Diana K. Sarko
- Department of AnatomySchool of Medicine, Southern Illinois University975 S. NormalCarbondaleIL62901U.S.A.
| | - Andrei Seluanov
- Departments of BiologyUniversity of Rochester402 Hutchison HallRochesterNY14627U.S.A.
| | - Alyssa Shepard
- Department of Cancer BiologyThe Scripps Research InstituteScripps FloridaJupiterFL33458U.S.A.
| | - Megan Smith
- Calico Life Sciences LLC1170 Veterans BlvdSouth San FranciscoCA94080U.S.A.
| | - Kenneth B. Storey
- Department of BiologyCarleton University1125 Colonel By DriveOttawaONK1S 5B6Canada
| | - Xiao Tian
- Department of Genetics – Blavatnik InstituteHarvard Medical School77 Avenue Louis PasteurBostonMA02115U.S.A.
| | - Emily N. Vice
- Department of Biological SciencesUniversity of Illinois at ChicagoChicagoIL60607U.S.A.
| | - Mélanie Viltard
- Fondation pour la recherche en PhysiologieUniversité Catholique de LouvainClos Chapelle‐aux‐Champs 30Woluwe‐saint Lambert1200Belgium
| | - Akiyuki Watarai
- Companion Animal Research, School of Veterinary MedicineAzabu UniversitySagamihara252‐5201Japan
| | - Ewa Wywial
- Biology DepartmentThe City College of New York138th Street and Convent AvenueNew YorkNY10031U.S.A.
| | - Masanori Yamakawa
- Department of Evolutionary Studies of BiosystemsThe Graduate University for Advanced StudiesHayama240‐0193Japan
| | - Elena D. Zemlemerova
- A.N. Severtsov Institute of Ecology and EvolutionRussian Academy of SciencesLeninskii pr. 33Moscow119071Russia
| | - Michael Zions
- Graduate Center City University of New York365 Fifth AvenueNew YorkNY10016U.S.A.
| | - Ewan St. John Smith
- The School of the Biological SciencesUniversity of CambridgeTennis Court RoadCambridgeCB2 1PDU.K.
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3
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Anderson EC, Frankino PA, Higuchi-Sanabria R, Yang Q, Bian Q, Podshivalova K, Shin A, Kenyon C, Dillin A, Meyer BJ. X Chromosome Domain Architecture Regulates Caenorhabditis elegans Lifespan but Not Dosage Compensation. Dev Cell 2019; 51:192-207.e6. [PMID: 31495695 DOI: 10.1016/j.devcel.2019.08.004] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/26/2019] [Accepted: 08/06/2019] [Indexed: 12/21/2022]
Abstract
Mechanisms establishing higher-order chromosome structures and their roles in gene regulation are elusive. We analyzed chromosome architecture during nematode X chromosome dosage compensation, which represses transcription via a dosage-compensation condensin complex (DCC) that binds hermaphrodite Xs and establishes megabase-sized topologically associating domains (TADs). We show that DCC binding at high-occupancy sites (rex sites) defines eight TAD boundaries. Single rex deletions disrupted boundaries, and single insertions created new boundaries, demonstrating that a rex site is necessary and sufficient to define DCC-dependent boundary locations. Deleting eight rex sites (8rexΔ) recapitulated TAD structure of DCC mutants, permitting analysis when chromosome-wide domain architecture was disrupted but most DCC binding remained. 8rexΔ animals exhibited no changes in X expression and lacked dosage-compensation mutant phenotypes. Hence, TAD boundaries are neither the cause nor the consequence of DCC-mediated gene repression. Abrogating TAD structure did, however, reduce thermotolerance, accelerate aging, and shorten lifespan, implicating chromosome architecture in stress responses and aging.
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Affiliation(s)
- Erika C Anderson
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Phillip A Frankino
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ryo Higuchi-Sanabria
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Qiming Yang
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Qian Bian
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - Aram Shin
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Cynthia Kenyon
- Calico Life Sciences, South San Francisco, CA 94080, USA
| | - Andrew Dillin
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Barbara J Meyer
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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Podshivalova K, Wang EA, Hart T, Salomon DR. Expression of the miR-150 tumor suppressor is restored by and synergizes with rapamycin in a human leukemia T-cell line. Leuk Res 2018; 74:1-9. [PMID: 30269036 PMCID: PMC6290994 DOI: 10.1016/j.leukres.2018.09.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 07/21/2018] [Accepted: 09/18/2018] [Indexed: 02/06/2023]
Abstract
miR-150 functions as a tumor suppressor in malignancies of the lymphocyte lineage and its expression is significantly reduced in these cells. However, the mechanism of miR-150 repression is unknown and so are pharmacological interventions that can reverse it. Here, we report that reduced expression of miR-150 in human Jurkat T-cell acute lymphoblastic leukemia (T-ALL) cells is mediated by constitutive mTOR signaling, a common characteristic of T-ALL cell lines and clinical isolates. Activating mTOR signaling in non-malignant T cells also resulted in a significant miR-150 down-regulation. Conversely, treatment with a pharmacological mTOR inhibitor, rapamycin, increased miR-150 expression in a dose-dependent manner in Jurkat cells, as well as in other leukemia cells. Interestingly, ectopic over-expression of miR-150 acted in a feed-forward loop and further sensitized Jurkat cells to a rapamycin-induced cell cycle arrest by targeting a large network of cell cycle genes. These findings suggest that miR-150 is normally expressed in quiescent T lymphocytes to reinforce an anti-proliferative state, and that mTOR signaling promotes cell proliferation in part by inhibiting miR-150 expression. Restoration of the miR-150-dependent anti-proliferative loop constitutes a novel mechanism underlying the efficacy of rapamycin in a T-ALL cell line. Further investigation of this mechanism in clinical isolates of T-ALL and other hematopoietic malignancies could help better guide development of targeted therapies.
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Affiliation(s)
- Katie Podshivalova
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, United States.
| | - Eileen A Wang
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Traver Hart
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Daniel R Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, United States
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5
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Podshivalova K, Kerr RA, Kenyon C. How a Mutation that Slows Aging Can Also Disproportionately Extend End-of-Life Decrepitude. Cell Rep 2017; 19:441-450. [PMID: 28423308 DOI: 10.1016/j.celrep.2017.03.062] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [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: 10/24/2016] [Revised: 02/18/2017] [Accepted: 03/21/2017] [Indexed: 12/26/2022] Open
Abstract
The goal of aging research is to extend healthy, active life. For decades, C. elegans daf-2 insulin/insulin-like growth factor 1 (IGF-1) receptor mutants have served as a model for extended lifespan and youthfulness. However, a recent report suggested that their longevity is associated with an undesirable phenotype: a disproportionately long period of decrepitude at the end of life. In the human population, such an outcome would be a burden to society, bringing into question the relevance of daf-2 mutants as a model for life extension. However, here we report that, following an extended period of movement, daf-2 mutants survive longer in a decrepit state because of a beneficial trait: they are resistant to colonization of the digestive tract by dietary bacteria, a condition that leads to premature death in the wild-type and prevents their manifestation of decrepitude. If bacterial colonization is prevented, then daf-2 mutants lead both chronologically and proportionately healthier lives relative to the wild-type.
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Affiliation(s)
- Katie Podshivalova
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Calico Life Sciences LLC, South San Francisco, CA 94080, USA
| | - Rex A Kerr
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Calico Life Sciences LLC, South San Francisco, CA 94080, USA
| | - Cynthia Kenyon
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Calico Life Sciences LLC, South San Francisco, CA 94080, USA.
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Podshivalova K, Salomon DR. MicroRNA regulation of T-lymphocyte immunity: modulation of molecular networks responsible for T-cell activation, differentiation, and development. Crit Rev Immunol 2014; 33:435-76. [PMID: 24099302 DOI: 10.1615/critrevimmunol.2013006858] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNA) are a class of small non-coding RNAs that constitute an essential and evolutionarily conserved mechanism for post-transcriptional gene regulation. Multiple miRNAs have been described to play key roles in T-lymphocyte development, differentiation, and function. In this review, we highlight the current literature regarding the differential expression of miRNAs in various models of murine and human T-cell biology. We emphasize mechanistic understandings of miRNA regulation of thymocyte development, T-cell activation, and differentiation into effector and memory subsets. We describe the participation of miRNAs in complex regulatory circuits shaping T-cell proteomes in a context-dependent manner. It is striking that some miRNAs regulate multiple processes, while others only appear in limited functional contexts. It is also evident that the expression and function of specific miRNAs can differ between murine and human systems. Ultimately, it is not always correct to simplify the complex events of T-cell biology into a model driven by only one or two master regulator miRNAs. In reality, T-cell activation and differentiation involve the expression of multiple miRNAs with many mRNA targets; thus, the true extent of miRNA regulation of T-cell biology is likely far more vast than currently appreciated.
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Affiliation(s)
- Katie Podshivalova
- Laboratory for Functional Genomics, Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
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Hart T, Komori HK, LaMere S, Podshivalova K, Salomon DR. Finding the active genes in deep RNA-seq gene expression studies. BMC Genomics 2013; 14:778. [PMID: 24215113 PMCID: PMC3870982 DOI: 10.1186/1471-2164-14-778] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [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: 07/12/2013] [Accepted: 10/29/2013] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Early application of second-generation sequencing technologies to transcript quantitation (RNA-seq) has hinted at a vast mammalian transcriptome, including transcripts from nearly all known genes, which might be fully measured only by ultradeep sequencing. Subsequent studies suggested that low-abundance transcripts might be the result of technical or biological noise rather than active transcripts; moreover, most RNA-seq experiments did not provide enough read depth to generate high-confidence estimates of gene expression for low-abundance transcripts. As a result, the community adopted several heuristics for RNA-seq analysis, most notably an arbitrary expression threshold of 0.3 - 1 FPKM for downstream analysis. However, advances in RNA-seq library preparation, sequencing technology, and informatic analysis have addressed many of the systemic sources of uncertainty and undermined the assumptions that drove the adoption of these heuristics. We provide an updated view of the accuracy and efficiency of RNA-seq experiments, using genomic data from large-scale studies like the ENCODE project to provide orthogonal information against which to validate our conclusions. RESULTS We show that a human cell's transcriptome can be divided into active genes carrying out the work of the cell and other genes that are likely the by-products of biological or experimental noise. We use ENCODE data on chromatin state to show that ultralow-expression genes are predominantly associated with repressed chromatin; we provide a novel normalization metric, zFPKM, that identifies the threshold between active and background gene expression; and we show that this threshold is robust to experimental and analytical variations. CONCLUSIONS The zFPKM normalization method accurately separates the biologically relevant genes in a cell, which are associated with active promoters, from the ultralow-expression noisy genes that have repressed promoters. A read depth of twenty to thirty million mapped reads allows high-confidence quantitation of genes expressed at this threshold, providing important guidance for the design of RNA-seq studies of gene expression. Moreover, we offer an example for using extensive ENCODE chromatin state information to validate RNA-seq analysis pipelines.
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Affiliation(s)
- Traver Hart
- Donnelly Centre, Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - H Kiyomi Komori
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Sarah LaMere
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Katie Podshivalova
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Daniel R Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
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Podshivalova K, Wang E, Salomon D. mTOR complex signaling inhibits expression of a specific set of microRNAs during T cell activation that regulate G1 cell cycle progression (P1180). The Journal of Immunology 2013. [DOI: 10.4049/jimmunol.190.supp.190.15] [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
microRNAs are a class of small non-coding RNAs that post-transcriptionally regulate gene expression. T cell activation results in dramatic changes in the expression of individual microRNAs. Mammalian target of rapamycin (mTOR) is activated promptly after TCR stimulation via the PI3K signaling branch and promotes T cell exit from the quiescent resting state into a highly proliferative activated state. Bringing these two important regulatory pathways together, we show that mTOR signals the down-regulation of several specific microRNAs after activation of T cells. Inhibition of mTOR in human T cells by rapamycin or PP242 results in up-regulation of a unique set of microRNAs. Conversely, the same miRNAs are dramatically reduced with T cell activation. Regulation of these miRNAs by mTOR appears to be T cell specific, as their expression does not change in B cells, fibroblasts or epithelial cells treated with mTOR inhibitors. Mechanistically, we show that mTOR-dependent microRNAs negatively regulate proliferation and induce G1 cell cycle arrest by targeting multiple genes, acting either additively or synergistically with mTOR inhibitors. Our data demonstrate that several microRNAs help maintain the quiescent state of resting T cells, are down-regulated with activation due to negative regulation by mTOR and because these microRNAs contribute to the induction of a cell cycle arrest, they may have potential roles as tumor suppressor genes.
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Affiliation(s)
- Katie Podshivalova
- 1Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - Eileen Wang
- 1Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - Daniel Salomon
- 1Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
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Van Nieuwerburgh F, Soetaert S, Podshivalova K, Ay-Lin Wang E, Schaffer L, Deforce D, Salomon DR, Head SR, Ordoukhanian P. Quantitative bias in Illumina TruSeq and a novel post amplification barcoding strategy for multiplexed DNA and small RNA deep sequencing. PLoS One 2011; 6:e26969. [PMID: 22046424 PMCID: PMC3203936 DOI: 10.1371/journal.pone.0026969] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 10/06/2011] [Indexed: 01/29/2023] Open
Abstract
Here we demonstrate a method for unbiased multiplexed deep sequencing of RNA and DNA libraries using a novel, efficient and adaptable barcoding strategy called Post Amplification Ligation-Mediated (PALM). PALM barcoding is performed as the very last step of library preparation, eliminating a potential barcode-induced bias and allowing the flexibility to synthesize as many barcodes as needed. We sequenced PALM barcoded micro RNA (miRNA) and DNA reference samples and evaluated the quantitative barcode-induced bias in comparison to the same reference samples prepared using the Illumina TruSeq barcoding strategy. The Illumina TruSeq small RNA strategy introduces the barcode during the PCR step using differentially barcoded primers, while the TruSeq DNA strategy introduces the barcode before the PCR step by ligation of differentially barcoded adaptors. Results show virtually no bias between the differentially barcoded miRNA and DNA samples, both for the PALM and the TruSeq sample preparation methods. We also multiplexed miRNA reference samples using a pre-PCR barcode ligation. This barcoding strategy results in significant bias.
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Verdino P, Witherden DA, Podshivalova K, Rieder SE, Havran WL, Wilson IA. cDNA sequence and Fab crystal structure of HL4E10, a hamster IgG lambda light chain antibody stimulatory for γδ T cells. PLoS One 2011; 6:e19828. [PMID: 21629689 PMCID: PMC3101210 DOI: 10.1371/journal.pone.0019828] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [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: 08/23/2010] [Accepted: 04/18/2011] [Indexed: 01/10/2023] Open
Abstract
Hamsters are widely used to generate monoclonal antibodies against mouse, rat, and human antigens, but sequence and structural information for hamster immunoglobulins is sparse. To our knowledge, only three hamster IgG sequences have been published, all of which use kappa light chains, and no three-dimensional structure of a hamster antibody has been reported. We generated antibody HL4E10 as a probe to identify novel costimulatory molecules on the surface of γδ T cells which lack the traditional αβ T cell co-receptors CD4, CD8, and the costimulatory molecule CD28. HL4E10 binding to γδ T cell, surface-expressed, Junctional Adhesion Molecule-Like (JAML) protein leads to potent costimulation via activation of MAP kinase pathways and cytokine production, resulting in cell proliferation. The cDNA sequence of HL4E10 is the first example of a hamster lambda light chain and only the second known complete hamster heavy chain sequence. The crystal structure of the HL4E10 Fab at 2.95 Å resolution reveals a rigid combining site with pockets faceted by solvent-exposed tyrosine residues, which are structurally optimized for JAML binding. The characterization of HL4E10 thus comprises a valuable addition to the spartan database of hamster immunoglobulin genes and structures. As the HL4E10 antibody is uniquely costimulatory for γδ T cells, humanized versions thereof may be of clinical relevance in treating γδ T cell dysfunction-associated diseases, such as chronic non-healing wounds and cancer.
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Affiliation(s)
- Petra Verdino
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Deborah A. Witherden
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
| | - Katie Podshivalova
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
| | - Stephanie E. Rieder
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
| | - Wendy L. Havran
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
| | - Ian A. Wilson
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail:
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Mills RE, Taylor KR, Podshivalova K, McKay DB, Jameson JM. Defects in skin gamma delta T cell function contribute to delayed wound repair in rapamycin-treated mice. J Immunol 2008; 181:3974-83. [PMID: 18768852 DOI: 10.4049/jimmunol.181.6.3974] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Disruptions in the normal program of tissue repair can result in poor wound healing, which perturbs the integrity of barrier tissues such as the skin. Such defects in wound repair occur in transplant recipients treated with the immunosuppressant drug rapamycin (sirolimus). Intraepithelial lymphocytes, such as gammadelta T cells in the skin, mediate tissue repair through the production of cytokines and growth factors. The capacity of skin-resident T cells to function during rapamycin treatment was analyzed in a mouse model of wound repair. Rapamycin treatment renders skin gammadelta T cells unable to proliferate, migrate, and produce normal levels of growth factors. The observed impairment of skin gammadelta T cell function is directly related to the inhibitory action of rapamycin on mammalian target of rapamycin. Skin gammadelta T cells treated with rapamycin are refractory to IL-2 stimulation and attempt to survive in the absence of cytokine and growth factor signaling by undergoing autophagy. Normal wound closure can be restored in rapamycin-treated mice by addition of the skin gammadelta T cell-produced factor, insulin-like growth factor-1. These studies not only reveal that mammalian target of rapamycin is a master regulator of gammadelta T cell function but also provide a novel mechanism for the increased susceptibility to nonhealing wounds that occurs during rapamycin administration.
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Affiliation(s)
- Robyn E Mills
- Department of Immunology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Jameson J, Mills R, Podshivalova K. Rapamycin impairs skin γδ T cell function resulting in autophagy. FASEB J 2008. [DOI: 10.1096/fasebj.22.1_supplement.854.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Robyn Mills
- ImmunologyThe Scripps Research InstituteLa JollaCA
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Stoyan T, Podshivalova K, Stevens D, Eardley D, Sears D. Teaching Basic Immunology Using Flow Cytometry. FASEB J 2008. [DOI: 10.1096/fasebj.22.1_supplement.574.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tanja Stoyan
- MCDBUniversity of California at Santa BarbaraSanta BarbaraCA
| | - Katie Podshivalova
- MCDBUniversity of California at Santa BarbaraSanta BarbaraCA
- The Scripps Research InstituteLa JollaCA
| | - Daniel Stevens
- MCDBUniversity of California at Santa BarbaraSanta BarbaraCA
| | - Diane Eardley
- MCDBUniversity of California at Santa BarbaraSanta BarbaraCA
| | - Duane Sears
- MCDBUniversity of California at Santa BarbaraSanta BarbaraCA
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