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Amaro IA, Wohl MP, Pitcher S, Alfonso-Parra C, Avila FW, Paige AS, Helinski MEH, Duvall LB, Harrington LC, Wolfner MF, McMeniman CJ. Sex peptide receptor is not required for refractoriness to remating or induction of egg laying in Aedes aegypti. Genetics 2024; 227:iyae034. [PMID: 38551457 PMCID: PMC11075561 DOI: 10.1093/genetics/iyae034] [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: 01/14/2024] [Accepted: 02/09/2024] [Indexed: 05/08/2024] Open
Abstract
Across diverse insect taxa, the behavior and physiology of females dramatically changes after mating-processes largely triggered by the transfer of seminal proteins from their mates. In the vinegar fly Drosophila melanogaster, the seminal protein sex peptide (SP) decreases the likelihood of female flies remating and causes additional behavioral and physiological changes that promote fertility including increasing egg production. Although SP is only found in the Drosophila genus, its receptor, sex peptide receptor (SPR), is the widely conserved myoinhibitory peptide (MIP) receptor. To test the functional role of SPR in mediating postmating responses in a non-Drosophila dipteran, we generated 2 independent Spr-knockout alleles in the yellow fever mosquito, Aedes aegypti. Although SPR is needed for postmating responses in Drosophila and the cotton bollworm Helicoverpa armigera, Spr mutant Ae. aegypti show completely normal postmating decreases in remating propensity and increases in egg laying. In addition, injection of synthetic SP or accessory gland homogenate from D. melanogaster into virgin female mosquitoes did not elicit these postmating responses. Our results demonstrate that Spr is not required for these canonical postmating responses in Ae. aegypti, indicating that other, as yet unknown, signaling pathways are likely responsible for these behavioral switches in this disease vector.
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Affiliation(s)
| | - Margot P Wohl
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sylvie Pitcher
- Department of Entomology, Cornell University, Ithaca, NY 14853, USA
| | | | - Frank W Avila
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Andrew S Paige
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | | | - Laura B Duvall
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | | | - Mariana F Wolfner
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Conor J McMeniman
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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2
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Lughmani H, Patel H, Chakravarti R. Structural Features and Physiological Associations of Human 14-3-3ζ Pseudogenes. Genes (Basel) 2024; 15:399. [PMID: 38674334 PMCID: PMC11049341 DOI: 10.3390/genes15040399] [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: 03/05/2024] [Revised: 03/15/2024] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
There are about 14,000 pseudogenes that are mutated or truncated sequences resembling functional parent genes. About two-thirds of pseudogenes are processed, while others are duplicated. Although initially thought dead, emerging studies indicate they have functional and regulatory roles. We study 14-3-3ζ, an adaptor protein that regulates cytokine signaling and inflammatory diseases, including rheumatoid arthritis, cancer, and neurological disorders. To understand how 14-3-3ζ (gene symbol YWHAZ) performs diverse functions, we examined the human genome and identified nine YWHAZ pseudogenes spread across many chromosomes. Unlike the 32 kb exon-to-exon sequence in YWHAZ, all pseudogenes are much shorter and lack introns. Out of six, four YWHAZ exons are highly conserved, but the untranslated region (UTR) shows significant diversity. The putative amino acid sequence of pseudogenes is 78-97% homologous, resulting in striking structural similarities with the parent protein. The OMIM and Decipher database searches revealed chromosomal loci containing pseudogenes are associated with human diseases that overlap with the parent gene. To the best of our knowledge, this is the first report on pseudogenes of the 14-3-3 family protein and their implications for human health. This bioinformatics-based study introduces a new insight into the complexity of 14-3-3ζ's functions in biology.
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Affiliation(s)
| | | | - Ritu Chakravarti
- Department of Physiology and Pharmacology, The University of Toledo, Toledo, OH 43614, USA; (H.L.); (H.P.)
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3
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Li L, Li Z, Meng X, Wang X, Song D, Liu Y, Xu T, Qin J, Sun N, Tian K, Zhong J, Yu D, Song Y, Hou T, Jiang C, Chen Q, Cai J. Histone lactylation-derived LINC01127 promotes the self-renewal of glioblastoma stem cells via the cis-regulating the MAP4K4 to activate JNK pathway. Cancer Lett 2023; 579:216467. [PMID: 38084701 DOI: 10.1016/j.canlet.2023.216467] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 10/19/2023] [Accepted: 10/25/2023] [Indexed: 12/18/2023]
Abstract
Gliomas are the most prevalent and aggressive brain tumors, exhibiting high proliferation, abnormal glycolysis, and poor prognosis. LncRNAs act as regulatory molecules and play crucial roles in the malignant behaviors of GBM cells, including cell self-renewal. However, the regulatory mechanisms involved are largely unknown. In this study, we performed bioinformatics analysis to explore NF-κB pathway-related lncRNAs. ECAR and qRT-PCR were used to measure the relationship between glycolytic activity and lncRNA expression. Assays such as RIP-PCR and ChIP-PCR were employed to reveal the regulatory mechanisms of the lncRNA. Neurosphere formation and limiting dilution assays were performed to evaluate the self-renewal capacity of GBM cells. In our study, we identified an NF-κB pathway-related lncRNA named LINC01127 in GBM, which was found to be associated with poor progression of GBM. Functionally, the NF-κB pathway promoted warburg effect, which, in turn, induced the lactylation of H3 histone and increased the expression of LINC01127. Consequently, this enhancement of LINC01127 expression led to the promotion of self-renewal in GBM cells. Furthermore, LINC01127 regulated MAP4K4 expression in cis by directly guiding POLR2A to the MAP4K4 promoter regions, thereby leading to JNK pathway activation, and ultimately modulating the self-renewal of GBM cells. Moreover, the activated JNK pathway promoted the phosphorylation of IκBα. Overall, targeting LINC01127-mediated axis impeded orthotopic tumor growth in GBM xenografts. Taken together these results revealed that warburg effect-induced histone lactylation drives NF-κB-related LINC01127 expression, thereby promoting the self-renewal of GBM cells through the MAP4K4/JNK/NF-κB axis, and providing substantial evidence that LINC01127 might provide a novel therapeutic strategy for GBM patients.
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Affiliation(s)
- Lulu Li
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, #246 Xuefu Road, 150086, Harbin, Heilongjiang Province, PR China; Department of Vascular Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021, Jinan, Shandong Province, PR China
| | - Ziwei Li
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, #246 Xuefu Road, 150086, Harbin, Heilongjiang Province, PR China; Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 100070, Beijing, PR China
| | - Xiangqi Meng
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, #246 Xuefu Road, 150086, Harbin, Heilongjiang Province, PR China
| | - Xinyu Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, #246 Xuefu Road, 150086, Harbin, Heilongjiang Province, PR China
| | - Dan Song
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, #246 Xuefu Road, 150086, Harbin, Heilongjiang Province, PR China
| | - Yuxiang Liu
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, #246 Xuefu Road, 150086, Harbin, Heilongjiang Province, PR China
| | - Tianye Xu
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, #246 Xuefu Road, 150086, Harbin, Heilongjiang Province, PR China
| | - Jie Qin
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, #246 Xuefu Road, 150086, Harbin, Heilongjiang Province, PR China
| | - Nan Sun
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, #246 Xuefu Road, 150086, Harbin, Heilongjiang Province, PR China
| | - Kaifu Tian
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, #246 Xuefu Road, 150086, Harbin, Heilongjiang Province, PR China
| | - Junzhe Zhong
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, #246 Xuefu Road, 150086, Harbin, Heilongjiang Province, PR China
| | - Daohan Yu
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, #246 Xuefu Road, 150086, Harbin, Heilongjiang Province, PR China
| | - Yu Song
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, #246 Xuefu Road, 150086, Harbin, Heilongjiang Province, PR China
| | - Tianlang Hou
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, #246 Xuefu Road, 150086, Harbin, Heilongjiang Province, PR China
| | - Chuanlu Jiang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, #246 Xuefu Road, 150086, Harbin, Heilongjiang Province, PR China; The Six Affiliated Hospital of Harbin Medical University, 150028, Harbin, Heilongjiang Province, PR China.
| | - Qun Chen
- Department of Neurosurgery, The First Affiliated Hospital, Zhejiang University School of Medicine, #79 Qingchun Road, 310003, Hangzhou, Zhejiang Province, PR China.
| | - Jinquan Cai
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, #246 Xuefu Road, 150086, Harbin, Heilongjiang Province, PR China.
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Villanueva RA, Loyola A. Pre- and Post-Transcriptional Control of HBV Gene Expression: The Road Traveled towards the New Paradigm of HBx, Its Isoforms, and Their Diverse Functions. Biomedicines 2023; 11:1674. [PMID: 37371770 DOI: 10.3390/biomedicines11061674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/04/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Hepatitis B virus (HBV) is an enveloped DNA human virus belonging to the Hepadnaviridae family. Perhaps its main distinguishable characteristic is the replication of its genome through a reverse transcription process. The HBV circular genome encodes only four overlapping reading frames, encoding for the main canonical proteins named core, P, surface, and X (or HBx protein). However, pre- and post-transcriptional gene regulation diversifies the full HBV proteome into diverse isoform proteins. In line with this, hepatitis B virus X protein (HBx) is a viral multifunctional and regulatory protein of 16.5 kDa, whose canonical reading frame presents two phylogenetically conserved internal in-frame translational initiation codons, and which results as well in the expression of two divergent N-terminal smaller isoforms of 8.6 and 5.8 kDa, during translation. The canonical HBx, as well as the smaller isoform proteins, displays different roles during viral replication and subcellular localizations. In this article, we reviewed the different mechanisms of pre- and post-transcriptional regulation of protein expression that take place during viral replication. We also investigated all the past and recent evidence about HBV HBx gene regulation and its divergent N-terminal isoform proteins. Evidence has been collected for over 30 years. The accumulated evidence simply strengthens the concept of a new paradigm of the canonical HBx, and its smaller divergent N-terminal isoform proteins, not only during viral replication, but also throughout cell pathogenesis.
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Affiliation(s)
| | - Alejandra Loyola
- Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago 8580702, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago 7510602, Chile
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5
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Man HSJ, Subramaniam N, Downs T, Sukumar AN, Saha AD, Nair R, Chen L, Teitelbaum D, Turgeon PJ, Ku KH, Tran E, de Perrot M, Marsden PA. Long noncoding RNA GATA2-AS1 augments endothelial Hypoxia Inducible Factor 1-α induction and regulates hypoxic signaling. J Biol Chem 2023; 299:103029. [PMID: 36806681 PMCID: PMC10148162 DOI: 10.1016/j.jbc.2023.103029] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 02/18/2023] Open
Abstract
Vascular endothelial cells form the inner cellular lining of blood vessels and have myriad physiologic functions including angiogenesis and response to hypoxia. We recently identified a set of endothelial cell (EC)-enriched long noncoding RNAs (lncRNAs) in differentiated human primary cell types and described the role of the STEEL lncRNA in angiogenic patterning. We sought to further understand the role of EC-enriched lncRNAs in physiologic adaptation of the vascular endothelium. In this work, we describe an abundant, cytoplasmic, and EC-enriched lncRNA, GATA2-AS1, that is divergently transcribed from the EC-enriched developmental regulator, GATA2. While GATA2-AS1 is largely co-expressed with GATA2 in ECs, GATA2-AS1 and GATA2 appear to be complementary rather than synergistic as they have mostly distinct target genes. Common single nucleotide variants (SNVs) in GATA2-AS1 exons are associated with early onset coronary artery disease (CAD) and decreased expression of GATA2-AS1 in endothelial cell lines. In most cells, HIF1-α is central to the transcriptional response to hypoxia, while in ECs, both HIF1-α and HIF2-α are required to coordinate an acute and chronic response respectively. In this setting, GATA2-AS1 contributes to the "HIF switch" and augments HIF1-α induction in acute hypoxia to regulate HIF1-α/ HIF2-α balance. In hypoxia, GATA2-AS1 orchestrates HIF1-α-dependent induction of the glycolytic pathway, and HIF1-α-independent maintenance of mitochondrial biogenesis. Similarly, GATA2-AS1 coordinates both metabolism and "tip/stalk" cell signaling to regulate angiogenesis in hypoxic ECs. Furthermore, we find that GATA2-AS1 expression patterns are perturbed in atherosclerotic disease. Together, these results define a role for GATA2-AS1 in the EC-specific response to hypoxia.
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Affiliation(s)
- H S Jeffrey Man
- Institute of Medical Science, Toronto, Ontario, Canada; Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, Toronto, Ontario, Canada; Department of Respirology, University Health Network, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Noeline Subramaniam
- Institute of Medical Science, Toronto, Ontario, Canada; Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Tiana Downs
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Aravin N Sukumar
- Institute of Medical Science, Toronto, Ontario, Canada; Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Aninda D Saha
- Institute of Medical Science, Toronto, Ontario, Canada; Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Ranju Nair
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Lucy Chen
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Daniel Teitelbaum
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Paul J Turgeon
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Kyung Ha Ku
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Eileen Tran
- Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Marc de Perrot
- Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, Toronto, Ontario, Canada; Division of Thoracic Surgery, Toronto General Hospital, Toronto, Ontario, Canada
| | - Philip A Marsden
- Institute of Medical Science, Toronto, Ontario, Canada; Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada.
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6
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Ghorbani A, Khataeipour SJ, Solbakken MH, Huebert DNG, Khoddami M, Eslamloo K, Collins C, Hori T, Jentoft S, Rise ML, Larijani M. Ancestral reconstruction reveals catalytic inactivation of activation-induced cytidine deaminase concomitant with cold water adaption in the Gadiformes bony fish. BMC Biol 2022; 20:293. [PMID: 36575514 PMCID: PMC9795746 DOI: 10.1186/s12915-022-01489-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 11/30/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Antibody affinity maturation in vertebrates requires the enzyme activation-induced cytidine deaminase (AID) which initiates secondary antibody diversification by mutating the immunoglobulin loci. AID-driven antibody diversification is conserved across jawed vertebrates since bony and cartilaginous fish. Two exceptions have recently been reported, the Pipefish and Anglerfish, in which the AID-encoding aicda gene has been lost. Both cases are associated with unusual reproductive behavior, including male pregnancy and sexual parasitism. Several cold water fish in the Atlantic cod (Gadinae) family carry an aicda gene that encodes for a full-length enzyme but lack affinity-matured antibodies and rely on antibodies of broad antigenic specificity. Hence, we examined the functionality of their AID. RESULTS By combining genomics, transcriptomics, immune responsiveness, and functional enzymology of AID from 36 extant species, we demonstrate that AID of that Atlantic cod and related fish have extremely lethargic or no catalytic activity. Through ancestral reconstruction and functional enzymology of 71 AID enzymes, we show that this enzymatic inactivation likely took place relatively recently at the emergence of the true cod family (Gadidae) from their ancestral Gadiformes order. We show that this AID inactivation is not only concordant with the previously shown loss of key adaptive immune genes and expansion of innate and cell-based immune genes in the Gadiformes but is further reflected in the genomes of these fish in the form of loss of AID-favored sequence motifs in their immunoglobulin variable region genes. CONCLUSIONS Recent demonstrations of the loss of the aicda gene in two fish species challenge the paradigm that AID-driven secondary antibody diversification is absolutely conserved in jawed vertebrates. These species have unusual reproductive behaviors forming an evolutionary pressure for a certain loss of immunity to avoid tissue rejection. We report here an instance of catalytic inactivation and functional loss of AID rather than gene loss in a conventionally reproducing vertebrate. Our data suggest that an expanded innate immunity, in addition to lower pathogenic pressures in a cold environment relieved the pressure to maintain robust secondary antibody diversification. We suggest that in this unique scenario, the AID-mediated collateral genome-wide damage would form an evolutionary pressure to lose AID function.
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Affiliation(s)
- Atefeh Ghorbani
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada ,grid.25055.370000 0000 9130 6822Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
| | - S. Javad Khataeipour
- grid.25055.370000 0000 9130 6822Department of Computer Science, Faculty of Science, Memorial University of Newfoundland, St. John’s, Canada
| | - Monica H. Solbakken
- grid.5510.10000 0004 1936 8921Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - David N. G. Huebert
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada ,grid.25055.370000 0000 9130 6822Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
| | - Minasadat Khoddami
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Khalil Eslamloo
- grid.25055.370000 0000 9130 6822Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, Canada
| | - Cassandra Collins
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Tiago Hori
- grid.25055.370000 0000 9130 6822Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, Canada
| | - Sissel Jentoft
- grid.5510.10000 0004 1936 8921Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Matthew L. Rise
- grid.25055.370000 0000 9130 6822Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, Canada
| | - Mani Larijani
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada ,grid.25055.370000 0000 9130 6822Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
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Sharova M, Skoblov M, Dadali E, Demina N, Shchagina O, Konovalov F, Ampleeva M, Sharkova I, Kutsev S. Case report: Unusual episodic myopathy in a patient with novel homozygous deletion of first coding exon of MICU1 gene. Front Neurol 2022; 13:1008937. [PMID: 36425804 PMCID: PMC9679209 DOI: 10.3389/fneur.2022.1008937] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/06/2022] [Indexed: 11/17/2023] Open
Abstract
We present a patient with unusual episodes of muscular weakness due to homozygous deletion of exon 2 in the MICU1 gene. Forty-three patients from 33 families were previously described with homozygous and compound heterozygous, predominantly loss of function (LoF) variants in the MICU1 gene that lead to autosomal recessive myopathy with extrapyramidal signs. Most described patients developed muscle weakness and elevated CK levels, and half of the patients had progressive extrapyramidal signs and learning disabilities. Our patient had a few severe acute episodes of muscle weakness with minimal myopathy features between episodes and a strongly elevated Creatinine Kinase (CK). Whole exome sequencing (WES) was performed and the homozygous deletion of exon 2 was suspected. To validate the diagnosis, we performed an RNA analysis of all family members. To investigate the possible impact of this deletion on the phenotype, we predicted a new Kozak sequence in exon 4 that could lead to the formation of a truncated MICU1 protein that could partly interact with MCU protein in a mitochondrial Ca2+ complex. We suspect that this unusual phenotype of the proband with MICU1-related myopathy could be explained by the presence of the truncated but partly functional protein. This work helps to define the clinical polymorphism of MICU1 deficiency better.
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Affiliation(s)
| | | | - Elena Dadali
- Research Centre for Medical Genetics, Moscow, Russia
| | - Nina Demina
- Research Centre for Medical Genetics, Moscow, Russia
| | | | - Fedor Konovalov
- Independent Clinical Bioinformatics Laboratory, Moscow, Russia
| | - Maria Ampleeva
- Independent Clinical Bioinformatics Laboratory, Moscow, Russia
| | - Inna Sharkova
- Research Centre for Medical Genetics, Moscow, Russia
| | - Sergey Kutsev
- Research Centre for Medical Genetics, Moscow, Russia
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8
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Sharova M, Guseva D, Kurenkov A, Novoselova O, Murtazina A, Skoblov M. Congenital myopathy as a new phenotype caused by two undescribed variants in ASCC1 gene. Am J Med Genet A 2022; 188:3100-3105. [PMID: 35838082 DOI: 10.1002/ajmg.a.62898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 05/19/2022] [Accepted: 06/02/2022] [Indexed: 01/31/2023]
Abstract
We present a patient with congenital myopathy and an inborn epiphysiolysis of the ulna. Whole-exome sequencing analysis revealed two novel mutations in Activation Signal Cointegrator Complex 1 (ASCC1) gene in a compound heterozygous state-a splicing variant c.395-2A>G and a deletion of the first two coding exons. Homozygous and compound heterozygous LoF variants in ASCC1 gene lead to a severe phenotype of spinal muscular atrophy with congenital bone fractures 2 (SMABF2). All patients described to date presented with a severe muscular hypotony, inborn fractures, and passed away shortly after birth while our proband had moderate hypotony, no fractures, but epiphysiolysis and he was 3.5 years old at the time of examination. To explain the phenotype of our patient, we performed an RNA analysis of all family members. We discovered that the c.395-2A>G variant results in two aberrant mRNA isoforms. We also validated the deletion of two exons in ASCC1 gene that lead to the increased expression of this truncated transcript by 1.8 times. To investigate the possible impact of this deletion on the phenotype we predicted a new Kozak sequence in exon 4 that could lead to the formation of a truncated protein with shortened KH domain and a full RNA ligase-like domain. We suggest that this unexpectedly different phenotype of the proband with ASCC1-related disorder could be explained by the presence of the truncated protein with an increased expression.
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Affiliation(s)
| | - Darya Guseva
- Research Centre for Medical Genetics, Moscow, Russia
| | - Alexey Kurenkov
- National Medical Research Center for Children's Health, the Russian Federation Ministry of Healthcare, Moscow, Russia
| | - Olga Novoselova
- Genomed Ltd., Genetic Diagnostic Lab, Moscow, Russia.,Filatov N.F. Children's City Hospital 103001, Moscow, Russia
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9
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Harter TS, Clifford AM, Tresguerres M. Adrenergically induced translocation of red blood cell β-adrenergic sodium-proton exchangers has ecological relevance for hypoxic and hypercapnic white seabass. Am J Physiol Regul Integr Comp Physiol 2021; 321:R655-R671. [PMID: 34494485 DOI: 10.1152/ajpregu.00175.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
White seabass (Atractoscion nobilis) increasingly experience periods of low oxygen (O2; hypoxia) and high carbon dioxide (CO2, hypercapnia) due to climate change and eutrophication of the coastal waters of California. Hemoglobin (Hb) is the principal O2 carrier in the blood and in many teleost fishes Hb-O2 binding is compromised at low pH; however, the red blood cells (RBC) of some species regulate intracellular pH with adrenergically stimulated sodium-proton-exchangers (β-NHEs). We hypothesized that RBC β-NHEs in white seabass are an important mechanism that can protect the blood O2-carrying capacity during hypoxia and hypercapnia. We determined the O2-binding characteristics of white seabass blood, the cellular and subcellular response of RBCs to adrenergic stimulation, and quantified the protective effect of β-NHE activity on Hb-O2 saturation. White seabass had typical teleost Hb characteristics, with a moderate O2 affinity (Po2 at half-saturation; P50 2.9 kPa) that was highly pH-sensitive (Bohr coefficient -0.92; Root effect 52%). Novel findings from super-resolution microscopy revealed β-NHE protein in vesicle-like structures and its translocation into the membrane after adrenergic stimulation. Microscopy data were corroborated by molecular and phylogenetic results and a functional characterization of β-NHE activity. The activation of RBC β-NHEs increased Hb-O2 saturation by ∼8% in normoxic hypercapnia and by up to ∼20% in hypoxic normocapnia. Our results provide novel insight into the cellular mechanism of adrenergic RBC stimulation within an ecologically relevant context. β-NHE activity in white seabass has great potential to protect arterial O2 transport during hypoxia and hypercapnia but is less effective during combinations of these stressors.
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Affiliation(s)
- Till S Harter
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California
| | - Alexander M Clifford
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California
| | - Martin Tresguerres
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California
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10
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Stress hematopoiesis induces a proliferative advantage in TET2 deficiency. Leukemia 2021; 36:809-820. [PMID: 34588613 DOI: 10.1038/s41375-021-01427-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 09/02/2021] [Accepted: 09/14/2021] [Indexed: 11/08/2022]
Abstract
TET2 loss-of-function mutations are recurrent events in a wide range of hematological malignancies and a physiologic occurrence in blood cells of healthy older adults. It is currently unknown what determines if a person harboring a somatic TET2 mutation will progress to myelodysplastic syndrome or acute myeloid leukemia. Here we develop a zebrafish tet2 mutant through which we show that tet2 loss leads to restricted hematopoietic differentiation combined with a modest upregulation of p53, which is also characteristic of many inherited bone marrow failure syndromes. Uniquely in the context of emergency hematopoiesis by external stimuli, such as infection or cytokine stimulation, lack of tet2 leads hematopoietic stem cells to undergo excessive proliferation, resulting in an accumulation of immature cells, which are poised to become leukemogenic following additional genetic/epigenetic perturbations. This same phenomenon observed in zebrafish extends to human hematopoietic stem cells, identifying TET2 as a critical relay switch in the context of stress hematopoiesis.
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11
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Scheurer L, Das Gupta RR, Saebisch A, Grampp T, Benke D, Zeilhofer HU, Wildner H. Expression of immunoglobulin constant domain genes in neurons of the mouse central nervous system. Life Sci Alliance 2021; 4:4/11/e202101154. [PMID: 34433614 PMCID: PMC8403770 DOI: 10.26508/lsa.202101154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/16/2021] [Accepted: 08/17/2021] [Indexed: 11/24/2022] Open
Abstract
General consensus states that immunoglobulins are exclusively expressed by B lymphocytes to form the first line of defense against common pathogens. Here, we provide compelling evidence for the expression of two heavy chain immunoglobulin genes in subpopulations of neurons in the mouse brain and spinal cord. RNA isolated from excitatory and inhibitory neurons through ribosome affinity purification revealed Ighg3 and Ighm transcripts encoding for the constant (Fc), but not the variable regions of IgG3 and IgM. Because, in the absence of the variable immunoglobulin regions, these transcripts lack the canonical transcription initiation site used in lymphocytes, we screened for alternative 5' transcription start sites and identified a novel 5' exon adjacent to a proposed promoter element. Immunohistochemical, Western blot, and in silico analyses strongly support that these neuronal transcripts are translated into proteins containing four Immunoglobulin domains. Our data thus demonstrate the expression of two Fc-encoding genes Ighg3 and Ighm in spinal and supraspinal neurons of the murine CNS and suggest a hitherto unknown function of the encoded proteins.
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Affiliation(s)
- Louis Scheurer
- Institute of Pharmacology and Toxicology, University of Zurich, Zürich, Switzerland
| | - Rebecca R Das Gupta
- Institute of Pharmacology and Toxicology, University of Zurich, Zürich, Switzerland.,Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
| | - Annika Saebisch
- Institute of Pharmacology and Toxicology, University of Zurich, Zürich, Switzerland
| | - Thomas Grampp
- Institute of Pharmacology and Toxicology, University of Zurich, Zürich, Switzerland
| | - Dietmar Benke
- Institute of Pharmacology and Toxicology, University of Zurich, Zürich, Switzerland
| | - Hanns Ulrich Zeilhofer
- Institute of Pharmacology and Toxicology, University of Zurich, Zürich, Switzerland .,Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
| | - Hendrik Wildner
- Institute of Pharmacology and Toxicology, University of Zurich, Zürich, Switzerland
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12
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Koprulu M, Shabbir RMK, Zaman Q, Nalbant G, Malik S, Tolun A. CRADD and USP44 mutations in intellectual disability, mild lissencephaly, brain atrophy, developmental delay, strabismus, behavioural problems and skeletal anomalies. Eur J Med Genet 2021; 64:104181. [PMID: 33647455 DOI: 10.1016/j.ejmg.2021.104181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 02/10/2021] [Accepted: 02/20/2021] [Indexed: 11/29/2022]
Abstract
In a consanguineous Pakistani kinship afflicted with mild to moderate intellectual disability (ID), mild lissencephaly, brain atrophy and skeletal anomalies, we detected homozygous CRADD c.2T > G (p.Met1?) and USP44 c.873_886delinsT (p.Leu291Phefs*8), two good candidates 1.85-Mb apart that segregated with the disorder. Biallelic damaging variants in CRADD cause recessive mental retardation-34 (MRT34; MIM 614499) with mild to moderate ID, "thin" lissencephaly, and variable megalencephaly and seizures. For USP44, only a single ID family has been reported with a homozygous deleterious variant, which is the same as the variant we detected. In affected individuals we present, at ages 29-32 years, clinical findings are similar yet not fully concordant with phenotypes for either gene considering the skeletal findings, and ID is not as severe as would be expected for defects in two genes with additive effect. Some variable CRADD-related features such as language impairment and seizures are not observed in the presented family. The presence of the two variants in the family is a very rare example of familial linked homozygous variants, and whether the damaging USP44 variant contributed to the disease in the family we present is not clear. As for the skeletal findings, facial dysmorphism and digestive problems, we did not find a candidate variant. This study is an example of both clinical variation and difficulty in variant detection and evaluation. Our findings highlight that even an extensive exome sequence analysis can fail to fully uncover the complex molecular basis of a syndrome even if potentially causative variants are identified.
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Affiliation(s)
- Mine Koprulu
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey
| | - Rana Muhammad Kamran Shabbir
- Human Genetics Program, Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Qamar Zaman
- Human Genetics Program, Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Gökhan Nalbant
- Department of Bioinformatics and Biostatistics, Institute of Health Sciences, Mehmet Ali Aydinlar Acibadem University, Istanbul, Turkey
| | - Sajid Malik
- Human Genetics Program, Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.
| | - Aslıhan Tolun
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey.
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13
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Goel N, Singh S, Aseri TC. Global sequence features based translation initiation site prediction in human genomic sequences. Heliyon 2020; 6:e04825. [PMID: 32964155 PMCID: PMC7490824 DOI: 10.1016/j.heliyon.2020.e04825] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 05/25/2020] [Accepted: 08/26/2020] [Indexed: 11/26/2022] Open
Abstract
Gene prediction has been increasingly important in genome annotation due to advancements in sequencing technology. Genome annotation further helps in determining the structure and function of these genes. Translation initiation site prediction (TIS) in human genomic sequences is one of the fundamental and essential steps in gene prediction. Thus, accurate prediction of TIS in these sequences is highly desirable. Although many computational methods were developed for this problem, none of them focused on finding these sites in human genomic sequences. In this paper, a new TIS prediction method is proposed by incorporating global sequence based features. Support vector machine is used to assess the prediction power of these features. The proposed method achieved accuracy of above 90% when tested for genomic as well as cDNA sequences. The experimental results indicate that the method works well for both genomic and cDNA sequences. The method can be integrated into gene prediction system in future.
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Affiliation(s)
- Neelam Goel
- Department of Information Technology, University Institute of Engineering and Technology, Sector-25, Panjab University, Chandigarh 160014, India
| | - Shailendra Singh
- Department of Computer Science and Engineering, Punjab Engineering College (Deemed to be University), Sector-12, Chandigarh 160012, India
| | - Trilok Chand Aseri
- Department of Computer Science and Engineering, Punjab Engineering College (Deemed to be University), Sector-12, Chandigarh 160012, India
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14
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Fu Y, Cao R, Schäfer M, Stephan S, Braspenning-Wesch I, Schmitt L, Bischoff R, Müller M, Schäfer K, Vinzón SE, Rösl F, Hasche D. Expression of different L1 isoforms of Mastomys natalensis papillomavirus as mechanism to circumvent adaptive immunity. eLife 2020; 9:e57626. [PMID: 32746966 PMCID: PMC7402679 DOI: 10.7554/elife.57626] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/03/2020] [Indexed: 12/11/2022] Open
Abstract
Although many high-risk mucosal and cutaneous human papillomaviruses (HPVs) theoretically have the potential to synthesize L1 isoforms differing in length, previous seroepidemiological studies only focused on the short L1 variants, co-assembling with L2 to infectious virions. Using the multimammate mouse Mastomys coucha as preclinical model, this is the first study demonstrating seroconversion against different L1 isoforms during the natural course of papillomavirus infection. Intriguingly, positivity with the cutaneous MnPV was accompanied by a strong seroresponse against a longer L1 isoform, but to our surprise, the raised antibodies were non-neutralizing. Only after a delay of around 4 months, protecting antibodies against the short L1 appeared, enabling the virus to successfully establish an infection. This argues for a novel humoral immune escape mechanism that may also have important implications on the interpretation of epidemiological data in terms of seropositivity and protection of PV infections in general.
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Affiliation(s)
- Yingying Fu
- Division of Viral Transformation Mechanisms, Research Program 'Infection, Inflammation and Cancer', German Cancer Research CenterHeidelbergGermany
| | - Rui Cao
- Division of Viral Transformation Mechanisms, Research Program 'Infection, Inflammation and Cancer', German Cancer Research CenterHeidelbergGermany
| | - Miriam Schäfer
- Division of Viral Transformation Mechanisms, Research Program 'Infection, Inflammation and Cancer', German Cancer Research CenterHeidelbergGermany
| | - Sonja Stephan
- Division of Viral Transformation Mechanisms, Research Program 'Infection, Inflammation and Cancer', German Cancer Research CenterHeidelbergGermany
| | - Ilona Braspenning-Wesch
- Division of Viral Transformation Mechanisms, Research Program 'Infection, Inflammation and Cancer', German Cancer Research CenterHeidelbergGermany
| | - Laura Schmitt
- Division of Viral Transformation Mechanisms, Research Program 'Infection, Inflammation and Cancer', German Cancer Research CenterHeidelbergGermany
| | - Ralf Bischoff
- Division of Functional Genome Analysis, Research Program 'Functional and Structural Genomics', German Cancer Research CenterHeidelbergGermany
| | - Martin Müller
- Research Group Tumorvirus-specific Vaccination Strategies, Research Program 'Infection, Inflammation and Cancer', German Cancer Research CenterHeidelbergGermany
| | - Kai Schäfer
- Division of Viral Transformation Mechanisms, Research Program 'Infection, Inflammation and Cancer', German Cancer Research CenterHeidelbergGermany
| | - Sabrina E Vinzón
- Division of Viral Transformation Mechanisms, Research Program 'Infection, Inflammation and Cancer', German Cancer Research CenterHeidelbergGermany
| | - Frank Rösl
- Division of Viral Transformation Mechanisms, Research Program 'Infection, Inflammation and Cancer', German Cancer Research CenterHeidelbergGermany
| | - Daniel Hasche
- Division of Viral Transformation Mechanisms, Research Program 'Infection, Inflammation and Cancer', German Cancer Research CenterHeidelbergGermany
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15
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La Bella T, Imbeaud S, Peneau C, Mami I, Datta S, Bayard Q, Caruso S, Hirsch TZ, Calderaro J, Morcrette G, Guettier C, Paradis V, Amaddeo G, Laurent A, Possenti L, Chiche L, Bioulac-Sage P, Blanc JF, Letouze E, Nault JC, Zucman-Rossi J. Adeno-associated virus in the liver: natural history and consequences in tumour development. Gut 2020; 69:737-747. [PMID: 31375600 DOI: 10.1136/gutjnl-2019-318281] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 06/28/2019] [Accepted: 06/29/2019] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Adeno-associated virus (AAV) is a defective mono-stranded DNA virus, endemic in human population (35%-80%). Recurrent clonal AAV2 insertions are associated with the pathogenesis of rare human hepatocellular carcinoma (HCC) developed on normal liver. This study aimed to characterise the natural history of AAV infection in the liver and its consequence in tumour development. DESIGN Viral DNA was quantified in tumour and non-tumour liver tissues of 1461 patients. Presence of episomal form and viral mRNA expression were analysed using a DNAse/TaqMan-based assay and quantitative RT-PCR. In silico analyses using viral capture data explored viral variants and new clonal insertions. RESULTS AAV DNA was detected in 21% of the patients, including 8% of the tumour tissues, equally distributed in two major viral subtypes: one similar to AAV2, the other hybrid between AAV2 and AAV13 sequences. Episomal viral forms were found in 4% of the non-tumour tissues, frequently associated with viral RNA expression and human herpesvirus type 6, the candidate natural AAV helper virus. In 30 HCC, clonal AAV insertions were recurrently identified in CCNA2, CCNE1, TERT, TNFSF10, KMT2B and GLI1/INHBE. AAV insertion triggered oncogenic overexpression through multiple mechanisms that differ according to the localisation of the integration site. CONCLUSION We provided an integrated analysis of the wild-type AAV infection in the liver with the identification of viral genotypes, molecular forms, helper virus relationship and viral integrations. Clonal AAV insertions were positive selected during HCC development on non-cirrhotic liver challenging the notion of AAV as a non-pathogenic virus.
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Affiliation(s)
- Tiziana La Bella
- Centre de Recherche des Cordeliers, Sorbonne Universités, INSERM, Paris, Île-de-France, France.,Functional Genomics of Solid Tumor, Labex Immuno- Oncology, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, Île-de-France, France
| | - Sandrine Imbeaud
- Centre de Recherche des Cordeliers, Sorbonne Universités, INSERM, Paris, Île-de-France, France.,Functional Genomics of Solid Tumor, Labex Immuno- Oncology, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, Île-de-France, France
| | - Camille Peneau
- Centre de Recherche des Cordeliers, Sorbonne Universités, INSERM, Paris, Île-de-France, France.,Functional Genomics of Solid Tumor, Labex Immuno- Oncology, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, Île-de-France, France
| | - Iadh Mami
- Centre de Recherche des Cordeliers, Sorbonne Universités, INSERM, Paris, Île-de-France, France.,Functional Genomics of Solid Tumor, Labex Immuno- Oncology, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, Île-de-France, France
| | - Shalini Datta
- Centre de Recherche des Cordeliers, Sorbonne Universités, INSERM, Paris, Île-de-France, France.,Functional Genomics of Solid Tumor, Labex Immuno- Oncology, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, Île-de-France, France.,Indian Statistical Institute, University of Kalyani, Kalyani, West Bengal, India
| | - Quentin Bayard
- Centre de Recherche des Cordeliers, Sorbonne Universités, INSERM, Paris, Île-de-France, France.,Functional Genomics of Solid Tumor, Labex Immuno- Oncology, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, Île-de-France, France
| | - Stefano Caruso
- Centre de Recherche des Cordeliers, Sorbonne Universités, INSERM, Paris, Île-de-France, France.,Functional Genomics of Solid Tumor, Labex Immuno- Oncology, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, Île-de-France, France
| | - Theo Z Hirsch
- Centre de Recherche des Cordeliers, Sorbonne Universités, INSERM, Paris, Île-de-France, France.,Functional Genomics of Solid Tumor, Labex Immuno- Oncology, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, Île-de-France, France
| | - Julien Calderaro
- Centre de Recherche des Cordeliers, Sorbonne Universités, INSERM, Paris, Île-de-France, France.,Functional Genomics of Solid Tumor, Labex Immuno- Oncology, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, Île-de-France, France.,Pathology Department, APHP, CHU Henri Mondor, Créteil, Île-de-France, France
| | - Guillaume Morcrette
- Centre de Recherche des Cordeliers, Sorbonne Universités, INSERM, Paris, Île-de-France, France.,Functional Genomics of Solid Tumor, Labex Immuno- Oncology, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, Île-de-France, France.,Pathology Department, APHP, Bicetre-Paul Brousse Hospitals, Le Kremlin Bicêtre, Île-de-France, France.,Physiopathogenesis and treatment of liver diseases, INSERM, Paris, Île-de-France, France
| | - Catherine Guettier
- Pathology Department, APHP, Bicetre-Paul Brousse Hospitals, Le Kremlin Bicêtre, Île-de-France, France.,Physiopathogenesis and treatment of liver diseases, INSERM, Paris, Île-de-France, France
| | - Valerie Paradis
- Functional Genomics of Solid Tumor, Labex Immuno- Oncology, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, Île-de-France, France.,Pathology Department, APHP, Beaujon Hospital, Paris, Île-de-France, France.,The Research Center on Inflammation labeled, INSERM, Paris, Île-de-France
| | - Giuliana Amaddeo
- Hepatology Department, APHP, Henri Mondor Hospital, Créteil, Île-de-France, France.,Molecular virology and immunology, INSERM, Institut Mondor de Recherche Biomédicale, Créteil, Île-de-France, France
| | - Alexis Laurent
- Department of Digestive Surgery, APHP, Henri Mondor Hospital, Créteil, Île-de-France, France
| | - Laurent Possenti
- Department of Hepato-Gastroenterology and Digestive Oncology, CHU de Bordeaux, Haut-Lévêque Hospital, Bordeaux, Aquitaine, France
| | - Laurence Chiche
- Department of Digestive Surgery, Centre Médico Chirurgical Magellan, CHU de Bordeaux, Haut-Lévêque Hospital, Bordeaux, Aquitaine, France
| | - Paulette Bioulac-Sage
- Department of Pathology, CHU de Bordeaux, Pellegrin Hospital, Bordeaux, Aquitaine, France.,Bordeaux Research in Translational Oncology, Université Bordeaux, Bordeaux, Aquitaine, France
| | - Jean-Frederic Blanc
- Department of Hepato-Gastroenterology and Digestive Oncology, CHU de Bordeaux, Haut-Lévêque Hospital, Bordeaux, Aquitaine, France.,Department of Pathology, CHU de Bordeaux, Pellegrin Hospital, Bordeaux, Aquitaine, France.,Bordeaux Research in Translational Oncology, Université Bordeaux, Bordeaux, Aquitaine, France
| | - Eric Letouze
- Centre de Recherche des Cordeliers, Sorbonne Universités, INSERM, Paris, Île-de-France, France.,Functional Genomics of Solid Tumor, Labex Immuno- Oncology, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, Île-de-France, France
| | - Jean-Charles Nault
- Centre de Recherche des Cordeliers, Sorbonne Universités, INSERM, Paris, Île-de-France, France.,Functional Genomics of Solid Tumor, Labex Immuno- Oncology, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, Île-de-France, France.,Department of Hepatology, Université Paris Nord, APHP, Hospital Jean Verdier, Bondy, Île-de-France, France
| | - Jessica Zucman-Rossi
- Centre de Recherche des Cordeliers, Sorbonne Universités, INSERM, Paris, Île-de-France, France.,Functional Genomics of Solid Tumor, Labex Immuno- Oncology, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, Île-de-France, France.,Department of Oncology, APHP, Hospital Européen Georges Pompidou, Paris, Île-de-France, France
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16
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Wu P, Cai J, Chen Q, Han B, Meng X, Li Y, Li Z, Wang R, Lin L, Duan C, Kang C, Jiang C. Lnc-TALC promotes O 6-methylguanine-DNA methyltransferase expression via regulating the c-Met pathway by competitively binding with miR-20b-3p. Nat Commun 2019; 10:2045. [PMID: 31053733 PMCID: PMC6499807 DOI: 10.1038/s41467-019-10025-2] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 04/12/2019] [Indexed: 12/15/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have emerged as new regulatory molecules implicated in diverse biological processes, including therapeutic resistance. However, the mechanisms underlying lncRNA-mediated temozolomide (TMZ) resistance in glioblastoma (GBM) remain largely unknown. To illustrate the role of lncRNA in TMZ resistance, we induce TMZ-resistant GBM cells, perform a lncRNA microarray of the parental and TMZ-resistant cells, and find an unreported lncRNA in GBM, lnc-TALC (temozolomide-associated lncRNA in glioblastoma recurrence), correlated with TMZ resistance via competitively binding miR-20b-3p to facilitate c-Met expression. A phosphorylated AKT/FOXO3 axis regulated lnc-TALC expression in TMZ-resistant GBM cells. Furthermore, lnc-TALC increased MGMT expression by mediating the acetylation of H3K9, H3K27 and H3K36 in MGMT promoter regions through the c-Met/Stat3/p300 axis. In clinical patients, lnc-TALC is required for TMZ resistance and GBM recurrence. Our results reveal that lnc-TALC in GBM could serve as a therapeutic target to overcome TMZ resistance, enhancing the clinical benefits of TMZ chemotherapy. Temozolomide resistance in glioblastoma is associated with MGMT overexpression. Here, the authors identify a lncRNA that is a competitive endogenous RNA for miR-20b-3p, which causes c-Met activation to modulate acetylation of histone H3 on MGMT promoter through Stat3/p300 complex to increase MGMT expression and temozolomide resistance.
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Affiliation(s)
- Pengfei Wu
- Department of Neurosurgery, the Second Affiliated Hospital of Harbin Medical University, Neuroscience Institute, Heilongjiang Academy of Medical Sciences, 150086, Harbin, China
| | - Jinquan Cai
- Department of Neurosurgery, the Second Affiliated Hospital of Harbin Medical University, Neuroscience Institute, Heilongjiang Academy of Medical Sciences, 150086, Harbin, China.
| | - Qun Chen
- Department of Neurosurgery, the Second Affiliated Hospital of Harbin Medical University, Neuroscience Institute, Heilongjiang Academy of Medical Sciences, 150086, Harbin, China
| | - Bo Han
- Department of Neurosurgery, the Second Affiliated Hospital of Harbin Medical University, Neuroscience Institute, Heilongjiang Academy of Medical Sciences, 150086, Harbin, China
| | - Xiangqi Meng
- Department of Neurosurgery, the Second Affiliated Hospital of Harbin Medical University, Neuroscience Institute, Heilongjiang Academy of Medical Sciences, 150086, Harbin, China
| | - Yansheng Li
- Department of Neurosurgery, Tianjin Medical University General Hospital, Lab of Neuro-oncology, Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, 300052, Tianjin, China
| | - Ziwei Li
- Department of Neurosurgery, the Second Affiliated Hospital of Harbin Medical University, Neuroscience Institute, Heilongjiang Academy of Medical Sciences, 150086, Harbin, China
| | - Ruijia Wang
- Department of Neurosurgery, the Second Affiliated Hospital of Harbin Medical University, Neuroscience Institute, Heilongjiang Academy of Medical Sciences, 150086, Harbin, China
| | - Lin Lin
- Department of Neurosurgery, the Second Affiliated Hospital of Harbin Medical University, Neuroscience Institute, Heilongjiang Academy of Medical Sciences, 150086, Harbin, China
| | - Chunbin Duan
- Department of Neurosurgery, the Second Affiliated Hospital of Harbin Medical University, Neuroscience Institute, Heilongjiang Academy of Medical Sciences, 150086, Harbin, China
| | - Chunsheng Kang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Lab of Neuro-oncology, Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, 300052, Tianjin, China.
| | - Chuanlu Jiang
- Department of Neurosurgery, the Second Affiliated Hospital of Harbin Medical University, Neuroscience Institute, Heilongjiang Academy of Medical Sciences, 150086, Harbin, China.
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17
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Bernardo-Garcia FJ, Syed M, Jékely G, Sprecher SG. Glass confers rhabdomeric photoreceptor identity in Drosophila, but not across all metazoans. EvoDevo 2019; 10:4. [PMID: 30873275 PMCID: PMC6399963 DOI: 10.1186/s13227-019-0117-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 02/15/2019] [Indexed: 12/14/2022] Open
Abstract
Across metazoans, visual systems employ different types of photoreceptor neurons (PRs) to detect light. These include rhabdomeric PRs, which exist in distantly related phyla and possess an evolutionarily conserved phototransduction cascade. While the development of rhabdomeric PRs has been thoroughly studied in the fruit fly Drosophila melanogaster, we still know very little about how they form in other species. To investigate this question, we tested whether the transcription factor Glass, which is crucial for instructing rhabdomeric PR formation in Drosophila, may play a similar role in other metazoans. Glass homologues exist throughout the animal kingdom, indicating that this protein evolved prior to the metazoan radiation. Interestingly, our work indicates that glass is not expressed in rhabdomeric photoreceptors in the planarian Schmidtea mediterranea nor in the annelid Platynereis dumerilii. Combined with a comparative analysis of the Glass DNA-binding domain, our data suggest that the fate of rhabdomeric PRs is controlled by Glass-dependent and Glass-independent mechanisms in different animal clades.
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Affiliation(s)
- F Javier Bernardo-Garcia
- 1Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland.,2Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158 USA
| | - Maryam Syed
- 1Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Gáspár Jékely
- 3Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD UK
| | - Simon G Sprecher
- 1Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
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18
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Jobst-Schwan T, Hoogstraten CA, Kolvenbach CM, Schmidt JM, Kolb A, Eddy K, Schneider R, Ashraf S, Widmeier E, Majmundar AJ, Hildebrandt F. Corticosteroid treatment exacerbates nephrotic syndrome in a zebrafish model of magi2a knockout. Kidney Int 2019; 95:1079-1090. [PMID: 31010479 DOI: 10.1016/j.kint.2018.12.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/21/2018] [Accepted: 12/13/2018] [Indexed: 01/31/2023]
Abstract
Recently, recessive mutations of MAGI2 were identified as a cause of steroid-resistant nephrotic syndrome (SRNS) in humans and mice. To further delineate the pathogenesis of MAGI2 loss of function, we generated stable knockout lines for the two zebrafish orthologues magi2a and magi2b by CRISPR/Cas9. We also developed a novel assay for the direct detection of proteinuria in zebrafish independent of transgenic background. Whereas knockout of magi2b did not yield a nephrotic syndrome phenotype, magi2a-/- larvae developed ascites, periorbital edema, and proteinuria, as indicated by increased excretion of low molecular weight protein. Electron microscopy demonstrated extensive podocyte foot process effacement. As in human SRNS, we observed genotype/phenotype correlation, with edema onset occurring earlier in zebrafish with truncating alleles (5-6 days post fertilization) versus hypomorphic alleles (19-20 days post fertilization). Paradoxically, corticosteroid treatment exacerbated the phenotype, with earlier onset of edema. In contrast, treatment with cyclosporine A or tacrolimus had no significant effect. Although RhoA signaling has been implicated as a downstream mediator of MAGI2 activity, targeting of the RhoA pathway did not modify the nephrotic syndrome phenotype. In the first CRISPR/Cas9 zebrafish knockout model of SRNS, we found that corticosteroids may have a paradoxical effect in the setting of specific genetic mutations.
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Affiliation(s)
- Tilman Jobst-Schwan
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Charlotte A Hoogstraten
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Caroline M Kolvenbach
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Johanna Magdalena Schmidt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Amy Kolb
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kaitlyn Eddy
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ronen Schneider
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Shazia Ashraf
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Eugen Widmeier
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Amar J Majmundar
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
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19
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Xie Z, Hou Y, Yu M, Liu Y, Fan Y, Zhang W, Wang Z, Xiong H, Yuan Y. Clinical and genetic spectrum of sarcoglycanopathies in a large cohort of Chinese patients. Orphanet J Rare Dis 2019; 14:43. [PMID: 30764848 PMCID: PMC6376703 DOI: 10.1186/s13023-019-1021-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 02/03/2019] [Indexed: 11/20/2022] Open
Abstract
Background Sarcoglycanopathies comprise four subtypes of autosomal recessive limb-girdle muscular dystrophy (LGMD2C, LGMD2D, LGMD2E, and LGMD2F) that are caused, respectively, by mutations in the SGCG, SGCA, SGCB, and SGCD genes. Knowledge about the clinical and genetic features of sarcoglycanopathies in Chinese patients is limited. The aims of this study were to investigate in detail the clinical manifestations, sarcoglycan expression, and gene mutations in Chinese patients with sarcoglycanopathies and to identify possible correlations between them. Results Of 3638 patients for suspected neuromuscular diseases (1733 with inherited myopathies, 1557 with acquired myopathies, and 348 unknown), 756 patients had next-generation sequencing (NGS) diagnostic panel. Twenty-five patients with sarcoglycanopathies (11.5%) were identified from 218 confirmed LGMDs, comprising 18 with LGMD2D, 6 with LGMD2E, and one with LGMD2C. One patient with LGMD2D also had Charcot-Marie-Tooth 1A. The clinical phenotypes of the patients with LGMD2D or LGMD2E were markedly heterogeneous. Muscle biopsy showed a dystrophic pattern in 19 patients and mild myopathic changes in 6. The percentage of correct prediction of genotype based on expression of sarcoglycan was 36.0% (4 LGMD2D, 4 LGMD2E, and one LGMD2C). There was a statistically significant positive correlation between reduction of α-sarcoglycan level and disease severity in LGMD2D. Thirty-five mutations were identified in SGCA, SGCB, SGCG, and PMP22, 16 of which were novel. Exon 3 of SGCA was a hotspot region for mutations in LGMD2D. The missense mutation c.662G > A (p.R221H) was the most common mutation in SGCA. Missense mutations in both alleles of SGCA were associated with a relative benign disease course. No obvious clinical, sarcoglycan expression, and genetic correlation was found in LGMD2E. Conclusions This study expands the clinical and genetic spectrum of sarcoglycanopathies in Chinese patients and provides evidence that disease severity of LGMD2D may be predicted by α-sarcoglycan expression and SGCA mutation. Electronic supplementary material The online version of this article (10.1186/s13023-019-1021-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhiying Xie
- Department of Neurology, Peking University First Hospital, 8 Xishiku St, Xicheng District, Beijing, 100034, China
| | - Yue Hou
- Department of Neurology, Peking University First Hospital, 8 Xishiku St, Xicheng District, Beijing, 100034, China
| | - Meng Yu
- Department of Neurology, Peking University First Hospital, 8 Xishiku St, Xicheng District, Beijing, 100034, China
| | - Yilin Liu
- Department of Neurology, Peking University First Hospital, 8 Xishiku St, Xicheng District, Beijing, 100034, China
| | - Yanbin Fan
- Department of Pediatrics, Peking University First Hospital, Xishiku St, Xicheng District, Beijing, 100034, China
| | - Wei Zhang
- Department of Neurology, Peking University First Hospital, 8 Xishiku St, Xicheng District, Beijing, 100034, China
| | - Zhaoxia Wang
- Department of Neurology, Peking University First Hospital, 8 Xishiku St, Xicheng District, Beijing, 100034, China
| | - Hui Xiong
- Department of Pediatrics, Peking University First Hospital, Xishiku St, Xicheng District, Beijing, 100034, China
| | - Yun Yuan
- Department of Neurology, Peking University First Hospital, 8 Xishiku St, Xicheng District, Beijing, 100034, China.
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20
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Migraine-Associated TRESK Mutations Increase Neuronal Excitability through Alternative Translation Initiation and Inhibition of TREK. Neuron 2018; 101:232-245.e6. [PMID: 30573346 DOI: 10.1016/j.neuron.2018.11.039] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 10/03/2018] [Accepted: 11/20/2018] [Indexed: 12/12/2022]
Abstract
It is often unclear why some genetic mutations to a given gene contribute to neurological disorders and others do not. For instance, two mutations have previously been found to produce a dominant negative for TRESK, a two-pore-domain K+ channel implicated in migraine: TRESK-MT, a 2-bp frameshift mutation, and TRESK-C110R. Both mutants inhibit TRESK, but only TRESK-MT increases sensory neuron excitability and is linked to migraine. Here, we identify a new mechanism, termed frameshift mutation-induced alternative translation initiation (fsATI), that may explain why only TRESK-MT is associated with migraine. fsATI leads to the production of a second protein fragment, TRESK-MT2, which co-assembles with and inhibits TREK1 and TREK2, two other two-pore-domain K+ channels, to increase trigeminal sensory neuron excitability, leading to a migraine-like phenotype in rodents. These findings identify TREK1 and TREK2 as potential molecular targets in migraine and suggest that fsATI should be considered as a distinct class of mutations.
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21
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Bayard Q, Meunier L, Peneau C, Renault V, Shinde J, Nault JC, Mami I, Couchy G, Amaddeo G, Tubacher E, Bacq D, Meyer V, La Bella T, Debaillon-Vesque A, Bioulac-Sage P, Seror O, Blanc JF, Calderaro J, Deleuze JF, Imbeaud S, Zucman-Rossi J, Letouzé E. Cyclin A2/E1 activation defines a hepatocellular carcinoma subclass with a rearrangement signature of replication stress. Nat Commun 2018; 9:5235. [PMID: 30531861 PMCID: PMC6286353 DOI: 10.1038/s41467-018-07552-9] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/08/2018] [Indexed: 02/07/2023] Open
Abstract
Cyclins A2 and E1 regulate the cell cycle by promoting S phase entry and progression. Here, we identify a hepatocellular carcinoma (HCC) subgroup exhibiting cyclin activation through various mechanisms including hepatitis B virus (HBV) and adeno-associated virus type 2 (AAV2) insertions, enhancer hijacking and recurrent CCNA2 fusions. Cyclin A2 or E1 alterations define a homogenous entity of aggressive HCC, mostly developed in non-cirrhotic patients, characterized by a transcriptional activation of E2F and ATR pathways and a high frequency of RB1 and PTEN inactivation. Cyclin-driven HCC display a unique signature of structural rearrangements with hundreds of tandem duplications and templated insertions frequently activating TERT promoter. These rearrangements, strongly enriched in early-replicated active chromatin regions, are consistent with a break-induced replication mechanism. Pan-cancer analysis reveals a similar signature in BRCA1-mutated breast and ovarian cancers. Together, this analysis reveals a new poor prognosis HCC entity and a rearrangement signature related to replication stress. Cyclins A2 and E1 are known to regulate the cell cycle by promoting S phase entry and progression. Here, they identify an aggressive hepatocellular carcinoma subgroup exhibiting cyclin activation through various mechanisms and find this subgroup to display replication stress-induced structural rearrangements frequently activating TERT promoter.
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Affiliation(s)
- Quentin Bayard
- INSERM, UMR-1162, Génomique Fonctionnelle des Tumeurs Solides, Equipe Labellisée Ligue Contre le Cancer, Institut Universitaire d'Hématologie, Paris, 75010, France.,Université Paris Descartes, Labex Immuno-Oncology, Sorbonne Paris Cité, Faculté de Médecine, Paris, 75006, France.,Université Paris 13, Sorbonne Paris Cité, Unité de Formation et de Recherche Santé, Médecine, Biologie Humaine, Bobigny, 93017, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, 75013, France
| | - Léa Meunier
- INSERM, UMR-1162, Génomique Fonctionnelle des Tumeurs Solides, Equipe Labellisée Ligue Contre le Cancer, Institut Universitaire d'Hématologie, Paris, 75010, France.,Université Paris Descartes, Labex Immuno-Oncology, Sorbonne Paris Cité, Faculté de Médecine, Paris, 75006, France.,Université Paris 13, Sorbonne Paris Cité, Unité de Formation et de Recherche Santé, Médecine, Biologie Humaine, Bobigny, 93017, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, 75013, France
| | - Camille Peneau
- INSERM, UMR-1162, Génomique Fonctionnelle des Tumeurs Solides, Equipe Labellisée Ligue Contre le Cancer, Institut Universitaire d'Hématologie, Paris, 75010, France.,Université Paris Descartes, Labex Immuno-Oncology, Sorbonne Paris Cité, Faculté de Médecine, Paris, 75006, France.,Université Paris 13, Sorbonne Paris Cité, Unité de Formation et de Recherche Santé, Médecine, Biologie Humaine, Bobigny, 93017, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, 75013, France
| | - Victor Renault
- Laboratory for Bioinformatics, Fondation Jean Dausset - CEPH, Paris, 75010, France
| | - Jayendra Shinde
- INSERM, UMR-1162, Génomique Fonctionnelle des Tumeurs Solides, Equipe Labellisée Ligue Contre le Cancer, Institut Universitaire d'Hématologie, Paris, 75010, France.,Université Paris Descartes, Labex Immuno-Oncology, Sorbonne Paris Cité, Faculté de Médecine, Paris, 75006, France.,Université Paris 13, Sorbonne Paris Cité, Unité de Formation et de Recherche Santé, Médecine, Biologie Humaine, Bobigny, 93017, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, 75013, France
| | - Jean-Charles Nault
- INSERM, UMR-1162, Génomique Fonctionnelle des Tumeurs Solides, Equipe Labellisée Ligue Contre le Cancer, Institut Universitaire d'Hématologie, Paris, 75010, France.,Université Paris Descartes, Labex Immuno-Oncology, Sorbonne Paris Cité, Faculté de Médecine, Paris, 75006, France.,Université Paris 13, Sorbonne Paris Cité, Unité de Formation et de Recherche Santé, Médecine, Biologie Humaine, Bobigny, 93017, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, 75013, France.,Liver unit, Hôpital Jean Verdier, Hôpitaux Universitaires Paris-Seine-Saint-Denis, Assistance-Publique Hôpitaux de Paris, APHP, Bondy, 93140, France.,Unité de Formation et de Recherche Santé Médecine et Biologie Humaine, Université Paris 13, Communauté d'Universités et Etablissements Sorbonne Paris Cité, Bobigny, 93017, France
| | - Iadh Mami
- INSERM, UMR-1162, Génomique Fonctionnelle des Tumeurs Solides, Equipe Labellisée Ligue Contre le Cancer, Institut Universitaire d'Hématologie, Paris, 75010, France.,Université Paris Descartes, Labex Immuno-Oncology, Sorbonne Paris Cité, Faculté de Médecine, Paris, 75006, France.,Université Paris 13, Sorbonne Paris Cité, Unité de Formation et de Recherche Santé, Médecine, Biologie Humaine, Bobigny, 93017, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, 75013, France
| | - Gabrielle Couchy
- INSERM, UMR-1162, Génomique Fonctionnelle des Tumeurs Solides, Equipe Labellisée Ligue Contre le Cancer, Institut Universitaire d'Hématologie, Paris, 75010, France.,Université Paris Descartes, Labex Immuno-Oncology, Sorbonne Paris Cité, Faculté de Médecine, Paris, 75006, France.,Université Paris 13, Sorbonne Paris Cité, Unité de Formation et de Recherche Santé, Médecine, Biologie Humaine, Bobigny, 93017, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, 75013, France
| | - Giuliana Amaddeo
- Inserm, U955, Team 18, Université Paris-Est Créteil, Faculté de Médecine, Créteil, 94010, France.,Assistance Publique-Hôpitaux de Paris, Service d'Hépatologie, CHU Henri Mondor, Créteil, 94010, France
| | - Emmanuel Tubacher
- Laboratory for Bioinformatics, Fondation Jean Dausset - CEPH, Paris, 75010, France
| | - Delphine Bacq
- Centre National de Recherche en Génomique Humaine, CEA, Evry, 91000, France
| | - Vincent Meyer
- Centre National de Recherche en Génomique Humaine, CEA, Evry, 91000, France
| | - Tiziana La Bella
- INSERM, UMR-1162, Génomique Fonctionnelle des Tumeurs Solides, Equipe Labellisée Ligue Contre le Cancer, Institut Universitaire d'Hématologie, Paris, 75010, France.,Université Paris Descartes, Labex Immuno-Oncology, Sorbonne Paris Cité, Faculté de Médecine, Paris, 75006, France.,Université Paris 13, Sorbonne Paris Cité, Unité de Formation et de Recherche Santé, Médecine, Biologie Humaine, Bobigny, 93017, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, 75013, France
| | - Audrey Debaillon-Vesque
- Service Hépato-Gastroentérologie et Oncologie Digestive, Hôpital Haut-Lévêque, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, 33076, France
| | - Paulette Bioulac-Sage
- Université Bordeaux, Bordeaux Research in Translational Oncology, Bordeaux, 33076, France.,Service de Pathologie, Hôpital Pellegrin, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, 33000, France
| | - Olivier Seror
- INSERM, UMR-1162, Génomique Fonctionnelle des Tumeurs Solides, Equipe Labellisée Ligue Contre le Cancer, Institut Universitaire d'Hématologie, Paris, 75010, France.,Radiology Department, Jean Verdier Hospital, Hôpitaux Universitaires Paris-Seine-Saint-Denis, APHP, Bondy, 93140, France
| | - Jean-Frédéric Blanc
- Service Hépato-Gastroentérologie et Oncologie Digestive, Hôpital Haut-Lévêque, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, 33076, France.,Université Bordeaux, Bordeaux Research in Translational Oncology, Bordeaux, 33076, France
| | - Julien Calderaro
- Inserm, U955, Team 18, Université Paris-Est Créteil, Faculté de Médecine, Créteil, 94010, France.,Assistance Publique-Hôpitaux de Paris, Département de Pathologie, Hôpital Henri Mondor, Créteil, 94010, France
| | - Jean-François Deleuze
- Laboratory for Bioinformatics, Fondation Jean Dausset - CEPH, Paris, 75010, France.,Centre National de Recherche en Génomique Humaine, CEA, Evry, 91000, France
| | - Sandrine Imbeaud
- INSERM, UMR-1162, Génomique Fonctionnelle des Tumeurs Solides, Equipe Labellisée Ligue Contre le Cancer, Institut Universitaire d'Hématologie, Paris, 75010, France.,Université Paris Descartes, Labex Immuno-Oncology, Sorbonne Paris Cité, Faculté de Médecine, Paris, 75006, France.,Université Paris 13, Sorbonne Paris Cité, Unité de Formation et de Recherche Santé, Médecine, Biologie Humaine, Bobigny, 93017, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, 75013, France
| | - Jessica Zucman-Rossi
- INSERM, UMR-1162, Génomique Fonctionnelle des Tumeurs Solides, Equipe Labellisée Ligue Contre le Cancer, Institut Universitaire d'Hématologie, Paris, 75010, France. .,Université Paris Descartes, Labex Immuno-Oncology, Sorbonne Paris Cité, Faculté de Médecine, Paris, 75006, France. .,Université Paris 13, Sorbonne Paris Cité, Unité de Formation et de Recherche Santé, Médecine, Biologie Humaine, Bobigny, 93017, France. .,Université Paris Diderot, Sorbonne Paris Cité, Paris, 75013, France. .,Assistance Publique-Hôpitaux de Paris, Hopital Européen Georges Pompidou, 75015, Paris, France.
| | - Eric Letouzé
- INSERM, UMR-1162, Génomique Fonctionnelle des Tumeurs Solides, Equipe Labellisée Ligue Contre le Cancer, Institut Universitaire d'Hématologie, Paris, 75010, France. .,Université Paris Descartes, Labex Immuno-Oncology, Sorbonne Paris Cité, Faculté de Médecine, Paris, 75006, France. .,Université Paris 13, Sorbonne Paris Cité, Unité de Formation et de Recherche Santé, Médecine, Biologie Humaine, Bobigny, 93017, France. .,Université Paris Diderot, Sorbonne Paris Cité, Paris, 75013, France.
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22
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Mayr SJ, Sass JO, Vry J, Kirschner J, Mader I, Hövener JB, Reiss J, Santamaria-Araujo JA, Schwarz G, Grünert SC. A mild case of molybdenum cofactor deficiency defines an alternative route of MOCS1 protein maturation. J Inherit Metab Dis 2018; 41:187-196. [PMID: 29368224 DOI: 10.1007/s10545-018-0138-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/29/2017] [Accepted: 01/04/2018] [Indexed: 02/07/2023]
Abstract
Molybdenum cofactor deficiency is an autosomal recessive inborn error of metabolism, which results from mutations in genes involved in Moco biosynthesis. Moco serves as a cofactor of several enzymes, including sulfite oxidase. MoCD is clinically characterized by intractable seizures and severe, rapidly progressing neurodegeneration leading to death in early childhood in the majority of known cases. Here we report a patient with an unusual late disease onset and mild phenotype, characterized by a lack of seizures, normal early development, a decline triggered by febrile illness and a subsequent dystonic movement disorder. Genetic analysis revealed a homozygous c.1338delG MOCS1 mutation causing a frameshift (p.S442fs) with a premature termination of the MOCS1AB translation product at position 477 lacking the entire MOCS1B domain. Surprisingly, urine analysis detected trace amounts (1% of control) of the Moco degradation product urothione, suggesting a residual Moco synthesis in the patient, which was consistent with the mild clinical presentation. Therefore, we performed bioinformatic analysis of the patient's mutated MOCS1 transcript and found a potential Kozak-sequence downstream of the mutation site providing the possibility of an independent expression of a MOCS1B protein. Following the expression of the patient's MOCS1 cDNA in HEK293 cells we detected two proteins: a truncated MOCS1AB protein and a 22.4 kDa protein representing MOCS1B. Functional studies of both proteins confirmed activity of MOCS1B, but not of the truncated MOCS1AB. This finding demonstrates an unusual mechanism of translation re-initiation in the MOCS1 transcript, which results in trace amounts of functional MOCS1B protein being sufficient to partially protect the patient from the most severe symptoms of MoCD.
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Affiliation(s)
- Simon Julius Mayr
- Institute of Biochemistry, Department of Chemistry, University of Cologne, Zülpicher Str. 47, 50674, Köln, Germany
| | - Jörn Oliver Sass
- Bioanalytics & Biochemistry, Department of Natural Science, Bonn-Rhein Sieg University of Applied Sciences, Rheinbach, Germany
| | - Julia Vry
- Department of Neuropediatrics and Muscle Disorders, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Janbernd Kirschner
- Department of Neuropediatrics and Muscle Disorders, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Irina Mader
- Faculty of Medicine, Department of Neuroradiology, University of Freiburg, Freiburg, Germany
| | - Jan-Bernd Hövener
- Department of Radiology, Medical Physics, Faculty of Medicine, Medical Center - University of Freiburg, University of Freiburg, Freiburg, Germany
- Section for Biomedical Imaging and MOIN CC, University Medical Center Schleswig Holstein, University of Kiel, Kiel, Germany
| | - Jochen Reiss
- Institut für Humangenetik, Universität Göttingen, Göttingen, Germany
| | - José Angel Santamaria-Araujo
- Institute of Biochemistry, Department of Chemistry, University of Cologne, Zülpicher Str. 47, 50674, Köln, Germany
| | - Günter Schwarz
- Institute of Biochemistry, Department of Chemistry, University of Cologne, Zülpicher Str. 47, 50674, Köln, Germany.
- Center for Molecular Medicine Cologne), University of Cologne, Cologne, Germany.
| | - Sarah Catharina Grünert
- Department of General Pediatrics, Adolescent Medicine and Neonatology, Faculty of Medicine, Medical Center - University of Freiburg, Mathildenstr. 1, 79106, Freiburg, Germany.
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23
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Wei MM, Zhou YC, Wen ZS, Zhou B, Huang YC, Wang GZ, Zhao XC, Pan HL, Qu LW, Zhang J, Zhang C, Cheng X, Zhou GB. Long non-coding RNA stabilizes the Y-box-binding protein 1 and regulates the epidermal growth factor receptor to promote lung carcinogenesis. Oncotarget 2018; 7:59556-59571. [PMID: 27322209 PMCID: PMC5312331 DOI: 10.18632/oncotarget.10006] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 05/29/2016] [Indexed: 01/11/2023] Open
Abstract
Indoor and outdoor air pollution has been classified as group I carcinogen in humans, but the underlying tumorigenesis remains unclear. Here, we screened for abnormal long noncoding RNAs (lncRNAs) in lung cancers from patients living in Xuanwei city which has the highest lung cancer incidence in China due to smoky coal combustion-generated air pollution. We reported that Xuanwei patients had much more dysregulated lncRNAs than patients from control regions where smoky coal was not used. The lncRNA CAR intergenic 10 (CAR10) was up-regulated in 39/62 (62.9%) of the Xuanwei patients, which was much higher than in patients from control regions (32/86, 37.2%; p=0.002). A multivariate regression analysis showed an association between CAR10 overexpression and air pollution, and a smoky coal combustion-generated carcinogen dibenz[a,h]anthracene up-regulated CAR10 by increasing transcription factor FoxF2 expression. CAR10 bound and stabilized transcription factor Y-box-binding protein 1 (YB-1), leading to up-regulation of the epidermal growth factor receptor (EGFR) and proliferation of lung cancer cells. Knockdown of CAR10 inhibited cell growth in vitro and tumor growth in vivo. These results demonstrate the role of lncRNAs in environmental lung carcinogenesis, and CAR10-YB-1 represents a potential therapeutic target.
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Affiliation(s)
- Ming-Ming Wei
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yong-Chun Zhou
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University (Yunnan Tumor Hospital), Kunming 650106, China
| | - Zhe-Sheng Wen
- Department of Thoracic Surgery, The Cancer Hospital, Sun Yat-Sen University, Guangzhou 510060, China
| | - Bo Zhou
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yun-Chao Huang
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University (Yunnan Tumor Hospital), Kunming 650106, China
| | - Gui-Zhen Wang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xin-Chun Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hong-Li Pan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Li-Wei Qu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chen Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xin Cheng
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guang-Biao Zhou
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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24
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Harasimczuk E, Øvergård AC, Grotmol S, Nilsen F, Dalvin S. Characterization of three salmon louse (Lepeophtheirus salmonis) genes with fibronectin II domains expressed by tegumental type 1 glands. Mol Biochem Parasitol 2017; 219:1-9. [PMID: 29246806 DOI: 10.1016/j.molbiopara.2017.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 10/30/2017] [Accepted: 12/11/2017] [Indexed: 10/18/2022]
Abstract
The salmon louse, Lepeophtheirus salmonis (Copepoda: Caligidae), is currently the most significant pathogen affecting the salmon farming industry in the Northern Hemisphere. Exocrine glands of blood-feeding parasites are believed to be important for the host-parasite interaction, but also in the production of substances for integument lubrication and antifouling. In L. salmonis; however, we have limited knowledge about the exocrine glands. The aim of this study was therefore to examine three genes containing fibronectin type II (FNII) domains expressed in L. salmonis tegumental type 1 (teg 1) glands, namely LsFNII1, 2 and 3. LsFNII1, 2 and 3 contains four, three, and two FNII domains respectively. Sequence alignment of LsFNII domains showed conservation of amino acids that may indicate a possible involvement of LsFNII domains in collagen binding. Ontogenetic analysis of LsFNII1, 2 and 3 revealed highest expression in pre-adult and adult lice. Localization of LsFNII1, 2 and 3 transcripts showed expression in teg 1 glands only, which are the most abundant exocrine gland type in L. salmonis. LsFNII1, 2 and 3 were successfully knocked-down by RNAi, however, alteration in gland morphology was not detected between the knock-down and control groups. Overall, this study gives first insight into FNII domain containing proteins in L. salmonis.
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Affiliation(s)
- Ewa Harasimczuk
- SLCR Sea Lice Research Center, Institute of Marine Research, 5817 Bergen, Norway.
| | - Aina-Cathrine Øvergård
- SLRC Sea Lice Research Center, Department of Biology, University of Bergen, Thormøhlensgt. 55, 5008 Bergen, Norway.
| | - Sindre Grotmol
- SLRC Sea Lice Research Center, Department of Biology, University of Bergen, Thormøhlensgt. 55, 5008 Bergen, Norway.
| | - Frank Nilsen
- SLRC Sea Lice Research Center, Department of Biology, University of Bergen, Thormøhlensgt. 55, 5008 Bergen, Norway.
| | - Sussie Dalvin
- SLCR Sea Lice Research Center, Institute of Marine Research, 5817 Bergen, Norway.
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25
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Nieke S, Yasmin N, Kakugawa K, Yokomizo T, Muroi S, Taniuchi I. Unique N-terminal sequences in two Runx1 isoforms are dispensable for Runx1 function. BMC DEVELOPMENTAL BIOLOGY 2017; 17:14. [PMID: 29047338 PMCID: PMC5648507 DOI: 10.1186/s12861-017-0156-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 10/01/2017] [Indexed: 01/19/2023]
Abstract
Background The Runt-related transcription factors (Runx) are a family of evolutionarily conserved transcriptional regulators that play multiple roles in the developmental control of various cell types. Among the three mammalian Runx proteins, Runx1 is essential for definitive hematopoiesis and its dysfunction leads to human leukemogenesis. There are two promoters, distal (P1) and proximal (P2), in the Runx1 gene, which produce two Runx1 isoforms with distinct N-terminal amino acid sequences, P1-Runx1 and P2-Runx1. However, it remains unclear whether P2-Runx specific N-terminal sequence have any specific function for Runx1 protein. Results To address the function of the P2-Runx1 isoform, we established novel mutant mouse models in which the translational initiation AUG (+1) codon for P2-Runx1 isoform was modulated. We found that a truncated P2-Runx1 isoform is translated from a downstream non-canonical AUG codon. Importantly, the truncated P2-Runx1 isoform is sufficient to support primary hematopoiesis, even in the absence of the P1-Runx1 isoform. Furthermore, the truncated P2-Runx1 isoform was able to restore defect in basophil development caused by loss of the P1-Runx1 isoform. The truncated P2-Runx1 isoform was more stable than the canonical P2-Runx1 isoform. Conclusions Our results demonstrate that the N-terminal sequences specific for P2-Runx1 are dispensable for Runx1 function, and likely serve as a de-stabilization module to regulate Runx1 production. Electronic supplementary material The online version of this article (10.1186/s12861-017-0156-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sebastian Nieke
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences (IMS). 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,Abteilung Immunologie, Interfakultaeres Institute fuer Zellbiologie, Auf der Morgenstelle 15, 72076, Tuebingen, Germany
| | - Nighat Yasmin
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences (IMS). 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,Faculty of Life Sciences (Microbiology), University of Central Punjab, 1 - Khayaban-e-Jinnah Road, Johar Town, Pakistan
| | - Kiyokazu Kakugawa
- Laboratory for Immune Crosstalk, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Tomomasa Yokomizo
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, #12-01, Singapore, 117599, Singapore.,International Research Center for Medical Sciences, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto City, 860-0811, Japan
| | - Sawako Muroi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences (IMS). 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences (IMS). 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
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26
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Hassan AO, Vemula SV, Sharma A, Bangari DS, Mishra KK, Mittal SK. 155R is a novel structural protein of bovine adenovirus type 3, but it is not essential for virus replication. J Gen Virol 2017; 98:749-753. [PMID: 28086071 DOI: 10.1099/jgv.0.000707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bovine adenovirus (AdV) type 3 (BAdV-3) E1 region shares functional homology with E1 of human AdV type C5. Sequence analysis of the BAdV-3 E1 region revealed the presence of a novel 155R ORF that is not observed in other AdVs, on the lower strand antiparallel to a portion of the E1B region. The 155R gene products in BAdV-3-infected cells were identified by Northern blot, reverse transcriptase PCR followed by sequencing and Western blot analysis using the155R-specific antibody. 155R seems to be a late protein and is present in purified BAdV-3 particles. Replication kinetics of BAdV mutants with either one (BAdV/155R/mt1) or two (BAdV/155R/mt2) stop codons in the 155R ORF were comparable to those of BAdV-3, indicating that 155R is not essential for virus replication in cell culture. These results suggest that 155R-deleted BAdV-3 vectors could be generated in a cell line that fully complements BAdV-3 E1 functions.
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Affiliation(s)
- Ahmed O Hassan
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA.,Purdue Institute for Immunology, Inflammation and Infectious Diseases, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA.,Purdue University Center for Cancer Research, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA
| | - Sai V Vemula
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA.,Purdue University Center for Cancer Research, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA.,Present address: Merck Sharp and Dohme, West Point, PA, USA
| | - Anurag Sharma
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA.,Purdue University Center for Cancer Research, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA.,Present address: Department of Pediatrics, Weill Cornell Medical College, New York, NY, USA
| | - Dinesh S Bangari
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA.,Purdue University Center for Cancer Research, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA.,Present address: Department of Pathology, Sanofi Genzyme, 5 Mountain Road, Framingham, MA, USA
| | - Krishna K Mishra
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA.,Purdue University Center for Cancer Research, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA.,Present address: Department of Biology, Ivy Tech Community College, Lafayette, IN, USA
| | - Suresh K Mittal
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA.,Purdue Institute for Immunology, Inflammation and Infectious Diseases, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA.,Purdue University Center for Cancer Research, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA
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27
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Braune K, Volkmer I, Staege MS. Characterization of Alstrom Syndrome 1 (ALMS1) Transcript Variants in Hodgkin Lymphoma Cells. PLoS One 2017; 12:e0170694. [PMID: 28135309 PMCID: PMC5279758 DOI: 10.1371/journal.pone.0170694] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 01/09/2017] [Indexed: 12/31/2022] Open
Abstract
The Alstrom syndrome gene (ALMS1) is one of the largest disease associated genes identified today in the human genome and is implicated in cell cycle control, ciliogenesis, endosome recycling and intracellular transport mechanisms. ALMS1 mutations cause Alstrom syndrome, a rare genetic disorder. However, its function is not completely understood. DNA microarray analysis suggested that ALMS1 might be differentially expressed between Hodgkin lymphoma (HL) cells and normal tissues. By using reverse transcription-polymerase chain reaction (RT-PCR) we detected low but variable expression of ALMS1 in HL cell lines with highest expression in KM-H2 cells. Immunofluorescence indicated centrosomal accumulation of ALMS1 protein in HL cells. Knock-down of ALMS1 in KM-H2 cells had no impact on viability or cytotoxic drug sensitivity of these cells. Sequencing of RT-PCR products from HL cell lines identified three variable regions in ALMS1 transcripts that affect exons 2, 13, and 23. One of these variants was characterized by splicing out of exon 13. The other variants are characterized by two alternative 5 prime ends or alternative 3 prime ends. Structure prediction of the corresponding RNAs and proteins suggest that the different transcript variants might affect posttranscriptional regulation and ligand binding.
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Affiliation(s)
- Katarina Braune
- Department of Pediatrics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Ines Volkmer
- Department of Pediatrics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Martin S. Staege
- Department of Pediatrics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- * E-mail:
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28
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Expression of the prospective mesoderm genes twist, snail, and mef2 in penaeid shrimp. Dev Genes Evol 2016; 226:317-24. [PMID: 27129985 DOI: 10.1007/s00427-016-0544-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 04/05/2016] [Indexed: 10/21/2022]
Abstract
In penaeid shrimp, mesoderm forms from two sources: naupliar mesoderm founder cells, which invaginate during gastrulation, and posterior mesodermal stem cells called mesoteloblasts, which undergo characteristic teloblastic divisions. The primordial mesoteloblast descends from the ventral mesendoblast, which arrests in cell division at the 32-cell stage and ingresses with its sister dorsal mesendoblast prior to naupliar mesoderm invagination. The naupliar mesoderm forms the muscles of the naupliar appendages (first and second antennae and mandibles), while the mesoteloblasts form the mesoderm, including the muscles, of subsequently formed posterior segments. To better understand the mechanism of mesoderm and muscle formation in penaeid shrimp, twist, snail, and mef2 cDNAs were identified from transcriptomes of Penaeus vannamei, P. japonicus, P. chinensis, and P. monodon. A single Twist ortholog was found, with strong inferred amino acid conservation across all three species. Multiple Snail protein variants were detected, which clustered in a phylogenetic tree with other decapod crustacean Snail sequences. Two closely-related mef2 variants were found in P. vannamei. The developmental mRNA expression of these genes was studied by qPCR in P. vannamei embryos, larvae, and postlarvae. Expression of Pv-twist and Pv-snail began during the limb bud stage and continued through larval stages to the postlarva. Surprisingly, Pv-mef2 expression was found in all stages from the zygote to the postlarva, with the highest expression in the limb bud and protozoeal stages. The results add comparative data on the development of anterior and posterior mesoderm in malacostracan crustaceans, and should stimulate further studies on mesoderm and muscle development in penaeid shrimp.
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Adam I, Mendoza E, Kobalz U, Wohlgemuth S, Scharff C. FoxP2 directly regulates the reelin receptor VLDLR developmentally and by singing. Mol Cell Neurosci 2016; 74:96-105. [PMID: 27105823 DOI: 10.1016/j.mcn.2016.04.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 03/10/2016] [Accepted: 04/18/2016] [Indexed: 12/15/2022] Open
Abstract
Mutations of the transcription factor FOXP2 cause a severe speech and language disorder. In songbirds, FoxP2 is expressed in the medium spiny neurons (MSNs) of the avian basal ganglia song nucleus, Area X, which is crucial for song learning and adult song performance. Experimental downregulation of FoxP2 in Area X affects spine formation, prevents neuronal plasticity induced by social context and impairs song learning. Direct target genes of FoxP2 relevant for song learning and song production are unknown. Here we show that a lentivirally mediated FoxP2 knockdown in Area X of zebra finches downregulates the expression of VLDLR, one of the two reelin receptors. Zebra finch FoxP2 binds to the promoter of VLDLR and activates it, establishing VLDLR as a direct FoxP2 target. Consistent with these findings, VLDLR expression is co-regulated with FoxP2 as a consequence of adult singing and during song learning. We also demonstrate that knockdown of FoxP2 affects glutamatergic transmission at the corticostriatal MSN synapse. These data raise the possibility that the regulatory relationship between FoxP2 and VLDLR guides structural plasticity towards the subset of FoxP2-positive MSNs in an activity dependent manner via the reelin pathway.
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Affiliation(s)
- Iris Adam
- Department for Animal Behavior, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany.
| | - Ezequiel Mendoza
- Department for Animal Behavior, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany.
| | - Ursula Kobalz
- Department for Animal Behavior, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany.
| | - Sandra Wohlgemuth
- Department for Animal Behavior, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany.
| | - Constance Scharff
- Department for Animal Behavior, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany.
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30
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A novel long non-coding RNA in the rheumatoid arthritis risk locus TRAF1-C5 influences C5 mRNA levels. Genes Immun 2015; 17:85-92. [PMID: 26673966 DOI: 10.1038/gene.2015.54] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 11/06/2015] [Accepted: 11/11/2015] [Indexed: 01/05/2023]
Abstract
Long non-coding RNAs (lncRNAs) can regulate the transcript levels of genes in the same genomic region. These locally acting lncRNAs have been found deregulated in human disease and some have been shown to harbour quantitative trait loci (eQTLs) in autoimmune diseases. However, lncRNAs linked to the transcription of candidate risk genes in loci associated to rheumatoid arthritis (RA) have not yet been identified. The TRAF1 and C5 risk locus shows evidence of multiple eQTLs and transcription of intergenic non-coding sequences. Here, we identified a non-coding transcript (C5T1lncRNA) starting in the 3' untranslated region (UTR) of C5. RA-relevant cell types express C5T1lncRNA and RNA levels are further enhanced by specific immune stimuli. C5T1lncRNA is expressed predominantly in the nucleus and its expression correlates positively with C5 mRNA in various tissues (P=0.001) and in peripheral blood mononuclear cells (P=0.02) indicating transcriptional co-regulation. Knockdown results in a concurrent decrease in C5 mRNA levels but not of other neighbouring genes. Overall, our data show the identification of a novel lncRNA C5T1lncRNA that is fully located in the associated region and influences transcript levels of C5, a gene previously linked to RA pathogenesis.
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31
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Fakhraldeen SA, Clark RJ, Roopra A, Chin EN, Huang W, Castorino J, Wisinski KB, Kim T, Spiegelman VS, Alexander CM. Two Isoforms of the RNA Binding Protein, Coding Region Determinant-binding Protein (CRD-BP/IGF2BP1), Are Expressed in Breast Epithelium and Support Clonogenic Growth of Breast Tumor Cells. J Biol Chem 2015; 290:13386-400. [PMID: 25861986 DOI: 10.1074/jbc.m115.655175] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Indexed: 11/06/2022] Open
Abstract
CRD-BP/IGF2BP1 has been characterized as an "oncofetal" RNA binding protein typically highly expressed in embryonic tissues, suppressed in normal adult tissues, but induced in many tumor types. In this study, we show that adult breast tissues express ubiquitous but low levels of CRD-BP protein and mRNA. Although CRD-BP mRNA expression is induced in breast tumor cells, levels remain ∼1000-fold lower than in embryonic tissues. Despite low expression levels, CRD-BP is required for clonogenic growth of breast cancer cells. We reveal that because the most common protein isoform in normal adult breast and breast tumors has an N-terminal deletion (lacking two RNA recognition motif (RRM) domains) and is therefore missing antibody epitopes, CRD-BP expression has been under-reported by previous studies. We show that a CRD-BP mutant mouse strain retains expression of the shorter transcript (ΔN-CRD-BP), which originates in intron 2, suggesting that the impact of complete ablation of this gene in mice is not yet known. Either the full-length CRD-BP or the N-terminally truncated version can rescue the clonogenicity of CRD-BP knockdown breast cancer cells, suggesting that clonogenic function is served by either CRD-BP isoform. In summary, although CRD-BP expression levels are low in breast cancer cells, this protein is necessary for clonogenic activity.
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Affiliation(s)
| | - Rod J Clark
- From the McArdle Laboratory for Cancer Research and
| | | | - Emily N Chin
- From the McArdle Laboratory for Cancer Research and
| | | | - John Castorino
- the School of Natural Sciences, Hampshire College, Amherst, Massachusetts 01002
| | | | - TaeWon Kim
- Dermatology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705-2276 and
| | - Vladimir S Spiegelman
- Dermatology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705-2276 and
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32
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Semplicini C, Vissing J, Dahlqvist JR, Stojkovic T, Bello L, Witting N, Duno M, Leturcq F, Bertolin C, D'Ambrosio P, Eymard B, Angelini C, Politano L, Laforêt P, Pegoraro E. Clinical and genetic spectrum in limb-girdle muscular dystrophy type 2E. Neurology 2015; 84:1772-81. [PMID: 25862795 DOI: 10.1212/wnl.0000000000001519] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 01/20/2015] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To determine the clinical spectrum of limb-girdle muscular dystrophy 2E (LGMD2E) and to investigate whether genetic or biochemical features can predict the phenotype of the disease. METHODS All LGMD2E patients followed in participating centers were included. A specific clinical protocol was created, including quantitative evaluation of motor, respiratory, and cardiac function. Phenotype was defined as severe or mild if the age at loss of ambulation occurred before or after 18 years. Molecular analysis of SGCB gene and biochemical features of muscle biopsies were reviewed. RESULTS Thirty-two patients were included (16 male, 16 female; age 7-67 years; 15 severe, 12 mild, and 5 unknown). Neurologic examination showed proximal muscle weakness in all patients, but distal involvement was also observed in patients with severe disease early in the disease course. Cardiac involvement was observed in 20 patients (63%) even before overt muscle involvement. Six patients had restrictive respiratory insufficiency requiring assisted ventilation (19%). Seventeen different mutations were identified, and 3 were recurrent. The c.377_384dup (13 alleles) was associated with the severe form, the c.-22_10dup (10) with the milder form, and the c.341C>T (9) with both. The entire sarcoglycan complex was undetectable by muscle immunohistochemistry or Western blot in 9/10 severe cases and reduced in 7/7 mild cases. The residual amount of sarcoglycan in muscle resulted a predictor of age at loss of ambulation. CONCLUSIONS This study expands the spectrum of phenotype in β-sarcoglycanopathy and provides strong evidence that severity of clinical involvement may be predicted by SGCB gene mutation and sarcoglycan protein expression.
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Affiliation(s)
- Claudio Semplicini
- From the Neuromuscular Center (C.S., L.B., C.B., E.P.), Department of Neurosciences, University of Padova, Italy; the Neuromuscular Clinic and Research Unit (J.V., J.R.D., N.W.), Department of Neurology, Rigshospitalet, University of Copenhagen, Denmark; Paris-Est Neuromuscular Center (T.S., B.E., P.L.), Institut of Myology, Pitié-Salpêtrière Hospital, Paris, France; the Department of Clinical Genetics (M.D.), University of Copenhagen, Rigshospitalet, Denmark; Laboratoire de Biochimie et Génétique Moléculaire (F.L.), Groupe Hospitalier Cochin, Paris, France; Cardiomyology and Medical Genetics (P.D., L.P.), Department of Experimental Medicine, Second University of Naples; and the IRCCS San Camillo (C.A.), Venezia, Italy
| | - John Vissing
- From the Neuromuscular Center (C.S., L.B., C.B., E.P.), Department of Neurosciences, University of Padova, Italy; the Neuromuscular Clinic and Research Unit (J.V., J.R.D., N.W.), Department of Neurology, Rigshospitalet, University of Copenhagen, Denmark; Paris-Est Neuromuscular Center (T.S., B.E., P.L.), Institut of Myology, Pitié-Salpêtrière Hospital, Paris, France; the Department of Clinical Genetics (M.D.), University of Copenhagen, Rigshospitalet, Denmark; Laboratoire de Biochimie et Génétique Moléculaire (F.L.), Groupe Hospitalier Cochin, Paris, France; Cardiomyology and Medical Genetics (P.D., L.P.), Department of Experimental Medicine, Second University of Naples; and the IRCCS San Camillo (C.A.), Venezia, Italy
| | - Julia R Dahlqvist
- From the Neuromuscular Center (C.S., L.B., C.B., E.P.), Department of Neurosciences, University of Padova, Italy; the Neuromuscular Clinic and Research Unit (J.V., J.R.D., N.W.), Department of Neurology, Rigshospitalet, University of Copenhagen, Denmark; Paris-Est Neuromuscular Center (T.S., B.E., P.L.), Institut of Myology, Pitié-Salpêtrière Hospital, Paris, France; the Department of Clinical Genetics (M.D.), University of Copenhagen, Rigshospitalet, Denmark; Laboratoire de Biochimie et Génétique Moléculaire (F.L.), Groupe Hospitalier Cochin, Paris, France; Cardiomyology and Medical Genetics (P.D., L.P.), Department of Experimental Medicine, Second University of Naples; and the IRCCS San Camillo (C.A.), Venezia, Italy
| | - Tanya Stojkovic
- From the Neuromuscular Center (C.S., L.B., C.B., E.P.), Department of Neurosciences, University of Padova, Italy; the Neuromuscular Clinic and Research Unit (J.V., J.R.D., N.W.), Department of Neurology, Rigshospitalet, University of Copenhagen, Denmark; Paris-Est Neuromuscular Center (T.S., B.E., P.L.), Institut of Myology, Pitié-Salpêtrière Hospital, Paris, France; the Department of Clinical Genetics (M.D.), University of Copenhagen, Rigshospitalet, Denmark; Laboratoire de Biochimie et Génétique Moléculaire (F.L.), Groupe Hospitalier Cochin, Paris, France; Cardiomyology and Medical Genetics (P.D., L.P.), Department of Experimental Medicine, Second University of Naples; and the IRCCS San Camillo (C.A.), Venezia, Italy
| | - Luca Bello
- From the Neuromuscular Center (C.S., L.B., C.B., E.P.), Department of Neurosciences, University of Padova, Italy; the Neuromuscular Clinic and Research Unit (J.V., J.R.D., N.W.), Department of Neurology, Rigshospitalet, University of Copenhagen, Denmark; Paris-Est Neuromuscular Center (T.S., B.E., P.L.), Institut of Myology, Pitié-Salpêtrière Hospital, Paris, France; the Department of Clinical Genetics (M.D.), University of Copenhagen, Rigshospitalet, Denmark; Laboratoire de Biochimie et Génétique Moléculaire (F.L.), Groupe Hospitalier Cochin, Paris, France; Cardiomyology and Medical Genetics (P.D., L.P.), Department of Experimental Medicine, Second University of Naples; and the IRCCS San Camillo (C.A.), Venezia, Italy
| | - Nanna Witting
- From the Neuromuscular Center (C.S., L.B., C.B., E.P.), Department of Neurosciences, University of Padova, Italy; the Neuromuscular Clinic and Research Unit (J.V., J.R.D., N.W.), Department of Neurology, Rigshospitalet, University of Copenhagen, Denmark; Paris-Est Neuromuscular Center (T.S., B.E., P.L.), Institut of Myology, Pitié-Salpêtrière Hospital, Paris, France; the Department of Clinical Genetics (M.D.), University of Copenhagen, Rigshospitalet, Denmark; Laboratoire de Biochimie et Génétique Moléculaire (F.L.), Groupe Hospitalier Cochin, Paris, France; Cardiomyology and Medical Genetics (P.D., L.P.), Department of Experimental Medicine, Second University of Naples; and the IRCCS San Camillo (C.A.), Venezia, Italy
| | - Morten Duno
- From the Neuromuscular Center (C.S., L.B., C.B., E.P.), Department of Neurosciences, University of Padova, Italy; the Neuromuscular Clinic and Research Unit (J.V., J.R.D., N.W.), Department of Neurology, Rigshospitalet, University of Copenhagen, Denmark; Paris-Est Neuromuscular Center (T.S., B.E., P.L.), Institut of Myology, Pitié-Salpêtrière Hospital, Paris, France; the Department of Clinical Genetics (M.D.), University of Copenhagen, Rigshospitalet, Denmark; Laboratoire de Biochimie et Génétique Moléculaire (F.L.), Groupe Hospitalier Cochin, Paris, France; Cardiomyology and Medical Genetics (P.D., L.P.), Department of Experimental Medicine, Second University of Naples; and the IRCCS San Camillo (C.A.), Venezia, Italy
| | - France Leturcq
- From the Neuromuscular Center (C.S., L.B., C.B., E.P.), Department of Neurosciences, University of Padova, Italy; the Neuromuscular Clinic and Research Unit (J.V., J.R.D., N.W.), Department of Neurology, Rigshospitalet, University of Copenhagen, Denmark; Paris-Est Neuromuscular Center (T.S., B.E., P.L.), Institut of Myology, Pitié-Salpêtrière Hospital, Paris, France; the Department of Clinical Genetics (M.D.), University of Copenhagen, Rigshospitalet, Denmark; Laboratoire de Biochimie et Génétique Moléculaire (F.L.), Groupe Hospitalier Cochin, Paris, France; Cardiomyology and Medical Genetics (P.D., L.P.), Department of Experimental Medicine, Second University of Naples; and the IRCCS San Camillo (C.A.), Venezia, Italy
| | - Cinzia Bertolin
- From the Neuromuscular Center (C.S., L.B., C.B., E.P.), Department of Neurosciences, University of Padova, Italy; the Neuromuscular Clinic and Research Unit (J.V., J.R.D., N.W.), Department of Neurology, Rigshospitalet, University of Copenhagen, Denmark; Paris-Est Neuromuscular Center (T.S., B.E., P.L.), Institut of Myology, Pitié-Salpêtrière Hospital, Paris, France; the Department of Clinical Genetics (M.D.), University of Copenhagen, Rigshospitalet, Denmark; Laboratoire de Biochimie et Génétique Moléculaire (F.L.), Groupe Hospitalier Cochin, Paris, France; Cardiomyology and Medical Genetics (P.D., L.P.), Department of Experimental Medicine, Second University of Naples; and the IRCCS San Camillo (C.A.), Venezia, Italy
| | - Paola D'Ambrosio
- From the Neuromuscular Center (C.S., L.B., C.B., E.P.), Department of Neurosciences, University of Padova, Italy; the Neuromuscular Clinic and Research Unit (J.V., J.R.D., N.W.), Department of Neurology, Rigshospitalet, University of Copenhagen, Denmark; Paris-Est Neuromuscular Center (T.S., B.E., P.L.), Institut of Myology, Pitié-Salpêtrière Hospital, Paris, France; the Department of Clinical Genetics (M.D.), University of Copenhagen, Rigshospitalet, Denmark; Laboratoire de Biochimie et Génétique Moléculaire (F.L.), Groupe Hospitalier Cochin, Paris, France; Cardiomyology and Medical Genetics (P.D., L.P.), Department of Experimental Medicine, Second University of Naples; and the IRCCS San Camillo (C.A.), Venezia, Italy
| | - Bruno Eymard
- From the Neuromuscular Center (C.S., L.B., C.B., E.P.), Department of Neurosciences, University of Padova, Italy; the Neuromuscular Clinic and Research Unit (J.V., J.R.D., N.W.), Department of Neurology, Rigshospitalet, University of Copenhagen, Denmark; Paris-Est Neuromuscular Center (T.S., B.E., P.L.), Institut of Myology, Pitié-Salpêtrière Hospital, Paris, France; the Department of Clinical Genetics (M.D.), University of Copenhagen, Rigshospitalet, Denmark; Laboratoire de Biochimie et Génétique Moléculaire (F.L.), Groupe Hospitalier Cochin, Paris, France; Cardiomyology and Medical Genetics (P.D., L.P.), Department of Experimental Medicine, Second University of Naples; and the IRCCS San Camillo (C.A.), Venezia, Italy
| | - Corrado Angelini
- From the Neuromuscular Center (C.S., L.B., C.B., E.P.), Department of Neurosciences, University of Padova, Italy; the Neuromuscular Clinic and Research Unit (J.V., J.R.D., N.W.), Department of Neurology, Rigshospitalet, University of Copenhagen, Denmark; Paris-Est Neuromuscular Center (T.S., B.E., P.L.), Institut of Myology, Pitié-Salpêtrière Hospital, Paris, France; the Department of Clinical Genetics (M.D.), University of Copenhagen, Rigshospitalet, Denmark; Laboratoire de Biochimie et Génétique Moléculaire (F.L.), Groupe Hospitalier Cochin, Paris, France; Cardiomyology and Medical Genetics (P.D., L.P.), Department of Experimental Medicine, Second University of Naples; and the IRCCS San Camillo (C.A.), Venezia, Italy
| | - Luisa Politano
- From the Neuromuscular Center (C.S., L.B., C.B., E.P.), Department of Neurosciences, University of Padova, Italy; the Neuromuscular Clinic and Research Unit (J.V., J.R.D., N.W.), Department of Neurology, Rigshospitalet, University of Copenhagen, Denmark; Paris-Est Neuromuscular Center (T.S., B.E., P.L.), Institut of Myology, Pitié-Salpêtrière Hospital, Paris, France; the Department of Clinical Genetics (M.D.), University of Copenhagen, Rigshospitalet, Denmark; Laboratoire de Biochimie et Génétique Moléculaire (F.L.), Groupe Hospitalier Cochin, Paris, France; Cardiomyology and Medical Genetics (P.D., L.P.), Department of Experimental Medicine, Second University of Naples; and the IRCCS San Camillo (C.A.), Venezia, Italy
| | - Pascal Laforêt
- From the Neuromuscular Center (C.S., L.B., C.B., E.P.), Department of Neurosciences, University of Padova, Italy; the Neuromuscular Clinic and Research Unit (J.V., J.R.D., N.W.), Department of Neurology, Rigshospitalet, University of Copenhagen, Denmark; Paris-Est Neuromuscular Center (T.S., B.E., P.L.), Institut of Myology, Pitié-Salpêtrière Hospital, Paris, France; the Department of Clinical Genetics (M.D.), University of Copenhagen, Rigshospitalet, Denmark; Laboratoire de Biochimie et Génétique Moléculaire (F.L.), Groupe Hospitalier Cochin, Paris, France; Cardiomyology and Medical Genetics (P.D., L.P.), Department of Experimental Medicine, Second University of Naples; and the IRCCS San Camillo (C.A.), Venezia, Italy.
| | - Elena Pegoraro
- From the Neuromuscular Center (C.S., L.B., C.B., E.P.), Department of Neurosciences, University of Padova, Italy; the Neuromuscular Clinic and Research Unit (J.V., J.R.D., N.W.), Department of Neurology, Rigshospitalet, University of Copenhagen, Denmark; Paris-Est Neuromuscular Center (T.S., B.E., P.L.), Institut of Myology, Pitié-Salpêtrière Hospital, Paris, France; the Department of Clinical Genetics (M.D.), University of Copenhagen, Rigshospitalet, Denmark; Laboratoire de Biochimie et Génétique Moléculaire (F.L.), Groupe Hospitalier Cochin, Paris, France; Cardiomyology and Medical Genetics (P.D., L.P.), Department of Experimental Medicine, Second University of Naples; and the IRCCS San Camillo (C.A.), Venezia, Italy.
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Guo G, Kang Q, Zhu X, Chen Q, Wang X, Chen Y, Ouyang J, Zhang L, Tan H, Chen R, Huang S, Chen JL. A long noncoding RNA critically regulates Bcr-Abl-mediated cellular transformation by acting as a competitive endogenous RNA. Oncogene 2014; 34:1768-79. [DOI: 10.1038/onc.2014.131] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 03/25/2014] [Accepted: 03/26/2014] [Indexed: 12/15/2022]
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Sikora KM, Nosavanh LM, Kantheti P, Burmeister M, Hortsch M. Expression of Caytaxin protein in Cayman Ataxia mouse models correlates with phenotype severity. PLoS One 2012; 7:e50570. [PMID: 23226316 PMCID: PMC3511541 DOI: 10.1371/journal.pone.0050570] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 10/22/2012] [Indexed: 02/06/2023] Open
Abstract
Caytaxin is a highly-conserved protein, which is encoded by the Atcay/ATCAY gene. Mutations in Atcay/ATCAY have been identified as causative of cerebellar disorders such as the rare hereditary disease Cayman ataxia in humans, generalized dystonia in the dystonic (dt) rat, and marked motor defects in three ataxic mouse lines. While several lines of evidence suggest that Caytaxin plays a critical role in maintaining nervous system processes, the physiological function of Caytaxin has not been fully characterized. In the study presented here, we generated novel specific monoclonal antibodies against full-length Caytaxin to examine endogenous Caytaxin expression in wild type and Atcay mutant mouse lines. Caytaxin protein is absent from brain tissues in the two severely ataxic Atcayjit (jittery) and Atcayswd (sidewinder) mutant lines, and markedly decreased in the mildly ataxic/dystonic Atcayji-hes (hesitant) line, indicating a correlation between Caytaxin expression and disease severity. As the expression of wild type human Caytaxin in mutant sidewinder and jittery mice rescues the ataxic phenotype, Caytaxin’s physiological function appears to be conserved between the human and mouse orthologs. Across multiple species and in several neuronal cell lines Caytaxin is expressed as several protein isoforms, the two largest of which are caused by the usage of conserved methionine translation start sites. The work described in this manuscript presents an initial characterization of the Caytaxin protein and its expression in wild type and several mutant mouse models. Utilizing these animal models of human Cayman Ataxia will now allow an in-depth analysis to elucidate Caytaxin’s role in maintaining normal neuronal function.
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Affiliation(s)
- Kristine M. Sikora
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- Molecular & Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - LaGina M. Nosavanh
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Prameela Kantheti
- Molecular & Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Margit Burmeister
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- Molecular & Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Psychiatry and Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Michael Hortsch
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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Semler O, Garbes L, Keupp K, Swan D, Zimmermann K, Becker J, Iden S, Wirth B, Eysel P, Koerber F, Schoenau E, Bohlander S, Wollnik B, Netzer C. A mutation in the 5'-UTR of IFITM5 creates an in-frame start codon and causes autosomal-dominant osteogenesis imperfecta type V with hyperplastic callus. Am J Hum Genet 2012; 91:349-57. [PMID: 22863195 DOI: 10.1016/j.ajhg.2012.06.011] [Citation(s) in RCA: 162] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Revised: 06/05/2012] [Accepted: 06/21/2012] [Indexed: 10/28/2022] Open
Abstract
Osteogenesis imperfecta (OI) is a clinically and genetically heterogeneous disorder associated with bone fragility and susceptibility to fractures after minimal trauma. OI type V has an autosomal-dominant pattern of inheritance and is not caused by mutations in the type I collagen genes COL1A1 and COL1A2. The most remarkable and pathognomonic feature, observed in ~65% of affected individuals, is a predisposition to develop hyperplastic callus after fractures or surgical interventions. To identify the molecular cause of OI type V, we performed whole-exome sequencing in a female with OI type V and her unaffected parents and searched for de novo mutations. We found a heterozygous de novo mutation in the 5'-untranslated region of IFITM5 (the gene encoding Interferon induced transmembrane protein 5), 14 bp upstream of the annotated translation initiation codon (c.-14C>T). Subsequently, we identified an identical heterozygous de novo mutation in a second individual with OI type V by Sanger sequencing, thereby confirming that this is the causal mutation for the phenotype. IFITM5 is a protein that is highly enriched in osteoblasts and has a putative function in bone formation and osteoblast maturation. The mutation c.-14C>T introduces an upstream start codon that is in frame with the reference open-reading frame of IFITM5 and is embedded into a stronger Kozak consensus sequence for translation initiation than the annotated start codon. In vitro, eukaryotic cells were able to recognize this start codon, and they used it instead of the reference translation initiation signal. This suggests that five amino acids (Met-Ala-Leu-Glu-Pro) are added to the N terminus and alter IFITM5 function in individuals with the mutation.
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Bali DS, Goldstein JL, Banugaria S, Dai J, Mackey J, Rehder C, Kishnani PS. Predicting cross-reactive immunological material (CRIM) status in Pompe disease using GAA mutations: lessons learned from 10 years of clinical laboratory testing experience. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2012; 160C:40-9. [PMID: 22252923 DOI: 10.1002/ajmg.c.31319] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Enzyme replacement therapy (ERT) for Pompe disease using recombinant acid alpha-glucosidase (rhGAA) has resulted in increased survival although the clinical response is variable. Cross-reactive immunological material (CRIM)-negative status has been recognized as a poor prognostic factor. CRIM-negative patients make no GAA protein and develop sustained high antibody titers to ERT that render the treatment ineffective. Antibody titers are generally low for the majority of CRIM-positive patients and there is typically a better clinical outcome. Because immunomodulation has been found to be most effective in CRIM-negative patients prior to, or shortly after, initiation of ERT, knowledge of CRIM status is important before ERT is begun. We have analyzed 243 patients with infantile Pompe disease using a Western blot method for determining CRIM status and using cultured skin fibroblasts. Sixty-one out of 243 (25.1%) patients tested from various ethnic backgrounds were found to be CRIM-negative. We then correlated the CRIM results with GAA gene mutations where available (52 CRIM-negative and 88 CRIM-positive patients). We found that, in most cases, CRIM status can be predicted from GAA mutations, potentially circumventing the need for invasive skin biopsy and time wasted in culturing cells in the future. Continued studies in this area will help to increase the power of GAA gene mutations in predicting CRIM status as well as possibly identifying CRIM-positive patients who are at risk for developing high antibody titers.
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Affiliation(s)
- Deeksha S Bali
- Duke Biochemical Genetics Laboratory, Durham, NC 27713, USA.
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37
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Identification and characterization of novel splice variants of the human EPM2A gene mutated in Lafora progressive myoclonus epilepsy. Genomics 2012; 99:36-43. [DOI: 10.1016/j.ygeno.2011.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 09/21/2011] [Accepted: 10/03/2011] [Indexed: 11/24/2022]
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Tzanis G, Berberidis C, Vlahavas I. StackTIS: A stacked generalization approach for effective prediction of translation initiation sites. Comput Biol Med 2012; 42:61-9. [DOI: 10.1016/j.compbiomed.2011.10.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Accepted: 10/20/2011] [Indexed: 10/15/2022]
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Maruyama Y, Kawamura Y, Nishikawa T, Isogai T, Nomura N, Goshima N. HGPD: Human Gene and Protein Database, 2012 update. Nucleic Acids Res 2011; 40:D924-9. [PMID: 22140100 PMCID: PMC3245012 DOI: 10.1093/nar/gkr1188] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Human Gene and Protein Database (HGPD; http://www.HGPD.jp/) is a unique database that stores information on a set of human Gateway entry clones in addition to protein expression and protein synthesis data. The HGPD was launched in November 2008, and 33,275 human Gateway entry clones have been constructed from the open reading frames (ORFs) of full-length cDNA, thus representing the largest collection in the world. Recently, research objectives have focused on the development of new medicines and the establishment of novel diagnostic methods and medical treatments. And, studies using proteins and protein information, which are closely related to gene function, have been undertaken. For this update, we constructed an additional 9974 human Gateway entry clones, giving a total of 43,249. This set of human Gateway entry clones was named the Human Proteome Expression Resource, known as the 'HuPEX'. In addition, we also classified the clones into 10 groups according to protein function. Moreover, in vivo cellular localization data of proteins for 32,651 human Gateway entry clones were included for retrieval from the HGPD. In 'Information Overview', which presents the search results, the ORF region of each cDNA is now displayed allowing the Gateway entry clones to be searched more easily.
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Affiliation(s)
- Yukio Maruyama
- National Institute of Advanced Industrial Science and Technology, Japan Biological Informatics Consortium, Aomi, Koto-ku, Tokyo 135-0064, Japan
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Matagne V, Mastronardi C, Shapiro RA, Dorsa DM, Ojeda SR. Hypothalamic expression of Eap1 is not directly controlled by ovarian steroids. Endocrinology 2009; 150:1870-8. [PMID: 19022886 PMCID: PMC2659281 DOI: 10.1210/en.2008-0779] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A gene termed EAP1 (enhanced at puberty 1) was recently identified as a transcriptional regulator of female neuroendocrine reproductive function. We have now used in vivo and in vitro assays, and the female rat as an animal model, to determine whether Eap1 gene expression is regulated by ovarian steroids. Eap1 mRNA abundance decreases in both the hypothalamus and cerebral cortex during the infantile-juvenile phases of development, but it increases selectively in the hypothalamus at puberty, suggesting that in contrast to the general decline in expression observed in immature animals, the region-specific increase in Eap1 mRNA levels that occurs at puberty might be elicited by ovarian steroids. This is, however, not the case, because hypothalamic Eap1 mRNA levels increase at the expected time of puberty in rats ovariectomized at the beginning of the juvenile period. Although a subpopulation of EAP1-containing cells in the medial basal hypothalamus (MBH) and preoptic area express estrogen receptor-alpha (ERalpha), the 5'-flanking region of the rat Eap1 (rEap1) gene does not contain a complete estrogen-responsive element, and no such estrogen-responsive element is detected within 100 kb of the rEap1 locus. Functional promoter assays showed that neither estradiol (E(2)) alone nor a combination of E(2) plus progesterone increases rEap1 gene transcription. Likewise, E(2) administered to ovariectomized immature rats elicited a robust surge of LH but increased neither preoptic area nor MBH Eap1 mRNA levels. E(2)/progesterone-treated rats showed a massive elevation in plasma LH but only a modest increase in Eap1 mRNA levels, limited to the MBH. These results indicate that hypothalamic Eap1 expression is not directly controlled by ovarian steroids and suggest that Eap1 expression increases at puberty driven by ovary-independent, centrally initiated events.
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Affiliation(s)
- Valerie Matagne
- Division of Neuroscience, Oregon National Primate Research Center/Oregon Health and Science University, Beaverton, Oregon 97006, USA
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Maruyama Y, Wakamatsu A, Kawamura Y, Kimura K, Yamamoto JI, Nishikawa T, Kisu Y, Sugano S, Goshima N, Isogai T, Nomura N. Human Gene and Protein Database (HGPD): a novel database presenting a large quantity of experiment-based results in human proteomics. Nucleic Acids Res 2009; 37:D762-6. [PMID: 19073703 PMCID: PMC2686585 DOI: 10.1093/nar/gkn872] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Completion of human genome sequencing has greatly accelerated functional genomic research. Full-length cDNA clones are essential experimental tools for functional analysis of human genes. In one of the projects of the New Energy and Industrial Technology Development Organization (NEDO) in Japan, the full-length human cDNA sequencing project (FLJ project), nucleotide sequences of approximately 30 000 human cDNA clones have been analyzed. The Gateway system is a versatile framework to construct a variety of expression clones for various experiments. We have constructed 33 275 human Gateway entry clones from full-length cDNAs, representing to our knowledge the largest collection in the world. Utilizing these clones with a highly efficient cell-free protein synthesis system based on wheat germ extract, we have systematically and comprehensively produced and analyzed human proteins in vitro. Sequence information for both amino acids and nucleotides of open reading frames of cDNAs cloned into Gateway entry clones and in vitro expression data using those clones can be retrieved from the Human Gene and Protein Database (HGPD, http://www.HGPD.jp). HGPD is a unique database that stores the information of a set of human Gateway entry clones and protein expression data and helps the user to search the Gateway entry clones.
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Affiliation(s)
- Yukio Maruyama
- Japan Biological Informatics Consortium, Aomi, Koto-ku, Tokyo 135-8073, Japan
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Sparks ME, Brendel V. MetWAMer: eukaryotic translation initiation site prediction. BMC Bioinformatics 2008; 9:381. [PMID: 18801175 PMCID: PMC2603428 DOI: 10.1186/1471-2105-9-381] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2008] [Accepted: 09/18/2008] [Indexed: 11/20/2022] Open
Abstract
Background Translation initiation site (TIS) identification is an important aspect of the gene annotation process, requisite for the accurate delineation of protein sequences from transcript data. We have developed the MetWAMer package for TIS prediction in eukaryotic open reading frames of non-viral origin. MetWAMer can be used as a stand-alone, third-party tool for post-processing gene structure annotations generated by external computational programs and/or pipelines, or directly integrated into gene structure prediction software implementations. Results MetWAMer currently implements five distinct methods for TIS prediction, the most accurate of which is a routine that combines weighted, signal-based translation initiation site scores and the contrast in coding potential of sequences flanking TISs using a perceptron. Also, our program implements clustering capabilities through use of the k-medoids algorithm, thereby enabling cluster-specific TIS parameter utilization. In practice, our static weight array matrix-based indexing method for parameter set lookup can be used with good results in data sets exhibiting moderate levels of 5'-complete coverage. Conclusion We demonstrate that improvements in statistically-based models for TIS prediction can be achieved by taking the class of each potential start-methionine into account pending certain testing conditions, and that our perceptron-based model is suitable for the TIS identification task. MetWAMer represents a well-documented, extensible, and freely available software system that can be readily re-trained for differing target applications and/or extended with existing and novel TIS prediction methods, to support further research efforts in this area.
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Affiliation(s)
- Michael E Sparks
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA.
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Faria-Campos AC, Moratelli FS, Mendes IK, Ortolani PL, Oliveira GC, Campos SVA, Ortega JM, Franco GR. Production of full-length cDNA sequences by sequencing and analysis of expressed sequence tags from Schistosoma mansoni. Mem Inst Oswaldo Cruz 2008; 101 Suppl 1:161-5. [PMID: 17308765 DOI: 10.1590/s0074-02762006000900026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2006] [Accepted: 06/26/2006] [Indexed: 11/21/2022] Open
Abstract
The number of sequences generated by genome projects has increased exponentially, but gene characterization has not followed at the same rate. Sequencing and analysis of full-length cDNAs is an important step in gene characterization that has been used nowadays by several research groups. In this work, we have selected Schistosoma mansoni clones for full-length sequencing, using an algorithm that investigates the presence of the initial methionine in the parasite sequence based on the positions of alignment start between two sequences. BLAST searches to produce such alignments have been performed using parasite expressed sequence tags produced by Minas Gerais Genome Network against sequences from the database Eukaryotic Cluster of Orthologous Groups (KOG). This procedure has allowed the selection of clones representing 398 proteins which have not been deposited as S. mansoni complete CDS in any public database. Dedicated sequencing of 96 of such clones with reads from both 5' and 3' ends has been performed. These reads have been assembled using PHRAP, resulting in the production of 33 full-length sequences that represent novel S. mansoni proteins. These results shall contribute to construct a more complete view of the biology of this important parasite.
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Affiliation(s)
- Alessandra C Faria-Campos
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, 31270-901 Belo Horzonte, MG, Brazil
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44
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Tzanis G, Berberidis C, Vlahavas I. MANTIS: A Data Mining Methodology for Effective Translation Initiation Site Prediction. ACTA ACUST UNITED AC 2007; 2007:6344-8. [DOI: 10.1109/iembs.2007.4353806] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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45
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Saeys Y, Abeel T, Degroeve S, Van de Peer Y. Translation initiation site prediction on a genomic scale: beauty in simplicity. Bioinformatics 2007; 23:i418-23. [PMID: 17646326 DOI: 10.1093/bioinformatics/btm177] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION The correct identification of translation initiation sites (TIS) remains a challenging problem for computational methods that automatically try to solve this problem. Furthermore, the lion's share of these computational techniques focuses on the identification of TIS in transcript data. However, in the gene prediction context the identification of TIS occurs on the genomic level, which makes things even harder because at the genome level many more pseudo-TIS occur, resulting in models that achieve a higher number of false positive predictions. RESULTS In this article, we evaluate the performance of several 'simple' TIS recognition methods at the genomic level, and compare them to state-of-the-art models for TIS prediction in transcript data. We conclude that the simple methods largely outperform the complex ones at the genomic scale, and we propose a new model for TIS recognition at the genome level that combines the strengths of these simple models. The new model obtains a false positive rate of 0.125 at a sensitivity of 0.80 on a well annotated human chromosome (chromosome 21). Detailed analyses show that the model is useful, both on its own and in a simple gene prediction setting. AVAILABILITY Datafiles and a web interface for the StartScan program are available at http://bioinformatics.psb.ugent.be/supplementary_data/.
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Affiliation(s)
- Yvan Saeys
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Ghent, Belgium.
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Lee B, Hong T, Byun SJ, Woo T, Choi YJ. ESTpass: a web-based server for processing and annotating expressed sequence tag (EST) sequences. Nucleic Acids Res 2007; 35:W159-62. [PMID: 17526512 PMCID: PMC1933161 DOI: 10.1093/nar/gkm369] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We present a web-based server, called ESTpass, for processing and annotating sequence data from expressed sequence tag (EST) projects. ESTpass accepts a FASTA-formatted EST file and its quality file as inputs, and it then executes a back-end EST analysis pipeline consisting of three consecutive steps. The first is cleansing the input EST sequences. The second is clustering and assembling the cleansed EST sequences using d2_cluster and CAP3 programs and producing putative transcripts. From the CAP3 output, ESTpass detects chimeric EST sequences which are confirmed through comparison with the nr database. The last step is annotating the putative transcript sequences using RefSeq, InterPro, GO and KEGG gene databases according to user-specified options. The major advantages of ESTpass are the integration of cleansing and annotating processes, rigorous chimeric EST detection, exhaustive annotation, and email reporting to inform the user about the progress and to send the analysis results. The ESTpass results include three reports (summary, cleansing and annotation) and download function, as well as graphic statistics. They can be retrieved and downloaded using a standard web browser. The server is available at http://estpass.kobic.re.kr/.
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Affiliation(s)
- Byungwook Lee
- Korean BioInformation Center, KRIBB, Daejeon 305-817, Korea, Department of BioSystems, KAIST, Daejeon 305-701, Korea and Bioinformatics team, Bioneer, 49-3 Munpyeong-dong, Daedeok-gu, Daejeon 306-220, Korea
| | - Taehui Hong
- Korean BioInformation Center, KRIBB, Daejeon 305-817, Korea, Department of BioSystems, KAIST, Daejeon 305-701, Korea and Bioinformatics team, Bioneer, 49-3 Munpyeong-dong, Daedeok-gu, Daejeon 306-220, Korea
| | - Sang Jin Byun
- Korean BioInformation Center, KRIBB, Daejeon 305-817, Korea, Department of BioSystems, KAIST, Daejeon 305-701, Korea and Bioinformatics team, Bioneer, 49-3 Munpyeong-dong, Daedeok-gu, Daejeon 306-220, Korea
| | - Taeha Woo
- Korean BioInformation Center, KRIBB, Daejeon 305-817, Korea, Department of BioSystems, KAIST, Daejeon 305-701, Korea and Bioinformatics team, Bioneer, 49-3 Munpyeong-dong, Daedeok-gu, Daejeon 306-220, Korea
| | - Yoon Jeong Choi
- Korean BioInformation Center, KRIBB, Daejeon 305-817, Korea, Department of BioSystems, KAIST, Daejeon 305-701, Korea and Bioinformatics team, Bioneer, 49-3 Munpyeong-dong, Daedeok-gu, Daejeon 306-220, Korea
- *To whom correspondence should be addressed. +82 42 879 8521+82-42-879-8519
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Prediction of Translation Initiation Sites Using Classifier Selection. ADVANCES IN ARTIFICIAL INTELLIGENCE 2006. [DOI: 10.1007/11752912_37] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Min XJ, Butler G, Storms R, Tsang A. TargetIdentifier: a webserver for identifying full-length cDNAs from EST sequences. Nucleic Acids Res 2005; 33:W669-72. [PMID: 15980559 PMCID: PMC1160197 DOI: 10.1093/nar/gki436] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
TargetIdentifier is a webserver that identifies full-length cDNA sequences from the expressed sequence tag (EST)-derived contig and singleton data. To accomplish this TargetIdentifier uses BLASTX alignments as a guide to locate protein coding regions and potential start and stop codons. This information is then used to determine whether the EST-derived sequences include their translation start codons. The algorithm also uses the BLASTX output to assign putative functions to the query sequences. The server is available at .
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Affiliation(s)
- Xiang Jia Min
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec H4B 1R6, Canada.
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Li GL, Leong TY. Feature selection for the prediction of translation initiation sites. GENOMICS, PROTEOMICS & BIOINFORMATICS 2005; 3:73-83. [PMID: 16393144 PMCID: PMC5172590 DOI: 10.1016/s1672-0229(05)03012-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Translation initiation sites (TISs) are important signals in cDNA sequences. In many previous attempts to predict TISs in cDNA sequences, three major factors affect the prediction performance: the nature of the cDNA sequence sets, the relevant features selected, and the classification methods used. In this paper, we examine different approaches to select and integrate relevant features for TIS prediction. The top selected significant features include the features from the position weight matrix and the propensity matrix, the number of nucleotide C in the sequence downstream ATG, the number of downstream stop codons, the number of upstream ATGs, and the number of some amino acids, such as amino acids A and D. With the numerical data generated from these features, different classification methods, including decision tree, naïve Bayes, and support vector machine, were applied to three independent sequence sets. The identified significant features were found to be biologically meaningful, while the experiments showed promising results.
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Affiliation(s)
- Guo Liang Li
- Medical Computing Laboratory, School of Computing, National University of Singapore.
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