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Cai Z, Duan Y, Li W, Liu Z, Gong Z, Hong S, He X, Xuanyuan X, Chen Y, Bi X, Wang W. FANCI serve as a prognostic biomarker correlated with immune infiltrates in skin cutaneous melanoma. Front Immunol 2023; 14:1295831. [PMID: 38077326 PMCID: PMC10703153 DOI: 10.3389/fimmu.2023.1295831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 11/07/2023] [Indexed: 12/18/2023] Open
Abstract
Background As a member of tumor, Skin cutaneous melanoma (SKCM) poses a serious threat to people's health because of its strong malignancy. Unfortunately, effective treatment methods for SKCM remain lacking. FANCI plays a vital role in the occurrence and metastasis of various tumor types. However, its regulatory role in SKCM is unclear. The purpose of this study was to explore the association of FANCI with SKCM. Methods This study investigated the expression of FANCI in GSE46517, GSE15605, and GSE114445 from the Gene Expression Omnibus database and The Cancer Genome Atlas (TCGA)-SKCM datasets using the package "limma" or "DESeq2" in R environment and also investigated the prognostic significance of FANCI by utilizing the GEPIA database. Additionally, our research made use of real-time quantitative polymerase chain reaction (RT-qPCR) and immunohistochemical (IHC) staining to verify FANCI expression between SKCM and normal tissues and developed the knockdown of FANCI in A375 and A875 cells to further analyze the function of FANCI. Finally, this study analyzed the correlation of FANCI and tumor-infiltrating immune cells by CIBERSORT, ESTIMATE, and ssGSEA algorithms. Results The FANCI level was increasing in SKCM tissues from GSE46517, GSE15605, GSE114445, and TCGA-SKCM. However, high FANCI expression correlated with poor overall survival. The RT-qPCR and IHC confirmed the accuracy of bioinformatics. Knocking down FANCI suppresses A375 and A875 cell proliferation, migration, and invasion. FANCI could be involved in the immunological milieu of SKCM by regulating immune responses and infiltrating numerous immune cells, particularly neutrophils, CD8+ T cells, and B cells. Furthermore, patients with SKCM who have a high FANCI expression level are reported to exhibit immunosuppression, whereas those with a low FANCI expression level are more likely to experience positive outcomes from immunotherapy. Conclusions The increased FANCI expression in SKCM can be a prognostic biomarker. Knockdown FANCI can reduce the occurrence and progression of SKCM. The FANCI expression provides a foundation for predicting the immune status and treatment of SKCM.
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Affiliation(s)
- Zhenguo Cai
- Department of Dermatology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Dermatology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Yanjuan Duan
- Department of Dermatology, Seventh People’s Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wen Li
- Department of Dermatology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zhuohang Liu
- Department of Neurology, Minhang Hospital, Fudan University/Central Hospital of Minhang District, Shanghai, China
| | - Zijun Gong
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Sheng Hong
- Department of Dermatology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Xu He
- Department of Dermatology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Xinyang Xuanyuan
- Department of Dermatology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Youdong Chen
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xinling Bi
- Department of Dermatology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Wuqing Wang
- Department of Dermatology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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2
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Fierheller CT, Alenezi WM, Serruya C, Revil T, Amuzu S, Bedard K, Subramanian DN, Fewings E, Bruce JP, Prokopec S, Bouchard L, Provencher D, Foulkes WD, El Haffaf Z, Mes-Masson AM, Tischkowitz M, Campbell IG, Pugh TJ, Greenwood CMT, Ragoussis J, Tonin PN. Molecular Genetic Characteristics of FANCI, a Proposed New Ovarian Cancer Predisposing Gene. Genes (Basel) 2023; 14:genes14020277. [PMID: 36833203 PMCID: PMC9956348 DOI: 10.3390/genes14020277] [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: 12/01/2022] [Revised: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 01/26/2023] Open
Abstract
FANCI was recently identified as a new candidate ovarian cancer (OC)-predisposing gene from the genetic analysis of carriers of FANCI c.1813C>T; p.L605F in OC families. Here, we aimed to investigate the molecular genetic characteristics of FANCI, as they have not been described in the context of cancer. We first investigated the germline genetic landscape of two sisters with OC from the discovery FANCI c.1813C>T; p.L605F family (F1528) to re-affirm the plausibility of this candidate. As we did not find other conclusive candidates, we then performed a candidate gene approach to identify other candidate variants in genes involved in the FANCI protein interactome in OC families negative for pathogenic variants in BRCA1, BRCA2, BRIP1, RAD51C, RAD51D, and FANCI, which identified four candidate variants. We then investigated FANCI in high-grade serous ovarian carcinoma (HGSC) from FANCI c.1813C>T carriers and found evidence of loss of the wild-type allele in tumour DNA from some of these cases. The somatic genetic landscape of OC tumours from FANCI c.1813C>T carriers was investigated for mutations in selected genes, copy number alterations, and mutational signatures, which determined that the profiles of tumours from carriers were characteristic of features exhibited by HGSC cases. As other OC-predisposing genes such as BRCA1 and BRCA2 are known to increase the risk of other cancers including breast cancer, we investigated the carrier frequency of germline FANCI c.1813C>T in various cancer types and found overall more carriers among cancer cases compared to cancer-free controls (p = 0.007). In these different tumour types, we also identified a spectrum of somatic variants in FANCI that were not restricted to any specific region within the gene. Collectively, these findings expand on the characteristics described for OC cases carrying FANCI c.1813C>T; p.L605F and suggest the possible involvement of FANCI in other cancer types at the germline and/or somatic level.
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Affiliation(s)
- Caitlin T. Fierheller
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Wejdan M. Alenezi
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- Department of Medical Laboratory Technology, Taibah University, Medina 42353, Saudi Arabia
| | - Corinne Serruya
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Timothée Revil
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
- McGill Genome Centre, McGill University, Montreal, QC H3A 0G1, Canada
| | - Setor Amuzu
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
- McGill Genome Centre, McGill University, Montreal, QC H3A 0G1, Canada
| | - Karine Bedard
- Laboratoire de Diagnostic Moléculaire, Centre Hospitalier de l’Université de Montréal (CHUM), Montreal, QC H2X 3E4, Canada
- Département de Pathologie et Biologie Cellulaire, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Deepak N. Subramanian
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Eleanor Fewings
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge CB2 1TN, UK
| | - Jeffrey P. Bruce
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Stephenie Prokopec
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Luigi Bouchard
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
- Department of Medical Biology, Centres Intégrés Universitaires de Santé et de Services Sociaux du Saguenay-Lac-Saint-Jean Hôpital Universitaire de Chicoutimi, Saguenay, QC G7H 7K9, Canada
- Centre de Recherche du Centre Hospitalier l’Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Diane Provencher
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal and Institut du Cancer de Montréal, Montreal, QC H2X 0A9, Canada
- Division of Gynecologic Oncology, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - William D. Foulkes
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
- Department of Medicine, McGill University, Montreal, QC H3G 2M1, Canada
| | - Zaki El Haffaf
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Anne-Marie Mes-Masson
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal and Institut du Cancer de Montréal, Montreal, QC H2X 0A9, Canada
- Department of Medicine, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge CB2 1TN, UK
| | - Ian G. Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Trevor J. Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Celia M. T. Greenwood
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H4A 3T2, Canada
- Department of Epidemiology, Biostatistics & Occupational Health, McGill University, Montreal, QC H3A 1Y7, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
- McGill Genome Centre, McGill University, Montreal, QC H3A 0G1, Canada
| | - Patricia N. Tonin
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- Department of Medicine, McGill University, Montreal, QC H3G 2M1, Canada
- Correspondence:
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Sora V, Laspiur AO, Degn K, Arnaudi M, Utichi M, Beltrame L, De Menezes D, Orlandi M, Stoltze UK, Rigina O, Sackett PW, Wadt K, Schmiegelow K, Tiberti M, Papaleo E. RosettaDDGPrediction for high-throughput mutational scans: From stability to binding. Protein Sci 2023; 32:e4527. [PMID: 36461907 PMCID: PMC9795540 DOI: 10.1002/pro.4527] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/25/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022]
Abstract
Reliable prediction of free energy changes upon amino acid substitutions (ΔΔGs) is crucial to investigate their impact on protein stability and protein-protein interaction. Advances in experimental mutational scans allow high-throughput studies thanks to multiplex techniques. On the other hand, genomics initiatives provide a large amount of data on disease-related variants that can benefit from analyses with structure-based methods. Therefore, the computational field should keep the same pace and provide new tools for fast and accurate high-throughput ΔΔG calculations. In this context, the Rosetta modeling suite implements effective approaches to predict folding/unfolding ΔΔGs in a protein monomer upon amino acid substitutions and calculate the changes in binding free energy in protein complexes. However, their application can be challenging to users without extensive experience with Rosetta. Furthermore, Rosetta protocols for ΔΔG prediction are designed considering one variant at a time, making the setup of high-throughput screenings cumbersome. For these reasons, we devised RosettaDDGPrediction, a customizable Python wrapper designed to run free energy calculations on a set of amino acid substitutions using Rosetta protocols with little intervention from the user. Moreover, RosettaDDGPrediction assists with checking completed runs and aggregates raw data for multiple variants, as well as generates publication-ready graphics. We showed the potential of the tool in four case studies, including variants of uncertain significance in childhood cancer, proteins with known experimental unfolding ΔΔGs values, interactions between target proteins and disordered motifs, and phosphomimetics. RosettaDDGPrediction is available, free of charge and under GNU General Public License v3.0, at https://github.com/ELELAB/RosettaDDGPrediction.
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Affiliation(s)
- Valentina Sora
- Cancer Structural Biology, Danish Cancer Society Research CenterCopenhagenDenmark
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and TechnologyTechnical University of DenmarkLyngbyDenmark
| | - Adrian Otamendi Laspiur
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and TechnologyTechnical University of DenmarkLyngbyDenmark
| | - Kristine Degn
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and TechnologyTechnical University of DenmarkLyngbyDenmark
| | - Matteo Arnaudi
- Cancer Structural Biology, Danish Cancer Society Research CenterCopenhagenDenmark
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and TechnologyTechnical University of DenmarkLyngbyDenmark
| | - Mattia Utichi
- Cancer Structural Biology, Danish Cancer Society Research CenterCopenhagenDenmark
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and TechnologyTechnical University of DenmarkLyngbyDenmark
| | - Ludovica Beltrame
- Cancer Structural Biology, Danish Cancer Society Research CenterCopenhagenDenmark
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and TechnologyTechnical University of DenmarkLyngbyDenmark
| | - Dayana De Menezes
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and TechnologyTechnical University of DenmarkLyngbyDenmark
| | - Matteo Orlandi
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and TechnologyTechnical University of DenmarkLyngbyDenmark
| | - Ulrik Kristoffer Stoltze
- Department of Clinical GeneticsCopenhagen University Hospital RigshospitaletCopenhagenDenmark
- Department of Pediatrics and Adolescent MedicineUniversity Hospital RigshospitaletCopenhagenDenmark
- Institute of Clinical Medicine, Faculty of MedicineUniversity of CopenhagenCopenhagenDenmark
| | - Olga Rigina
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and TechnologyTechnical University of DenmarkLyngbyDenmark
| | - Peter Wad Sackett
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and TechnologyTechnical University of DenmarkLyngbyDenmark
| | - Karin Wadt
- Department of Clinical GeneticsCopenhagen University Hospital RigshospitaletCopenhagenDenmark
- Institute of Clinical Medicine, Faculty of MedicineUniversity of CopenhagenCopenhagenDenmark
| | - Kjeld Schmiegelow
- Department of Pediatrics and Adolescent MedicineUniversity Hospital RigshospitaletCopenhagenDenmark
- Institute of Clinical Medicine, Faculty of MedicineUniversity of CopenhagenCopenhagenDenmark
| | - Matteo Tiberti
- Cancer Structural Biology, Danish Cancer Society Research CenterCopenhagenDenmark
| | - Elena Papaleo
- Cancer Structural Biology, Danish Cancer Society Research CenterCopenhagenDenmark
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and TechnologyTechnical University of DenmarkLyngbyDenmark
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4
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Hunter JE, Campbell AE, Kerridge S, Fraser C, Hannaway NL, Luli S, Ivanova I, Brownridge PJ, Coxhead J, Taylor L, Leary P, Hasoon MSR, Eyers CE, Perkins ND. Up-regulation of the PI3K/AKT and RHO/RAC/PAK signalling pathways in CHK1 inhibitor resistant Eµ-Myc lymphoma cells. Biochem J 2022; 479:2131-2151. [PMID: 36240067 PMCID: PMC9704644 DOI: 10.1042/bcj20220103] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 12/14/2022]
Abstract
The development of resistance and the activation of bypass pathway signalling represents a major problem for the clinical application of protein kinase inhibitors. While investigating the effect of either a c-Rel deletion or RelAT505A phosphosite knockin on the Eµ-Myc mouse model of B-cell lymphoma, we discovered that both NF-κB subunit mutations resulted in CHK1 inhibitor resistance, arising from either loss or alteration of CHK1 activity, respectively. However, since Eµ-Myc lymphomas depend on CHK1 activity to cope with high levels of DNA replication stress and consequent genomic instability, it was not clear how these mutant NF-κB subunit lymphomas were able to survive. To understand these survival mechanisms and to identify potential compensatory bypass signalling pathways in these lymphomas, we applied a multi-omics strategy. With c-Rel-/- Eµ-Myc lymphomas we observed high levels of Phosphatidyl-inositol 3-kinase (PI3K) and AKT pathway activation. Moreover, treatment with the PI3K inhibitor Pictilisib (GDC-0941) selectively inhibited the growth of reimplanted c-Rel-/- and RelAT505A, but not wild type (WT) Eµ-Myc lymphomas. We also observed up-regulation of a RHO/RAC pathway gene expression signature in both Eµ-Myc NF-κB subunit mutation models. Further investigation demonstrated activation of the RHO/RAC effector p21-activated kinase (PAK) 2. Here, the PAK inhibitor, PF-3758309 successfully overcame resistance of RelAT505A but not WT lymphomas. These findings demonstrate that up-regulation of multiple bypass pathways occurs in CHK1 inhibitor resistant Eµ-Myc lymphomas. Consequently, drugs targeting these pathways could potentially be used as either second line or combinatorial therapies to aid the successful clinical application of CHK1 inhibitors.
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Affiliation(s)
- Jill E. Hunter
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Newcastle University, Level 6, Herschel Building, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
| | - Amy E. Campbell
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Scott Kerridge
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Newcastle University, Level 6, Herschel Building, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
| | - Callum Fraser
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Newcastle University, Level 6, Herschel Building, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
| | - Nicola L. Hannaway
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Newcastle University, Level 6, Herschel Building, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
| | - Saimir Luli
- Newcastle University Clinical and Translational Research Institute, Preclinical In Vivo Imaging (PIVI), Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Iglika Ivanova
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Newcastle University, Level 6, Herschel Building, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
| | - Philip J. Brownridge
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Jonathan Coxhead
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Newcastle University, Level 6, Herschel Building, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
| | - Leigh Taylor
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Newcastle University, Level 6, Herschel Building, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
| | - Peter Leary
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Megan S. R. Hasoon
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Claire E. Eyers
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Neil D. Perkins
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Newcastle University, Level 6, Herschel Building, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
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Georgescu MM, Whipple SG, Notarianni CM. Novel neoplasms associated with syndromic pediatric medulloblastoma: integrated pathway delineation for personalized therapy. Cell Commun Signal 2022; 20:123. [PMID: 35978432 PMCID: PMC9382778 DOI: 10.1186/s12964-022-00930-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/05/2022] [Indexed: 11/16/2022] Open
Abstract
Medulloblastoma is the most common pediatric embryonal brain tumor, and may occur in cancer predisposition syndromes. We describe novel associations of medulloblastoma with atypical prolactinoma and dural high-grade sarcoma in Li-Fraumeni syndrome (LFS), and epidural desmoid fibromatosis in familial adenomatous polyposis (FAP)/Turcot syndrome. Genomic analysis showing XRCC3 alterations suggested radiotherapy as contributing factor to the progression of LFS-associated medulloblastoma, and demonstrated different mechanisms of APC inactivation in the FAP-associated tumors. The integrated genomic-transcriptomic analysis uncovered the growth pathways driving tumorigenesis, including the prolactin-prolactin receptor (PRLR) autocrine loop and Shh pathway in the LFS-associated prolactinoma and medulloblastoma, respectively, the Wnt pathway in both FAP-associated neoplasms, and the TGFβ and Hippo pathways in the soft tissue tumors, regardless of germline predisposition. In addition, the comparative analysis of paired syndromic neoplasms revealed several growth pathways susceptible to therapeutic intervention by PARP, PRLR, and selective receptor tyrosine kinase (RTK) inhibitors. These could target the defective DNA damage repair in the LFS-associated medulloblastoma, the prolactin autocrine loop in the atypical prolactinoma, the EPHA3/7 and ALK overexpression in the FAP-associated medulloblastoma, and the multi-RTK upregulation in the soft tissue neoplasms. This study presents the spatiotemporal evolution of novel neoplastic associations in syndromic medulloblastoma, and discusses the post-radiotherapy risk for secondary malignancies in syndromic pediatric patients, with important implications for the biology, diagnosis, and therapy of these tumors. Video Abstract
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Affiliation(s)
| | - Stephen G Whipple
- Department of Neurosurgery, Louisiana State University Shreveport, Shreveport, LA, 71103, USA
| | - Christina M Notarianni
- Department of Neurosurgery, Louisiana State University Shreveport, Shreveport, LA, 71103, USA
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Zhang J, Wang J, Wu J, Huang J, Lin Z, Lin X. UBE2T regulates FANCI monoubiquitination to promote NSCLC progression by activating EMT. Oncol Rep 2022; 48:139. [PMID: 35703356 PMCID: PMC9245069 DOI: 10.3892/or.2022.8350] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 05/06/2022] [Indexed: 12/24/2022] Open
Abstract
Fanconi anemia complementation group I (FANCI) is a critical protein for maintaining DNA stability. However, the exact role of FANCI in tumors remains to be elucidated. The present study aimed to explore the role and potential mechanism of action of FANCI in non-small cell lung cancer (NSCLC). To quantify the expression levels of FANCI and ubiquitin-conjugating enzyme E2T (UBE2T) in NSCLC tissues, reverse-transcription quantitative PCR and western blotting were employed. Cell Counting Kit-8, wound healing and Transwell assays along with flow cytometry analysis and tumor xenograft were used to investigate the biological effects of FANCI in NSCLC in vitro and in vivo. The binding of FANCI with UBE2T was confirmed using a co-immunoprecipitation assay. Epithelial-to-mesenchymal transition (EMT) protein markers were quantified via western blotting. The results showed that FANCI expression level was higher in NSCLC tumor tissues, compared with adjacent tissues. In A549 and H1299 cells, knockdown of FANCI inhibited cell proliferation, migration, invasion, cell cycle and EMT in vitro. Tumor growth was repressed in vitro, upon downregulation of FANCI expression. UBE2T was observed to directly bind to FANCI and regulate its monoubiquitination. Overexpression of UBE2T reversed the effects induced by FANCI knockdown in NSCLC cells. Furthermore, it was noted that FANCI interacted with WD repeat domain 48 (WDR48). Overexpression of WDR48 reversed the effects of FANCI on cell proliferation, migration and EMT. In conclusion, FANCI was identified to be a putative oncogene in NSCLC, wherein FANCI was monouniubiquitinated by UBE2T to regulate cell growth, migration and EMT through WDR48. The findings suggested that FANCI could be used as a prognostic biomarker and therapeutic target for NSCLC.
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Affiliation(s)
- Jiguang Zhang
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, Fujian 350001, P.R. China
| | - Jingdong Wang
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, Fujian 350001, P.R. China
| | - Jincheng Wu
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, Fujian 350001, P.R. China
| | - Jianyuan Huang
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, Fujian 350001, P.R. China
| | - Zhaoxian Lin
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, Fujian 350001, P.R. China
| | - Xing Lin
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, Fujian 350001, P.R. China
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7
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Fierheller CT, Guitton-Sert L, Alenezi WM, Revil T, Oros KK, Gao Y, Bedard K, Arcand SL, Serruya C, Behl S, Meunier L, Fleury H, Fewings E, Subramanian DN, Nadaf J, Bruce JP, Bell R, Provencher D, Foulkes WD, El Haffaf Z, Mes-Masson AM, Majewski J, Pugh TJ, Tischkowitz M, James PA, Campbell IG, Greenwood CMT, Ragoussis J, Masson JY, Tonin PN. A functionally impaired missense variant identified in French Canadian families implicates FANCI as a candidate ovarian cancer-predisposing gene. Genome Med 2021; 13:186. [PMID: 34861889 PMCID: PMC8642877 DOI: 10.1186/s13073-021-00998-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 10/27/2021] [Indexed: 12/14/2022] Open
Abstract
Background Familial ovarian cancer (OC) cases not harbouring pathogenic variants in either of the BRCA1 and BRCA2 OC-predisposing genes, which function in homologous recombination (HR) of DNA, could involve pathogenic variants in other DNA repair pathway genes. Methods Whole exome sequencing was used to identify rare variants in HR genes in a BRCA1 and BRCA2 pathogenic variant negative OC family of French Canadian (FC) ancestry, a population exhibiting genetic drift. OC cases and cancer-free individuals from FC and non-FC populations were investigated for carrier frequency of FANCI c.1813C>T; p.L605F, the top-ranking candidate. Gene and protein expression were investigated in cancer cell lines and tissue microarrays, respectively. Results In FC subjects, c.1813C>T was more common in familial (7.1%, 3/42) than sporadic (1.6%, 7/439) OC cases (P = 0.048). Carriers were detected in 2.5% (74/2950) of cancer-free females though female/male carriers were more likely to have a first-degree relative with OC (121/5249, 2.3%; Spearman correlation = 0.037; P = 0.011), suggesting a role in risk. Many of the cancer-free females had host factors known to reduce risk to OC which could influence cancer risk in this population. There was an increased carrier frequency of FANCI c.1813C>T in BRCA1 and BRCA2 pathogenic variant negative OC families, when including the discovery family, compared to cancer-free females (3/23, 13%; OR = 5.8; 95%CI = 1.7–19; P = 0.005). In non-FC subjects, 10 candidate FANCI variants were identified in 4.1% (21/516) of Australian OC cases negative for pathogenic variants in BRCA1 and BRCA2, including 10 carriers of FANCI c.1813C>T. Candidate variants were significantly more common in familial OC than in sporadic OC (P = 0.04). Localization of FANCD2, part of the FANCI-FANCD2 (ID2) binding complex in the Fanconi anaemia (FA) pathway, to sites of induced DNA damage was severely impeded in cells expressing the p.L605F isoform. This isoform was expressed at a reduced level, destabilized by DNA damaging agent treatment in both HeLa and OC cell lines, and exhibited sensitivity to cisplatin but not to a poly (ADP-ribose) polymerase inhibitor. By tissue microarray analyses, FANCI protein was consistently expressed in fallopian tube epithelial cells and only expressed at low-to-moderate levels in 88% (83/94) of OC samples. Conclusions This is the first study to describe candidate OC variants in FANCI, a member of the ID2 complex of the FA DNA repair pathway. Our data suggest that pathogenic FANCI variants may modify OC risk in cancer families. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00998-5.
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Affiliation(s)
- Caitlin T Fierheller
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada
| | - Laure Guitton-Sert
- Genome Stability Laboratory, CHU de Québec-Université Laval Research Center, Oncology Division, Quebec City, Quebec, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, Quebec, Canada
| | - Wejdan M Alenezi
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada.,Department of Medical Laboratory Technology, Taibah University, Medina, Saudi Arabia
| | - Timothée Revil
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill Genome Centre, McGill University, Montreal, Quebec, Canada
| | - Kathleen K Oros
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Yuandi Gao
- Genome Stability Laboratory, CHU de Québec-Université Laval Research Center, Oncology Division, Quebec City, Quebec, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, Quebec, Canada
| | - Karine Bedard
- Laboratoire de Diagnostic Moléculaire, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, Quebec, Canada.,Département de pathologie et biologie cellulaire, Université de Montréal, Montreal, Quebec, Canada
| | - Suzanna L Arcand
- Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada
| | - Corinne Serruya
- Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada
| | - Supriya Behl
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Liliane Meunier
- Centre de recherche du Centre hospitalier de l'Université de Montréal and Institut du cancer de Montréal, Montreal, Quebec, Canada
| | - Hubert Fleury
- Centre de recherche du Centre hospitalier de l'Université de Montréal and Institut du cancer de Montréal, Montreal, Quebec, Canada
| | - Eleanor Fewings
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Deepak N Subramanian
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Javad Nadaf
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill Genome Centre, McGill University, Montreal, Quebec, Canada
| | - Jeffrey P Bruce
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Rachel Bell
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Diane Provencher
- Centre de recherche du Centre hospitalier de l'Université de Montréal and Institut du cancer de Montréal, Montreal, Quebec, Canada.,Division of Gynecologic Oncology, Université de Montréal, Montreal, Quebec, Canada
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.,Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Zaki El Haffaf
- Centre de recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
| | - Anne-Marie Mes-Masson
- Centre de recherche du Centre hospitalier de l'Université de Montréal and Institut du cancer de Montréal, Montreal, Quebec, Canada.,Department of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Paul A James
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.,The Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Ian G Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Celia M T Greenwood
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada.,Department of Epidemiology, Biostatistics & Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill Genome Centre, McGill University, Montreal, Quebec, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec-Université Laval Research Center, Oncology Division, Quebec City, Quebec, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, Quebec, Canada
| | - Patricia N Tonin
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada. .,Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada. .,Department of Medicine, McGill University, Montreal, Quebec, Canada.
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8
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Zhan S, Siu J, Wang Z, Yu H, Bezabeh T, Deng Y, Du W, Fei P. Focal Point of Fanconi Anemia Signaling. Int J Mol Sci 2021; 22:12976. [PMID: 34884777 PMCID: PMC8657418 DOI: 10.3390/ijms222312976] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/26/2021] [Accepted: 11/26/2021] [Indexed: 12/11/2022] Open
Abstract
Among human genetic diseases, Fanconi Anemia (FA) tops all with its largest number of health complications in nearly all human organ systems, suggesting the significant roles played by FA genes in the maintenance of human health. With the accumulated research on FA, the encoded protein products by FA genes have been building up to the biggest cell defense signaling network, composed of not only 22+ FA proteins but also ATM, ATR, and many other non-FA proteins. The FA D2 group protein (FANCD2) and its paralog form the focal point of FA signaling to converge the effects of its upstream players in response to a variety of cellular insults and simultaneously with downstream players to protect humans from contracting diseases, including aging and cancer. In this review, we update and discuss how the FA signaling crucially eases cellular stresses through understanding its focal point.
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Affiliation(s)
- Sudong Zhan
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI 96813, USA; (S.Z.); (Z.W.); (H.Y.)
| | - Jolene Siu
- Student Research Experience Program of University of Hawaii, Honolulu, HI 96822, USA;
| | - Zhanwei Wang
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI 96813, USA; (S.Z.); (Z.W.); (H.Y.)
| | - Herbert Yu
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI 96813, USA; (S.Z.); (Z.W.); (H.Y.)
| | - Tedros Bezabeh
- Department of Chemistry, University of Guam, Mangilao, GU 96923, USA;
| | - Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA;
| | - Wei Du
- Division of Hematology and Oncology, University of Pittsburgh School of Medicine, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA;
| | - Peiwen Fei
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI 96813, USA; (S.Z.); (Z.W.); (H.Y.)
- Student Research Experience Program of University of Hawaii, Honolulu, HI 96822, USA;
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9
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Cagnan I, Keles M, Keskus AG, Tombaz M, Sahan OB, Aerts-Kaya F, Uckan-Cetinkaya D, Konu O, Gunel-Ozcan A. Global miRNA expression of bone marrow mesenchymal stem/stromal cells derived from Fanconi anemia patients. Hum Cell 2021; 35:111-124. [PMID: 34792755 DOI: 10.1007/s13577-021-00626-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 09/26/2021] [Indexed: 11/24/2022]
Abstract
Fanconi anemia (FA) is a rare genetic disorder characterized by genomic instability, developmental defects, and bone marrow (BM) failure. Hematopoietic stem cells (HSCs) in BM interact with the mesenchymal stem/stromal cells (MSCs); and this partly sustains the tissue homeostasis. MicroRNAs (miRNAs) can play a critical role during these interactions possibly via paracrine mechanisms. This is the first study addressing the miRNA profile of FA BM-MSCs obtained before and after BM transplantation (preBMT and postBMT, respectively). Non-coding RNA expression profiling and quality control analyses were performed in Donors (n = 13), FA preBMT (n = 11), and FA postBMT (n = 6) BM-MSCs using GeneChip miRNA 2.0 Array. Six Donor-FA preBMT pairs were used to identify a differentially expressed miRNA expression signature containing 50 miRNAs, which exhibited a strong correlation with the signature obtained from unpaired samples. Five miRNAs (hsa-miR-146a-5p, hsa-miR-148b-3p, hsa-miR-187-3p, hsa-miR-196b-5p, and hsa-miR-25-3p) significantly downregulated in both the paired and unpaired analyses were used to generate the BM-MSCs' miRNA-BM mononuclear mRNA networks upon integration of a public dataset (GSE16334; studying Donor versus FA samples). Functionally enriched KEGG pathways included cellular senescence, miRNAs, and pathways in cancer. Here, we showed that hsa-miR-146a-5p and hsa-miR-874-3p were rescued upon BMT (n = 3 triplets). The decrease in miR-146a-5p was also validated using RT-qPCR and emerged as a strong candidate as a modulator of BM mRNAs in FA patients.
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Affiliation(s)
- Ilgin Cagnan
- Department of Stem Cell Sciences, Graduate School of Health Sciences, Center for Stem Cell Research and Development, Hacettepe University, 06100, Sihhiye, Ankara, Turkey.,Department of Biological Sciences, Faculty of Arts and Sciences, Eastern Mediterranean University, 99628, Famagusta, North Cyprus, via Mersin-10, Turkey
| | - Mustafa Keles
- Department of Stem Cell Sciences, Graduate School of Health Sciences, Center for Stem Cell Research and Development, Hacettepe University, 06100, Sihhiye, Ankara, Turkey.,Center for Stem Cell Research and Development, PEDI-STEM, Hacettepe University, 06100, Sihhiye, Ankara, Turkey
| | - Ayse Gokce Keskus
- Interdisciplinary Neuroscience Program, Bilkent University, Ankara, Turkey
| | - Melike Tombaz
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Ozge Burcu Sahan
- Department of Stem Cell Sciences, Graduate School of Health Sciences, Center for Stem Cell Research and Development, Hacettepe University, 06100, Sihhiye, Ankara, Turkey.,Center for Stem Cell Research and Development, PEDI-STEM, Hacettepe University, 06100, Sihhiye, Ankara, Turkey
| | - Fatima Aerts-Kaya
- Department of Stem Cell Sciences, Graduate School of Health Sciences, Center for Stem Cell Research and Development, Hacettepe University, 06100, Sihhiye, Ankara, Turkey.,Center for Stem Cell Research and Development, PEDI-STEM, Hacettepe University, 06100, Sihhiye, Ankara, Turkey
| | - Duygu Uckan-Cetinkaya
- Department of Stem Cell Sciences, Graduate School of Health Sciences, Center for Stem Cell Research and Development, Hacettepe University, 06100, Sihhiye, Ankara, Turkey.,Center for Stem Cell Research and Development, PEDI-STEM, Hacettepe University, 06100, Sihhiye, Ankara, Turkey.,Department of Pediatrics, Division of Bone Marrow Transplantation Unit, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Ozlen Konu
- Interdisciplinary Neuroscience Program, Bilkent University, Ankara, Turkey. .,Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey.
| | - Aysen Gunel-Ozcan
- Department of Stem Cell Sciences, Graduate School of Health Sciences, Center for Stem Cell Research and Development, Hacettepe University, 06100, Sihhiye, Ankara, Turkey. .,Center for Stem Cell Research and Development, PEDI-STEM, Hacettepe University, 06100, Sihhiye, Ankara, Turkey.
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10
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Wang T, Chen X, Jing F, Li Z, Tan H, Luo Y, Shi H. Identifying the hub genes in non-small cell lung cancer by integrated bioinformatics methods and analyzing the prognostic values. Pathol Res Pract 2021; 228:153654. [PMID: 34749208 DOI: 10.1016/j.prp.2021.153654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 10/07/2021] [Accepted: 10/09/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND Lung cancer, a malignant tumor, has the highest mortality and second most common morbidity worldwide. Non-small cell lung cancer (NSCLC) is the most common pathological subtype of lung cancer. This study aimed to identify the gene signature associated with the NSCLC prognosis using bioinformatics analysis. MATERIALS AND METHODS The dataset GSE103512 was utilized to construct co-expression networks using weighted gene co-expression network analysis (WGCNA). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed using Database for Annotation, Visualization, and Integrated Discovery. Gene set enrichment analysis was conducted to ascertain the function of the hub genes more accurately. The relationship between the hub genes and immune infiltration was investigated using a single sample gene set enrichment analysis. Hub genes were screened and validated by other datasets and online websites. RESULTS The results of WGCNA demonstrated that the blue module was most significantly related to tumor progression in NSCLC. Functional enrichment analysis showed that the blue module was associated with DNA replication, cell division, mitotic nuclear division, and cell cycle. A total of five hub genes (RFC5, UBE2S, CHAF1A, FANCI, and TMEM194A) were chosen to be identified and validated at transcriptional and translational levels. Receiver operating characteristic curve verified that the mRNA levels of these five genes can excellently discriminate between normal and tumor tissues. Survival analysis was also performed. Additionally, the protein levels of these five genes were also significantly different between tumor and normal tissues. Immune infiltration analysis showed that the expression levels of the hub genes had a negative correlation with the infiltration levels of many cells related to innate immune response, antigen-presenting process, humoral immune response, or T cell-mediated immune responses. CONCLUSIONS We identified five hub genes associated with the NSCLC tumorigenesis. NSCLC patients with higher expressions of each hub gene had a worse prognosis than those with lower expressions. Moreover, the hub genes might serve as biomarkers and therapeutic targets for precise diagnosis, target therapy, and immunotherapy of NSCLC in the future.
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Affiliation(s)
- Tengyong Wang
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
| | - Xiaoxuan Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
| | - Fangqi Jing
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zehua Li
- West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Huaicheng Tan
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yiqiao Luo
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Huashan Shi
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
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11
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Lemoine KA, Fassas JM, Ohannesian SH, Purcell NH. On the PHLPPside: Emerging roles of PHLPP phosphatases in the heart. Cell Signal 2021; 86:110097. [PMID: 34320369 PMCID: PMC8403656 DOI: 10.1016/j.cellsig.2021.110097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 02/07/2023]
Abstract
PH domain leucine-rich repeat protein phosphatase (PHLPP) is a family of enzymes made up of two isoforms (PHLPP1 and PHLPP2), whose actions modulate intracellular activity via the dephosphorylation of specific serine/threonine (Ser/Thr) residues on proteins such as Akt. Recent data generated in our lab, supported by findings from others, implicates the divergent roles of PHLPP1 and PHLPP2 in maintaining cellular homeostasis since dysregulation of these enzymes has been linked to various pathological states including cardiovascular disease, diabetes, ischemia/reperfusion injury, musculoskeletal disease, and cancer. Therefore, development of therapies to modulate specific isoforms of PHLPP could prove to be therapeutically beneficial in several diseases especially those targeting the cardiovascular system. This review is intended to provide a comprehensive summary of current literature detailing the role of the PHLPP isoforms in the development and progression of heart disease.
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Affiliation(s)
- Kellie A Lemoine
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92039, USA
| | - Julianna M Fassas
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92039, USA
| | - Shirag H Ohannesian
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92039, USA
| | - Nicole H Purcell
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92039, USA; Cardiovascular Molecular Signaling, Huntington Medical Research Institutes, Pasadena, CA 91105, USA.
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12
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Ji L, Fu J, Hao J, Ji Y, Wang H, Wang Z, Wang P, Xiao H. Proteomics analysis of tissue small extracellular vesicles reveals protein panels for the reoccurrence prediction of colorectal cancer. J Proteomics 2021; 249:104347. [PMID: 34384913 DOI: 10.1016/j.jprot.2021.104347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 07/25/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023]
Abstract
Many stage II/III colorectal cancer (CRC) patients might relapse after routine treatment and there is a great need of reliable biomarkers for predicting its reoccurrence risk. Small extracellular vesicles (sEVs) could regulate many pathophysiological processes of diseases, which are promising source for biomarker discovery. In this study, we implemented a MS-based workflow that utilizes data-dependent acquisition (DDA) for discovery and parallel reaction monitoring (PRM) for validation of high relapse risk related biomarkers. We compared the protein profiling of sEVs from CRC tissues and paired adjacent tissues in relapsed group (n = 5) and non-relapsed group (n = 5). 417 and 1140 proteins were differentially expressed between the tumor tissues and adjacent tissues in relapsed group and non-relapsed group, respectively. Bioinformatics analysis showed that immunity of the relapsed patients (Z-score - 0.69) was relatively poorer than the non-relapsed patients (Z-score 2.59), while chronic inflammatory response was activated (Z-score 3.0), which might enhance the reoccurrence risk. Four proteins (HLA-DPA1, S100P, NUP205, PCNA) showed significant expressions in the adjacent tissues of the relapsed group by PRM validation. ROC analysis of HLA-DPA1 (AUC = 0.96) achieved the best classification accuracy in separating the relapsed group and the non-relapsed group. Our data demonstrate that tissue-derived sEVs harbor prognostic proteomic signatures of CRC. SIGNIFICANCE: In this research, our proteomics analysis of tissue sEVs revealed that poor immunity as well as chronic inflammatory of the CRC relapsed patient likely lead to poor prognosis and high risk of reoccurrence. The significant expression levels of four proteins (HLA-DPA1, S100P, NUP205, PCNA) in the adjacent tissues of the relapsed group might be used to predict the risk of relapse in postoperative follow-ups.
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Affiliation(s)
- Liyun Ji
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jihong Fu
- Department of Colorectal Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, Shanghai 200092, China
| | - Jie Hao
- Shanghai Centre for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yin Ji
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Pharmaceutical Co., Ltd, Nanjing 210042, China
| | - Huiyu Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zeyuan Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Peng Wang
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Pharmaceutical Co., Ltd, Nanjing 210042, China.
| | - Hua Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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13
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Saei AA, Beusch CM, Sabatier P, Wells JA, Gharibi H, Meng Z, Chernobrovkin A, Rodin S, Näreoja K, Thorsell AG, Karlberg T, Cheng Q, Lundström SL, Gaetani M, Végvári Á, Arnér ESJ, Schüler H, Zubarev RA. System-wide identification and prioritization of enzyme substrates by thermal analysis. Nat Commun 2021; 12:1296. [PMID: 33637753 PMCID: PMC7910609 DOI: 10.1038/s41467-021-21540-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 01/26/2021] [Indexed: 02/06/2023] Open
Abstract
Despite the immense importance of enzyme-substrate reactions, there is a lack of general and unbiased tools for identifying and prioritizing substrate proteins that are modified by the enzyme on the structural level. Here we describe a high-throughput unbiased proteomics method called System-wide Identification and prioritization of Enzyme Substrates by Thermal Analysis (SIESTA). The approach assumes that the enzymatic post-translational modification of substrate proteins is likely to change their thermal stability. In our proof-of-concept studies, SIESTA successfully identifies several known and novel substrate candidates for selenoprotein thioredoxin reductase 1, protein kinase B (AKT1) and poly-(ADP-ribose) polymerase-10 systems. Wider application of SIESTA can enhance our understanding of the role of enzymes in homeostasis and disease, opening opportunities to investigate the effect of post-translational modifications on signal transduction and facilitate drug discovery.
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Affiliation(s)
- Amir Ata Saei
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
| | - Christian M Beusch
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Pierre Sabatier
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Juan Astorga Wells
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Hassan Gharibi
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Zhaowei Meng
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Alexey Chernobrovkin
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Pelago Bioscience AB, Solna, Sweden
| | - Sergey Rodin
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Katja Näreoja
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Ann-Gerd Thorsell
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Tobias Karlberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Qing Cheng
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Susanna L Lundström
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Massimiliano Gaetani
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- SciLifeLab, Stockholm, Sweden
- Chemical Proteomics Core Facility, Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ákos Végvári
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Proteomics Biomedicum, Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Elias S J Arnér
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Herwig Schüler
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Roman A Zubarev
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
- Department of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow, Russia.
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14
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The PHLPP1 N-Terminal Extension Is a Mitotic Cdk1 Substrate and Controls an Interactome Switch. Mol Cell Biol 2021; 41:e0033320. [PMID: 33397691 PMCID: PMC8088274 DOI: 10.1128/mcb.00333-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
PH domain leucine-rich repeat protein phosphatase 1 (PHLPP1) is a tumor suppressor that directly dephosphorylates a wide array of substrates, most notably the prosurvival kinase Akt. However, little is known about the molecular mechanisms governing PHLPP1 itself. Here, we report that PHLPP1 is dynamically regulated in a cell cycle-dependent manner and deletion of PHLPP1 results in mitotic delays and increased rates of chromosomal segregation errors. We show that PHLPP1 is hyperphosphorylated during mitosis by Cdk1 in a functionally uncharacterized region known as the PHLPP1 N-terminal extension (NTE). A proximity-dependent biotin identification (BioID) interaction screen revealed that during mitosis, PHLPP1 dissociates from plasma membrane scaffolds, such as Scribble, by a mechanism that depends on its NTE and gains proximity to kinetochore and mitotic spindle proteins such as KNL1 and TPX2. Our data are consistent with a model in which phosphorylation of PHLPP1 during mitosis regulates binding to its mitotic partners and allows accurate progression through mitosis. The finding that PHLPP1 binds mitotic proteins in a cell cycle- and phosphorylation-dependent manner may have relevance to its tumor-suppressive function.
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15
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Baffi TR, Cohen-Katsenelson K, Newton AC. PHLPPing the Script: Emerging Roles of PHLPP Phosphatases in Cell Signaling. Annu Rev Pharmacol Toxicol 2021; 61:723-743. [PMID: 32997603 PMCID: PMC11003498 DOI: 10.1146/annurev-pharmtox-031820-122108] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Whereas protein kinases have been successfully targeted for a variety of diseases, protein phosphatases remain an underutilized therapeutic target, in part because of incomplete characterization of their effects on signaling networks. The pleckstrin homology domain leucine-rich repeat protein phosphatase (PHLPP) is a relatively new player in the cell signaling field, and new roles in controlling the balance among cell survival, proliferation, and apoptosis are being increasingly identified. Originally characterized for its tumor-suppressive function in deactivating the prosurvival kinase Akt, PHLPP may have an opposing role in promoting survival, as recent evidence suggests. Additionally, identification of the transcription factor STAT1 as a substrate unveils a role for PHLPP as a critical mediator of transcriptional programs in cancer and the inflammatory response. This review summarizes the current knowledge of PHLPP as both a tumor suppressor and an oncogene and highlights emerging functions in regulating gene expression and the immune system. Understanding the context-dependent functions of PHLPP is essential for appropriate therapeutic intervention.
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Affiliation(s)
- Timothy R Baffi
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0721, USA;
| | - Ksenya Cohen-Katsenelson
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0721, USA;
| | - Alexandra C Newton
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0721, USA;
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16
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Ma J, Cai X, Kang L, Chen S, Liu H. Identification of novel biomarkers and candidate small-molecule drugs in cutaneous melanoma by comprehensive gene microarrays analysis. J Cancer 2021; 12:1307-1317. [PMID: 33531976 PMCID: PMC7847648 DOI: 10.7150/jca.49702] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 12/04/2020] [Indexed: 12/15/2022] Open
Abstract
Background: Melanoma is a pernicious skin cancer with high aggressiveness. This study aimed to identify potential novel biomarkers associated with the prognosis and pathogenesis of cutaneous melanoma and to explore new targeted drugs for melanoma. Methods: Two Gene Expression Omnibus (GEO) microarray datasets, GSE3189 and GSE7553 were combined to analyze the differentially expressed genes (DEGs). To better understand the DEGs in the melanoma pathogenesis, we performed gene enrichment analyses and established a protein-protein interaction network (PPI). The survival analyses for key genes were conducted based on the GEPIA platform. Finally, we mined the CMap database to explore potential small-molecule drugs to target the obtained DEGs. Results: In short, we identified 500 DEGs between cutaneous melanoma samples and normal samples. The PPI network was established with 349 nodes and 1251 edges. Signaling pathway analysis showed that these genes play a vital role in ECM-receptor interactions, the PPAR signaling pathway and pathways in cancer. Eight DEGs with a relatively high degree of connectivity (CDC45, CENPF, DTL, FANCI, GINS2, HJURP, TPX2 and TRIP13) were selected as hub-genes that remarkably correlated to a poor survival rate. Based on 500 DEGs, 20 small-molecule drugs that potentially target genes with abnormal expression in cutaneous melanoma were obtained from the CMap database. Among these compounds, we found that menadione has the greatest therapeutic value for melanoma. Conclusions: In conclusion, we identified the 8 candidate biomarkers and potential key signaling pathways in cutaneous melanoma through comprehensive microarray analyses. The identified candidate drugs have provided several directive significances for the synthesis medicine for melanoma.
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Affiliation(s)
- Jilei Ma
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Xin Cai
- Department of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, Henan 455000, PR China
| | - Li Kang
- Department of Human Anatomy and Histoembryology, Henan Vocational College of Nursing, Anyang, Henan, 400500, China
| | - Songfeng Chen
- Department of Orthopaedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Hongjian Liu
- Department of Orthopaedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
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17
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PARP Inhibition Increases the Reliance on ATR/CHK1 Checkpoint Signaling Leading to Synthetic Lethality-An Alternative Treatment Strategy for Epithelial Ovarian Cancer Cells Independent from HR Effectiveness. Int J Mol Sci 2020; 21:ijms21249715. [PMID: 33352723 PMCID: PMC7766831 DOI: 10.3390/ijms21249715] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 12/20/2022] Open
Abstract
Poly (ADP-ribose) polymerase inhibitor (PARPi, olaparib) impairs the repair of DNA single-strand breaks (SSBs), resulting in double-strand breaks (DSBs) that cannot be repaired efficiently in homologous recombination repair (HRR)-deficient cancers such as BRCA1/2-mutant cancers, leading to synthetic lethality. Despite the efficacy of olaparib in the treatment of BRCA1/2 deficient tumors, PARPi resistance is common. We hypothesized that the combination of olaparib with anticancer agents that disrupt HRR by targeting ataxia telangiectasia and Rad3-related protein (ATR) or checkpoint kinase 1 (CHK1) may be an effective strategy to reverse ovarian cancer resistance to olaparib. Here, we evaluated the effect of olaparib, the ATR inhibitor AZD6738, and the CHK1 inhibitor MK8776 alone and in combination on cell survival, colony formation, replication stress response (RSR) protein expression, DNA damage, and apoptotic changes in BRCA2 mutated (PEO-1) and HRR-proficient BRCA wild-type (SKOV-3 and OV-90) cells. Combined treatment caused the accumulation of DNA DSBs. PARP expression was associated with sensitivity to olaparib or inhibitors of RSR. Synergistic effects were weaker when olaparib was combined with CHK1i and occurred regardless of the BRCA2 status of tumor cells. Because PARPi increases the reliance on ATR/CHK1 for genome stability, the combination of PARPi with ATR inhibition suppressed ovarian cancer cell growth independently of the efficacy of HRR. The present results were obtained at sub-lethal doses, suggesting the potential of these inhibitors as monotherapy as well as in combination with olaparib.
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18
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Chen W, Gao C, Liu Y, Wen Y, Hong X, Huang Z. Bioinformatics Analysis of Prognostic miRNA Signature and Potential Critical Genes in Colon Cancer. Front Genet 2020; 11:478. [PMID: 32582275 PMCID: PMC7296168 DOI: 10.3389/fgene.2020.00478] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 04/17/2020] [Indexed: 12/14/2022] Open
Abstract
This study aims to lay a foundation for studying the regulation of microRNAs (miRNAs) in colon cancer by applying bioinformatics methods to identify miRNAs and their potential critical target genes associated with colon cancer and prognosis. Data of differentially expressed miRNAs (DEMs) and genes (DEGs) downloaded from two independent databases (TCGA and GEO) and analyzed by R software resulted in 472 DEMs and 565 DEGs in colon cancers, respectively. Next, we developed an 8-miRNA (hsa-mir-6854, hsa-mir-4437, hsa-mir-216a, hsa-mir-3677, hsa-mir-887, hsa-mir-4999, hsa-mir-34b, and hsa-mir-3189) prognostic signature for patients with colon cancer by Cox proportional hazards regression analysis. To predict the target genes of these miRNAs, we used TargetScan and miRDB. The intersection of DEGs with the target genes predicted for these eight miRNAs retrieved 112 consensus genes. GO and KEGG pathway enrichment analyses showed these 112 genes were mainly involved in protein binding, one-carbon metabolic process, nitrogen metabolism, proteoglycans in cancer, and chemokine signaling pathways. The protein-protein interaction network of the consensus genes, constructed using the STRING database and imported into Cytoscape, identified 14 critical genes in the pathogenesis of colon cancer (CEP55, DTL, FANCI, HMMR, KIF15, MCM6, MKI67, NCAPG2, NEK2, RACGAP1, RRM2, TOP2A, UBE2C, and ZWILCH). Finally, we verified the critical genes by weighted gene co-expression network analysis (WGCNA) of the GEO data, and further mined the core genes involved in colon cancer. In summary, this study identified an 8-miRNA model that can effectively predict the prognosis of colon cancer patients and 14 critical genes with vital roles in colon cancer carcinogenesis. Our findings contribute new ideas for elucidating the molecular mechanisms of colon cancer carcinogenesis and provide new therapeutic targets and biomarkers for future treatment and prognosis.
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Affiliation(s)
- Weigang Chen
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Guangdong Medical University, Dongguan, China.,Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Chang Gao
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Guangdong Medical University, Dongguan, China.,Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Yong Liu
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Guangdong Medical University, Dongguan, China.,Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Ying Wen
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Guangdong Medical University, Dongguan, China.,Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Xiaoling Hong
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Guangdong Medical University, Dongguan, China.,Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Zunnan Huang
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Guangdong Medical University, Dongguan, China.,The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, China.,Institute of Marine Biomedical Research, Guangdong Medical University, Zhanjiang, China
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19
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Gralewska P, Gajek A, Marczak A, Rogalska A. Participation of the ATR/CHK1 pathway in replicative stress targeted therapy of high-grade ovarian cancer. J Hematol Oncol 2020; 13:39. [PMID: 32316968 PMCID: PMC7175546 DOI: 10.1186/s13045-020-00874-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/08/2020] [Indexed: 12/15/2022] Open
Abstract
Ovarian cancer is one of the most lethal gynecologic malignancies reported throughout the world. The initial, standard-of-care, adjuvant chemotherapy in epithelial ovarian cancer is usually a platinum drug, such as cisplatin or carboplatin, combined with a taxane. However, despite surgical removal of the tumor and initial high response rates to first-line chemotherapy, around 80% of women will develop cancer recurrence. Effective strategies, including chemotherapy and new research models, are necessary to improve the prognosis. The replication stress response (RSR) is characteristic of the development of tumors, including ovarian cancer. Hence, RSR pathway and DNA repair proteins have emerged as a new area for anticancer drug development. Although clinical trials have shown poly (ADP-ribose) polymerase inhibitors (PARPi) response rates of around 40% in women who carry a mutation in the BRCA1/2 genes, PARPi is responsible for tumor suppression, but not for complete tumor regression. Recent reports suggest that cells with impaired homologous recombination (HR) activities due to mutations in TP53 gene or specific DNA repair proteins are specifically sensitive to ataxia telangiectasia and Rad3-related protein (ATR) inhibitors. Replication stress activates DNA repair checkpoint proteins (ATR, CHK1), which prevent further DNA damage. This review describes the use of DNA repair checkpoint inhibitors as single agents and strategies combining these inhibitors with DNA-damaging compounds for ovarian cancer therapy, as well as the new platforms used for optimizing ovarian cancer therapy.
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Affiliation(s)
- Patrycja Gralewska
- Department of Medical Biophysics, Faculty of Biology and Environmental Protection, Institute of Biophysics, University of Lodz, Pomorska 141/143, 90-236, Lodz, Poland
| | - Arkadiusz Gajek
- Department of Medical Biophysics, Faculty of Biology and Environmental Protection, Institute of Biophysics, University of Lodz, Pomorska 141/143, 90-236, Lodz, Poland
| | - Agnieszka Marczak
- Department of Medical Biophysics, Faculty of Biology and Environmental Protection, Institute of Biophysics, University of Lodz, Pomorska 141/143, 90-236, Lodz, Poland
| | - Aneta Rogalska
- Department of Medical Biophysics, Faculty of Biology and Environmental Protection, Institute of Biophysics, University of Lodz, Pomorska 141/143, 90-236, Lodz, Poland.
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20
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Georgescu MM, Olar A. Genetic and histologic spatiotemporal evolution of recurrent, multifocal, multicentric and metastatic glioblastoma. Acta Neuropathol Commun 2020; 8:10. [PMID: 32014051 PMCID: PMC6998196 DOI: 10.1186/s40478-020-0889-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 01/27/2020] [Indexed: 12/14/2022] Open
Abstract
Glioblastoma is the most frequent and aggressive primary brain tumor, characterized by extensive brain invasion and rarely, systemic metastases. The pathogenesis of metastatic glioblastoma is largely unknown. We present the first integrated clinical/histologic/genetic analysis of 5 distinct brain and lung foci from a unique case of recurrent, multifocal, multicentric and metastatic glioblastoma. The initial right frontotemporal gliosarcoma received standard surgical/chemoradiation therapy and recurred 1.5 years later, co-occurring with three additional masses localized to the ipsilateral temporal lobe, cerebellum and lung. Synchronous metastatic lung carcinoma was suspected in this long-term smoker patient with family history of cancer. However, glioblastoma was confirmed in all tumors, although with different morphologic patterns, including ependymomatous and epithelioid. Genomic profiling revealed a germline FANCD2 variant of unknown significance, and a 4-gene somatic mutation signature shared by all tumors, consisting of TERT promoter and PTEN, RB1 and TP53 tumor suppressor mutations. Additional GRIN2A and ATM heterozygous mutations were selected in the cerebellar and lung foci, but were variably present in the supratentorial foci, indicating reduced post-therapeutic genetic evolution in brain foci despite morphologic variability. Significant genetic drift characterized the lung metastasis, likely explaining the known resistance of circulating glioblastoma cells to systemic seeding. MET overexpression was detected in the initial gliosarcoma and lung metastasis, possibly contributing to invasiveness. This comprehensive analysis sheds light on the temporospatial evolution of glioblastoma and underscores the importance of genetic testing for diagnosis and personalized therapy.
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21
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Fan S, Tang J, Li N, Zhao Y, Ai R, Zhang K, Wang M, Du W, Wang W. Integrative analysis with expanded DNA methylation data reveals common key regulators and pathways in cancers. NPJ Genom Med 2019; 4:2. [PMID: 30729033 PMCID: PMC6358616 DOI: 10.1038/s41525-019-0077-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/02/2019] [Indexed: 11/09/2022] Open
Abstract
The integration of genomic and DNA methylation data has been demonstrated as a powerful strategy in understanding cancer mechanisms and identifying therapeutic targets. The TCGA consortium has mapped DNA methylation in thousands of cancer samples using Illumina Infinium Human Methylation 450 K BeadChip (Illumina 450 K array) that only covers about 1.5% of CpGs in the human genome. Therefore, increasing the coverage of the DNA methylome would significantly leverage the usage of the TCGA data. Here, we present a new model called EAGLING that can expand the Illumina 450 K array data 18 times to cover about 30% of the CpGs in the human genome. We applied it to analyze 13 cancers in TCGA. By integrating the expanded methylation, gene expression, and somatic mutation data, we identified the genes showing differential patterns in each of the 13 cancers. Many of the triple-evidenced genes identified in majority of the cancers are biomarkers or potential biomarkers. Pan-cancer analysis also revealed the pathways in which the triple-evidenced genes are enriched, which include well known ones as well as new ones, such as axonal guidance signaling pathway and pathways related to inflammatory processing or inflammation response. Triple-evidenced genes, particularly TNXB, RRM2, CELSR3, SLC16A3, FANCI, MMP9, MMP11, SIK1, and TRIM59 showed superior predictive power in both tumor diagnosis and prognosis. These results have demonstrated that the integrative analysis using the expanded methylation data is powerful in identifying critical genes/pathways that may serve as new therapeutic targets.
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Affiliation(s)
- Shicai Fan
- 1School of Automation Engineering, University of Electronic Science and Technology of China, 611731 Chengdu, Sichuan China.,2Center for Informational Biology, University of Electronic Science and Technology of China, 611731 Chengdu, Sichuan China.,3Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093-0359 USA.,4Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, 130012 Changchun, China
| | - Jianxiong Tang
- 1School of Automation Engineering, University of Electronic Science and Technology of China, 611731 Chengdu, Sichuan China
| | - Nan Li
- 3Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093-0359 USA
| | - Ying Zhao
- 3Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093-0359 USA
| | - Rizi Ai
- 3Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093-0359 USA
| | - Kai Zhang
- 3Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093-0359 USA
| | - Mengchi Wang
- 3Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093-0359 USA
| | - Wei Du
- 4Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, 130012 Changchun, China
| | - Wei Wang
- 3Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093-0359 USA.,5Department of Cellular and Molecular Medicine, University of California, San Diego, CA 92093-0359 USA
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22
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Gorrepati KDD, Lupse B, Annamalai K, Yuan T, Maedler K, Ardestani A. Loss of Deubiquitinase USP1 Blocks Pancreatic β-Cell Apoptosis by Inhibiting DNA Damage Response. iScience 2018; 1:72-86. [PMID: 30227958 PMCID: PMC6135944 DOI: 10.1016/j.isci.2018.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 01/09/2023] Open
Abstract
Impaired pancreatic β-cell survival contributes to the reduced β-cell mass in diabetes, but underlying regulatory mechanisms and key players in this process remain incompletely understood. Here, we identified the deubiquitinase ubiquitin-specific protease 1 (USP1) as an important player in the regulation of β-cell apoptosis under diabetic conditions. Genetic silencing and pharmacological suppression of USP1 blocked β-cell death in several experimental models of diabetes in vitro and ex vivo without compromising insulin content and secretion and without impairing β-cell maturation/identity genes in human islets. Our further analyses showed that USP1 inhibition attenuated DNA damage response (DDR) signals, which were highly elevated in diabetic β-cells, suggesting a USP1-dependent regulation of DDR in stressed β-cells. Our findings highlight a novel function of USP1 in the control of β-cell survival, and its inhibition may have a potential therapeutic relevance for the suppression of β-cell death in diabetes. Genetic and chemical inhibition of USP1 promoted β-cell survival USP1 inhibitors blocked β-cell death in human islets without affecting β-cell function USP1 inhibition reduced DDR signals in stressed β-cells
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Affiliation(s)
- Kanaka Durga Devi Gorrepati
- Islet Biology Laboratory, University of Bremen, Centre for Biomolecular Interactions Bremen, Leobener Straße NW2, Room B2080, 28359 Bremen, Germany
| | - Blaz Lupse
- Islet Biology Laboratory, University of Bremen, Centre for Biomolecular Interactions Bremen, Leobener Straße NW2, Room B2080, 28359 Bremen, Germany
| | - Karthika Annamalai
- Islet Biology Laboratory, University of Bremen, Centre for Biomolecular Interactions Bremen, Leobener Straße NW2, Room B2080, 28359 Bremen, Germany
| | - Ting Yuan
- Islet Biology Laboratory, University of Bremen, Centre for Biomolecular Interactions Bremen, Leobener Straße NW2, Room B2080, 28359 Bremen, Germany
| | - Kathrin Maedler
- Islet Biology Laboratory, University of Bremen, Centre for Biomolecular Interactions Bremen, Leobener Straße NW2, Room B2080, 28359 Bremen, Germany.
| | - Amin Ardestani
- Islet Biology Laboratory, University of Bremen, Centre for Biomolecular Interactions Bremen, Leobener Straße NW2, Room B2080, 28359 Bremen, Germany.
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23
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Che R, Zhang J, Nepal M, Han B, Fei P. Multifaceted Fanconi Anemia Signaling. Trends Genet 2018; 34:171-183. [PMID: 29254745 PMCID: PMC5858900 DOI: 10.1016/j.tig.2017.11.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 11/28/2017] [Indexed: 01/26/2023]
Abstract
In 1927 Guido Fanconi described a hereditary condition presenting panmyelopathy accompanied by short stature and hyperpigmentation, now better known as Fanconi anemia (FA). With this discovery the genetic and molecular basis underlying FA has emerged as a field of great interest. FA signaling is crucial in the DNA damage response (DDR) to mediate the repair of damaged DNA. This has attracted a diverse range of investigators, especially those interested in aging and cancer. However, recent evidence suggests FA signaling also regulates functions outside the DDR, with implications for many other frontiers of research. We discuss here the characteristics of FA functions and expand upon current perspectives regarding the genetics of FA, indicating that FA plays a role in a myriad of molecular and cellular processes.
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Affiliation(s)
- Raymond Che
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, USA; Graduate Program of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI, USA
| | - Jun Zhang
- Department of Laboratory Medicine and Pathology, Mayo Clinic Foundation, USA
| | - Manoj Nepal
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, USA; Graduate Program of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI, USA
| | - Bing Han
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, USA
| | - Peiwen Fei
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, USA; Graduate Program of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI, USA.
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24
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Wever CM, Geoffrion D, Grande BM, Yu S, Alcaide M, Lemaire M, Riazalhosseini Y, Hébert J, Gavino C, Vinh DC, Petrogiannis-Haliotis T, Dmitrienko S, Mann KK, Morin RD, Johnson NA. The genomic landscape of two Burkitt lymphoma cases and derived cell lines: comparison between primary and relapse samples. Leuk Lymphoma 2018; 59:2159-2174. [PMID: 29295643 DOI: 10.1080/10428194.2017.1413186] [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] [Indexed: 12/30/2022]
Abstract
Relapse occurs in 10-40% of Burkitt lymphoma (BL) patients that have completed intensive chemotherapy regimens and is typically fatal. While treatment-naive BL has been characterized, the genomic landscape of BL at the time of relapse (rBL) has never been reported. Here, we present a genomic characterization of two rBL patients. The diagnostic samples had mutations common in BL, including MYC and CCND3. Additional mutations were detected at relapse, affecting important pathways such as NFκB (IKBKB) and MEK/ERK (NRAS) signaling, glutamine metabolism (SIRT4), and RNA processing (ZFP36L2). Genes implicated in drug resistance were also mutated at relapse (TP53, BAX, ALDH3A1, APAF1, FANCI). This concurrent genomic profiling of samples obtained at diagnosis and relapse has revealed mutations not previously reported in this disease. The patient-derived cell lines will be made available and, along with their detailed genetics, will be a valuable resource to examine the role of specific mutations in therapeutic resistance.
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Affiliation(s)
- Claudia M Wever
- a Department of Medicine , McGill University, Lady Davis Institute, Jewish General Hospital , Montreal , Canada.,b Lady Davis Institute, Jewish General Hospital , Montreal , Canada
| | | | - Bruno M Grande
- c Department of Molecular Biology and Biochemistry , Simon Fraser University , Burnaby , Canada.,d Genome Sciences Centre, BC Cancer Agency , Vancouver , Canada
| | - Stephen Yu
- c Department of Molecular Biology and Biochemistry , Simon Fraser University , Burnaby , Canada
| | - Miguel Alcaide
- c Department of Molecular Biology and Biochemistry , Simon Fraser University , Burnaby , Canada
| | - Maryse Lemaire
- b Lady Davis Institute, Jewish General Hospital , Montreal , Canada
| | - Yasser Riazalhosseini
- e Department of Human Genetics , McGill University , Montreal , Canada.,f McGill University and Genome Quebec Innovation Centre , Montreal , Canada
| | - Josée Hébert
- g Department of Medicine, Faculty of Medicine , Université de Montréal , Montreal , Canada.,h Research Centre and Division of Hematology-Oncology Maisonneuve-Rosemont Hospital , The Québec Leukemia Cell Bank , Montreal , Canada
| | - Christina Gavino
- i Infectious Disease Susceptibility Program (Research Institute-McGill University Health Centre) , Montreal , Canada.,j Department of Medicine , Medical Microbiology and Human Genetics (McGill University Health Centre) , Montreal , Canada
| | - Donald C Vinh
- i Infectious Disease Susceptibility Program (Research Institute-McGill University Health Centre) , Montreal , Canada.,j Department of Medicine , Medical Microbiology and Human Genetics (McGill University Health Centre) , Montreal , Canada
| | | | | | - Koren K Mann
- a Department of Medicine , McGill University, Lady Davis Institute, Jewish General Hospital , Montreal , Canada.,b Lady Davis Institute, Jewish General Hospital , Montreal , Canada
| | - Ryan D Morin
- c Department of Molecular Biology and Biochemistry , Simon Fraser University , Burnaby , Canada.,d Genome Sciences Centre, BC Cancer Agency , Vancouver , Canada
| | - Nathalie A Johnson
- a Department of Medicine , McGill University, Lady Davis Institute, Jewish General Hospital , Montreal , Canada.,b Lady Davis Institute, Jewish General Hospital , Montreal , Canada
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Nepal M, Che R, Ma C, Zhang J, Fei P. FANCD2 and DNA Damage. Int J Mol Sci 2017; 18:ijms18081804. [PMID: 28825622 PMCID: PMC5578191 DOI: 10.3390/ijms18081804] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/08/2017] [Accepted: 08/12/2017] [Indexed: 02/07/2023] Open
Abstract
Investigators have dedicated considerable effort to understanding the molecular basis underlying Fanconi Anemia (FA), a rare human genetic disease featuring an extremely high incidence of cancer and many congenital defects. Among those studies, FA group D2 protein (FANCD2) has emerged as the focal point of FA signaling and plays crucial roles in multiple aspects of cellular life, especially in the cellular responses to DNA damage. Here, we discuss the recent and relevant studies to provide an updated review on the roles of FANCD2 in the DNA damage response.
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Affiliation(s)
- Manoj Nepal
- Cancer Biology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA.
- Graduate Program of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96813, USA.
| | - Raymond Che
- Cancer Biology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA.
- Graduate Program of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96813, USA.
| | - Chi Ma
- Cancer Biology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA.
| | - Jun Zhang
- Department of Laboratory Medicine and Pathology, Mayo Clinic Foundation, Rochester, MN 55905, USA.
| | - Peiwen Fei
- Cancer Biology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA.
- Graduate Program of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96813, USA.
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