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Deepak K, Roy PK, Das CK, Mukherjee B, Mandal M. Mitophagy at the crossroads of cancer development: Exploring the role of mitophagy in tumor progression and therapy resistance. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119752. [PMID: 38776987 DOI: 10.1016/j.bbamcr.2024.119752] [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: 01/17/2024] [Revised: 04/27/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024]
Abstract
Preserving a functional mitochondrial network is crucial for cellular well-being, considering the pivotal role of mitochondria in ensuring cellular survival, especially under stressful conditions. Mitophagy, the selective removal of damaged mitochondria through autophagy, plays a pivotal role in preserving cellular homeostasis by preventing the production of harmful reactive oxygen species from dysfunctional mitochondria. While the involvement of mitophagy in neurodegenerative diseases has been thoroughly investigated, it is becoming increasingly evident that mitophagy plays a significant role in cancer biology. Perturbations in mitophagy pathways lead to suboptimal mitochondrial quality control, catalyzing various aspects of carcinogenesis, including establishing metabolic plasticity, stemness, metabolic reconfiguration of cancer-associated fibroblasts, and immunomodulation. While mitophagy performs a delicate balancing act at the intersection of cell survival and cell death, mounting evidence indicates that, particularly in the context of stress responses induced by cancer therapy, it predominantly promotes cell survival. Here, we showcase an overview of the current understanding of the role of mitophagy in cancer biology and its potential as a target for cancer therapy. Gaining a more comprehensive insight into the interaction between cancer therapy and mitophagy has the potential to reveal novel targets and pathways, paving the way for enhanced treatment strategies for therapy-resistant tumors in the near future.
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Affiliation(s)
- K Deepak
- Cancer Biology Lab, School of Medical Science & Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India.
| | - Pritam Kumar Roy
- Cancer Biology Lab, School of Medical Science & Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India.
| | - Chandan Kanta Das
- Cancer Biology Lab, School of Medical Science & Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India; Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, BRBII/III, Philadelphia, PA, 19104, USA
| | - Budhaditya Mukherjee
- Infectious Disease and Immunology Lab, School of Medical Science & Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India.
| | - Mahitosh Mandal
- Cancer Biology Lab, School of Medical Science & Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India.
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Daida K, Yoshino H, Malik L, Baker B, Ishiguro M, Genner R, Paquette K, Li Y, Nishioka K, Masuzugawa S, Hirano M, Takahashi K, Kolmogolv M, Billingsley KJ, Funayama M, Blauwendraat C, Hattori N. The Utility of Long-Read Sequencing in Diagnosing Genetic Autosomal Recessive Parkinson's Disease: a genetic screening study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.14.24308784. [PMID: 39108517 PMCID: PMC11302705 DOI: 10.1101/2024.06.14.24308784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Background Mutations within the genes PRKN and PINK1 are the leading cause of early onset autosomal recessive Parkinson's disease (PD). However, the genetic cause of most early-onset PD (EOPD) cases still remains unresolved. Long-read sequencing has successfully identified many pathogenic structural variants that cause disease, but this technology has not been widely applied to PD. We recently identified the genetic cause of EOPD in a pair of monozygotic twins by uncovering a complex structural variant that spans over 7 Mb, utilizing Oxford Nanopore Technologies (ONT) long-read sequencing. In this study, we aimed to expand on this and assess whether a second variant could be detected with ONT long-read sequencing in other unresolved EOPD cases reported to carry one heterozygous variant in PRKN or PINK1. Methods ONT long-read sequencing was performed on patients with one reported PRKN/PINK1 pathogenic variant. EOPD patients with an age at onset younger than 50 were included in this study. As a positive control, we also included EOPD patients who had already been identified to carry two known PRKN pathogenic variants. Initial genetic testing was performed using either short-read targeted panel sequencing for single nucleotide variants and multiplex ligation-dependent probe amplification (MLPA) for copy number variants. Results 48 patients were included in this study (PRKN "one-variant" n = 24, PINK1 "one-variant" n = 12, PRKN "two-variants" n = 12). Using ONT long-read sequencing, we detected a second pathogenic variant in six PRKN "one-variant" patients (26%, 6/23) but none in the PINK1 "one-variant" patients (0%, 0/12). Long-read sequencing identified one case with a complex inversion, two instances of structural variant overlap, and three cases of duplication. In addition, in the positive control PRKN "two-variants" group, we were able to identify both pathogenic variants in PRKN in all the patients (100%, 12/12). Conclusions This data highlights that ONT long-read sequencing is a powerful tool to identify a pathogenic structural variant at the PRKN locus that is often missed by conventional methods. Therefore, for cases where conventional methods fail to detect a second variant for EOPD, long-read sequencing should be considered as an alternative and complementary approach.
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Affiliation(s)
- Kensuke Daida
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Department of Neurology, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Hiroyo Yoshino
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Laksh Malik
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Breeana Baker
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Mayu Ishiguro
- Department of Neurology, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Rylee Genner
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Kimberly Paquette
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Yuanzhe Li
- Department of Neurology, Faculty of Medicine, Juntendo University, Tokyo, Japan
- Department of Diagnosis, Prevention and Treatment of Dementia, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kenya Nishioka
- Department of Neurology, Juntendo Tokyo Koto Geriatric Medical Center, Koto-ku, Tokyo, Japan
| | | | - Makito Hirano
- Department of Neurology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Kenta Takahashi
- Division of Neurology and Gerontology, Department of Internal Medicine, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Mikhail Kolmogolv
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kimberley J Billingsley
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Manabu Funayama
- Department of Neurology, Faculty of Medicine, Juntendo University, Tokyo, Japan
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Cornelis Blauwendraat
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Nobutaka Hattori
- Department of Neurology, Faculty of Medicine, Juntendo University, Tokyo, Japan
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Neurodegenerative Disorders Collaborative Laboratory, RIKEN Center for Brain Science, Wako, Saitama, Japan
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Cogan G, Daida K, Billingsley KJ, Tesson C, Forlani S, Jornea L, Arnaud L, Tissier L, LeGuern E, Singleton AB, Ferrien M, Gervais Bernard H, Lesage S, Blauwendraat C, Brice A. Long-read sequencing unravels the complexity of structural variants in PRKN in two individuals with early-onset Parkinson's disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.02.24306523. [PMID: 38746197 PMCID: PMC11092742 DOI: 10.1101/2024.05.02.24306523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Background PRKN biallelic pathogenic variants are the most common cause of autosomal recessive early-onset Parkinson's disease (PD). However, the variants responsible for suspected PRKN- PD individuals are not always identified with standard genetic testing. Objectives Identify the genetic cause in two siblings with a PRKN -PD phenotype using long-read sequencing (LRS). Methods The genetic investigation involved standard testing using successively multiple ligation probe amplification (MLPA), Sanger sequencing, targeted sequencing, whole-exome sequencing and LRS. Results MLPA and targeted sequencing identified one copy of exon four in PRKN but no other variants were identified. Subsequently, LRS unveiled a large deletion encompassing exon 3 to 4 on one allele and a duplication of exon 3 on the second allele; explaining the siblings' phenotype. MLPA could not identify the balanced rearrangement of exon 3. Conclusions This study highlights the potential utility of long-read sequencing in the context of unsolved typical PRKN- PD individuals.
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Miano-Burkhardt A, Alvarez Jerez P, Daida K, Bandres Ciga S, Billingsley KJ. The Role of Structural Variants in the Genetic Architecture of Parkinson's Disease. Int J Mol Sci 2024; 25:4801. [PMID: 38732020 PMCID: PMC11084710 DOI: 10.3390/ijms25094801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/17/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
Parkinson's disease (PD) significantly impacts millions of individuals worldwide. Although our understanding of the genetic foundations of PD has advanced, a substantial portion of the genetic variation contributing to disease risk remains unknown. Current PD genetic studies have primarily focused on one form of genetic variation, single nucleotide variants (SNVs), while other important forms of genetic variation, such as structural variants (SVs), are mostly ignored due to the complexity of detecting these variants with traditional sequencing methods. Yet, these forms of genetic variation play crucial roles in gene expression and regulation in the human brain and are causative of numerous neurological disorders, including forms of PD. This review aims to provide a comprehensive overview of our current understanding of the involvement of coding and noncoding SVs in the genetic architecture of PD.
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Affiliation(s)
- Abigail Miano-Burkhardt
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD 20892, USA; (A.M.-B.); (K.D.)
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD 20892, USA; (P.A.J.); (S.B.C.)
| | - Pilar Alvarez Jerez
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD 20892, USA; (P.A.J.); (S.B.C.)
| | - Kensuke Daida
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD 20892, USA; (A.M.-B.); (K.D.)
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD 20892, USA; (P.A.J.); (S.B.C.)
| | - Sara Bandres Ciga
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD 20892, USA; (P.A.J.); (S.B.C.)
| | - Kimberley J. Billingsley
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD 20892, USA; (A.M.-B.); (K.D.)
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD 20892, USA; (P.A.J.); (S.B.C.)
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Daida K, Funayama M, Billingsley KJ, Malik L, Miano-Burkhardt A, Leonard HL, Makarious MB, Iwaki H, Ding J, Gibbs JR, Ishiguro M, Yoshino H, Ogaki K, Oyama G, Nishioka K, Nonaka R, Akamatsu W, Blauwendraat C, Hattori N. Long-Read Sequencing Resolves a Complex Structural Variant in PRKN Parkinson's Disease. Mov Disord 2023; 38:2249-2257. [PMID: 37926948 PMCID: PMC10843047 DOI: 10.1002/mds.29610] [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: 06/27/2023] [Revised: 08/17/2023] [Accepted: 09/11/2023] [Indexed: 11/07/2023] Open
Abstract
BACKGROUND Parkin RBR E3 ubiquitin-protein ligase (PRKN) mutations are the most common cause of young onset and autosomal recessive Parkinson's disease (PD). PRKN is located in FRA6E, which is one of the common fragile sites in the human genome, making this region prone to structural variants. However, complex structural variants such as inversions of PRKN are seldom reported, suggesting that there are potentially unrevealed complex pathogenic PRKN structural variants. OBJECTIVES To identify complex structural variants in PRKN using long-read sequencing. METHODS We investigated the genetic cause of monozygotic twins presenting with a young onset dystonia-parkinsonism using targeted sequencing, whole exome sequencing, multiple ligation probe amplification, and long-read sequencing. We assessed the presence and frequency of complex inversions overlapping PRKN using whole-genome sequencing data of Accelerating Medicines Partnership Parkinson's disease (AMP-PD) and United Kingdom (UK)-Biobank datasets. RESULTS Multiple ligation probe amplification identified a heterozygous exon three deletion in PRKN and long-read sequencing identified a large novel inversion spanning over 7 Mb, including a large part of the coding DNA sequence of PRKN. We could diagnose the affected subjects as compound heterozygous carriers of PRKN. We analyzed whole genome sequencing data of 43,538 participants of the UK-Biobank and 4941 participants of the AMP-PD datasets. Nine inversions in the UK-Biobank and two in AMP PD were identified and were considered potentially damaging and likely to affect PRKN expression. CONCLUSIONS This is the first report describing a large 7 Mb inversion involving breakpoints outside of PRKN. This study highlights the importance of using long-read sequencing for structural variant analysis in unresolved young-onset PD cases. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
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Affiliation(s)
- Kensuke Daida
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
| | - Manabu Funayama
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kimberley J Billingsley
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Laksh Malik
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Abigail Miano-Burkhardt
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Hampton L. Leonard
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Mary B. Makarious
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK, WC1N 3BG
- UCL Movement Disorders Centre, University College London, London, UK, WC1N 3BG
| | - Hirotaka Iwaki
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
| | - Jinhui Ding
- Computational Biology Group, Laboratory of Neurogenetics,National Institute on Aging, NIH, PorterNeuroscience ResearchCenter,Bethesda, MD, USA
| | - J. Raphael Gibbs
- Computational Biology Group, Laboratory of Neurogenetics,National Institute on Aging, NIH, PorterNeuroscience ResearchCenter,Bethesda, MD, USA
| | - Mayu Ishiguro
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
| | - Hiroyo Yoshino
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kotaro Ogaki
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
| | - Genko Oyama
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
| | - Kenya Nishioka
- Department of Neurology, Juntendo Tokyo Koto Geriatric Medical Center 3-3-20 Shinsuna, Koto-ku, Tokyo 136-0075
| | - Risa Nonaka
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
- Department of Clinical Data of Parkinson’s Disease, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Center for Genomic and Regenerative Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Wado Akamatsu
- Center for Genomic and Regenerative Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Cornelis Blauwendraat
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Nobutaka Hattori
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Neurodegenerative Disorders Collaborative Laboratory, RIKEN Center for Brain Science, Wako, Saitama, Japan
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Kitada T, Ardah MT, Haque ME. History of Parkinson's Disease-Associated Gene, Parkin: Research over a Quarter Century in Quest of Finding the Physiological Substrate. Int J Mol Sci 2023; 24:16734. [PMID: 38069057 PMCID: PMC10706564 DOI: 10.3390/ijms242316734] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
Parkin, the gene responsible for hereditary Parkinson's disease (PD) called "Autosomal Recessive Juvenile Parkinsonism (AR-JP)" was discovered a quarter of a century ago. Owing to its huge gene structure and unique protein functions, parkin has become a subject of interest to those involved in PD research and researchers and clinicians in various fields and is being vigorously studied worldwide in relation to its nature and disease. The gene structure was registered under the gene name "parkin" in the GenBank in 1997. In 1998, deletion and point mutations in the parkin gene were reported, thereby demonstrating parkin is the causative gene for hereditary PD. Although 25 years have passed since the gene's discovery and many researchers have worked tirelessly to elucidate the function of the Parkin protein and the mechanism of its role against neuronal cell death and pathogenesis remain unknown, which raises a major question concerning the current leading hypothesis. In this review, we present the results of related research on the parkin gene in chronological order and discuss unresolved problems concerning its function and pathology as well as new trends in the research conducted to solve them. The relationship between parkin and tumorigenesis has also been addressed from the perspective of Parkin's redox molecule.
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Affiliation(s)
- Tohru Kitada
- Otawa-Kagaku, Parkinson Clinic and Research, Kamakura 247-0061, Japan;
| | - Mustafa T. Ardah
- Department of Biochemistry and Molecular Biology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates;
| | - M. Emdadul Haque
- Department of Biochemistry and Molecular Biology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates;
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
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7
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Daida K, Funayama M, Billingsley KJ, Malik L, Miano-Burkhardt A, Leonard HL, Makarious MB, Iwaki H, Ding J, Gibbs JR, Ishiguro M, Yoshino H, Ogaki K, Oyama G, Nishioka K, Nonaka R, Akamatsu W, Blauwendraat C, Hattori N. Long-read sequencing resolves a complex structural variant in PRKN Parkinson's disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.14.23293948. [PMID: 37790330 PMCID: PMC10543050 DOI: 10.1101/2023.08.14.23293948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Background PRKN mutations are the most common cause of young onset and autosomal recessive Parkinson's disease (PD). PRKN is located in FRA6E which is one of the common fragile sites in the human genome, making this region prone to structural variants. However, complex structural variants such as inversions of PRKN are seldom reported, suggesting that there are potentially unrevealed complex pathogenic PRKN structural variants. Objectives To identify complex structural variants in PRKN using long-read sequencing. Methods We investigated the genetic cause of monozygotic twins presenting with a young onset dystonia-parkinsonism using targeted sequencing, whole exome sequencing, multiple ligation probe amplification, and long-read. We assessed the presence and frequency of complex inversions overlapping PRKN using whole-genome sequencing data of AMP-PD and UK-Biobank datasets. Results Multiple ligation probe amplification identified a heterozygous exon 3 deletion in PRKN and long-read sequencing identified a large novel inversion spanning over 7Mb, including a large part of the coding DNA sequence of PRKN. We could diagnose the affected subjects as compound heterozygous carriers of PRKN. We analyzed whole genome sequencing data of 43,538 participants of the UK-Biobank and 4,941 participants of the AMP-PD datasets. Nine inversions in the UK-Biobank and two in AMP PD were identified and were considered potentially damaging and likely to affect PRKN isoforms. Conclusions This is the first report describing a large 7Mb inversion involving breakpoints outside of PRKN. This study highlights the importance of using long-read whole genome sequencing for structural variant analysis in unresolved young-onset PD cases.
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Affiliation(s)
- Kensuke Daida
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
| | - Manabu Funayama
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kimberley J Billingsley
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Laksh Malik
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Abigail Miano-Burkhardt
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Hampton L. Leonard
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
- German Center for Neurodegenerative Diseases (DZNE), Tubingen, Germany
| | - Mary B. Makarious
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK, WC1N 3BG
- UCL Movement Disorders Centre, University College London, London, UK, WC1N 3BG
| | - Hirotaka Iwaki
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
| | - Jinhui Ding
- BiocomputationalGroup, Laboratory of Neurogenetics,National Institute on Aging, NIH, PorterNeuroscience ResearchCenter,Bethesda, MD, USA
| | - J. Raphael Gibbs
- BiocomputationalGroup, Laboratory of Neurogenetics,National Institute on Aging, NIH, PorterNeuroscience ResearchCenter,Bethesda, MD, USA
| | - Mayu Ishiguro
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
| | - Hiroyo Yoshino
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kotaro Ogaki
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
| | - Genko Oyama
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
| | - Kenya Nishioka
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
| | - Risa Nonaka
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
- Department of Clinical Data of Parkinson’s Disease, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Center for Genomic and Regenerative Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Wado Akamatsu
- Center for Genomic and Regenerative Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Cornelis Blauwendraat
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Nobutaka Hattori
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Neurodegenerative Disorders Collaborative Laboratory, RIKEN Center for Brain Science, Wako, Saitama, Japan
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Hyblova M, Gnip A, Kucharik M, Budis J, Sekelska M, Minarik G. Maternal Copy Number Imbalances in Non-Invasive Prenatal Testing: Do They Matter? Diagnostics (Basel) 2022; 12:diagnostics12123056. [PMID: 36553064 PMCID: PMC9777446 DOI: 10.3390/diagnostics12123056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Non-invasive prenatal testing (NIPT) has become a routine practice in screening for common aneuploidies of chromosomes 21, 18, and 13 and gonosomes X and Y in fetuses worldwide since 2015 and has even expanded to include smaller subchromosomal events. In fact, the fetal fraction represents only a small proportion of cell-free DNA on a predominant background of maternal DNA. Unlike fetal findings that have to be confirmed using invasive testing, it has been well documented that NIPT provides information on maternal mosaicism, occult malignancies, and hidden health conditions due to copy number variations (CNVs) with diagnostic resolution. Although large duplications or deletions associated with certain medical conditions or syndromes are usually well recognized and easy to interpret, very little is known about small, relatively common copy number variations on the order of a few hundred kilobases and their potential impact on human health. We analyzed data from 6422 NIPT patient samples with a CNV detection resolution of 200 kb for the maternal genome and identified 942 distinct CNVs; 328 occurred repeatedly. We defined them as multiple occurring variants (MOVs). We scrutinized the most common ones, compared them with frequencies in the gnomAD SVs v2.1, dbVar, and DGV population databases, and analyzed them with an emphasis on genomic content and potential association with specific phenotypes.
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Affiliation(s)
- Michaela Hyblova
- Medirex Group Academy n.o., Novozamocka 67, 949 05 Nitra, Slovakia
- Trisomy Test s.r.o., Novozamocka 67, 949 05 Nitra, Slovakia
- Correspondence:
| | - Andrej Gnip
- Medirex a.s., Galvaniho 17/C, 820 16 Bratislava, Slovakia
| | | | - Jaroslav Budis
- Geneton s.r.o., Ilkovicova 8, 841 04 Bratislava, Slovakia
| | - Martina Sekelska
- Medirex Group Academy n.o., Novozamocka 67, 949 05 Nitra, Slovakia
- Trisomy Test s.r.o., Novozamocka 67, 949 05 Nitra, Slovakia
| | - Gabriel Minarik
- Medirex Group Academy n.o., Novozamocka 67, 949 05 Nitra, Slovakia
- Trisomy Test s.r.o., Novozamocka 67, 949 05 Nitra, Slovakia
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9
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Grimaldo L, Sandoval A, Duran P, Gómez Flores-Ramos L, Felix R. The ubiquitin E3 ligase Parkin regulates neuronal Ca V1.3 channel functional expression. J Neurophysiol 2022; 128:1555-1564. [PMID: 36350063 DOI: 10.1152/jn.00287.2022] [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: 11/11/2022] Open
Abstract
Neuronal L-type Ca2+ channels of the CaV1.3 subclass are transmembrane protein complexes that contribute to the pacemaker activity in the adult substantia nigra dopaminergic neurons. The altered function of these channels may play a role in the development and progress of neurodegenerative mechanisms implicated in Parkinson's disease (PD). Although L-type channel expression is precisely regulated, an increased functional expression has been observed in PD. Previously, we showed that Parkin, an E3 enzyme of the ubiquitin-proteasome system (UPS) interacts with neuronal CaV2.2 channels promoting their ubiquitin-mediated degradation. In addition, previous studies show an increase in CaV1.3 channel activity in dopaminergic neurons of the SNc and that Parkin expression is reduced in PD. These findings suggest that the decrease in Parkin may affect the proteasomal degradation of CaV1.3, which helps explain the increase in channel activity. Therefore, the present report aims to gain insight into the degradation mechanisms of the neuronal CaV1.3 channel by the UPS. Immunoprecipitation assays showed the interaction between Parkin and the CaV1.3 channels expressed in HEK-293 cells and neural tissues. Likewise, Parkin overexpression reduced the total and membrane channel levels and decreased the current density. Consistent with this, patch-clamp recordings in the presence of an inhibitor of the UPS, MG132, prevented the effects of Parkin, suggesting enhanced channel proteasomal degradation. In addition, the half-life of the pore-forming CaV1.3α1 protein was significantly reduced by Parkin overexpression. Finally, electrophysiological recordings using a PRKN knockout HEK-293 cell line generated by CRISPR/Cas9 showed increased current density. These results suggest that Parkin promotes the proteasomal degradation of CaV1.3, which may be a relevant aspect for the pathophysiology of PD.NEW & NOTEWORTHY The increased expression of CaV1.3 calcium channels is a crucial feature of Parkinson's disease (PD) pathophysiology. However, the mechanisms that determine this increase are not yet defined. Parkin, an enzyme of the ubiquitin-proteasome system, is known to interact with neuronal channels promoting their ubiquitin-mediated degradation. Interestingly, Parkin mutations also play a role in PD. Here, the degradation mechanisms of CaV1.3 channels and their relationship with the pathophysiology of PD are studied in detail.
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Affiliation(s)
- Lizbeth Grimaldo
- Conacyt, Population Health Research Center, National Institute of Public Health, Cuernavaca, Mexico
| | - Alejandro Sandoval
- School of Medicine FES Iztacala, National Autonomous University of Mexico (UNAM), Tlalnepantla, Mexico
| | - Paz Duran
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, New York
| | | | - Ricardo Felix
- Department of Cell Biology, Centre for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav-IPN), Mexico City, Mexico
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10
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Aksoy Yasar FB, Shingu T, Zamler DB, Zaman MF, Chien DL, Zhang Q, Ren J, Hu J. Quaking but not parkin is the major tumor suppressor in 6q deleted region in glioblastoma. Front Cell Dev Biol 2022; 10:931387. [PMID: 36051438 PMCID: PMC9424994 DOI: 10.3389/fcell.2022.931387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Glioblastoma (GBM) is a high-grade, aggressive brain tumor with dismal median survival time of 15 months. Chromosome 6q (Ch6q) is a hotspot of genomic alterations, which is commonly deleted or hyper-methylated in GBM. Two neighboring genes in this region, QKI and PRKN have been appointed as tumor suppressors in GBM. While a genetically modified mouse model (GEMM) of GBM has been successfully generated with Qk deletion in the central nervous system (CNS), in vivo genetic evidence supporting the tumor suppressor function of Prkn has not been established. In the present study, we generated a mouse model with Prkn-null allele and conditional Trp53 and Pten deletions in the neural stem cells (NSCs) and compared the tumorigenicity of this model to our previous GBM model with Qk deletion within the same system. We find that Qk but not Prkn is the potent tumor suppressor in the frequently altered Ch6q region in GBM.
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Affiliation(s)
- Fatma Betul Aksoy Yasar
- Department of Cancer Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
| | - Takashi Shingu
- Department of Cancer Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
| | - Daniel B. Zamler
- Department of Cancer Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Mohammad Fayyad Zaman
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
| | - Derek Lin Chien
- School of Arts and Sciences, University of Rochester, Rochester, NY, United States
| | - Qiang Zhang
- Department of Cancer Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
| | - Jiangong Ren
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jian Hu
- Department of Cancer Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
- *Correspondence: Jian Hu,
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11
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Zhang F, Wu Z, Long F, Tan J, Gong N, Li X, Lin C. The Roles of ATP13A2 Gene Mutations Leading to Abnormal Aggregation of α-Synuclein in Parkinson’s Disease. Front Cell Neurosci 2022; 16:927682. [PMID: 35875356 PMCID: PMC9296842 DOI: 10.3389/fncel.2022.927682] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
Parkinson’s disease (PD) is the second most common neurodegenerative disease. PARK9 (also known as ATP13A2) is recognized as one of the key genes that cause PD, and a mutation in this gene was first discovered in a rare case of PD in an adolescent. Lewy bodies (LBs) formed by abnormal aggregation of α-synuclein, which is encoded by the SNCA gene, are one of the pathological diagnostic criteria for PD. LBs are also recognized as one of the most important features of PD pathogenesis. In this article, we first summarize the types of mutations in the ATP13A2 gene and their effects on ATP13A2 mRNA and protein structure; then, we discuss lysosomal autophagy inhibition and the molecular mechanism of abnormal α-synuclein accumulation caused by decreased levels and dysfunction of the ATP13A2 protein in lysosomes. Finally, this article provides a new direction for future research on the pathogenesis and therapeutic targets for ATP13A2 gene-related PD from the perspective of ATP13A2 gene mutations and abnormal aggregation of α-synuclein.
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Affiliation(s)
- Fan Zhang
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Zhiwei Wu
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Fei Long
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Jieqiong Tan
- Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Key Laboratory of Molecular Precision Medicine of Hunan Province, Center for Medical Genetics, Institute of Molecular Precision Medicine, Xiangya Hospital of Central South University, Changsha, China
| | - Ni Gong
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Xiaorong Li
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Changwei Lin
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- *Correspondence: Changwei Lin, orcid.org/0000-0003-1676-0912
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12
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Genotype–Phenotype Correlations for Putative Haploinsufficient Genes in Deletions of 6q26-q27: Report of Eight Patients and Review of Literature. Glob Med Genet 2022; 9:166-174. [PMID: 35707784 PMCID: PMC9192176 DOI: 10.1055/s-0042-1743568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 01/11/2022] [Indexed: 11/06/2022] Open
Abstract
Background
Cytogenomic analyses have been used to detect pathogenic copy number variants. Patients with deletions at 6q26-q27 present variable clinical features. We reported clinical and cytogenomic findings of eight unrelated patients with a deletion of 6q26-q27. A systematic review of the literature found 28 patients with a deletion of 6q26-q27 from 2010 to 2020.
Results
For these 36 patients, the sex ratio showed equal occurrence between males and females; 29 patients (81%) had a terminal deletion and seven patients (19%) had a proximal or distal interstitial deletion. Of the 22 patients with parental studies, deletions of de novo, maternal, paternal, and bi-parental inheritance accounted for 64, 18, 14, and 4% of patients, respectively. The most common clinical findings were brain abnormalities (100%) in fetuses observed by ultrasonography followed by developmental delay and intellectual disability (81%), brain abnormalities (72%), facial dysmorphism (66%), hypotonia (63%), learning difficulty or language delay (50%), and seizures (47%) in pediatric and adult patients. Anti-epilepsy treatment showed the effect on controlling seizures in these patients. Cytogenomic mapping defined one proximal critical region at 6q26 containing the putative haploinsufficient gene
PRKN
and one distal critical region at 6q27 containing two haploinsufficient genes
DLL1
and
TBP
. Deletions involving the
PRKN
gene could associate with early-onset Parkinson disease and autism spectrum disorder; deletions involving the
DLL1
gene correlate with the 6q terminal deletion syndrome.
Conclusion
The genotype–phenotype correlations for putative haploinsufficient genes in deletions of 6q26-q27 provided evidence for precise diagnostic interpretation, genetic counseling, and clinical management of patients with a deletion of 6q26-q27.
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Kapadia BB, Roychowdhury A, Kayastha F, Nanaji N, Gartenhaus RB. PARK2 regulates eIF4B-driven lymphomagenesis. Mol Cancer Res 2022; 20:molcanres.MCR-21-0729-A.2021. [PMID: 35191952 PMCID: PMC9339581 DOI: 10.1158/1541-7786.mcr-21-0729] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/07/2021] [Accepted: 01/26/2022] [Indexed: 01/09/2023]
Abstract
Patients with high-risk diffuse large B-cell lymphoma (DLBCL) have poor outcomes following first-line cyclophosphamide, doxorubicin, vincristine, prednisone, and rituximab (R-CHOP); thus, treatment of this fatal disease remains an area of unmet medical need and requires identification of novel therapeutic approaches. Dysregulation of protein translation initiation has emerged as a common downstream node in several malignancies, including lymphoma. Ubiquitination, a prominent post-translational modification associated with substrate degradation, has recently been shown to be a key modulator of nascent peptide synthesis by limiting several translational initiation factors. While a few deubiquitinases have been identified, the E3-ligase responsible for the critical ubiquitination of these translational initiation factors is still unknown. In this study, using complementary cellular models along with clinical readouts, we establish that PARK2 ubiquitinates eIF4B and consequently regulates overall protein translational activity. The formation of this interaction depends on upstream signaling, which is negatively regulated at the protein level of PARK2. Through biochemical, mutational, and genetic studies, we identified PARK2 as a mTORC1 substrate. mTORC1 phosphorylates PARK2 at Ser127, which blocks its cellular ubiquitination activity, thereby hindering its tumor suppressor effect on eIF4B's stability. This resultant increase of eIF4B protein level helps drive enhanced overall protein translation. These data support a novel paradigm in which PARK2-generated eIF4B ubiquitination serves as an anti-oncogenic intracellular inhibitor of protein translation, attenuated by mTORC1 signaling. Implications: Our data implicates the FASN/mTOR-PARK2-eIF4B axis as a critical driver of enhanced oncogene expression contributing to lymphomagenesis.
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Affiliation(s)
- Bandish B. Kapadia
- Section of Hematology and Oncology, Medicine Service, McGuire Cancer Center, Hunter Holmes McGuire VA Medical Center, Richmond, Virginia
- Division of Hematology, Oncology, and Palliative Care, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Anirban Roychowdhury
- Section of Hematology and Oncology, Medicine Service, McGuire Cancer Center, Hunter Holmes McGuire VA Medical Center, Richmond, Virginia
- Division of Hematology, Oncology, and Palliative Care, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Forum Kayastha
- Section of Hematology and Oncology, Medicine Service, McGuire Cancer Center, Hunter Holmes McGuire VA Medical Center, Richmond, Virginia
- Division of Hematology, Oncology, and Palliative Care, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Nahid Nanaji
- Department of Veteran Affairs, Maryland Healthcare System, Baltimore, Maryland
| | - Ronald B. Gartenhaus
- Section of Hematology and Oncology, Medicine Service, McGuire Cancer Center, Hunter Holmes McGuire VA Medical Center, Richmond, Virginia
- Division of Hematology, Oncology, and Palliative Care, Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
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14
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Lokanga RA, Kumari D, Usdin K. Common Threads: Aphidicolin-Inducible and Folate-Sensitive Fragile Sites in the Human Genome. Front Genet 2021; 12:708860. [PMID: 34567068 PMCID: PMC8456018 DOI: 10.3389/fgene.2021.708860] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/28/2021] [Indexed: 11/13/2022] Open
Abstract
The human genome has many chromosomal regions that are fragile, demonstrating chromatin breaks, gaps, or constrictions on exposure to replication stress. Common fragile sites (CFSs) are found widely distributed in the population, with the largest subset of these sites being induced by aphidicolin (APH). Other fragile sites are only found in a subset of the population. One group of these so-called rare fragile sites (RFSs) is induced by folate stress. APH-inducible CFSs are generally located in large transcriptionally active genes that are A + T rich and often enriched for tracts of AT-dinucleotide repeats. In contrast, all the folate-sensitive sites mapped to date consist of transcriptionally silenced CGG microsatellites. Thus, all the folate-sensitive fragile sites may have a very similar molecular basis that differs in key ways from that of the APH CFSs. The folate-sensitive FSs include FRAXA that is associated with Fragile X syndrome (FXS), the most common heritable form of intellectual disability. Both CFSs and RFSs can cause chromosomal abnormalities. Recent work suggests that both APH-inducible fragile sites and FRAXA undergo Mitotic DNA synthesis (MiDAS) when exposed to APH or folate stress, respectively. Interestingly, blocking MiDAS in both cases prevents chromosome fragility but increases the risk of chromosome mis-segregation. MiDAS of both APH-inducible and FRAXA involves conservative DNA replication and POLD3, an accessory subunit of the replicative polymerase Pol δ that is essential for break-induced replication (BIR). Thus, MiDAS is thought to proceed via some form of BIR-like process. This review will discuss the recent work that highlights the similarities and differences between these two groups of fragile sites and the growing evidence for the presence of many more novel fragile sites in the human genome.
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Affiliation(s)
| | - Daman Kumari
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Karen Usdin
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
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15
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Murillo-González FE, García-Aguilar R, Vega L, Elizondo G. Regulation of Parkin expression as the key balance between neural survival and cancer cell death. Biochem Pharmacol 2021; 190:114650. [PMID: 34111426 DOI: 10.1016/j.bcp.2021.114650] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 11/25/2022]
Abstract
Parkin is a cytosolic E3 ubiquitin ligase that plays an important role in neuroprotection by targeting several proteins to be degraded by the 26S proteasome. Its dysfunction has been associated not only with Parkinson's disease (PD) but also with other neurodegenerative pathologies, such as Alzheimer's disease and Huntington's disease. More recently, Parkin has been identified as a tumor suppressor gene implicated in cancer development. Due to the important roles that this E3 ubiquitin ligase plays in cellular homeostasis, its expression, activity, and turnover are tightly regulated. Several reviews have addressed Parkin regulation; however, genetic and epigenetic regulation have been excluded. In addition to posttranslational modifications (PTMs), this review examines the regulatory mechanisms that control Parkin function through gene expression, epigenetic regulation, and degradation. Furthermore, the consequences of disrupting these regulatory processes on human health are discussed.
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Affiliation(s)
| | | | - Libia Vega
- Department of Toxicology, CINVESTAV-IPN, Av. IPN 2508, C.P. 07360 Mexico City, Mexico
| | - Guillermo Elizondo
- Department of Cellular Biology, CINVESTAV-IPN, Av. IPN 2508, C.P. 07360 Mexico City, Mexico.
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16
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Perwez A, Wahabi K, Rizvi MA. Parkin: A targetable linchpin in human malignancies. Biochim Biophys Acta Rev Cancer 2021; 1876:188533. [PMID: 33785381 DOI: 10.1016/j.bbcan.2021.188533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/21/2021] [Accepted: 03/21/2021] [Indexed: 12/16/2022]
Abstract
Parkin, an E3 ubiquitin ligase has been found to be deregulated in a variety of human cancers. Our current understanding is endowed with strong evidences that Parkin plays crucial role in the pathogenesis of cancer by controlling/interfering with major hallmarks of cancer delineated till today. Consistent with the idea of mitophagy, the existing studies imitates the tumor suppressive potential of Parkin, resolved by its capacity to regulate cell proliferation, cell migration, angiogenesis, apoptosis and overall cellular survival. Dysfunction of Parkin has resulted in the loss of ubiquitination of cell cycle components followed by their accumulation leading to genomic instability, perturbed cell cycle and eventually tumor progression. In this review, we provide an overview of current knowledge about the critical role of Parkin in cancer development and progression and have focussed on its therapeutic implications highlighting the diagnostic and prognostic value of Parkin as a biomarker. We earnestly hope that an in-depth knowledge of Parkin will provide a linchpin to target in various cancers that will open a new door of clinical applications and therapeutics.
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Affiliation(s)
- Ahmad Perwez
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Khushnuma Wahabi
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Moshahid A Rizvi
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India.
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17
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Brewer K, Nip I, Bellizzi J, Costa-Guda J, Arnold A. Molecular analysis of cyclin D1 modulators PRKN and FBX4 as candidate tumor suppressors in sporadic parathyroid adenomas. Endocr Connect 2021; 10:302-308. [PMID: 33617468 PMCID: PMC8052572 DOI: 10.1530/ec-21-0055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 02/17/2021] [Indexed: 11/10/2022]
Abstract
OBJECTIVE Primary hyperparathyroidism is most often caused by a sporadic single-gland parathyroid adenoma (PTA), a tumor type for which cyclin D1 is the only known and experimentally validated oncoprotein. However, the molecular origins of its frequent overexpression have remained mostly elusive. In this study, we explored a potential tumorigenic mechanism that could increase cyclin D1 stability through a defect in molecules responsible for its degradation. METHODS We examined two tumor suppressor genes known to modulate cyclin D1 ubiquitination, PRKN and FBXO4 (FBX4), for evidence of classic two-hit tumor suppressor inactivation within a cohort of 82 PTA cases. We examined the cohort for intragenic inactivating and splice site mutations by Sanger sequencing and for locus-associated loss of heterozygosity (LOH) by microsatellite analysis. RESULTS We identified no evidence of bi-allelic tumor suppressor inactivation of PRKN or FBXO4 via inactivating mutation or splice site perturbation, neither in combination with nor independent of LOH. Among the 82 cases, we encountered previously documented benign single nucleotide polymorphisms (SNPs) in 35 tumors at frequencies similar to those reported in the germlines of the general population. Eight cases exhibited intragenic LOH at the PRKN locus, in some cases extending to cover at least an additional 1.7 Mb of chromosome 6q25-26. FBXO4 was not affected by LOH. CONCLUSION The absence of evidence for specific bi-allelic inactivation in PRKN and FBXO4 in this sizeable cohort suggests that these genes only rarely, if ever, serve as classic driver tumor suppressors responsible for the growth of PTAs.
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Affiliation(s)
- Kelly Brewer
- Center for Molecular Oncology, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Isabel Nip
- Center for Molecular Oncology, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Justin Bellizzi
- Center for Molecular Oncology, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Jessica Costa-Guda
- Center for Molecular Oncology, University of Connecticut School of Medicine, Farmington, Connecticut, USA
- Center for Regenerative Medicine and Skeletal Development, Department of Reconstructive Sciences, University of Connecticut School of Dental Medicine, Farmington, Connecticut, USA
| | - Andrew Arnold
- Center for Molecular Oncology, University of Connecticut School of Medicine, Farmington, Connecticut, USA
- Division of Endocrinology and Metabolism, University of Connecticut School of Medicine, Farmington, Connecticut, USA
- Correspondence should be addressed to A Arnold:
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Kamienieva I, Duszyński J, Szczepanowska J. Multitasking guardian of mitochondrial quality: Parkin function and Parkinson's disease. Transl Neurodegener 2021; 10:5. [PMID: 33468256 PMCID: PMC7816312 DOI: 10.1186/s40035-020-00229-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/30/2020] [Indexed: 12/27/2022] Open
Abstract
The familial form of Parkinson’s disease (PD) is linked to mutations in specific genes. The mutations in parkin are one of the most common causes of early-onset PD. Mitochondrial dysfunction is an emerging active player in the pathology of neurodegenerative diseases, because mitochondria are highly dynamic structures integrated with many cellular functions. Herein, we overview and discuss the role of the parkin protein product, Parkin E3 ubiquitin ligase, in the cellular processes related to mitochondrial function, and how parkin mutations can result in pathology in vitro and in vivo.
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Affiliation(s)
- Iryna Kamienieva
- Nencki Institute of Experimental Biology, Polish Academy of Science, 02-093, Warsaw, Poland
| | - Jerzy Duszyński
- Nencki Institute of Experimental Biology, Polish Academy of Science, 02-093, Warsaw, Poland
| | - Joanna Szczepanowska
- Nencki Institute of Experimental Biology, Polish Academy of Science, 02-093, Warsaw, Poland.
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Comprehensive germline genomic profiles of children, adolescents and young adults with solid tumors. Nat Commun 2020; 11:2206. [PMID: 32371905 PMCID: PMC7200683 DOI: 10.1038/s41467-020-16067-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 04/08/2020] [Indexed: 02/07/2023] Open
Abstract
Compared to adult carcinomas, there is a paucity of targeted treatments for solid tumors in children, adolescents, and young adults (C-AYA). The impact of germline genomic signatures has implications for heritability, but its impact on targeted therapies has not been fully appreciated. Performing variant-prioritization analysis on germline DNA of 1,507 C-AYA patients with solid tumors, we show 12% of these patients carrying germline pathogenic and/or likely pathogenic variants (P/LP) in known cancer-predisposing genes (KCPG). An additional 61% have germline pathogenic variants in non-KCPG genes, including PRKN, SMARCAL1, SMAD7, which we refer to as candidate genes. Despite germline variants in a broad gene spectrum, pathway analysis leads to top networks centering around p53. Our drug-target analysis shows 1/3 of patients with germline P/LP variants have at least one druggable alteration, while more than half of them are from our candidate gene group, which would otherwise go unidentified in routine clinical care. Targeted therapies for solid tumors in children, adolescents, and young adults (C-AYA) lag behind that of adult carcinomas. Here, the authors study the germline genomic signatures of 1,507 C-AYA patients with solid tumors and find pathogenic/likely pathogenic germline variants in diverse genes of which 1/3 of these alterations are druggable.
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Impaired Replication Timing Promotes Tissue-Specific Expression of Common Fragile Sites. Genes (Basel) 2020; 11:genes11030326. [PMID: 32204553 PMCID: PMC7140878 DOI: 10.3390/genes11030326] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 02/27/2020] [Accepted: 03/06/2020] [Indexed: 12/24/2022] Open
Abstract
Common fragile sites (CFSs) are particularly vulnerable regions of the genome that become visible as breaks, gaps, or constrictions on metaphase chromosomes when cells are under replicative stress. Impairment in DNA replication, late replication timing, enrichment of A/T nucleotides that tend to form secondary structures, the paucity of active or inducible replication origins, the generation of R-loops, and the collision between replication and transcription machineries on particularly long genes are some of the reported characteristics of CFSs that may contribute to their tissue-specific fragility. Here, we validated the induction of two CFSs previously found in the human fetal lung fibroblast line, Medical Research Council cell strain 5 (MRC-5), in another cell line derived from the same fetal tissue, Institute for Medical Research-90 cells (IMR-90). After induction of CFSs through aphidicolin, we confirmed the expression of the CFS 1p31.1 on chromosome 1 and CFS 3q13.3 on chromosome 3 in both fetal lines. Interestingly, these sites were found to not be fragile in lymphocytes, suggesting a role for epigenetic or transcriptional programs for this tissue specificity. Both these sites contained late-replicating genes NEGR1 (neuronal growth regulator 1) at 1p31.1 and LSAMP (limbic system-associated membrane protein) at 3q13.3, which are much longer, 0.880 and 1.4 Mb, respectively, than the average gene length. Given the established connection between long genes and CFS, we compiled information from the literature on all previously identified CFSs expressed in fibroblasts and lymphocytes in response to aphidicolin, including the size of the genes contained in each fragile region. Our comprehensive analysis confirmed that the genes found within CFSs are longer than the average human gene; interestingly, the two longest genes in the human genome are found within CFSs: Contactin Associated Protein 2 gene (CNTNAP2) in a lymphocytes’ CFS, and Duchenne muscular dystrophy gene (DMD) in a CFS expressed in both lymphocytes and fibroblasts. This indicates that the presence of very long genes is a unifying feature of all CFSs. We also obtained replication profiles of the 1p31.1 and 3q13.3 sites under both perturbed and unperturbed conditions using a combination of fluorescent in situ hybridization (FISH) and immunofluorescence against bromodeoxyuridine (BrdU) on interphase nuclei. Our analysis of the replication dynamics of these CFSs showed that, compared to lymphocytes where these regions are non-fragile, fibroblasts display incomplete replication of the fragile alleles, even in the absence of exogenous replication stress. Our data point to the existence of intrinsic features, in addition to the presence of long genes, which affect DNA replication of the CFSs in fibroblasts, thus promoting chromosomal instability in a tissue-specific manner.
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Koyano F, Yamano K, Kosako H, Kimura Y, Kimura M, Fujiki Y, Tanaka K, Matsuda N. Parkin-mediated ubiquitylation redistributes MITOL/March5 from mitochondria to peroxisomes. EMBO Rep 2019; 20:e47728. [PMID: 31602805 PMCID: PMC6893362 DOI: 10.15252/embr.201947728] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 08/30/2019] [Accepted: 09/11/2019] [Indexed: 12/23/2022] Open
Abstract
Ubiquitylation of outer mitochondrial membrane (OMM) proteins is closely related to the onset of familial Parkinson's disease. Typically, a reduction in the mitochondrial membrane potential results in Parkin-mediated ubiquitylation of OMM proteins, which are then targeted for proteasomal and mitophagic degradation. The role of ubiquitylation of OMM proteins with non-degradative fates, however, remains poorly understood. In this study, we find that the mitochondrial E3 ubiquitin ligase MITOL/March5 translocates from depolarized mitochondria to peroxisomes following mitophagy stimulation. This unusual redistribution is mediated by peroxins (peroxisomal biogenesis factors) Pex3/16 and requires the E3 ligase activity of Parkin, which ubiquitylates K268 in the MITOL C-terminus, essential for p97/VCP-dependent mitochondrial extraction of MITOL. These findings imply that ubiquitylation directs peroxisomal translocation of MITOL upon mitophagy stimulation and reveal a novel role for ubiquitin as a sorting signal that allows certain specialized proteins to escape from damaged mitochondria.
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Affiliation(s)
- Fumika Koyano
- Ubiquitin ProjectTokyo Metropolitan Institute of Medical ScienceTokyoJapan
| | - Koji Yamano
- Ubiquitin ProjectTokyo Metropolitan Institute of Medical ScienceTokyoJapan
| | - Hidetaka Kosako
- Division of Cell SignalingFujii Memorial Institute of Medical SciencesTokushima UniversityTokushimaJapan
| | - Yoko Kimura
- Department of Agriculture Graduate School of Integrated Science and TechnologyShizuoka UniversityShizuokaJapan
| | - Mayumi Kimura
- Ubiquitin ProjectTokyo Metropolitan Institute of Medical ScienceTokyoJapan
| | - Yukio Fujiki
- Medical Institute of BioregulationKyushu UniversityHigashi‐kuFukuokaJapan
| | - Keiji Tanaka
- Laboratory of Protein MetabolismTokyo Metropolitan Institute of Medical ScienceTokyoJapan
| | - Noriyuki Matsuda
- Ubiquitin ProjectTokyo Metropolitan Institute of Medical ScienceTokyoJapan
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22
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Alonso-Peña M, Espinosa-Escudero RA, Soto-Muñiz M, Sanchon-Sanchez P, Sanchez-Martin A, Marin JJ. Role of transportome in the pharmacogenomics of hepatocellular carcinoma and hepatobiliary cancer. Pharmacogenomics 2019; 20:957-970. [PMID: 31486734 DOI: 10.2217/pgs-2019-0033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
An important factor determining the pharmacological response to antitumor drugs is their concentrations in cancer cells, which accounts for the net interaction with their intracellular molecular targets. Accordingly, mechanisms leading to reduced intracellular levels of active agents play a crucial role in cancer chemoresistance. These include impaired drug uptake through solute carrier (SLC) proteins and efficient drug export by ATP-dependent pumps belonging to the ATP-binding cassette (ABC) superfamily of proteins. Since the net movement of drugs in-and-out the cells depends on the overall expression of carrier proteins, defining the so-called transportome, special attention has been devoted to the study of transcriptome regarding these proteins. Nevertheless, genetic variants affecting SLC and ABC genes may markedly affect the bioavailability and, hence, the efficacy of anticancer drugs.
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Affiliation(s)
- Marta Alonso-Peña
- Experimental Hepatology & Drug Targeting (HEVEFARM), IBSAL, University of Salamanca, Salamanca, 37007, Spain
| | - Ricardo A Espinosa-Escudero
- Experimental Hepatology & Drug Targeting (HEVEFARM), IBSAL, University of Salamanca, Salamanca, 37007, Spain
| | - Meraris Soto-Muñiz
- Experimental Hepatology & Drug Targeting (HEVEFARM), IBSAL, University of Salamanca, Salamanca, 37007, Spain
| | - Paula Sanchon-Sanchez
- Experimental Hepatology & Drug Targeting (HEVEFARM), IBSAL, University of Salamanca, Salamanca, 37007, Spain
| | - Anabel Sanchez-Martin
- Experimental Hepatology & Drug Targeting (HEVEFARM), IBSAL, University of Salamanca, Salamanca, 37007, Spain
| | - Jose Jg Marin
- Experimental Hepatology & Drug Targeting (HEVEFARM), IBSAL, University of Salamanca, Salamanca, 37007, Spain.,Center for the Study of Liver & Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, 28029, Spain
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23
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Zheglo D, Brueckner LM, Sepman O, Wecht EM, Kuligina E, Suspitsin E, Imyanitov E, Savelyeva L. The FRA14B
common fragile site maps to a region prone to somatic and germline rearrangements within the large GPHN
gene. Genes Chromosomes Cancer 2018; 58:284-294. [DOI: 10.1002/gcc.22706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 01/27/2023] Open
Affiliation(s)
- Diana Zheglo
- FSBI Research Centre for Medical Genetics; Moscow Russia
| | - Lena M. Brueckner
- Division of Neuroblastoma Genomics; German Cancer Research Center (DKFZ); Heidelberg Germany
| | - Olga Sepman
- Klinik fuer Allgemein-, Viszeral-, Thorax- und minimal-invasive Chirurgie; Pforzheim Germany
| | - Elisa M. Wecht
- Division of Neuroblastoma Genomics; German Cancer Research Center (DKFZ); Heidelberg Germany
| | | | - Evgenij Suspitsin
- Petrov Institute of Oncology; St Petersburg Russia
- St. Petersburg Pediatric Medical University; Sankt-Peterburg Russia
| | - Evgenij Imyanitov
- Petrov Institute of Oncology; St Petersburg Russia
- Mechnikov North-Western Medical University; Saint Petersburg Russia
| | - Larissa Savelyeva
- Division of Neuroblastoma Genomics; German Cancer Research Center (DKFZ); Heidelberg Germany
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24
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Shi R, Guberman M, Kirshenbaum LA. Mitochondrial quality control: The role of mitophagy in aging. Trends Cardiovasc Med 2018; 28:246-260. [DOI: 10.1016/j.tcm.2017.11.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 11/27/2017] [Accepted: 11/28/2017] [Indexed: 12/25/2022]
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25
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Parkin in Parkinson’s Disease and Cancer: a Double-Edged Sword. Mol Neurobiol 2018; 55:6788-6800. [DOI: 10.1007/s12035-018-0879-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 01/07/2018] [Indexed: 12/19/2022]
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26
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Mitophagy and age-related pathologies: Development of new therapeutics by targeting mitochondrial turnover. Pharmacol Ther 2017; 178:157-174. [DOI: 10.1016/j.pharmthera.2017.04.005] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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27
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Abstract
Ever since initial suggestions that instability at common fragile sites (CFSs) could be responsible for chromosome rearrangements in cancers, CFSs and associated genes have been the subject of numerous studies, leading to questions and controversies about their role and importance in cancer. It is now clear that CFSs are not frequently involved in translocations or other cancer-associated recurrent gross chromosome rearrangements. However, recent studies have provided new insights into the mechanisms of CFS instability, their effect on genome instability, and their role in generating focal copy number alterations that affect the genomic landscape of many cancers.
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Affiliation(s)
- Thomas W Glover
- Department of Human Genetics; the Department of Pathology; and the Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Thomas E Wilson
- Department of Human Genetics; and the Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Martin F Arlt
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
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28
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Madireddy A, Gerhardt J. Replication Through Repetitive DNA Elements and Their Role in Human Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:549-581. [PMID: 29357073 DOI: 10.1007/978-981-10-6955-0_23] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Human cells contain various repetitive DNA sequences, which can be a challenge for the DNA replication machinery to travel through and replicate correctly. Repetitive DNA sequence can adopt non-B DNA structures, which could block the DNA replication. Prolonged stalling of the replication fork at the endogenous repeats in human cells can have severe consequences such as genome instability that includes repeat expansions, contractions, and chromosome fragility. Several neurological and muscular diseases are caused by a repeat expansion. Furthermore genome instability is the major cause of cancer. This chapter describes some of the important classes of repetitive DNA sequences in the mammalian genome, their ability to form secondary DNA structures, their contribution to replication fork stalling, and models for repeat expansion as well as chromosomal fragility. Included in this chapter are also some of the strategies currently employed to detect changes in DNA replication and proteins that could prevent the repeat-mediated disruption of DNA replication in human cells. Additionally summarized are the consequences of repeat-associated perturbation of the DNA replication, which could lead to specific human diseases.
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29
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Hazan I, Hofmann TG, Aqeilan RI. Tumor Suppressor Genes within Common Fragile Sites Are Active Players in the DNA Damage Response. PLoS Genet 2016; 12:e1006436. [PMID: 27977694 PMCID: PMC5157955 DOI: 10.1371/journal.pgen.1006436] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The role of common fragile sites (CFSs) in cancer remains controversial. Two main views dominate the discussion: one suggests that CFS loci are hotspots of genomic instability leading to inactivation of genes encoded within them, while the other view proposes that CFSs are functional units and that loss of the encoded genes confers selective pressure, leading to cancer development. The latter view is supported by emerging evidence showing that expression of a given CFS is associated with genome integrity and that inactivation of CFS-resident tumor suppressor genes leads to dysregulation of the DNA damage response (DDR) and increased genomic instability. These two viewpoints of CFS function are not mutually exclusive but rather coexist; when breaks at CFSs are not repaired accurately, this can lead to deletions by which cells acquire growth advantage because of loss of tumor suppressor activities. Here, we review recent advances linking some CFS gene products with the DDR, genomic instability, and carcinogenesis and discuss how their inactivation might represent a selective advantage for cancer cells.
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Affiliation(s)
- Idit Hazan
- Lautenberg Center for Immunology and Cancer Research, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Thomas G. Hofmann
- Cellular Senescence Group, Department of Epigenetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rami I. Aqeilan
- Lautenberg Center for Immunology and Cancer Research, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America
- Department of Biochemistry, University of Vermont College of Medicine, Burlington, Vermont, United States of America
- * E-mail:
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30
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Parkin and mitophagy in cancer. Oncogene 2016; 36:1315-1327. [PMID: 27593930 DOI: 10.1038/onc.2016.302] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 07/04/2016] [Accepted: 07/04/2016] [Indexed: 02/07/2023]
Abstract
Mitophagy, the selective engulfment and clearance of mitochondria, is essential for the homeostasis of a healthy network of functioning mitochondria and prevents excessive production of cytotoxic reactive oxygen species from damaged mitochondria. The mitochondrially targeted PTEN-induced kinase-1 (PINK1) and the E3 ubiquitin ligase Parkin are well-established synergistic mediators of the mitophagy of dysfunctional mitochondria. This pathway relies on the ubiquitination of a number of mitochondrial outer membrane substrates and subsequent docking of autophagy receptor proteins to selectively clear mitochondria. There are also alternate Parkin-independent mitophagy pathways mediated by BCL2/adenovirus E1B 19 kDa protein-interacting protein 3 and Nip-3 like protein X as well as other effectors. There is increasing evidence that ablation of mitophagy accelerates a number of pathologies. Familial Parkinsonism is associated with loss-of-function mutations in PINK1 and Parkin. A growing number of studies have observed a correlation between impaired Parkin activity and enhanced cancer development, leading to the emerging concept that Parkin activity, or mitophagy in general, is a tumour suppression mechanism. This review examines the molecular mechanisms of mitophagy and highlights the potential links between Parkin and the hallmarks of cancer that may influence tumour development and progression.
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31
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Morais S, Bastos-Ferreira R, Sequeiros J, Alonso I. Genomic mechanisms underlying PARK2 large deletions identified in a cohort of patients with PD. NEUROLOGY-GENETICS 2016; 2:e73. [PMID: 27182553 PMCID: PMC4856358 DOI: 10.1212/nxg.0000000000000073] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 03/09/2016] [Indexed: 11/15/2022]
Abstract
OBJECTIVES To identify the genomic mechanisms that result in PARK2 large gene deletions. METHODS We conducted mutation screening using PCR amplification of PARK2-coding regions and exon-intron boundaries, followed by sequencing to evaluate a large series of 244 unrelated Portuguese patients with symptoms of Parkinson disease. For the detection of large gene rearrangements, we performed multiplex ligation-dependent probe amplification, followed by long-range PCR and sequencing to map deletion breakpoints. RESULTS We identified biallelic pathogenic parkin mutations in 40 of the 244 patients. There were 18 different mutations, some of them novel. This study included mapping of 17 deletion breakpoints showing that nonhomologous end joining is the most common mechanism responsible for these gene rearrangements. None of these deletion breakpoints were previously described, and only one was present in 2 unrelated families, indicating that most of the deletions result from independent events. CONCLUSIONS The c.155delA mutation is highly prevalent in the Portuguese population (62.5% of the cases). Large deletions were present in 42.5% of the patients. We present the largest study on the molecular mechanisms that mediate PARK2 deletions in a homogeneous population.
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Affiliation(s)
- Sara Morais
- UnIGENe (S.M., J.S., I.A.), Institute for Molecular and Cell Biology; i3S (S.M., R.B.-F., J.S., I.A.), Instituto de Investigação e Inovação em Saúde; CGPP (R.B.-F., J.S., I.A.), Institute for Molecular and Cell Biology; and Instituto de Ciências Biomédicas Abel Salazar (J.S., I.A.), University of Porto, Portugal
| | - Rita Bastos-Ferreira
- UnIGENe (S.M., J.S., I.A.), Institute for Molecular and Cell Biology; i3S (S.M., R.B.-F., J.S., I.A.), Instituto de Investigação e Inovação em Saúde; CGPP (R.B.-F., J.S., I.A.), Institute for Molecular and Cell Biology; and Instituto de Ciências Biomédicas Abel Salazar (J.S., I.A.), University of Porto, Portugal
| | - Jorge Sequeiros
- UnIGENe (S.M., J.S., I.A.), Institute for Molecular and Cell Biology; i3S (S.M., R.B.-F., J.S., I.A.), Instituto de Investigação e Inovação em Saúde; CGPP (R.B.-F., J.S., I.A.), Institute for Molecular and Cell Biology; and Instituto de Ciências Biomédicas Abel Salazar (J.S., I.A.), University of Porto, Portugal
| | - Isabel Alonso
- UnIGENe (S.M., J.S., I.A.), Institute for Molecular and Cell Biology; i3S (S.M., R.B.-F., J.S., I.A.), Instituto de Investigação e Inovação em Saúde; CGPP (R.B.-F., J.S., I.A.), Institute for Molecular and Cell Biology; and Instituto de Ciências Biomédicas Abel Salazar (J.S., I.A.), University of Porto, Portugal
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32
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Landais E, Leroy C, Kleinfinger P, Brunet S, Koubi V, Pietrement C, Poli-Mérol ML, Fiquet C, Souchon PF, Beri M, Jonveaux P, Garnotel R, Gaillard D, Doco-Fenzy M. A pure familial 6q15q21 split duplication associated with obesity and transmitted with partial reduction. Am J Med Genet A 2015; 167:1275-84. [PMID: 25900228 DOI: 10.1002/ajmg.a.36995] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 12/29/2014] [Indexed: 01/06/2023]
Abstract
Familial transmission of chromosome 6 duplications is rare. We report on the first observation of a maternally-inherited pure segmental 6q duplication split into two segments, 6q15q16.3 and 6q16.3q21, and associated with obesity. Obesity has previously been correlated to chromosome 6 q-arm deletion but has not yet been assessed in duplications. The aim of this study was to characterize the structure of these intrachromosomal insertional translocations by classic cytogenetic banding, array-CGH, FISH, M-banding and genotyping using microsatellites and SNP array analysis, in a mother and four offspring. The duplicated 6q segments, 9.75 Mb (dup 1) and 7.05 Mb (dup 2) in size in the mother, were inserted distally into two distinct chromosome 6q regions. They were transmitted to four offspring. A son and a daughter inherited the two unbalanced insertions and displayed, like the mother, an abnormal phenotype with facial dysmorphism, intellectual disability, and morbid obesity. Curiously, two daughters with a normal phenotype inherited only the smaller segment, 6q16.3q21. The abnormal phenotype was associated with the larger proximal 6q15q16.3 duplication. We hypothesize a mechanism for this exceptional phenomenon of recurrent reduction and transmission of the duplication during meiosis in a family. We expect the interpretation of our findings to be useful for genetic counseling and for understanding the mechanisms underlying these large segmental 6q duplications and their evolution.
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Affiliation(s)
- Emilie Landais
- CHU-Reims, HMB, Service de Génétique, France.,CHU-Reims, HMB, Plateforme Régionale de Biologie Innovante, France
| | - Camille Leroy
- CHU-Reims, HMB, Service de Génétique, France.,Université de Reims Champagne-Ardenne, UFR de médecine, France
| | | | | | - Valérie Koubi
- Service de génétique Médicale, Laboratoire de génétique moléculaire, CHU Hopital Necker enfants malades, Paris, France
| | | | - Marie-Laurence Poli-Mérol
- Université de Reims Champagne-Ardenne, UFR de médecine, France.,CHU-Reims, American Memorial Hospital, Service de Chirurgie pédiatrique, France
| | - Caroline Fiquet
- CHU-Reims, American Memorial Hospital, Service de Chirurgie pédiatrique, France.,SFR CAP Santé, Reims, EA 3801, France
| | | | - Mylène Beri
- CHU-Nancy, Laboratoire de Génétique Médicale, Nancy Université, France
| | - Philippe Jonveaux
- CHU-Nancy, Laboratoire de Génétique Médicale, Nancy Université, France
| | - Roselyne Garnotel
- CHU-Reims, Laboratoire de Biochimie Médicale et Biologie Moléculaire, CNRS UMR 6198, UFR, Médecine, France
| | - Dominique Gaillard
- CHU-Reims, HMB, Service de Génétique, France.,Université de Reims Champagne-Ardenne, UFR de médecine, France
| | - Martine Doco-Fenzy
- CHU-Reims, HMB, Service de Génétique, France.,SFR CAP Santé, Reims, EA 3801, France
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33
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Ambroziak W, Koziorowski D, Duszyc K, Górka-Skoczylas P, Potulska-Chromik A, Sławek J, Hoffman-Zacharska D. Genomic instability in the PARK2 locus is associated with Parkinson's disease. J Appl Genet 2015; 56:451-461. [PMID: 25833766 PMCID: PMC4617850 DOI: 10.1007/s13353-015-0282-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 03/05/2015] [Accepted: 03/05/2015] [Indexed: 12/01/2022]
Abstract
Parkinson’s disease (PD) is a common neurodegenerative disorder affecting mostly elderly people, although there is a group of patients developing so-called early-onset PD (EOPD). Mutations in the PARK2 gene are a common cause of autosomal recessive EOPD. PARK2 belongs to the family of extremely large human genes which are often localised in genomic common fragile sites (CFSs) and exhibit gross instability. PARK2 is located in the centre of FRA6E, the third most mutation-susceptible CFS of the human genome. The gene encompasses a region of 1.3 Mbp and, among its mutations, large rearrangements of single or multiple exons account for around 50 %. We performed an analysis of the PARK2 gene in a group of 344 PD patients with EOPD and classical form of the disease. Copy number changes were first identified using multiplex ligation probe amplification (MLPA), with their ranges characterised by array comparative genomic hybridisation (aCGH). Exact breakpoints were mapped using direct sequencing. Rearrangements were found in eight subjects, including five deletions and three duplications. Rearrangements were mostly non-recurrent and no repetitive sequences or extended homologies were identified in the regions flanking breakpoint junctions. However, in most cases, 1–3 bp microhomologies were present, strongly suggesting that microhomology-mediated mechanisms, specifically non-homologous end joining (NHEJ) and fork stalling and template switching (FoSTeS)/microhomology-mediated break-induced replication (MMBIR), are predominantly involved in the rearrangement processes in this genomic region.
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Affiliation(s)
- Wojciech Ambroziak
- Department of Medical Genetics, Institute of Mother and Child, Kasprzaka 17A, 01-211, Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Dariusz Koziorowski
- Department of Neurology, Faculty of Heath Science, Medical University of Warsaw, Kondratowicza 8, 03-242, Warsaw, Poland
| | - Kinga Duszyc
- Department of Medical Genetics, Institute of Mother and Child, Kasprzaka 17A, 01-211, Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Paulina Górka-Skoczylas
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Anna Potulska-Chromik
- Department of Neurology, Medical University of Warsaw, Banacha 1, 02-097, Warsaw, Poland
| | - Jarosław Sławek
- Department of Neurological and Psychiatric Nursing, Medical University of Gdańsk, Dębinki 7, 80-952, Gdańsk, Poland
| | - Dorota Hoffman-Zacharska
- Department of Medical Genetics, Institute of Mother and Child, Kasprzaka 17A, 01-211, Warsaw, Poland. .,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawińskiego 5a, 02-106, Warsaw, Poland.
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34
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Abstract
WWOX is a gene that spans an extremely large chromosomal region. It is derived from within chromosomal band 16q23.2 which is a region with frequent deletions and other alterations in a variety of different cancers. This chromosomal band also contains the FRA16D common fragile site (CFS). CFSs are chromosomal regions found in all individuals which are highly unstable. WWOX has also been demonstrated to function as a tumor suppressor that is involved in the development of many cancers. Two other highly unstable CFSs, FRA3B (3p14.2) and FRA6E (6q26), also span extremely large genes, FHIT and PARK2, respectively, and these two genes are also found to be important tumor suppressors. There are a number of interesting similarities between these three large CFS genes. In spite of the fact that they are derived from some of the most unstable chromosomal regions in the genome, they are found to be highly evolutionarily conserved and the chromosomal region spanning the mouse homologs of both WWOX and FHIT are also CFSs in mice. Many of the other CFSs also span extremely large genes and many of these are very attractive tumor suppressor candidates. WWOX is therefore a member of a very interesting family of very large CFS genes.
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Affiliation(s)
- Ge Gao
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - David I Smith
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
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35
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Prognostic significance of decreased expression of six large common fragile site genes in oropharyngeal squamous cell carcinomas. Transl Oncol 2014; 7:726-31. [PMID: 25500082 PMCID: PMC4311028 DOI: 10.1016/j.tranon.2014.09.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 09/22/2014] [Accepted: 09/26/2014] [Indexed: 11/20/2022] Open
Abstract
Common fragile sites (CFSs) are large regions with profound genomic instability that often span extremely large genes a number of which have been found to be important tumor suppressors. RNA sequencing previously revealed that there was a group of six large CFS genes which frequently had decreased expression in oropharyngeal squamous cell carcinomas (OPSCCs) and real-time reverse transcriptase polymerase chain reaction experiments validated that these six large CFS genes (PARK2, DLG2, NBEA, CTNNA3, DMD, and FHIT) had decreased expression in most of the tumor samples. In this study, we investigated whether the decreased expression of these genes has any clinical significance in OPSCCs. We analyzed the six CFS large genes in 45 OPSCC patients and found that 27 (60%) of the OPSCC tumors had decreased expression of these six genes. When we correlated the expression of these six genes to each patient's clinical records, for 11 patients who had tumor recurrence, 10 of them had decreased expression of almost all 6 genes. When we divided the patients into two groups, one group with decreased expression of the six genes and the other group with either slight changes or increased expression of the six genes, we found that there is significant difference in the incidence of tumor recurrence between these two groups by Kaplan-Meier plot analysis (P < .05). Our results demonstrated that those OPSCC tumors with decreased expression of this select group of six large CFS genes were much more likely to be associated with tumor recurrence and these genes are potential prognostic markers for predicting tumor recurrence in OPSCC.
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Gao G, Smith DI. Very large common fragile site genes and their potential role in cancer development. Cell Mol Life Sci 2014; 71:4601-15. [PMID: 25300511 PMCID: PMC11113612 DOI: 10.1007/s00018-014-1753-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 09/30/2014] [Indexed: 10/24/2022]
Abstract
Common fragile sites (CFSs) are large chromosomal regions that are hot-spots for alterations especially within cancer cells. The three most frequently expressed CFS regions (FRA3B, FRA16D and FRA6E) contain genes that span extremely large genomic regions (FHIT, WWOX and PARK2, respectively), and these genes were found to function as important tumor suppressors. Many other CFS regions contain extremely large genes that are also targets of alterations in multiple cancers, but none have yet been demonstrated to function as tumor suppressors. The loss of expression of just FHIT or WWOX has been found to be associated with a worse overall clinical outcome. Studies in different cancers have revealed that some cancers have decreased expression of multiple large CFS genes. This loss of expression could have a profound phenotypic effect on these cells. In this review, we will summarize the known large common fragile site genes and discuss their potential relationship to cancer development.
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Affiliation(s)
- Ge Gao
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905 USA
| | - David I. Smith
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905 USA
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Ozeri-Galai E, Tur-Sinai M, Bester AC, Kerem B. Interplay between genetic and epigenetic factors governs common fragile site instability in cancer. Cell Mol Life Sci 2014; 71:4495-506. [PMID: 25297918 PMCID: PMC11113459 DOI: 10.1007/s00018-014-1719-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 08/28/2014] [Indexed: 11/28/2022]
Abstract
Common fragile sites (CFSs) are regions within the normal chromosomal structure that were characterized as hotspots for genomic instability in cancer almost 30 years ago. In recent years, many efforts have been made to understand the basis of CFS fragility and their involvement in the genomic signature of instability found in malignant tumors. CFSs are among the first regions to undergo genomic instability during cancer development because of their intrinsic sensitivity to replication stress conditions, which result from oncogene expression. The preferred sensitivity of CFSs to replication stress stems from various mechanisms including: replication fork arrest at AT-rich repeats, origin paucity along large genomic regions, failure in activation of dormant origins, late replication timing, collision between replication and transcription along large genes, all leading to incomplete replication of the CFS region and resulting in chromosomal instability. Here we review shared and unique characteristics of CFSs, their underlying causes and implications, particularly for the development of cancer.
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Affiliation(s)
- Efrat Ozeri-Galai
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Edmond J. Safra Campus, 91904 Jerusalem, Israel
| | - Michal Tur-Sinai
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Edmond J. Safra Campus, 91904 Jerusalem, Israel
| | - Assaf C. Bester
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Edmond J. Safra Campus, 91904 Jerusalem, Israel
| | - Batsheva Kerem
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Edmond J. Safra Campus, 91904 Jerusalem, Israel
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Mazouzi A, Velimezi G, Loizou JI. DNA replication stress: causes, resolution and disease. Exp Cell Res 2014; 329:85-93. [PMID: 25281304 DOI: 10.1016/j.yexcr.2014.09.030] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 09/20/2014] [Accepted: 09/22/2014] [Indexed: 12/17/2022]
Abstract
DNA replication is a fundamental process of the cell that ensures accurate duplication of the genetic information and subsequent transfer to daughter cells. Various pertubations, originating from endogenous or exogenous sources, can interfere with proper progression and completion of the replication process, thus threatening genome integrity. Coordinated regulation of replication and the DNA damage response is therefore fundamental to counteract these challenges and ensure accurate synthesis of the genetic material under conditions of replication stress. In this review, we summarize the main sources of replication stress and the DNA damage signaling pathways that are activated in order to preserve genome integrity during DNA replication. We also discuss the association of replication stress and DNA damage in human disease and future perspectives in the field.
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Affiliation(s)
- Abdelghani Mazouzi
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Georgia Velimezi
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Joanna I Loizou
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria.
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Georgakilas AG, Tsantoulis P, Kotsinas A, Michalopoulos I, Townsend P, Gorgoulis VG. Are common fragile sites merely structural domains or highly organized "functional" units susceptible to oncogenic stress? Cell Mol Life Sci 2014; 71:4519-44. [PMID: 25238782 PMCID: PMC4232749 DOI: 10.1007/s00018-014-1717-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 08/28/2014] [Indexed: 01/07/2023]
Abstract
Common fragile sites (CFSs) are regions of the genome with a predisposition to DNA double-strand breaks in response to intrinsic (oncogenic) or extrinsic replication stress. CFS breakage is a common feature in carcinogenesis from its earliest stages. Given that a number of oncogenes and tumor suppressors are located within CFSs, a question that emerges is whether fragility in these regions is only a structural “passive” incident or an event with a profound biological effect. Furthermore, there is sparse evidence that other elements, like non-coding RNAs, are positioned with them. By analyzing data from various libraries, like miRbase and ENCODE, we show a prevalence of various cancer-related genes, miRNAs, and regulatory binding sites, such as CTCF within CFSs. We propose that CFSs are not only susceptible structural domains, but highly organized “functional” entities that when targeted, severe repercussion for cell homeostasis occurs.
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Affiliation(s)
- Alexandros G Georgakilas
- Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Zografou, 15780, Athens, Greece
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Anatomical, molecular and pathological consideration of the circumventricular organs. Neurochirurgie 2014; 61:90-100. [PMID: 24974365 DOI: 10.1016/j.neuchi.2013.04.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 04/15/2013] [Accepted: 04/23/2013] [Indexed: 01/25/2023]
Abstract
BACKGROUND AND PURPOSE Circumventricular organs (CVOs) are a diverse group of specialised structures characterized by peculiar vascular and position around the third and fourth ventricles of the brain. In humans, these organs are present during the fetal period and some become vestigial after birth. Some, such as the pineal gland (PG), subcommissural organ (SCO) and organum vasculosum of the lamina terminalis (OVLT), which are located around the third ventricle, might be the site of origin of periventricular tumours. In contrast to humans, CVOs are present in the adult rat and can be dissected by laser capture microdissection (LCM). METHODS In this study, we used LCM and microarrays to analyse the transcriptomes of three CVOs, the SCO, the subfornical organ (SFO) and the PG and the third ventricle ependyma of the adult rat, in order to better characterise these organs at the molecular level. Furthermore, an immunohistochemical study of Claudin-3 (CLDN3), a membrane protein involved in forming cellular tight junctions, was performed at the level of the SCO. RESULTS This study highlighted some potentially new or already described specific markers of these structures as Erbb2 and Col11a1 in ependyma, Epcam and CLDN3 in the SCO, Ren1 and Slc22a3 in the SFO and Tph, Anat and Asmt in the PG. Moreover, we found that CLDN3 expression was restricted to the apical pole of ependymocytes in the SCO.
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Kim D, Shin H, Sohn KA, Verma A, Ritchie MD, Kim JH. Incorporating inter-relationships between different levels of genomic data into cancer clinical outcome prediction. Methods 2014; 67:344-53. [PMID: 24561168 DOI: 10.1016/j.ymeth.2014.02.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Revised: 01/25/2014] [Accepted: 02/07/2014] [Indexed: 01/06/2023] Open
Abstract
In order to improve our understanding of cancer and develop multi-layered theoretical models for the underlying mechanism, it is essential to have enhanced understanding of the interactions between multiple levels of genomic data that contribute to tumor formation and progression. Although there exist recent approaches such as a graph-based framework that integrates multi-omics data including copy number alteration, methylation, gene expression, and miRNA data for cancer clinical outcome prediction, most of previous methods treat each genomic data as independent and the possible interplay between them is not explicitly incorporated to the model. However, cancer is dysregulated by multiple levels in the biological system through genomic, epigenomic, transcriptomic, and proteomic level. Thus, genomic features are likely to interact with other genomic features in the different genomic levels. In order to deepen our knowledge, it would be desirable to incorporate such inter-relationship information when integrating multi-omics data for cancer clinical outcome prediction. In this study, we propose a new graph-based framework that integrates not only multi-omics data but inter-relationship between them for better elucidating cancer clinical outcomes. In order to highlight the validity of the proposed framework, serous cystadenocarcinoma data from TCGA was adopted as a pilot task. The proposed model incorporating inter-relationship between different genomic features showed significantly improved performance compared to the model that does not consider inter-relationship when integrating multi-omics data. For the pair between miRNA and gene expression data, the model integrating miRNA, for example, gene expression, and inter-relationship between them with an AUC of 0.8476 (REI) outperformed the model combining miRNA and gene expression data with an AUC of 0.8404. Similar results were also obtained for other pairs between different levels of genomic data. Integration of different levels of data and inter-relationship between them can aid in extracting new biological knowledge by drawing an integrative conclusion from many pieces of information collected from diverse types of genomic data, eventually leading to more effective screening strategies and alternative therapies that may improve outcomes.
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Affiliation(s)
- Dokyoon Kim
- Seoul National University Biomedical Informatics (SNUBI), Div. of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110799, Republic of Korea; Center for Systems Genomics, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
| | - Hyunjung Shin
- Department of Industrial & Information Systems Engineering, Ajou University, San 5, Wonchun-dong, Yeoungtong-gu, 443-749 Suwon, Republic of Korea.
| | - Kyung-Ah Sohn
- Department of Information and Computer Engineering, Ajou University, Suwon 443-749, Republic of Korea.
| | - Anurag Verma
- Center for Systems Genomics, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
| | - Marylyn D Ritchie
- Center for Systems Genomics, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
| | - Ju Han Kim
- Seoul National University Biomedical Informatics (SNUBI), Div. of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110799, Republic of Korea; Systems Biomedical Informatics Research Center, Seoul National University, Seoul 110799, Republic of Korea.
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Oczkowska A, Kozubski W, Lianeri M, Dorszewska J. Mutations in PRKN and SNCA Genes Important for the Progress of Parkinson's Disease. Curr Genomics 2014; 14:502-17. [PMID: 24532983 PMCID: PMC3924246 DOI: 10.2174/1389202914666131210205839] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Revised: 11/12/2013] [Accepted: 11/25/2013] [Indexed: 11/30/2022] Open
Abstract
Although Parkinson’s disease (PD) was first described almost 200 years ago, it remains an incurable disease
with a cause that is not fully understood. Nowadays it is known that disturbances in the structure of pathological proteins
in PD can be caused by more than environmental and genetic factors. Despite numerous debates and controversies in the
literature about the role of mutations in the SNCA and PRKN genes in the pathogenesis of PD, it is evident that these
genes play a key role in maintaining dopamine (DA) neuronal homeostasis and that the dysfunction of this homeostasis is
relevant to both familial (FPD) and sporadic (SPD) PD with different onset. In recent years, the importance of alphasynuclein
(ASN) in the process of neurodegeneration and neuroprotective function of the Parkin is becoming better understood.
Moreover, there have been an increasing number of recent reports indicating the importance of the interaction between
these proteins and their encoding genes. Among others interactions, it is suggested that even heterozygous substitution
in the PRKN gene in the presence of the variants +2/+2 or +2/+3 of NACP-Rep1 in the SNCA promoter, may increase
the risk of PD manifestation, which is probably due to ineffective elimination of over-expressed ASN by the mutated
Parkin protein. Finally, it seems that genetic testing may be an important part of diagnostics in patients with PD and may
improve the prognostic process in the course of PD. However, only full knowledge of the mechanism of the interaction
between the genes associated with the pathogenesis of PD is likely to help explain the currently unknown pathways of selective
damage to dopaminergic neurons in the course of PD.
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Affiliation(s)
- Anna Oczkowska
- Laboratory of Neurobiology, Department of Neurology, Poznan University of Medical Sciences, Poznan, Poland
| | - Wojciech Kozubski
- Chair and Department of Neurology, Poznan University of Medical Sciences, Poznan, Poland
| | - Margarita Lianeri
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Poznan, Poland
| | - Jolanta Dorszewska
- Laboratory of Neurobiology, Department of Neurology, Poznan University of Medical Sciences, Poznan, Poland
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Gao G, Kasperbauer JL, Tombers NM, Wang V, Mayer K, Smith DI. A selected group of large common fragile site genes have decreased expression in oropharyngeal squamous cell carcinomas. Genes Chromosomes Cancer 2014; 53:392-401. [DOI: 10.1002/gcc.22150] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 01/14/2013] [Accepted: 01/15/2013] [Indexed: 01/11/2023] Open
Affiliation(s)
- Ge Gao
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology; Mayo Clinic; Rochester MN
| | | | | | - Vivian Wang
- Mayo Medical Genome Facilities; Mayo Clinic; Rochester MN
| | - Kevin Mayer
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology; Mayo Clinic; Rochester MN
| | - David I. Smith
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology; Mayo Clinic; Rochester MN
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Abstract
PARK2 (PARKIN) is an E3 ubiquitin ligase involved in multiple signaling pathways and cellular processes. Activity of PARK2 is tightly regulated through inter- and intra-molecular interactions. Dysfunction of PARK2 is associated with the progression of parkinsonism. Notably, frequent PARK2 inactivation has been identified in various human cancers. Park2-deficient mice are more susceptible to tumorigenesis, indicating its crucial role as a tumor suppressor. However, biological studies also show that PARK2 possesses both pro-survival and growth suppressive functions. Here, we summarize the genetic lesions of PARK2 in human cancers and discuss the current knowledge of PARK2 in cancer progression. We further highlight future efforts for the study of PARK2 in cancer.
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45
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Parkin induces upregulation of 40S ribosomal protein SA and posttranslational modification of cytokeratins 8 and 18 in human cervical cancer cells. Appl Biochem Biotechnol 2013; 171:1630-8. [PMID: 23990477 DOI: 10.1007/s12010-013-0443-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 08/06/2013] [Indexed: 10/26/2022]
Abstract
Parkin was originally identified as a protein associated with Parkinson's disease. Recently, numerous research studies have suggested that parkin acts as a tumor suppressor. In accordance with these studies, we previously reported that overexpression of parkin in HeLa cells induced growth inhibition. To elucidate possible mechanisms by which parkin may inhibit cell growth, HeLa cells were infected with adenoviruses expressing either the parkin gene or adenovirus alone for 72 h and a total proteomic analysis was performed using 2-D gel electrophoresis followed by LC-MS/MS. We identified three proteins whose expression changed between the two groups: the 40S ribosomal protein SA (RPSA) was downregulated in parkin virus-infected cells, and cytokeratins 8 and 18 exhibited an acid shift in pI value without a change in molecular weight, suggesting that these proteins became phosphorylated in parkin virus-infected cells. The changes in these three proteins were first observed at 60 h postinfection and were most dramatic at 72 h postinfection. Because upregulation of RPSA and dephosphorylation of cytokeratins 8/18 have been linked with tumor progression, these data suggest that parkin may inhibit cell growth, at least in part, by decreasing RPSA expression and inducing phosphorylation of cytokeratin 8/18.
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Mackinnon RN, Campbell LJ. Chromothripsis under the microscope: a cytogenetic perspective of two cases of AML with catastrophic chromosome rearrangement. Cancer Genet 2013; 206:238-51. [PMID: 23911237 DOI: 10.1016/j.cancergen.2013.05.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 05/16/2013] [Accepted: 05/28/2013] [Indexed: 12/21/2022]
Abstract
Chromothripsis is a recently described phenomenon identified in cancer cells that produces catastrophic chromosome reorganization of one or a small number of chromosomes. It has been proposed that the multiple breakage events occur at a single point in time. Here we introduce the term anachromosome to describe an abnormal chromosome produced by chromothripsis. We report two cases of acute myeloid leukemia matching the description of chromothripsis that illustrate different aspects of this phenomenon from a cytogenetic perspective. Fluorescence in situ hybridization (FISH) analyses, including multicolor FISH and FISH for repeat elements that are not present on microarrays and that are resistant to sequencing, helped interpret the rearrangements but did not reveal their level of complexity. The anachromosomes conformed to the normal constraints of chromosome structure by including segments that provide two telomeres and a centromere. In patient samples, there are mixtures of cells with and without deletions. The deletion B allele frequencies for heterozygous loci in a mixture of cells with and without the deletions create a distinctive array pattern that is consistent with all the deletions in the anachromosomes having occurred concurrently. This evidence supporting the single-event hypothesis for chromothripsis has not previously been highlighted, to our knowledge. In the context of exploring mechanisms for chromosome shattering, we discuss a possible connection between chromosome pulverization and fragile sites. Understanding chromothripsis in the context of chromosome biology will help us identify its causes and consequences.
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Affiliation(s)
- Ruth N Mackinnon
- Victorian Cancer Cytogenetics Service, St Vincent's Hospital Melbourne, Fitzroy, Australia.
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Common Fragile Site Profiling in Epithelial and Erythroid Cells Reveals that Most Recurrent Cancer Deletions Lie in Fragile Sites Hosting Large Genes. Cell Rep 2013; 4:420-8. [DOI: 10.1016/j.celrep.2013.07.003] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 06/05/2013] [Accepted: 07/02/2013] [Indexed: 01/22/2023] Open
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Lee K, Lee MH, Kang YW, Rhee KJ, Kim TU, Kim YS. Parkin induces apoptotic cell death in TNF-α-treated cervical cancer cells. BMB Rep 2013; 45:526-31. [PMID: 23010174 DOI: 10.5483/bmbrep.2012.45.9.104] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many malignant tumors become resistant to tumor necrosis factor-alpha (TNF-α)-induced cell death during carcinogenesis. In the present study, we examined whether parkin acts as a tumor suppressor in HeLa cells, a human cervical cancer cell line resistant to TNF-α-induced cell death. TNF-α-treatment alone did not affect HeLa cell viability. However, expression of parkin restored TNF-α-induced apoptosis in HeLa cells. Increased cell death was due to the activation of the apoptotic pathway. Expression of parkin in TNF-α-treated HeLa cells stimulated cleavage of the pro-apoptotic proteins caspase-8, -9, -3, -7 and poly ADP ribose polymerase (PARP). In addition, parkin expression resulted in decreased expression of the caspase inhibitory protein, survivin. These results suggest that parkin acts as a tumor suppressor in human cervical cancer cells by modulating survivin expression and caspase activity. We propose that this pathway is a novel molecular mechanism by which parkin functions as a tumor suppressor.
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Affiliation(s)
- Kyunghong Lee
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju 220-710, Korea
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49
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Abstract
Two genes responsible for the juvenile Parkinson’s disease (PD), PINK1 and Parkin, have been implicated in mitochondrial quality control. The inactivation of PINK1, which encodes a mitochondrial kinase, leads to age-dependent mitochondrial degeneration in Drosophila. The phenotype is closely associated with the impairment of mitochondrial respiratory chain activity and defects in mitochondrial dynamics. Drosophila genetic studies have further revealed that PINK1 is an upstream regulator of Parkin and is involved in the mitochondrial dynamics and motility. A series of cell biological studies have given rise to a model in which the activation of PINK1 in damaged mitochondria induces the selective elimination of mitochondria in cooperation with Parkin through the ubiquitin-proteasome and autophagy machineries. Although the relevance of this pathway to PD etiology is still unclear, approaches using stem cells from patients and animal models will help to understand the significance of mitochondrial quality control by the PINK1-Parkin pathway in PD and in healthy individuals. Here I will review recent advances in our understanding of the PINK1-Parkin signaling and will discuss the roles of PINK1-Parkin signaling for mitochondrial maintenance and how the failure of this signaling leads to neurodegeneration.
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Affiliation(s)
- Yuzuru Imai
- Department of Neuroscience for Neurodegenerative Disorders, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
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50
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Toma MI, Wuttig D, Kaiser S, Herr A, Weber T, Zastrow S, Koch R, Meinhardt M, Baretton GB, Wirth MP, Fuessel S. PARK2 and PACRG are commonly downregulated in clear-cell renal cell carcinoma and are associated with aggressive disease and poor clinical outcome. Genes Chromosomes Cancer 2012; 52:265-73. [PMID: 23125027 DOI: 10.1002/gcc.22026] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 10/05/2012] [Indexed: 01/24/2023] Open
Abstract
PARK2 is an E3 ligase, known to be involved in ubiquitination of several proteins and to play a role in neuronal protection. The gene PARK2 and its potentially co-regulated gene PACRG have been previously found to be deleted in clear-cell renal cell carcinomas (ccRCCs). The aim of our study was to evaluate the mRNA and protein expression of PARK2 and PACRG in a large cohort of ccRCC, and to investigate their association with outcome. The expression of both genes was measured by quantitative PCR in 94 primary ccRCCs and autologous nonmalignant kidney tissues. PACRG and PARK2 protein expression was determined immunohistochemically using tissue microarrays comprising 133 ccRCCs. The mRNA and protein expression of PARK2 and PACRG was significantly downregulated in ccRCCs compared with nonmalignant tissues. Low levels of PARK2 mRNA were associated with high-grade ccRCC and lymph node metastasis. Patients with low PARK2 mRNA levels showed a higher tumor-specific mortality rate and a shorter overall survival (OS) than those with high PARK2 expression. Patients without PACRG mRNA expression in the tumor had a shorter disease-free survival and OS than those with tumors expressing PACRG. In multivariate analyses, neither PARK2 nor PACRG expression were independent prognostic factors. The protein expression of PARK2 and PACRG was significantly downregulated in ccRCCs (82.8, and 96.9%, respectively), but no association with clinical outcome was noticed.
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Affiliation(s)
- Marieta I Toma
- Institute of Pathology, University Hospital Carl Gustav Carus Tehnical University of Dresden, Germany.
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