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Min YG, Lee SY, Lim E, Park MY, Kim DH, Byun JM, Koh Y, Hong J, Shin DY, Yoon SS, Sung JJ, Oh SB, Kim I. Genetic Risk Factors for Bortezomib-induced Neuropathic Pain in an Asian Population: A Genome-wide Association Study in South Korea. THE JOURNAL OF PAIN 2024:104552. [PMID: 38692398 DOI: 10.1016/j.jpain.2024.104552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/22/2024] [Accepted: 04/22/2024] [Indexed: 05/03/2024]
Abstract
Bortezomib-induced neuropathic pain (BINP) poses a challenge in multiple myeloma (MM) treatment. Genetic factors play a key role in BINP susceptibility, but research has predominantly focused on Caucasian populations. This research explored novel genetic risk loci and pathways associated with BINP development in Korean MM patients while evaluating the reproducibility of variants from Caucasians. Clinical data and buffy coat samples from 185 MM patients on bortezomib were collected. The cohort was split into discovery and validation cohorts through random stratification of clinical risk factors for BINP. Genome-wide association study was performed on the discovery cohort (n = 74) with Infinium Global Screening Array-24 v3.0 BeadChip (654,027 single nucleotide polymorphism [SNPs]). Relevant biological pathways were identified using the pathway scoring algorithm. The top 20 SNPs were validated in the validation cohort (n = 111). Previously reported SNPs were validated in the entire cohort (n = 185). Pathway analysis of the genome-wide association study results identified 31 relevant pathways, including immune systems and endosomal vacuolar pathways. Among the top 20 SNPs from the discovery cohort, 16 were replicated, which included intronic variants in ASIC2 and SMOC2, recently implicated in nociception, as well as intergenic variants or long noncoding RNAs. None of the 17 previously reported SNPs remained significant in our cohort (rs2274578, P = .085). This study represents the first investigation of novel genetic loci and biological pathways associated with BINP occurrence. Our findings, in conjunction with existing Caucasian studies, expand the understanding of personalized risk prediction and disease mechanisms. PERSPECTIVE: This article is the first to explore novel genetic loci and pathways linked to BINP in Korean MM patients, offering novel insights beyond the existing research focused on Caucasian populations into personalized risk assessment and therapeutic strategies of BINP.
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Affiliation(s)
- Young Gi Min
- Department of Translational Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; Department of Neurology, Seoul National University Hospital, Seoul, South Korea
| | | | | | | | | | - Ja Min Byun
- Department of Internal Medicine, Seoul National University Hospital, Biomedical Research Institute, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Youngil Koh
- Department of Internal Medicine, Seoul National University Hospital, Biomedical Research Institute, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Junshik Hong
- Department of Internal Medicine, Seoul National University Hospital, Biomedical Research Institute, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dong-Yeop Shin
- Department of Internal Medicine, Seoul National University Hospital, Biomedical Research Institute, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung-Soo Yoon
- Department of Internal Medicine, Seoul National University Hospital, Biomedical Research Institute, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jung-Joon Sung
- Department of Translational Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; Department of Neurology, Seoul National University Hospital, Seoul, South Korea; Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, South Korea; Wide River Institute of Immunology, Seoul National University, Hongcheon, Gangwon-do, South Korea
| | - Seog Bae Oh
- Department of Neurobiology and Physiology, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, Republic of Korea; ADA Forsyth Institute, Cambridge, Massachusetts.
| | - Inho Kim
- Department of Internal Medicine, Seoul National University Hospital, Biomedical Research Institute, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
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Sands B, Yun SR, Oshima J, Mendenhall AR. Maternal histone methyltransferases antagonistically regulate monoallelic expression in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576748. [PMID: 38328214 PMCID: PMC10849558 DOI: 10.1101/2024.01.22.576748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Undefined epigenetic programs act to probabilistically silence individual autosomal alleles, generating unique individuals, even from genetic clones. This sort of random monoallelic expression can explain variation in traits and diseases that differences in genes and environments cannot. Here, we developed the nematode Caenorhabditis elegans to study monoallelic expression in whole tissues, and defined a developmental genetic regulation pathway. We found maternal H3K9 histone methyltransferase (HMT) SET-25/SUV39/G9a works with HPL-2/HP1 and LIN-61/L3MBTL2 to randomly silence alleles in the intestinal progenitor E-cell of 8-cell embryos to cause monoallelic expression. SET-25 was antagonized by another maternal H3K9 HMT, MET-2/SETDB1, which works with LIN-65/ATF7ZIP and ARLE-14/ARL14EP to prevent monoallelic expression. The HMT-catalytic SET domains of both MET-2 and SET-25 were required for regulating monoallelic expression. Our data support a model wherein SET-25 and MET-2 regulate histones during development to generate patterns of somatic monoallelic expression that are persistent but not heritable.
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Peng F, Nordgren CE, Murray JI. A spatiotemporally resolved atlas of mRNA decay in the C. elegans embryo reveals differential regulation of mRNA stability across stages and cell types. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.15.575757. [PMID: 38293118 PMCID: PMC10827189 DOI: 10.1101/2024.01.15.575757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
During embryonic development, cells undergo dynamic changes in gene expression that are required for appropriate cell fate specification. Although both transcription and mRNA degradation contribute to gene expression dynamics, patterns of mRNA decay are less well-understood. Here we directly measured spatiotemporally resolved mRNA decay rates transcriptome-wide throughout C. elegans embryogenesis by transcription inhibition followed by bulk and single-cell RNA-sequencing. This allowed us to calculate mRNA half-lives within specific cell types and developmental stages and identify differentially regulated mRNA decay throughout embryonic development. We identified transcript features that are correlated with mRNA stability and found that mRNA decay rates are associated with distinct peaks in gene expression over time. Moreover, we provide evidence that, on average, mRNA is more stable in the germline compared to in the soma and in later embryonic stages compared to in earlier stages. This work suggests that differential mRNA decay across cell states and time helps to shape developmental gene expression, and it provides a valuable resource for studies of mRNA turnover regulatory mechanisms.
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Affiliation(s)
- Felicia Peng
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - C Erik Nordgren
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - John Isaac Murray
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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4
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Wolfe AD, Koberstein JN, Smith CB, Stewart ML, Gonzalez IJ, Hammarlund M, Hyman AA, Stork PJS, Goodman RH, Colón-Ramos DA. Local and dynamic regulation of neuronal glycolysis in vivo. Proc Natl Acad Sci U S A 2024; 121:e2314699121. [PMID: 38198527 PMCID: PMC10801914 DOI: 10.1073/pnas.2314699121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/01/2023] [Indexed: 01/12/2024] Open
Abstract
Energy metabolism supports neuronal function. While it is well established that changes in energy metabolism underpin brain plasticity and function, less is known about how individual neurons modulate their metabolic states to meet varying energy demands. This is because most approaches used to examine metabolism in living organisms lack the resolution to visualize energy metabolism within individual circuits, cells, or subcellular regions. Here, we adapted a biosensor for glycolysis, HYlight, for use in Caenorhabditis elegans to image dynamic changes in glycolysis within individual neurons and in vivo. We determined that neurons cell-autonomously perform glycolysis and modulate glycolytic states upon energy stress. By examining glycolysis in specific neurons, we documented a neuronal energy landscape comprising three general observations: 1) glycolytic states in neurons are diverse across individual cell types; 2) for a given condition, glycolytic states within individual neurons are reproducible across animals; and 3) for varying conditions of energy stress, glycolytic states are plastic and adapt to energy demands. Through genetic analyses, we uncovered roles for regulatory enzymes and mitochondrial localization in the cellular and subcellular dynamic regulation of glycolysis. Our study demonstrates the use of a single-cell glycolytic biosensor to examine how energy metabolism is distributed across cells and coupled to dynamic states of neuronal function and uncovers unique relationships between neuronal identities and metabolic landscapes in vivo.
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Affiliation(s)
- Aaron D. Wolfe
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT06536
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT06536
| | | | - Chadwick B. Smith
- Vollum Institute, Oregon Health & Science University, Portland, OR97239
| | | | - Ian J. Gonzalez
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT06536
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT06536
| | - Marc Hammarlund
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT06536
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT06536
| | - Anthony A. Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden01307, Germany
| | | | - Richard H. Goodman
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT06536
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT06536
- Vollum Institute, Oregon Health & Science University, Portland, OR97239
| | - Daniel A. Colón-Ramos
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT06536
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT06536
- Wu Tsai Institute, Yale University, New Haven, CT06510
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Toperzer KM, Brennan SJ, Carroll DJ, Guisbert EA, Kim Guisbert KS. Visualization of the biphasic calcium wave during fertilization in Caenorhabditis elegans using a genetically encoded calcium indicator. Biol Open 2023; 12:bio059832. [PMID: 37602653 PMCID: PMC10655868 DOI: 10.1242/bio.059832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 08/03/2023] [Indexed: 08/22/2023] Open
Abstract
Fertilization is a critical step in development, yet internal fertilization events are notoriously difficult to visualize. Taking advantage of the calcium response that is a hallmark of sperm-egg fusion, we adapted the genetically encoded calcium indicator jGCaMP7s to visualize the moment of fertilization in Caenorhabditis elegans using fluorescence. We termed this tool the 'CaFE' reporter, for 'calcium during fertilization in C. elegans'. The CaFE reporter produced a robust signal that recapitulated the previously reported, biphasic nature of the calcium wave and had no significant deleterious effects on worm physiology or fecundity. Calcium waves were not observed at the restrictive temperature in the spe-9(hc88) strain, in which sperm can still trigger meiotic maturation but can no longer fuse with the oocyte. Demonstrating the utility of the CaFE reporter, we analyzed polyspermy induced by inhibition of egg-3 via RNAi and observed late calcium waves in the uterus. This finding provides support to the idea that calcium release is not restricted to the first sperm fusion event during polyspermy. Establishment of the CaFE reporter in the genetically tractable and optically transparent worm provides a powerful tool to dissect the oocyte-to-embryo transition inside a living animal.
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Affiliation(s)
- Katie M. Toperzer
- Florida Institute of Technology, Biomedical Sciences Program, 150 W. University Blvd, Melbourne, FL 32901, USA
| | - Savannah J. Brennan
- Florida Institute of Technology, Biomedical Sciences Program, 150 W. University Blvd, Melbourne, FL 32901, USA
| | - David J. Carroll
- Midwestern University, Department of Biochemistry and Molecular Genetics, 19555 N 59th Ave, Glendale, AZ 85308, USA
| | - Eric A. Guisbert
- Florida Institute of Technology, Biomedical Sciences Program, 150 W. University Blvd, Melbourne, FL 32901, USA
| | - Karen S. Kim Guisbert
- Florida Institute of Technology, Biomedical Sciences Program, 150 W. University Blvd, Melbourne, FL 32901, USA
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Wolfe AD, Koberstein JN, Smith CB, Stewart ML, Hammarlund M, Hyman A, Stork PJ, Goodman R, Colón-Ramos DA. Local and dynamic regulation of neuronal glycolysis in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.25.554774. [PMID: 37662365 PMCID: PMC10473759 DOI: 10.1101/2023.08.25.554774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Energy metabolism supports neuronal function. While it is well established that changes in energy metabolism underpin brain plasticity and function, less is known about how individual neurons modulate their metabolic states to meet varying energy demands. This is because most approaches used to examine metabolism in living organisms lack the resolution to visualize energy metabolism within individual circuits, cells, or subcellular regions. Here we adapted a biosensor for glycolysis, HYlight, for use in C. elegans to image dynamic changes in glycolysis within individual neurons and in vivo. We determined that neurons perform glycolysis cell-autonomously, and modulate glycolytic states upon energy stress. By examining glycolysis in specific neurons, we documented a neuronal energy landscape comprising three general observations: 1) glycolytic states in neurons are diverse across individual cell types; 2) for a given condition, glycolytic states within individual neurons are reproducible across animals; and 3) for varying conditions of energy stress, glycolytic states are plastic and adapt to energy demands. Through genetic analyses, we uncovered roles for regulatory enzymes and mitochondrial localization in the cellular and subcellular dynamic regulation of glycolysis. Our study demonstrates the use of a single-cell glycolytic biosensor to examine how energy metabolism is distributed across cells and coupled to dynamic states of neuronal function, and uncovers new relationships between neuronal identities and metabolic landscapes in vivo.
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Affiliation(s)
- Aaron D Wolfe
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine; New Haven, CT 06536, USA
| | - John N Koberstein
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Chadwick B Smith
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Melissa L Stewart
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Marc Hammarlund
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine; New Haven, CT 06536, USA
| | - Anthony Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, Dresden, Germany
| | - Philip Js Stork
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Richard Goodman
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine; New Haven, CT 06536, USA
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Daniel A Colón-Ramos
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine; New Haven, CT 06536, USA
- Wu Tsai Institute, Yale University; New Haven, CT 06510, USA
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7
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Dvorak P, Hanicinec V, Soucek P. The position of the longest intron is related to biological functions in some human genes. Front Genet 2023; 13:1085139. [PMID: 36712854 PMCID: PMC9875286 DOI: 10.3389/fgene.2022.1085139] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/27/2022] [Indexed: 01/12/2023] Open
Abstract
The evidence that introns can influence different levels of transfer of genetic information between DNA and the final product is increasing. Longer first introns were found to be a general property of eukaryotic gene structure and shown to contain a higher fraction of conserved sequence and different functional elements. Our work brings more precise information about the position of the longest introns in human protein-coding genes and possible connection with biological function and gene expression. According to our results, the position of the longest intron can be localized to the first third of introns in 64%, the second third in 19%, and the third in 17%, with notable peaks at the middle and last introns of approximately 5% and 6%, respectively. The median lengths of the longest introns decrease with increasing distance from the start of the gene from approximately 15,000 to 5,000 bp. We have shown that the position of the longest intron is in some cases linked to the biological function of the given gene. For example, DNA repair genes have the longest intron more often in the second or third. In the distribution of gene expression according to the position of the longest intron, tissue-specific profiles can be traced with the highest expression usually at the absolute positions of intron 1 and 2. In this work, we present arguments supporting the hypothesis that the position of the longest intron in a gene is another biological factor modulating the transmission of genetic information. The position of the longest intron is related to biological functions in some human genes.
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Affiliation(s)
- Pavel Dvorak
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia,Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia,Institute of Medical Genetics, University Hospital Pilsen, Pilsen, Czechia,*Correspondence: Pavel Dvorak,
| | - Vojtech Hanicinec
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
| | - Pavel Soucek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia,Toxicogenomics Unit, National Institute of Public Health, Prague, Czechia
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Eigenfeld M, Kerpes R, Whitehead I, Becker T. Autofluorescence prediction model for fluorescence unmixing and age determination. Biotechnol J 2022; 17:e2200091. [DOI: 10.1002/biot.202200091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Marco Eigenfeld
- Technical University of Munich, School of Life Science Institute of Brewing and Beverage Technology Freising Germany
| | - Roland Kerpes
- Technical University of Munich, School of Life Science Institute of Brewing and Beverage Technology Freising Germany
| | - Iain Whitehead
- Technical University of Munich, School of Life Science Institute of Brewing and Beverage Technology Freising Germany
| | - Thomas Becker
- Technical University of Munich, School of Life Science Institute of Brewing and Beverage Technology Freising Germany
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Konzman D, Fukushige T, Dagnachew M, Krause M, Hanover JA. O-GlcNAc transferase plays a non-catalytic role in C. elegans male fertility. PLoS Genet 2022; 18:e1010273. [PMID: 36383567 PMCID: PMC9710795 DOI: 10.1371/journal.pgen.1010273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/30/2022] [Accepted: 11/08/2022] [Indexed: 11/17/2022] Open
Abstract
Animal behavior is influenced by the competing drives to maintain energy and to reproduce. The balance between these evolutionary pressures and how nutrient signaling pathways intersect with mating remains unclear. The nutrient sensor O-GlcNAc transferase, which post-translationally modifies intracellular proteins with a single monosaccharide, is responsive to cellular nutrient status and regulates diverse biological processes. Though essential in most metazoans, O-GlcNAc transferase (ogt-1) is dispensable in Caenorhabditis elegans, allowing genetic analysis of its physiological roles. Compared to control, ogt-1 males had a four-fold reduction in mean offspring, with nearly two thirds producing zero progeny. Interestingly, we found that ogt-1 males transferred sperm less often, and virgin males had reduced sperm count. ogt-1 males were also less likely to engage in mate-searching and mate-response behaviors. Surprisingly, we found normal fertility for males with hypodermal expression of ogt-1 and for ogt-1 strains with catalytic-dead mutations. This suggests OGT-1 serves a non-catalytic function in the hypodermis impacting male fertility and mating behavior. This study builds upon research on the nutrient sensor O-GlcNAc transferase and demonstrates a role it plays in the interplay between the evolutionary drives for reproduction and survival.
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Affiliation(s)
- Daniel Konzman
- Laboratory of Cellular and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Tetsunari Fukushige
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mesgana Dagnachew
- Laboratory of Cellular and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Michael Krause
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - John A. Hanover
- Laboratory of Cellular and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
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Liao TJ, Pan B, Hong H, Hayashi P, Rule JA, Ganger D, Lee WM, Rakela J, Chen M. Whole Exome Sequencing Reveals Genetic Variants in HLA Class II Genes Associated With Transplant-free Survival of Indeterminate Acute Liver Failure. Clin Transl Gastroenterol 2022; 13:e00502. [PMID: 35905417 PMCID: PMC10476814 DOI: 10.14309/ctg.0000000000000502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/17/2022] [Indexed: 09/06/2023] Open
Abstract
INTRODUCTION Indeterminate acute liver failure (IND-ALF) is a rare clinical syndrome with a high mortality rate. Lacking a known etiology makes rapid evaluation and treatment difficult, with liver transplantation often considered as the only therapeutic option. Our aim was to identify genetic variants from whole exome sequencing data that might be associated with IND-ALF clinical outcomes. METHODS Bioinformatics analysis was performed on whole exome sequencing data for 22 patients with IND-ALF. A 2-tier approach was used to identify significant single-nucleotide polymorphisms (SNPs) associated with IND-ALF clinical outcomes. Tier 1 identified the SNPs with a higher relative risk in the IND-ALF population compared with those identified in control populations. Tier 2 determined the SNPs connected to transplant-free survival and associated with model for end-stage liver disease serum sodium and Acute Liver Failure Study Group prognostic scores. RESULTS Thirty-one SNPs were found associated with a higher relative risk in the IND-ALF population compared with those in controls, of which 11 belong to the human leukocyte antigen (HLA) class II genes but none for the class I. Further analysis showed that 5 SNPs: rs796202376, rs139189937, and rs113473719 of HLA-DRB5; rs9272712 of HLA-DQA1; and rs747397929 of IDO1 were associated with a higher probability of IND-ALF transplant-free survival. Using 3 selected SNPs, a model for the polygenic risk score was developed to predict IND-ALF prognoses, which are comparable with those by model for end-stage liver disease serum sodium and Acute Liver Failure Study Group prognostic scores. DISCUSSION Certain gene variants in HLA-DRB5, HLA-DQA1, and IDO1 were found associated with IND-ALF transplant-free survival. Once validated, these identified SNPs may help elucidate the mechanism of IND-ALF and assist in its diagnosis and management.
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Affiliation(s)
- Tsung-Jen Liao
- Division of Bioinformatics and Biostatistics, U.S. Food and Drug Administration (FDA) National Center for Toxicological Research, Jefferson, Arkansas, USA;
| | - Bohu Pan
- Division of Bioinformatics and Biostatistics, U.S. Food and Drug Administration (FDA) National Center for Toxicological Research, Jefferson, Arkansas, USA;
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, U.S. Food and Drug Administration (FDA) National Center for Toxicological Research, Jefferson, Arkansas, USA;
| | - Paul Hayashi
- Division of Hepatology and Nutrition, Office of New Drugs, FDA Center for Drug Evaluation and Research, Silver Spring, Maryland, USA;
| | - Jody A. Rule
- Division of Gastroenterology and Hepatology, University of Texas Southwestern, Dallas, Texas, USA;
| | - Daniel Ganger
- Division of Gastroenterology and Hepatology, Northwestern University, Chicago, Illinois, USA;
| | - William M. Lee
- Division of Gastroenterology and Hepatology, University of Texas Southwestern, Dallas, Texas, USA;
| | - Jorge Rakela
- Division of Gastroenterology and Hepatology, Mayo Clinic, Phoenix, Arizona, USA.
| | - Minjun Chen
- Division of Bioinformatics and Biostatistics, U.S. Food and Drug Administration (FDA) National Center for Toxicological Research, Jefferson, Arkansas, USA;
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Adams DE, Zhen Y, Qi X, Shao WH. Axl Expression in Renal Mesangial Cells Is Regulated by Sp1, Ap1, MZF1, and Ep300, and the IL-6/miR-34a Pathway. Cells 2022; 11:cells11121869. [PMID: 35740998 PMCID: PMC9221537 DOI: 10.3390/cells11121869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/31/2022] [Accepted: 06/06/2022] [Indexed: 12/10/2022] Open
Abstract
Axl receptor tyrosine kinase expression in the kidney contributes to a variety of inflammatory renal disease by promoting glomerular proliferation. Axl expression in the kidney is negligible in healthy individuals but upregulated under inflammatory conditions. Little is known about Axl transcriptional regulation. We analyzed the 4.4 kb mouse Axl promoter region and found that many transcription factor (TF)-binding sites and regulatory elements are located within a 600 bp fragment proximal to the translation start site. Among four TFs (Sp1, Ap1, MZF1, and Ep300) identified, Sp1 was the most potent TF that promotes Axl expression. Luciferase assays confirmed the siRNA results and revealed additional mechanisms that regulate Axl expression, including sequences encoding a 5'-UTR mini-intron and potential G-quadruplex forming regions. Deletion of the Axl 5'-UTR mini-intron resulted in a 3.2-fold increases in luciferase activity over the full-length UTR (4.4 kb Axl construct). The addition of TMPyP4, a G-quadruplex stabilizer, resulted in a significantly decreased luciferase activity. Further analysis of the mouse Axl 3'-UTR revealed a miRNA-34a binding site, which inversely regulates Axl expression. The inhibitory role of miRNA-34a in Axl expression was demonstrated in mesangial cells using miRNA-34a mimicry and in primary kidney cells with IL-6 stimulated STAT3 activation. Taken together, Axl expression in mouse kidney is synergistically regulated by multiple factors, including TFs and secondary structures, such as mini-intron and G-quadruplex. A unique IL6/STAT3/miRNA-34a pathway was revealed to be critical in inflammatory renal Axl expression.
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Affiliation(s)
- David E. Adams
- Division of Rheumatology, Allergy, and Immunology, Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA; (D.E.A.); (Y.Z.)
| | - Yuxuan Zhen
- Division of Rheumatology, Allergy, and Immunology, Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA; (D.E.A.); (Y.Z.)
| | - Xiaoyang Qi
- Division of Hematology/Oncology, Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA;
| | - Wen-Hai Shao
- Division of Rheumatology, Allergy, and Immunology, Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA; (D.E.A.); (Y.Z.)
- Correspondence:
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12
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Calumenin knockdown, by intronic artificial microRNA, to improve expression efficiency of the recombinant human coagulation factor IX. Biotechnol Lett 2022; 44:713-728. [PMID: 35412165 DOI: 10.1007/s10529-022-03249-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 03/25/2022] [Indexed: 11/02/2022]
Abstract
OBJECTIVES To improve the expression efficiency of recombinant hFIX, by enhancing its γ-carboxylation, which is inhibited by Calumenin (CALU), we used intronic artificial microRNAs (amiRNAs) for the CALU downregulation. METHODS Two human CALU (hCALU)-specific amiRNAs were designed, validated and inserted within a truncated form of the hFIX intron 1, in either 3'- or 5'-untranslated regions of the hFIX cDNA, in an expression vector. After transfections of a human cell line with the recombinant constructs, processing of the miRNAs confirmed by RT-PCR, using stem-loop primers. The hFIX and hCALU expression assessments were done based on RT-PCR results. The Gamma(γ)-carboxylation of the expressed hFIX was examined by a barium citrate precipitation method, followed by Enzyme-Linked Immunosorbent Assay. RESULTS Efficient CALU down regulations, with more than 30-fold decrease, occurred in the cells carrying either of the two examined the 3'-located amiRNAs. The CALU downregulation in the same cells doubled the FIX γ-carboxylation, although the transcription of the FIX decreased significantly. On the other hand, while the expression of the amiRNAs from the 5'-located intron had no decreasing effect on the expression level of CALU, the level of hFIX transcription in these cells increased almost twofold compared to the construct without amiRNA. CONCLUSION The CALU downregulation, consistent with efficient hFIX γ-carboxylation, occurred in the cells carrying either of the two amiRNAs containing constructs, although it was affected by the locations of the amiRNA carrying introns, suggesting a possible need to optimize the conditions for the amiRNAs expression.
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Garcia G, Homentcovschi S, Kelet N, Higuchi-Sanabria R. Imaging of Actin Cytoskeletal Integrity During Aging in C. elegans. Methods Mol Biol 2022; 2364:101-137. [PMID: 34542850 DOI: 10.1007/978-1-0716-1661-1_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The actin cytoskeleton plays a fundamental role in the regulation of multiple cellular pathways, including trafficking and locomotion. The functional integrity of the cytoskeleton is important during aging, as the decline of cytoskeletal integrity contributes to the physiological consequence of aging. Moreover, improving cytoskeletal form and function throughout aging is sufficient to drive life span extension and promote organismal health in multiple model systems. For these reasons, optimized protocols for visualization of the actin cytoskeleton and its downstream consequences on health span and life span are critical for understanding the aging process. In C. elegans, the actin cytoskeleton shows diverse morphologies across tissues, potentially due to the significantly different functions of each cell type. This chapter describes an imaging platform utilizing LifeAct to visualize the actin cytoskeleton in live, whole nematodes throughout the aging process and methods to perform follow-up studies on the life span and health span of these organisms.
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Affiliation(s)
- Gilberto Garcia
- Department of Molecular & Cellular Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Stefan Homentcovschi
- Department of Molecular & Cellular Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Naame Kelet
- Department of Molecular & Cellular Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ryo Higuchi-Sanabria
- Department of Molecular & Cellular Biology, University of California, Berkeley, Berkeley, CA, USA.
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA.
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Sands B, Yun S, Mendenhall AR. Introns control stochastic allele expression bias. Nat Commun 2021; 12:6527. [PMID: 34764277 PMCID: PMC8585970 DOI: 10.1038/s41467-021-26798-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 10/19/2021] [Indexed: 01/26/2023] Open
Abstract
Monoallelic expression (MAE) or extreme allele bias can account for incomplete penetrance, missing heritability and non-Mendelian diseases. In cancer, MAE is associated with shorter patient survival times and higher tumor grade. Prior studies showed that stochastic MAE is caused by stochastic epigenetic silencing, in a gene and tissue-specific manner. Here, we used C. elegans to study stochastic MAE in vivo. We found allele bias/MAE to be widespread within C. elegans tissues, presenting as a continuum from fully biallelic to MAE. We discovered that the presence of introns within alleles robustly decreases MAE. We determined that introns control MAE at distinct loci, in distinct cell types, with distinct promoters, and within distinct coding sequences, using a 5'-intron position-dependent mechanism. Bioinformatic analysis showed human intronless genes are significantly enriched for MAE. Our experimental evidence demonstrates a role for introns in regulating MAE, possibly explaining why some mutations within introns result in disease.
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Affiliation(s)
- Bryan Sands
- grid.34477.330000000122986657Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA USA
| | - Soo Yun
- grid.34477.330000000122986657Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA USA
| | - Alexander R. Mendenhall
- grid.34477.330000000122986657Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA USA
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15
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Tanaka T, Maeda Y, Suhaimi N, Tsuneoka C, Nonoyama T, Yoshino T, Kato N, Lauersen KJ. Intron-mediated enhancement of transgene expression in the oleaginous diatom Fistulifera solaris towards bisabolene production. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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16
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Back G, Walther D. Identification of cis-regulatory motifs in first introns and the prediction of intron-mediated enhancement of gene expression in Arabidopsis thaliana. BMC Genomics 2021; 22:390. [PMID: 34039279 PMCID: PMC8157754 DOI: 10.1186/s12864-021-07711-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/11/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Intron mediated enhancement (IME) is the potential of introns to enhance the expression of its respective gene. This essential function of introns has been observed in a wide range of species, including fungi, plants, and animals. However, the mechanisms underlying the enhancement are as of yet poorly understood. The goal of this study was to identify potential IME-related sequence motifs and genomic features in first introns of genes in Arabidopsis thaliana. RESULTS Based on the rationale that functional sequence motifs are evolutionarily conserved, we exploited the deep sequencing information available for Arabidopsis thaliana, covering more than one thousand Arabidopsis accessions, and identified 81 candidate hexamer motifs with increased conservation across all accessions that also exhibit positional occurrence preferences. Of those, 71 were found associated with increased correlation of gene expression of genes harboring them, suggesting a cis-regulatory role. Filtering further for effect on gene expression correlation yielded a set of 16 hexamer motifs, corresponding to five consensus motifs. While all five motifs represent new motif definitions, two are similar to the two previously reported IME-motifs, whereas three are altogether novel. Both consensus and hexamer motifs were found associated with higher expression of alleles harboring them as compared to alleles containing mutated motif variants as found in naturally occurring Arabidopsis accessions. To identify additional IME-related genomic features, Random Forest models were trained for the classification of gene expression level based on an array of sequence-related features. The results indicate that introns contain information with regard to gene expression level and suggest sequence-compositional features as most informative, while position-related features, thought to be of central importance before, were found with lower than expected relevance. CONCLUSIONS Exploiting deep sequencing and broad gene expression information and on a genome-wide scale, this study confirmed the regulatory role on first-introns, characterized their intra-species conservation, and identified a set of novel sequence motifs located in first introns of genes in the genome of the plant Arabidopsis thaliana that may play a role in inducing high and correlated gene expression of the genes harboring them.
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Affiliation(s)
- Georg Back
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Dirk Walther
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany.
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17
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Bryant AS, Hallem EA. The Wild Worm Codon Adapter: a web tool for automated codon adaptation of transgenes for expression in non-Caenorhabditis nematodes. G3 (BETHESDA, MD.) 2021; 11:6259089. [PMID: 33914084 PMCID: PMC8496300 DOI: 10.1093/g3journal/jkab146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/22/2021] [Indexed: 01/22/2023]
Abstract
Advances in genomics techniques are expanding the range of nematode species that are amenable to transgenesis. Due to divergent codon usage biases across species, codon optimization is often a critical step for the successful expression of exogenous transgenes in nematodes. Platforms for generating DNA sequences codon-optimized for the free-living model nematode Caenorhabditis elegans are broadly available. However, until now such tools did not exist for non-Caenorhabditis nematodes. We therefore developed the Wild Worm Codon Adapter, a tool for rapid transgene codon optimization for expression in non-Caenorhabditis nematodes. The app includes built-in optimization for parasitic nematodes in the Strongyloides, Nippostrongylus, and Brugia genera as well as the predatory nematode Pristionchus pacificus. The app also supports custom optimization for any species using user-provided optimization rules. In addition, the app supports automated insertion of synthetic or native introns, as well as the analysis of codon bias in transgene and native sequences. Here, we describe this web-based tool and demonstrate how it may be used to analyze genome-wide codon bias in Strongyloides species.
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Affiliation(s)
- Astra S Bryant
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Elissa A Hallem
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Corresponding author: University of California, Los Angeles, MIMG, 237 BSRB, 615 Charles E. Young Dr. S., Los Angeles, CA 90095, USA.
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18
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Skopenkova VV, Egorova TV, Bardina MV. Muscle-Specific Promoters for Gene Therapy. Acta Naturae 2021; 13:47-58. [PMID: 33959386 PMCID: PMC8084301 DOI: 10.32607/actanaturae.11063] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 07/30/2020] [Indexed: 12/19/2022] Open
Abstract
Many genetic diseases that are responsible for muscular disorders have been described to date. Gene replacement therapy is a state-of-the-art strategy used to treat such diseases. In this approach, the functional copy of a gene is delivered to the affected tissues using viral vectors. There is an urgent need for the design of short, regulatory sequences that would drive a high and robust expression of a therapeutic transgene in skeletal muscles, the diaphragm, and the heart, while exhibiting limited activity in non-target tissues. This review focuses on the development and improvement of muscle-specific promoters based on skeletal muscle α-actin, muscle creatine kinase, and desmin genes, as well as other genes expressed in muscles. The current approaches used to engineer synthetic muscle-specific promoters are described. Other elements of the viral vectors that contribute to tissue-specific expression are also discussed. A special feature of this review is the presence of up-to-date information on the clinical and preclinical trials of gene therapy drug candidates that utilize muscle-specific promoters.
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Affiliation(s)
- V. V. Skopenkova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
- Marlin Biotech LLC, Moscow, 121205 Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - T. V. Egorova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
- Marlin Biotech LLC, Moscow, 121205 Russia
| | - M. V. Bardina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
- Marlin Biotech LLC, Moscow, 121205 Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
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Han Z, Lo WS, Lightfoot JW, Witte H, Sun S, Sommer RJ. Improving Transgenesis Efficiency and CRISPR-Associated Tools Through Codon Optimization and Native Intron Addition in Pristionchus Nematodes. Genetics 2020; 216:947-956. [PMID: 33060138 PMCID: PMC7768246 DOI: 10.1534/genetics.120.303785] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/14/2020] [Indexed: 12/12/2022] Open
Abstract
A lack of appropriate molecular tools is one obstacle that prevents in-depth mechanistic studies in many organisms. Transgenesis, clustered regularly interspaced short palindromic repeats (CRISPR)-associated engineering, and related tools are fundamental in the modern life sciences, but their applications are still limited to a few model organisms. In the phylum Nematoda, transgenesis can only be performed in a handful of species other than Caenorhabditis elegans, and additionally, other species suffer from significantly lower transgenesis efficiencies. We hypothesized that this may in part be due to incompatibilities of transgenes in the recipient organisms. Therefore, we investigated the genomic features of 10 nematode species from three of the major clades representing all different lifestyles. We found that these species show drastically different codon usage bias and intron composition. With these findings, we used the species Pristionchus pacificus as a proof of concept for codon optimization and native intron addition. Indeed, we were able to significantly improve transgenesis efficiency, a principle that may be usable in other nematode species. In addition, with the improved transgenes, we developed a fluorescent co-injection marker in P. pacificus for the detection of CRISPR-edited individuals, which helps considerably to reduce associated time and costs.
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Affiliation(s)
- Ziduan Han
- Max Planck Institute for Developmental Biology, Tuebingen 72076, Germany
| | - Wen-Sui Lo
- Max Planck Institute for Developmental Biology, Tuebingen 72076, Germany
| | - James W Lightfoot
- Max Planck Institute for Developmental Biology, Tuebingen 72076, Germany
| | - Hanh Witte
- Max Planck Institute for Developmental Biology, Tuebingen 72076, Germany
| | - Shuai Sun
- Max Planck Institute for Developmental Biology, Tuebingen 72076, Germany
| | - Ralf J Sommer
- Max Planck Institute for Developmental Biology, Tuebingen 72076, Germany
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20
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Burnaevskiy N, Sands B, Yun S, Tedesco PM, Johnson TE, Kaeberlein M, Brent R, Mendenhall A. Chaperone biomarkers of lifespan and penetrance track the dosages of many other proteins. Nat Commun 2019; 10:5725. [PMID: 31844058 PMCID: PMC6914778 DOI: 10.1038/s41467-019-13664-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 11/11/2019] [Indexed: 12/27/2022] Open
Abstract
Many traits vary among isogenic individuals in homogeneous environments. In microbes, plants and animals, variation in the protein chaperone system affects many such traits. In the animal model C. elegans, the expression level of hsp-16.2 chaperone biomarkers correlates with or predicts the penetrance of mutations and lifespan after heat shock. But the physiological mechanisms causing cells to express different amounts of the biomarker were unknown. Here, we used an in vivo microscopy approach to dissect different contributions to cell-to-cell variation in hsp-16.2 expression in the intestines of young adult animals, which generate the most lifespan predicting signal. While we detected both cell autonomous intrinsic noise and signaling noise, we found both contributions were relatively unimportant. The major contributor to cell-to-cell variation in biomarker expression was general differences in protein dosage. The hsp-16.2 biomarker reveals states of high or low effective dosage for many genes.
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Affiliation(s)
| | - Bryan Sands
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Soo Yun
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Patricia M Tedesco
- Department of Integrative Physiology, University of Colorado, Boulder, CO, USA
| | - Thomas E Johnson
- Department of Integrative Physiology, University of Colorado, Boulder, CO, USA
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Roger Brent
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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