1
|
Li C, Lin Y, Chen Y, Song X, Zheng X, Li J, He J, Chen X, Huang C, Wang W, Wu J, Wu J, Gao J, Tu Z, Li XJ, Yan S, Li S. A Specific Mini-Intrabody Mediates Lysosome Degradation of Mutant Huntingtin. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301120. [PMID: 37688357 PMCID: PMC10625127 DOI: 10.1002/advs.202301120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 08/01/2023] [Indexed: 09/10/2023]
Abstract
Accumulation of misfolded proteins leads to many neurodegenerative diseases that can be treated by lowering or removing mutant proteins. Huntington's disease (HD) is characterized by the intracellular accumulation of mutant huntingtin (mHTT) that can be soluble and aggregated in the central nervous system and causes neuronal damage and death. Here, an intracellular antibody (intrabody) fragment is generated that can specifically bind mHTT and link to the lysosome for degradation. It is found that delivery of this peptide by either brain injection or intravenous administration can efficiently clear the soluble and aggregated mHTT by activating the lysosomal degradation pathway, resulting in amelioration of gliosis and dyskinesia in HD knock-in (KI-140Q) mice. These findings suggest that the small intrabody peptide linked to lysosomes can effectively lower mutant proteins and provide a new approach for treating neurodegenerative diseases that are caused by the accumulation of mutant proteins.
Collapse
Affiliation(s)
- Caijuan Li
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), GHM Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Yingqi Lin
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), GHM Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Yizhi Chen
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), GHM Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Xichen Song
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), GHM Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Xiao Zheng
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), GHM Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Jiawei Li
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), GHM Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Jun He
- Institute of Laboratory Animal Science, Jinan University, Guangzhou, 510632, China
| | - Xiusheng Chen
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), GHM Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Chunhui Huang
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), GHM Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Wei Wang
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), GHM Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Jianhao Wu
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), GHM Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Jiaxi Wu
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), GHM Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Jiale Gao
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), GHM Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Zhuchi Tu
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), GHM Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Xiao-Jiang Li
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), GHM Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Sen Yan
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), GHM Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Shihua Li
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), GHM Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| |
Collapse
|
2
|
Comorbidities and clinical outcomes in adult- and juvenile-onset Huntington's disease: a study of linked Swedish National Registries (2002-2019). J Neurol 2023; 270:864-876. [PMID: 36253622 PMCID: PMC9886595 DOI: 10.1007/s00415-022-11418-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 09/30/2022] [Accepted: 10/02/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND Huntington's disease (HD) is a rare, neurodegenerative disease and its complex motor, cognitive and psychiatric symptoms exert a lifelong clinical burden on both patients and their families. OBJECTIVE To describe the clinical burden and natural history of HD. METHODS This longitudinal cohort study used data from the linked Swedish national registries to describe the occurrence of comorbidities (acute and chronic), symptomatic treatments and mortality in an incident cohort of individuals who either received the first diagnosis of HD above (adult onset HD; AoHD) or below (juvenile-onset HD; JoHD) 20 years of age, compared with a matched cohort without HD from the general population. Disease burden of all individuals alive in Sweden was described during a single calendar year (2018), including the occurrence of key symptoms, treatments and hospitalizations. RESULTS The prevalence of HD in 2018 was approximately 10.2 per 100,000. Of 1492 individuals with a diagnosis of HD during 2002 and 2018, 1447 had AoHD and 45 had JoHD. Individuals with AoHD suffered a higher incidence of obsessive-compulsive disorder, acute psychotic episodes, pneumonia, constipation and fractures compared with matched controls. Individuals with JoHD had higher incidence rates of epilepsy, constipation and acute respiratory symptoms. Median time to all-cause mortality in AoHD was 12.1 years from diagnosis. Patients alive with HD in Sweden in 2018 displayed a pattern of increased clinical burden for a number of years since diagnosis. CONCLUSIONS This study demonstrates the significant and progressive clinical burden in individuals with HD and presents novel insights into the natural history of JoHD.
Collapse
|
3
|
Freischel AR, Teer JK, Luddy K, Cunningham J, Artzy-Randrup Y, Epstein T, Tsai KY, Berglund A, Cleveland JL, Gillies RJ, Brown JS, Gatenby RA. Evolutionary Analysis of TCGA Data Using Over- and Under- Mutated Genes Identify Key Molecular Pathways and Cellular Functions in Lung Cancer Subtypes. Cancers (Basel) 2022; 15:18. [PMID: 36612014 PMCID: PMC9817988 DOI: 10.3390/cancers15010018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/30/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Abstract
We identify critical conserved and mutated genes through a theoretical model linking a gene’s fitness contribution to its observed mutational frequency in a clinical cohort. “Passenger” gene mutations do not alter fitness and have mutational frequencies determined by gene size and the mutation rate. Driver mutations, which increase fitness (and proliferation), are observed more frequently than expected. Non-synonymous mutations in essential genes reduce fitness and are eliminated by natural selection resulting in lower prevalence than expected. We apply this “evolutionary triage” principle to TCGA data from EGFR-mutant, KRAS-mutant, and NEK (non-EGFR/KRAS) lung adenocarcinomas. We find frequent overlap of evolutionarily selected non-synonymous gene mutations among the subtypes suggesting enrichment for adaptations to common local tissue selection forces. Overlap of conserved genes in the LUAD subtypes is rare suggesting negative evolutionary selection is strongly dependent on initiating mutational events during carcinogenesis. Highly expressed genes are more likely to be conserved and significant changes in expression (>20% increased/decreased) are common in genes with evolutionarily selected mutations but not in conserved genes. EGFR-mut cancers have fewer average mutations (89) than KRAS-mut (228) and NEK (313). Subtype-specific variation in conserved and mutated genes identify critical molecular components in cell signaling, extracellular matrix remodeling, and membrane transporters. These findings demonstrate subtype-specific patterns of co-adaptations between the defining driver mutation and somatically conserved genes as well as novel insights into epigenetic versus genetic contributions to cancer evolution.
Collapse
Affiliation(s)
- Audrey R. Freischel
- Departments of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
- Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Jamie K. Teer
- Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
- Departments of Tumor Biology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Kimberly Luddy
- Departments of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Jessica Cunningham
- Departments of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Yael Artzy-Randrup
- Departments of Cancer Physiology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Tamir Epstein
- Departments of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Kenneth Y. Tsai
- Departments of Tumor Biology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
- Departments of Cancer Physiology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Anders Berglund
- Departments of Tumor Biology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - John L. Cleveland
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Robert J. Gillies
- Departments of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
- Departments of Pathology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
- Department of Diagnostic Imaging & Interventional Radiology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Joel S. Brown
- Departments of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
- Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Robert A. Gatenby
- Departments of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
- Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
- Department of Diagnostic Imaging & Interventional Radiology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| |
Collapse
|
4
|
Chan LL, Hill A, Lu G, Van Raamsdonk J, Gascoyne R, Hayden MR, Leavitt BR. Huntingtin Overexpression Does Not Alter Overall Survival in Murine Cancer Models. J Huntingtons Dis 2022; 11:383-389. [PMID: 36442204 DOI: 10.3233/jhd-220554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A reduced incidence of various forms of cancer has been reported in Huntington's disease patients and may be due to pro-apoptotic effects of mutant huntingtin. We tested this hypothesis by assessing the effects of huntingtin protein overexpression on survival in two murine cancer models. We generated YAC HD mice containing human huntingtin transgenes with various CAG tract lengths (YAC18, YAC72, YAC128) on either an Msh2 or p53 null background which have increased cancer incidence. In both mouse models of cancer, the overexpression of either mutant or wild-type huntingtin had no significant effect on overall survival. These results do not support the hypothesis that mutant huntingtin expression is protective against cancer.
Collapse
Affiliation(s)
- Laura Lynn Chan
- Department of Medical Genetics and Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Austin Hill
- Department of Medical Genetics and Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Ge Lu
- Department of Medical Genetics and Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Jeremy Van Raamsdonk
- Laboratory of Aging and Neurodegenerative Disease, Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, USA.,Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada.,Metabolic Disorders and Complications Program, and Brain Repair and Integrative Neuroscience Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Randy Gascoyne
- Center for Lymphoid Cancer, British Columbia Cancer, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Michael R Hayden
- Department of Medical Genetics and Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Blair R Leavitt
- Department of Medical Genetics and Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
5
|
dos Santos FRC, Guardia GDA, dos Santos FF, Ohara D, Galante PAF. Reboot: a straightforward approach to identify genes and splicing isoforms associated with cancer patient prognosis. NAR Cancer 2021; 3:zcab024. [PMID: 34316711 PMCID: PMC8210018 DOI: 10.1093/narcan/zcab024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/26/2021] [Accepted: 06/03/2021] [Indexed: 12/20/2022] Open
Abstract
Nowadays, the massive amount of data generated by modern sequencing technologies provides an unprecedented opportunity to find genes associated with cancer patient prognosis, connecting basic and translational research. However, treating high dimensionality of gene expression data and integrating it with clinical variables are major challenges to perform these analyses. Here, we present Reboot, an integrative approach to find and validate genes and transcripts (splicing isoforms) associated with cancer patient prognosis from high dimensional expression datasets. Reboot innovates by using a multivariate strategy with penalized Cox regression (LASSO method) combined with a bootstrap approach, in addition to statistical tests and plots to support the findings. Applying Reboot on data from 154 glioblastoma patients, we identified a three-gene signature (IKBIP, OSMR, PODNL1) whose increased derived risk score was significantly associated with worse patients' prognosis. Similarly, Reboot was able to find a seven-splicing isoforms signature related to worse overall survival in 177 pancreatic adenocarcinoma patients with elevated risk scores after uni- and multivariate analyses. In summary, Reboot is an efficient, intuitive and straightforward way of finding genes or splicing isoforms signatures relevant to patient prognosis, which can democratize this kind of analysis and shed light on still under-investigated cancer-related genes and splicing isoforms.
Collapse
Affiliation(s)
- Felipe R C dos Santos
- Centro de Oncologia Molecular, Hospital Sirio-Libanes, Sao Paulo, SP 01308-060, Brazil
- Programa Interunidades em Bioinformatica, Universidade de São Paulo, Sao Paulo, SP 05508-090, Brazil
| | - Gabriela D A Guardia
- Centro de Oncologia Molecular, Hospital Sirio-Libanes, Sao Paulo, SP 01308-060, Brazil
| | - Filipe F dos Santos
- Centro de Oncologia Molecular, Hospital Sirio-Libanes, Sao Paulo, SP 01308-060, Brazil
- Departamento de Bioquimica, Universidade de Sao Paulo, SP 05508-000, Brazil
| | - Daniel T Ohara
- Centro de Oncologia Molecular, Hospital Sirio-Libanes, Sao Paulo, SP 01308-060, Brazil
| | - Pedro A F Galante
- Centro de Oncologia Molecular, Hospital Sirio-Libanes, Sao Paulo, SP 01308-060, Brazil
| |
Collapse
|
6
|
Tan X, Liu Y, Liu Y, Zhang T, Cong S. Dysregulation of long non-coding RNAs and their mechanisms in Huntington's disease. J Neurosci Res 2021; 99:2074-2090. [PMID: 34031910 DOI: 10.1002/jnr.24825] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 01/19/2021] [Accepted: 02/26/2021] [Indexed: 12/31/2022]
Abstract
Extensive alterations in gene regulatory networks are a typical characteristic of Huntington's disease (HD); these include alterations in protein-coding genes and poorly understood non-coding RNAs (ncRNAs), which are associated with pathology caused by mutant huntingtin. Long non-coding RNAs (lncRNAs) are an important class of ncRNAs involved in a variety of biological functions, including transcriptional regulation and post-transcriptional modification of many targets, and likely contributed to the pathogenesis of HD. While a number of changes in lncRNAs expression have been observed in HD, little is currently known about their functions. Here, we discuss their possible mechanisms and molecular functions, with a particular focus on their roles in transcriptional regulation. These findings give us a better insight into HD pathogenesis and may provide new targets for the treatment of this neurodegenerative disease.
Collapse
Affiliation(s)
- Xiaoping Tan
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, P.R. China
| | - Yang Liu
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, P.R. China
| | - Yan Liu
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, P.R. China
| | - Taiming Zhang
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, P.R. China
| | - Shuyan Cong
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, P.R. China
| |
Collapse
|
7
|
Marquilly C, Busto GU, Leger BS, Boulanger A, Giniger E, Walker JA, Fradkin LG, Dura JM. Htt is a repressor of Abl activity required for APP-induced axonal growth. PLoS Genet 2021; 17:e1009287. [PMID: 33465062 PMCID: PMC7845969 DOI: 10.1371/journal.pgen.1009287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 01/29/2021] [Accepted: 11/18/2020] [Indexed: 11/18/2022] Open
Abstract
Huntington’s disease is a progressive autosomal dominant neurodegenerative disorder caused by the expansion of a polyglutamine tract at the N-terminus of a large cytoplasmic protein. The Drosophila huntingtin (htt) gene is widely expressed during all developmental stages from embryos to adults. However, Drosophila htt mutant individuals are viable with no obvious developmental defects. We asked if such defects could be detected in htt mutants in a background that had been genetically sensitized to reveal cryptic developmental functions. Amyloid precursor protein (APP) is linked to Alzheimer’s disease. Appl is the Drosophila APP ortholog and Appl signaling modulates axon outgrowth in the mushroom bodies (MBs), the learning and memory center in the fly, in part by recruiting Abl tyrosine kinase. Here, we find that htt mutations suppress axon outgrowth defects of αβ neurons in Appl mutant MB by derepressing the activity of Abl. We show that Abl is required in MB αβ neurons for their axon outgrowth. Importantly, both Abl overexpression and lack of expression produce similar phenotypes in the MBs, indicating the necessity of tightly regulating Abl activity. We find that Htt behaves genetically as a repressor of Abl activity, and consistent with this, in vivo FRET-based measurements reveal a significant increase in Abl kinase activity in the MBs when Htt levels are reduced. Thus, Appl and Htt have essential but opposing roles in MB development, promoting and suppressing Abl kinase activity, respectively, to maintain the appropriate intermediate level necessary for axon growth. Understanding the normal physiological roles of proteins involved in neurodegenerative diseases can provide significant insight into disease mechanisms. Drosophila offers a powerful system in which to ask these fundamental questions. Both Htt, related to Huntington’s disease, and Appl, related to Alzheimer’s disease, have well-conserved single orthologs in the fly genome. Appl has been shown to be a conserved modulator of a Wnt-PCP signaling pathway required for axon outgrowth in the mushroom body (MB) in the Drosophila brain. However, roles for Htt in fly brain development have not been reported. Unexpectedly, we found that htt mutations suppress the axon outgrowth defects of Appl mutants in the MB, indicating a link between these two neurodegenerative proteins and a cryptic role of Htt during development. Abl tyrosine kinase is a downstream effector of the Appl receptor, and we show here that Abl is also required for MB axon outgrowth. Importantly, Abl activity must be tightly regulated as evidenced by our observations that both under and overexpression of Abl result in similar axonal defects. We demonstrate that Htt is an inhibitor of Abl activity and provide evidence that the phenotypic rescue of αβ axons in Appl mutants by reducing htt is mediated by the restoration of proper levels of Abl signaling. These data, therefore, suggest that Appl and Htt act antagonistically to maintain an optimal balance of activation and inhibition of Abl, and thereby promote the growth of MB αβ axons.
Collapse
Affiliation(s)
- Claire Marquilly
- IGH, Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
| | - Germain U. Busto
- IGH, Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
| | - Brittany S. Leger
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Ana Boulanger
- IGH, Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
| | - Edward Giniger
- Intramural Research Program, NINDS, NIH, Bethesda, Maryland, United States of America
| | - James A. Walker
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Lee G. Fradkin
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jean-Maurice Dura
- IGH, Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
- * E-mail:
| |
Collapse
|
8
|
Amador MDM, Gargiulo M, Boucher C, Herson A, Staraci S, Salachas F, Clot F, Cazeneuve C, Le Ber I, Durr A. Who and Why? Requests for Presymptomatic Genetic Testing for Amyotrophic Lateral Sclerosis/Frontotemporal Dementia vs Huntington Disease. NEUROLOGY-GENETICS 2020; 7:e538. [PMID: 33376800 PMCID: PMC7768924 DOI: 10.1212/nxg.0000000000000538] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/20/2020] [Indexed: 11/15/2022]
Abstract
Objective We aimed to describe the population of subjects seeking presymptomatic counseling for amyotrophic lateral sclerosis and/or frontotemporal dementia (ALS/FTD) and compared them with those demanding the well-established presymptomatic test for Huntington disease (HD). Methods We retrospectively examined the requests of a cohort of individuals at risk of familial ALS/FTD and 1 at risk of HD over the same time frame of 11 years. The individuals were seen in the referral center of our neurogenetics unit. Results Of the 106 presymptomatic testing (PT) requests from subjects at risk of ALS/FTD, 65% were seen in the last 3 years. Over two-thirds of the subjects were at risk of carrying mutations responsible for ALS, FTD, or both. Sixty-two percent of the subjects came from families with a known hexanucleotide repeat expansion in C9ORF72. During the same period, we counseled 840 subjects at risk of HD. Subjects at risk of ALS/FTD had the presymptomatic test significantly sooner after being aware of their risk, but were older than those at risk of HD. The youngest subjects requesting the test had the highest disease load in the family (p < 0.05). Conclusions Demands for PT for ALS/FTD have been increasingly growing, particularly since the discovery of the C9ORF72 gene. The major specificity of the genetic counseling for these diseases is the unpredictability of the clinical phenotype for most of the genes involved. Awareness of this added uncertainty does not prevent individuals from taking the test, as the dropout rate is not higher than that for HD.
Collapse
Affiliation(s)
- Maria Del Mar Amador
- Maria del Mar Amador, Département de Neurologie (M.d.M.A., F.S.), Centre de Référence SLA de Paris, Assistance Publique-Hôpitaux de Paris, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France; Département de Génétique (M.d.M.A., M.G., C.B., A.H., S.S., A.D.), Assistance Publique-Hôpitaux de Paris, Sorbonne Université, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France; Laboratory of Clinical Psychology (M.G.), Psychopathology and Psychoanalysis PCPP, EA 4056, University Paris Descartes, Sorbonne Paris City, Psychology Institute, Boulogne-Billancourt, France; Département de Génétique (F.C., C.C.), UF de Neurogénétique, Assistance Publique-Hôpitaux de Paris, Sorbonne Université Hospital Pitié-Salpêtrière; Centre de Référence des Démences Rares ou Précoces (I.L.B.), IM2A, Département de Neurologie, Assistance Publique-Hôpitaux de Paris, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France; and Sorbonne Université, Institut du Cerveau et de la Moelle épinière (ICM) (I.L.B., A.D.), Assistance Publique-Hôpitaux de Paris, INSERM, CNRS, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France
| | - Marcela Gargiulo
- Maria del Mar Amador, Département de Neurologie (M.d.M.A., F.S.), Centre de Référence SLA de Paris, Assistance Publique-Hôpitaux de Paris, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France; Département de Génétique (M.d.M.A., M.G., C.B., A.H., S.S., A.D.), Assistance Publique-Hôpitaux de Paris, Sorbonne Université, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France; Laboratory of Clinical Psychology (M.G.), Psychopathology and Psychoanalysis PCPP, EA 4056, University Paris Descartes, Sorbonne Paris City, Psychology Institute, Boulogne-Billancourt, France; Département de Génétique (F.C., C.C.), UF de Neurogénétique, Assistance Publique-Hôpitaux de Paris, Sorbonne Université Hospital Pitié-Salpêtrière; Centre de Référence des Démences Rares ou Précoces (I.L.B.), IM2A, Département de Neurologie, Assistance Publique-Hôpitaux de Paris, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France; and Sorbonne Université, Institut du Cerveau et de la Moelle épinière (ICM) (I.L.B., A.D.), Assistance Publique-Hôpitaux de Paris, INSERM, CNRS, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France
| | - Christilla Boucher
- Maria del Mar Amador, Département de Neurologie (M.d.M.A., F.S.), Centre de Référence SLA de Paris, Assistance Publique-Hôpitaux de Paris, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France; Département de Génétique (M.d.M.A., M.G., C.B., A.H., S.S., A.D.), Assistance Publique-Hôpitaux de Paris, Sorbonne Université, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France; Laboratory of Clinical Psychology (M.G.), Psychopathology and Psychoanalysis PCPP, EA 4056, University Paris Descartes, Sorbonne Paris City, Psychology Institute, Boulogne-Billancourt, France; Département de Génétique (F.C., C.C.), UF de Neurogénétique, Assistance Publique-Hôpitaux de Paris, Sorbonne Université Hospital Pitié-Salpêtrière; Centre de Référence des Démences Rares ou Précoces (I.L.B.), IM2A, Département de Neurologie, Assistance Publique-Hôpitaux de Paris, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France; and Sorbonne Université, Institut du Cerveau et de la Moelle épinière (ICM) (I.L.B., A.D.), Assistance Publique-Hôpitaux de Paris, INSERM, CNRS, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France
| | - Ariane Herson
- Maria del Mar Amador, Département de Neurologie (M.d.M.A., F.S.), Centre de Référence SLA de Paris, Assistance Publique-Hôpitaux de Paris, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France; Département de Génétique (M.d.M.A., M.G., C.B., A.H., S.S., A.D.), Assistance Publique-Hôpitaux de Paris, Sorbonne Université, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France; Laboratory of Clinical Psychology (M.G.), Psychopathology and Psychoanalysis PCPP, EA 4056, University Paris Descartes, Sorbonne Paris City, Psychology Institute, Boulogne-Billancourt, France; Département de Génétique (F.C., C.C.), UF de Neurogénétique, Assistance Publique-Hôpitaux de Paris, Sorbonne Université Hospital Pitié-Salpêtrière; Centre de Référence des Démences Rares ou Précoces (I.L.B.), IM2A, Département de Neurologie, Assistance Publique-Hôpitaux de Paris, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France; and Sorbonne Université, Institut du Cerveau et de la Moelle épinière (ICM) (I.L.B., A.D.), Assistance Publique-Hôpitaux de Paris, INSERM, CNRS, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France
| | - Stéphanie Staraci
- Maria del Mar Amador, Département de Neurologie (M.d.M.A., F.S.), Centre de Référence SLA de Paris, Assistance Publique-Hôpitaux de Paris, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France; Département de Génétique (M.d.M.A., M.G., C.B., A.H., S.S., A.D.), Assistance Publique-Hôpitaux de Paris, Sorbonne Université, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France; Laboratory of Clinical Psychology (M.G.), Psychopathology and Psychoanalysis PCPP, EA 4056, University Paris Descartes, Sorbonne Paris City, Psychology Institute, Boulogne-Billancourt, France; Département de Génétique (F.C., C.C.), UF de Neurogénétique, Assistance Publique-Hôpitaux de Paris, Sorbonne Université Hospital Pitié-Salpêtrière; Centre de Référence des Démences Rares ou Précoces (I.L.B.), IM2A, Département de Neurologie, Assistance Publique-Hôpitaux de Paris, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France; and Sorbonne Université, Institut du Cerveau et de la Moelle épinière (ICM) (I.L.B., A.D.), Assistance Publique-Hôpitaux de Paris, INSERM, CNRS, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France
| | - François Salachas
- Maria del Mar Amador, Département de Neurologie (M.d.M.A., F.S.), Centre de Référence SLA de Paris, Assistance Publique-Hôpitaux de Paris, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France; Département de Génétique (M.d.M.A., M.G., C.B., A.H., S.S., A.D.), Assistance Publique-Hôpitaux de Paris, Sorbonne Université, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France; Laboratory of Clinical Psychology (M.G.), Psychopathology and Psychoanalysis PCPP, EA 4056, University Paris Descartes, Sorbonne Paris City, Psychology Institute, Boulogne-Billancourt, France; Département de Génétique (F.C., C.C.), UF de Neurogénétique, Assistance Publique-Hôpitaux de Paris, Sorbonne Université Hospital Pitié-Salpêtrière; Centre de Référence des Démences Rares ou Précoces (I.L.B.), IM2A, Département de Neurologie, Assistance Publique-Hôpitaux de Paris, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France; and Sorbonne Université, Institut du Cerveau et de la Moelle épinière (ICM) (I.L.B., A.D.), Assistance Publique-Hôpitaux de Paris, INSERM, CNRS, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France
| | - Fabienne Clot
- Maria del Mar Amador, Département de Neurologie (M.d.M.A., F.S.), Centre de Référence SLA de Paris, Assistance Publique-Hôpitaux de Paris, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France; Département de Génétique (M.d.M.A., M.G., C.B., A.H., S.S., A.D.), Assistance Publique-Hôpitaux de Paris, Sorbonne Université, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France; Laboratory of Clinical Psychology (M.G.), Psychopathology and Psychoanalysis PCPP, EA 4056, University Paris Descartes, Sorbonne Paris City, Psychology Institute, Boulogne-Billancourt, France; Département de Génétique (F.C., C.C.), UF de Neurogénétique, Assistance Publique-Hôpitaux de Paris, Sorbonne Université Hospital Pitié-Salpêtrière; Centre de Référence des Démences Rares ou Précoces (I.L.B.), IM2A, Département de Neurologie, Assistance Publique-Hôpitaux de Paris, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France; and Sorbonne Université, Institut du Cerveau et de la Moelle épinière (ICM) (I.L.B., A.D.), Assistance Publique-Hôpitaux de Paris, INSERM, CNRS, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France
| | - Cécile Cazeneuve
- Maria del Mar Amador, Département de Neurologie (M.d.M.A., F.S.), Centre de Référence SLA de Paris, Assistance Publique-Hôpitaux de Paris, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France; Département de Génétique (M.d.M.A., M.G., C.B., A.H., S.S., A.D.), Assistance Publique-Hôpitaux de Paris, Sorbonne Université, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France; Laboratory of Clinical Psychology (M.G.), Psychopathology and Psychoanalysis PCPP, EA 4056, University Paris Descartes, Sorbonne Paris City, Psychology Institute, Boulogne-Billancourt, France; Département de Génétique (F.C., C.C.), UF de Neurogénétique, Assistance Publique-Hôpitaux de Paris, Sorbonne Université Hospital Pitié-Salpêtrière; Centre de Référence des Démences Rares ou Précoces (I.L.B.), IM2A, Département de Neurologie, Assistance Publique-Hôpitaux de Paris, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France; and Sorbonne Université, Institut du Cerveau et de la Moelle épinière (ICM) (I.L.B., A.D.), Assistance Publique-Hôpitaux de Paris, INSERM, CNRS, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France
| | - Isabelle Le Ber
- Maria del Mar Amador, Département de Neurologie (M.d.M.A., F.S.), Centre de Référence SLA de Paris, Assistance Publique-Hôpitaux de Paris, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France; Département de Génétique (M.d.M.A., M.G., C.B., A.H., S.S., A.D.), Assistance Publique-Hôpitaux de Paris, Sorbonne Université, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France; Laboratory of Clinical Psychology (M.G.), Psychopathology and Psychoanalysis PCPP, EA 4056, University Paris Descartes, Sorbonne Paris City, Psychology Institute, Boulogne-Billancourt, France; Département de Génétique (F.C., C.C.), UF de Neurogénétique, Assistance Publique-Hôpitaux de Paris, Sorbonne Université Hospital Pitié-Salpêtrière; Centre de Référence des Démences Rares ou Précoces (I.L.B.), IM2A, Département de Neurologie, Assistance Publique-Hôpitaux de Paris, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France; and Sorbonne Université, Institut du Cerveau et de la Moelle épinière (ICM) (I.L.B., A.D.), Assistance Publique-Hôpitaux de Paris, INSERM, CNRS, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France
| | - Alexandra Durr
- Maria del Mar Amador, Département de Neurologie (M.d.M.A., F.S.), Centre de Référence SLA de Paris, Assistance Publique-Hôpitaux de Paris, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France; Département de Génétique (M.d.M.A., M.G., C.B., A.H., S.S., A.D.), Assistance Publique-Hôpitaux de Paris, Sorbonne Université, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France; Laboratory of Clinical Psychology (M.G.), Psychopathology and Psychoanalysis PCPP, EA 4056, University Paris Descartes, Sorbonne Paris City, Psychology Institute, Boulogne-Billancourt, France; Département de Génétique (F.C., C.C.), UF de Neurogénétique, Assistance Publique-Hôpitaux de Paris, Sorbonne Université Hospital Pitié-Salpêtrière; Centre de Référence des Démences Rares ou Précoces (I.L.B.), IM2A, Département de Neurologie, Assistance Publique-Hôpitaux de Paris, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France; and Sorbonne Université, Institut du Cerveau et de la Moelle épinière (ICM) (I.L.B., A.D.), Assistance Publique-Hôpitaux de Paris, INSERM, CNRS, Sorbonne Université Hospital Pitié-Salpêtrière, Paris, France
| |
Collapse
|
9
|
Wang L, Chen Y, Yan Y, Guo X, Fang Y, Su Y, Wang L, Pathak JL, Ge L. miR-146a Overexpression in Oral Squamous Cell Carcinoma Potentiates Cancer Cell Migration and Invasion Possibly via Targeting HTT. Front Oncol 2020; 10:585976. [PMID: 33282738 DOI: 10.3389/fonc.2020.585976] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/14/2020] [Indexed: 01/04/2023] Open
Abstract
Huntingtin (HTT) is one of the target genes of miR-146-a and regulates various cancer cell activities. This study aims to explore the miR-146a expression pattern in oral squamous cell carcinoma (OSCC) and its role and mechanism in OSCC progression and metastasis via targeting the HTT gene. OSCC tissue and non-cancerous matched tissue (NCMT) were obtained from 14 patients. OSCC cell lines and normal HOK cells were used to analyze migration and invasion assay. OSCC-induced miR-146a knockout mice (B6.Cg-Mir146tm1.1Bal) model was developed. Transwell cell migration/invasion and scratch wound assays were used to investigate the OSCC cell migration and invasion in vitro. Kaplan-Meier survival analysis was used to investigate the association of HTT expression patterns in cancer tissue with patient survival percentage and duration. Pearson's correlation analysis tested the association between miR-146a and HTT expression in OSCC tissues. miR-146a mimic and inhibitor transfection were performed to overexpress and knockdown the miR-146a in OSCC cells, respectively. miR-146a expression was highly upregulated in OSCC tissues and OSCC cell lines. Cancer cell migration/invasion was enhanced in miR-146a overexpressed cells and reduced in mi-R146a knockdowned cells. HTT expression was reduced in OSCC tissues and cell lines compared to NCMT and HOK cells, respectively. HTT expression was downregulated in miR-146a overexpressed OSCC cells and upregulated in miR-146a knockdowned OSCC cells. The expression pattern of miR-146a in OSCC cell lines and tissues was inversely correlated with HTT expression. Prediction of miRNA target analysis showed that HTT possesses the binding sites for miR-146a. HTT overexpression in OSCC tissues was associated with patients' higher survival percentage and duration. HTT knockdown in OSCC cells enhanced miR-146a expression and cell migration/invasion. Inducing OSCC in miR-146a knockout mice increased the HTT expression in tongue tissue and alleviated the cancer aggressiveness and epithelial damage. Overexpressed miR-146a in OSCC targets the HTT gene and enhances cancer cell migration/invasion unraveling the possible role of HTT in miR146a-mediated OSCC cell migration and invasion.
Collapse
Affiliation(s)
- Liping Wang
- Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China
| | - Yunxin Chen
- Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China
| | - Yongyong Yan
- Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China.,Institute of Oral Disease, Guangzhou Medical University, Guangzhou, China
| | - Xueqi Guo
- Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China
| | - Ying Fang
- Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China
| | - Yucheng Su
- Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Lijing Wang
- Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China.,School of Life Science and Biopharmaceutics, Vascular Biology Research Institute, Guangdong Pharmaceutical University, Guangzhou, China
| | - Janak L Pathak
- Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China.,Institute of Oral Disease, Guangzhou Medical University, Guangzhou, China
| | - Linhu Ge
- Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China.,Institute of Oral Disease, Guangzhou Medical University, Guangzhou, China
| |
Collapse
|
10
|
Seçilmiş D, Hillerton T, Morgan D, Tjärnberg A, Nelander S, Nordling TEM, Sonnhammer ELL. Uncovering cancer gene regulation by accurate regulatory network inference from uninformative data. NPJ Syst Biol Appl 2020; 6:37. [PMID: 33168813 PMCID: PMC7652823 DOI: 10.1038/s41540-020-00154-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 10/15/2020] [Indexed: 01/11/2023] Open
Abstract
The interactions among the components of a living cell that constitute the gene regulatory network (GRN) can be inferred from perturbation-based gene expression data. Such networks are useful for providing mechanistic insights of a biological system. In order to explore the feasibility and quality of GRN inference at a large scale, we used the L1000 data where ~1000 genes have been perturbed and their expression levels have been quantified in 9 cancer cell lines. We found that these datasets have a very low signal-to-noise ratio (SNR) level causing them to be too uninformative to infer accurate GRNs. We developed a gene reduction pipeline in which we eliminate uninformative genes from the system using a selection criterion based on SNR, until reaching an informative subset. The results show that our pipeline can identify an informative subset in an overall uninformative dataset, allowing inference of accurate subset GRNs. The accurate GRNs were functionally characterized and potential novel cancer-related regulatory interactions were identified.
Collapse
Affiliation(s)
- Deniz Seçilmiş
- Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121, Solna, Sweden
| | - Thomas Hillerton
- Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121, Solna, Sweden
| | - Daniel Morgan
- Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121, Solna, Sweden
| | - Andreas Tjärnberg
- Center for Developmental Genetics, New York University, New York, NY, USA
| | - Sven Nelander
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Torbjörn E M Nordling
- Department of Mechanical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Erik L L Sonnhammer
- Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121, Solna, Sweden.
| |
Collapse
|
11
|
Svrzikapa N, Longo KA, Prasad N, Boyanapalli R, Brown JM, Dorset D, Yourstone S, Powers J, Levy SE, Morris AJ, Vargeese C, Goyal J. Investigational Assay for Haplotype Phasing of the Huntingtin Gene. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 19:162-173. [PMID: 33209959 PMCID: PMC7648085 DOI: 10.1016/j.omtm.2020.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 09/04/2020] [Indexed: 01/20/2023]
Abstract
Novel treatments for Huntington's disease (HD), a progressive neurodegenerative disorder, include selective targeting of the mutant allele of the huntingtin gene (mHTT) carrying the abnormally expanded disease-causing cytosine-adenine-guanine (CAG) repeat. WVE-120101 and WVE-120102 are investigational stereopure antisense oligonucleotides that enable selective suppression of mHTT by targeting single-nucleotide polymorphisms (SNPs) that are in haplotype phase with the CAG repeat expansion. Recently developed long-read sequencing technologies can capture CAG expansions and distant SNPs of interest and potentially facilitate haplotype-based identification of patients for clinical trials of oligonucleotide therapies. However, improved methods are needed to phase SNPs with CAG repeat expansions directly and reliably without need for familial genotype/haplotype data. Our haplotype phasing method uses single-molecule real-time sequencing and a custom algorithm to determine with confidence bases at SNPs on mutant alleles, even without familial data. Herein, we summarize this methodology and validate the approach using patient-derived samples with known phasing results. Comparison of experimentally measured CAG repeat lengths, heterozygosity, and phasing with previously determined results showed improved performance. Our methodology enables the haplotype phasing of SNPs of interest and the disease-causing, expanded CAG repeat of the huntingtin gene, enabling accurate identification of patients with HD eligible for allele-selective clinical studies.
Collapse
Affiliation(s)
- Nenad Svrzikapa
- Wave Life Sciences Ltd., Cambridge, MA 02138, USA.,Department of Paediatrics, Medical Sciences Division, University of Oxford, Oxford OX3 9DU, UK
| | | | - Nripesh Prasad
- HudsonAlpha Discovery, Discovery Life Sciences, Huntsville, AL 35806, USA.,Genomic Services Laboratory, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | | | - Daniel Dorset
- HudsonAlpha Discovery, Discovery Life Sciences, Huntsville, AL 35806, USA.,Genomic Services Laboratory, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | - Jason Powers
- Q Solutions
- EA Genomics, LLC, Morrisville, NC 27560, USA
| | - Shawn E Levy
- HudsonAlpha Discovery, Discovery Life Sciences, Huntsville, AL 35806, USA.,Genomic Services Laboratory, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | | | - Jaya Goyal
- Wave Life Sciences Ltd., Cambridge, MA 02138, USA
| |
Collapse
|
12
|
Advani D, Gupta R, Tripathi R, Sharma S, Ambasta RK, Kumar P. Protective role of anticancer drugs in neurodegenerative disorders: A drug repurposing approach. Neurochem Int 2020; 140:104841. [PMID: 32853752 DOI: 10.1016/j.neuint.2020.104841] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/24/2020] [Accepted: 08/18/2020] [Indexed: 12/13/2022]
Abstract
The disease heterogeneity and little therapeutic progress in neurodegenerative diseases justify the need for novel and effective drug discovery approaches. Drug repurposing is an emerging approach that reinvigorates the classical drug discovery method by divulging new therapeutic uses of existing drugs. The common biological background and inverse tuning between cancer and neurodegeneration give weight to the conceptualization of repurposing of anticancer drugs as novel therapeutics. Many studies are available in the literature, which highlights the success story of anticancer drugs as repurposed therapeutics. Among them, kinase inhibitors, developed for various oncology indications evinced notable neuroprotective effects in neurodegenerative diseases. In this review, we shed light on the salient role of multiple protein kinases in neurodegenerative disorders. We also proposed a feasible explanation of the action of kinase inhibitors in neurodegenerative disorders with more attention towards neurodegenerative disorders. The problem of neurotoxicity associated with some anticancer drugs is also highlighted. Our review encourages further research to better encode the hidden potential of anticancer drugs with the aim of developing prospective repurposed drugs with no toxicity for neurodegenerative disorders.
Collapse
Affiliation(s)
- Dia Advani
- Department of Biotechnology, Molecular Neuroscience and Functional Genomics Laboratory, Room# FW4TF3, Mechanical Engineering Building, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Rohan Gupta
- Department of Biotechnology, Molecular Neuroscience and Functional Genomics Laboratory, Room# FW4TF3, Mechanical Engineering Building, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Rahul Tripathi
- Department of Biotechnology, Molecular Neuroscience and Functional Genomics Laboratory, Room# FW4TF3, Mechanical Engineering Building, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Sudhanshu Sharma
- Department of Biotechnology, Molecular Neuroscience and Functional Genomics Laboratory, Room# FW4TF3, Mechanical Engineering Building, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Rashmi K Ambasta
- Department of Biotechnology, Molecular Neuroscience and Functional Genomics Laboratory, Room# FW4TF3, Mechanical Engineering Building, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Pravir Kumar
- Department of Biotechnology, Molecular Neuroscience and Functional Genomics Laboratory, Room# FW4TF3, Mechanical Engineering Building, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India.
| |
Collapse
|
13
|
Laverde EE, Lai Y, Leng F, Balakrishnan L, Freudenreich CH, Liu Y. R-loops promote trinucleotide repeat deletion through DNA base excision repair enzymatic activities. J Biol Chem 2020; 295:13902-13913. [PMID: 32763971 DOI: 10.1074/jbc.ra120.014161] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 08/04/2020] [Indexed: 12/27/2022] Open
Abstract
Trinucleotide repeat (TNR) expansion and deletion are responsible for over 40 neurodegenerative diseases and associated with cancer. TNRs can undergo somatic instability that is mediated by DNA damage and repair and gene transcription. Recent studies have pointed toward a role for R-loops in causing TNR expansion and deletion, and it has been shown that base excision repair (BER) can result in CAG repeat deletion from R-loops in yeast. However, it remains unknown how BER in R-loops can mediate TNR instability. In this study, using biochemical approaches, we examined BER enzymatic activities and their influence on TNR R-loops. We found that AP endonuclease 1 incised an abasic site on the nontemplate strand of a TNR R-loop, creating a double-flap intermediate containing an RNA:DNA hybrid that subsequently inhibited polymerase β (pol β) synthesis of TNRs. This stimulated flap endonuclease 1 (FEN1) cleavage of TNRs engaged in an R-loop. Moreover, we showed that FEN1 also efficiently cleaved the RNA strand, facilitating pol β loop/hairpin bypass synthesis and the resolution of TNR R-loops through BER. Consequently, this resulted in fewer TNRs synthesized by pol β than those removed by FEN1, thereby leading to repeat deletion. Our results indicate that TNR R-loops preferentially lead to repeat deletion during BER by disrupting the balance between the addition and removal of TNRs. Our discoveries open a new avenue for the treatment and prevention of repeat expansion diseases and cancer.
Collapse
Affiliation(s)
- Eduardo E Laverde
- Biochemistry Ph.D. Program, Florida International University, Miami, Florida, USA
| | - Yanhao Lai
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
| | - Fenfei Leng
- Biochemistry Ph.D. Program, Florida International University, Miami, Florida, USA; Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA; Biomolecular Sciences Institute, Florida International University, Miami, Florida, USA
| | - Lata Balakrishnan
- Department of Biology, Indiana Purdue University Indianapolis, Indianapolis, Indiana, USA
| | | | - Yuan Liu
- Biochemistry Ph.D. Program, Florida International University, Miami, Florida, USA; Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA; Biomolecular Sciences Institute, Florida International University, Miami, Florida, USA.
| |
Collapse
|
14
|
Analysis of the Circadian Regulation of Cancer Hallmarks by a Cross-Platform Study of Colorectal Cancer Time-Series Data Reveals an Association with Genes Involved in Huntington's Disease. Cancers (Basel) 2020; 12:cancers12040963. [PMID: 32295075 PMCID: PMC7226183 DOI: 10.3390/cancers12040963] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/07/2020] [Accepted: 04/10/2020] [Indexed: 02/06/2023] Open
Abstract
Accumulating evidence points to a link between circadian clock dysfunction and the molecular events that drive tumorigenesis. Here, we investigated the connection between the circadian clock and the hallmarks of cancer in an in vitro model of colorectal cancer (CRC). We used a cross-platform data normalization method to concatenate and compare available microarray and RNA-sequencing time series data of CRC cell lines derived from the same patient at different disease stages. Our data analysis suggests differential regulation of molecular pathways between the CRC cells and identifies several of the circadian and likely clock-controlled genes (CCGs) as cancer hallmarks and circadian drug targets. Notably, we found links of the CCGs to Huntington’s disease (HD) in the metastasis-derived cells. We then investigated the impact of perturbations of our candidate genes in a cohort of 439 patients with colon adenocarcinoma retrieved from the Cancer Genome Atlas (TCGA). The analysis revealed a correlation of the differential expression levels of the candidate genes with the survival of patients. Thus, our study provides a bioinformatics workflow that allows for a comprehensive analysis of circadian properties at different stages of colorectal cancer, and identifies a new association between cancer and HD.
Collapse
|
15
|
Srinageshwar B, Petersen RB, Dunbar GL, Rossignol J. Prion-like mechanisms in neurodegenerative disease: Implications for Huntington's disease therapy. Stem Cells Transl Med 2020; 9:559-566. [PMID: 31997581 PMCID: PMC7180288 DOI: 10.1002/sctm.19-0248] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 01/14/2020] [Indexed: 12/18/2022] Open
Abstract
Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder caused by a CAG repeat expansions in the huntingtin gene resulting in the synthesis of a misfolded form of the huntingtin protein (mHTT) which is toxic. The current treatments for HD are only palliative. Some of the potential therapies for HD include gene therapy (using antisense oligonucleotides and clustered regularly interspaced short palindromic repeats-Cas9 system) and stem-cell-based therapies. Various types of stem cell transplants, such as mesenchymal stem cells, neural stem cells, and reprogrammed stem cells, have the potential to either replace the lost neurons or support the existing neurons by releasing trophic factors. Most of the transplants are xenografts and allografts; however, recent reports on HD patients who received grafts suggest that the mHTT aggregates are transferred from the host neurons to the grafted cells as well as to the surrounding areas of the graft by a "prion-like" mechanism. This observation seems to be true for autotransplantation paradigms, as well. This article reviews the different types of stem cells that have been transplanted into HD patients and their therapeutic efficacy, focusing on the transfer of mHTT from the host cells to the graft. Autotransplants of reprogramed stem cells in HD patients are a promising therapeutic option. However, this needs further attention to ensure a better understanding of the transfer of mHTT aggregates following transplantation of the gene-corrected cells back into the patient.
Collapse
Affiliation(s)
- Bhairavi Srinageshwar
- College of Medicine, Central Michigan University, Mount Pleasant, Michigan.,Field Neurosciences Institute Laboratory for Restorative Neurology, Central Michigan University, Mount Pleasant, Michigan.,Program in Neuroscience, Central Michigan University, Mount Pleasant, Michigan
| | - Robert B Petersen
- College of Medicine, Central Michigan University, Mount Pleasant, Michigan.,Program in Neuroscience, Central Michigan University, Mount Pleasant, Michigan
| | - Gary L Dunbar
- Field Neurosciences Institute Laboratory for Restorative Neurology, Central Michigan University, Mount Pleasant, Michigan.,Program in Neuroscience, Central Michigan University, Mount Pleasant, Michigan.,Department of Psychology, Central Michigan University, Mount Pleasant, Michigan.,Field Neurosciences Institute, Saginaw, Michigan
| | - Julien Rossignol
- College of Medicine, Central Michigan University, Mount Pleasant, Michigan.,Field Neurosciences Institute Laboratory for Restorative Neurology, Central Michigan University, Mount Pleasant, Michigan.,Program in Neuroscience, Central Michigan University, Mount Pleasant, Michigan
| |
Collapse
|
16
|
Hashimoto M, Ho G, Takamatsu Y, Wada R, Sugama S, Takenouchi T, Masliah E, Waragai M. Possible Role of the Polyglutamine Elongation in Evolution of Amyloid-Related Evolvability. J Huntingtons Dis 2018; 7:297-307. [PMID: 30372687 PMCID: PMC6294593 DOI: 10.3233/jhd-180309] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The polyglutamine (polyQ) diseases, such as Huntington's disease and the spinocerebellar ataxias, are characterized by the accumulation of elongated polyQ sequences (epolyQ) and mostly occur during midlife. Considering that polyQ disorders have not been selected out in evolution, there might be important physiological functions of epolyQ during development and/or reproduction. In a similar context, the physiological functions of neurodegeneration-associated amyloidogenic proteins (APs), such as β-amyloid in Alzheimer's disease and α-synuclein in Parkinson's disease, remain elusive. In this regard, we recently proposed that evolvability for coping with diverse stressors in the brain, which is beneficial for offspring, might be relevant to the physiological functions of APs. Given analogous properties of APs and epolyQ in terms of neurotoxic amyloid-fibril formation, the objective of this paper is to determine whether evolvability could also be applied to the physiological functions of epolyQ. Indeed, APs and epolyQ are similar in many ways, including functional redundancy of non-amyloidogenic homologues, hormesis conferred by the heterogeneity of the stress-induced protein aggregates, the transgenerational prion-like transmission of the protein aggregates via germ cells, and the antagonistic pleiotropy relationship between evolvability and neurodegenerative disease. Given that epolyQ is widely expressed from microorganisms to human brain, whereas APs are only identified in vertebrates, evolvability of epolyQ is considered to be much more primitive compared to those of APs during evolution. Collectively, epolyQ may be not only be important in the pathophysiology of polyQ diseases, but also in the evolution of amyloid-related evolvability.
Collapse
Affiliation(s)
- Makoto Hashimoto
- Tokyo Metropolitan Institute of Medical Science, Kamikitazawa, Setagaya-ku, Tokyo, Japan
| | - Gilbert Ho
- PCND Neuroscience Research Institute, Poway, CA, USA
| | - Yoshiki Takamatsu
- Tokyo Metropolitan Institute of Medical Science, Kamikitazawa, Setagaya-ku, Tokyo, Japan
| | - Ryoko Wada
- Tokyo Metropolitan Institute of Medical Science, Kamikitazawa, Setagaya-ku, Tokyo, Japan
| | - Shuei Sugama
- Department of Physiology, Nippon Medical School, Tokyo, Japan
| | - Takato Takenouchi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Eliezer Masliah
- Division of Neurosciences, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Masaaki Waragai
- Tokyo Metropolitan Institute of Medical Science, Kamikitazawa, Setagaya-ku, Tokyo, Japan
| |
Collapse
|