1
|
Paumier JM, Gowrishankar S. Disruptions in axonal lysosome transport and its contribution to neurological disease. Curr Opin Cell Biol 2024; 89:102382. [PMID: 38905918 DOI: 10.1016/j.ceb.2024.102382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/23/2024]
Abstract
Lysosomes are central to the maintenance of protein and organelle homeostasis in cells. Optimal lysosome function is particularly critical for neurons which are long-lived, non-dividing and highly polarized with specialized compartments such as axons and dendrites with distinct architecture, cargo, and turnover requirements. In recent years, there has been a growing appreciation for the role played by axonal lysosome transport in regulating neuronal development, its maintenance and functioning. Perturbations to optimal axonal lysosome abundance leading to either strong accumulations or dearth of lysosomes are both linked to altered neuronal health and functioning. In this review we highlight how two critical regulators of axonal lysosome transport and abundance, the small GTPase Arl8 and the adaptor protein JIP3, aid in maintaining axonal lysosome homeostasis and how alterations to their levels and activity could contribute to neurodevelopmental and neurodegenerative diseases.
Collapse
Affiliation(s)
- Jean-Michel Paumier
- Department of Anatomy and Cell Biology, University of Illinois Chicago, 808 S Wood St, Chicago, IL 60612, USA
| | - Swetha Gowrishankar
- Department of Anatomy and Cell Biology, University of Illinois Chicago, 808 S Wood St, Chicago, IL 60612, USA.
| |
Collapse
|
2
|
Drozd CJ, Chowdhury TA, Quinn CC. UNC-16 interacts with LRK-1 and WDFY-3 to regulate the termination of axon growth. Genetics 2024; 227:iyae053. [PMID: 38581414 PMCID: PMC11151918 DOI: 10.1093/genetics/iyae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 02/27/2024] [Accepted: 03/28/2024] [Indexed: 04/08/2024] Open
Abstract
In humans, MAPK8IP3 (also known as JIP3) is a neurodevelopmental disorder-associated gene. In Caenorhabditis elegans, the UNC-16 ortholog of the MAPK8IP3 protein can regulate the termination of axon growth. However, its role in this process is not well understood. Here, we report that UNC-16 promotes axon termination through a process that includes the LRK-1 (LRRK-1/LRRK-2) kinase and the WDFY-3 (WDFY3/Alfy) selective autophagy protein. Genetic analysis suggests that UNC-16 promotes axon termination through an interaction between its RH1 domain and the dynein complex. Loss of unc-16 function causes accumulation of late endosomes specifically in the distal axon. Moreover, we observe synergistic interactions between loss of unc-16 function and disruptors of endolysosomal function, indicating that the endolysosomal system promotes axon termination. We also find that the axon termination defects caused by loss of UNC-16 function require the function of a genetic pathway that includes lrk-1 and wdfy-3, 2 genes that have been implicated in autophagy. These observations suggest a model where UNC-16 promotes axon termination by interacting with the endolysosomal system to regulate a pathway that includes LRK-1 and WDFY-3.
Collapse
Affiliation(s)
- Cody J Drozd
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53201, USA
| | - Tamjid A Chowdhury
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53201, USA
| | - Christopher C Quinn
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53201, USA
| |
Collapse
|
3
|
Orlowski A, Karippaparambil J, Paumier JM, Ghanta S, Pallares E, Tandukar J, Gao R, Gowrishankar S. Axonal organelle buildup from loss of AP-4 complex function causes exacerbation of amyloid plaque pathology and gliosis in Alzheimer's disease mouse model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.31.587499. [PMID: 38617351 PMCID: PMC11014495 DOI: 10.1101/2024.03.31.587499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Lysosomes and related precursor organelles robustly build up in swollen axons that surround amyloid plaques and disrupted axonal lysosome transport has been implicated in worsening Alzheimer's pathology. Our prior studies have revealed that loss of Adaptor protein-4 (AP-4) complex function, linked primarily to Spastic Paraplegia (HSP), leads to a similar build of lysosomes in structures we term "AP-4 dystrophies". Surprisingly, these AP-4 dystrophies were also characterized by enrichment of components of APP processing machinery, β-site cleaving enzyme 1 (BACE1) and Presenilin 2. Our studies examining whether the abnormal axonal lysosome build up resulting from AP-4 loss could lead to amyloidogenesis revealed that the loss of AP-4 complex function in an Alzheimer's disease model resulted in a strong increase in size and abundance of amyloid plaques in the hippocampus and corpus callosum as well as increased microglial association with the plaques. Interestingly, we found a further increase in enrichment of the secretase, BACE1, in the axonal swellings of the plaques of Alzheimer model mice lacking AP-4 complex compared to those having normal AP-4 complex function, suggestive of increased amyloidogenic processing under this condition. Additionally, the exacerbation of plaque pathology was region-specific as it did not increase in the cortex. The burden of the AP-4 linked axonal dystrophies/AP-4 dystrophies was higher in the corpus callosum and hippocampus compared to the cortex, establishing the critical role of AP-4 -dependent axonal lysosome transport and maturation in regulating amyloidogenic amyloid precursor protein processing.
Collapse
Affiliation(s)
- Alex Orlowski
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois Chicago, Chicago, IL 60612 USA
| | - Joseph Karippaparambil
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois Chicago, Chicago, IL 60612 USA
| | - Jean-Michel Paumier
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois Chicago, Chicago, IL 60612 USA
| | - Shraddha Ghanta
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois Chicago, Chicago, IL 60612 USA
| | - Eduardo Pallares
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois Chicago, Chicago, IL 60612 USA
| | - Jamuna Tandukar
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL 60607 USA
| | - Ruixuan Gao
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL 60607 USA
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL 60607 USA
| | - Swetha Gowrishankar
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois Chicago, Chicago, IL 60612 USA
| |
Collapse
|
4
|
Drozd CJ, Chowdhury TA, Quinn CC. UNC-16 interacts with LRK-1 and WDFY-3 to regulate the termination of axon growth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.15.580526. [PMID: 38405875 PMCID: PMC10888800 DOI: 10.1101/2024.02.15.580526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
MAPK8IP3 (unc-16/JIP3) is a neurodevelopmental-disorder associated gene that can regulate the termination of axon growth. However, its role in this process is not well understood. Here, we report that UNC-16 promotes axon termination through a process that includes the LRK-1(LRRK-1/LRRK-2) kinase and the WDFY-3 (WDFY3/Alfy) selective autophagy protein. Genetic analysis suggests that UNC-16 promotes axon termination through an interaction between its RH1 domain and the dynein complex. Loss of unc-16 function causes accumulation of late endosomes specifically in the distal axon. Moreover, we observe synergistic interactions between loss of unc-16 function and disruptors of endolysosomal function, indicating that the endolysosomal system promotes axon termination. We also find that the axon termination defects caused by loss of UNC-16 function require the function of a genetic pathway that includes lrk-1 and wdfy-3, two genes that have been implicated in autophagy. These observations suggest a model where UNC-16 promotes axon termination by interacting with the endolysosomal system to regulate a pathway that includes LRK-1 and WDFY-3.
Collapse
Affiliation(s)
- Cody J. Drozd
- Department of Biological Sciences, University of Wisconsin-Milwaukee; Milwaukee, WI, 53201, U.S.A
| | - Tamjid A. Chowdhury
- Department of Biological Sciences, University of Wisconsin-Milwaukee; Milwaukee, WI, 53201, U.S.A
| | - Christopher C. Quinn
- Department of Biological Sciences, University of Wisconsin-Milwaukee; Milwaukee, WI, 53201, U.S.A
| |
Collapse
|
5
|
Sasazawa Y, Hattori N, Saiki S. JNK-interacting protein 4 is a central molecule for lysosomal retrograde trafficking. Bioessays 2023; 45:e2300052. [PMID: 37559169 DOI: 10.1002/bies.202300052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 08/11/2023]
Abstract
Lysosomal positioning is an important factor in regulating cellular responses, including autophagy. Because proteins encoded by disease-responsible genes are involved in lysosomal trafficking, proper intracellular lysosomal trafficking is thought to be essential for cellular homeostasis. In the past few years, the mechanisms of lysosomal trafficking have been elucidated with a focus on adapter proteins linking motor proteins to lysosomes. Here, we outline recent findings on the mechanisms of lysosomal trafficking by focusing on adapter protein c-Jun NH2 -terminal kinase-interacting protein (JIP) 4, which plays a central role in this process, and other JIP4 functions and JIP family proteins. Additionally, we discuss neuronal diseases associated with aberrance in the JIP family protein. Accumulating evidence suggests that chemical manipulation of lysosomal positioning may be a therapeutic approach for these neuronal diseases.
Collapse
Affiliation(s)
- Yukiko Sasazawa
- Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan
- Department of Neurology, Juntendo University Faculty of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Nobutaka Hattori
- Department of Neurology, Juntendo University Faculty of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Shinji Saiki
- Department of Neurology, Juntendo University Faculty of Medicine, Bunkyo-ku, Tokyo, Japan
- Department of Neurology, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| |
Collapse
|
6
|
Liang H, Zhang L, Zhao X, Rong J. The therapeutic potential of exosomes in lung cancer. Cell Oncol (Dordr) 2023; 46:1181-1212. [PMID: 37365450 DOI: 10.1007/s13402-023-00815-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Lung cancer (LC) is one of the most common malignancies globally. Besides early detection and surgical resection, there is currently no effective curative treatment for metastatic advanced LC. Exosomes are endogenous nano-extracellular vesicles produced by somatic cells that play an important role in the development and maintenance of normal physiology. Exosomes can carry proteins, peptides, lipids, nucleic acids, and various small molecules for intra- and intercellular material transport or signal transduction. LC cells can maintain their survival, proliferation, migration, invasion, and metastasis, by producing or interacting with exosomes. Basic and clinical data also show that exosomes can be used to suppress LC cell proliferation and viability, induce apoptosis, and enhance treatment sensitivity. Due to the high stability and target specificity, good biocompatibility, and low immunogenicity of exosomes, they show promise as vehicles of LC therapy. CONCLUSION We have written this comprehensive review to communicate the LC treatment potential of exosomes and their underlying molecular mechanisms. We found that overall, LC cells can exchange substances or crosstalk with themselves or various other cells in the surrounding TME or distant organs through exosomes. Through this, they can modulate their survival, proliferation, stemness, migration, and invasion, EMT, metastasis, and apoptotic resistance.
Collapse
Affiliation(s)
- Hongyuan Liang
- Department of Radiology, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Shenyang, 110004, China
| | - Lingyun Zhang
- Department of Medical Oncology, the First Hospital of China Medical University, No. 210, BaiTa Street, Hunnan District, Shenyang, 110001, People's Republic of China
| | - Xiangxuan Zhao
- Health Sciences Institute, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, 110022, People's Republic of China.
| | - Jian Rong
- Department of Pediatrics, PICU, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Shenyang, Liaoning Province, 110004, People's Republic of China.
| |
Collapse
|
7
|
Kárteszi J, Ziegler A, Tihanyi M, Elmont B, Zhang Y, Patócs B, Molnár MJ, Méhes G, Wells K, Jakus R, Bessenyei B, Ranatunga W, Morava É. Compound heterozygous variants in MAPK8IP3 were detected in severe congenital hypotonia mimicking lethal spinal muscular atrophy. Am J Med Genet A 2023; 191:2428-2432. [PMID: 37462082 DOI: 10.1002/ajmg.a.63340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/09/2023] [Accepted: 06/20/2023] [Indexed: 08/20/2023]
Abstract
Mitogen-activated protein kinase 8-interacting protein 3 gene (MAPK8IP3) encodes the c-Jun-amino-terminal kinase-interacting protein 3 (JIP3) and is involved in retrograde axonal transport. Heterozygous de novo pathogenic variants in MAPK8IP3 result in a neurodevelopmental disorder with or without brain abnormalities and possible axonal peripheral neuropathy. Whole-exome sequencing was performed on an individual presenting with severe congenital muscle hypotonia of neuronal origin mimicking lethal spinal muscular atrophy. Compound heterozygous rare variants (a splice and a missense) were detected in MAPK8IP3, inherited from the healthy parents. Western blot analysis in a muscle biopsy sample showed a more than 60% decrease in JIP3 expression. Here, we suggest a novel autosomal recessive phenotype of a lower motor neuron disease caused by JIP3 deficiency.
Collapse
Affiliation(s)
- Judit Kárteszi
- Genetic Counselling, Hospital of Zala County, Zalaegerszeg, Hungary
| | - Alban Ziegler
- Department of Genetics, University Hospital of Angers, and Mitovasc UMR INSERM 1083 - CNRS 6015, University of Angers, Angers, France
| | - Mariann Tihanyi
- Genetic Counselling, Hospital of Zala County, Zalaegerszeg, Hungary
| | - Beatrix Elmont
- Pediatric Ward, Hospital of Zala County, Zalaegerszeg, Hungary
| | - Yuebo Zhang
- Department of Clinical Genomics and Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Barbara Patócs
- Department of Child Neurology, Bethesda Child Hospital, Budapest, Hungary
| | - Mária Judit Molnár
- Department of Genomic Medicine and Rare Diseases, Semmelweis University, Budapest, Hungary
| | - Gábor Méhes
- Department of Pathology, University of Debrecen, Debrecen, Hungary
| | | | - Rita Jakus
- Department of Child Neurology, Bethesda Child Hospital, Budapest, Hungary
| | - Beáta Bessenyei
- Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Wasantha Ranatunga
- Department of Clinical Genomics and Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Éva Morava
- Department of Clinical Genomics and Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| |
Collapse
|
8
|
Silvaieh S, König T, Wurm R, Parvizi T, Berger-Sieczkowski E, Goeschl S, Hotzy C, Wagner M, Berutti R, Sammler E, Stögmann E, Zimprich A. Comprehensive genetic screening of early-onset dementia patients in an Austrian cohort-suggesting new disease-contributing genes. Hum Genomics 2023; 17:55. [PMID: 37330543 PMCID: PMC10276391 DOI: 10.1186/s40246-023-00499-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/31/2023] [Indexed: 06/19/2023] Open
Abstract
Early-onset dementia (EOD), with symptom onset before age 65, has a strong genetic burden. Due to genetic and clinical overlaps between different types of dementia, whole-exome sequencing (WES) has emerged as an appropriate screening method for diagnostic testing and novel gene-finding approaches. We performed WES and C9orf72 repeat testing in 60 well-defined Austrian EOD patients. Seven patients (12%) carried likely disease-causing variants in monogenic genes, PSEN1, MAPT, APP, and GRN. Five patients (8%) were APOE4 homozygote carriers. Definite and possible risk variants were detected in the genes TREM2, SORL1, ABCA7 and TBK1. In an explorative approach, we cross-checked rare gene variants in our cohort with a curated neurodegeneration candidate gene list and identified DCTN1, MAPK8IP3, LRRK2, VPS13C and BACE1 as promising candidate genes. Conclusively, 12 cases (20%) carried variants relevant to patient counseling, comparable to previously reported studies, and can thus be considered genetically resolved. Reduced penetrance, oligogenic inheritance and not yet identified high-risk genes might explain the high number of unresolved cases. To address this issue, we provide complete genetic and phenotypic information (uploaded to the European Genome-phenome Archive), enabling other researchers to cross-check variants. Thereby, we hope to increase the chance of independently finding the same gene/variant-hit in other well-defined EOD patient cohorts, thus confirming new genetic risk variants or variant combinations.
Collapse
Affiliation(s)
- Sara Silvaieh
- Department of Neurology, Medical University of Vienna, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Theresa König
- Department of Neurology, Medical University of Vienna, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Raphael Wurm
- Department of Neurology, Medical University of Vienna, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Tandis Parvizi
- Department of Neurology, Medical University of Vienna, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Evelyn Berger-Sieczkowski
- Department of Neurology, Medical University of Vienna, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Stella Goeschl
- Department of Neurology, Medical University of Vienna, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Christoph Hotzy
- Department of Neurology, Medical University of Vienna, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Matias Wagner
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Centrum, Munich, Germany
| | - Riccardo Berutti
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Esther Sammler
- Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Elisabeth Stögmann
- Department of Neurology, Medical University of Vienna, Vienna, Austria.
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria.
| | - Alexander Zimprich
- Department of Neurology, Medical University of Vienna, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| |
Collapse
|
9
|
Ji G, Tang Q, Zhu S, Zhu J, Ye P, Xia S, Wu X. stAPAminer: Mining Spatial Patterns of Alternative Polyadenylation for Spatially Resolved Transcriptomic Studies. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:601-618. [PMID: 36669641 PMCID: PMC10787175 DOI: 10.1016/j.gpb.2023.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 12/07/2022] [Accepted: 01/08/2023] [Indexed: 01/19/2023]
Abstract
Alternative polyadenylation (APA) contributes to transcriptome complexity and gene expression regulation and has been implicated in various cellular processes and diseases. Single-cell RNA sequencing (scRNA-seq) has enabled the profiling of APA at the single-cell level; however, the spatial information of cells is not preserved in scRNA-seq. Alternatively, spatial transcriptomics (ST) technologies provide opportunities to decipher the spatial context of the transcriptomic landscape. Pioneering studies have revealed potential spatially variable genes and/or splice isoforms; however, the pattern of APA usage in spatial contexts remains unappreciated. In this study, we developed a toolkit called stAPAminer for mining spatial patterns of APA from spatially barcoded ST data. APA sites were identified and quantified from the ST data. In particular, an imputation model based on the k-nearest neighbors algorithm was designed to recover APA signals, and then APA genes with spatial patterns of APA usage variation were identified. By analyzing well-established ST data of the mouse olfactory bulb (MOB), we presented a detailed view of spatial APA usage across morphological layers of the MOB. We compiled a comprehensive list of genes with spatial APA dynamics and obtained several major spatial expression patterns that represent spatial APA dynamics in different morphological layers. By extending this analysis to two additional replicates of the MOB ST data, we observed that the spatial APA patterns of several genes were reproducible among replicates. stAPAminer employs the power of ST to explore the transcriptional atlas of spatial APA patterns with spatial resolution. This toolkit is available at https://github.com/BMILAB/stAPAminer and https://ngdc.cncb.ac.cn/biocode/tools/BT007320.
Collapse
Affiliation(s)
- Guoli Ji
- Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou 215000, China; Department of Automation, Xiamen University, Xiamen 361005, China
| | - Qi Tang
- Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou 215000, China; Department of Automation, Xiamen University, Xiamen 361005, China
| | - Sheng Zhu
- Department of Automation, Xiamen University, Xiamen 361005, China
| | - Junyi Zhu
- Institute of Neuroscience, Soochow University, Suzhou 215000, China
| | - Pengchao Ye
- Department of Automation, Xiamen University, Xiamen 361005, China
| | - Shuting Xia
- Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou 215000, China; Institute of Neuroscience, Soochow University, Suzhou 215000, China
| | - Xiaohui Wu
- Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou 215000, China.
| |
Collapse
|
10
|
Khabibullina DA, Kolodkina AA, Vizerov TV, Zubkova NA, Bezlepkina OB. [Gonadotropin-dependent precocious puberty: genetic and clinical characteristics]. PROBLEMY ENDOKRINOLOGII 2023; 69:58-66. [PMID: 37448272 DOI: 10.14341/probl13215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/12/2023] [Accepted: 01/22/2023] [Indexed: 07/15/2023]
Abstract
BACKGROUND In 90% cases of girls and 25-60% cases of boys the cause of gonadotropin-dependent precocious puberty (PP) is unclear. Up to 25-27.5% of gonadotropin-dependent PP cases are monogenic and suggest autosomal-dominant inheritance with incomplete sex-dependent penetrance. To date, mutations in genes KISS1, KISS1R, MKRN3, DLK1 have been described as causal variants leading to precocious hypothalamic-pituitary axis activation in childhood. Genetic testing in patients with hereditary forms of PP can expand our knowledge of underlying molecular mechanisms of the disease and it is also necessary for genetic counselling. AIM To study clinical features and genetic characteristics of patients with idiopathic gonadotropin-dependent precocious puberty. MATERIALS AND METHODS A group of patients with idiopathic gonadotropin-dependent precocious puberty and positive family history (early or precocious puberty) was examined. Laboratory and instrumental diagnostic tests, full-exome sequencing (NGS, next-generation sequencing) were provided for all patients. RESULTS The study included 30 patients (29 girls, 1 boy) with idiopathic gonadotropin-dependent precocious puberty. The median of patients age at the time of the examination was 7,2 years [6,5; 7,7]. Positive family history presented in all cases: in 40% of patients on father's side, in 37% - on mother's side, in 23% of patients PP was diagnosed in siblings. The fullexome sequencing was conducted to 21 patients: in 61,9% of cases (95% CI [40;79]) nucleotide variants were identified in genes, associated with gonadotropin-dependent precocious puberty. MKRN3 gene defect was detected in most cases (77% cases (95% CI [49; 92]), which consistent with international data on its highest prevalence in the monogenic forms of PP. In 23% of cases (95% CI [7; 50]) nucleotide variants were identified in other candidate genes associated with neuroontogenesis and neuroendocrine regulation mechanisms of hypothalamic-pituitary axis. CONCLUSION Our study confirms that detailed family history data in children with PP provides a rational approach to molecular-genetic testing. Data of inheritance pattern and clinical manifestations will simplify the diagnosis of hereditary forms of disease and enhance genetic counselling of families, followed by timely examination and administration of pathogenetic therapy.
Collapse
|
11
|
Majumder P, Edmison D, Rodger C, Patel S, Reid E, Gowrishankar S. AP-4 regulates neuronal lysosome composition, function, and transport via regulating export of critical lysosome receptor proteins at the trans-Golgi network. Mol Biol Cell 2022; 33:ar102. [PMID: 35976706 PMCID: PMC9635302 DOI: 10.1091/mbc.e21-09-0473] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The adaptor protein complex-4 or AP-4 is known to mediate autophagosome maturation through regulating sorting of transmembrane cargo such as ATG9A at the Golgi. There is a need to understand AP-4 function in neurons, as mutations in any of its four subunits cause a complex form of hereditary spastic paraplegia (HSP) with intellectual disability. While AP-4 has been implicated in regulating trafficking and distribution of cargo such as ATG9A and APP, little is known about its effect on neuronal lysosomal protein traffic, lysosome biogenesis and function. In this study, we demonstrate that in human iPSC-derived neurons AP-4 regulates lysosome composition, function and transport via regulating export of critical lysosomal receptors, including Sortilin 1, from the trans-Golgi network to endo-lysosomes. Additionally, loss of AP-4 causes endo-lysosomes to stall and build up in axonal swellings potentially through reduced recruitment of retrograde transport machinery to the organelle. These findings of axonal lysosome build-up are highly reminiscent of those observed in Alzheimer's disease as well as in neurons modelling the most common form of HSP, caused by spastin mutations. Our findings implicate AP-4 as a critical regulator of neuronal lysosome biogenesis and altered lysosome function and axonal endo-lysosome transport as an underlying defect in AP-4 deficient HSP. Additionally, our results also demonstrate the utility of the human i3Neuronal model system in investigating neuronal phenotypes observed in AP-4 deficient mice and/or the human AP-4 deficiency syndrome. [Media: see text] [Media: see text].
Collapse
Affiliation(s)
- Piyali Majumder
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Daisy Edmison
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Catherine Rodger
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England, UK
| | - Sruchi Patel
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Evan Reid
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England, UK
| | - Swetha Gowrishankar
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| |
Collapse
|
12
|
Celestino R, Gama JB, Castro-Rodrigues AF, Barbosa DJ, Rocha H, d’Amico EA, Musacchio A, Carvalho AX, Morais-Cabral JH, Gassmann R. JIP3 interacts with dynein and kinesin-1 to regulate bidirectional organelle transport. J Cell Biol 2022; 221:213353. [PMID: 35829703 PMCID: PMC9284427 DOI: 10.1083/jcb.202110057] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 06/04/2022] [Accepted: 06/23/2022] [Indexed: 01/16/2023] Open
Abstract
The MAP kinase and motor scaffold JIP3 prevents excess lysosome accumulation in axons of vertebrates and invertebrates. How JIP3's interaction with dynein and kinesin-1 contributes to organelle clearance is unclear. We show that human dynein light intermediate chain (DLIC) binds the N-terminal RH1 domain of JIP3, its paralog JIP4, and the lysosomal adaptor RILP. A point mutation in RH1 abrogates DLIC binding without perturbing the interaction between JIP3's RH1 domain and kinesin heavy chain. Characterization of this separation-of-function mutation in Caenorhabditis elegans shows that JIP3-bound dynein is required for organelle clearance in the anterior process of touch receptor neurons. Unlike JIP3 null mutants, JIP3 that cannot bind DLIC causes prominent accumulation of endo-lysosomal organelles at the neurite tip, which is rescued by a disease-associated point mutation in JIP3's leucine zipper that abrogates kinesin light chain binding. These results highlight that RH1 domains are interaction hubs for cytoskeletal motors and suggest that JIP3-bound dynein and kinesin-1 participate in bidirectional organelle transport.
Collapse
Affiliation(s)
- Ricardo Celestino
- Instituto de Investigação e Inovação em Saúde—i3S, Universidade do Porto, Porto, Portugal
| | - José B. Gama
- Instituto de Investigação e Inovação em Saúde—i3S, Universidade do Porto, Porto, Portugal
| | | | - Daniel J. Barbosa
- Instituto de Investigação e Inovação em Saúde—i3S, Universidade do Porto, Porto, Portugal,TOXRUN—Toxicology Research Unit, University Institute of Health Sciences, Advanced Polytechnic and University Cooperative (CESPU), Cooperative of Limited Liability (CRL), Gandra, Portugal
| | - Helder Rocha
- Instituto de Investigação e Inovação em Saúde—i3S, Universidade do Porto, Porto, Portugal
| | - Ennio A. d’Amico
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Andrea Musacchio
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany,Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Ana Xavier Carvalho
- Instituto de Investigação e Inovação em Saúde—i3S, Universidade do Porto, Porto, Portugal
| | - João H. Morais-Cabral
- Instituto de Investigação e Inovação em Saúde—i3S, Universidade do Porto, Porto, Portugal
| | - Reto Gassmann
- Instituto de Investigação e Inovação em Saúde—i3S, Universidade do Porto, Porto, Portugal,Correspondence to Reto Gassmann:
| |
Collapse
|
13
|
Snead AM, Gowrishankar S. Loss of MAPK8IP3 Affects Endocytosis in Neurons. Front Cell Neurosci 2022; 16:828071. [PMID: 35711470 PMCID: PMC9196590 DOI: 10.3389/fncel.2022.828071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
Perturbations in endo-lysosomal trafficking pathways are linked to many neurodevelopmental and neurodegenerative diseases. Of relevance to our current study, MAPK8IP3/JIP3, a brain enriched putative adaptor between lysosomes and motors has been previously implicated as a key regulator of axonal lysosome transport. Since de novo variants in MAPK8IP3 have recently been linked to a neurodevelopmental disorder with intellectual disability, there is a need to better understand the functioning of this protein in human neurons. To this end, using induced neurons (i3Neurons) derived from human iPSCs lacking MAPK8IP3, we demonstrate that loss of hMAPK8IP3 affects endocytic uptake in neurons but does not affect the proteolytic activity of lysosomes in neuronal cell bodies. Our findings indicate that MAPK8IP3 may be a regulator of bulk endocytosis in neurons and that altered endocytic uptake may play a role in MAPK8IP3-linked neurodevelopmental disorders.
Collapse
|
14
|
Gui L, Lu W, Shi M, Hu R, Yan zhou, Shen Y, Xu X, Liu J, Xia H, Wang Y, Li W, Lu Y. Liver DNA methylation and transcriptome between 1- and 3-year-old grass carp. AQUACULTURE AND FISHERIES 2022. [DOI: 10.1016/j.aaf.2020.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
15
|
Takahashi Y, Date H, Oi H, Adachi T, Imanishi N, Kimura E, Takizawa H, Kosugi S, Matsumoto N, Kosaki K, Matsubara Y, Mizusawa H. Six years' accomplishment of the Initiative on Rare and Undiagnosed Diseases: nationwide project in Japan to discover causes, mechanisms, and cures. J Hum Genet 2022; 67:505-513. [PMID: 35318459 PMCID: PMC9402437 DOI: 10.1038/s10038-022-01025-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/07/2022] [Accepted: 02/07/2022] [Indexed: 11/09/2022]
Abstract
The identification of causative genetic variants for hereditary diseases has revolutionized clinical medicine and an extensive collaborative framework with international cooperation has become a global trend to understand rare disorders. The Initiative on Rare and Undiagnosed Diseases (IRUD) was established in Japan to provide accurate diagnosis, discover causes, and ultimately provide cures for rare and undiagnosed diseases. The fundamental IRUD system consists of three pillars: IRUD diagnostic coordination, analysis centers (IRUD-ACs), and a data center (IRUD-DC). IRUD diagnostic coordination consists of clinical centers (IRUD-CLs) and clinical specialty subgroups (IRUD-CSSs). In addition, the IRUD coordinating center (IRUD-CC) manages the entire IRUD system and temporarily operates the IRUD resource center (IRUD-RC). By the end of March 2021, 6301 pedigrees consisting of 18,136 individuals were registered in the IRUD. The whole-exome sequencing method was completed in 5136 pedigrees, and a final diagnosis was established in 2247 pedigrees (43.8%). The total number of aberrated genes and pathogenic variants was 657 and 1718, among which 1113 (64.8%) were novel. In addition, 39 novel disease entities or phenotypes with 41 aberrated genes were identified. The 6-year endeavor of IRUD has been an overwhelming success, establishing an all-Japan comprehensive diagnostic and research system covering all geographic areas and clinical specialties/subspecialties. IRUD has accurately diagnosed diseases, identified novel aberrated genes or disease entities, discovered many candidate genes, and enriched phenotypic and pathogenic variant databases. Further promotion of the IRUD is essential for determining causes and developing cures for rare and undiagnosed diseases.
Collapse
Affiliation(s)
- Yuji Takahashi
- Department of Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Hidetoshi Date
- Department of Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Hideki Oi
- Department of Clinical Data Science, Clinical Research and Education Promotion Division, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Takeya Adachi
- Keio Frontier Research & Education Collaborative Square (K-FRECS) at Tonomachi, Keio University, Kawasaki, Japan.,Department of Medical Regulatory Science, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kyoto, Japan.,Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
| | - Noriaki Imanishi
- Japan Agency for Medical Research and Development (AMED), Tokyo, Japan.,Department of Research Promotion and Management, National Cerebral and Cardiovascular Center, Suita, Japan
| | - En Kimura
- Department of Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Japan.,Japan Agency for Medical Research and Development (AMED), Tokyo, Japan.,Astellas Pharma Incorporated, Tokyo, Japan
| | - Hotake Takizawa
- Department of Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Japan.,Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
| | - Shinji Kosugi
- Department of Medical Ethics/Medical Genetics, Kyoto University School of Public Health, Kyoto, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | | | | | - Hidehiro Mizusawa
- Department of Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Japan.
| |
Collapse
|
16
|
Louros N, Ramakers M, Michiels E, Konstantoulea K, Morelli C, Garcia T, Moonen N, D'Haeyer S, Goossens V, Thal DR, Audenaert D, Rousseau F, Schymkowitz J. Mapping the sequence specificity of heterotypic amyloid interactions enables the identification of aggregation modifiers. Nat Commun 2022; 13:1351. [PMID: 35292653 PMCID: PMC8924238 DOI: 10.1038/s41467-022-28955-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 02/11/2022] [Indexed: 02/07/2023] Open
Abstract
Heterotypic amyloid interactions between related protein sequences have been observed in functional and disease amyloids. While sequence homology seems to favour heterotypic amyloid interactions, we have no systematic understanding of the structural rules determining such interactions nor whether they inhibit or facilitate amyloid assembly. Using structure-based thermodynamic calculations and extensive experimental validation, we performed a comprehensive exploration of the defining role of sequence promiscuity in amyloid interactions. Using tau as a model system we demonstrate that proteins with local sequence homology to tau amyloid nucleating regions can modify fibril nucleation, morphology, assembly and spreading of aggregates in cultured cells. Depending on the type of mutation such interactions inhibit or promote aggregation in a manner that can be predicted from structure. We find that these heterotypic amyloid interactions can result in the subcellular mis-localisation of these proteins. Moreover, equilibrium studies indicate that the critical concentration of aggregation is altered by heterotypic interactions. Our findings suggest a structural mechanism by which the proteomic background can modulate the aggregation propensity of amyloidogenic proteins and we discuss how such sequence-specific proteostatic perturbations could contribute to the selective cellular susceptibility of amyloid disease progression. In this work, Louros et al. uncover a rule book for interactions of amyloids with other proteins. This grammar was shown to promote cellular spreading of tau aggregates in cells, but can also be harvested to develop structure-based aggregation blockers.
Collapse
Affiliation(s)
- Nikolaos Louros
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Meine Ramakers
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Emiel Michiels
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Katerina Konstantoulea
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Chiara Morelli
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Teresa Garcia
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Nele Moonen
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Sam D'Haeyer
- VIB Screening Core, Ghent, Belgium.,Centre for Bioassay Development and Screening (C-BIOS), Ghent University, Ghent, Belgium
| | - Vera Goossens
- VIB Screening Core, Ghent, Belgium.,Centre for Bioassay Development and Screening (C-BIOS), Ghent University, Ghent, Belgium
| | - Dietmar Rudolf Thal
- KU Leuven, Leuven Brain Institute, 3000, Leuven, Belgium.,Laboratory for Neuropathology, KU Leuven, and Department of Pathology, UZ Leuven, 3000, Leuven, Belgium
| | - Dominique Audenaert
- VIB Screening Core, Ghent, Belgium.,Centre for Bioassay Development and Screening (C-BIOS), Ghent University, Ghent, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium. .,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium. .,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
| |
Collapse
|
17
|
Wang Z, Zhao H, Xu Y, Zhao J, Song Z, Bi Y, Li Y, Lan X, Pan C, Foulkes NS, Zhang S. Early-life lead exposure induces long-term toxicity in the central nervous system: From zebrafish larvae to juveniles and adults. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 804:150185. [PMID: 34509844 DOI: 10.1016/j.scitotenv.2021.150185] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 06/13/2023]
Abstract
Lead induced neurotoxicity has been extensively investigated. However, the potential connections between early-life lead exposure and the frequently observed aberrant neurobehavior in juveniles and adults remain unclear. In this study, zebrafish model was used to explore the immediate and long-term effects of early-life exposure to environmental levels of lead on the central nervous system, and the cellular and molecular mechanisms underlying the consequent abnormal neurobehavior. Lead exposed zebrafish larvae exhibited neurologic damage and defective neurobehavior. Consistent with clinical studies, despite being raised in lead-free conditions, the juvenile and adult fish experienced lead exposure earlier, presented ADHD-like symptoms, and the adult fish exhibited remarkably affected vitality and shoaling behavior. Their anxiety levels were elevated, whereas their social interaction, as well as learning and memory were strongly depressed. The expression profiles of key genes involved in neurodevelopment and neurotransmitter systems were significantly modulated, in similar patterns as in the larval stage. Notably, the density of neurons was decreased and varicosities in neuronal axons were frequently observed in the lead-exposed groups. It's tempting to speculate that the disruption of early neurodevelopment as well as the prolonged modulation of neuromorphic and neurotransmitter systems contribute to the lead-induced neurobehavioral disorders observed in juveniles and adulthood.
Collapse
Affiliation(s)
- Zuo Wang
- School of Life Sciences, Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, No. 222 South Tianshui Road, Lanzhou 730000, Gansu Province, China
| | - Haiyu Zhao
- School of Life Sciences, Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, No. 222 South Tianshui Road, Lanzhou 730000, Gansu Province, China.
| | - Yanyi Xu
- School of Life Sciences, Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, No. 222 South Tianshui Road, Lanzhou 730000, Gansu Province, China
| | - Jianing Zhao
- School of Life Sciences, Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, No. 222 South Tianshui Road, Lanzhou 730000, Gansu Province, China; Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling 712100, Shaanxi Province, China
| | - Zan Song
- School of Life Sciences, Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, No. 222 South Tianshui Road, Lanzhou 730000, Gansu Province, China
| | - Yi Bi
- School of Life Sciences, Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, No. 222 South Tianshui Road, Lanzhou 730000, Gansu Province, China; Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling 712100, Shaanxi Province, China
| | - Yang Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling 712100, Shaanxi Province, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling 712100, Shaanxi Province, China
| | - Chuanying Pan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling 712100, Shaanxi Province, China
| | - Nicholas S Foulkes
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Shengxiang Zhang
- School of Life Sciences, Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, No. 222 South Tianshui Road, Lanzhou 730000, Gansu Province, China
| |
Collapse
|
18
|
JIP3 links lysosome transport to regulation of multiple components of the axonal cytoskeleton. Commun Biol 2022; 5:5. [PMID: 35013510 PMCID: PMC8748971 DOI: 10.1038/s42003-021-02945-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 12/02/2021] [Indexed: 12/11/2022] Open
Abstract
Lysosome axonal transport is important for the clearance of cargoes sequestered by the endocytic and autophagic pathways. Building on observations that mutations in the JIP3 (MAPK8IP3) gene result in lysosome-filled axonal swellings, we analyzed the impact of JIP3 depletion on the cytoskeleton of human neurons. Dynamic focal lysosome accumulations were accompanied by disruption of the axonal periodic scaffold (spectrin, F-actin and myosin II) throughout each affected axon. Additionally, axonal microtubule organization was locally disrupted at each lysosome-filled swelling. This local axonal microtubule disorganization was accompanied by accumulations of both F-actin and myosin II. These results indicate that transport of axonal lysosomes is functionally interconnected with mechanisms that control the organization and maintenance of the axonal cytoskeleton. They have potential relevance to human neurological disease arising from JIP3 mutations as well as for neurodegenerative diseases associated with the focal accumulations of lysosomes within axonal swellings such as Alzheimer’s disease. Rafiq et al. report that disruption of JIP3-dependent control of axonal lysosome transport in human neurons results in unexpected changes to the organization of multiple cytoskeletal proteins. This study provides new insights that improve our understanding of intellectual disabilities caused by mutations in JIP3, and are relevant for neurodegenerative diseases associated with accumulations of lysosomes such as the Alzheimer’s disease
Collapse
|
19
|
Jones AM. In Pursuit: A Mother's Account of Her Son's Rare Disease Diagnosis Journey. J Patient Cent Res Rev 2021; 8:360-362. [PMID: 34722806 DOI: 10.17294/2330-0698.1845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
|
20
|
Li S, DeLisi LE, McDonough SI. Rare germline variants in individuals diagnosed with schizophrenia within multiplex families. Psychiatry Res 2021; 303:114038. [PMID: 34174581 DOI: 10.1016/j.psychres.2021.114038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 05/27/2021] [Indexed: 12/30/2022]
Abstract
An extensive catalog of common and rare genetic variants contributes to overall risk for schizophrenia and related disorders. As a complement to population genetics efforts, here we present whole genome sequences of multiple affected probands within individual families to search for possible high penetrance driver variants. From a total of 15 families diagnostically evaluated by a single research psychiatrist, we performed whole genome sequencing of a total of 61 affected individuals, called SNPs, indels, and copy number variants, and compared to reference genomes. In fourteen out of fifteen families, the schizophrenia polygenic risk score for each proband was within the control range defined by the Thousand Genomes cohort. In six families, each affected member carried a very rare or private, predicted-damaging, variant in at least one gene. Among these genes, variants in LRP1 and TENM2 suggest these are candidate disease-related genes when taken into context with existing population genetic studies and biological information. Results add to the number of pedigree sequences reported, suggest pathways for the investigation of biological mechanisms, and are consistent with the overall accumulating evidence that very rare damaging variants contribute to the heritability of schizophrenia.
Collapse
Affiliation(s)
| | - Lynn E DeLisi
- Cambridge Health Alliance, Cambridge, MA, United States; Harvard Medical School, Boston, MA, United States
| | | |
Collapse
|
21
|
Yechieli M, Gulsuner S, Ben-Pazi H, Fattal A, Aran A, Kuzminsky A, Sagi L, Guttman D, Schneebaum Sender N, Gross-Tsur V, Klopstock T, Walsh T, Renbaum P, Zeligson S, Shemer Meiri L, Lev D, Shmueli D, Blumkin L, Lahad A, King MC, Levy EL, Segel R. Diagnostic yield of chromosomal microarray and trio whole exome sequencing in cryptogenic cerebral palsy. J Med Genet 2021; 59:759-767. [PMID: 34321325 DOI: 10.1136/jmedgenet-2021-107884] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 07/14/2021] [Indexed: 11/03/2022]
Abstract
OBJECTIVE To determine the yield of genetic diagnoses using chromosomal microarray (CMA) and trio whole exome sequencing (WES), separately and combined, among patients with cryptogenic cerebral palsy (CP). METHODS Trio WES of patients with prior CMA analysis for cryptogenic CP, defined as disabling, non-progressive motor symptoms beginning before the age of 3 years without known cause. RESULTS Given both CMA analysis and trio WES, clinically significant genetic findings were identified for 58% of patients (26 of 45). Diagnoses were eight large CNVs detected by CMA and 18 point mutations detected by trio WES. None had more than one severe mutation. Approximately half of events (14 of 26) were de novo. Yield was significantly higher in patients with CP with comorbidities (69%, 22 of 32) than in those with pure motor CP (31%, 4 of 13; p=0.02). Among patients with genetic diagnoses, CNVs were more frequent than point mutations among patients with congenital anomalies (OR 7.8, 95% CI 1.2 to 52.4) or major dysmorphic features (OR 10.5, 95% CI 1.4 to 73.7). Clinically significant mutations were identified in 18 different genes: 14 with known involvement in CP-related disorders and 4 responsible for other neurodevelopmental conditions. Three possible new candidate genes for CP were ARGEF10, RTF1 and TAOK3. CONCLUSIONS Cryptogenic CP is genetically highly heterogeneous. Genomic analysis has a high yield and is warranted in all these patients. Trio WES has higher yield than CMA, except in patients with congenital anomalies or major dysmorphic features, but these methods are complementary. Patients with negative results with one approach should also be tested by the other.
Collapse
Affiliation(s)
- Michal Yechieli
- Obstetrics and Gynecology, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Suleyman Gulsuner
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Hilla Ben-Pazi
- Pediatric Neurology, Shaare Zedek Medical Center, Jerusalem, Israel.,Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Aviva Fattal
- Pediatric Neurology Unit, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Adi Aran
- Pediatric Neurology, Shaare Zedek Medical Center, Jerusalem, Israel.,Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Alla Kuzminsky
- Pediatric Neurology Institute, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
| | - Liora Sagi
- Pediatric Neurology Unit, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Dafna Guttman
- Pediatric Rehabilitation Department, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Nira Schneebaum Sender
- Pediatric Neurology Unit, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Varda Gross-Tsur
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.,Pediatric Neurology Unit, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Tehila Klopstock
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.,Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Tom Walsh
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Paul Renbaum
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Sharon Zeligson
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | | | - Dorit Lev
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Institute of Medical Genetics, Edith Wolfson Medical Center, Holon, Israel
| | - Dorit Shmueli
- Child Development Services, Clalit Health Services, Tel Aviv, Israel
| | - Luba Blumkin
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Neurology, Edith Wolfson Hospital, Holon, Israel
| | - Amnon Lahad
- Braun School of Public Health, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.,Department of Family Medicine, Clalit Health Services, Jerusalem, Israel
| | - Mary-Claire King
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Ephrat Lahad Levy
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.,Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Reeval Segel
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel .,Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| |
Collapse
|
22
|
Gunarta IK, Yuliana D, Erdenebaatar P, Kishi Y, Boldbaatar J, Suzuki R, Odongoo R, Davaakhuu G, Hohjoh H, Yoshioka K. c-Jun NH 2-terminal kinase (JNK)/stress-activated protein kinase-associated protein 1 (JSAP1) attenuates curcumin-induced cell death differently from its family member, JNK-associated leucine zipper protein (JLP). Drug Discov Ther 2021; 15:66-72. [PMID: 33716240 DOI: 10.5582/ddt.2021.01021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Curcumin, a major component of turmeric, is known to exhibit multiple biological functions including antitumor activity. We previously reported that the mitogen-activated protein kinase (MAPK) scaffold protein c-Jun NH2-terminal kinase (JNK)-associated leucine zipper protein (JLP) reduces curcumin-induced cell death by modulating p38 MAPK and autophagy through the regulation of lysosome positioning. In this study, we investigated the role of JNK/stress-activated protein kinase-associated protein 1 (JSAP1), a JLP family member, in curcumin-induced stress, and found that JSAP1 also attenuates curcumin-induced cell death. However, JSAP1 knockout showed no or little effect on the activation of JNK and p38 MAPKs in response to curcumin. In addition, small molecule inhibitors of JNK and p38 MAPKs did not increase curcumin-induced cell death. Furthermore, JSAP1 depletion did not impair lysosome positioning and autophagosome-lysosome fusion. Instead, we noticed substantial autolysosome accumulation accompanied by an inefficient autophagic flux in JSAP1 knockout cells. Taken together, these results indicate that JSAP1 is involved in curcumin-induced cell death differently from JLP, and may suggest that JSAP1 plays a role in autophagosome degradation and its dysfunction results in enhanced cell death. The findings of this study may contribute to the development of novel therapeutic approaches using curcumin for cancer.
Collapse
Affiliation(s)
- I Ketut Gunarta
- Division of Molecular Cell Signaling, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
| | - Dewi Yuliana
- Division of Molecular Cell Signaling, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
| | - Purev Erdenebaatar
- Division of Molecular Cell Signaling, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
| | - Yuhei Kishi
- Division of Molecular Cell Signaling, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
| | - Jambaldorj Boldbaatar
- Division of Molecular Cell Signaling, Cancer Research Institute, Kanazawa University, Kanazawa, Japan.,Present address: School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Ryusuke Suzuki
- Division of Molecular Cell Signaling, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
| | - Ravdandorj Odongoo
- Division of Molecular Cell Signaling, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
| | - Gantulga Davaakhuu
- Laboratory of Molecular Biology, Institute of General and Experimental Biology, Mongolian Academy of Sciences, Ulaanbaatar, Mongolia
| | - Hirohiko Hohjoh
- Department of Molecular Pharmacology, National Institute of Neuroscience, NCNP, Kodaira, Tokyo, Japan
| | - Katsuji Yoshioka
- Division of Molecular Cell Signaling, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
| |
Collapse
|
23
|
Gowrishankar S, Lyons L, Rafiq NM, Roczniak-Ferguson A, De Camilli P, Ferguson SM. Overlapping roles of JIP3 and JIP4 in promoting axonal transport of lysosomes in human iPSC-derived neurons. Mol Biol Cell 2021; 32:1094-1103. [PMID: 33788575 PMCID: PMC8351540 DOI: 10.1091/mbc.e20-06-0382] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The dependence of neurons on microtubule-based motors for the movement of lysosomes over long distances raises questions about adaptations that allow neurons to meet these demands. Recently, JIP3/MAPK8IP3, a neuronally enriched putative adaptor between lysosomes and motors, was identified as a critical regulator of axonal lysosome abundance. In this study, we establish a human induced pluripotent stem cell (iPSC)-derived neuron model for the investigation of axonal lysosome transport and maturation and show that loss of JIP3 results in the accumulation of axonal lysosomes and the Alzheimer’s disease–related amyloid precursor protein (APP)-derived Aβ42 peptide. We furthermore reveal an overlapping role of the homologous JIP4 gene in lysosome axonal transport. These results establish a cellular model for investigating the relationship between lysosome axonal transport and amyloidogenic APP processing and more broadly demonstrate the utility of human iPSC–derived neurons for the investigation of neuronal cell biology and pathology.
Collapse
Affiliation(s)
- Swetha Gowrishankar
- Departments of Cell Biology and.,Neuroscience.,Program in Cellular Neuroscience, Neurodegeneration and Repair.,Howard Hughes Medical Institute, and
| | - Lila Lyons
- Departments of Cell Biology and.,Neuroscience.,Program in Cellular Neuroscience, Neurodegeneration and Repair.,Howard Hughes Medical Institute, and
| | - Nisha Mohd Rafiq
- Departments of Cell Biology and.,Neuroscience.,Program in Cellular Neuroscience, Neurodegeneration and Repair.,Howard Hughes Medical Institute, and
| | - Agnes Roczniak-Ferguson
- Departments of Cell Biology and.,Neuroscience.,Program in Cellular Neuroscience, Neurodegeneration and Repair
| | - Pietro De Camilli
- Departments of Cell Biology and.,Neuroscience.,Program in Cellular Neuroscience, Neurodegeneration and Repair.,Howard Hughes Medical Institute, and.,Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT 06510
| | - Shawn M Ferguson
- Departments of Cell Biology and.,Neuroscience.,Program in Cellular Neuroscience, Neurodegeneration and Repair
| |
Collapse
|
24
|
Edmison D, Wang L, Gowrishankar S. Lysosome Function and Dysfunction in Hereditary Spastic Paraplegias. Brain Sci 2021; 11:152. [PMID: 33498913 PMCID: PMC7911997 DOI: 10.3390/brainsci11020152] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/15/2021] [Accepted: 01/21/2021] [Indexed: 12/13/2022] Open
Abstract
Hereditary Spastic Paraplegias (HSPs) are a genetically diverse group of inherited neurological diseases with over 80 associated gene loci. Over the last decade, research into mechanisms underlying HSPs has led to an emerging interest in lysosome dysfunction. In this review, we highlight the different classes of HSPs that have been linked to lysosome defects: (1) a subset of complex HSPs where mutations in lysosomal genes are causally linked to the diseases, (2) other complex HSPs where mutation in genes encoding membrane trafficking adaptors lead to lysosomal defects, and (3) a subset of HSPs where mutations affect genes encoding proteins whose function is primarily linked to a different cellular component or organelle such as microtubule severing and Endoplasmic Reticulum-shaping, while also altering to lysosomes. Interestingly, aberrant axonal lysosomes, associated with the latter two subsets of HSPs, are a key feature observed in other neurodegenerative diseases such as Alzheimer's disease. We discuss how altered lysosome function and trafficking may be a critical contributor to HSP pathology and highlight the need for examining these features in the cortico-spinal motor neurons of HSP mutant models.
Collapse
Affiliation(s)
| | | | - Swetha Gowrishankar
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA; (D.E.); (L.W.)
| |
Collapse
|
25
|
Ilinca A, Englund E, Samuelsson S, Truvé K, Kafantari E, Martinez-Majander N, Putaala J, Håkansson C, Lindgren AG, Puschmann A. MAP3K6 Mutations in a Neurovascular Disease Causing Stroke, Cognitive Impairment, and Tremor. NEUROLOGY-GENETICS 2021; 7:e548. [PMID: 33728376 PMCID: PMC7958314 DOI: 10.1212/nxg.0000000000000548] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 11/09/2020] [Indexed: 12/20/2022]
Abstract
Objective To describe a possible novel genetic mechanism for cerebral small vessel disease (cSVD) and stroke. Methods We studied a Swedish kindred with ischemic stroke and intracerebral hemorrhage, tremor, dysautonomia, and mild cognitive decline. Members were examined clinically, radiologically, and by histopathology. Genetic workup included whole-exome sequencing (WES) and whole-genome sequencing (WGS) and intrafamilial cosegregation analyses. Results Fifteen family members were examined clinically. Twelve affected individuals had white matter hyperintensities and 1 or more of (1) stroke episodes, (2) clinically silent lacunar ischemic lesions, and (3) cognitive dysfunction. All affected individuals had tremor and/or atactic gait disturbance. Mild symmetric basal ganglia calcifications were seen in 3 affected members. Postmortem examination of 1 affected member showed pathologic alterations in both small and large arteries the brain. Skin biopsies of 3 affected members showed extracellular amorphous deposits within the subepidermal zone, which may represent degenerated arterioles. WES or WGS did not reveal any potentially disease-causing variants in known genes for cSVDs or idiopathic basal ganglia calcification, but identified 1 heterozygous variant, NM_004672.4 MAP3K6 c.322G>A p.(Asp108Asn), that cosegregated with the disease in this large family. MAP3K6 has known functions in angiogenesis and affects vascular endothelial growth factor expression, which may be implicated in cerebrovascular disease. Conclusions Our data strongly suggest the MAP3K6 variant to be causative for this novel disease phenotype, but the absence of functional data and the present lack of additional families with this disease and MAP3K6 mutations still limit the formal evidence for the variant's pathogenicity.
Collapse
Affiliation(s)
- Andreea Ilinca
- Department of Clinical Sciences Lund, Neurology (A.I., E.K., A.G.L., A.P.), Lund University; Section of Neurology (A.I., E.K., A.G.L., A.P.), Skåne University Hospital, Lund; Department of Clinical Genetics and Pathology (E.E., S.S.), Laboratory Medicine, Region Skåne; Department of Clinical Sciences Lund (E.E.), Division of Pathology, Lund University; Bioinformatics Core Facility (K.T.), Sahlgrenska Academy at University of Gothenburg, Sweden; Neurology (N.M.-M., J.P.), University of Helsinki, and Helsinki University Hospital, Finland; Department of Imaging and Function (C.H.), Skånes University Hospital, Lund; and Department of Clinical Sciences, Diagnostic Radiology (C.H.), Lund University, Sweden
| | - Elisabet Englund
- Department of Clinical Sciences Lund, Neurology (A.I., E.K., A.G.L., A.P.), Lund University; Section of Neurology (A.I., E.K., A.G.L., A.P.), Skåne University Hospital, Lund; Department of Clinical Genetics and Pathology (E.E., S.S.), Laboratory Medicine, Region Skåne; Department of Clinical Sciences Lund (E.E.), Division of Pathology, Lund University; Bioinformatics Core Facility (K.T.), Sahlgrenska Academy at University of Gothenburg, Sweden; Neurology (N.M.-M., J.P.), University of Helsinki, and Helsinki University Hospital, Finland; Department of Imaging and Function (C.H.), Skånes University Hospital, Lund; and Department of Clinical Sciences, Diagnostic Radiology (C.H.), Lund University, Sweden
| | - Sofie Samuelsson
- Department of Clinical Sciences Lund, Neurology (A.I., E.K., A.G.L., A.P.), Lund University; Section of Neurology (A.I., E.K., A.G.L., A.P.), Skåne University Hospital, Lund; Department of Clinical Genetics and Pathology (E.E., S.S.), Laboratory Medicine, Region Skåne; Department of Clinical Sciences Lund (E.E.), Division of Pathology, Lund University; Bioinformatics Core Facility (K.T.), Sahlgrenska Academy at University of Gothenburg, Sweden; Neurology (N.M.-M., J.P.), University of Helsinki, and Helsinki University Hospital, Finland; Department of Imaging and Function (C.H.), Skånes University Hospital, Lund; and Department of Clinical Sciences, Diagnostic Radiology (C.H.), Lund University, Sweden
| | - Katarina Truvé
- Department of Clinical Sciences Lund, Neurology (A.I., E.K., A.G.L., A.P.), Lund University; Section of Neurology (A.I., E.K., A.G.L., A.P.), Skåne University Hospital, Lund; Department of Clinical Genetics and Pathology (E.E., S.S.), Laboratory Medicine, Region Skåne; Department of Clinical Sciences Lund (E.E.), Division of Pathology, Lund University; Bioinformatics Core Facility (K.T.), Sahlgrenska Academy at University of Gothenburg, Sweden; Neurology (N.M.-M., J.P.), University of Helsinki, and Helsinki University Hospital, Finland; Department of Imaging and Function (C.H.), Skånes University Hospital, Lund; and Department of Clinical Sciences, Diagnostic Radiology (C.H.), Lund University, Sweden
| | - Efthymia Kafantari
- Department of Clinical Sciences Lund, Neurology (A.I., E.K., A.G.L., A.P.), Lund University; Section of Neurology (A.I., E.K., A.G.L., A.P.), Skåne University Hospital, Lund; Department of Clinical Genetics and Pathology (E.E., S.S.), Laboratory Medicine, Region Skåne; Department of Clinical Sciences Lund (E.E.), Division of Pathology, Lund University; Bioinformatics Core Facility (K.T.), Sahlgrenska Academy at University of Gothenburg, Sweden; Neurology (N.M.-M., J.P.), University of Helsinki, and Helsinki University Hospital, Finland; Department of Imaging and Function (C.H.), Skånes University Hospital, Lund; and Department of Clinical Sciences, Diagnostic Radiology (C.H.), Lund University, Sweden
| | - Nicolas Martinez-Majander
- Department of Clinical Sciences Lund, Neurology (A.I., E.K., A.G.L., A.P.), Lund University; Section of Neurology (A.I., E.K., A.G.L., A.P.), Skåne University Hospital, Lund; Department of Clinical Genetics and Pathology (E.E., S.S.), Laboratory Medicine, Region Skåne; Department of Clinical Sciences Lund (E.E.), Division of Pathology, Lund University; Bioinformatics Core Facility (K.T.), Sahlgrenska Academy at University of Gothenburg, Sweden; Neurology (N.M.-M., J.P.), University of Helsinki, and Helsinki University Hospital, Finland; Department of Imaging and Function (C.H.), Skånes University Hospital, Lund; and Department of Clinical Sciences, Diagnostic Radiology (C.H.), Lund University, Sweden
| | - Jukka Putaala
- Department of Clinical Sciences Lund, Neurology (A.I., E.K., A.G.L., A.P.), Lund University; Section of Neurology (A.I., E.K., A.G.L., A.P.), Skåne University Hospital, Lund; Department of Clinical Genetics and Pathology (E.E., S.S.), Laboratory Medicine, Region Skåne; Department of Clinical Sciences Lund (E.E.), Division of Pathology, Lund University; Bioinformatics Core Facility (K.T.), Sahlgrenska Academy at University of Gothenburg, Sweden; Neurology (N.M.-M., J.P.), University of Helsinki, and Helsinki University Hospital, Finland; Department of Imaging and Function (C.H.), Skånes University Hospital, Lund; and Department of Clinical Sciences, Diagnostic Radiology (C.H.), Lund University, Sweden
| | - Claes Håkansson
- Department of Clinical Sciences Lund, Neurology (A.I., E.K., A.G.L., A.P.), Lund University; Section of Neurology (A.I., E.K., A.G.L., A.P.), Skåne University Hospital, Lund; Department of Clinical Genetics and Pathology (E.E., S.S.), Laboratory Medicine, Region Skåne; Department of Clinical Sciences Lund (E.E.), Division of Pathology, Lund University; Bioinformatics Core Facility (K.T.), Sahlgrenska Academy at University of Gothenburg, Sweden; Neurology (N.M.-M., J.P.), University of Helsinki, and Helsinki University Hospital, Finland; Department of Imaging and Function (C.H.), Skånes University Hospital, Lund; and Department of Clinical Sciences, Diagnostic Radiology (C.H.), Lund University, Sweden
| | - Arne G Lindgren
- Department of Clinical Sciences Lund, Neurology (A.I., E.K., A.G.L., A.P.), Lund University; Section of Neurology (A.I., E.K., A.G.L., A.P.), Skåne University Hospital, Lund; Department of Clinical Genetics and Pathology (E.E., S.S.), Laboratory Medicine, Region Skåne; Department of Clinical Sciences Lund (E.E.), Division of Pathology, Lund University; Bioinformatics Core Facility (K.T.), Sahlgrenska Academy at University of Gothenburg, Sweden; Neurology (N.M.-M., J.P.), University of Helsinki, and Helsinki University Hospital, Finland; Department of Imaging and Function (C.H.), Skånes University Hospital, Lund; and Department of Clinical Sciences, Diagnostic Radiology (C.H.), Lund University, Sweden
| | - Andreas Puschmann
- Department of Clinical Sciences Lund, Neurology (A.I., E.K., A.G.L., A.P.), Lund University; Section of Neurology (A.I., E.K., A.G.L., A.P.), Skåne University Hospital, Lund; Department of Clinical Genetics and Pathology (E.E., S.S.), Laboratory Medicine, Region Skåne; Department of Clinical Sciences Lund (E.E.), Division of Pathology, Lund University; Bioinformatics Core Facility (K.T.), Sahlgrenska Academy at University of Gothenburg, Sweden; Neurology (N.M.-M., J.P.), University of Helsinki, and Helsinki University Hospital, Finland; Department of Imaging and Function (C.H.), Skånes University Hospital, Lund; and Department of Clinical Sciences, Diagnostic Radiology (C.H.), Lund University, Sweden
| |
Collapse
|
26
|
Fourel G, Boscheron C. Tubulin mutations in neurodevelopmental disorders as a tool to decipher microtubule function. FEBS Lett 2020; 594:3409-3438. [PMID: 33064843 DOI: 10.1002/1873-3468.13958] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 09/28/2020] [Accepted: 10/05/2020] [Indexed: 01/08/2023]
Abstract
Malformations of cortical development (MCDs) are a group of severe brain malformations associated with intellectual disability and refractory childhood epilepsy. Human missense heterozygous mutations in the 9 α-tubulin and 10 β-tubulin isoforms forming the heterodimers that assemble into microtubules (MTs) were found to cause MCDs. However, how a single mutated residue in a given tubulin isoform can perturb the entire microtubule population in a neuronal cell remains a crucial question. Here, we examined 85 MCD-associated tubulin mutations occurring in TUBA1A, TUBB2, and TUBB3 and their location in a three-dimensional (3D) microtubule cylinder. Mutations hitting residues exposed on the outer microtubule surface are likely to alter microtubule association with partners, while alteration of intradimer contacts may impair dimer stability and straightness. Other types of mutations are predicted to alter interdimer and lateral contacts, which are responsible for microtubule cohesion, rigidity, and dynamics. MCD-associated tubulin mutations surprisingly fall into all categories, thus providing unexpected insights into how a single mutation may impair microtubule function and elicit dominant effects in neurons.
Collapse
|
27
|
Guo K, Eid SA, Elzinga SE, Pacut C, Feldman EL, Hur J. Genome-wide profiling of DNA methylation and gene expression identifies candidate genes for human diabetic neuropathy. Clin Epigenetics 2020; 12:123. [PMID: 32787975 PMCID: PMC7425575 DOI: 10.1186/s13148-020-00913-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/27/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Diabetic peripheral neuropathy (DPN) is the most common complication of type 2 diabetes (T2D). Although the cellular and molecular mechanisms of DPN are poorly understood, we and others have shown that altered gene expression and DNA methylation are implicated in disease pathogenesis. However, how DNA methylation might functionally impact gene expression and contribute to nerve damage remains unclear. Here, we analyzed genome-wide transcriptomic and methylomic profiles of sural nerves from T2D patients with DPN. RESULTS Unbiased clustering of transcriptomics data separated samples into groups, which correlated with HbA1c levels. Accordingly, we found 998 differentially expressed genes (DEGs) and 929 differentially methylated genes (DMGs) between the groups with the highest and lowest HbA1c levels. Functional enrichment analysis revealed that DEGs and DMGs were enriched for pathways known to play a role in DPN, including those related to the immune system, extracellular matrix (ECM), and axon guidance. To understand the interaction between the transcriptome and methylome in DPN, we performed an integrated analysis of the overlapping genes between DEGs and DMGs. Integrated functional and network analysis identified genes and pathways modulating functions such as immune response, ECM regulation, and PI3K-Akt signaling. CONCLUSION These results suggest for the first time that DNA methylation is a mechanism regulating gene expression in DPN. Overall, DPN patients with high HbA1c have distinct alterations in sural nerve DNA methylome and transcriptome, suggesting that optimal glycemic control in DPN patients is an important factor in maintaining epigenetic homeostasis and nerve function.
Collapse
Affiliation(s)
- Kai Guo
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, 1301 North Columbia Rd. Stop 9037, Grand Forks, ND 58202-9037 USA
| | - Stephanie A. Eid
- Department of Neurology, School of Medicine, University of Michigan, Ann Arbor, MI 48109 USA
| | - Sarah E. Elzinga
- Department of Neurology, School of Medicine, University of Michigan, Ann Arbor, MI 48109 USA
| | - Crystal Pacut
- Department of Neurology, School of Medicine, University of Michigan, Ann Arbor, MI 48109 USA
| | - Eva L. Feldman
- Department of Neurology, School of Medicine, University of Michigan, Ann Arbor, MI 48109 USA
| | - Junguk Hur
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, 1301 North Columbia Rd. Stop 9037, Grand Forks, ND 58202-9037 USA
| |
Collapse
|
28
|
Sanderson MR, Badior KE, Fahlman RP, Wevrick R. The necdin interactome: evaluating the effects of amino acid substitutions and cell stress using proximity-dependent biotinylation (BioID) and mass spectrometry. Hum Genet 2020; 139:1513-1529. [PMID: 32529326 DOI: 10.1007/s00439-020-02193-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/03/2020] [Indexed: 02/07/2023]
Abstract
Prader-Willi syndrome (PWS) is a neurodevelopmental disorder caused by the loss of function of a set of imprinted genes on chromosome 15q11-15q13. One of these genes, NDN, encodes necdin, a protein that is important for neuronal differentiation and survival. Loss of Ndn in mice causes defects in the formation and function of the nervous system. Necdin is a member of the melanoma-associated antigen gene (MAGE) protein family. The functions of MAGE proteins depend highly on their interactions with other proteins, and in particular MAGE proteins interact with E3 ubiquitin ligases and deubiquitinases to form MAGE-RING E3 ligase-deubiquitinase complexes. Here, we used proximity-dependent biotin identification (BioID) and mass spectrometry (MS) to determine the network of protein-protein interactions (interactome) of the necdin protein. This process yielded novel as well as known necdin-proximate proteins that cluster into a protein network. Next, we used BioID-MS to define the interactomes of necdin proteins carrying coding variants. Variant necdin proteins had interactomes that were distinct from wildtype necdin. BioID-MS is not only a useful tool to identify protein-protein interactions, but also to analyze the effects of variants of unknown significance on the interactomes of proteins involved in genetic disease.
Collapse
Affiliation(s)
| | - Katherine E Badior
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.,Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada
| | - Richard P Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.,Department of Oncology, University of Alberta, Edmonton, AB, Canada
| | - Rachel Wevrick
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada.
| |
Collapse
|