1
|
Wieder N, D'Souza EN, Martin-Geary AC, Lassen FH, Talbot-Martin J, Fernandes M, Chothani SP, Rackham OJL, Schafer S, Aspden JL, MacArthur DG, Davies RW, Whiffin N. Differences in 5'untranslated regions highlight the importance of translational regulation of dosage sensitive genes. Genome Biol 2024; 25:111. [PMID: 38685090 PMCID: PMC11057154 DOI: 10.1186/s13059-024-03248-0] [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: 05/17/2023] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Untranslated regions (UTRs) are important mediators of post-transcriptional regulation. The length of UTRs and the composition of regulatory elements within them are known to vary substantially across genes, but little is known about the reasons for this variation in humans. Here, we set out to determine whether this variation, specifically in 5'UTRs, correlates with gene dosage sensitivity. RESULTS We investigate 5'UTR length, the number of alternative transcription start sites, the potential for alternative splicing, the number and type of upstream open reading frames (uORFs) and the propensity of 5'UTRs to form secondary structures. We explore how these elements vary by gene tolerance to loss-of-function (LoF; using the LOEUF metric), and in genes where changes in dosage are known to cause disease. We show that LOEUF correlates with 5'UTR length and complexity. Genes that are most intolerant to LoF have longer 5'UTRs, greater TSS diversity, and more upstream regulatory elements than their LoF tolerant counterparts. We show that these differences are evident in disease gene-sets, but not in recessive developmental disorder genes where LoF of a single allele is tolerated. CONCLUSIONS Our results confirm the importance of post-transcriptional regulation through 5'UTRs in tight regulation of mRNA and protein levels, particularly for genes where changes in dosage are deleterious and lead to disease. Finally, to support gene-based investigation we release a web-based browser tool, VuTR, that supports exploration of the composition of individual 5'UTRs and the impact of genetic variation within them.
Collapse
Affiliation(s)
- Nechama Wieder
- Big Data Institute, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Elston N D'Souza
- Big Data Institute, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Alexandra C Martin-Geary
- Big Data Institute, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Frederik H Lassen
- Big Data Institute, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Maria Fernandes
- Big Data Institute, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sonia P Chothani
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore, 169857, Singapore
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore, 169857, Singapore
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Sebastian Schafer
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore, 169857, Singapore
| | - Julie L Aspden
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
- LeedsOmics, University of Leeds, Leeds, LS2 9JT, United Kingdom
- Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Daniel G MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, NSW, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Robert W Davies
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Nicola Whiffin
- Big Data Institute, University of Oxford, Oxford, UK.
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| |
Collapse
|
2
|
Bracey NA, Platnich JM, Lau A, Chung H, Hyndman ME, MacDonald JA, Chun J, Beck PL, Girardin SE, Gordon PM, Muruve DA. Tissue-selective alternate promoters guide NLRP6 expression. Life Sci Alliance 2020; 4:4/3/e202000897. [PMID: 33376129 PMCID: PMC7772780 DOI: 10.26508/lsa.202000897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/12/2020] [Accepted: 12/15/2020] [Indexed: 12/14/2022] Open
Abstract
The NLRP6 innate immune sensor is regulated by tissue-selective alternate promoters that facilitate translational gene silencing outside of the intestinal epithelium in both humans and mice. The pryin domain (PYD) domain is involved in protein interactions that lead to assembly of immune-sensing complexes such as inflammasomes. The repertoire of PYD-containing genes expressed by a cell type arms tissues with responses against a range of stimuli. The transcriptional regulation of the PYD gene family however is incompletely understood. Alternative promoter utilization was identified as a mechanism regulating the tissue distribution of human PYD gene family members, including NLRP6 that is translationally silenced outside of intestinal tissue. Results show that alternative transcriptional promoters mediate NLRP6 silencing in mice and humans, despite no upstream genomic synteny. Human NLRP6 contains an internal alternative promoter within exon 2 of the PYD, resulting in a truncated mRNA in nonintestinal tissue. In mice, a proximal promoter was used that expanded the 5′ leader sequence restricting nuclear export and abolishing translational efficiency. Nlrp6 was dispensable in disease models targeting the kidney, which expresses noncanonical isoforms. Thus, alternative promoter use is a critical mechanism not just for isoform modulation but for determining expression profile and function of PYD family members.
Collapse
Affiliation(s)
- Nathan A Bracey
- Department of Medicine, University of Calgary, Calgary, Canada.,Snyder Institute for Chronic Disease, University of Calgary, Calgary, Canada
| | - Jaye M Platnich
- Department of Medicine, University of Alberta, Edmonton, Canada
| | - Arthur Lau
- Department of Medicine, University of Calgary, Calgary, Canada.,Snyder Institute for Chronic Disease, University of Calgary, Calgary, Canada
| | - Hyunjae Chung
- Department of Medicine, University of Calgary, Calgary, Canada.,Snyder Institute for Chronic Disease, University of Calgary, Calgary, Canada
| | - M Eric Hyndman
- Department of Surgery, University of Calgary, Calgary, Canada
| | - Justin A MacDonald
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Justin Chun
- Department of Medicine, University of Calgary, Calgary, Canada.,Snyder Institute for Chronic Disease, University of Calgary, Calgary, Canada
| | - Paul L Beck
- Department of Medicine, University of Calgary, Calgary, Canada.,Snyder Institute for Chronic Disease, University of Calgary, Calgary, Canada
| | - Stephen E Girardin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Paul Mk Gordon
- Centre for Health Genomics and Informatics, University of Calgary, Calgary, Canada
| | - Daniel A Muruve
- Department of Medicine, University of Calgary, Calgary, Canada .,Snyder Institute for Chronic Disease, University of Calgary, Calgary, Canada
| |
Collapse
|
3
|
Chen S, Wang X, Nisar MF, Lin M, Zhong JL. Heme Oxygenases: Cellular Multifunctional and Protective Molecules against UV-Induced Oxidative Stress. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:5416728. [PMID: 31885801 PMCID: PMC6907065 DOI: 10.1155/2019/5416728] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 10/29/2019] [Indexed: 12/20/2022]
Abstract
Ultraviolet (UV) irradiation can be considered as a double-edged sword: not only is it a crucial environmental factor that can cause skin-related disorders but it can also be used for phototherapy of skin diseases. Inducible heme oxygenase-1 (HO-1) in response to a variety of stimuli, including UV exposure, is vital to maintain cell homeostasis. Heme oxygenase-2 (HO-2), another member of the heme oxygenase family, is constitutively expressed. In this review, we discuss how heme oxygenase (HO), a vital rate-limiting enzyme, participates in heme catabolism and cytoprotection. Phylogenetic analysis showed that there may exist a functional differentiation between HO-1 and HO-2 during evolution. Furthermore, depending on functions in immunomodulation and antioxidation, HO-1 participates in disease progression, especially in pathogenesis of skin diseases, such as vitiligo and psoriasis. To further investigate the particular role of HO-1 in diseases, we summarized the profile of the HO enzyme system and its related signaling pathways, such as Nrf2 and endoplasmic reticulum crucial signaling, both known to regulate HO-1 expression. Furthermore, we report on a C-terminal truncation of HO-1, which is generally considered as a signal molecule. Also, a newly identified alternative splice isoform of HO-1 not only provides us a novel perspective on comprehensive HO-1 alternative splicing but also offers us a basis to clarify the relationship between HO-1 transcripts and oxidative diseases. To conclude, the HO system is not only involved in heme catabolism but also involved in biological processes related to the pathogenesis of certain diseases, even though the mechanism of disease progression still remains sketchy. Further understanding the role of the HO system and its relationship to UV is helpful for revealing the HO-related signaling networks and the pathogenesis of many diseases.
Collapse
Affiliation(s)
- ShiDa Chen
- The Base of “111 Project” for Biomechanics & Tissue Repair Engineering; Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China
| | - XiaoYu Wang
- The Base of “111 Project” for Biomechanics & Tissue Repair Engineering; Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Muhammad Farrukh Nisar
- The Base of “111 Project” for Biomechanics & Tissue Repair Engineering; Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Mao Lin
- Chongqing Traditional Chinese Medicine Hospital, Chongqing 400011, China
| | - Julia Li Zhong
- The Base of “111 Project” for Biomechanics & Tissue Repair Engineering; Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China
- Chongqing Traditional Chinese Medicine Hospital, Chongqing 400011, China
| |
Collapse
|
4
|
Yeh HS, Yong J. mTOR-coordinated Post-Transcriptional Gene Regulations: from Fundamental to Pathogenic Insights. J Lipid Atheroscler 2019; 9:8-22. [PMID: 32821719 PMCID: PMC7379075 DOI: 10.12997/jla.2020.9.1.8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 09/13/2019] [Accepted: 09/22/2019] [Indexed: 12/26/2022] Open
Abstract
Post-transcriptional regulations of mRNA transcripts such as alternative splicing and alternative polyadenylation can affect the expression of genes without changing the transcript levels. Recent studies have demonstrated that these post-transcriptional events can have significant physiological impacts on various biological systems and play important roles in the pathogenesis of a number of diseases, including cancers. Nevertheless, how cellular signaling pathways control these post-transcriptional processes in cells are not very well explored in the field yet. The mammalian target of rapamycin complex 1 (mTORC1) pathway plays a key role in sensing cellular nutrient and energy status and regulating the proliferation and growth of cells by controlling various anabolic and catabolic processes. Dysregulation of mTORC1 pathway can tip the metabolic balance of cells and is associated with a number of pathological conditions, including various types of cancers, diabetes, and cardiovascular diseases. Numerous reports have shown that mTORC1 controls its downstream pathways through translational and/or transcriptional regulation of the expression of key downstream effectors. And, recent studies have also shown that mTORC1 can control downstream pathways via post-transcriptional regulations. In this review, we will discuss the roles of post-transcriptional processes in gene expression regulations and how mTORC1-mediated post-transcriptional regulations contribute to cellular physiological changes. We highlight post-transcriptional regulation as an additional layer of gene expression control by mTORC1 to steer cellular biology. These emphasize the importance of studying post-transcriptional events in transcriptome datasets for gaining a fuller understanding of gene expression regulations in the biological systems of interest.
Collapse
Affiliation(s)
- Hsin-Sung Yeh
- Department of Biochemistry, Molecular Biology and Biophysics, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Jeongsik Yong
- Department of Biochemistry, Molecular Biology and Biophysics, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| |
Collapse
|
5
|
Watanabe T, Minaga K, Kamata K, Sakurai T, Komeda Y, Nagai T, Kitani A, Tajima M, Fuss IJ, Kudo M, Strober W. RICK/RIP2 is a NOD2-independent nodal point of gut inflammation. Int Immunol 2019; 31:669-683. [PMID: 31132297 DOI: 10.1093/intimm/dxz045] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/25/2019] [Indexed: 12/19/2022] Open
Abstract
Previous studies have shown that inhibition of receptor-interacting serine/threonine kinase (RICK) (also known as RIP2) results in amelioration of experimental colitis. This role has largely been attributed to nucleotide-binding oligomerization domain 2 (NOD2) signaling since the latter is considered a major inducer of RICK activation. In this study, we explored the molecular mechanisms accounting for RICK-mediated inhibition of inflammatory bowel disease (IBD). In an initial series of studies focused on trinitrobenzene sulfonic acid (TNBS)-colitis and dextran sodium sulfate (DSS)-colitis we showed that down-regulation of intestinal RICK expression in NOD2-intact mice by intra-rectal administration of a plasmid expressing RICK-specific siRNA was accompanied by down-regulation of pro-inflammatory cytokine responses in the colon and protection of the mice from experimental colitis. Somewhat surprisingly, intra-rectal administration of RICK-siRNA also inhibited TNBS-colitis and DSS-colitis in NOD2-deficient and in NOD1/NOD2-double deficient mice. In complementary studies of humans with IBD we found that expression of RICK, cellular inhibitor of apoptosis protein 2 (cIAP2) and downstream signaling partners were markedly increased in inflamed tissue of IBD compared to controls without marked elevations of NOD1 or NOD2 expression. In addition, the increase in RICK expression correlated with disease activity and pro-inflammatory cytokine responses. These studies thus suggest that NOD1- or NOD2-independenent activation of RICK plays a major role in both murine experimental colitis and human IBD.
Collapse
Affiliation(s)
- Tomohiro Watanabe
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Ohno-Higashi, Osaka-Sayama, Osaka, Japan.,Mucosal Immunity Section, Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kosuke Minaga
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Ohno-Higashi, Osaka-Sayama, Osaka, Japan
| | - Ken Kamata
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Ohno-Higashi, Osaka-Sayama, Osaka, Japan
| | - Toshiharu Sakurai
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Ohno-Higashi, Osaka-Sayama, Osaka, Japan
| | - Yoriaki Komeda
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Ohno-Higashi, Osaka-Sayama, Osaka, Japan
| | - Tomoyuki Nagai
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Ohno-Higashi, Osaka-Sayama, Osaka, Japan
| | - Atsushi Kitani
- Mucosal Immunity Section, Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Masaki Tajima
- Mucosal Immunity Section, Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ivan J Fuss
- Mucosal Immunity Section, Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Masatoshi Kudo
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Ohno-Higashi, Osaka-Sayama, Osaka, Japan
| | - Warren Strober
- Mucosal Immunity Section, Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
6
|
Ping Z, Xiaomu W, Xufang X, Wenfeng C, Liang S, Tao W. GAPDH rs1136666 SNP indicates a high risk of Parkinson's disease. Neurosci Lett 2018; 685:55-62. [PMID: 29886133 DOI: 10.1016/j.neulet.2018.06.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/16/2018] [Accepted: 06/06/2018] [Indexed: 01/24/2023]
Abstract
BACKGROUND Development of Parkinson's disease (PD) is attributed to both genetic and environmental factors. Furthermore,GAPDH may play a key role in the development of neurodegenerative disease. Examination of genetic polymorphism in patients with sporadic PD will help uncover the mechanisms of PD pathogenesis and provide new insights into the treatment of PD. METHODS AND RESULTS The SNaPshot method was applied to determine the gene sequences in 265 patients with idiopathic PD and 269 control cases (sex- and age-matched). The rs1136666 polymorphism of GAPDH was determined to be closely associated with PD. Subsequently, the CC genotype of the rs1136666 fragment was transfected into SH-SY5Y cells via a plasmid. The genetic expression of rs1136666 CC could induce SH-SY5Y cell injury and apoptosis via regulation of the oxidant-antioxidant and apoptosis-antiapoptosis balance. rs1136666 CC of the GAPDH had a pro-apoptotic effect similar to that of rotenone, and combination of the rs1136666 CC genetic variation and the rotenone neurotoxic effect could aggravate oxidative stress, cell injury, and apoptosis better than either single treatment alone. CONCLUSION This study confirmed that the rs1136666 CC allele of theGAPDH increased the risk of PD, particularly in older male patients.
Collapse
Affiliation(s)
- Zhang Ping
- Department of Neurology, Jiangxi Provincial People's Hospital, No, 92 Aiguo Road, Donghu District, Nanchang, 330006, Jiangxi, China; Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, China.
| | - Wu Xiaomu
- Department of Neurology, Jiangxi Provincial People's Hospital, No, 92 Aiguo Road, Donghu District, Nanchang, 330006, Jiangxi, China
| | - Xie Xufang
- Department of Neurology, Jiangxi Provincial People's Hospital, No, 92 Aiguo Road, Donghu District, Nanchang, 330006, Jiangxi, China
| | - Cao Wenfeng
- Department of Neurology, Jiangxi Provincial People's Hospital, No, 92 Aiguo Road, Donghu District, Nanchang, 330006, Jiangxi, China
| | - Shao Liang
- Department of Cardiology, Jiangxi Provincial People's Hospital, No, 92 Aiguo Road, Donghu District, Nanchang, 330006, Jiangxi, China.
| | - Wang Tao
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, China.
| |
Collapse
|
7
|
Identification and Characterization of a Splicing Variant in the 5' UTR of the Human TLR5 Gene. BIOMED RESEARCH INTERNATIONAL 2017; 2017:8727434. [PMID: 28948171 PMCID: PMC5602658 DOI: 10.1155/2017/8727434] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 08/02/2017] [Accepted: 08/02/2017] [Indexed: 11/17/2022]
Abstract
Toll-like receptors (TLRs) are essential components of the innate immune system. TLR5 is the receptor for flagellin, the principal protein component of bacterial flagella. The TLR5 gene has 6 exons. In an RT-PCR analysis, we found long TLR5 transcripts, in addition to those of the expected size (short TLR5 transcripts). A sequence analysis revealed that the long TLR5 transcripts contain a new exon of 94 nucleotides located between previously reported exons IV and V in the 5' untranslated region (5' UTR). A real-time PCR analysis of the two alternatively spliced variants in various cell lines showed that the long TLR5 transcripts are abundantly expressed in nonimmune cells. The ratios of long/short transcripts in human nonimmune cell lines, such as A549, T98G, HaCaT, H460, HEK-293, and Caco-2 cells, and primary mesenchymal stem cells were in the range of 1.25 to 4.31. In contrast, those of human monocytic THP-1 and U937 cells and E6.1 T cells and Ramos B cells were around 0.9. These ratios in human monocytic THP-1 cells were decreased by treatment with IFN-γ in a concentration-dependent manner. Based on our findings, we suggest that the newly found long TLR5 transcripts may be involved in the negative regulation of TLR5 expression and function.
Collapse
|
8
|
Alternative Pre-mRNA Splicing in Mammals and Teleost Fish: A Effective Strategy for the Regulation of Immune Responses Against Pathogen Infection. Int J Mol Sci 2017; 18:ijms18071530. [PMID: 28714877 PMCID: PMC5536018 DOI: 10.3390/ijms18071530] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 07/10/2017] [Accepted: 07/12/2017] [Indexed: 12/14/2022] Open
Abstract
Pre-mRNA splicing is the process by which introns are removed and the protein coding elements assembled into mature mRNAs. Alternative pre-mRNA splicing provides an important source of transcriptome and proteome complexity through selectively joining different coding elements to form mRNAs, which encode proteins with similar or distinct functions. In mammals, previous studies have shown the role of alternative splicing in regulating the function of the immune system, especially in the regulation of T-cell activation and function. As lower vertebrates, teleost fish mainly rely on a large family of pattern recognition receptors (PRRs) to recognize pathogen-associated molecular patterns (PAMPs) from various invading pathogens. In this review, we summarize recent advances in our understanding of alternative splicing of piscine PRRs including peptidoglycan recognition proteins (PGRPs), nucleotide binding and oligomerization domain (NOD)-like receptors (NLRs), retinoic acid-inducible gene-I (RIG-I)-like receptors (RLRs) and their downstream signaling molecules, compared to splicing in mammals. We also discuss what is known and unknown about the function of splicing isoforms in the innate immune responses against pathogens infection in mammals and teleost fish. Finally, we highlight the consequences of alternative splicing in the innate immune system and give our view of important directions for future studies.
Collapse
|
9
|
Mallarino R, Linden TA, Linnen CR, Hoekstra HE. The role of isoforms in the evolution of cryptic coloration inPeromyscusmice. Mol Ecol 2016; 26:245-258. [DOI: 10.1111/mec.13663] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 04/12/2016] [Accepted: 04/17/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Ricardo Mallarino
- Departments of Organismic & Evolutionary Biology and Molecular & Cellular Biology; Museum of Comparative Zoology; Howard Hughes Medical Institute; Harvard University; 26 Oxford Street Cambridge MA 02138 USA
| | - Tess A. Linden
- Departments of Organismic & Evolutionary Biology and Molecular & Cellular Biology; Museum of Comparative Zoology; Howard Hughes Medical Institute; Harvard University; 26 Oxford Street Cambridge MA 02138 USA
| | - Catherine R. Linnen
- Department of Biology; University of Kentucky; 675 Rose Street Lexington KY 40506 USA
| | - Hopi E. Hoekstra
- Departments of Organismic & Evolutionary Biology and Molecular & Cellular Biology; Museum of Comparative Zoology; Howard Hughes Medical Institute; Harvard University; 26 Oxford Street Cambridge MA 02138 USA
| |
Collapse
|
10
|
Brahma B, Patra MC, Mishra P, De BC, Kumar S, Maharana J, Vats A, Ahlawat S, Datta TK, De S. Computational studies on receptor-ligand interactions between novel buffalo (Bubalus bubalis) nucleotide-binding oligomerization domain-containing protein 2 (NOD2) variants and muramyl dipeptide (MDP). J Mol Graph Model 2016; 65:15-26. [PMID: 26897084 DOI: 10.1016/j.jmgm.2016.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 01/25/2016] [Accepted: 02/08/2016] [Indexed: 11/19/2022]
Abstract
Nucleotide binding and oligomerization domain 2 (NOD2), a member of intracellular NOD-like receptors (NLRs) family, recognizes the bacterial peptidoglycan, muramyl dipeptide (MDP) and initiates host immune response. The precise ligand recognition mechanism of NOD2 has remained elusive, although studies have suggested leucine rich repeat (LRR) region of NOD2 as the possible binding site of MDP. In this study, we identified multiple transcripts of NOD2 gene in buffalo (buNOD2) and at least five LRR variants (buNOD2-LRRW (wild type), buNOD2-LRRV1-V4) were found to be expressed in buffalo peripheral blood mononuclear cells. The newly identified buNOD2 transcripts were shorter in lengths as a result of exon-skipping and frame-shift mutations. Among the variants, buNOD2-LRRW, V1, and V3 were expressed more frequently in the animals studied. A comparative receptor-ligand interaction study through modeling of variants, docking, and molecular dynamics simulation revealed that the binding affinity of buNOD2-LRRW towards MDP was greater than that of the shorter variants. The absence of a LRR segment in the buNOD2 variants had probably affected their affinity toward MDP. Notwithstanding a high homology among the variants, the amino acid residues that interact with MDP were located on different LRR motifs. The binding free energy calculation revealed that the amino acids Arg850(LRR4) and Glu932(LRR7) of buNOD2-LRRW, Lys810(LRR3) of buNOD2-LRRV1, and Lys830(LRR3) of buNOD2-LRRV3 largely contributed towards MDP recognition. The knowledge of MDP recognition and binding modes on buNOD2 variants could be useful to understand the regulation of NOD-mediated immune response as well as to develop next generation anti-inflammatory compounds.
Collapse
Affiliation(s)
- Biswajit Brahma
- Animal Genomics Lab., Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Mahesh Chandra Patra
- Animal Genomics Lab., Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Purusottam Mishra
- Animal Genomics Lab., Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Bidhan Chandra De
- Animal Genomics Lab., Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Sushil Kumar
- Animal Genomics Lab., Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Jitendra Maharana
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar 751003, Odisha, India
| | - Ashutosh Vats
- Animal Genomics Lab., Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Sonika Ahlawat
- Animal Genomics Lab., Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Tirtha Kumar Datta
- Animal Genomics Lab., Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Sachinandan De
- Animal Genomics Lab., Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India.
| |
Collapse
|
11
|
Hayrabedyan S, Todorova K, Jabeen A, Metodieva G, Toshkov S, Metodiev MV, Mincheff M, Fernández N. Sertoli cells have a functional NALP3 inflammasome that can modulate autophagy and cytokine production. Sci Rep 2016; 6:18896. [PMID: 26744177 PMCID: PMC4705529 DOI: 10.1038/srep18896] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 11/27/2015] [Indexed: 02/07/2023] Open
Abstract
Sertoli cells, can function as non-professional tolerogenic antigen-presenting cells, and sustain the blood-testis barrier formed by their tight junctions. The NOD-like receptor family members and the NALP3 inflammasome play a key role in pro-inflammatory innate immunity signalling pathways. Limited data exist on NOD1 and NOD2 expression in human and mouse Sertoli cells. Currently, there is no data on inflammasome expression or function in Sertoli cells. We found that in primary pre-pubertal Sertoli cells and in adult Sertoli line, TLR4\NOD1 and NOD2 crosstalk converged in NFκB activation and elicited a NALP3 activation, leading to de novo synthesis and inflammasome priming. This led to caspase-1 activation and IL-1β secretion. We demonstrated this process was controlled by mechanisms linked to autophagy. NOD1 promoted pro-IL-1β restriction and autophagosome maturation arrest, while NOD2 promoted caspase-1 activation, IL-1β secretion and autophagy maturation. NALP3 modulated NOD1 and pro-IL-1β expression, while NOD2 inversely promoted IL-1β. This study is proof of concept that Sertoli cells, upon specific stimulation, could participate in male infertility pathogenesis via inflammatory cytokine induction.
Collapse
Affiliation(s)
- Soren Hayrabedyan
- Institute of Biology and Immunology of Reproduction, Laboratory of Reproductive Omics Technologies, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Krassimira Todorova
- Institute of Biology and Immunology of Reproduction, Laboratory of Reproductive Omics Technologies, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Asma Jabeen
- School of Biological Sciences, Wivenhoe Park, University of Essex, Colchester, UK
| | - Gergana Metodieva
- School of Biological Sciences, Wivenhoe Park, University of Essex, Colchester, UK
| | - Stavri Toshkov
- Cellular and Gene Therapy Ward, National Specialized Haematology Hospital, Sofia, Bulgaria
| | - Metodi V Metodiev
- School of Biological Sciences, Wivenhoe Park, University of Essex, Colchester, UK
| | - Milcho Mincheff
- Cellular and Gene Therapy Ward, National Specialized Haematology Hospital, Sofia, Bulgaria
| | - Nelson Fernández
- School of Biological Sciences, Wivenhoe Park, University of Essex, Colchester, UK
| |
Collapse
|
12
|
Buggiano V, Petrillo E, Alló M, Lafaille C, Redal MA, Alghamdi MA, Khoder MI, Shamy M, Muñoz MJ, Kornblihtt AR. Effects of airborne particulate matter on alternative pre-mRNA splicing in colon cancer cells. ENVIRONMENTAL RESEARCH 2015; 140:185-190. [PMID: 25863591 DOI: 10.1016/j.envres.2015.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 02/28/2015] [Accepted: 04/01/2015] [Indexed: 06/04/2023]
Abstract
Alternative pre-mRNA splicing plays key roles in determining tissue- and species-specific cell differentiation as well as in the onset of hereditary disease and cancer, being controlled by multiple post- and co-transcriptional regulatory mechanisms. We report here that airborne particulate matter, resulting from industrial pollution, inhibits expression and specifically affects alternative splicing at the 5' untranslated region of the mRNA encoding the bone morphogenetic protein BMP4 in human colon cells in culture. These effects are consistent with a previously reported role for BMP4 in preventing colon cancer development, suggesting that ingestion of particulate matter could contribute to the onset of colon cell proliferation. We also show that the underlying mechanism might involve changes in transcriptional elongation. This is the first study to demonstrate that particulate matter causes non-pleiotropic changes in alternative splicing.
Collapse
Affiliation(s)
- Valeria Buggiano
- Laboratorio de Fisiología y Biología Molecular, Departamento de Fisiología, Biología Molecular y Celular, IFIBYNE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - Ezequiel Petrillo
- Laboratorio de Fisiología y Biología Molecular, Departamento de Fisiología, Biología Molecular y Celular, IFIBYNE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - Mariano Alló
- Laboratorio de Fisiología y Biología Molecular, Departamento de Fisiología, Biología Molecular y Celular, IFIBYNE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - Celina Lafaille
- Laboratorio de Fisiología y Biología Molecular, Departamento de Fisiología, Biología Molecular y Celular, IFIBYNE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - María Ana Redal
- Instituto de Ciencias Básicas y Medicina Experimental, Hospital Italiano de Buenos Aires, Argentina
| | - Mansour A Alghamdi
- Department of Environmental Sciences, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mamdouh I Khoder
- Department of Environmental Sciences, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia; Center of Excellence in Environmental Studies, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Magdy Shamy
- Department of Environmental Sciences, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Manuel J Muñoz
- Laboratorio de Fisiología y Biología Molecular, Departamento de Fisiología, Biología Molecular y Celular, IFIBYNE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina.
| | - Alberto R Kornblihtt
- Laboratorio de Fisiología y Biología Molecular, Departamento de Fisiología, Biología Molecular y Celular, IFIBYNE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina.
| |
Collapse
|
13
|
Nerlich A, Ruangkiattikul N, Laarmann K, Janze N, Dittrich-Breiholz O, Kracht M, Goethe R. C/EBPβ is a transcriptional key regulator of IL-36α in murine macrophages. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:966-78. [PMID: 26066982 DOI: 10.1016/j.bbagrm.2015.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 05/15/2015] [Accepted: 06/01/2015] [Indexed: 12/25/2022]
Abstract
Interleukin (IL)-36α - one of the novel members of the IL-1 family of cytokines - is a potent regulator of dendritic and T cells and plays an important role in inflammatory processes like experimental skin inflammation in mice and in mouse models for human psoriasis. Here, we demonstrate that C/EBPβ, a transcription factor required for the selective expression of inflammatory genes, is a key activator of the Il36A gene in murine macrophages. RNAi-mediated suppression of C/EBPβ expression in macrophages (C/EBPβ(low) cells) significantly impaired Il36A gene induction following challenge with LPS. Despite the presence of five predicted C/EBP binding sites, luciferase reporter assays demonstrated that C/EBPβ confers responsiveness to LPS primarily through a half-CRE•C/EBP element in the proximal Il36A promoter. Electrophoretic mobility shift assays showed that C/EBPβ but not CREB proteins interact with this critical half-CRE•C/EBP element. In addition, overexpression of C/EBPβ in C/EBPβ(low) cells enhanced the expression of Il36A whereas CREB-1 had no effect. Finally, chromatin immunoprecipitation confirmed that C/EBPβ but neither CREB-1, ATF-2 nor ATF4 is directly recruited to the proximal promoter region of the Il36A gene. Together, these findings demonstrate an essential role of C/EBPβ in the regulation of the Il36A gene via the proximal half-CRE•C/EBP element in response to inflammatory stimuli.
Collapse
Affiliation(s)
- Andreas Nerlich
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine, Foundation Hannover, 30173 Hannover, Germany.
| | - Nanthapon Ruangkiattikul
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine, Foundation Hannover, 30173 Hannover, Germany
| | - Kristin Laarmann
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine, Foundation Hannover, 30173 Hannover, Germany
| | - Nina Janze
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine, Foundation Hannover, 30173 Hannover, Germany
| | | | - Michael Kracht
- Rudolf -Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Ralph Goethe
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine, Foundation Hannover, 30173 Hannover, Germany
| |
Collapse
|
14
|
Alternative 5' untranslated regions are involved in expression regulation of human heme oxygenase-1. PLoS One 2013; 8:e77224. [PMID: 24098580 PMCID: PMC3788786 DOI: 10.1371/journal.pone.0077224] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 09/02/2013] [Indexed: 01/19/2023] Open
Abstract
The single nucleotide polymorphism rs2071746 and a (GT)n microsatellite within the human gene encoding heme oxygenase-1 (HMOX1) are associated with incidence or outcome in a variety of diseases. Most of these associations involve either release of heme or oxidative stress. Both polymorphisms are localized in the promoter region, but previously reported correlations with heme oxygenase-1 expression remain not coherent. This ambiguity suggests a more complex organization of the 5’ gene region which we sought to investigate more fully. We evaluated the 5‘ end of HMOX1 and found a novel first exon 1a placing the two previously reported polymorphisms in intronic or exonic positions within the 5’ untranslated region respectively. Expression of exon 1a can be induced in HepG2 hepatoma cells by hemin and is a repressor of heme oxygenase-1 translation as shown by luciferase reporter assays. Moreover, minigene approaches revealed that the quantitative outcome of alternative splicing within the 5’ untranslated region is affected by the (GT)n microsatellite. This data supporting an extended HMOX1 gene model and provide further insights into expression regulation of heme oxygenase-1. Alternative splicing within the HMOX1 5' untranslated region contributes to translational regulation and is a mechanistic feature involved in the interplay between genetic variations, heme oxygenase-1 expression and disease outcome.
Collapse
|
15
|
Arribere JA, Gilbert WV. Roles for transcript leaders in translation and mRNA decay revealed by transcript leader sequencing. Genome Res 2013; 23:977-87. [PMID: 23580730 PMCID: PMC3668365 DOI: 10.1101/gr.150342.112] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Transcript leaders (TLs) can have profound effects on mRNA translation and stability. To map TL boundaries genome-wide, we developed TL-sequencing (TL-seq), a technique combining enzymatic capture of m7G-capped mRNA 5′ ends with high-throughput sequencing. TL-seq identified mRNA start sites for the majority of yeast genes and revealed many examples of intragenic TL heterogeneity. Surprisingly, TL-seq identified transcription initiation sites within 6% of protein-coding regions, and these sites were concentrated near the 5′ ends of ORFs. Furthermore, ribosome density analysis showed these truncated mRNAs are translated. Translation-associated TL-seq (TATL-seq), which combines TL-seq with polysome fractionation, enabled annotation of TLs, and simultaneously assayed their function in translation. Using TATL-seq to address relationships between TL features and translation of the downstream ORF, we observed that upstream AUGs (uAUGs), and no other upstream codons, were associated with poor translation and nonsense-mediated mRNA decay (NMD). We also identified hundreds of genes with very short TLs, and demonstrated that short TLs were associated with poor translation initiation at the annotated start codon and increased initiation at downstream AUGs. This frequently resulted in out-of-frame translation and subsequent termination at premature termination codons, culminating in NMD of the transcript. Unlike previous approaches, our technique enabled observation of alternative TL variants for hundreds of genes and revealed significant differences in translation in genes with distinct TL isoforms. TL-seq and TATL-seq are useful tools for annotation and functional characterization of TLs, and can be applied to any eukaryotic system to investigate TL-mediated regulation of gene expression.
Collapse
Affiliation(s)
- Joshua A Arribere
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | |
Collapse
|
16
|
Oehlers SH, Flores MV, Hall CJ, Swift S, Crosier KE, Crosier PS. The inflammatory bowel disease (IBD) susceptibility genes NOD1 and NOD2 have conserved anti-bacterial roles in zebrafish. Dis Model Mech 2011; 4:832-41. [PMID: 21729873 PMCID: PMC3209652 DOI: 10.1242/dmm.006122] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Inflammatory bowel disease (IBD), in the form of Crohn's disease (CD) or ulcerative colitis (UC), is a debilitating chronic immune disorder of the intestine. A complex etiology resulting from dysfunctional interactions between the intestinal immune system and its microflora, influenced by host genetic susceptibility, makes disease modeling challenging. Mutations in NOD2 have the highest disease-specific risk association for CD, and a related gene, NOD1, is associated with UC. NOD1 and NOD2 encode intracellular bacterial sensor proteins acting as innate immune triggers, and represent promising therapeutic targets. The zebrafish has the potential to aid in modeling genetic and environmental aspects of IBD pathogenesis. Here, we report the characterization of the Nod signaling components in the zebrafish larval intestine. The nod1 and nod2 genes are expressed in intestinal epithelial cells and neutrophils together with the Nod signaling pathway genes ripk2, a20, aamp, cd147, centaurin b1, erbin and grim-19. Using a zebrafish embryo Salmonella infection model, morpholino-mediated depletion of Nod1 or Nod2 reduced the ability of embryos to control systemic infection. Depletion of Nod1 or Nod2 decreased expression of dual oxidase in the intestinal epithelium and impaired the ability of larvae to reduce intracellular bacterial burden. This work highlights the potential use of zebrafish larvae in the study of components of IBD pathogenesis.
Collapse
Affiliation(s)
- Stefan H Oehlers
- Department of Molecular Medicine and Pathology, School of Medical Sciences, The University of Auckland, Auckland 1001, New Zealand
| | | | | | | | | | | |
Collapse
|
17
|
Häsler R, Kerick M, Mah N, Hultschig C, Richter G, Bretz F, Sina C, Lehrach H, Nietfeld W, Schreiber S, Rosenstiel P. Alterations of pre-mRNA splicing in human inflammatory bowel disease. Eur J Cell Biol 2011; 90:603-11. [PMID: 21324547 DOI: 10.1016/j.ejcb.2010.11.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2010] [Revised: 11/18/2010] [Accepted: 11/22/2010] [Indexed: 12/11/2022] Open
Abstract
Alternative pre-mRNA splicing is regarded as a pivotal mechanism for generating proteome diversity and complexity from a limited inventory of mammalian genes. Aberrant splicing has been described as a predisposing factor for a number of diseases, but very little is known about its role in chronic inflammation. In this study, we systematically screened 149 splicing factors and 145 potential intron retention events for occurrence and differential expression in inflammatory bowel diseases (IBD). As a result, we identified 47 splicing factors and 33 intron retention events that were differentially regulated in mucosal tissue of IBD patients at transcript level. Despite the fact that Crohn's disease and ulcerative colitis, two subtypes of IBD, share the expression patterns of splicing factors and intron retention events in the majority of cases, we observed significant differences. To investigate these subtype-specific changes in detail we determined the expression levels of seven splicing factors (DUSP11, HNRPAB, HNRPH3, SLU7, SFR2IP, SFPQ, SF3B14) and three intron retention events (PARC, IER3, FGD2) in a cohort of 165 patients with inflammatory diseases of the colon (120 with IBD) and 30 healthy controls by real time PCR (TaqMan). This study demonstrates the potential impact of regulated splicing factors on subsequent regulated intron retention in the pathogenesis of chronic inflammation, exemplified by IBD.
Collapse
Affiliation(s)
- Robert Häsler
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Schittenhelmstrasse 12, 24105 Kiel, Germany.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Henderson P, van Limbergen JE, Wilson DC, Satsangi J, Russell RK. Genetics of childhood-onset inflammatory bowel disease. Inflamm Bowel Dis 2011; 17:346-61. [PMID: 20839313 DOI: 10.1002/ibd.21283] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Nearly a third of inflammatory bowel disease (IBD) patients present in childhood or adolescence, with epidemiological and natural history studies clearly demonstrating a rising incidence in this population. Although early-onset disease has a distinct phenotype, such as more extensive disease at onset and rapid progression, two recent genome-wide association studies (GWAS) carried out exclusively in this age group have demonstrated marked genetic similarities to adult disease. Although these parallels exist, this review will focus on the novel regions associated with early-onset IBD susceptibility identified by these early-onset GWAS. These new loci reaffirm the dysregulated pathways previously implicated in adult IBD pathogenesis and provide further insight into the pathophysiology of intestinal inflammation. The newly identified loci and expression data suggest mutations in genes encoding IL-27, which is involved in Th17 effector cell physiology; MTMR3, which we demonstrate is an essential component of autophagy; and CAPN10, which is necessary in regulating endoplasmic reticulum stress. In addition, the roles of PSMG1, TNFRSF6B, ZMIZ1 and SMAD3 are also discussed in relation to abnormal protein degradation and the secondary immune response. It is clear that with increasing technology our understanding of IBD pathogenesis is deepening at the genomic level and that the use of early patient selection coupled with ongoing work on therapeutic targets will lead to improved disease-modifying treatments in the near future.
Collapse
Affiliation(s)
- Paul Henderson
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Royal Hospital for Sick Children, Edinburgh, UK.
| | | | | | | | | |
Collapse
|
19
|
Billmann-Born S, Lipinski S, Böck J, Till A, Rosenstiel P, Schreiber S. The complex interplay of NOD-like receptors and the autophagy machinery in the pathophysiology of Crohn disease. Eur J Cell Biol 2010; 90:593-602. [PMID: 21146253 DOI: 10.1016/j.ejcb.2010.10.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 10/20/2010] [Accepted: 10/22/2010] [Indexed: 02/07/2023] Open
Abstract
Several coding variants of NOD2 and ATG16L1 are associated with increased risk of Crohn disease (CD). NOD2, a cytosolic receptor of the innate immune system activates pro-inflammatory signalling cascades upon recognition of bacterial muramyl dipeptide, but seems also to be involved in antiviral and anti-parasitic defence programs. The CD associated variant L1007fsinsC leads to impaired pro-inflammatory signalling and diminished bacterial clearance. ATG16L1 is a protein essential for autophagosome formation at the phagophore assembly site. The CD associated T300A variant is located in the c-terminal WD40 domain, whose function is still unknown. Basal autophagy is not affected by the T300A variant, but antibacterial autophagy (xenophagy) is impaired, a finding that relates ATG16L1 as well as NOD2 to pathogen defence. Notably, combination of disease-associated alleles of ATG16L1 and NOD2/CARD15 leads to synergistically increased susceptibility for CD, indicating a possible crosstalk between NOD2- and ATG16L1-mediated processes in the pathogenesis of CD. This review surveys current research results and discusses the functional models of potential interplay between NLR-pathways and xenophagy. Interaction between pathways is discussed in the context of reactive oxygen species (ROS), membrane co-localisation, antigen processing and implications of disturbed Paneth cell vesicle export. These effects on pathogen response might imbalance the intestinal barrier epithelia towards chronic inflammation and promote development of Crohn disease. Further elucidation of NOD2/ATG16L1 interplay in xenophagy is relevant for understanding the aetiology of chronic intestinal inflammation and host-microbe interaction in general and could lead to principal new insights to xenophagy induction.
Collapse
Affiliation(s)
- Susanne Billmann-Born
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | | | | | | | | | | |
Collapse
|
20
|
Kramer M, Boeck J, Reichenbach D, Kaether C, Schreiber S, Platzer M, Rosenstiel P, Huse K. NOD2-C2 - a novel NOD2 isoform activating NF-kappaB in a muramyl dipeptide-independent manner. BMC Res Notes 2010; 3:224. [PMID: 20698950 PMCID: PMC2931527 DOI: 10.1186/1756-0500-3-224] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Accepted: 08/10/2010] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The innate immune system employs several receptor families that form the basis of sensing pathogen-associated molecular patterns. NOD (nucleotide-binding and oligomerization domain) like receptors (NLRs) comprise a group of cytosolic proteins that trigger protective responses upon recognition of intracellular danger signals. NOD2 displays a tandem caspase recruitment domain (CARD) architecture, which is unique within the NLR family. FINDINGS Here, we report a novel alternative transcript of the NOD2 gene, which codes for a truncated tandem CARD only protein, called NOD2-C2. The transcript isoform is highest expressed in leucocytes, a natural barrier against pathogen invasion, and is strictly linked to promoter usage as well as predominantly to one allele of the single nucleotide polymorphism rs2067085. Contrary to a previously identified truncated single CARD NOD2 isoform, NOD2-S, NOD2-C2 is able to activate NF-kappaB in a dose dependent manner independently of muramyl dipeptide (MDP). On the other hand NOD2-C2 competes with MDPs ability to activate the NOD2-driven NF-kappaB signaling cascade. CONCLUSION NOD2 transcripts having included an alternative exon downstream of exon 3 (exon 3a) are the endogenous equivalents of a previously described in vitro construct with the putative protein composed of only the two N-terminal CARDs. This protein form (NOD2-C2) activates NF-kappaB independent of an MDP stimulus and is a potential regulator of NOD2 signaling.
Collapse
Affiliation(s)
- Marcel Kramer
- Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstrasse 11, 07745 Jena, Germany.
| | | | | | | | | | | | | | | |
Collapse
|
21
|
Cenik C, Derti A, Mellor JC, Berriz GF, Roth FP. Genome-wide functional analysis of human 5' untranslated region introns. Genome Biol 2010; 11:R29. [PMID: 20222956 PMCID: PMC2864569 DOI: 10.1186/gb-2010-11-3-r29] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Accepted: 03/11/2010] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Approximately 35% of human genes contain introns within the 5' untranslated region (UTR). Introns in 5'UTRs differ from those in coding regions and 3'UTRs with respect to nucleotide composition, length distribution and density. Despite their presumed impact on gene regulation, the evolution and possible functions of 5'UTR introns remain largely unexplored. RESULTS We performed a genome-scale computational analysis of 5'UTR introns in humans. We discovered that the most highly expressed genes tended to have short 5'UTR introns rather than having long 5'UTR introns or lacking 5'UTR introns entirely. Although we found no correlation in 5'UTR intron presence or length with variance in expression across tissues, which might have indicated a broad role in expression-regulation, we observed an uneven distribution of 5'UTR introns amongst genes in specific functional categories. In particular, genes with regulatory roles were surprisingly enriched in having 5'UTR introns. Finally, we analyzed the evolution of 5'UTR introns in non-receptor protein tyrosine kinases (NRTK), and identified a conserved DNA motif enriched within the 5'UTR introns of human NRTKs. CONCLUSIONS Our results suggest that human 5'UTR introns enhance the expression of some genes in a length-dependent manner. While many 5'UTR introns are likely to be evolving neutrally, their relationship with gene expression and overrepresentation among regulatory genes, taken together, suggest that complex evolutionary forces are acting on this distinct class of introns.
Collapse
Affiliation(s)
- Can Cenik
- Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, 250 Longwood Avenue, SGMB-322, Boston, MA 02115, USA.
| | | | | | | | | |
Collapse
|
22
|
Abstract
From epidemiological data, based on concordance data in family studies, via linkage analysis to genome-wide association studies, we and others have accumulated robust evidence implicating more than 30 distinct genomic loci involved in the genetic susceptibility to Crohn's disease (CD). These loci encode genes involved in a number of homeostatic mechanisms: innate pattern recognition receptors (NOD2/CARD15, TLR4, CARD9), the differentiation of Th17-lymphocytes (IL-23R, JAK2, STAT3, CCR6, ICOSLG), autophagy (ATG16L1, IRGM, LRRK2), maintenance of epithelial barrier integrity (IBD5, DLG5, PTGER4, ITLN1, DMBT1, XBP1), and the orchestration of the secondary immune response (HLA-region, TNFSF15/TL1A, IRF5, PTPN2, PTPN22, NKX2-3, IL-12B, IL-18RAP, MST1). While many of these loci also predispose to pediatric CD, an additional number of childhood-onset loci have been identified recently (e.g., TNFRSF6B). Not only has the identification of these loci improved our understanding of the pathophysiology of CD, this knowledge also holds real promise for clinical practice.
Collapse
Affiliation(s)
- Johan Van Limbergen
- Department of Pediatric Gastroenterology and Nutrition, Royal Hospital for Sick Children, Edinburgh EH9 1LF, United Kingdom.
| | | | | |
Collapse
|
23
|
Meloni I, Parri V, De Filippis R, Ariani F, Artuso R, Bruttini M, Katzaki E, Longo I, Mari F, Bellan C, Dotti CG, Renieri A. The XLMR gene ACSL4 plays a role in dendritic spine architecture. Neuroscience 2008; 159:657-69. [PMID: 19166906 DOI: 10.1016/j.neuroscience.2008.11.056] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2008] [Revised: 11/21/2008] [Accepted: 11/22/2008] [Indexed: 12/13/2022]
Abstract
ACSL4 is a gene involved in non-syndromic X-linked mental retardation. It encodes for a ubiquitous protein that adds coenzyme A to long-chain fatty acids, with a high substrate preference for arachidonic acid. It presents also a brain-specific isoform deriving from an alternative splicing and containing 41 additional N-terminal amino acids. To start to unravelling the link between ACSL4 and mental retardation, we have performed molecular and cell biological studies. By retro-transcription polymerase chain reaction analyses we identified a new transcript with a shorter 5'-UTR region. By immunofluorescence microscopy in embryonic rat hippocampal neurons we report that ACSL4 is associated preferentially to endoplasmic reticulum tubules. ACSL4 knockdown by siRNAs in hippocampal neurons indicated that this protein is largely dispensable for these cells' gross architectural features (i.e. axonal and dendritic formation and final length) yet it is required for the presence of normal spines. In fact, reduced levels of ACSL4 led to a significant reduction in dendritic spine density and an alteration in spine/filopodia distribution. The possible mechanisms behind this phenotype are discussed.
Collapse
Affiliation(s)
- I Meloni
- Medical Genetics Unit, Department of Molecular Biology, University of Siena, Policlinico Le Scotte, Viale Bracci 2, 53100 Siena, Italy
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Anderson JP, Mueller JL, Misaghi A, Anderson S, Sivagnanam M, Kolodner RD, Hoffman HM. Initial description of the human NLRP3 promoter. Genes Immun 2008; 9:721-6. [PMID: 18719602 PMCID: PMC4477692 DOI: 10.1038/gene.2008.66] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Revised: 07/24/2008] [Accepted: 07/24/2008] [Indexed: 01/06/2023]
Abstract
Mutations in NLRP3 (CIAS1) are identified in a continuum of related inflammatory disorders, known as cryopyrinopathies since NLRP3 codes for the protein cryopyrin. Approximately 40% of patients with classic presentation lack mutations in the coding region of NLRP3 suggesting heterogeneity or epigenetic factors. Cryopyrin is a key regulator of proinflammatory cytokine release. Therefore, variations in the NLRP3 promoter sequence may have effects on disease state in patients with cryopyrinopathies and other inflammatory diseases. In this report, we confirmed three 5'-untranslated region splice forms with two separate transcriptional start sites, and identified potential promoter regions and six new DNA promoter variants. One variant is unique to a mutation negative cryopyrinopathy patient and increases in vitro gene expression. Additional studies can now be performed to further characterize the NLRP3 promoter and sequence variants, which will lead to better understanding of the regulation of NLRP3 expression and its role in disease.
Collapse
Affiliation(s)
- JP Anderson
- Department of Emergency Medicine, Harbor-UCLA Medical Center, Torrance, CA, USA
- School of Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - JL Mueller
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA
- Ludwig Institute of Cancer Research, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - A Misaghi
- School of Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - S Anderson
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - M Sivagnanam
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - RD Kolodner
- Ludwig Institute of Cancer Research, University of California San Diego School of Medicine, La Jolla, CA, USA
- Department of Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine and Cancer Center, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - HM Hoffman
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA
- Ludwig Institute of Cancer Research, University of California San Diego School of Medicine, La Jolla, CA, USA
- Division of Rheumatology, Allergy, and Immunology, University of California San Diego School of Medicine, La Jolla, CA, USA
| |
Collapse
|