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Hasan MDN, Rahman MM, Husna AA, Arif M, Jasineviciute I, Kato D, Nakagawa T, Miura N. Upregulation and functional roles of miR-450b in canine oral melanoma. Noncoding RNA Res 2024; 9:376-387. [PMID: 38511062 PMCID: PMC10950611 DOI: 10.1016/j.ncrna.2024.01.017] [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: 11/22/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 03/22/2024] Open
Abstract
Canine oral melanoma (COM) is a common and highly aggressive disease with the potential to model human melanomas. Dysregulated microRNAs represent an interesting line of research for COM because they are implicated in tumor progression. One example is miR-450b, which has been investigated for its molecular mechanisms and biological functions in multiple human cancers, but not human or canine melanoma. Here, we aimed to investigate miR-450b as a potential diagnostic biomarker of COM and its functional roles in metastatic and non-metastatic forms of the disease. We investigated the expression of miR-450b and its target mRNA genes in clinical (tumor tissue and plasma) samples and metastatic and primary-tumor cell lines. Knockdown and overexpression experiments were performed to determine the influence of miR-450b on cell proliferation, migration, colony formation, and apoptosis. miR-450b was significantly upregulated in COM and differentiated between metastatic and non-metastatic tumors, and its potential as a biomarker of metastatic and non-metastatic COM was further confirmed in ROC analysis. miR-450b knockdown promoted cell proliferation, migration, and clonogenicity and inhibited apoptosis, whereas its overexpression yielded the reverse pattern. miR-450b directly binds 3' UTR of PAX9 mRNA and modulates its function leading to BMP4 downregulation and MMP9 upregulation at the transcript level. Furthermore, we surmised that miR-450b activates the Wnt signaling pathway based on gene ontology and enrichment analyses. We concluded that miR-450b has the potential as a diagnostic biomarker and could be a target candidate for COM treatment.
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Affiliation(s)
- MD Nazmul Hasan
- Joint Graduate School of Veterinary Medicine, Kagoshima University, 1-21-24, Korimoto, Kagoshima, 890-0065, Japan
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24, Korimoto, Kagoshima, 890-0065, Japan
| | - Md. Mahfuzur Rahman
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Al Asmaul Husna
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24, Korimoto, Kagoshima, 890-0065, Japan
| | - Mohammad Arif
- Joint Graduate School of Veterinary Medicine, Kagoshima University, 1-21-24, Korimoto, Kagoshima, 890-0065, Japan
| | - Indre Jasineviciute
- Department of Anatomy and Physiology, Veterinary Faculty, Lithuanian University of Health Sciences, LT-47181, Kaunas, Lithuania
| | - Daiki Kato
- Laboratory of Veterinary Surgery, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Takayuki Nakagawa
- Laboratory of Veterinary Surgery, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Naoki Miura
- Joint Graduate School of Veterinary Medicine, Kagoshima University, 1-21-24, Korimoto, Kagoshima, 890-0065, Japan
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24, Korimoto, Kagoshima, 890-0065, Japan
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2
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Coutant K, Magne B, Ferland K, Fuentes-Rodriguez A, Chancy O, Mitchell A, Germain L, Landreville S. Melanocytes in regenerative medicine applications and disease modeling. J Transl Med 2024; 22:336. [PMID: 38589876 PMCID: PMC11003097 DOI: 10.1186/s12967-024-05113-x] [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: 11/08/2023] [Accepted: 03/20/2024] [Indexed: 04/10/2024] Open
Abstract
Melanocytes are dendritic cells localized in skin, eyes, hair follicles, ears, heart and central nervous system. They are characterized by the presence of melanosomes enriched in melanin which are responsible for skin, eye and hair pigmentation. They also have different functions in photoprotection, immunity and sound perception. Melanocyte dysfunction can cause pigmentary disorders, hearing and vision impairments or increased cancer susceptibility. This review focuses on the role of melanocytes in homeostasis and disease, before discussing their potential in regenerative medicine applications, such as for disease modeling, drug testing or therapy development using stem cell technologies, tissue engineering and extracellular vesicles.
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Affiliation(s)
- Kelly Coutant
- Department of Ophthalmology and Otorhinolaryngology-Cervico-Facial Surgery, Faculty of Medicine, Université Laval, Quebec City, QC, Canada
- Regenerative Medicine Division, CHU de Québec-Université Laval Research Centre, Quebec City, QC, Canada
- Centre de recherche en organogénèse expérimentale de l'Université Laval/LOEX, Quebec City, QC, Canada
- Université Laval Cancer Research Center, Quebec City, QC, Canada
| | - Brice Magne
- Regenerative Medicine Division, CHU de Québec-Université Laval Research Centre, Quebec City, QC, Canada
- Centre de recherche en organogénèse expérimentale de l'Université Laval/LOEX, Quebec City, QC, Canada
- Department of Surgery, Faculty of Medicine, Université Laval, Quebec City, QC, Canada
| | - Karel Ferland
- Regenerative Medicine Division, CHU de Québec-Université Laval Research Centre, Quebec City, QC, Canada
- Centre de recherche en organogénèse expérimentale de l'Université Laval/LOEX, Quebec City, QC, Canada
- Department of Surgery, Faculty of Medicine, Université Laval, Quebec City, QC, Canada
| | - Aurélie Fuentes-Rodriguez
- Department of Ophthalmology and Otorhinolaryngology-Cervico-Facial Surgery, Faculty of Medicine, Université Laval, Quebec City, QC, Canada
- Regenerative Medicine Division, CHU de Québec-Université Laval Research Centre, Quebec City, QC, Canada
- Centre de recherche en organogénèse expérimentale de l'Université Laval/LOEX, Quebec City, QC, Canada
- Université Laval Cancer Research Center, Quebec City, QC, Canada
| | - Olivier Chancy
- Department of Ophthalmology and Otorhinolaryngology-Cervico-Facial Surgery, Faculty of Medicine, Université Laval, Quebec City, QC, Canada
- Regenerative Medicine Division, CHU de Québec-Université Laval Research Centre, Quebec City, QC, Canada
- Centre de recherche en organogénèse expérimentale de l'Université Laval/LOEX, Quebec City, QC, Canada
- Université Laval Cancer Research Center, Quebec City, QC, Canada
| | - Andrew Mitchell
- Department of Ophthalmology and Otorhinolaryngology-Cervico-Facial Surgery, Faculty of Medicine, Université Laval, Quebec City, QC, Canada
- Regenerative Medicine Division, CHU de Québec-Université Laval Research Centre, Quebec City, QC, Canada
- Centre de recherche en organogénèse expérimentale de l'Université Laval/LOEX, Quebec City, QC, Canada
- Université Laval Cancer Research Center, Quebec City, QC, Canada
| | - Lucie Germain
- Regenerative Medicine Division, CHU de Québec-Université Laval Research Centre, Quebec City, QC, Canada.
- Centre de recherche en organogénèse expérimentale de l'Université Laval/LOEX, Quebec City, QC, Canada.
- Department of Surgery, Faculty of Medicine, Université Laval, Quebec City, QC, Canada.
| | - Solange Landreville
- Department of Ophthalmology and Otorhinolaryngology-Cervico-Facial Surgery, Faculty of Medicine, Université Laval, Quebec City, QC, Canada.
- Regenerative Medicine Division, CHU de Québec-Université Laval Research Centre, Quebec City, QC, Canada.
- Centre de recherche en organogénèse expérimentale de l'Université Laval/LOEX, Quebec City, QC, Canada.
- Université Laval Cancer Research Center, Quebec City, QC, Canada.
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3
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Taskaeva I, Shatruk A, Bgatova N, Yeremina A, Trunov A, Kononova N, Chernykh V. Autophagy and vesicular trafficking in human uveal melanoma: A histopathological study. Microsc Res Tech 2024; 87:122-132. [PMID: 37698482 DOI: 10.1002/jemt.24417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 08/04/2023] [Accepted: 09/03/2023] [Indexed: 09/13/2023]
Abstract
Uveal melanoma is an ocular tumor with a high risk of developing metastases. The endo-lysosomal system can affect the melanoma progression by accelerating and facilitating invasion or metastasis. This study aims to conduct comparative analysis of normal choroidal melanocytes and uveal melanoma cells ultrastructure with a focus on intracellular transport system, and to examine the patterns of autophagy- and vesicular trafficking-related proteins expression in a case series of uveal melanomas. Transmission electron microscopy was used to assess the ultrastructure of normal choroidal melanocytes and uveal melanoma cells. The expression levels of autophagy- and vesicular trafficking-related proteins in three histological types of uveal melanoma were analyzed by immunofluorescence staining. Electron microscopy results showed that the autophagic vacuoles were more abundant in normal choroidal melanocytes, than in uveal melanoma cells. The normal choroidal melanocytes were characterized by active intracellular vesicular trafficking; however, the proportion of caveolae was higher in uveal melanoma cells. The spindle type of tumor was characterized by a high expression levels of LC3 beta, while Rab7 and Rab11 proteins expression was significantly up-regulated in the mixed-type tumor cells. The results indicate that uveal melanoma cells probably have lower basal levels of autophagy and higher receptor-mediated endocytic trafficking-associated with caveolae than normal choroidal melanocytes. RESEARCH HIGHLIGHTS: The autophagic vacuoles are abundant in normal choroidal melanocytes. Uveal melanoma cells are characterized by a high proportion of caveolae. The high expression levels of LC3 beta were revealed in a spindle type of tumor, while Rab7 and Rab11 proteins expression was up-regulated in the mixed-type tumor cells.
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Affiliation(s)
- Iuliia Taskaeva
- Laboratory of Ultrastructural Research, Research Institute of Clinical and Experimental Lymphology - Branch of the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anastasia Shatruk
- Laboratory of Ultrastructural Research, Research Institute of Clinical and Experimental Lymphology - Branch of the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Nataliya Bgatova
- Laboratory of Ultrastructural Research, Research Institute of Clinical and Experimental Lymphology - Branch of the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alena Yeremina
- S. N. Fyodorov Federal State Institution National Medical Research Center Intersectoral Research and Technology Complex "Eye Microsurgery" Ministry of Health of the Russian Federation, Novosibirsk, Russia
| | - Aleksander Trunov
- S. N. Fyodorov Federal State Institution National Medical Research Center Intersectoral Research and Technology Complex "Eye Microsurgery" Ministry of Health of the Russian Federation, Novosibirsk, Russia
| | - Natalya Kononova
- S. N. Fyodorov Federal State Institution National Medical Research Center Intersectoral Research and Technology Complex "Eye Microsurgery" Ministry of Health of the Russian Federation, Novosibirsk, Russia
| | - Valeriy Chernykh
- S. N. Fyodorov Federal State Institution National Medical Research Center Intersectoral Research and Technology Complex "Eye Microsurgery" Ministry of Health of the Russian Federation, Novosibirsk, Russia
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Targeting VPS41 induces methuosis and inhibits autophagy in cancer cells. Cell Chem Biol 2023; 30:130-143.e5. [PMID: 36708709 DOI: 10.1016/j.chembiol.2023.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 11/09/2022] [Accepted: 01/09/2023] [Indexed: 01/28/2023]
Abstract
The homotypic fusion and vacuole protein sorting (HOPS) complex mediates membrane trafficking involved in endocytosis, autophagy, lysosome biogenesis, and phagocytosis. Defects in HOPS subunits are associated with various forms of cancer, but their potential as drug targets has rarely been examined. Here, we identified vacuolar protein sorting-associated protein 41 homolog (VPS41), a subunit of the HOPS complex, as a target of methyl 2,4-dihydroxy-3-(3-methyl-2-butenyl)-6-phenethylbenzoate (DMBP), a natural small molecule with preferable anticancer activity. DMBP induced methuosis and inhibited autophagic flux in cancer cells by inhibiting the function of VPS41, leading to the restrained fusion of late endosomes and autophagosomes with lysosomes. Moreover, DMBP effectively inhibited metastasis in a mouse metastatic melanoma model. Collectively, the current work revealed that targeting VPS41 would provide a valuable method of inhibiting cancer proliferation through methuosis.
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Said NM, Yassin F, Elkreem EA. Wnt10a missense gene polymorphism association with obesity risk: List of literature and a case-control study with Roc analysis for serum β-catenin level in Egypt. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Ramakrishnan S, Baptista RP, Asady B, Huang G, Docampo R. TbVps41 regulates trafficking of endocytic but not biosynthetic cargo to lysosomes of bloodstream forms of Trypanosoma brucei. FASEB J 2021; 35:e21641. [PMID: 34041791 DOI: 10.1096/fj.202100487r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/15/2021] [Accepted: 04/19/2021] [Indexed: 11/11/2022]
Abstract
The bloodstream stage of Trypanosoma brucei, the causative agent of African trypanosomiasis, is characterized by its high rate of endocytosis, which is involved in remodeling of its surface coat. Here we present evidence that RNAi-mediated expression down-regulation of vacuolar protein sorting 41 (Vps41), a component of the homotypic fusion and vacuole protein sorting (HOPS) complex, leads to a strong inhibition of endocytosis, vesicle accumulation, enlargement of the flagellar pocket ("big eye" phenotype), and dramatic effect on cell growth. Unexpectedly, other functions described for Vps41 in mammalian cells and yeasts, such as delivery of proteins to lysosomes, and lysosome-related organelles (acidocalcisomes) were unaffected, indicating that in trypanosomes post-Golgi trafficking is distinct from that of mammalian cells and yeasts. The essentiality of TbVps41 suggests that it is a potential drug target.
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Affiliation(s)
| | | | - Beejan Asady
- Center for Tropical and Emerging Global Diseases, Athens, GA, USA
| | - Guozhong Huang
- Center for Tropical and Emerging Global Diseases, Athens, GA, USA
| | - Roberto Docampo
- Center for Tropical and Emerging Global Diseases, Athens, GA, USA.,Department of Cellular Biology, University of Georgia, Athens, GA, USA
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7
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van der Welle REN, Jobling R, Burns C, Sanza P, van der Beek JA, Fasano A, Chen L, Zwartkruis FJ, Zwakenberg S, Griffin EF, ten Brink C, Veenendaal T, Liv N, van Ravenswaaij‐Arts CMA, Lemmink HH, Pfundt R, Blaser S, Sepulveda C, Lozano AM, Yoon G, Santiago‐Sim T, Asensio CS, Caldwell GA, Caldwell KA, Chitayat D, Klumperman J. Neurodegenerative VPS41 variants inhibit HOPS function and mTORC1-dependent TFEB/TFE3 regulation. EMBO Mol Med 2021; 13:e13258. [PMID: 33851776 PMCID: PMC8103106 DOI: 10.15252/emmm.202013258] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 11/09/2022] Open
Abstract
Vacuolar protein sorting 41 (VPS41) is as part of the Homotypic fusion and Protein Sorting (HOPS) complex required for lysosomal fusion events and, independent of HOPS, for regulated secretion. Here, we report three patients with compound heterozygous mutations in VPS41 (VPS41S285P and VPS41R662* ; VPS41c.1423-2A>G and VPS41R662* ) displaying neurodegeneration with ataxia and dystonia. Cellular consequences were investigated in patient fibroblasts and VPS41-depleted HeLa cells. All mutants prevented formation of a functional HOPS complex, causing delayed lysosomal delivery of endocytic and autophagic cargo. By contrast, VPS41S285P enabled regulated secretion. Strikingly, loss of VPS41 function caused a cytosolic redistribution of mTORC1, continuous nuclear localization of Transcription Factor E3 (TFE3), enhanced levels of LC3II, and a reduced autophagic response to nutrient starvation. Phosphorylation of mTORC1 substrates S6K1 and 4EBP1 was not affected. In a C. elegans model of Parkinson's disease, co-expression of VPS41S285P /VPS41R662* abolished the neuroprotective function of VPS41 against α-synuclein aggregates. We conclude that the VPS41 variants specifically abrogate HOPS function, which interferes with the TFEB/TFE3 axis of mTORC1 signaling, and cause a neurodegenerative disease.
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Affiliation(s)
- Reini E N van der Welle
- Section Cell BiologyCenter for Molecular MedicineInstitute of BiomembranesUniversity Medical Center UtrechtUtrecht UniversityUtrechtThe Netherlands
| | - Rebekah Jobling
- Department of PediatricsDivision of Clinical and Metabolic GeneticsThe Hospital for Sick ChildrenUniversity of TorontoTorontoONCanada
| | - Christian Burns
- Department of Biological SciencesDivision of Natural Sciences and MathematicsUniversity of DenverDenverCOUSA
| | - Paolo Sanza
- Section Cell BiologyCenter for Molecular MedicineInstitute of BiomembranesUniversity Medical Center UtrechtUtrecht UniversityUtrechtThe Netherlands
| | - Jan A van der Beek
- Section Cell BiologyCenter for Molecular MedicineInstitute of BiomembranesUniversity Medical Center UtrechtUtrecht UniversityUtrechtThe Netherlands
| | - Alfonso Fasano
- Edmond J. Safra Program in Parkinson’s DiseaseMorton and Gloria Shulman Movement Disorders ClinicToronto Western Hospital, UHNTorontoONCanada
- Division of NeurologyUniversity of TorontoTorontoONCanada
- Krembil Brain InstituteTorontoONCanada
- Center for Advancing Neurotechnological Innovation to Application (CRANIA)TorontoONCanada
| | - Lan Chen
- Department of Biological SciencesDivision of Natural Sciences and MathematicsUniversity of DenverDenverCOUSA
| | - Fried J Zwartkruis
- Section Molecular Cancer ResearchCenter for Molecular MedicineUniversity Medical Center UtrechtUtrecht UniversityUtrechtThe Netherlands
| | - Susan Zwakenberg
- Section Molecular Cancer ResearchCenter for Molecular MedicineUniversity Medical Center UtrechtUtrecht UniversityUtrechtThe Netherlands
| | - Edward F Griffin
- Department of Biological SciencesThe University of AlabamaTuscaloosaALUSA
- Department of NeurologyCenter for Neurodegeneration and Experimental TherapeuticsNathan Shock Center for Basic Research in the Biology of AgingUniversity of Alabama at Birmingham School of MedicineBirminghamALUSA
| | - Corlinda ten Brink
- Section Cell BiologyCenter for Molecular MedicineInstitute of BiomembranesUniversity Medical Center UtrechtUtrecht UniversityUtrechtThe Netherlands
| | - Tineke Veenendaal
- Section Cell BiologyCenter for Molecular MedicineInstitute of BiomembranesUniversity Medical Center UtrechtUtrecht UniversityUtrechtThe Netherlands
| | - Nalan Liv
- Section Cell BiologyCenter for Molecular MedicineInstitute of BiomembranesUniversity Medical Center UtrechtUtrecht UniversityUtrechtThe Netherlands
| | | | - Henny H Lemmink
- Department of GeneticsUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
| | - Rolph Pfundt
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
| | - Susan Blaser
- Department of Diagnostic ImagingHospital for Sick ChildrenTorontoONCanada
| | - Carolina Sepulveda
- Edmond J. Safra Program in Parkinson’s DiseaseMorton and Gloria Shulman Movement Disorders ClinicToronto Western Hospital, UHNTorontoONCanada
- Division of NeurologyUniversity of TorontoTorontoONCanada
| | - Andres M Lozano
- Krembil Brain InstituteTorontoONCanada
- Center for Advancing Neurotechnological Innovation to Application (CRANIA)TorontoONCanada
- Department of NeurosurgeryToronto Western Hospital, UHNTorontoONCanada
- University of TorontoTorontoONCanada
| | - Grace Yoon
- Department of PediatricsDivision of Clinical and Metabolic GeneticsThe Hospital for Sick ChildrenUniversity of TorontoTorontoONCanada
| | | | - Cedric S Asensio
- Department of Biological SciencesDivision of Natural Sciences and MathematicsUniversity of DenverDenverCOUSA
| | - Guy A Caldwell
- Department of Biological SciencesThe University of AlabamaTuscaloosaALUSA
- Department of NeurologyCenter for Neurodegeneration and Experimental TherapeuticsNathan Shock Center for Basic Research in the Biology of AgingUniversity of Alabama at Birmingham School of MedicineBirminghamALUSA
| | - Kim A Caldwell
- Department of Biological SciencesThe University of AlabamaTuscaloosaALUSA
- Department of NeurologyCenter for Neurodegeneration and Experimental TherapeuticsNathan Shock Center for Basic Research in the Biology of AgingUniversity of Alabama at Birmingham School of MedicineBirminghamALUSA
| | - David Chitayat
- Department of PediatricsDivision of Clinical and Metabolic GeneticsThe Hospital for Sick ChildrenUniversity of TorontoTorontoONCanada
- The Prenatal Diagnosis and Medical Genetics ProgramDepartment of Obstetrics and GynecologyUniversity of TorontoTorontoONCanada
| | - Judith Klumperman
- Section Cell BiologyCenter for Molecular MedicineInstitute of BiomembranesUniversity Medical Center UtrechtUtrecht UniversityUtrechtThe Netherlands
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Rotunno M, Barajas R, Clyne M, Hoover E, Simonds NI, Lam TK, Mechanic LE, Goldstein AM, Gillanders EM. A Systematic Literature Review of Whole Exome and Genome Sequencing Population Studies of Genetic Susceptibility to Cancer. Cancer Epidemiol Biomarkers Prev 2020; 29:1519-1534. [PMID: 32467344 DOI: 10.1158/1055-9965.epi-19-1551] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 03/17/2020] [Accepted: 05/13/2020] [Indexed: 01/03/2023] Open
Abstract
The application of next-generation sequencing (NGS) technologies in cancer research has accelerated the discovery of somatic mutations; however, progress in the identification of germline variation associated with cancer risk is less clear. We conducted a systematic literature review of cancer genetic susceptibility studies that used NGS technologies at an exome/genome-wide scale to obtain a fuller understanding of the research landscape to date and to inform future studies. The variability across studies on methodologies and reporting was considerable. Most studies sequenced few high-risk (mainly European) families, used a candidate analysis approach, and identified potential cancer-related germline variants or genes in a small fraction of the sequenced cancer cases. This review highlights the importance of establishing consensus on standards for the application and reporting of variants filtering strategies. It also describes the progress in the identification of cancer-related germline variation to date. These findings point to the untapped potential in conducting studies with appropriately sized and racially diverse families and populations, combining results across studies and expanding beyond a candidate analysis approach to advance the discovery of genetic variation that accounts for the unexplained cancer heritability.
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Affiliation(s)
- Melissa Rotunno
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland.
| | - Rolando Barajas
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Mindy Clyne
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Elise Hoover
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | | | - Tram Kim Lam
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Leah E Mechanic
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Alisa M Goldstein
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Elizabeth M Gillanders
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
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A Humanized Yeast Phenomic Model of Deoxycytidine Kinase to Predict Genetic Buffering of Nucleoside Analog Cytotoxicity. Genes (Basel) 2019; 10:genes10100770. [PMID: 31575041 PMCID: PMC6826991 DOI: 10.3390/genes10100770] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/17/2019] [Accepted: 09/23/2019] [Indexed: 12/22/2022] Open
Abstract
Knowledge about synthetic lethality can be applied to enhance the efficacy of anticancer therapies in individual patients harboring genetic alterations in their cancer that specifically render it vulnerable. We investigated the potential for high-resolution phenomic analysis in yeast to predict such genetic vulnerabilities by systematic, comprehensive, and quantitative assessment of drug–gene interaction for gemcitabine and cytarabine, substrates of deoxycytidine kinase that have similar molecular structures yet distinct antitumor efficacy. Human deoxycytidine kinase (dCK) was conditionally expressed in the Saccharomyces cerevisiae genomic library of knockout and knockdown (YKO/KD) strains, to globally and quantitatively characterize differential drug–gene interaction for gemcitabine and cytarabine. Pathway enrichment analysis revealed that autophagy, histone modification, chromatin remodeling, and apoptosis-related processes influence gemcitabine specifically, while drug–gene interaction specific to cytarabine was less enriched in gene ontology. Processes having influence over both drugs were DNA repair and integrity checkpoints and vesicle transport and fusion. Non-gene ontology (GO)-enriched genes were also informative. Yeast phenomic and cancer cell line pharmacogenomics data were integrated to identify yeast–human homologs with correlated differential gene expression and drug efficacy, thus providing a unique resource to predict whether differential gene expression observed in cancer genetic profiles are causal in tumor-specific responses to cytotoxic agents.
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10
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Galván I, Inácio Â, Dañino M, Corbí-Llopis R, Monserrat MT, Bernabeu-Wittel J. High SLC7A11 expression in normal skin of melanoma patients. Cancer Epidemiol 2019; 62:101582. [PMID: 31419780 DOI: 10.1016/j.canep.2019.101582] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/23/2019] [Accepted: 08/05/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND Melanoma is one of the highest metastatic cancers and its incidence is rapidly increasing. A great effort has been devoted to determine gene mutations and expression profiles in melanoma cells, but less attention has been given to the possible influence of melanin synthesis in melanocytes on melanomagenesis. SLC7A11 encodes the cystine/glutamate antiporter xCT and its expression increases the antioxidant capacity of cells by providing cysteine that may be used for glutathione (GSH) synthesis. Melanocytes, however, can also use cysteine for pheomelanin synthesis and pigmentation. Therefore, pheomelanin synthesis may lead to chronic oxidative stress. Possible consequences of this for melanomagenesis have never been explored. METHODS We quantified the expression of SLC7A11 and other genes that are involved in the synthesis of pheomelanin but do not regulate the transport of cysteine from the extracellular medium to the cytosol (CTNS, MC1R, ASIP and SLC45A2) in non-tumorous skin of 45 patients of cutaneous melanoma and 50 healthy individuals. We controlled for the effects of Fitzpatrick skin type, age, gender, body mass, frequency of sun exposure and sunburns and number of melanocytic nevi, as well as for the intrinsic antioxidant capacity as given by the expression of the gene NFE2L2. RESULTS The expression of SLC7A11, but not of the other genes, was significantly higher in melanoma patients than in healthy individuals. This was independent of phenotypic factors and antioxidant capacity, thus supporting an effect of pheomelanin-induced oxidative stress on melanomagenesis. CONCLUSION Our findings indicate that SLC7A11 downregulation in normal epidermal melanocytes may represent a preventive treatment against melanoma.
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Affiliation(s)
- Ismael Galván
- Department of Evolutionary Ecology, Doñana Biological Station, Consejo Superior de Investigaciones Científicas (CSIC), C/ Américo Vespucio 26, 41092 Sevilla, Spain.
| | - Ângela Inácio
- Laboratório de Genética, Instituto de Saúde Ambiental, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, Edifício Egas Moniz, 1649-028 Lisboa, Portugal
| | - María Dañino
- Department of Dermatology, Virgen del Rocío University Hospital, Avda. Manuel Siurot s/n, 41013 Sevilla, Spain
| | - Rosa Corbí-Llopis
- Department of Dermatology, Virgen del Rocío University Hospital, Avda. Manuel Siurot s/n, 41013 Sevilla, Spain
| | - María T Monserrat
- Department of Dermatology, Virgen del Rocío University Hospital, Avda. Manuel Siurot s/n, 41013 Sevilla, Spain
| | - José Bernabeu-Wittel
- Department of Dermatology, Virgen del Rocío University Hospital, Avda. Manuel Siurot s/n, 41013 Sevilla, Spain
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van der Beek J, Jonker C, van der Welle R, Liv N, Klumperman J. CORVET, CHEVI and HOPS – multisubunit tethers of the endo-lysosomal system in health and disease. J Cell Sci 2019; 132:132/10/jcs189134. [DOI: 10.1242/jcs.189134] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
ABSTRACT
Multisubunit tethering complexes (MTCs) are multitasking hubs that form a link between membrane fusion, organelle motility and signaling. CORVET, CHEVI and HOPS are MTCs of the endo-lysosomal system. They regulate the major membrane flows required for endocytosis, lysosome biogenesis, autophagy and phagocytosis. In addition, individual subunits control complex-independent transport of specific cargoes and exert functions beyond tethering, such as attachment to microtubules and SNARE activation. Mutations in CHEVI subunits lead to arthrogryposis, renal dysfunction and cholestasis (ARC) syndrome, while defects in CORVET and, particularly, HOPS are associated with neurodegeneration, pigmentation disorders, liver malfunction and various forms of cancer. Diseases and phenotypes, however, vary per affected subunit and a concise overview of MTC protein function and associated human pathologies is currently lacking. Here, we provide an integrated overview on the cellular functions and pathological defects associated with CORVET, CHEVI or HOPS proteins, both with regard to their complexes and as individual subunits. The combination of these data provides novel insights into how mutations in endo-lysosomal proteins lead to human pathologies.
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Affiliation(s)
- Jan van der Beek
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Institute for Biomembranes, Utrecht University, Utrecht 3584 CX, The Netherlands
| | - Caspar Jonker
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Institute for Biomembranes, Utrecht University, Utrecht 3584 CX, The Netherlands
| | - Reini van der Welle
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Institute for Biomembranes, Utrecht University, Utrecht 3584 CX, The Netherlands
| | - Nalan Liv
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Institute for Biomembranes, Utrecht University, Utrecht 3584 CX, The Netherlands
| | - Judith Klumperman
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Institute for Biomembranes, Utrecht University, Utrecht 3584 CX, The Netherlands
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12
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MITF has a central role in regulating starvation-induced autophagy in melanoma. Sci Rep 2019; 9:1055. [PMID: 30705290 PMCID: PMC6355916 DOI: 10.1038/s41598-018-37522-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/07/2018] [Indexed: 01/27/2023] Open
Abstract
The MITF transcription factor is a master regulator of melanocyte development and a critical factor in melanomagenesis. The related transcription factors TFEB and TFE3 regulate lysosomal activity and autophagy processes known to be important in melanoma. Here we show that MITF binds the CLEAR-box element in the promoters of lysosomal and autophagosomal genes in melanocytes and melanoma cells. The crystal structure of MITF bound to the CLEAR-box reveals how the palindromic nature of this motif induces symmetric MITF homodimer binding. In metastatic melanoma tumors and cell lines, MITF positively correlates with the expression of lysosomal and autophagosomal genes, which, interestingly, are different from the lysosomal and autophagosomal genes correlated with TFEB and TFE3. Depletion of MITF in melanoma cells and melanocytes attenuates the response to starvation-induced autophagy, whereas the overexpression of MITF in melanoma cells increases the number of autophagosomes but is not sufficient to induce autophagic flux. Our results suggest that MITF and the related factors TFEB and TFE3 have separate roles in regulating a starvation-induced autophagy response in melanoma. Understanding the normal and pathophysiological roles of MITF and related transcription factors may provide important clinical insights into melanoma therapy.
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Fesenko DO, Abramov IS, Shershov VE, Kuznetsova VE, Surzhikov SA, Grechishnikova IV, Barsky VE, Chudinov AV, Nasedkina TV. Multiplex Assay to Evaluate the Genetic Risk of Developing Human Melanoma. Mol Biol 2018. [DOI: 10.1134/s0026893318060079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Inman GJ, Wang J, Nagano A, Alexandrov LB, Purdie KJ, Taylor RG, Sherwood V, Thomson J, Hogan S, Spender LC, South AP, Stratton M, Chelala C, Harwood CA, Proby CM, Leigh IM. The genomic landscape of cutaneous SCC reveals drivers and a novel azathioprine associated mutational signature. Nat Commun 2018; 9:3667. [PMID: 30202019 PMCID: PMC6131170 DOI: 10.1038/s41467-018-06027-1] [Citation(s) in RCA: 188] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 08/07/2018] [Indexed: 02/07/2023] Open
Abstract
Cutaneous squamous cell carcinoma (cSCC) has a high tumour mutational burden (50 mutations per megabase DNA pair). Here, we combine whole-exome analyses from 40 primary cSCC tumours, comprising 20 well-differentiated and 20 moderately/poorly differentiated tumours, with accompanying clinical data from a longitudinal study of immunosuppressed and immunocompetent patients and integrate this analysis with independent gene expression studies. We identify commonly mutated genes, copy number changes and altered pathways and processes. Comparisons with tumour differentiation status suggest events which may drive disease progression. Mutational signature analysis reveals the presence of a novel signature (signature 32), whose incidence correlates with chronic exposure to the immunosuppressive drug azathioprine. Characterisation of a panel of 15 cSCC tumour-derived cell lines reveals that they accurately reflect the mutational signatures and genomic alterations of primary tumours and provide a valuable resource for the validation of tumour drivers and therapeutic targets.
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Affiliation(s)
- Gareth J Inman
- Division of Cancer Research, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee, DD1 9SY, UK.
| | - Jun Wang
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK.
| | - Ai Nagano
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Karin J Purdie
- Centre for Cell Biology and Cutaneous Research, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
| | - Richard G Taylor
- Division of Cancer Research, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee, DD1 9SY, UK
| | - Victoria Sherwood
- Division of Cancer Research, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee, DD1 9SY, UK
| | - Jason Thomson
- Centre for Cell Biology and Cutaneous Research, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
| | - Sarah Hogan
- Centre for Cell Biology and Cutaneous Research, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
| | - Lindsay C Spender
- Division of Cancer Research, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee, DD1 9SY, UK
| | - Andrew P South
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Michael Stratton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Claude Chelala
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Catherine A Harwood
- Centre for Cell Biology and Cutaneous Research, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
| | - Charlotte M Proby
- Division of Cancer Research, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee, DD1 9SY, UK
| | - Irene M Leigh
- Division of Cancer Research, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee, DD1 9SY, UK.
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15
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Xie H, Xue L, Hua W, Jia B, Zhang L, Li L. Whole genome sequencing and 6-year follow-up of a mother and daughter with frontometaphyseal dysplasia associated with keratitis, xerosis, poikiloderma, and acro-osteolysis: A case report. Medicine (Baltimore) 2018; 97:e11283. [PMID: 29995760 PMCID: PMC6076188 DOI: 10.1097/md.0000000000011283] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
RATIONALE Frontometaphyseal dysplasia (FMD) is a dominant X-linked rare disease caused by mutations of FLNA. The distinctive features of FMD include skeletal dysplasia, facial dysmorphism, extremities anomalies, deafness, cleft palate and eye anterior segment anomalies, yet none of the complications, such as acro-osteolysis, keratitis, xerosis or poikiloderma, have been reported in FMD. PATIENT CONCERNS A 29-year-old mother and her 7-year-old daughter, both presented with congenital glaucoma, craniofacial dysmorphism, xerosis and poikiloderma, were admitted to our hospital in 2011. Additionally, the mother also suffered from acro-osteolysis, keratitis, camptodactyly of hands and metastatic cutaneous squamous cell carcinoma (SCC) which turned out to be fatal 5 years later. In 2017, keratitis and acro-osteolysis were noticed in the daughter as well. Radiography showed bowed long bones with thickening cortex, and distal phalangeal osteolysis. DIAGNOSES Whole genome sequencing (WGS) was conducted in 2016, resulting in 71491 single-nucleotide polymorphisms and 7616 indels shared by patients while the father was taken as control. A FLNA variant was classified likely pathogenic, supporting the diagnoses of FMD. In addition, though our patients' symptoms were highly consistent with xeroderma pigmentosum variant, a mild subtype of xeroderma pigmentosum (XP) with merely accumulated UV-induced lesions like xerosis and poikiloderma limited to sun-exposure sites, higher risks of cutaneous neoplasms and absence of classical XP features, WGS didn't find supportive genetical evidence, but 2 HERC2 variants were assigned highest suspicion in both XP and SCC by bioinformatical analyses. INTERVENTIONS Anti-inflammatory treatment, sunscreens and moisturizers were administered. OUTCOMES The daughter's cutaneous lesions developed slowly during the 6-year follow-up, but the keratitis seriously weakened her sight. LESSONS To our knowledge, it's the first report of cases carrying FMD, keratitis, xerosis, poikiloderma and acro-osteolysis simultaneously, and 3 likely pathogenic variants were identified. Whole genome/exon sequencing is recommended as a common test for patients with rare phenotypes.
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Affiliation(s)
| | - Li Xue
- Department of Dermatology
| | | | | | - Liang Zhang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Implant Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Li Li
- Department of Dermatology
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16
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Amber S, Zahid S. Data integration for functional annotation of regulatory single nucleotide polymorphisms associated with Alzheimer's disease susceptibility. Gene 2018; 672:115-125. [PMID: 29883757 DOI: 10.1016/j.gene.2018.06.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 05/30/2018] [Accepted: 06/04/2018] [Indexed: 01/10/2023]
Abstract
BACKGROUND Alzheimer's disease (AD), the most common form of dementia affects 24.3 million people worldwide. More than twenty genetic loci have been associated with AD and a significant number of genetic variants were mapped within these loci. A large proportion of genome wide significant variants lie outside the coding region. However, the plausible function of these variants is still unexplored. OBJECTIVE The present study aimed to unravel the regulatory role of proxy single nucleotide polymorphisms (SNPs), to determine their risk of developing AD. METHODS The RegulomeDB was employed to predict the regulatory role of proxy SNPs. Protein association network and functional enrichment analysis was performed using String10.5 and gene ontology, respectively. RESULTS A total of 451 SNPs were examined through SNAP web portal (r2 ≤ 0.80) which returned 2186 proxy SNPs in linkage disequilibrium (LD) with genome wide significant SNPs for AD. Out of 2186 SNPs analyzed in RegulomeDB, 151 had the scores < 3 that indicates the high degree of their potential regulatory function. Further analysis revealed that out of these 151 SNPs, 37 were genome wide significant for AD, 17 were significantly associated with diseases other than AD, 89 were proxy SNPs (not genome wide significant) for various diseases including AD while 8 SNPs were novel proxy SNPs for AD. CONCLUSION These findings support the notion that the non-coding variants can be strongly associated with disease risk. Further validation through genome wide association studies will be helpful for the elucidation of their regulatory potential.
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Affiliation(s)
- Sanila Amber
- Neurobiology Research Laboratory, Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Saadia Zahid
- Neurobiology Research Laboratory, Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan.
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17
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Franzoni A, Markova-Car E, Dević-Pavlić S, Jurišić D, Puppin C, Mio C, De Luca M, Petruz G, Damante G, Pavelić SK. A polymorphic GGC repeat in the NPAS2 gene and its association with melanoma. Exp Biol Med (Maywood) 2017; 242:1553-1558. [PMID: 28799406 DOI: 10.1177/1535370217724093] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Circadian clock regulation in mammals is controlled by feedback loops of a set of circadian genes. One of these circadian genes, NPAS2, encodes for a member of the bHLH-PAS class of transcription factors and is expressed in the forebrain and in some peripheral organs such as liver and skin. Other biological processes are also regulated by circadian genes. For example, NPAS2 is involved in cell proliferation, DNA damage repair and malignant transformation. Aberrant expression of clock genes has been previously observed in melanoma which led to our effort to sequence the NPAS2 promoter region in this cancer type. The NPAS2 putative promoter and 5' untranslated region of ninety-three melanoma patients and ninety-six control subjects were sequenced and several variants were identified. Among these is a novel microsatellite comprising a GGC repeat with different alleles ranging from 7 to 13 repeats located in the 5' untranslated exon. Homozygosity of an allele with nine repeats (9/9) was more prevalent in melanoma than in control subjects (22.6% and 13.5%, respectively, P: 0.0206) suggesting that some NPAS2 variants might contribute to melanoma susceptibility. Impact statement This report describes a variable microsatellite repeat sequence located in the 5' untranslated exon of NSPAS2, a gene encoding a clock transcription factor. Significantly, this study is the first to show that a variant copy number GGC repeat sequence in the NPAS2 clock gene associates with melanoma risk and which may be useful in the assessment of melanoma predisposition.
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Affiliation(s)
- Alessandra Franzoni
- 1 Medical Genetics Institute, Azienda Ospedaliero-Universitaria di Udine, Udine 33017, Italy
| | - Elitza Markova-Car
- 2 Department of Biotechnology, Centre for High-Throughput Technologies, University of Rijeka, Rijeka 51000, Croatia
| | - Sanja Dević-Pavlić
- 2 Department of Biotechnology, Centre for High-Throughput Technologies, University of Rijeka, Rijeka 51000, Croatia
| | - Davor Jurišić
- 3 Department for Plastic and Reconstructive Surgery, Clinic for Surgery, University Hospital Centre Rijeka, Rijeka 51000, Croatia
| | - Cinzia Puppin
- 4 Department of Medical and Biological Sciences, University of Udine, Udine 33100, Italy
| | - Catia Mio
- 4 Department of Medical and Biological Sciences, University of Udine, Udine 33100, Italy
| | - Marila De Luca
- 4 Department of Medical and Biological Sciences, University of Udine, Udine 33100, Italy
| | - Giulia Petruz
- 4 Department of Medical and Biological Sciences, University of Udine, Udine 33100, Italy
| | - Giuseppe Damante
- 1 Medical Genetics Institute, Azienda Ospedaliero-Universitaria di Udine, Udine 33017, Italy.,4 Department of Medical and Biological Sciences, University of Udine, Udine 33100, Italy
| | - Sandra Kraljević Pavelić
- 2 Department of Biotechnology, Centre for High-Throughput Technologies, University of Rijeka, Rijeka 51000, Croatia
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18
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Shi Q, Liu H, Han P, Li C, Wang Y, Wu W, Zhu D, Amos CI, Fang S, Lee JE, Han J, Wei Q. Genetic Variants in WNT2B and BTRC Predict Melanoma Survival. J Invest Dermatol 2017; 137:1749-1756. [PMID: 28499756 PMCID: PMC5548422 DOI: 10.1016/j.jid.2017.04.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 04/01/2017] [Accepted: 04/23/2017] [Indexed: 12/12/2022]
Abstract
Cutaneous melanoma (CM) is the most lethal skin cancer. The Wnt pathway has an impact on development, invasion, and metastasis of CM, thus likely affecting CM prognosis. Using data from a published genome-wide association study from The University of Texas MD Anderson Cancer Center, we assessed the associations of 19,830 common single-nucleotide polymorphisms (SNPs) in 151 Wnt pathway autosomal genes with CM-specific survival and then validated significant SNPs in another genome-wide association study from Harvard University. In the single-locus analysis, 1,855 SNPs were significantly associated with CM-specific survival at P < 0.05, of which 547 SNPs were still considered noteworthy after the correction by the false-positive report probability. In the replication, two SNPs remained significantly associated with CM-specific survival after multiple comparison correction. By performing functional prediction and stepwise selection, we identified two independent SNPs (i.e., WNT2B rs1175649 G>T and BTRC rs61873997 G>A) that showed a predictive role in CM-specific survival, with an effect-allele-attributed hazards ratio (adjusted hazards ratio) of 1.99 (95% confidence interval = 1.41-2.81, P = 8.10 × 10-5) and 0.61 (0.46-0.80, 3.12×10-4), respectively. Collectively, these variants in the Wnt pathway genes may be biomarkers for outcomes of patients with CM, if validated by larger studies.
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Affiliation(s)
- Qiong Shi
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China; Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA; Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA; Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Peng Han
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA; Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA; Department of Otorhinolaryngology Head and Neck Surgery, First Affiliated Hospital, Xi'an Jiaotong University College of Medicine, Xi'an, Shaanxi, China
| | - Chunying Li
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Yanru Wang
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA; Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Wenting Wu
- Department of Epidemiology, Fairbanks School of Public Health, Indiana University Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, Indiana, USA
| | - Dakai Zhu
- Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Christopher I Amos
- Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Shenying Fang
- Department of Surgical Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA
| | - Jeffrey E Lee
- Department of Surgical Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA
| | - Jiali Han
- Department of Epidemiology, Fairbanks School of Public Health, Indiana University Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, Indiana, USA; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA; Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.
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Hernando B, Peña-Chilet M, Ibarrola-Villava M, Martin-Gonzalez M, Gomez-Fernandez C, Ribas G, Martinez-Cadenas C. Genetic 3'UTR variation is associated with human pigmentation characteristics and sensitivity to sunlight. Exp Dermatol 2017; 26:896-903. [PMID: 28266728 DOI: 10.1111/exd.13333] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2017] [Indexed: 12/14/2022]
Abstract
Sunlight exposure induces signalling pathways leading to the activation of melanin synthesis and tanning response. MicroRNAs (miRNAs) can regulate the expression of genes involved in pigmentation pathways by binding to the complementary sequence in their 3'untranslated regions (3'UTRs). Therefore, 3'UTR SNPs are predicted to modify the ability of miRNAs to target genes, resulting in differential gene expression. In this study, we investigated the role in pigmentation and sun-sensitivity traits, as well as in melanoma susceptibility, of 38 different 3'UTR SNPs from 38 pigmentation-related genes. A total of 869 individuals of Spanish origin (526 melanoma cases and 343 controls) were analysed. The association of genotypic data with pigmentation traits was analysed via logistic regression. Web-based tools for predicting the effect of genetic variants in microRNA-binding sites in 3'UTR gene regions were also used. Seven 3'UTR SNPs showed a potential implication in melanoma risk phenotypes. This association is especially noticeable for two of them, rs2325813 in the MLPH gene and rs752107 in the WNT3A gene. These two SNPs were predicted to disrupt a miRNA-binding site and to impact on miRNA-mRNA interaction. To our knowledge, this is the first time that these two 3'UTR SNPs have been associated with sun-sensitivity traits. We state the potential implication of these SNPs in human pigmentation and sensitivity to sunlight, possibly as a result of changes in the level of gene expression through the disruption of putative miRNA-binding sites.
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Affiliation(s)
- Barbara Hernando
- Department of Medicine, Jaume I University of Castellon, Castellon, Spain
| | - Maria Peña-Chilet
- Department of Medical Oncology, Biomedical Research Institute - INCLIVA, Valencia, Spain.,Network Centre for Biomedical Cancer Research (CIBERONC), Valencia, Spain
| | - Maider Ibarrola-Villava
- Department of Medical Oncology, Biomedical Research Institute - INCLIVA, Valencia, Spain.,Network Centre for Biomedical Cancer Research (CIBERONC), Valencia, Spain
| | | | | | - Gloria Ribas
- Department of Medical Oncology, Biomedical Research Institute - INCLIVA, Valencia, Spain.,Network Centre for Biomedical Cancer Research (CIBERONC), Valencia, Spain
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20
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Fesenko DO, Chudinov AV, Surzhikov SA, Zasedatelev AS. Biochip-Based Genotyping Assay for Detection of Polymorphisms in Pigmentation Genes Associated with Cutaneous Melanoma. Genet Test Mol Biomarkers 2016; 20:208-12. [PMID: 26848990 DOI: 10.1089/gtmb.2015.0272] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
AIMS The purpose of the study was to develop a new assay for genotyping nine single nucleotide polymorphisms (SNPs) that are known to be associated with melanoma. METHODS Two-stage single tube polymerase chain reaction (PCR) followed by hybridization on a biochip was developed and applied in the study. RESULTS A total of nine SNPs were selected from five genes: MC1R (rs1805006, rs1805007, rs1805009, rs11547464), HERC2 (rs12913832), OCA2 (rs1800407), SLC45A2 (rs16891982), TYR (rs1393350), and a SNP from the intergenic locus rs12896399 were used for the synthesis of ssDNAs via a single-stage PCR process. The assays were performed on a biochip-based platform that is capable of SNP genotyping via a single reaction-tube PCR, followed by on chip hybridization. We tested 69 DNAs obtained from healthy persons and demonstrated the assays' ability to discriminate all three genotypes for almost all of the SNPs. CONCLUSIONS The developed approach proved robust, suggesting that it might be useful for the personalized genotyping of large cohorts of patients.
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Affiliation(s)
- Denis O Fesenko
- 1 Engelhardt Institute of Molecular Biology , Russian Academy of Sciences, Moscow, Russia
- 2 N.N. Blokhin Russian Cancer Research Center , Russian Academy of Sciences, Moscow, Russia
| | - Alexander V Chudinov
- 1 Engelhardt Institute of Molecular Biology , Russian Academy of Sciences, Moscow, Russia
| | - Sergey A Surzhikov
- 1 Engelhardt Institute of Molecular Biology , Russian Academy of Sciences, Moscow, Russia
| | - Alexander S Zasedatelev
- 1 Engelhardt Institute of Molecular Biology , Russian Academy of Sciences, Moscow, Russia
- 2 N.N. Blokhin Russian Cancer Research Center , Russian Academy of Sciences, Moscow, Russia
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21
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Hernando B, Ibarrola-Villava M, Fernandez LP, Peña-Chilet M, Llorca-Cardeñosa M, Oltra SS, Alonso S, Boyano MD, Martinez-Cadenas C, Ribas G. Sex-specific genetic effects associated with pigmentation, sensitivity to sunlight, and melanoma in a population of Spanish origin. Biol Sex Differ 2016; 7:17. [PMID: 26998216 PMCID: PMC4797181 DOI: 10.1186/s13293-016-0070-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 03/07/2016] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Human pigmentation is a polygenic quantitative trait with high heritability. In addition to genetic factors, it has been shown that pigmentation can be modulated by oestrogens and androgens via up- or down-regulation of melanin synthesis. Our aim was to identify possible sex differences in pigmentation phenotype as well as in melanoma association in a melanoma case-control population of Spanish origin. METHODS Five hundred and ninety-nine females (316 melanoma cases and 283 controls) and 458 males (234 melanoma cases and 224 controls) were analysed. We genotyped 363 polymorphisms (single nucleotide polymorphisms (SNPs)) from 65 pigmentation gene regions. RESULTS When samples were stratified by sex, we observed more SNPs associated with dark pigmentation and good sun tolerance in females than in males (107 versus 75; P = 2.32 × 10(-6)), who were instead associated with light pigmentation and poor sun tolerance. Furthermore, six SNPs in TYR, SILV/CDK2, GPR143, and F2RL1 showed strong differences in melanoma risk by sex (P < 0.01). CONCLUSIONS We demonstrate that these genetic variants are important for pigmentation as well as for melanoma risk, and also provide suggestive evidence for potential differences in genetic effects by sex.
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Affiliation(s)
- Barbara Hernando
- Department of Medicine, Jaume I University of Castellon, Av. Sos Baynat s/n, 12071 Castellon, Spain
| | - Maider Ibarrola-Villava
- Department of Medical Oncology, Biomedical Research Institute - INCLIVA, University of Valencia, Av. Menendez Pelayo 4 accesorio, 46010 Valencia, Spain
| | - Lara P Fernandez
- Molecular Oncology and Nutritional Genomics of Cancer Group, IMDEA Food Institute, CEI UAM + CSIC, Madrid, Spain
| | - Maria Peña-Chilet
- Department of Medical Oncology, Biomedical Research Institute - INCLIVA, University of Valencia, Av. Menendez Pelayo 4 accesorio, 46010 Valencia, Spain
| | - Marta Llorca-Cardeñosa
- Department of Medical Oncology, Biomedical Research Institute - INCLIVA, University of Valencia, Av. Menendez Pelayo 4 accesorio, 46010 Valencia, Spain
| | - Sara S Oltra
- Department of Medical Oncology, Biomedical Research Institute - INCLIVA, University of Valencia, Av. Menendez Pelayo 4 accesorio, 46010 Valencia, Spain
| | - Santos Alonso
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Leioa, Bizkaia Spain
| | - Maria Dolores Boyano
- Department of Cell Biology and Histology, University of the Basque Country UPV/EHU, Leioa, Bizkaia Spain.,BioCruces Health Research Institute, Cruces University Hospital, Cruces-Barakaldo, Bizkaia Spain
| | - Conrado Martinez-Cadenas
- Department of Medicine, Jaume I University of Castellon, Av. Sos Baynat s/n, 12071 Castellon, Spain
| | - Gloria Ribas
- Department of Medical Oncology, Biomedical Research Institute - INCLIVA, University of Valencia, Av. Menendez Pelayo 4 accesorio, 46010 Valencia, Spain
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Overexpression of Rab25 promotes hepatocellular carcinoma cell proliferation and invasion. Tumour Biol 2015; 37:7713-8. [PMID: 26692100 DOI: 10.1007/s13277-015-4606-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 12/07/2015] [Indexed: 01/17/2023] Open
Abstract
Rab25 was reported to be associated with several human cancers and malignant biological behavior of cancer cells. The goal of the present study was to determine its expression pattern and biological function in human hepatocellular carcinoma (HCC). We examined Rab25 protein in 92 cases of HCC tissues and 3 HCC cell lines. The results showed that Rab25 was upregulated in HCC tissues and cells compared with normal liver tissues and cell line. Rab25 overexpression correlated with advanced tumor stage and nodal metastasis. Rab25 small interfering RNA (siRNA) was employed in Bel7402 and SK-Hep-1 cell lines. Cell Counting Kit-8 (CCK-8) assay and colony formation assay showed that Rab25 depletion blocked cell growth rate and inhibited colony formation ability. Transwell assay showed that Rab25 depletion negatively regulated the invading ability of HCC cells. To explore the possible mechanisms, we checked several signaling pathways and found that Rab25 depletion downregulated AKT phosphorylation. In addition, luciferase reporter assay showed that Rab25 depletion inhibited the Wnt signaling pathway and its target genes such as cyclin D1, c-myc, and MMP7. In conclusion, Rab25 is overexpressed in human HCC and contributes to cancer cell proliferation and invasion possibly through regulation of the Wnt signaling pathway.
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MITF drives endolysosomal biogenesis and potentiates Wnt signaling in melanoma cells. Proc Natl Acad Sci U S A 2015; 112:E420-9. [PMID: 25605940 DOI: 10.1073/pnas.1424576112] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Canonical Wnt signaling plays an important role in development and disease, regulating transcription of target genes and stabilizing many proteins phosphorylated by glycogen synthase kinase 3 (GSK3). We observed that the MiT family of transcription factors, which includes the melanoma oncogene MITF (micropthalmia-associated transcription factor) and the lysosomal master regulator TFEB, had the highest phylogenetic conservation of three consecutive putative GSK3 phosphorylation sites in animal proteomes. This finding prompted us to examine the relationship between MITF, endolysosomal biogenesis, and Wnt signaling. Here we report that MITF expression levels correlated with the expression of a large subset of lysosomal genes in melanoma cell lines. MITF expression in the tetracycline-inducible C32 melanoma model caused a marked increase in vesicular structures, and increased expression of late endosomal proteins, such as Rab7, LAMP1, and CD63. These late endosomes were not functional lysosomes as they were less active in proteolysis, yet were able to concentrate Axin1, phospho-LRP6, phospho-β-catenin, and GSK3 in the presence of Wnt ligands. This relocalization significantly enhanced Wnt signaling by increasing the number of multivesicular bodies into which the Wnt signalosome/destruction complex becomes localized upon Wnt signaling. We also show that the MITF protein was stabilized by Wnt signaling, through the novel C-terminal GSK3 phosphorylations identified here. MITF stabilization caused an increase in multivesicular body biosynthesis, which in turn increased Wnt signaling, generating a positive-feedback loop that may function during the proliferative stages of melanoma. The results underscore the importance of misregulated endolysosomal biogenesis in Wnt signaling and cancer.
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