1
|
Bidooki SH, Navarro MA, Fernandes SCM, Osada J. Thioredoxin Domain Containing 5 (TXNDC5): Friend or Foe? Curr Issues Mol Biol 2024; 46:3134-3163. [PMID: 38666927 PMCID: PMC11049379 DOI: 10.3390/cimb46040197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/25/2024] [Accepted: 03/30/2024] [Indexed: 04/28/2024] Open
Abstract
This review focuses on the thioredoxin domain containing 5 (TXNDC5), also known as endoplasmic reticulum protein 46 (ERp46), a member of the protein disulfide isomerase (PDI) family with a dual role in multiple diseases. TXNDC5 is highly expressed in endothelial cells, fibroblasts, pancreatic β-cells, liver cells, and hypoxic tissues, such as cancer endothelial cells and atherosclerotic plaques. TXNDC5 plays a crucial role in regulating cell proliferation, apoptosis, migration, and antioxidative stress. Its potential significance in cancer warrants further investigation, given the altered and highly adaptable metabolism of tumor cells. It has been reported that both high and low levels of TXNDC5 expression are associated with multiple diseases, such as arthritis, cancer, diabetes, brain diseases, and infections, as well as worse prognoses. TXNDC5 has been attributed to both oncogenic and tumor-suppressive features. It has been concluded that in cancer, TXNDC5 acts as a foe and responds to metabolic and cellular stress signals to promote the survival of tumor cells against apoptosis. Conversely, in normal cells, TXNDC5 acts as a friend to safeguard cells against oxidative and endoplasmic reticulum stress. Therefore, TXNDC5 could serve as a viable biomarker or even a potential pharmacological target.
Collapse
Affiliation(s)
- Seyed Hesamoddin Bidooki
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Veterinaria, Instituto de Investigación Sanitaria de Aragón, Universidad de Zaragoza, E-50013 Zaragoza, Spain; (S.H.B.); (M.A.N.)
- Centre National de la Recherche Scientifique (CNRS), Institute of Analytical Sciences and Physico-Chemistry for Environment and Materials (IPREM), Universite de Pau et des Pays de l’Adour, E2S UPPA, 64 000 Pau, France;
- MANTA—Marine Materials Research Group, Universite de Pau et des Pays de l’Adour, E2S UPPA, 64 600 Anglet, France
| | - María A. Navarro
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Veterinaria, Instituto de Investigación Sanitaria de Aragón, Universidad de Zaragoza, E-50013 Zaragoza, Spain; (S.H.B.); (M.A.N.)
- Instituto Agroalimentario de Aragón, CITA-Universidad de Zaragoza, E-50013 Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, E-28029 Madrid, Spain
| | - Susana C. M. Fernandes
- Centre National de la Recherche Scientifique (CNRS), Institute of Analytical Sciences and Physico-Chemistry for Environment and Materials (IPREM), Universite de Pau et des Pays de l’Adour, E2S UPPA, 64 000 Pau, France;
- MANTA—Marine Materials Research Group, Universite de Pau et des Pays de l’Adour, E2S UPPA, 64 600 Anglet, France
| | - Jesus Osada
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Veterinaria, Instituto de Investigación Sanitaria de Aragón, Universidad de Zaragoza, E-50013 Zaragoza, Spain; (S.H.B.); (M.A.N.)
- Instituto Agroalimentario de Aragón, CITA-Universidad de Zaragoza, E-50013 Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, E-28029 Madrid, Spain
| |
Collapse
|
2
|
Wirthlin ME, Schmid TA, Elie JE, Zhang X, Kowalczyk A, Redlich R, Shvareva VA, Rakuljic A, Ji MB, Bhat NS, Kaplow IM, Schäffer DE, Lawler AJ, Wang AZ, Phan BN, Annaldasula S, Brown AR, Lu T, Lim BK, Azim E, Clark NL, Meyer WK, Pond SLK, Chikina M, Yartsev MM, Pfenning AR, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements. Science 2024; 383:eabn3263. [PMID: 38422184 DOI: 10.1126/science.abn3263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/20/2024] [Indexed: 03/02/2024]
Abstract
Vocal production learning ("vocal learning") is a convergently evolved trait in vertebrates. To identify brain genomic elements associated with mammalian vocal learning, we integrated genomic, anatomical, and neurophysiological data from the Egyptian fruit bat (Rousettus aegyptiacus) with analyses of the genomes of 215 placental mammals. First, we identified a set of proteins evolving more slowly in vocal learners. Then, we discovered a vocal motor cortical region in the Egyptian fruit bat, an emergent vocal learner, and leveraged that knowledge to identify active cis-regulatory elements in the motor cortex of vocal learners. Machine learning methods applied to motor cortex open chromatin revealed 50 enhancers robustly associated with vocal learning whose activity tended to be lower in vocal learners. Our research implicates convergent losses of motor cortex regulatory elements in mammalian vocal learning evolution.
Collapse
Affiliation(s)
- Morgan E Wirthlin
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Tobias A Schmid
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94708, USA
| | - Julie E Elie
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94708, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94708, USA
| | - Xiaomeng Zhang
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Amanda Kowalczyk
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Ruby Redlich
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Varvara A Shvareva
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94708, USA
| | - Ashley Rakuljic
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94708, USA
| | - Maria B Ji
- Department of Psychology, University of California, Berkeley, Berkeley, CA 94708, USA
| | - Ninad S Bhat
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94708, USA
| | - Irene M Kaplow
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Daniel E Schäffer
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Alyssa J Lawler
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Andrew Z Wang
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - BaDoi N Phan
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Siddharth Annaldasula
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Ashley R Brown
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Tianyu Lu
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Byung Kook Lim
- Neurobiology section, Division of Biological Science, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eiman Azim
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Nathan L Clark
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Wynn K Meyer
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | | | - Maria Chikina
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Michael M Yartsev
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94708, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94708, USA
| | - Andreas R Pfenning
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
3
|
Tamura T, Shimojima Yamamoto K, Imaizumi T, Yamamoto H, Miyamoto Y, Yagasaki H, Morioka I, Kanno H, Yamamoto T. Breakpoint analysis for cytogenetically balanced translocation revealed unexpected complex structural abnormalities and suggested the position effect for MEF2C. Am J Med Genet A 2023; 191:1632-1638. [PMID: 36916329 DOI: 10.1002/ajmg.a.63182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/27/2023] [Accepted: 03/02/2023] [Indexed: 03/15/2023]
Abstract
Many disease-causing genes have been identified by determining the breakpoints of balanced chromosomal translocations. Recent progress in genomic analysis has accelerated the analysis of chromosomal translocation-breakpoints at the nucleotide level. Using a long-read whole-genome sequence, we analyzed the breakpoints of the cytogenetically balanced chromosomal translocation t(5;15)(q21;26.3), which was confirmed to be of de novo origin, in a patient with a neurodevelopmental disorder. The results showed complex rearrangements with seven fragments consisting of five breakpoint-junctions (BJs). Four of the five BJs showed microhomologies of 1-3-bp, and only one BJ displayed a signature of blunt-end ligation, indicating chromothripsis as the underlying mechanism. Although the BJs did not disrupt any disease-causing gene, the clinical features of the patient were compatible with MEF2C haploinsufficiency syndrome. Complex rearrangements were located approximately 2.5-Mb downstream of MEF2C. Therefore, position effects were considered the mechanism of the occurrence of MEF2C haploinsufficiency syndrome.
Collapse
Affiliation(s)
- Takeaki Tamura
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan.,Division of Gene Medicine, Graduate School of Medical Science, Tokyo Women's Medical University, Tokyo, Japan.,Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan
| | - Keiko Shimojima Yamamoto
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan.,Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Taichi Imaizumi
- Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Hisako Yamamoto
- Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yusaku Miyamoto
- Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Hiroshi Yagasaki
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| | - Ichiro Morioka
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| | - Hitoshi Kanno
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan.,Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Toshiyuki Yamamoto
- Division of Gene Medicine, Graduate School of Medical Science, Tokyo Women's Medical University, Tokyo, Japan.,Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| |
Collapse
|
4
|
Abstract
Thioredoxin domain-containing protein 5 (TXNDC5) is a member of the protein disulfide isomerase (PDI) family. It can promote the formation and rearrangement of disulfide bonds, ensuring proper protein folding. TXNDC5 has three Trx-like domains, which can act independently to introduce disulfide bonds rapidly and disorderly. TXNDC5 is abnormally expressed in various diseases, such as cancer, rheumatoid arthritis (RA), etc. It can protect cells from oxidative stress, promote cell proliferation, inhibit apoptosis and promote the progression of disease. Aberrant expression of TXNDC5 in different diseases suggests its role in disease diagnosis. In addition, targeting TXNDC5 in the treatment of diseases has shown promising application prospects. This article reviews the structure and function of TXNDC5 as well as its role and mechanism in cancer, RA and other diseases.
Collapse
Affiliation(s)
- Xueling Wang
- Medical Research Center of The Affiliated Hospital of Qingdao University, No 1677 Wutaishan Road, Huangdao District, Qingdao, China
| | - Haoran Li
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Qingdao University, No 16 Jiangsu Road, Qingdao, China
| | - Xiaotian Chang
- Medical Research Center of The Affiliated Hospital of Qingdao University, No 1677 Wutaishan Road, Huangdao District, Qingdao, China.
| |
Collapse
|
5
|
Poszewiecka B, Pienkowski VM, Nowosad K, Robin JD, Gogolewski K, Gambin A. TADeus2: a web server facilitating the clinical diagnosis by pathogenicity assessment of structural variations disarranging 3D chromatin structure. Nucleic Acids Res 2022; 50:W744-W752. [PMID: 35524567 PMCID: PMC9252839 DOI: 10.1093/nar/gkac318] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/12/2022] [Accepted: 04/21/2022] [Indexed: 01/01/2023] Open
Abstract
In recent years great progress has been made in identification of structural variants (SV) in the human genome. However, the interpretation of SVs, especially located in non-coding DNA, remains challenging. One of the reasons stems in the lack of tools exclusively designed for clinical SVs evaluation acknowledging the 3D chromatin architecture. Therefore, we present TADeus2 a web server dedicated for a quick investigation of chromatin conformation changes, providing a visual framework for the interpretation of SVs affecting topologically associating domains (TADs). This tool provides a convenient visual inspection of SVs, both in a continuous genome view as well as from a rearrangement’s breakpoint perspective. Additionally, TADeus2 allows the user to assess the influence of analyzed SVs within flaking coding/non-coding regions based on the Hi-C matrix. Importantly, the SVs pathogenicity is quantified and ranked using TADA, ClassifyCNV tools and sampling-based P-value. TADeus2 is publicly available at https://tadeus2.mimuw.edu.pl.
Collapse
Affiliation(s)
- Barbara Poszewiecka
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, 2 Banacha street, 02-097 Warsaw, Poland
| | - Victor Murcia Pienkowski
- Aix Marseille Univ, INSERM, Marseille Medical Genetics, MMG, Marseille, France.,Department of Medical Genetics, Medical University of Warsaw, Adolfa Pawińskiego 3c, 02-106 Warsaw, Poland
| | - Karol Nowosad
- Department of Cell Biology, Erasmus Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, Netherlands.,Department of Biomedical Sciences, Laboratory of Molecular Genetics, Medical University of Lublin, Doktora Witolda Chodźki 1, 20-400 Lublin, Poland.,The Postgraduate School of Molecular Medicine, Medical University of Warsaw, Żwirki i Wigury 61, 02-091 Warsaw, Poland
| | - Jérôme D Robin
- Aix Marseille Univ, INSERM, Marseille Medical Genetics, MMG, Marseille, France
| | - Krzysztof Gogolewski
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, 2 Banacha street, 02-097 Warsaw, Poland
| | - Anna Gambin
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, 2 Banacha street, 02-097 Warsaw, Poland
| |
Collapse
|
6
|
Argani P, Palsgrove DN, Anders RA, Smith SC, Saoud C, Kwon R, Voltaggio L, Assarzadegan N, Oshima K, Rooper L, Matoso A, Zhang L, Cantarel BL, Gagan J, Antonescu CR. A Novel NIPBL-NACC1 Gene Fusion Is Characteristic of the Cholangioblastic Variant of Intrahepatic Cholangiocarcinoma. Am J Surg Pathol 2021; 45:1550-1560. [PMID: 33999553 PMCID: PMC8516671 DOI: 10.1097/pas.0000000000001729] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
We report a novel NIPBL-NACC1 gene fusion in a rare primary hepatic neoplasm previously described as the "cholangioblastic variant of intrahepatic cholangiocarcinoma." The 2 index cases were identified within our consultation files as morphologically distinctive primary hepatic neoplasms in a 24-year-old female and a 54-year-old male. The neoplasms each demonstrated varied architecture, including trabecular, organoid, microcystic/follicular, and infiltrative glandular patterns, and biphasic cytology with large, polygonal eosinophilic cells and smaller basophilic cells. The neoplasms had a distinctive immunoprofile characterized by diffuse labeling for inhibin, and patchy labeling for neuroendocrine markers (chromogranin and synaptophysin) and biliary marker cytokeratin 19. RNA sequencing of both cases demonstrated an identical fusion of NIBPL exon 8 to NACC1 exon 2, which was further confirmed by break-apart fluorescence in situ hybridization assay for each gene. Review of a tissue microarray including 123 cases originally diagnosed as well-differentiated neuroendocrine neoplasm at one of our hospitals resulted in identification of a third case with similar morphology and immunophenotype in a 52-year-old male, and break-apart fluorescence in situ hybridization probes confirmed rearrangement of both NIPBL and NACC1. Review of The Cancer Genome Atlas (TCGA) sequencing data and digital images from 36 intrahepatic cholangiocarcinomas (www.cbioportal.org) revealed one additional case with the same gene fusion and the same characteristic solid, trabecular, and follicular/microcystic architectures and biphasic cytology as seen in our genetically confirmed cases. The NIPBL-NACC1 fusion represents the third type of gene fusion identified in intrahepatic cholangiocarcinoma, and correlates with a distinctive morphology described herein.
Collapse
Affiliation(s)
- Pedram Argani
- Departments of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Doreen N. Palsgrove
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Robert A. Anders
- Departments of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Steven C. Smith
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia
| | - Carla Saoud
- Departments of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Regina Kwon
- Departments of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Lysandra Voltaggio
- Departments of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Naziheh Assarzadegan
- Departments of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kiyoko Oshima
- Departments of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Lisa Rooper
- Departments of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Andres Matoso
- Departments of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Lei Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brandi L. Cantarel
- Bioinformatics Core Facility, Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jeffrey Gagan
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | |
Collapse
|
7
|
Sandal P, Jong CJ, Merrill RA, Song J, Strack S. Protein phosphatase 2A - structure, function and role in neurodevelopmental disorders. J Cell Sci 2021; 134:270819. [PMID: 34228795 DOI: 10.1242/jcs.248187] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Neurodevelopmental disorders (NDDs), including intellectual disability (ID), autism and schizophrenia, have high socioeconomic impact, yet poorly understood etiologies. A recent surge of large-scale genome or exome sequencing studies has identified a multitude of mostly de novo mutations in subunits of the protein phosphatase 2A (PP2A) holoenzyme that are strongly associated with NDDs. PP2A is responsible for at least 50% of total Ser/Thr dephosphorylation in most cell types and is predominantly found as trimeric holoenzymes composed of catalytic (C), scaffolding (A) and variable regulatory (B) subunits. PP2A can exist in nearly 100 different subunit combinations in mammalian cells, dictating distinct localizations, substrates and regulatory mechanisms. PP2A is well established as a regulator of cell division, growth, and differentiation, and the roles of PP2A in cancer and various neurodegenerative disorders, such as Alzheimer's disease, have been reviewed in detail. This Review summarizes and discusses recent reports on NDDs associated with mutations of PP2A subunits and PP2A-associated proteins. We also discuss the potential impact of these mutations on the structure and function of the PP2A holoenzymes and the etiology of NDDs.
Collapse
Affiliation(s)
- Priyanka Sandal
- Department of Neuroscience and Pharmacology, and Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa 52242, USA
| | - Chian Ju Jong
- Department of Neuroscience and Pharmacology, and Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa 52242, USA
| | - Ronald A Merrill
- Department of Neuroscience and Pharmacology, and Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa 52242, USA
| | - Jianing Song
- Department of Neuroscience and Pharmacology, and Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa 52242, USA
| | - Stefan Strack
- Department of Neuroscience and Pharmacology, and Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa 52242, USA
| |
Collapse
|
8
|
Jiménez de la Peña M, Jiménez de Domingo A, Tirado P, Calleja-Pérez B, Alcaraz LA, Álvarez S, Williams J, Hagman JR, Németh AH, Fernández-Jaén A. Neuroimaging Findings in Patients with EBF3 Mutations: Report of Two Cases. Mol Syndromol 2021; 12:186-193. [PMID: 34177436 DOI: 10.1159/000513583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 12/03/2020] [Indexed: 12/27/2022] Open
Abstract
Early B cell factor 3 (EBF3) is a transcription factor involved in brain development. Heterozygous, loss-of-function mutations in EBF3 have been reported in an autosomal dominant neurodevelopmental syndrome characterized by hypotonia, ataxia, and developmental delay (sometimes described as "HADD"s). We report 2 unrelated cases with novel de novo EBF3 mutations: c.455G>T (p.Arg152Leu) and c.962dup (p.Tyr321*) to expand the genotype/phenotype correlations of this disorder; clinical, neuropsychological, and MRI studies were used to define the phenotype. IQ was in the normal range and diffusion tensor imaging revealed asymmetric alterations of the longitudinal fasciculus in both cases. Our results demonstrate that EBF3 mutations can underlie neurodevelopmental disorders without intellectual disability. Long tract abnormalities have not been previously recognized and suggest that they may be an unrecognized and characteristic feature in this syndrome.
Collapse
Affiliation(s)
| | | | - Pilar Tirado
- Department of Pediatric Neurology, Hospital Universitario La Paz, Madrid, Spain
| | | | | | - Sara Álvarez
- Genomics and Medicine, NIMGenetics, Madrid, Spain
| | - Jonathan Williams
- Oxford Medical Genetics Laboratories, Churchill Hospital, Oxford, United Kingdom
| | - James R Hagman
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, USA
| | - Andrea H Németh
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom.,Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Alberto Fernández-Jaén
- Department of Pediatric Neurology, Hospital Universitario Quirónsalud, and Medicine School, Universidad Europea de Madrid, Madrid, Spain
| |
Collapse
|
9
|
Toraman B, Bilginer SÇ, Hesapçıoğlu ST, Göker Z, Soykam HO, Ergüner B, Dinçer T, Yıldız G, Ünsal S, Kasap BK, Kandil S, Kalay E. Finding underlying genetic mechanisms of two patients with autism spectrum disorder carrying familial apparently balanced chromosomal translocations. J Gene Med 2021; 23:e3322. [PMID: 33591602 DOI: 10.1002/jgm.3322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/26/2021] [Accepted: 02/14/2021] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Genetic etiologies of autism spectrum disorders (ASD) are complex, and the genetic factors identified so far are very diverse. In complex genetic diseases such as ASD, de novo or inherited chromosomal abnormalities are valuable findings for researchers with respect to identifying the underlying genetic risk factors. With gene mapping studies on these chromosomal abnormalities, dozens of genes have been associated with ASD and other neurodevelopmental genetic diseases. In the present study, we aimed to idenitfy the causative genetic factors in patients with ASD who have an apparently balanced chromosomal translocation in their karyotypes. METHODS For mapping the broken genes as a result of chromosomal translocations, we performed whole genome DNA sequencing. Chromosomal breakpoints and large DNA copy number variations (CNV) were determined after genome alignment. Identified CNVs and single nucleotide variations (SNV) were evaluated with VCF-BED intersect and Gemini tools, respectively. A targeted resequencing approach was performed on the JMJD1C gene in all of the ASD cohorts (220 patients). For molecular modeling, we used a homology modeling approach via the SWISS-MODEL. RESULTS We found that there was no contribution of the broken genes or regulator DNA sequences to ASD, whereas the SNVs on the JMJD1C, CNKSR2 and DDX11 genes were the most convincing genetic risk factors for underlying ASD phenotypes. CONCLUSIONS Genetic etiologies of ASD should be analyzed comprehensively by taking into account of the all chromosomal structural abnormalities and de novo or inherited CNV/SNVs with all possible inheritance patterns.
Collapse
Affiliation(s)
- Bayram Toraman
- Faculty of Medicine Department of Medical Biology, Karadeniz Technical University, Trabzon, Turkey
| | - Samiye Çilem Bilginer
- Faculty of Medicine Child and Adolescent Psychiatry Department, Karadeniz Technical University, Trabzon, Turkey
| | - Selma Tural Hesapçıoğlu
- Child and Adolescent Psychiatry Department, Yildirim Beyazit University Faculty of Medicine, Ankara, Turkey
| | - Zeynep Göker
- Ministry of Health Ankara City Hospital, Child-Adolescent and Mental Health, Cankaya, Ankara, Turkey
| | - Hüseyin Okan Soykam
- Department of Biostatistics and Bioinformatics, Acibadem Mehmet Ali Aydinlar University, Institute of Health Sciences, İstanbul, Turkey
| | - Bekir Ergüner
- Sabanci University Faculty of Engineering and Natural Sciences, Molecular Biology, Genetics and Bio engineering, Istanbul, Turkey
| | - Tuba Dinçer
- Faculty of Medicine Department of Medical Biology, Karadeniz Technical University, Trabzon, Turkey
| | - Gökhan Yıldız
- Faculty of Medicine Department of Medical Biology, Karadeniz Technical University, Trabzon, Turkey
| | - Serbülent Ünsal
- Graduate School of Health Science, Biostatistics and Medical Informatics Department, PhD Candidate, Karadeniz Technical University, Trabzon, Turkey
| | - Burak Kaan Kasap
- Graduate School of Health Science, Medical Biology Department, PhD Candidate, Karadeniz Technical University, Trabzon, Turkey
| | - Sema Kandil
- Faculty of Medicine Child and Adolescent Psychiatry Department, Karadeniz Technical University, Trabzon, Turkey
| | - Ersan Kalay
- Faculty of Medicine Department of Medical Biology, Karadeniz Technical University, Trabzon, Turkey
| |
Collapse
|
10
|
Bao M, Zhang L, Hu Y. Novel gene signatures for prognosis prediction in ovarian cancer. J Cell Mol Med 2020; 24:9972-9984. [PMID: 32666642 PMCID: PMC7520318 DOI: 10.1111/jcmm.15601] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 06/01/2020] [Accepted: 06/07/2020] [Indexed: 12/24/2022] Open
Abstract
Ovarian cancer (OV) is one of the leading causes of cancer deaths in women worldwide. Late diagnosis and heterogeneous treatment result to poor survival outcomes for patients with OV. Therefore, we aimed to develop novel biomarkers for prognosis prediction from the potential molecular mechanism of tumorigenesis. Eight eligible data sets related to OV in GEO database were integrated to identify differential expression genes (DEGs) between tumour tissues and normal. Enrichment analyses discovered DEGs were most significantly enriched in G2/M checkpoint signalling pathway. Subsequently, we constructed a multi‐gene signature based on the LASSO Cox regression model in the TCGA database and time‐dependent ROC curves showed good predictive accuracy for 1‐, 3‐ and 5‐year overall survival. Utility in various types of OV was validated through subgroup survival analysis. Risk scores formulated by the multi‐gene signature stratified patients into high‐risk and low‐risk, and the former inclined worse overall survival than the latter. By incorporating this signature with age and pathological tumour stage, a visual predictive nomogram was established, which was useful for clinicians to predict survival outcome of patients. Furthermore, SNRPD1 and EFNA5 were selected from the multi‐gene signature as simplified prognostic indicators. Higher EFNA5 expression or lower SNRPD1 indicated poorer outcome. The correlation between signature gene expression and clinical characteristics was observed through WGCNA. Drug‐gene interaction was used to identify 16 potentially targeted drugs for OV treatment. In conclusion, we established novel gene signatures as independent prognostic factors to stratify the risk of OV patients and facilitate the implementation of personalized therapies.
Collapse
Affiliation(s)
- Mingyang Bao
- State Key Laboratory of Genetic Engineering, Institute of Biostatistics, School of Life Sciences, Fudan University, Shanghai, China
| | - Lihua Zhang
- Department of Gynecology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, China
| | - Yueqing Hu
- State Key Laboratory of Genetic Engineering, Institute of Biostatistics, School of Life Sciences, Fudan University, Shanghai, China.,Shanghai Center for Mathematical Sciences, Fudan University, Shanghai, China
| |
Collapse
|
11
|
Pourpre R, Naudon L, Meziane H, Lakisic G, Jouneau L, Varet H, Legendre R, Wendling O, Selloum M, Proux C, Coppée JY, Herault Y, Bierne H. BAHD1 haploinsufficiency results in anxiety-like phenotypes in male mice. PLoS One 2020; 15:e0232789. [PMID: 32407325 PMCID: PMC7224496 DOI: 10.1371/journal.pone.0232789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/21/2020] [Indexed: 02/07/2023] Open
Abstract
BAHD1 is a heterochomatinization factor recently described as a component of a multiprotein complex associated with histone deacetylases HDAC1/2. The physiological and patho-physiological functions of BAHD1 are not yet well characterized. Here, we examined the consequences of BAHD1 deficiency in the brains of male mice. While Bahd1 knockout mice had no detectable defects in brain anatomy, RNA sequencing profiling revealed about 2500 deregulated genes in Bahd1-/- brains compared to Bahd1+/+ brains. A majority of these genes were involved in nervous system development and function, behavior, metabolism and immunity. Exploration of the Allen Brain Atlas and Dropviz databases, assessing gene expression in the brain, revealed that expression of the Bahd1 gene was limited to a few territories and cell subtypes, particularly in the hippocampal formation, the isocortex and the olfactory regions. The effect of partial BAHD1 deficiency on behavior was then evaluated on Bahd1 heterozygous male mice, which have no lethal or metabolic phenotypes. Bahd1+/- mice showed anxiety-like behavior and reduced prepulse inhibition (PPI) of the startle response. Altogether, these results suggest that BAHD1 plays a role in chromatin-dependent gene regulation in a subset of brain cells and support recent evidence linking genetic alteration of BAHD1 to psychiatric disorders in a human patient.
Collapse
Affiliation(s)
- Renaud Pourpre
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Laurent Naudon
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- Micalis Institute, Université Paris-Saclay, CNRS, INRAE, AgroParisTech, Jouy-en-Josas, France
| | - Hamid Meziane
- Institut Clinique de la Souris-ICS, Université de Strasbourg, CNRS, INSERM, PHENOMIN, Illkirch, France
| | - Goran Lakisic
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Luc Jouneau
- Université Paris-Saclay, INRAE, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Hugo Varet
- Institut Pasteur, Bioinformatics and Biostatistics Hub, C3BI, USR 3756 IP CNRS, Paris, France
- Institut Pasteur, Transcriptome and Epigenome Platform, Biomics Pole, Paris, France
| | - Rachel Legendre
- Institut Pasteur, Bioinformatics and Biostatistics Hub, C3BI, USR 3756 IP CNRS, Paris, France
- Institut Pasteur, Transcriptome and Epigenome Platform, Biomics Pole, Paris, France
| | - Olivia Wendling
- Institut Clinique de la Souris-ICS, Université de Strasbourg, CNRS, INSERM, PHENOMIN, Illkirch, France
| | - Mohammed Selloum
- Institut Clinique de la Souris-ICS, Université de Strasbourg, CNRS, INSERM, PHENOMIN, Illkirch, France
| | - Caroline Proux
- Institut Pasteur, Transcriptome and Epigenome Platform, Biomics Pole, Paris, France
| | - Jean-Yves Coppée
- Institut Pasteur, Transcriptome and Epigenome Platform, Biomics Pole, Paris, France
| | - Yann Herault
- Institut Clinique de la Souris-ICS, Université de Strasbourg, CNRS, INSERM, PHENOMIN, Illkirch, France
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique Biologie Moléculaire et Cellulaire (IGBMC), UMR7104, U1268, Illkirch, France
| | - Hélène Bierne
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| |
Collapse
|
12
|
Murcia Pienkowski V, Kucharczyk M, Rydzanicz M, Poszewiecka B, Pachota K, Młynek M, Stawiński P, Pollak A, Kosińska J, Wojciechowska K, Lejman M, Cieślikowska A, Wicher D, Stembalska A, Matuszewska K, Materna-Kiryluk A, Gambin A, Chrzanowska K, Krajewska-Walasek M, Płoski R. Breakpoint Mapping of Symptomatic Balanced Translocations Links the EPHA6, KLF13 and UBR3 Genes to Novel Disease Phenotype. J Clin Med 2020; 9:jcm9051245. [PMID: 32344861 PMCID: PMC7287862 DOI: 10.3390/jcm9051245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/19/2020] [Accepted: 04/23/2020] [Indexed: 12/18/2022] Open
Abstract
De novo balanced chromosomal aberrations (BCAs), such as reciprocal translocations and inversions, are genomic aberrations that, in approximately 25% of cases, affect the human phenotype. Delineation of the exact structure of BCAs may provide a precise diagnosis and/or point to new disease loci. We report on six patients with de novo balanced chromosomal translocations (BCTs) and one patient with a de novo inversion, in whom we mapped breakpoints to a resolution of 1 bp, using shallow whole-genome mate pair sequencing. In all seven cases, a disruption of at least one gene was found. In two patients, the phenotypic impact of the disrupted genes is well known (NFIA, ATP7A). In five patients, the aberration damaged genes: PARD3, EPHA6, KLF13, STK24, UBR3, MLLT10 and TLE3, whose influence on the human phenotype is poorly understood. In particular, our results suggest novel candidate genes for retinal degeneration with anophthalmia (EPHA6), developmental delay with speech impairment (KLF13), and developmental delay with brain dysembryoplastic neuroepithelial tumor (UBR3). In conclusion, identification of the exact structure of symptomatic BCTs using next generation sequencing is a viable method for both diagnosis and finding novel disease candidate genes in humans.
Collapse
Affiliation(s)
- Victor Murcia Pienkowski
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (V.M.P.); (M.R.); (P.S.); (A.P.); (J.K.)
| | - Marzena Kucharczyk
- Department of Medical Genetics, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.K.); (K.P.); (M.M.); (A.C.); (D.W.); (K.C.); (M.K.-W.)
| | - Małgorzata Rydzanicz
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (V.M.P.); (M.R.); (P.S.); (A.P.); (J.K.)
| | - Barbara Poszewiecka
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, 02-097 Warsaw, Poland; (B.P.); (A.G.)
| | - Katarzyna Pachota
- Department of Medical Genetics, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.K.); (K.P.); (M.M.); (A.C.); (D.W.); (K.C.); (M.K.-W.)
| | - Marlena Młynek
- Department of Medical Genetics, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.K.); (K.P.); (M.M.); (A.C.); (D.W.); (K.C.); (M.K.-W.)
| | - Piotr Stawiński
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (V.M.P.); (M.R.); (P.S.); (A.P.); (J.K.)
| | - Agnieszka Pollak
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (V.M.P.); (M.R.); (P.S.); (A.P.); (J.K.)
| | - Joanna Kosińska
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (V.M.P.); (M.R.); (P.S.); (A.P.); (J.K.)
| | - Katarzyna Wojciechowska
- Department of Pediatric Hematology Oncology and Transplantology, University Children’s Hospital, 20-093 Lublin, Poland;
| | - Monika Lejman
- Department of Pediatric Hematology Oncology and Transplantology, Medical University of Lublin, 20-093 Lublin, Poland;
| | - Agata Cieślikowska
- Department of Medical Genetics, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.K.); (K.P.); (M.M.); (A.C.); (D.W.); (K.C.); (M.K.-W.)
| | - Dorota Wicher
- Department of Medical Genetics, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.K.); (K.P.); (M.M.); (A.C.); (D.W.); (K.C.); (M.K.-W.)
| | | | - Karolina Matuszewska
- Department of Medical Genetics, University of Medical Sciences, 60-806 Poznan, Poland; (K.M.); (A.M.-K.)
- Centers for Medical Genetics GENESIS, Grudzieniec, 60-406 Poznan, Poland
| | - Anna Materna-Kiryluk
- Department of Medical Genetics, University of Medical Sciences, 60-806 Poznan, Poland; (K.M.); (A.M.-K.)
- Centers for Medical Genetics GENESIS, Grudzieniec, 60-406 Poznan, Poland
| | - Anna Gambin
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, 02-097 Warsaw, Poland; (B.P.); (A.G.)
| | - Krystyna Chrzanowska
- Department of Medical Genetics, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.K.); (K.P.); (M.M.); (A.C.); (D.W.); (K.C.); (M.K.-W.)
| | - Małgorzata Krajewska-Walasek
- Department of Medical Genetics, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.K.); (K.P.); (M.M.); (A.C.); (D.W.); (K.C.); (M.K.-W.)
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (V.M.P.); (M.R.); (P.S.); (A.P.); (J.K.)
- Correspondence: ; Tel.: +48-22-572-06-95; Fax: +48-22-572-06-96
| |
Collapse
|
13
|
Affiliation(s)
- Hanno J. Bolz
- Aff1 Senckenberg Zentrum für Humangenetik Frankfurt am Main Deutschland
| | - Alexander Hoischen
- Aff2 0000 0004 0444 9382 grid.10417.33 Department of Human Genetics & Department of Internal Medicine, Radboud Institute of Medical Life Sciences Radboud University Medical Center Nijmegen Niederlande
| |
Collapse
|