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Abstract
Complex multicellular organisms have evolved specific mechanisms to replenish cells in homeostasis and during repair. Here, we discuss how emerging technologies (e.g., single-cell RNA sequencing) challenge the concept that tissue renewal is fueled by unidirectional differentiation from a resident stem cell. We now understand that cell plasticity, i.e., cells adaptively changing differentiation state or identity, is a central tissue renewal mechanism. For example, mature cells can access an evolutionarily conserved program (paligenosis) to reenter the cell cycle and regenerate damaged tissue. Most tissues lack dedicated stem cells and rely on plasticity to regenerate lost cells. Plasticity benefits multicellular organisms, yet it also carries risks. For one, when long-lived cells undergo paligenotic, cyclical proliferation and redif-ferentiation, they can accumulate and propagate acquired mutations that activate oncogenes and increase the potential for developing cancer. Lastly, we propose a new framework for classifying patterns of cell proliferation in homeostasis and regeneration, with stem cells representing just one of the diverse methods that adult tissues employ.
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Affiliation(s)
- Jeffrey W. Brown
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Charles J. Cho
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA,Current affiliation: Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Jason C. Mills
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA,Current affiliation: Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA,Departments of Pathology and Immunology and Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA,Current affiliation: Departments of Medicine, Pathology and Immunology, and Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
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2
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Verhagen I, Laine VN, Mateman AC, Pijl A, de Wit R, van Lith B, Kamphuis W, Viitaniemi HM, Williams TD, Caro SP, Meddle SL, Gienapp P, van Oers K, Visser ME. Fine-tuning of seasonal timing of breeding is regulated downstream in the underlying neuro-endocrine system in a small songbird. ACTA ACUST UNITED AC 2019; 222:jeb.202481. [PMID: 31371403 DOI: 10.1242/jeb.202481] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 07/31/2019] [Indexed: 12/15/2022]
Abstract
The timing of breeding is under selection in wild populations as a result of climate change, and understanding the underlying physiological processes mediating this timing provides insight into the potential rate of adaptation. Current knowledge on this variation in physiology is, however, mostly limited to males. We assessed whether individual differences in the timing of breeding in females are reflected in differences in candidate gene expression and, if so, whether these differences occur in the upstream (hypothalamus) or downstream (ovary and liver) parts of the neuroendocrine system. We used 72 female great tits from two generations of lines artificially selected for early and late egg laying, which were housed in climate-controlled aviaries and went through two breeding cycles within 1 year. In the first breeding season we obtained individual egg-laying dates, while in the second breeding season, using the same individuals, we sampled several tissues at three time points based on the timing of the first breeding attempt. For each tissue, mRNA expression levels were measured using qPCR for a set of candidate genes associated with the timing of reproduction and subsequently analysed for differences between generations, time points and individual timing of breeding. We found differences in gene expression between generations in all tissues, with the most pronounced differences in the hypothalamus. Differences between time points, and early- and late-laying females, were found exclusively in the ovary and liver. Altogether, we show that fine-tuning of the seasonal timing of breeding, and thereby the opportunity for adaptation in the neuroendocrine system, is regulated mostly downstream in the neuro-endocrine system.
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Affiliation(s)
- Irene Verhagen
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
| | - Veronika N Laine
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
| | - A Christa Mateman
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
| | - Agata Pijl
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
| | - Ruben de Wit
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
| | - Bart van Lith
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
| | - Willem Kamphuis
- Netherlands Institute for Neuroscience (NIN-KNAW), 1105 BA Amsterdam-Zuidoost, The Netherlands
| | - Heidi M Viitaniemi
- Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland
| | - Tony D Williams
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6
| | - Samuel P Caro
- Departement d'Ecologie Evolutive, Centre d'Ecologie Fonctionnelle & Evolutive, 34293 Montpellier 5, France
| | - Simone L Meddle
- Department of Behavioural Neuroendocrinology, University of Edinburgh, Edinburgh EH8 9YL, UK
| | - Phillip Gienapp
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
| | - Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
| | - Marcel E Visser
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
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3
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Lewis MA, Sharabash N, Miao ZF, Lyons LN, Piccirillo J, Kallogjeri D, Schootman M, Mutch M, Yan Y, Levin MS, Castells A, Cuatrecasas M, Mills JC, Wang ZN, Rubin DC. Increased IFRD1 Expression in Human Colon Cancers Predicts Reduced Patient Survival. Dig Dis Sci 2017; 62:3460-3467. [PMID: 29094309 PMCID: PMC6167971 DOI: 10.1007/s10620-017-4819-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 10/19/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND Colon cancer (CRC) is the third most common cancer worldwide. CRC develops through combinations of genetic and epigenetic changes. However, there is marked heterogeneity in the "driver gene" mutational profiles within and among colon cancers from individual patients, and these are not sufficient to explain differences in colon cancer behavior and treatment response. Global modulation of the tumor landscape may play a role in cancer behavior. Interferon-related developmental regulator 1 (IFRD1) is a transcriptional co-regulator that modulates expression of large gene cassettes and plays a role in gut epithelial proliferation following massive intestinal resection. AIMS We address the hypothesis that increased IFRD1 expression in colon cancers is associated with poorer patient survival. METHODS Tumor and normal tissue from colon cancer patient cohorts from the USA, Spain, and China were used for this study. Cancers were scored for the intensity of IFRD1 immunostaining. The primary clinical outcome was overall survival defined as time from diagnosis to death due to cancer. Kaplan-Meier method and log-rank analysis were used to assess the association between IFRD1 expression and survival. RESULTS Almost all (98.7%) colon cancers showed readily detectable IFRD1 expression, with immunoreactivity primarily in the tumor cytoplasm. High IFRD1 colon cancer expression was significantly associated with decreased 5-year patient survival. Patients in the American cohort with high IFRD1 expression had a poorer prognosis. CONCLUSIONS We have demonstrated that high IFRD1 protein expression in colon cancer is associated with poorer patient prognosis, suggesting a potential role for IFRD1 in modulating tumor behavior.
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Affiliation(s)
- Mark A Lewis
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, 660 South Euclid Avenue, Box 8124, St. Louis, MO, 63110, USA
| | - Noura Sharabash
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, 660 South Euclid Avenue, Box 8124, St. Louis, MO, 63110, USA
- University of Illinois, Carle Clinics, 611 W. Park Street, Urbana, IL, 61801, USA
| | - Zhi-Feng Miao
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, 660 South Euclid Avenue, Box 8124, St. Louis, MO, 63110, USA
- Department of Surgical Oncology, First Hospital of China Medical University, No. 155 North Nanjing Street, Shenyang, Liaoning Province, China
| | - Lydia N Lyons
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, 660 South Euclid Avenue, Box 8124, St. Louis, MO, 63110, USA
| | - Jay Piccirillo
- Department of Surgery, Washington University School of Medicine, 660 South Euclid Avenue, Box 8115, St. Louis, MO, 63110, USA
| | - Donna Kallogjeri
- Department of Surgery, Washington University School of Medicine, 660 South Euclid Avenue, Box 8115, St. Louis, MO, 63110, USA
| | - Mario Schootman
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, 660 South Euclid Avenue, Box 8124, St. Louis, MO, 63110, USA
- St. Louis University School of Medicine, Salus Center, 3545 Lafayette Ave. Room 1401-K, St. Louis, MO, 63103, USA
| | - Matthew Mutch
- Department of Surgery, Washington University School of Medicine, 660 South Euclid Avenue, Box 8109, St. Louis, MO, 63110, USA
| | - Yan Yan
- Department of Surgery, Washington University School of Medicine, 660 South Euclid Avenue, Box 8100, St. Louis, MO, 63110, USA
| | - Marc S Levin
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, 660 South Euclid Avenue, Box 8124, St. Louis, MO, 63110, USA
- Veterans' Administration St. Louis Health Care System, St. Louis, MO, USA
| | | | | | - Jason C Mills
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, 660 South Euclid Avenue, Box 8124, St. Louis, MO, 63110, USA
- Department of Pathology, Washington University School of Medicine, 660 South Euclid Avenue, Box 8124, St. Louis, MO, 63110, USA
- Department of Developmental Biology, Washington University School of Medicine, 660 South Euclid Avenue, Box 8124, St. Louis, MO, 63110, USA
| | - Zhen-Ning Wang
- Department of Surgical Oncology, First Hospital of China Medical University, No. 155 North Nanjing Street, Shenyang, Liaoning Province, China
| | - Deborah C Rubin
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, 660 South Euclid Avenue, Box 8124, St. Louis, MO, 63110, USA.
- Department of Developmental Biology, Washington University School of Medicine, 660 South Euclid Avenue, Box 8124, St. Louis, MO, 63110, USA.
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Li FX, Liu Y, Miao XP, Fu GQ, Curry TE. Expression and regulation of the differentiation regulators ERBB Receptor Feedback Inhibitor 1 (ERRFI1) and Interferon-related Developmental Regulator 1 (IFRD1) during the periovulatory period in the rat ovary. Mol Reprod Dev 2016; 83:714-23. [DOI: 10.1002/mrd.22673] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 06/28/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Fei-xue Li
- Zhejiang Key Laboratory of Organ Development and Regeneration, Institute of Developmental and Regenerative Biology, College of Life and Environmental Sciences; Hangzhou Normal University; Hangzhou China
| | - Ying Liu
- Zhejiang Key Laboratory of Organ Development and Regeneration, Institute of Developmental and Regenerative Biology, College of Life and Environmental Sciences; Hangzhou Normal University; Hangzhou China
| | - Xiao-ping Miao
- Zhejiang Key Laboratory of Organ Development and Regeneration, Institute of Developmental and Regenerative Biology, College of Life and Environmental Sciences; Hangzhou Normal University; Hangzhou China
| | - Guo-quan Fu
- Zhejiang Key Laboratory of Organ Development and Regeneration, Institute of Developmental and Regenerative Biology, College of Life and Environmental Sciences; Hangzhou Normal University; Hangzhou China
| | - Thomas E. Curry
- Department of Obstetrics and Gynecology, Chandler Medical Center; University of Kentucky; Lexington Kentucky
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Rubin DC, Levin MS. Mechanisms of intestinal adaptation. Best Pract Res Clin Gastroenterol 2016; 30:237-48. [PMID: 27086888 PMCID: PMC4874810 DOI: 10.1016/j.bpg.2016.03.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/03/2016] [Accepted: 03/05/2016] [Indexed: 01/31/2023]
Abstract
Following loss of functional small bowel surface area due to surgical resection for therapy of Crohn's disease, ischemia, trauma or other disorders, the remnant gut undergoes a morphometric and functional compensatory adaptive response which has been best characterized in preclinical models. Increased crypt cell proliferation results in increased villus height, crypt depth and villus hyperplasia, accompanied by increased nutrient, fluid and electrolyte absorption. Clinical observations suggest that functional adaptation occurs in humans. In the immediate postoperative period, patients with substantial small bowel resection have massive fluid and electrolyte loss with reduced nutrient absorption. For many patients, the adaptive response permits partial or complete weaning from parenteral nutrition (PN), within two years following resection. However, others have life-long PN dependence. An understanding of the molecular mechanisms that regulate the gut adaptive response is critical for developing novel therapies for short bowel syndrome. Herein we present a summary of key studies that seek to elucidate the mechanisms that regulate post-resection adaptation, focusing on stem and crypt cell proliferation, epithelial differentiation, apoptosis, enterocyte function and the role of growth factors and the enteric nervous system.
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Affiliation(s)
- Deborah C Rubin
- Departments of Medicine and Developmental Biology, Washington University in St. Louis School of Medicine, 660 South Euclid Avenue, Box 8124, Saint Louis, MO, 63141, USA.
| | - Marc S Levin
- Veteran's Administration, St. Louis Health Care System and Department of Medicine, Divisions of Gastroenterology and VA Medicine, Washington University in St. Louis School of Medicine, 660 South Euclid Avenue, Box 8124, Saint Louis, MO, 63141, USA.
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6
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Tummers B, Goedemans R, Pelascini LPL, Jordanova ES, van Esch EMG, Meyers C, Melief CJM, Boer JM, van der Burg SH. The interferon-related developmental regulator 1 is used by human papillomavirus to suppress NFκB activation. Nat Commun 2015; 6:6537. [PMID: 26055519 PMCID: PMC4382698 DOI: 10.1038/ncomms7537] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 02/05/2015] [Indexed: 12/26/2022] Open
Abstract
High-risk human papillomaviruses (hrHPVs) infect keratinocytes and successfully evade host immunity despite the fact that keratinocytes are well equipped to respond to innate and adaptive immune signals. Using non-infected and freshly established or persistent hrHPV-infected keratinocytes we show that hrHPV impairs the acetylation of NFκB/RelA K310 in keratinocytes. As a consequence, keratinocytes display a decreased pro-inflammatory cytokine production and immune cell attraction in response to stimuli of the innate or adaptive immune pathways. HPV accomplishes this by augmenting the expression of interferon-related developmental regulator 1 (IFRD1) in an EGFR-dependent manner. Restoration of NFκB/RelA acetylation by IFRD1 shRNA, cetuximab treatment or the HDAC1/3 inhibitor entinostat increases basal and induced cytokine expression. Similar observations are made in IFRD1-overexpressing HPV-induced cancer cells. Thus, our study reveals an EGFR–IFRD1-mediated viral immune evasion mechanism, which can also be exploited by cancer cells. Human papillomavirus employs immune evasion strategies to establish a long-term infection. Here the authors show that the virus in the EGFR-dependent manner induces IFRD1, which blocks NFκB activating acetylation, and that this process can be suppressed by the EGFR inhibitor cetuximab.
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Affiliation(s)
- Bart Tummers
- Department of Clinical Oncology, Leiden University Medical Center, Albinusdreef 2, 2333ZA Leiden, The Netherlands
| | - Renske Goedemans
- Department of Clinical Oncology, Leiden University Medical Center, Albinusdreef 2, 2333ZA Leiden, The Netherlands
| | - Laetitia P L Pelascini
- Department of Molecular Cell Biology, Leiden University Medical Center, Albinusdreef 2, 2333ZA Leiden, The Netherlands
| | - Ekaterina S Jordanova
- Center for Gynaecological Oncology, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Edith M G van Esch
- Department of Gynaecology, Leiden University Medical Center, Albinusdreef 2, 2333ZA Leiden, The Netherlands
| | - Craig Meyers
- Department of Microbiology and Immunology, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, Pennsylvania 17033, USA
| | - Cornelis J M Melief
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333ZA Leiden, The Netherlands
| | - Judith M Boer
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, 2333ZA Leiden, The Netherlands
| | - Sjoerd H van der Burg
- Department of Clinical Oncology, Leiden University Medical Center, Albinusdreef 2, 2333ZA Leiden, The Netherlands
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7
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Garcia AM, Wakeman D, Lu J, Rowley C, Geisman T, Butler C, Bala S, Swietlicki EA, Warner BW, Levin MS, Rubin DC. Tis7 deletion reduces survival and induces intestinal anastomotic inflammation and obstruction in high-fat diet-fed mice with short bowel syndrome. Am J Physiol Gastrointest Liver Physiol 2014; 307:G642-54. [PMID: 25059825 PMCID: PMC4166722 DOI: 10.1152/ajpgi.00374.2013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Effective therapies are limited for patients with parenteral nutrition-dependent short bowel syndrome. We previously showed that intestinal expression of the transcriptional coregulator tetradecanoyl phorbol acetate-induced sequence 7 (tis7) is markedly increased during the adaptive response following massive small bowel resection and tis7 plays a role in normal gut lipid metabolism. Here, we further explore the functional implications of tis7 deletion in intestinal lipid metabolism and the adaptive response following small bowel resection. Intestinal tis7 transgenic (tis7(tg)), tis7(-/-), and wild-type (WT) littermates were subjected to 50% small bowel resection. Mice were fed a control or a high-saturated-fat (42% energy) diet for 21 days. Survival, body weight recovery, lipid absorption, mucosal lipid analysis, and the morphometric adaptive response were analyzed. Quantitative real-time PCR was performed to identify tis7 downstream gene targets. Postresection survival was markedly reduced in high-fat, but not control, diet-fed tis7(-/-) mice. Decreased survival was associated with anastomotic inflammation and intestinal obstruction postresection. High-fat, but not control, diet-fed tis7(-/-) mice had increased intestinal IL-6 expression. Intestinal lipid trafficking was altered in tis7(-/-) compared with WT mice postresection. In contrast, high-fat diet-fed tis7(tg) mice had improved survival postresection compared with WT littermates. High-fat diet feeding in the setting of tis7 deletion resulted in postresection anastomotic inflammation and small bowel obstruction. Tolerance of a calorie-rich, high-fat diet postresection may require tis7 and its target genes. The presence of luminal fat in the setting of tis7 deletion promotes an intestinal inflammatory response postresection.
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Affiliation(s)
- Amy M. Garcia
- 2Division of Pediatric Gastroenterology, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri;
| | - Derek Wakeman
- 3Department of Pediatric Surgery, Washington University School of Medicine, St. Louis, Missouri;
| | - Jianyun Lu
- 1Division of Gastroenterology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri;
| | - Christopher Rowley
- 1Division of Gastroenterology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri;
| | - Taylor Geisman
- 1Division of Gastroenterology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri;
| | - Catherine Butler
- 1Division of Gastroenterology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri;
| | - Shashi Bala
- 1Division of Gastroenterology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri;
| | - Elzbieta A. Swietlicki
- 1Division of Gastroenterology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri;
| | - Brad W. Warner
- 3Department of Pediatric Surgery, Washington University School of Medicine, St. Louis, Missouri;
| | - Marc S. Levin
- 1Division of Gastroenterology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri; ,4Department of Medicine, Veterans Affairs St. Louis Health Care System; St. Louis, Missouri; and
| | - Deborah C. Rubin
- 1Division of Gastroenterology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri; ,5Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri
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Rise ML, Nash GW, Hall JR, Booman M, Hori TS, Trippel EA, Gamperl AK. Variation in embryonic mortality and maternal transcript expression among Atlantic cod (Gadus morhua) broodstock: a functional genomics study. Mar Genomics 2014; 18 Pt A:3-20. [PMID: 24878168 DOI: 10.1016/j.margen.2014.05.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/13/2014] [Accepted: 05/13/2014] [Indexed: 12/22/2022]
Abstract
Early life stage mortality is an important issue for Atlantic cod aquaculture, yet the impact of the cod maternal (egg) transcriptome on egg quality and mortality during embryonic development is poorly understood. In the present work, we studied embryonic mortality and maternal transcript expression using eggs from 15 females. Total mortality at 7days post-fertilization (7 dpf, segmentation stage) was used as an indice of egg quality. A 20,000 probe (20K) microarray experiment compared the 7hours post-fertilization (7 hpf, ~2-cell stage) egg transcriptome of the two lowest quality females (>90% mortality at 7 dpf) to that of the highest quality female (~16% mortality at 7 dpf). Forty-three microarray probes were consistently differentially expressed in both low versus high quality egg comparisons (25 higher expressed in low quality eggs, and 18 higher expressed in high quality eggs). The microarray experiment also identified many immune-relevant genes [e.g. interferon (IFN) pathway genes ifngr1 and ifrd1)] that were highly expressed in eggs of all 3 females regardless of quality. Twelve of the 43 candidate egg quality-associated genes, and ifngr1, ifrd1 and irf7, were included in a qPCR study with 7 hpf eggs from all 15 females. Then, the genes that were confirmed by qPCR to be greater than 2-fold differentially expressed between 7 hpf eggs from the lowest and highest quality females (dcbld1, ddc, and acy3 more highly expressed in the 2 lowest quality females; kpna7 and hacd1 more highly expressed in the highest quality female), and the 3 IFN pathway genes, were included in a second qPCR study with unfertilized eggs. While some maternal transcripts included in these qPCR studies were associated with extremes in egg quality, there was little correlation between egg quality and gene expression when all females were considered. Both dcbld1 and ddc showed greater than 100-fold differences in transcript expression between females and were potentially influenced by family. The Atlantic cod ddc (dopa decarboxylase) complete cDNA was characterized, and has a 1461bp open reading frame encoding a 486 amino acid protein that contains all eight residues of the conserved pyridoxal 5'-phosphate binding site including the catalytic lysine. This study provides valuable new information and resources related to the Atlantic cod egg transcriptome. Some of these microarray-identified, qPCR-confirmed, Atlantic cod egg transcripts (e.g. ddc, kpna7) play important roles during embryonic development of other vertebrate species, and may have similar functions in Atlantic cod.
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Affiliation(s)
- Matthew L Rise
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada.
| | - Gordon W Nash
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada
| | - Jennifer R Hall
- Aquatic Research Cluster, CREAIT Network, Ocean Sciences Centre, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada
| | - Marije Booman
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada
| | - Tiago S Hori
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada
| | - Edward A Trippel
- Fisheries and Oceans Canada, St. Andrews Biological Station, St. Andrews, NB, E5B 2L9, Canada
| | - A Kurt Gamperl
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada
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9
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Nakamura Y, Hinoi E, Iezaki T, Takada S, Hashizume S, Takahata Y, Tsuruta E, Takahashi S, Yoneda Y. Repression of adipogenesis through promotion of Wnt/β-catenin signaling by TIS7 up-regulated in adipocytes under hypoxia. Biochim Biophys Acta Mol Basis Dis 2013; 1832:1117-28. [DOI: 10.1016/j.bbadis.2013.03.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 02/15/2013] [Accepted: 03/12/2013] [Indexed: 12/26/2022]
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10
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Weiler CA, Drumm ML. Genetic influences on cystic fibrosis lung disease severity. Front Pharmacol 2013; 4:40. [PMID: 23630497 PMCID: PMC3632778 DOI: 10.3389/fphar.2013.00040] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 03/21/2013] [Indexed: 12/19/2022] Open
Abstract
Understanding the causes of variation in clinical manifestations of disease should allow for design of new or improved therapeutic strategies to treat the disease. If variation is caused by genetic differences between individuals, identifying the genes involved should present therapeutic targets, either in the proteins encoded by those genes or the pathways in which they function. The technology to identify and genotype the millions of variants present in the human genome has evolved rapidly over the past two decades. Originally only a small number of polymorphisms in a small number of subjects could be studied realistically, but speed and scope have increased nearly as dramatically as cost has decreased, making it feasible to determine genotypes of hundreds of thousands of polymorphisms in thousands of subjects. The use of such genetic technology has been applied to cystic fibrosis (CF) to identify genetic variation that alters the outcome of this single gene disorder. Candidate gene strategies to identify these variants, referred to as “modifier genes,” has yielded several genes that act in pathways known to be important in CF and for these the clinical implications are relatively clear. More recently, whole-genome surveys that probe hundreds of thousands of variants have been carried out and have identified genes and chromosomal regions for which a role in CF is not at all clear. Identification of these genes is exciting, as it provides the possibility for new areas of therapeutic development.
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Affiliation(s)
- Colleen A Weiler
- Department of Pediatrics, Case Western Reserve University Cleveland, OH, USA
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Hector A, Kormann M, Kammermeier J, Burdi S, Marcos V, Rieber N, Mays L, Illig T, Klopp N, Falkenstein F, Kappler M, Riethmueller J, Graepler-Mainka U, Stern M, Eickmeier O, Serve F, Zielen S, Döring G, Griese M, Hartl D. Expression and Regulation of Interferon-Related Development Regulator–1 in Cystic Fibrosis Neutrophils. Am J Respir Cell Mol Biol 2013; 48:71-7. [DOI: 10.1165/rcmb.2012-0061oc] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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12
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Ait Ghezala H, Jolles B, Salhi S, Castrillo K, Carpentier W, Cagnard N, Bruhat A, Fafournoux P, Jean-Jean O. Translation termination efficiency modulates ATF4 response by regulating ATF4 mRNA translation at 5' short ORFs. Nucleic Acids Res 2012; 40:9557-70. [PMID: 22904092 PMCID: PMC3479206 DOI: 10.1093/nar/gks762] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The activating transcription factor 4 (ATF4) promotes transcriptional upregulation of specific target genes in response to cellular stress. ATF4 expression is regulated at the translational level by two short open reading frames (uORFs) in its 5′-untranslated region (5′-UTR). Here, we describe a mechanism regulating ATF4 expression in translation termination-deficient human cells. Using microarray analysis of total RNA and polysome-associated mRNAs, we show that depletion of the eucaryotic release factor 3a (eRF3a) induces upregulation of ATF4 and of ATF4 target genes. We show that eRF3a depletion modifies ATF4 translational control at regulatory uORFs increasing ATF4 ORF translation. Finally, we show that the increase of REDD1 expression, one of the upregulated targets of ATF4, is responsible for the mTOR pathway inhibition in eRF3a-depleted cells. Our results shed light on the molecular mechanisms connecting eRF3a depletion to mammalian target of rapamycin (mTOR) pathway inhibition and give an example of ATF4 activation that bypasses the signal transduction cascade leading to the phosphorylation of eIF2α. We propose that in mammals, in which the 5′-UTR regulatory elements of ATF4 mRNA are strictly conserved, variations in translation termination efficiency allow the modulation of the ATF4 response.
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Affiliation(s)
- Hayet Ait Ghezala
- UPMC Univ Paris 06, CNRS-FRE 3402, Biologie de l'ARN, 9 quai Saint Bernard, 75005 Paris, France
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Abstract
Wnts are conserved, secreted signaling proteins that can influence cell behavior by stabilizing β-catenin. Accumulated β-catenin enters the nucleus, where it physically associates with T-cell factor (TCF) family members to regulate target gene expression in many developmental and adult tissues. Recruitment of β-catenin to Wnt response element (WRE) chromatin converts TCFs from transcriptional repressors to activators. This review will outline the complex interplay between factors contributing to TCF repression and coactivators working with β-catenin to regulate Wnt targets. In addition, three variations of the standard transcriptional switch model will be discussed. One is the Wnt/β-catenin symmetry pathway in Caenorhabditis elegans, where Wnt-mediated nuclear efflux of TCF is crucial for activation of targets. Another occurs in vertebrates, where distinct TCF family members are associated with repression and activation, and recent evidence suggests that Wnt signaling facilitates a "TCF exchange" on WRE chromatin. Finally, a "reverse switch" mechanism for target genes that are directly repressed by Wnt/β-catenin signaling occurs in Drosophila cells. The diversity of TCF regulatory mechanisms may help to explain how a small group of transcription factors can function in so many different contexts to regulate target gene expression.
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Affiliation(s)
- Ken M Cadigan
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
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14
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Yu C, Jiang S, Lu J, Coughlin CC, Wang Y, Swietlicki EA, Wang L, Vietor I, Huber LA, Cikes D, Coleman T, Xie Y, Semenkovich CF, Davidson NO, Levin MS, Rubin DC. Deletion of Tis7 protects mice from high-fat diet-induced weight gain and blunts the intestinal adaptive response postresection. J Nutr 2010; 140:1907-14. [PMID: 20861213 PMCID: PMC2955873 DOI: 10.3945/jn.110.127084] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
After loss of intestinal surface area, the remaining bowel undergoes a morphometric and functional adaptive response. Enterocytic expression of the transcriptional coregulator tetradecanoyl phorbol acetate induced sequence 7 (Tis7) is markedly increased in a murine model of intestinal adaptation. Mice overexpressing Tis7 in intestine have greater triglyceride absorption and weight gain when fed a high-fat diet (42% energy) than their wild-type (WT) littermates fed the same diet. These and other data suggest that Tis7 has a unique role in nutrient absorptive and metabolic adaptation. Herein, male Tis7(-/-) and WT mice were fed a high-fat diet (42% energy) for 8 wk. Weight was monitored and metabolic analyses and hepatic and intestinal lipid concentrations were compared after 8 wk. Intestinal lipid absorption and metabolism studies and intestinal resection surgeries were performed in separate groups of Tis7(-/-) and WT mice. At 8 wk, weight gain was less and jejunal mucosal and hepatic triglyceride and cholesterol concentrations were lower in Tis7(-/-) mice than in the WT controls. Following corn oil gavage, serum cholesterol, triglyceride, and FFA concentrations were lower in the Tis7(-/-) mice than in the WT mice. Incorporation of oral (3)[H] triolein into intestinal mucosal cholesterol ester and FFA was less in Tis7(-/-) compared with WT mice. Following resection, crypt cell proliferation rates and villus heights were lower in Tis7(-/-) than in WT mice, indicating a blunted adaptive response. Our results suggest a novel physiologic function for Tis7 in the gut as a global regulator of lipid absorption and metabolism and epithelial cell proliferation.
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Affiliation(s)
- Cong Yu
- Divisions of Gastroenterology, Washington University School of Medicine, St. Louis, MO 63110
| | - Shujun Jiang
- Divisions of Gastroenterology, Washington University School of Medicine, St. Louis, MO 63110
| | - Jianyun Lu
- Divisions of Gastroenterology, Washington University School of Medicine, St. Louis, MO 63110
| | - Carrie C. Coughlin
- Divisions of Gastroenterology, Washington University School of Medicine, St. Louis, MO 63110
| | - Yuan Wang
- Divisions of Gastroenterology, Washington University School of Medicine, St. Louis, MO 63110
| | - Elzbieta A. Swietlicki
- Divisions of Gastroenterology, Washington University School of Medicine, St. Louis, MO 63110
| | - Lihua Wang
- Divisions of Gastroenterology, Washington University School of Medicine, St. Louis, MO 63110
| | - Ilja Vietor
- Biocenter, Division of Cell Biology, Innsbruck Medical University, Innsbruck 6010, Austria
| | - Lukas A. Huber
- Biocenter, Division of Cell Biology, Innsbruck Medical University, Innsbruck 6010, Austria
| | - Domagoj Cikes
- Biocenter, Division of Cell Biology, Innsbruck Medical University, Innsbruck 6010, Austria
| | - Trey Coleman
- Divisions of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110
| | - Yan Xie
- Divisions of Gastroenterology, Washington University School of Medicine, St. Louis, MO 63110
| | - Clay F. Semenkovich
- Divisions of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110
| | - Nicholas O. Davidson
- Divisions of Gastroenterology, Washington University School of Medicine, St. Louis, MO 63110,Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110
| | - Marc S. Levin
- Divisions of Gastroenterology, Washington University School of Medicine, St. Louis, MO 63110,Department of Medicine, St. Louis Veterans Administration Medical Center, St. Louis, MO 63106
| | - Deborah C. Rubin
- Divisions of Gastroenterology, Washington University School of Medicine, St. Louis, MO 63110,Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110,To whom correspondence should be addressed. E-mail:
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15
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Brimble S, Wollaston-Hayden EE, Teo CF, Morris AC, Wells L. The Role of the O-GlcNAc Modification in Regulating Eukaryotic Gene Expression. ACTA ACUST UNITED AC 2010; 5:12-24. [PMID: 25484640 DOI: 10.2174/157436210790226465] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
O-linked β-N-acetylglucosamine (O-GlcNAc) modification of proteins has been shown to be involved in many different cellular processes, such as cell cycle control, nutrient sensing, signal transduction, stress response and transcriptional regulation. Cells have developed complex regulatory systems in order to regulate gene expression appropriately in response to environmental and intracellular cues. Control of eukaryotic gene transcription often involves post-translational modification of a multitude of proteins including transcription factors, basal transcription machinery, and chromatin remodeling complexes to modulate their functions in a variety of manners. In this review we describe the emerging functional roles for and techniques to detect and modulate the O-GlcNAc modification and illustrate that the O-GlcNAc modification is intricately involved in at least seven different general mechanisms for the control of gene transcription.
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Affiliation(s)
- Sandii Brimble
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA 30602
| | - Edith E Wollaston-Hayden
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA 30602
| | - Chin Fen Teo
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA 30602
| | - Andrew C Morris
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA 30602
| | - Lance Wells
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA 30602 ; Department of Chemistry, University of Georgia, Athens, GA, USA 30602
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16
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Mutations to LmIFRD affect cell wall integrity, development and pathogenicity of the ascomycete Leptosphaeria maculans. Fungal Genet Biol 2009; 46:695-706. [DOI: 10.1016/j.fgb.2009.06.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Revised: 05/25/2009] [Accepted: 06/10/2009] [Indexed: 11/22/2022]
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17
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Ehrnhoefer DE. IFRD1 modulates disease severity in cystic fibrosis through the regulation of neutrophil effector function. Clin Genet 2009; 76:148-9. [PMID: 19673948 DOI: 10.1111/j.1399-0004.2009.01247_2.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- D E Ehrnhoefer
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, BC, Canada.
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18
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Klopstock N, Katzenellenbogen M, Pappo O, Sklair-Levy M, Olam D, Mizrahi L, Potikha T, Galun E, Goldenberg D. HCV tumor promoting effect is dependent on host genetic background. PLoS One 2009; 4:e5025. [PMID: 19340302 PMCID: PMC2660413 DOI: 10.1371/journal.pone.0005025] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2008] [Accepted: 02/27/2009] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The hepatitis C virus (HCV) is one of the major risk factors for the development of hepatocellular carcinoma (HCC). Nevertheless, transgenic mice which express the whole HCV polyprotein (HCV-Tg) do not develop HCC. Whereas chronic HCV infection causes inflammation in patients, in HCV-Tg mice, the host immune reaction against viral proteins is lacking. We aimed to test the role of HCV proteins in HCC development on the background of chronic inflammation in vivo. METHODOLOGY/PRINCIPAL FINDINGS We crossed HCV-Tg mice that do not develop HCC with the Mdr2-knockout (Mdr2-KO) mice which develop inflammation-associated HCC, to generate Mdr2-KO/HCV-Tg mice. We studied the effect of the HCV transgene on tumor incidence, hepatocyte mitosis and apoptosis, and investigated the potential contributing factors for the generated phenotype by gene expression and protein analyses. The Mdr2-KO/HCV-Tg females from the N2 generation of this breeding (having 75% of the FVB/N genome and 25% of the C57BL/6 genome) produced significantly larger tumors in comparison with Mdr2-KO mice. In parallel, the Mdr2-KO/HCV-Tg females had an enhanced inflammatory gene expression signature. However, in the N7 generation (having 99.2% of the FVB/N genome and 0.8% of the C57BL/6 genome) there was no difference in tumor development between Mdr2-KO/HCV-Tg and Mdr2-KO animals of both sexes. The HCV transgene was similarly expressed in the livers of Mdr2-KO/HCV-Tg females of both generations, as revealed by detection of the HCV transcript and the core protein. CONCLUSION These findings suggest that the HCV transgene accelerated inflammation-associated hepatocarcinogenesis in a host genetic background-dependent manner.
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Affiliation(s)
- Naama Klopstock
- Goldyne Savad Institute of Gene Therapy, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Mark Katzenellenbogen
- Bioinformatics and Microarray Unit, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Orit Pappo
- Department of Pathology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | | | - Devorah Olam
- Goldyne Savad Institute of Gene Therapy, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Lina Mizrahi
- Goldyne Savad Institute of Gene Therapy, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Tamara Potikha
- Goldyne Savad Institute of Gene Therapy, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Eithan Galun
- Goldyne Savad Institute of Gene Therapy, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Daniel Goldenberg
- Goldyne Savad Institute of Gene Therapy, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
- * E-mail:
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19
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Gu Y, Harley ITW, Henderson LB, Aronow BJ, Vietor I, Huber LA, Harley JB, Kilpatrick JR, Langefeld CD, Williams AH, Jegga AG, Chen J, Wills-Karp M, Arshad SH, Ewart SL, Thio CL, Flick LM, Filippi MD, Grimes HL, Drumm ML, Cutting GR, Knowles MR, Karp CL. Identification of IFRD1 as a modifier gene for cystic fibrosis lung disease. Nature 2009; 458:1039-42. [PMID: 19242412 PMCID: PMC2841516 DOI: 10.1038/nature07811] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2008] [Accepted: 01/20/2009] [Indexed: 01/11/2023]
Abstract
Lung disease is the major cause of morbidity and mortality in cystic fibrosis (CF), an autosomal recessive disease caused by mutations in CFTR. In CF, chronic infection and dysregulated neutrophilic inflammation lead to progressive airway destruction. The severity of CF lung disease has significant heritability, independent of CFTR genotype1. To identify genetic modifiers, we performed a genome-wide single nucleotide polymorphism (SNP) scan in one cohort of CF patients, replicating top candidates in an independent cohort. This approach identified IFRD1 as a modifier of CF lung disease severity. IFRD1 is a histone deacetylase (HDAC)-dependent transcriptional co-regulator expressed during terminal neutrophil differentiation. Neutrophils, but not macrophages, from Ifrd1-deficient mice exhibited blunted effector function, associated with decreased NF-κB p65 transactivation. In vivo, IFRD1 deficiency caused delayed bacterial clearance from the airway, but also less inflammation and disease—a phenotype primarily dependent on hematopoietic cell expression, or lack of expression, of IFRD1. In humans, IFRD1 polymorphisms were significantly associated with variation in neutrophil effector function. These data suggest that IFRD1 modulates the pathogenesis of CF lung disease through regulation of neutrophil effector function.
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Affiliation(s)
- YuanYuan Gu
- Division of Molecular Immunology, Cincinnati Children's Hospital Research Foundation and the University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA
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Rapid culling of the CD4+ T cell repertoire in the transition from effector to memory. Immunity 2008; 28:533-45. [PMID: 18356084 DOI: 10.1016/j.immuni.2008.02.014] [Citation(s) in RCA: 148] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2007] [Revised: 01/17/2008] [Accepted: 02/06/2008] [Indexed: 01/03/2023]
Abstract
Requirements for CD4+ T cell memory differentiation were analyzed with adoptively transferred SMARTA T cell receptor (TCR) transgenic cells specific for alymphocytic choriomeningitis virus (LCMV) epitope. LCMV-induced effector and memory differentiation of SMARTA cells mimicked the endogenous CD4+ T cell response. In contrast, infection with a recombinant Listeria expressing the LCMV epitope, although resulting initially in massive SMARTA expansion, led to loss of effector function and rapid cell death characterized by high expression of the apoptosis regulator Bim. Defective memory differentiation was seen after stimulation of naive but not memory SMARTA cells, was independent of precursor frequency, and correlated with a lower TCR avidity compared to endogenous responders. In addition, long-lived endogenous CD4+ memory T cells skewed to a higher functional avidity over time. These results support a model in which CD4+ T cell memory differentiation and longevity depend on the strength of the TCR signal during the primary response.
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