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Vicario R, Fragkogianni S, Weber L, Lazarov T, Hu Y, Hayashi SY, Craddock BP, Socci ND, Alberdi A, Baako A, Ay O, Ogishi M, Lopez-Rodrigo E, Kappagantula R, Viale A, Iacobuzio-Donahue CA, Zhou T, Ransohoff RM, Chesworth R, Abdel-Wahab O, Boisson B, Elemento O, Casanova JL, Miller WT, Geissmann F. A microglia clonal inflammatory disorder in Alzheimer's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.25.577216. [PMID: 38328106 PMCID: PMC10849735 DOI: 10.1101/2024.01.25.577216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Somatic genetic heterogeneity resulting from post-zygotic DNA mutations is widespread in human tissues and can cause diseases, however few studies have investigated its role in neurodegenerative processes such as Alzheimer's Disease (AD). Here we report the selective enrichment of microglia clones carrying pathogenic variants, that are not present in neuronal, glia/stromal cells, or blood, from patients with AD in comparison to age-matched controls. Notably, microglia-specific AD-associated variants preferentially target the MAPK pathway, including recurrent CBL ring-domain mutations. These variants activate ERK and drive a microglia transcriptional program characterized by a strong neuro-inflammatory response, both in vitro and in patients. Although the natural history of AD-associated microglial clones is difficult to establish in human, microglial expression of a MAPK pathway activating variant was previously shown to cause neurodegeneration in mice, suggesting that AD-associated neuroinflammatory microglial clones may contribute to the neurodegenerative process in patients. One-Sentence Summary A subset of Alzheimer Disease patients carry mutant microglia somatic clones which promote neuro-inflammation.
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Riley AK, Grant M, Snell A, Vichas A, Moorthi S, Urisman A, Castel P, Wan L, Berger AH. The deubiquitinase USP9X regulates RIT1 protein abundance and oncogenic phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569313. [PMID: 38077017 PMCID: PMC10705424 DOI: 10.1101/2023.11.30.569313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
RIT1 is a rare and understudied oncogene in lung cancer. Despite structural similarity to other RAS GTPase proteins such as KRAS, oncogenic RIT1 activity does not appear to be tightly regulated by nucleotide exchange or hydrolysis. Instead, there is a growing understanding that the protein abundance of RIT1 is important for its regulation and function. We previously identified the deubiquitinase USP9X as a RIT1 dependency in RIT1-mutant cells. Here, we demonstrate that both wild-type and mutant forms of RIT1 are substrates of USP9X. Depletion of USP9X leads to decreased RIT1 protein stability and abundance and resensitizes cells to EGFR tyrosine kinase inhibitors. Our work expands upon the current understanding of RIT1 protein regulation and presents USP9X as a key regulator of RIT1-driven oncogenic phenotypes.
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Affiliation(s)
- Amanda K. Riley
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Michael Grant
- Department of Molecular Oncology, Molecular Medicine Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Aidan Snell
- Department of Molecular Oncology, Molecular Medicine Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Athea Vichas
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Sitapriya Moorthi
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Anatoly Urisman
- Department of Pathology, University of California San Francisco, CA, USA
| | - Pau Castel
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Lixin Wan
- Department of Molecular Oncology, Molecular Medicine Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Alice H. Berger
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Herbold Computational Biology Program, Public Health Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Lead contact:
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3
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Su Y, Lin H, Yu J, Mao L, Jin W, Liu T, Jiang S, Wu Y, Zhang S, Geng Q, Ge C, Zhao F, Chen T, Cui Y, Li J, Hou H, Zhou X, Li H. RIT1 regulates mitosis and promotes proliferation by interacting with SMC3 and PDS5 in hepatocellular carcinoma. J Exp Clin Cancer Res 2023; 42:326. [PMID: 38017479 PMCID: PMC10685607 DOI: 10.1186/s13046-023-02892-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 11/10/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND As a small G protein of Ras family, Ras-like-without-CAAX-1 (RIT1) plays a critical role in various tumors. Our previous study has demonstrated the involvement of RIT1 in promoting malignant progression of hepatocellular carcinoma (HCC). However, its underlying mechanism remains unclear. METHODS Gene set enrichment analysis (GSEA) was conducted in the TCGA LIHC cohort to investigate the underlying biological mechanism of RIT1. Live cell imaging, immunofluorescence (IF) and flow cytometry assays were used to verify biological function of RIT1 in HCC mitosis. Subcutaneous xenografting of human HCC cells in BALB/c nude mice was utilized to assess tumor proliferation in vivo. RNA-seq, co-immunoprecipitation (Co-IP), mass spectrometry analyses, western blot and IF assays were employed to elucidate the mechanisms by which RIT1 regulates mitosis and promotes proliferation in HCC. RESULTS Our findings demonstrate that RIT1 plays a crucial role in regulating mitosis in HCC. Knockdown of RIT1 disrupts cell division, leading to G2/M phase arrest, mitotic catastrophe, and apoptosis in HCC cells. SMC3 is found to interact with RIT1 and knockdown of SMC3 attenuates the proliferative effects mediated by RIT1 both in vitro and in vivo. Mechanistically, RIT1 protects and maintains SMC3 acetylation by binding to SMC3 and PDS5 during mitosis, thereby promoting rapid cell division and proliferation in HCC. Notably, we have observed an upregulation of SMC3 expression in HCC tissues, which is associated with poor patient survival and promotion of HCC cell proliferation. Furthermore, there is a significant positive correlation between the expression levels of RIT1, SMC3, and PDS5. Importantly, HCC patients with high expression of both RIT1 and SMC3 exhibit worse prognosis compared to those with high RIT1 but low SMC3 expression. CONCLUSIONS Our findings underscore the crucial role of RIT1 in regulating mitosis in HCC and further demonstrate its potential as a promising therapeutic target for HCC treatment.
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Affiliation(s)
- Yang Su
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Hechun Lin
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Junming Yu
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Lin Mao
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Wenjiao Jin
- Department of Oncology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
| | - Tengfei Liu
- Department of Oncology, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China
| | - Shuqing Jiang
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Yunyu Wu
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Saihua Zhang
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Qin Geng
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Chao Ge
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Fangyu Zhao
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Taoyang Chen
- Qidong Liver Cancer Institute, Qidong, 226200, China
| | - Ying Cui
- Cancer Institute of Guangxi, Nanning, 530021, China
| | - Jinjun Li
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Helei Hou
- Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, Qingdao, 266003, China.
| | - Xinli Zhou
- Department of Oncology, Huashan Hospital, Fudan University, Shanghai, 200040, China.
| | - Hong Li
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China.
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4
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Cuevas-Navarro A, Wagner M, Van R, Swain M, Mo S, Columbus J, Allison MR, Cheng A, Messing S, Turbyville TJ, Simanshu DK, Sale MJ, McCormick F, Stephen AG, Castel P. RAS-dependent RAF-MAPK hyperactivation by pathogenic RIT1 is a therapeutic target in Noonan syndrome-associated cardiac hypertrophy. SCIENCE ADVANCES 2023; 9:eadf4766. [PMID: 37450595 PMCID: PMC10348673 DOI: 10.1126/sciadv.adf4766] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 06/14/2023] [Indexed: 07/18/2023]
Abstract
RIT1 is a RAS guanosine triphosphatase (GTPase) that regulates different aspects of signal transduction and is mutated in lung cancer, leukemia, and in the germline of individuals with Noonan syndrome. Pathogenic RIT1 proteins promote mitogen-activated protein kinase (MAPK) hyperactivation; however, this mechanism remains poorly understood. Here, we show that RAF kinases are direct effectors of membrane-bound mutant RIT1 necessary for MAPK activation. We identify critical residues in RIT1 that facilitate interaction with membrane lipids and show that these are necessary for association with RAF kinases and MAPK activation. Although mutant RIT1 binds to RAF kinases directly, it fails to activate MAPK signaling in the absence of classical RAS proteins. Consistent with aberrant RAF/MAPK activation as a driver of disease, we show that pathway inhibition alleviates cardiac hypertrophy in a mouse model of RIT1 mutant Noonan syndrome. These data shed light on the function of pathogenic RIT1 and identify avenues for therapeutic intervention.
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Affiliation(s)
- Antonio Cuevas-Navarro
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Morgan Wagner
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Richard Van
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Monalisa Swain
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Stephanie Mo
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - John Columbus
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Madeline R. Allison
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alice Cheng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Simon Messing
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Thomas J. Turbyville
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Dhirendra K. Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Matthew J. Sale
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Frank McCormick
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Andrew G. Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Pau Castel
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
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Zha P, Kong Y, Wang L, Wang Y, Qing Q, Dai L. Noonan syndrome caused by RIT1 gene mutation: A case report and literature review. Front Pediatr 2022; 10:934808. [PMID: 36160792 PMCID: PMC9490085 DOI: 10.3389/fped.2022.934808] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 08/18/2022] [Indexed: 11/26/2022] Open
Abstract
OBJECTIVE Noonan syndrome (NS), an autosomal dominant disease known as a RASopathy, is caused by germline mutations in mitogen-activated protein kinase pathway genes. A RIT1 gene mutation has been found to cause NS. The present study summarizes RIT1 gene mutation sites and associated clinical phenotypes. METHODS We retrospectively analyzed the clinical characteristics of a case of NS caused by RIT1 mutation in our hospital, and searched the PubMed database, China National Knowledge Infrastructure (CNKI) database and Wanfang database with the keywords Noonan syndrome and RIT1. Studies published between May 1, 2014 and July 1, 2021 were retrieved. By reviewing the abstracts and full text of the studies, we screened NS cases associated with RIT1 mutation in children 0-18 years of age. The clinical characteristics of these cases were summarized. RESULTS A total of 41 cases were analyzed, including 13 boys and 28 girls. There were 14 premature cases. The age at diagnosis was 4 days to 18 years, and 10 cases were diagnosed at 0-1 years of age. Common amino acid substitution positions included 57 (13/41), 95 (7/41), 82 (8/41), and 90 (4/41). A total of 63.63% cases had abnormal prenatal examination results, manifesting mainly as fetal neck edema, polyhydramnios and cardiac malformation. With respect to abnormal conditions after birth, 70-80% of patients had typical developmental malformations of the face, neck and thorax; 19/35 patients had abnormal lymphatic development; and a portion of patients had short stature and motor development disorders. A total of 87.80% (36/41) patients had cardiac dysplasia, among which hypertrophic cardiomyopathy (HCM) accounted for 58.53%. A total of 84.62% of patients carrying the p.A57G mutation had HCM, but no HCM was found in patients with the p.G95A mutation. A total of 34.15% of patients had pulmonary artery or pulmonary valve stenosis (PVS). In patients with the p.M90I mutation, 75% had PVS. Patients with concurrent HCM and PVS accounted for 19.51 and 48.78% of patients had supraventricular tachycardia. CONCLUSION A RIT1 gene mutation causing NS was associated with a high rate of abnormal prenatal examination findings. Most patients had typical NS craniofacial deformities, and some have short stature and motor development disorders. The cardiac deformity rate was high, and HCM was common. Some patients had supraventricular arrhythmias. Heart abnormalities showed high heterogeneity, given the various mutation loci.
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Affiliation(s)
- Ping Zha
- Department of Neonatology, Anhui Provincial Children's Hospital, Hefei, China
| | - Ying Kong
- Department of Neonatology, Anhui Provincial Children's Hospital, Hefei, China
| | - Lili Wang
- Department of Neonatology, Anhui Provincial Children's Hospital, Hefei, China
| | - Yujuan Wang
- Department of Neonatology, Anhui Provincial Children's Hospital, Hefei, China
| | - Qing Qing
- Department of Neonatology, Anhui Provincial Children's Hospital, Hefei, China
| | - Liying Dai
- Department of Neonatology, Anhui Provincial Children's Hospital, Hefei, China
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Lo A, Holmes K, Kamlapurkar S, Mundt F, Moorthi S, Fung I, Fereshetian S, Watson J, Carr SA, Mertins P, Berger AH. Multiomic characterization of oncogenic signaling mediated by wild-type and mutant RIT1. Sci Signal 2021; 14:eabc4520. [PMID: 34846918 PMCID: PMC8848860 DOI: 10.1126/scisignal.abc4520] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Aberrant activation of the RAS family of guanosine triphosphatases (GTPases) is prevalent in lung adenocarcinoma, with somatic mutation of KRAS occurring in ~30% of tumors. We previously identified somatic mutations and amplifications of the gene encoding RAS family GTPase RIT1 in lung adenocarcinomas. To explore the biological pathways regulated by RIT1 and how they relate to the oncogenic KRAS network, we performed quantitative proteomic, phosphoproteomic, and transcriptomic profiling of isogenic lung epithelial cells in which we ectopically expressed wild-type or cancer-associated variants of RIT1 and KRAS. We found that both mutant KRAS and mutant RIT1 promoted canonical RAS signaling and that overexpression of wild-type RIT1 partially phenocopied oncogenic RIT1 and KRAS, including induction of epithelial-to-mesenchymal transition. Our findings suggest that RIT1 protein abundance is a factor in its pathogenic function. Therefore, chromosomal amplification of wild-type RIT1 in lung and other cancers may be tumorigenic.
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Affiliation(s)
- April Lo
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Kristin Holmes
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Shriya Kamlapurkar
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Filip Mundt
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Oncology-Pathology, Karolinska Institute, 171 77 Stockholm, Sweden
- Present address: Proteomics technology platform, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health at Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
| | - Sitapriya Moorthi
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Iris Fung
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shaunt Fereshetian
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jacqueline Watson
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven A. Carr
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Philipp Mertins
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Current affiliation: Proteomics Platform, Max Delbrück Center for Molecular Medicine in the Helmholtz Society, 13092 Berlin, Germany
| | - Alice H. Berger
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
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7
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Zhao F, Bosler DS, Cook JR. Designing Myeloid Gene Panels. Arch Pathol Lab Med 2021; 146:1004-1011. [PMID: 34784413 DOI: 10.5858/arpa.2021-0124-oa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2021] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Next-generation sequencing studies are increasingly used in the evaluation of suspected chronic myeloid neoplasms (CMNs), but there is wide variability among laboratories in the genes analyzed for this purpose. Recently, the Association for Molecular Pathology CMN working group recommended a core 34-gene set as a minimum target list for evaluation of CMNs. This list was recommended based on literature review, and its diagnostic yield in clinical practice is unknown. OBJECTIVE.— To determine the diagnostic yield of the core 34 genes and assess the potential impact of including selected additional genes. DESIGN.— We retrospectively reviewed 185 patients with known or suspected CMNs tested using a 62-gene next-generation sequencing panel that included all 34 core genes. RESULTS.— The Association for Molecular Pathology's core 34 genes had a diagnostic yield of 158 of 185 (85.4%) to detect at least 1 variant with strong/potential clinical significance and 107 of 185 (57.8%) to detect at least 2 such variants. The 62-gene panel had a diagnostic yield of 160 of 185 (86.5%) and 112 of 185 (60.5%), respectively. Variants of unknown significance were identified in 49 of 185 (26.5%) using the core 34 genes versus 76 of 185 (41.1%) using the 62-gene panel. CONCLUSIONS.— This study demonstrates that the Association for Molecular Pathology-recommended core 34-gene set has a high diagnostic yield in CMNs. Inclusion of selected additional genes slightly increases the rate of abnormal results, while also increasing the detection of variants of unknown significance. We recommend inclusion of CUX1, DDX41, ETNK1, RIT1, and SUZ12 in addition to the Association for Molecular Pathology's 34-gene core set for routine evaluation of CMNs.
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Affiliation(s)
- Fang Zhao
- From the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio.,Zhao is currently located at the Center for Clinical Informatics Research and Education and Department of Pathology, The MetroHealth System/Case Western Reserve University, Cleveland, Ohio
| | - David S Bosler
- From the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio
| | - James R Cook
- From the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio
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8
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Riley AK, Berger AH. Genome-wide CRISPR screening reveals novel therapeutic targets in RIT1-driven lung cancer. Mol Cell Oncol 2021; 8:2000318. [PMID: 35419481 PMCID: PMC8997261 DOI: 10.1080/23723556.2021.2000318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 06/14/2023]
Abstract
In recent work, we performed CRISPR/Cas9 screening in RIT1 (Ras-like in all tissues)-mutant cancer cells. We found that RIT1-mutant cells are vulnerable to loss of mitotic regulators, and mutant RIT1 synergizes with YAP1 (yes-associated protein 1) in oncogenesis. These findings can be leveraged to identify targeted therapies for RIT1-mutant cancer.
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Affiliation(s)
- Amanda K. Riley
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Alice H. Berger
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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9
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Vichas A, Riley AK, Nkinsi NT, Kamlapurkar S, Parrish PCR, Lo A, Duke F, Chen J, Fung I, Watson J, Rees M, Gabel AM, Thomas JD, Bradley RK, Lee JK, Hatch EM, Baine MK, Rekhtman N, Ladanyi M, Piccioni F, Berger AH. Integrative oncogene-dependency mapping identifies RIT1 vulnerabilities and synergies in lung cancer. Nat Commun 2021; 12:4789. [PMID: 34373451 PMCID: PMC8352964 DOI: 10.1038/s41467-021-24841-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 07/12/2021] [Indexed: 12/13/2022] Open
Abstract
CRISPR-based cancer dependency maps are accelerating advances in cancer precision medicine, but adequate functional maps are limited to the most common oncogenes. To identify opportunities for therapeutic intervention in other rarer subsets of cancer, we investigate the oncogene-specific dependencies conferred by the lung cancer oncogene, RIT1. Here, genome-wide CRISPR screening in KRAS, EGFR, and RIT1-mutant isogenic lung cancer cells identifies shared and unique vulnerabilities of each oncogene. Combining this genetic data with small-molecule sensitivity profiling, we identify a unique vulnerability of RIT1-mutant cells to loss of spindle assembly checkpoint regulators. Oncogenic RIT1M90I weakens the spindle assembly checkpoint and perturbs mitotic timing, resulting in sensitivity to Aurora A inhibition. In addition, we observe synergy between mutant RIT1 and activation of YAP1 in multiple models and frequent nuclear overexpression of YAP1 in human primary RIT1-mutant lung tumors. These results provide a genome-wide atlas of oncogenic RIT1 functional interactions and identify components of the RAS pathway, spindle assembly checkpoint, and Hippo/YAP1 network as candidate therapeutic targets in RIT1-mutant lung cancer.
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Affiliation(s)
- Athea Vichas
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Amanda K Riley
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Naomi T Nkinsi
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Shriya Kamlapurkar
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Phoebe C R Parrish
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - April Lo
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Fujiko Duke
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Jennifer Chen
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Iris Fung
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | | | - Matthew Rees
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Austin M Gabel
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - James D Thomas
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Robert K Bradley
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - John K Lee
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Emily M Hatch
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Marina K Baine
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Natasha Rekhtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Federica Piccioni
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
- Merck Research Laboratories, Boston, MA, USA
| | - Alice H Berger
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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10
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Genomic variations in patients with myelodysplastic syndrome and karyotypes without numerical or structural changes. Sci Rep 2021; 11:2783. [PMID: 33531543 PMCID: PMC7854738 DOI: 10.1038/s41598-021-81467-2] [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: 09/08/2020] [Accepted: 12/23/2020] [Indexed: 01/30/2023] Open
Abstract
Myelodysplastic syndrome (MDS) is an onco-hematologic disease with distinct levels of peripheral blood cytopenias, dysplasias in cell differentiation and various forms of chromosomal and cytogenomic alterations. In this study, the Chromosomal Microarray Analysis (CMA) was performed in patients with primary MDS without numerical and/or structural chromosomal alterations in karyotypes. A total of 17 patients was evaluated by GTG banding and eight patients showed no numerical and/or structural alterations. Then, the CMA was carried out and identified gains and losses CNVs and long continuous stretches of homozygosity (LCSHs). They were mapped on chromosomes 1, 2, 3, 4, 5, 6, 7, 9, 10, 12, 14, 16, 17, 18, 19, 20, 21, X, and Y. Ninety-one genes that have already been implicated in molecular pathways important for cell viability were selected and in-silico expression analyses demonstrated 28 genes differentially expressed in mesenchymal stromal cells of patients. Alterations in these genes may be related to the inactivation of suppressor genes or the activation of oncogenes contributing to the evolution and malignization of MDS. CMA provided additional information in patients without visible changes in the karyotype and our findings could contribute with additional information to improve the prognostic and personalized stratification for patients.
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11
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Migliori AD, Patel LA, Neale C. The RIT1 C-terminus associates with lipid bilayers via charge complementarity. Comput Biol Chem 2021; 91:107437. [PMID: 33517146 DOI: 10.1016/j.compbiolchem.2021.107437] [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: 08/20/2020] [Revised: 12/30/2020] [Accepted: 01/14/2021] [Indexed: 12/13/2022]
Abstract
RIT1 is a member of the Ras superfamily of small GTPases involved in regulation of cellular signaling. Mutations to RIT1 are involved in cancer and developmental disorders. Like many Ras subfamily members, RIT1 is localized to the plasma membrane. However, RIT1 lacks the C-terminal prenylation that helps many other subfamily members adhere to cellular membranes. We used molecular dynamics simulations to examine the mechanisms by which the C-terminal peptide (CTP) of RIT1 associates with lipid bilayers. We show that the CTP is unstructured and that its membrane interactions depend on lipid composition. While a 12-residue region of the CTP binds strongly to anionic bilayers containing phosphatidylserine lipids, the CTP termini fray from the membrane allowing for accommodation of the RIT1 globular domain at the membrane-water interface.
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Affiliation(s)
- Amy D Migliori
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, 87545, United States; Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, 87545, United States
| | - Lara A Patel
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, 87545, United States; Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, 87545, United States
| | - Chris Neale
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, 87545, United States.
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12
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Van R, Cuevas-Navarro A, Castel P, McCormick F. The molecular functions of RIT1 and its contribution to human disease. Biochem J 2020; 477:2755-2770. [PMID: 32766847 PMCID: PMC7787054 DOI: 10.1042/bcj20200442] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 12/29/2022]
Abstract
RIT1 is a member of the Ras family of GTPases that direct broad cellular physiological responses through tightly controlled signaling networks. The canonical Ras GTPases are well-defined regulators of the RAF/MEK/ERK pathway and mutations in these are pathogenic in cancer and a class of developmental disorders termed RASopathies. Emerging clinical evidences have now demonstrated a role for RIT1 in RASopathies, namely Noonan syndrome, and various cancers including lung adenocarcinoma and myeloid malignancies. While RIT1 has been mostly described in the context of neuronal differentiation and survival, the mechanisms underlying aberrant RIT1-mediated signaling remain elusive. Here, we will review efforts undertaken to characterize the biochemical and functional properties of the RIT1 GTPase at the molecular, cellular, and organismal level, as well as provide a phenotypic overview of different human conditions caused by RIT1 mutations. Deeper understanding of RIT1 biological function and insight to its pathogenic mechanisms are imperative to developing effective therapeutic interventions for patients with RIT1-mutant Noonan syndrome and cancer.
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Affiliation(s)
- Richard Van
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, U.S.A
| | - Antonio Cuevas-Navarro
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, U.S.A
| | - Pau Castel
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, U.S.A
| | - Frank McCormick
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, U.S.A
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13
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OGAWA S. Genetic basis of myelodysplastic syndromes. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2020; 96:107-121. [PMID: 32161209 PMCID: PMC7167367 DOI: 10.2183/pjab.96.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 01/15/2020] [Indexed: 05/06/2023]
Abstract
During the past decade, substantial progress has been made in the field of the genetics of myelodysplastic syndromes (MDS). These comprise a group of chronic myeloid neoplasms with abnormal cell morphology and progression to acute myeloid leukemia (AML), where revolutionary sequencing technologies have played a major role. Through extensive sequencing of a large number of MDS genomes, a comprehensive registry of driver mutations involved in the pathogenesis of MDS has been revealed, along with their impacts on clinical phenotype and prognosis. The most frequently affected molecules are involved in DNA methylations, chromatin modification, RNA splicing, transcription, signal transduction, cohesin regulation, and DNA repair. These mutations show strong positive and negative correlations with each other, suggesting the presence of functional interactions between mutations, which dictate disease progression. Because these mutations are associated with disease phenotype, drug response, and clinical outcomes, it is essential to be familiar with MDS genetics not only for better understanding of MDS pathogenesis but also for management of patients.
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Affiliation(s)
- Seishi OGAWA
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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14
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Azrakhsh NA, Mensah-Glanowska P, Sand K, Kittang AO. Targeting Immune Signaling Pathways in Clonal Hematopoiesis. Curr Med Chem 2019; 26:5262-5277. [PMID: 30907306 DOI: 10.2174/0929867326666190325100636] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 03/05/2019] [Accepted: 03/12/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND Myeloid neoplasms are a diverse group of malignant diseases with different entities and numerous patho-clinical features. They arise from mutated clones of hematopoietic stem- and progenitor cells which expand by outperforming their normal counterparts. The intracellular signaling profile of cancer cells is the sum of genetic, epigenetic and microenvironmental influences, and the multiple interconnections between different signaling pathways make pharmacological targeting complicated. OBJECTIVE To present an overview of known somatic mutations in myeloproliferative neoplasms (MPN), myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) and the inflammatory signaling pathways affected by them, as well as current efforts to therapeutically modulate this aberrant inflammatory signaling. METHODS In this review, we extensively reviewed and compiled salient information with ClinicalTrials.gov as our source on ongoing studies, and PubMed as our authentic bibliographic source, using a focused review question. RESULTS Mutations affecting immune signal transduction are present to varying extents in clonal myeloid diseases. While MPN are dominated by a few common mutations, a multitude of different genes can be mutated in MDS and AML. Mutations can also occur in asymptomatic persons, a finding called clonal hematopoiesis of indeterminate potential (CHIP). Mutations in FLT3, JAK, STAT, CBL and RAS can lead to aberrant immune signaling. Protein kinase inhibitors are entering the clinic and are extensively investigated in clinical trials in MPN, MDS and AML. CONCLUSION In summary, this article summarizes recent research on aberrant inflammatory signaling in clonal myeloid diseases and the clinical therapeutic potential of modulation of signal transduction and effector proteins in the affected pathways.
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Affiliation(s)
| | - Patrycja Mensah-Glanowska
- Department of Hematology, Jagiellonian University Medical College / University Hospital, Krakow, Poland
| | - Kristoffer Sand
- Clinic of Medicine and Rehabilitation, More and Romsdal Hospital Trust, Alesund, Norway
| | - Astrid Olsnes Kittang
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Medicine, Section for Hematology, Haukeland University Hospital, Bergen, Norway
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15
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Choi MY, Kato S, Wang HY, Lin JH, Lanman RB, Kurzrock R. JAK2 V617F mutation in plasma cell-free DNA preceding clinically overt myelofibrosis: Implications for early diagnosis. Cancer Biol Ther 2019; 19:664-668. [PMID: 29565699 PMCID: PMC6067874 DOI: 10.1080/15384047.2018.1450120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A 52 year-old man with Erdheim-Chester Disease (ECD) (a non-Langerhans polyostotic sclerosing histiocytosis) had next-generation sequencing (NGS) performed as part of his diagnostic workup. In addition to the tissue BRAF V600E mutation that is found in over 50% of ECD cases, he was also found to have a JAK2 V617F alteration in cell-free circulating tumor DNA (ctDNA) (liquid biopsy). The latter was thought to be an "incidental" finding, perhaps due to clonal hematopoiesis (though this usually occurs in older individuals), as his blood counts were normal and he had no splenomegaly. Approximately 13 months after the ctDNA test showing JAK2 V617F, he developed anemia, thrombocytopenia, and splenomegaly. Marrow biopsy then showed megakaryocytic atypia and markedly increased marrow fibrosis, consistent with WHO grade 2 of 3 myelofibrosis. Therefore, the patient was determined to have ECD with a typical BRAF V600E mutation, as well as primary myelofibrosis, with the latter diagnosis manifesting clinically over one year after the JAK2 V617F was first detected in ctDNA. He recently was started on the JAK2 inhibitor ruxolitinib. This case demonstrates that genomic alterations detected by liquid biopsy for evaluation of specific malignancies already present may serve as an early harbinger of hematological disease.
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Affiliation(s)
- Michael Y Choi
- a Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine , University of California San Diego Moores Cancer Center , La Jolla , CA , USA
| | - Shumei Kato
- a Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine , University of California San Diego Moores Cancer Center , La Jolla , CA , USA
| | - Huan-You Wang
- b Department of Pathology , University of California San Diego , La Jolla , CA , USA
| | - Jonathan H Lin
- b Department of Pathology , University of California San Diego , La Jolla , CA , USA
| | | | - Razelle Kurzrock
- a Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine , University of California San Diego Moores Cancer Center , La Jolla , CA , USA
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16
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Song Z, Liu T, Chen J, Ge C, Zhao F, Zhu M, Chen T, Cui Y, Tian H, Yao M, Li J, Li H. HIF-1α-induced RIT1 promotes liver cancer growth and metastasis and its deficiency increases sensitivity to sorafenib. Cancer Lett 2019; 460:96-107. [PMID: 31247273 DOI: 10.1016/j.canlet.2019.06.016] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 06/21/2019] [Accepted: 06/21/2019] [Indexed: 12/12/2022]
Abstract
Ras-like-without-CAAX-1 (RIT1) belongs to the RAS superfamily of small GTPases, which plays critical roles in tumor progression. However, little is known about the roles of RIT1 in hepatocellular carcinoma (HCC). Here we found that RIT1 expression was positively associated with the presence of intrahepatic metastasis and the histological grade of HCC and higher RIT1 expression indicated shorter overall survival in HCC patients. In vitro and in vivo studies revealed that RIT1 functioned as an oncogene, as overexpression of RIT1 enhanced HCC cell proliferation and aggressive behavior, whereas silencing RIT1 expression repressed the malignant behaviors. Furthermore, RIT1 deficiency increased drug sensitivity to sorafenib treatment. We further demonstrated that hypoxia-inducible factor 1α (HIF-1α) directly transcriptionally upregulated RIT1, and its stableness was positively correlated with RIT1 expression in HCC tissues. Knockdown of RIT1 attenuated the invasion and migration induced by hypoxia. Collectively, our data highlight the significance of HIF-1α/RIT1 axis in driving HCC progression and sorafenib resistance.
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Affiliation(s)
- Zhen Song
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Tengfei Liu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Jing Chen
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Chao Ge
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Fangyu Zhao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Miaoxin Zhu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Taoyang Chen
- Qidong Liver Cancer Institute, Qidong, Jiangsu, 226200, China
| | - Ying Cui
- Cancer Institute of Guangxi, Nanning, Guangxi, 530021, China
| | - Hua Tian
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Ming Yao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Jinjun Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Hong Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China.
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17
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Takahara S, Inoue SI, Miyagawa-Tomita S, Matsuura K, Nakashima Y, Niihori T, Matsubara Y, Saiki Y, Aoki Y. New Noonan syndrome model mice with RIT1 mutation exhibit cardiac hypertrophy and susceptibility to β-adrenergic stimulation-induced cardiac fibrosis. EBioMedicine 2019; 42:43-53. [PMID: 30898653 PMCID: PMC6491386 DOI: 10.1016/j.ebiom.2019.03.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/27/2019] [Accepted: 03/06/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Noonan syndrome (NS) is a genetic disorder characterized by short stature, a distinctive facial appearance, and heart defects. We recently discovered a novel NS gene, RIT1, which is a member of the RAS subfamily of small GTPases. NS patients with RIT1 mutations have a high incidence of hypertrophic cardiomyopathy and edematous phenotype, but the specific role of RIT1 remains unclear. METHODS To investigate how germline RIT1 mutations cause NS, we generated knock-in mice that carried a NS-associated Rit1 A57G mutation (Rit1A57G/+). We investigated the phenotypes of Rit1A57G/+ mice in fetal and adult stages as well as the effects of isoproterenol on cardiac function in Rit1A57G/+ mice. FINDINGS Rit1A57G/+ embryos exhibited decreased viability, edema, subcutaneous hemorrhage and AKT activation. Surviving Rit1A57G/+ mice had a short stature, craniofacial abnormalities and splenomegaly. Cardiac hypertrophy and cardiac fibrosis with increased expression of S100A4, vimentin and periostin were observed in Rit1A57G/+ mice compared to Rit1+/+ mice. Upon isoproterenol stimulation, cardiac fibrosis was drastically increased in Rit1A57G/+ mice. Phosphorylated (at Thr308) AKT levels were also elevated in isoproterenol-treated Rit1A57G/+ hearts. INTERPRETATION The A57G mutation in Rit1 causes cardiac hypertrophy, fibrosis and other NS-associated features. Biochemical analysis indicates that the AKT signaling pathway might be related to downstream signaling in the RIT1 A57G mutant at a developmental stage and under β-adrenergic stimulation in the heart. FUND: The Grants-in-Aid were provided by the Practical Research Project for Rare/Intractable Diseases from the Japan Agency for Medical Research and Development, the Japan Society for the Promotion of Science KAKENHI Grant.
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Affiliation(s)
- Shingo Takahara
- Department of Medical Genetics, Tohoku University Graduate School of Medicine, Sendai, Japan; Division of Cardiovascular Surgery, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Shin-Ichi Inoue
- Department of Medical Genetics, Tohoku University Graduate School of Medicine, Sendai, Japan.
| | - Sachiko Miyagawa-Tomita
- Department of Pediatric Cardiology, Tokyo Women's Medical University, Tokyo, Japan; Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Animal Nursing Science, Yamazaki University of Animal Health Technology, Tokyo, Japan
| | - Katsuhisa Matsuura
- Institute of Advanced Biomedical Engineering and Science, Tokyo Women's Medical University, Tokyo, Japan; Department of Cardiology, Tokyo Women's Medical University, Tokyo, Japan
| | - Yasumi Nakashima
- Department of Pediatrics, Seirei Hamamatsu General Hospital, Hamamatsu, Japan
| | - Tetsuya Niihori
- Department of Medical Genetics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoichi Matsubara
- Department of Medical Genetics, Tohoku University Graduate School of Medicine, Sendai, Japan; National Center for Child Health and Development, Tokyo, Japan
| | - Yoshikatsu Saiki
- Division of Cardiovascular Surgery, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Yoko Aoki
- Department of Medical Genetics, Tohoku University Graduate School of Medicine, Sendai, Japan.
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Castel P, Cheng A, Cuevas-Navarro A, Everman DB, Papageorge AG, Simanshu DK, Tankka A, Galeas J, Urisman A, McCormick F. RIT1 oncoproteins escape LZTR1-mediated proteolysis. Science 2019; 363:1226-1230. [PMID: 30872527 PMCID: PMC6986682 DOI: 10.1126/science.aav1444] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 02/17/2019] [Indexed: 12/11/2022]
Abstract
RIT1 oncoproteins have emerged as an etiologic factor in Noonan syndrome and cancer. Despite the resemblance of RIT1 to other members of the Ras small guanosine triphosphatases (GTPases), mutations affecting RIT1 are not found in the classic hotspots but rather in a region near the switch II domain of the protein. We used an isogenic germline knock-in mouse model to study the effects of RIT1 mutation at the organismal level, which resulted in a phenotype resembling Noonan syndrome. By mass spectrometry, we detected a RIT1 interactor, leucine zipper-like transcription regulator 1 (LZTR1), that acts as an adaptor for protein degradation. Pathogenic mutations affecting either RIT1 or LZTR1 resulted in incomplete degradation of RIT1. This led to RIT1 accumulation and dysregulated growth factor signaling responses. Our results highlight a mechanism of pathogenesis that relies on impaired protein degradation of the Ras GTPase RIT1.
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Affiliation(s)
- Pau Castel
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Alice Cheng
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Antonio Cuevas-Navarro
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | | | - Alex G Papageorge
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, USA
| | - Alexandra Tankka
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Jacqueline Galeas
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Anatoly Urisman
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Frank McCormick
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
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19
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RIT1 suppresses esophageal squamous cell carcinoma growth and metastasis and predicts good prognosis. Cell Death Dis 2018; 9:1085. [PMID: 30348939 PMCID: PMC6197279 DOI: 10.1038/s41419-018-0979-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 06/23/2018] [Accepted: 06/26/2018] [Indexed: 01/05/2023]
Abstract
Ras-like without CAAX1 (RIT1) protein is a member of Ras family, which plays critical roles in signaling pathways and cellular process regulation. However, the role of RIT1 in esophageal squamous cell carcinoma (ESCC) is unclear. In this study, we found that the expression of RIT1 is downregulated in ESCC compared to corresponding non-tumor tissues. The low-level expression of RIT1 was correlated with poorer prognosis. Then we showed that RIT1 inhibited proliferation, invasion, and migration of ESCC cells, and silencing RIT1 by shRNA promoted tumorigenicity and metastasis in nude mice. We further demonstrated that RIT1 inhibited the malignant behaviors of ESCC through inhibiting the PI3K/AKT and MAPK pathway and epithelial–mesenchymal transition in ESCC cells. Our study also revealed that RIT1 increased drug sensitivity to cisplatin (CDDP), and this function could be carried out through downregulating stemness of ESCC. In conclusion, our study indicates for the first time that RIT1 displays tumor-suppressing functions in ESCC, and these functions were carried out by inhibiting MAPK and PI3K/AKT signaling pathway, inhibiting EMT, and downregulating cancer stemness of ESCC cells.
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20
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Aberrant splicing and defective mRNA production induced by somatic spliceosome mutations in myelodysplasia. Nat Commun 2018; 9:3649. [PMID: 30194306 PMCID: PMC6128865 DOI: 10.1038/s41467-018-06063-x] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 07/30/2018] [Indexed: 12/20/2022] Open
Abstract
Spliceosome mutations are frequently found in myelodysplasia. Splicing alterations induced by these mutations, their precise targets, and the effect at the transcript level have not been fully elucidated. Here we report transcriptomic analyses of 265 bone marrow samples from myelodysplasia patients, followed by a validation using CRISPR/Cas9-mediated gene editing and an assessment of nonsense-mediated decay susceptibility. Small but widespread reduction of intron-retaining isoforms is the most frequent splicing alteration in SF3B1-mutated samples. SF3B1 mutation is also associated with 3′ splice site alterations, leading to the most pronounced reduction of canonical transcripts. Target genes include tumor suppressors and genes of mitochondrial iron metabolism or heme biosynthesis. Alternative exon usage is predominant in SRSF2- and U2AF1-mutated samples. Usage of an EZH2 cryptic exon harboring a premature termination codon is increased in both SRSF2- and U2AF1-mutated samples. Our study reveals a landscape of splicing alterations and precise targets of various spliceosome mutations. Mutations to the splicing machinery may have an important role in myelodysplasia. Here, the authors describe splicing factor gene mutations in myelodysplasia and report tumor suppressor, epigenetic, iron metabolism and heme biosynthesis genes as their targets.
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21
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Meyer zum Büschenfelde U, Brandenstein LI, von Elsner L, Flato K, Holling T, Zenker M, Rosenberger G, Kutsche K. RIT1 controls actin dynamics via complex formation with RAC1/CDC42 and PAK1. PLoS Genet 2018; 14:e1007370. [PMID: 29734338 PMCID: PMC5937737 DOI: 10.1371/journal.pgen.1007370] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 04/18/2018] [Indexed: 12/12/2022] Open
Abstract
RIT1 belongs to the RAS family of small GTPases. Germline and somatic RIT1 mutations have been identified in Noonan syndrome (NS) and cancer, respectively. By using heterologous expression systems and purified recombinant proteins, we identified the p21-activated kinase 1 (PAK1) as novel direct effector of RIT1. We found RIT1 also to directly interact with the RHO GTPases CDC42 and RAC1, both of which are crucial regulators of actin dynamics upstream of PAK1. These interactions are independent of the guanine nucleotide bound to RIT1. Disease-causing RIT1 mutations enhance protein-protein interaction between RIT1 and PAK1, CDC42 or RAC1 and uncouple complex formation from serum and growth factors. We show that the RIT1-PAK1 complex regulates cytoskeletal rearrangements as expression of wild-type RIT1 and its mutant forms resulted in dissolution of stress fibers and reduction of mature paxillin-containing focal adhesions in COS7 cells. This effect was prevented by co-expression of RIT1 with dominant-negative CDC42 or RAC1 and kinase-dead PAK1. By using a transwell migration assay, we show that RIT1 wildtype and the disease-associated variants enhance cell motility. Our work demonstrates a new function for RIT1 in controlling actin dynamics via acting in a signaling module containing PAK1 and RAC1/CDC42, and highlights defects in cell adhesion and migration as possible disease mechanism underlying NS. Noonan syndrome (NS) belongs to the RASopathies, a group of developmental diseases caused by mutations in genes encoding RAS-MAPK pathway components. Germline mutations in RIT1 have been identified in NS. RIT1 belongs to the RAS superfamily, however, the cellular function of RIT1 remains elusive. We show that RIT1 binds p21-activated kinase 1 (PAK1), an effector of the RHO GTPases RAC1 and CDC42, which are important regulators of cytoskeletal dynamics. NS-associated RIT1 mutants enhance complex formation between RIT1, RAC1/CDC42 and PAK1. Expression of wild-type or mutant forms of RIT1 caused loss of stress fibers and mature focal adhesions and enhanced cell motility. Our data suggest that dysfunction in actin dynamics is a novel aspect in the pathophysiology of RASopathies.
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Affiliation(s)
| | | | - Leonie von Elsner
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kristina Flato
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tess Holling
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Zenker
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - Georg Rosenberger
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- * E-mail: (KK); (GR)
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- * E-mail: (KK); (GR)
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Hosono N, Makishima H, Mahfouz R, Przychodzen B, Yoshida K, Jerez A, LaFramboise T, Polprasert C, Clemente MJ, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Sanada M, Cui E, Verma AK, McDevitt MA, List AF, Saunthararajah Y, Sekeres MA, Boultwood J, Ogawa S, Maciejewski JP. Recurrent genetic defects on chromosome 5q in myeloid neoplasms. Oncotarget 2018; 8:6483-6495. [PMID: 28031539 PMCID: PMC5351647 DOI: 10.18632/oncotarget.14130] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 12/16/2016] [Indexed: 11/25/2022] Open
Abstract
Background Deletion of chromosome 5q (del(5q)) is the most common karyotypic abnormality in myeloid neoplasms. Materials and Methods To define the pathogenic molecular features associated with del(5q), next–generation sequencing was applied to 133 patients with myeloid neoplasms (MDS; N = 69, MDS/MPN; N = 5, sAML; N = 29, pAML; N = 30) with del(5q) as a sole abnormally or a part of complex karyotype and results were compared to molecular features of patients diploid for chr5. Findings A number of 5q genes with haploinsufficient expression and/or recurrent somatic mutations were identified; for these genes, CSNK1A1 and G3BP1 within the commonly deleted 5q region and DDX41 within a commonly retained region were most commonly affected by somatic mutations. These genes showed consistent haploinsufficiency in deleted cases; low expression/mutations of G3BP1 or DDX41 were associated with poor survival, likely due to decreased cellular function. The most common mutations on other chromosomes in patients with del(5q) included TP53, and mutations of FLT3 (ITD or TKD), NPM1 or TET2 and were mutually exclusive. Serial sequencing allowed for definition of clonal architecture and dynamics, in patients with exome sequencing allelic imbalance for informative SNPs facilitated simultaneous approximation of clonal size of del(5q) and clonal burden for somatic mutations. Interpretation Our results illuminate the spectrum of molecular defects characteristic of del(5q), their clinical impact and succession of stepwise evolution.
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Affiliation(s)
- Naoko Hosono
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.,First Department of Internal Medicine, Faculty of Medical Sciences, University of Fukui, Fukui, Japan
| | - Hideki Makishima
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Reda Mahfouz
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Bartlomiej Przychodzen
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Kenichi Yoshida
- Cancer Genomics Project, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Andres Jerez
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Thomas LaFramboise
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Chantana Polprasert
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Michael J Clemente
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Yuichi Shiraishi
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kenichi Chiba
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hiroko Tanaka
- Laboratory of Sequence Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Laboratory of Sequence Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Masashi Sanada
- Cancer Genomics Project, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Edward Cui
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Amit K Verma
- Department of Oncology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Michael A McDevitt
- Division of Hematology and Hematological Malignancy, Department of Internal Medicine and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alan F List
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Yogen Saunthararajah
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Mikkael A Sekeres
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.,Department of Hematology and Medical Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.,LLR Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Jacqueline Boultwood
- LLR Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Seishi Ogawa
- Cancer Genomics Project, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.,Leukemia Program, Cleveland Clinic, Taussig Cancer Institute, Cleveland, OH, USA
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23
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Makishima H. Somatic SETBP1 mutations in myeloid neoplasms. Int J Hematol 2017; 105:732-742. [PMID: 28447248 DOI: 10.1007/s12185-017-2241-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 04/18/2017] [Indexed: 01/06/2023]
Abstract
SETBP1 is a SET-binding protein regulating self-renewal potential through HOXA-protein activation. Somatic SETBP1 mutations were identified by whole exome sequencing in several phenotypes of myelodysplastic/myeloproliferative neoplasms (MDS/MPN), including atypical chronic myeloid leukemia, chronic myelomonocytic leukemia, and juvenile myelomonocytic leukemia as well as in secondary acute myeloid leukemia (sAML). Surprisingly, its recurrent somatic activated mutations are located at the identical positions of germline mutations reported in congenital Schinzel-Giedion syndrome. In general, somatic SETBP1 mutations have a significant clinical impact on the outcome as poor prognostic factor, due to downstream HOXA-pathway as well as associated aggressive types of chromosomal defects (-7/del(7q) and i(17q)), which is consistent with wild-type SETBP1 activation in aggressive types of acute myeloid leukemia and leukemic evolution. Biologically, mutant SETBP1 attenuates RUNX1 and activates MYB. The studies of mouse models confirmed biological significance of SETBP1 mutations in myeloid leukemogenesis, particularly associated with ASXL1 mutations. SETBP1 is a major oncogene in myeloid neoplasms, which cooperates with various genetic events and causes distinct phenotypes of MDS/MPN and sAML.
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MESH Headings
- Animals
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Chromosome Deletion
- Chromosomes, Human, Pair 7/genetics
- Core Binding Factor Alpha 2 Subunit/genetics
- Core Binding Factor Alpha 2 Subunit/metabolism
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/mortality
- Leukemia, Myeloid, Acute/therapy
- Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/genetics
- Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/metabolism
- Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/mortality
- Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/therapy
- Leukemia, Myelomonocytic, Chronic/genetics
- Leukemia, Myelomonocytic, Chronic/metabolism
- Leukemia, Myelomonocytic, Chronic/mortality
- Leukemia, Myelomonocytic, Chronic/therapy
- Leukemia, Myelomonocytic, Juvenile
- Mice
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Proto-Oncogene Proteins c-myb/genetics
- Proto-Oncogene Proteins c-myb/metabolism
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
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Affiliation(s)
- Hideki Makishima
- Department of Pathology and Tumor Biology, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
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24
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Fang Z, Marshall CB, Yin JC, Mazhab-Jafari MT, Gasmi-Seabrook GMC, Smith MJ, Nishikawa T, Xu Y, Neel BG, Ikura M. Biochemical Classification of Disease-associated Mutants of RAS-like Protein Expressed in Many Tissues (RIT1). J Biol Chem 2016; 291:15641-52. [PMID: 27226556 DOI: 10.1074/jbc.m116.714196] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Indexed: 01/09/2023] Open
Abstract
RAS-like protein expressed in many tissues 1 (RIT1) is a disease-associated RAS subfamily small guanosine triphosphatase (GTPase). Recent studies revealed that germ-line and somatic RIT1 mutations can cause Noonan syndrome (NS), and drive proliferation of lung adenocarcinomas, respectively, akin to RAS mutations in these diseases. However, the locations of these RIT1 mutations differ significantly from those found in RAS, and do not affect the three mutational "hot spots" of RAS. Moreover, few studies have characterized the GTPase cycle of RIT1 and its disease-associated mutants. Here we developed a real-time NMR-based GTPase assay for RIT1 and investigated the effect of disease-associated mutations on GTPase cycle. RIT1 exhibits an intrinsic GTP hydrolysis rate similar to that of H-RAS, but its intrinsic nucleotide exchange rate is ∼4-fold faster, likely as a result of divergent residues near the nucleotide binding site. All of the disease-associated mutations investigated increased the GTP-loaded, activated state of RIT1 in vitro, but they could be classified into two groups with different intrinsic GTPase properties. The S35T, A57G, and Y89H mutants exhibited more rapid nucleotide exchange, whereas F82V and T83P impaired GTP hydrolysis. A RAS-binding domain pulldown assay indicated that RIT1 A57G and Y89H were highly activated in HEK293T cells, whereas T83P and F82V exhibited more modest activation. All five mutations are associated with NS, whereas two (A57G and F82V) have also been identified in urinary tract cancers and myeloid malignancies. Characterization of the effects on the GTPase cycle of RIT1 disease-associated mutations should enable better understanding of their role in disease processes.
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Affiliation(s)
- Zhenhao Fang
- From the Department of Medical Biophysics, Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Christopher B Marshall
- From the Department of Medical Biophysics, Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Jiani C Yin
- From the Department of Medical Biophysics, Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Mohammad T Mazhab-Jafari
- From the Department of Medical Biophysics, Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Geneviève M C Gasmi-Seabrook
- From the Department of Medical Biophysics, Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Matthew J Smith
- From the Department of Medical Biophysics, Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Tadateru Nishikawa
- From the Department of Medical Biophysics, Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Yang Xu
- From the Department of Medical Biophysics, Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Benjamin G Neel
- From the Department of Medical Biophysics, Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Mitsuhiko Ikura
- From the Department of Medical Biophysics, Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario M5G 2M9, Canada
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25
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Milosavljević D, Overwater E, Tamminga S, de Boer K, Elting MW, van Hoorn ME, Rinne T, Houweling AC. Two cases ofRIT1associated Noonan syndrome: Further delineation of the clinical phenotype and review of the literature. Am J Med Genet A 2016; 170:1874-80. [DOI: 10.1002/ajmg.a.37657] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 03/20/2016] [Indexed: 02/01/2023]
Affiliation(s)
- Doris Milosavljević
- Department of Clinical Genetics; VU University Medical Center; Amsterdam The Netherlands
- Department of Experimental Cardiology; Academic Medical Center; Amsterdam The Netherlands
| | - Eline Overwater
- Department of Clinical Genetics; VU University Medical Center; Amsterdam The Netherlands
- Department of Clinical Genetics; Academic Medical Center; Amsterdam The Netherlands
| | - Saskia Tamminga
- Department of Clinical Genetics; VU University Medical Center; Amsterdam The Netherlands
| | - Karin de Boer
- Department of Cardiology; VU University Medical Center; Amsterdam The Netherlands
| | - Mariet W. Elting
- Department of Clinical Genetics; VU University Medical Center; Amsterdam The Netherlands
| | - Marion E. van Hoorn
- Department of Obstetrics and Gynecology; VU University Medical Center; Amsterdam The Netherlands
| | - Tuula Rinne
- Department of Human Genetics; Radboud University Medical Center; Nijmegen The Netherlands
| | - Arjan C. Houweling
- Department of Clinical Genetics; VU University Medical Center; Amsterdam The Netherlands
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26
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Kouz K, Lissewski C, Spranger S, Mitter D, Riess A, Lopez-Gonzalez V, Lüttgen S, Aydin H, von Deimling F, Evers C, Hahn A, Hempel M, Issa U, Kahlert AK, Lieb A, Villavicencio-Lorini P, Ballesta-Martinez MJ, Nampoothiri S, Ovens-Raeder A, Puchmajerová A, Satanovskij R, Seidel H, Unkelbach S, Zabel B, Kutsche K, Zenker M. Genotype and phenotype in patients with Noonan syndrome and a RIT1 mutation. Genet Med 2016; 18:1226-1234. [DOI: 10.1038/gim.2016.32] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 02/03/2016] [Indexed: 01/03/2023] Open
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27
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A novel heterozygous RIT1 mutation in a patient with Noonan syndrome, leukopenia, and transient myeloproliferation-a review of the literature. Eur J Pediatr 2016; 175:587-92. [PMID: 26518681 DOI: 10.1007/s00431-015-2658-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 10/15/2015] [Accepted: 10/19/2015] [Indexed: 01/26/2023]
Abstract
UNLABELLED Noonan syndrome (NS) is a genetic condition presenting with typical facies, cardiac defects, short stature, variable developmental deficit, cryptorchidism, skeletal, and other abnormalities. Germline mutations in genes involved in the RAS/MAPK signaling have been discovered to underlie NS. Recently, missense mutations in RIT1 have been reported as causative for individuals with clinical signs of NS. We report on a 2.5-year-old boy with NS phenotype with a novel heterozygous change in the RIT1 gene. The patient was born prematurely from pregnancy monitored for polyhydramnios. At 7 months of age, non-immune neutropenia and splenomegaly have been observed. During the severe pneumonia at 10 months, significant progression of hepatosplenomegaly, leukopenia with monocytosis (15-29 %), and thrombocytopenia occurred. Bone marrow evaluation showed myeloid hyperplasia and monocytosis, suggestive of myeloproliferative syndrome. Clinical phenotype (facial dysmorphism, soft hair, short neck, broad chest, widely spaced nipples, mild pectus carinatum, deep palmar creases, unilateral cryptorchidism), and moderate pulmonary valve stenosis with mild psychomotor delay were indicative of NS. DNA analysis identified a de novo heterozygous variant c.69A >T, p.(Lys23Asn) in exon 2 of the RIT1 gene, presumed to be causative. CONCLUSION We present a patient with a clinical suspicion of NS carrying a novel substitution in RIT1 and hematologic findings not being observed in RIT1 positive patients to date. Thus, the case broadens variability of hematologic symptoms in RIT1 positive NS individuals. WHAT IS KNOWN • Noonan syndrome is a common genetically heterogeneous disorder of autosomal dominant inheritance characterized by craniofacial dysmorphism, short stature, congenital heart defects, variable cognitive deficit, and other anomalies. What is new: • We report on a 2.5-year-old male patient with clinical signs of NS and hematologic abnormalities, in whom a novel heterozygous substitution in RIT1 with probable pathogenicity was detected.
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28
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Mutation allele burden remains unchanged in chronic myelomonocytic leukaemia responding to hypomethylating agents. Nat Commun 2016; 7:10767. [PMID: 26908133 PMCID: PMC4770084 DOI: 10.1038/ncomms10767] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 01/19/2016] [Indexed: 12/18/2022] Open
Abstract
The cytidine analogues azacytidine and 5-aza-2'-deoxycytidine (decitabine) are commonly used to treat myelodysplastic syndromes, with or without a myeloproliferative component. It remains unclear whether the response to these hypomethylating agents results from a cytotoxic or an epigenetic effect. In this study, we address this question in chronic myelomonocytic leukaemia. We describe a comprehensive analysis of the mutational landscape of these tumours, combining whole-exome and whole-genome sequencing. We identify an average of 14±5 somatic mutations in coding sequences of sorted monocyte DNA and the signatures of three mutational processes. Serial sequencing demonstrates that the response to hypomethylating agents is associated with changes in DNA methylation and gene expression, without any decrease in the mutation allele burden, nor prevention of new genetic alteration occurence. Our findings indicate that cytosine analogues restore a balanced haematopoiesis without decreasing the size of the mutated clone, arguing for a predominantly epigenetic effect.
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29
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Mutations in RIT1 cause Noonan syndrome with possible juvenile myelomonocytic leukemia but are not involved in acute lymphoblastic leukemia. Eur J Hum Genet 2016; 24:1124-31. [PMID: 26757980 DOI: 10.1038/ejhg.2015.273] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Revised: 12/01/2015] [Accepted: 12/02/2015] [Indexed: 11/09/2022] Open
Abstract
Noonan syndrome is a heterogeneous autosomal dominant disorder caused by mutations in at least eight genes involved in the RAS/MAPK signaling pathway. Recently, RIT1 (Ras-like without CAAX 1) has been shown to be involved in the pathogenesis of some patients. We report a series of 44 patients from 30 pedigrees (including nine multiplex families) with mutations in RIT1. These patients display a typical Noonan gestalt and facial phenotype. Among the probands, 8.7% showed postnatal growth retardation, 90% had congenital heart defects, 36% had hypertrophic cardiomyopathy (a lower incidence compared with previous report), 50% displayed speech delay and 52% had learning difficulties, but only 22% required special education. None had major skin anomalies. One child died perinatally of juvenile myelomonocytic leukemia. Compared with the canonical Noonan phenotype linked to PTPN11 mutations, patients with RIT1 mutations appear to be less severely growth retarded and more frequently affected by cardiomyopathy. Based on our experience, we estimate that RIT1 could be the cause of 5% of Noonan syndrome patients. Because mutations found constitutionally in Noonan syndrome are also found in several tumors in adulthood, we evaluated the potential contribution of RIT1 to leukemogenesis in Noonan syndrome. We screened 192 pediatric cases of acute lymphoblastic leukemias (96 B-ALL and 96 T-ALL) and 110 cases of juvenile myelomonocytic leukemias (JMML), but detected no variation in these tumoral samples, suggesting that Noonan patients with germline RIT1 mutations are not at high risk to developing JMML or ALL, and that RIT1 has at most a marginal role in these sporadic malignancies.
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30
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Spectrum of mutations and genotype-phenotype analysis in Noonan syndrome patients with RIT1 mutations. Hum Genet 2015; 135:209-22. [PMID: 26714497 DOI: 10.1007/s00439-015-1627-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 12/14/2015] [Indexed: 02/08/2023]
Abstract
RASopathies are autosomal dominant disorders caused by mutations in more than 10 known genes that regulate the RAS/MAPK pathway. Noonan syndrome (NS) is a RASopathy characterized by a distinctive facial appearance, musculoskeletal abnormalities, and congenital heart defects. We have recently identified mutations in RIT1 in patients with NS. To delineate the clinical manifestations in RIT1 mutation-positive patients, we further performed a RIT1 analysis in RASopathy patients and identified 7 RIT1 mutations, including two novel mutations, p.A77S and p.A77T, in 14 of 186 patients. Perinatal abnormalities, including nuchal translucency, fetal hydrops, pleural effusion, or chylothorax and congenital heart defects, are observed in all RIT1 mutation-positive patients. Luciferase assays in NIH 3T3 cells demonstrated that the newly identified RIT1 mutants, including p.A77S and p.A77T, and the previously identified p.F82V, p.T83P, p.Y89H, and p.M90I, enhanced Elk1 transactivation. Genotype-phenotype correlation analyses of previously reported NS patients harboring RIT1, PTPN11, SOS1, RAF1, and KRAS revealed that hypertrophic cardiomyopathy (56 %) was more frequent in patients harboring a RIT1 mutation than in patients harboring PTPN11 (9 %) and SOS1 mutations (10 %). The rates of hypertrophic cardiomyopathy were similar between patients harboring RIT1 mutations and patients harboring RAF1 mutations (75 %). Short stature (52 %) was less prevalent in patients harboring RIT1 mutations than in patients harboring PTPN11 (71 %) and RAF1 (83 %) mutations. These results delineate the clinical manifestations of RIT1 mutation-positive NS patients: high frequencies of hypertrophic cardiomyopathy, atrial septal defects, and pulmonary stenosis; and lower frequencies of ptosis and short stature.
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31
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Recent advances in RASopathies. J Hum Genet 2015; 61:33-9. [PMID: 26446362 DOI: 10.1038/jhg.2015.114] [Citation(s) in RCA: 239] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 08/09/2015] [Accepted: 08/24/2015] [Indexed: 12/21/2022]
Abstract
RASopathies or RAS/mitogen-activated protein kinase (MAPK) syndromes are a group of phenotypically overlapping syndromes caused by germline mutations that encode components of the RAS/MAPK signaling pathway. These disorders include neurofibromatosis type I, Legius syndrome, Noonan syndrome, Noonan syndrome with multiple lentigines (formerly called LEOPARD syndrome), Costello syndrome, cardiofaciocutaneous (CFC) syndrome, Noonan-like syndrome, hereditary gingival fibromatosis and capillary malformation-arteriovenous malformation. Recently, novel gene variants, including RIT1, RRAS, RASA2, A2ML1, SOS2 and LZTR1, have been shown to be associated with RASopathies, further expanding the disease entity. Although further analysis will be needed, these findings will help to better elucidate an understanding of the pathogenesis of these disorders and will aid in the development of potential therapeutic approaches. In this review, we summarize the novel genes that have been reported to be associated with RASopathies and highlight the cardiovascular abnormalities that may arise in affected individuals.
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32
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Devarakonda S, Morgensztern D, Govindan R. Genomic alterations in lung adenocarcinoma. Lancet Oncol 2015; 16:e342-51. [PMID: 26149886 DOI: 10.1016/s1470-2045(15)00077-7] [Citation(s) in RCA: 268] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 02/07/2015] [Accepted: 02/09/2015] [Indexed: 12/11/2022]
Abstract
Treatment for non-small-cell lung cancer is evolving from the use of cytotoxic chemotherapy to personalised treatment based on molecular alterations. This past decade has witnessed substantial progress in the treatment of patients with EGFR mutations and ALK rearrangements, and it is now possible to study complex genomic alterations in cancer using next-generation sequencing. Sequencing data from large-scale consortia, such as The Cancer Genome Atlas, as well as several independent groups, have helped identify novel drivers and potentially targetable alterations in lung adenocarcinomas. These data clearly suggest that lung adenocarcinoma is associated with distinct genomic alterations compared with other lung cancer subtypes, and highlight the widespread molecular heterogeneity that underlies the disease. In this Review, we discuss some of the key findings from genomic studies of lung adenocarcinoma.
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Affiliation(s)
- Siddhartha Devarakonda
- Division of Medical Oncology, Washington University School of Medicine, St Louis, MO, USA
| | - Daniel Morgensztern
- Division of Medical Oncology, Washington University School of Medicine, St Louis, MO, USA; Alvin J Siteman Cancer Center, St Louis, MO, USA
| | - Ramaswamy Govindan
- Division of Medical Oncology, Washington University School of Medicine, St Louis, MO, USA; Alvin J Siteman Cancer Center, St Louis, MO, USA.
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33
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Xu F, Sun S, Yan S, Guo H, Dai M, Teng Y. Elevated expression of RIT1 correlates with poor prognosis in endometrial cancer. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:10315-10324. [PMID: 26617739 PMCID: PMC4637554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 08/26/2015] [Indexed: 06/05/2023]
Abstract
RIT1, (Ras-like without CAAX1), the founding member of a novel branch of the Ras subfamily, mediates a wide variety of cellular functions, including cell proliferation, survival, and differentiation, and it may play crucial oncogenic role in human cancer. The purpose of the current study was to characterize the expression pattern of RIT1 and assess the clinical significance of RIT1 expression in endometrial cancer patients. The mRNA and protein expression of RIT1 was significantly overexpressed in 7 endometrial cancer cell lines by qPCR and Western blot, respectively. In addition, RIT1 mRNA expression was elevated in 36 freshly frozen endometrial cancer tissues compared to 21 non-cancerous endometrial tissue samples. Similar results were observed by analyzing GEO datasets. Immunohistochemistry was used to examine the protein expression of RIT1 in two tissue microarrays containing 257 cases of tumor and 31 non-tumor tissues, which showed that elevated expression of RIT1 was significantly correlated with pathological type, clinical stage, grade and vascular invasion. Importantly, Kaplan-Meier survival analysis indicated that RIT1 expression was associated with overall survival of endometrial cancer patients. Multivariate Cox regression analysis revealed that RIT1 expression was one of the independent prognostic factors for endometrial cancer patients. Furthermore, RIT1 combined with other clinicopathological risk factors was a more significant model in ROC curve comparison. In conclusion, elevated expression of RIT1 may contribute to the progression of endometrial cancer and thus may serve as a novel prognostic marker and a promising molecular target for the treatment of endometrial cancer.
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Affiliation(s)
- Fengjuan Xu
- Department of Obstetrics and Gynecology, The First People’s Hospital of TaicangJiangsu, PR China
| | - Su’an Sun
- Department of Obstetrics and Gynecology, Huai’an First People’s Hospital, Nanjing Medical UniversityHuai’an, Jiangsu, PR China
| | - Shilan Yan
- Department of Obstetrics and Gynecology, Huai’an First People’s Hospital, Nanjing Medical UniversityHuai’an, Jiangsu, PR China
| | - Hongling Guo
- Department of Obstetrics and Gynecology, The First People’s Hospital of TaicangJiangsu, PR China
| | - Miao Dai
- Department of Obstetric and Gynecology, Shanghai Jiao Tong University Affiliated Sixth People’s HospitalShanghai, PR China
| | - Yincheng Teng
- Department of Obstetric and Gynecology, Shanghai Jiao Tong University Affiliated Sixth People’s HospitalShanghai, PR China
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Visconte V, Tiu RV, Rogers HJ. Pathogenesis of myelodysplastic syndromes: an overview of molecular and non-molecular aspects of the disease. Blood Res 2014; 49:216-27. [PMID: 25548754 PMCID: PMC4278002 DOI: 10.5045/br.2014.49.4.216] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 12/12/2014] [Accepted: 12/12/2014] [Indexed: 12/21/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are a group of clonal disorders arising from hematopoietic stem cells generally characterized by inefficient hematopoiesis, dysplasia in one or more myeloid cell lineages, and variable degrees of cytopenias. Most MDS patients are diagnosed in their late 60s to early 70s. The estimated incidence of MDS in the United States and in Europe are 4.3 and 1.8 per 100,000 individuals per year, respectively with lower rates reported in some Asian countries and less well estimated in other parts of the world. Evolution to acute myeloid leukemia can occur in 10-15% of MDS patients. Three drugs are currently approved for the treatment of patients with MDS: immunomodulatory agents (lenalidomide), and hypomethylating therapy [HMT (decitabine and 5-azacytidine)]. All patients will eventually lose their response to therapy, and the survival outcome of MDS patients is poor (median survival of 4.5 months) especially for patients who fail (refractory/relapsed) HMT. The only potential curative treatment for MDS is hematopoietic cell transplantation. Genomic/chromosomal instability and various mechanisms contribute to the pathogenesis and prognosis of the disease. High throughput genetic technologies like single nucleotide polymorphism array analysis and next generation sequencing technologies have uncovered novel genetic alterations and increased our knowledge of MDS pathogenesis. We will review various genetic and non-genetic causes that are involved in the pathogenesis of MDS.
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Affiliation(s)
- Valeria Visconte
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Ramon V Tiu
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA. ; Department of Hematologic Oncology and Blood Disorders, Cleveland Clinic, Cleveland, OH, USA
| | - Heesun J Rogers
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH, USA
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Cai W, Andres DA. mTORC2 is required for rit-mediated oxidative stress resistance. PLoS One 2014; 9:e115602. [PMID: 25531880 PMCID: PMC4274107 DOI: 10.1371/journal.pone.0115602] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 11/30/2014] [Indexed: 01/13/2023] Open
Abstract
Rit, a member of the Ras family of GTPases, has been shown to promote cell survival in response to oxidative stress, in part by directing an evolutionarily conserved p38 MAPK-Akt survival cascade. Aberrant Rit signaling has recently been implicated as a driver mutation in human cancer, adding importance to the characterization of critical Rit effector pathways. However, the mechanism by which Rit-p38 signaling regulated Akt activity was unknown. Here, we identify mTORC2 as a critical downstream mediator of Rit-dependent survival signaling in response to reactive oxygen species (ROS) stress. Rit interacts with Sin1 (MAPKAP1), and Rit loss compromises ROS-dependent mTORC2 complex activation, blunting mTORC2-mediated phosphorylation of Akt kinase. Taken together, our findings demonstrate that the p38/mTORC2/Akt signaling cascade mediates Rit-dependent oxidative stress survival. Inhibition of this previously unrecognized cascade should be explored as a potential therapy of Rit-dependent malignancies.
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Affiliation(s)
- Weikang Cai
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Douglas A. Andres
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
- * E-mail:
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Capelletti M, Dodge ME, Ercan D, Hammerman PS, Park SI, Kim J, Sasaki H, Jablons DM, Lipson D, Young L, Stephens PJ, Miller VA, Lindeman NI, Munir KJ, Richards WG, Jänne PA. Identification of recurrent FGFR3-TACC3 fusion oncogenes from lung adenocarcinoma. Clin Cancer Res 2014; 20:6551-8. [PMID: 25294908 DOI: 10.1158/1078-0432.ccr-14-1337] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Targetable oncogenic alterations are detected more commonly in patients with non-small cell lung cancer (NSCLC) who never smoked cigarettes. For such patients, specific kinase inhibitors have emerged as effective clinical treatments. However, the currently known oncogenic alterations do not account for all never smokers who develop NSCLC. We sought to identify additional oncogenic alterations from patients with NSCLC to define additional treatment options. EXPERIMENTAL DESIGN We analyzed 576 lung adenocarcinomas from patients of Asian and Caucasian ethnicity. We identified a subset of cancers that did not harbor any known oncogenic alteration. We performed targeted next-generation sequencing (NGS) assay on 24 patients from this set with >75% tumor cell content. RESULTS EGFR mutations were the most common oncogenic alteration from both Asian (53%) and Caucasian (41.6%) patients. No known oncogenic alterations were present in 25.7% of Asian and 31% of Caucasian tumor specimens. We identified a FGFR3-TACC3 fusion event in one of 24 patients from this subset using targeted NGS. Two additional patients harboring FGFR3-TACC3 were identified by screening our entire cohort (overall prevalence, 0.5%). Expression of FGFR3-TACC3 led to IL3 independent growth in Ba/F3 cells. These cells were sensitive to pan-fibroblast growth factor receptor (pan-FGFR) inhibitors but not the epidermal growth factor (EGFR) inhibitor gefitinib. CONCLUSIONS FGFR3-TACC3 rearrangements occur in a subset of patients with lung adenocarcinoma. Such patients should be considered for clinical trials featuring FGFR inhibitors.
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Affiliation(s)
- Marzia Capelletti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Michael E Dodge
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Dalia Ercan
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Peter S Hammerman
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Seung-Il Park
- Department of Thoracic Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Jhingook Kim
- Department of Thoracic Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hidefumi Sasaki
- Department of Oncology, Immunology and Surgery, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - David M Jablons
- Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Doron Lipson
- Foundation Medicine, Inc., Cambridge, Massachusetts
| | - Lauren Young
- Foundation Medicine, Inc., Cambridge, Massachusetts
| | | | | | - Neal I Lindeman
- Department of Pathology and Center for Advanced Molecular Diagnostics, Brigham and Women's Hospital, Boston, Massachusetts
| | - Kiara J Munir
- Division of Thoracic Surgery, Brigham and Women's Hospital, Boston, Massachusetts
| | - William G Richards
- Division of Thoracic Surgery, Brigham and Women's Hospital, Boston, Massachusetts
| | - Pasi A Jänne
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. Belfer Institute for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts.
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Abstract
Context
The analysis of molecular biomarkers in lung adenocarcinoma (ACA) is now a central component of pathologic diagnosis and oncologic care. The identification of an EGFR mutation or ALK rearrangement in advanced-stage lung ACA will dictate a change in first-line treatment from standard chemotherapy to targeted inhibition of these oncogenic alterations. Viable approaches to therapeutic targeting of KRAS-mutated ACA are now under investigation, raising the possibility that this too will become an important predictive marker in this tumor type. The recognized array of less common oncogenic alterations in lung ACA, including in the ROS1, RET, BRAF, and ERBB2 genes, is growing rapidly. The therapeutic implications of these findings are, in many cases, still under investigation.
Objective
To focus on the major molecular biomarkers in lung ACA, recommended testing strategies, the implications for targeted therapies, and the mechanisms that drive development of resistance.
Data Sources
Our current understanding of predictive and prognostic markers in lung ACA is derived from a decade of technical advances, clinical trials, and epidemiologic studies. Many of the newest discoveries have emerged from application of high-throughput next-generation sequencing and gene expression analyses in clinically and pathologically defined cohorts of human lung tumors.
Conclusions
Best practices require a solid understanding of relevant biomarkers for diagnosis and treatment of patients with lung ACA.
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Affiliation(s)
- Lynette M. Sholl
- From the Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Harvard University, Boston, Massachusetts
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38
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Shen W, Clemente MJ, Hosono N, Yoshida K, Przychodzen B, Yoshizato T, Shiraishi Y, Miyano S, Ogawa S, Maciejewski JP, Makishima H. Deep sequencing reveals stepwise mutation acquisition in paroxysmal nocturnal hemoglobinuria. J Clin Invest 2014; 124:4529-38. [PMID: 25244093 DOI: 10.1172/jci74747] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 07/10/2014] [Indexed: 12/13/2022] Open
Abstract
Paroxysmal nocturnal hemoglobinuria (PNH) is a nonmalignant clonal disease of hematopoietic stem cells that is associated with hemolysis, marrow failure, and thrombophilia. PNH has been considered a monogenic disease that results from somatic mutations in the gene encoding PIGA, which is required for biosynthesis of glycosylphosphatidylinisotol-anchored (GPI-anchored) proteins. The loss of certain GPI-anchored proteins is hypothesized to provide the mutant clone with an extrinsic growth advantage, but some features of PNH argue that there are intrinsic drivers of clonal expansion. Here, we performed whole-exome sequencing of paired PNH+ and PNH- fractions on samples taken from 12 patients as well as targeted deep sequencing of an additional 36 PNH patients. We identified additional somatic mutations that resulted in a complex hierarchical clonal architecture, similar to that observed in myeloid neoplasms. In addition to mutations in PIGA, mutations were found in genes known to be involved in myeloid neoplasm pathogenesis, including TET2, SUZ12, U2AF1, and JAK2. Clonal analysis indicated that these additional mutations arose either as a subclone within the PIGA-mutant population, or prior to PIGA mutation. Together, our data indicate that in addition to PIGA mutations, accessory genetic events are frequent in PNH, suggesting a stepwise clonal evolution derived from a singular stem cell clone.
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Next-generation sequencing identifies rare variants associated with Noonan syndrome. Proc Natl Acad Sci U S A 2014; 111:11473-8. [PMID: 25049390 DOI: 10.1073/pnas.1324128111] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Noonan syndrome (NS) is a relatively common genetic disorder, characterized by typical facies, short stature, developmental delay, and cardiac abnormalities. Known causative genes account for 70-80% of clinically diagnosed NS patients, but the genetic basis for the remaining 20-30% of cases is unknown. We performed next-generation sequencing on germ-line DNA from 27 NS patients lacking a mutation in the known NS genes. We identified gain-of-function alleles in Ras-like without CAAX 1 (RIT1) and mitogen-activated protein kinase kinase 1 (MAP2K1) and previously unseen loss-of-function variants in RAS p21 protein activator 2 (RASA2) that are likely to cause NS in these patients. Expression of the mutant RASA2, MAP2K1, or RIT1 alleles in heterologous cells increased RAS-ERK pathway activation, supporting a causative role in NS pathogenesis. Two patients had more than one disease-associated variant. Moreover, the diagnosis of an individual initially thought to have NS was revised to neurofibromatosis type 1 based on an NF1 nonsense mutation detected in this patient. Another patient harbored a missense mutation in NF1 that resulted in decreased protein stability and impaired ability to suppress RAS-ERK activation; however, this patient continues to exhibit a NS-like phenotype. In addition, a nonsense mutation in RPS6KA3 was found in one patient initially diagnosed with NS whose diagnosis was later revised to Coffin-Lowry syndrome. Finally, we identified other potential candidates for new NS genes, as well as potential carrier alleles for unrelated syndromes. Taken together, our data suggest that next-generation sequencing can provide a useful adjunct to RASopathy diagnosis and emphasize that the standard clinical categories for RASopathies might not be adequate to describe all patients.
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40
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Gos M, Fahiminiya S, Poznański J, Klapecki J, Obersztyn E, Piotrowicz M, Wierzba J, Posmyk R, Bal J, Majewski J. Contribution of RIT1 mutations to the pathogenesis of Noonan syndrome: four new cases and further evidence of heterogeneity. Am J Med Genet A 2014; 164A:2310-6. [PMID: 24939608 DOI: 10.1002/ajmg.a.36646] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 05/21/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Monika Gos
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
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41
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Kurtovic-Kozaric A, Przychodzen B, Singh J, Konarska MM, Clemente MJ, Otrock ZK, Nakashima M, Hsi ED, Yoshida K, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Ogawa S, Boultwood J, Makishima H, Maciejewski JP, Padgett RA. PRPF8 defects cause missplicing in myeloid malignancies. Leukemia 2014; 29:126-36. [PMID: 24781015 PMCID: PMC4214909 DOI: 10.1038/leu.2014.144] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 04/07/2014] [Accepted: 04/21/2014] [Indexed: 11/26/2022]
Abstract
Mutations of spliceosome components are common in myeloid neoplasms. One of the affected genes, PRPF8, encodes the most evolutionarily conserved spliceosomal protein. We identified either recurrent somatic PRPF8 mutations or hemizygous deletions in 15/447 and 24/450 cases, respectively. 50% of PRPF8 mutant and del(17p) cases were found in AML and conveyed poor prognosis. PRPF8 defects correlated with increased myeloblasts and ring sideroblasts in cases without SF3B1 mutations. Knockdown of PRPF8 in K562 and CD34+ primary bone marrow cells increased proliferative capacity. Whole RNA deep sequencing of primary cells from patients with PRPF8 abnormalities demonstrated consistent missplicing defects. In yeast models, homologous mutations introduced into Prp8 abrogated a block experimentally produced in the second step of the RNA splicing process suggesting that the mutants have defects in proof-reading functions. In sum, the exploration of clinical and functional consequences suggests that PRPF8 is a novel leukemogenic gene in myeloid neoplasms with a distinct phenotype likely manifested through aberrant splicing.
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Affiliation(s)
- A Kurtovic-Kozaric
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland, OH, USA
| | - B Przychodzen
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland, OH, USA
| | - J Singh
- Department of Molecular Genetics, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | - M J Clemente
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland, OH, USA
| | - Z K Otrock
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland, OH, USA
| | - M Nakashima
- Department of Pathology, Cleveland Clinic, Cleveland, OH, USA
| | - E D Hsi
- Department of Pathology, Cleveland Clinic, Cleveland, OH, USA
| | - K Yoshida
- Cancer Genomics Project, Graduate School of Medicine, Tokyo, Japan
| | - Y Shiraishi
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - K Chiba
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - H Tanaka
- Laboratory of Sequence Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - S Miyano
- 1] Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan [2] Laboratory of Sequence Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - S Ogawa
- 1] Cancer Genomics Project, Graduate School of Medicine, Tokyo, Japan [2] Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - J Boultwood
- LLR Molecular Haematology Unit, NDCLS, RDM, John Radcliffe Hospital, Oxford, UK
| | - H Makishima
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland, OH, USA
| | - J P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland, OH, USA
| | - R A Padgett
- Department of Molecular Genetics, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
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42
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Berger AH, Imielinski M, Duke F, Wala J, Kaplan N, Shi GX, Andres DA, Meyerson M. Oncogenic RIT1 mutations in lung adenocarcinoma. Oncogene 2014; 33:4418-23. [PMID: 24469055 PMCID: PMC4150988 DOI: 10.1038/onc.2013.581] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 11/25/2013] [Accepted: 12/03/2013] [Indexed: 12/27/2022]
Abstract
Lung adenocarcinoma is comprised of distinct mutational subtypes characterized by mutually exclusive oncogenic mutations in RTK/RAS pathway members KRAS, EGFR, BRAF and ERBB2, and translocations involving ALK, RET and ROS1. Identification of these oncogenic events has transformed the treatment of lung adenocarcinoma via application of therapies targeted toward specific genetic lesions in stratified patient populations. However, such mutations have been reported in only ∼55% of lung adenocarcinoma cases in the United States, suggesting other mechanisms of malignancy are involved in the remaining cases. Here we report somatic mutations in the small GTPase gene RIT1 in ∼2% of lung adenocarcinoma cases that cluster in a hotspot near the switch II domain of the protein. RIT1 switch II domain mutations are mutually exclusive with all other known lung adenocarcinoma driver mutations. Ectopic expression of mutated RIT1 induces cellular transformation in vitro and in vivo, which can be reversed by combined PI3K and MEK inhibition. These data identify RIT1 as a driver oncogene in a specific subset of lung adenocarcinomas and suggest PI3K and MEK inhibition as a potential therapeutic strategy in RIT1-mutated tumors.
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Affiliation(s)
- A H Berger
- 1] Cancer Program, The Broad Institute of Harvard and M.I.T., 7 Cambridge Center, Cambridge, MA, USA [2] Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - M Imielinski
- 1] Cancer Program, The Broad Institute of Harvard and M.I.T., 7 Cambridge Center, Cambridge, MA, USA [2] Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA [3] Department of Pathology, Massachusetts General Hospital, Boston, MA, USA [4] Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - F Duke
- Cancer Program, The Broad Institute of Harvard and M.I.T., 7 Cambridge Center, Cambridge, MA, USA
| | - J Wala
- 1] Cancer Program, The Broad Institute of Harvard and M.I.T., 7 Cambridge Center, Cambridge, MA, USA [2] Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA [3] Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - N Kaplan
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - G-X Shi
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY, USA
| | - D A Andres
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY, USA
| | - M Meyerson
- 1] Cancer Program, The Broad Institute of Harvard and M.I.T., 7 Cambridge Center, Cambridge, MA, USA [2] Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA [3] Department of Pathology, Harvard Medical School, Boston, MA, USA
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44
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Itzykson R, Kosmider O, Fenaux P. Somatic mutations and epigenetic abnormalities in myelodysplastic syndromes. Best Pract Res Clin Haematol 2014; 26:355-64. [PMID: 24507812 DOI: 10.1016/j.beha.2014.01.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
During many years, very limited data had been available on specific gene mutations in MDS in particular due to the fact that balanced chromosomal translocations (which have allowed to discover many "leukemia" genes) are very rare in MDS, while chromosomal deletions are generally very large, making it difficult to identify genes of interest. Recently, the advent of next generation sequencing (NGS) techniques has helped identify somatic gene mutations in 75-80% of MDS, that cluster mainly in four functional groups, i.e. cytokine signaling (RAS genes), DNA methylation, (TET2, IDH1/2, DNMT3a genes) histone modifications (ASXL1 and EZH2 genes), and spliceosome (SF3B1 and SRSF2 genes) along with mutations of RUNX1 and TP 53 genes. Most of those mutations, except SF3B1 and TET2 mutations, are associated with an overall poorer prognosis, while some gene mutations (mainly TET2 mutation), may be associated to better response to hypomethylating agents. The frequent mutations of epigenetic modulators in MDS appear to largely contribute to the importance of epigenetic deregulation (in particular gene hypermethylation and histone deacetylation) in MDS progression, and may account at least partially for the efficacy of hypomethylating agents in the treatment of MDS.
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Affiliation(s)
- Raphael Itzykson
- Hematology Department, Hôpital Saint-Louis, Assistance Publique - Hôpitaux de Paris (AP-HP), France; Université Paris 7, France; INSERM Unit U944, Hôpital St Louis, Paris, France
| | - Olivier Kosmider
- Laboratoire d'hématologie, Hôpital Cochin, Assistance Publique - Hôpitaux de Paris (AP-HP), France; Université Paris 5, France
| | - Pierre Fenaux
- Hematology Department, Hôpital Saint-Louis, Assistance Publique - Hôpitaux de Paris (AP-HP), France; Université Paris 7, France; INSERM UMR-S-940, Hôpital St Louis, Paris, France.
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STAT3 mutations indicate the presence of subclinical T-cell clones in a subset of aplastic anemia and myelodysplastic syndrome patients. Blood 2013; 122:2453-9. [PMID: 23926297 DOI: 10.1182/blood-2013-04-494930] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Large granular lymphocyte leukemia (LGL) is often associated with immune cytopenias and can cooccur in the context of aplastic anemia (AA) and myelodysplastic syndromes (MDS). We took advantage of the recent description of signal transducer and activator of transcription 3 (STAT3) mutations in LGL clonal expansions to test, using sensitive methods, for the presence of these mutations in a large cohort of 367 MDS and 140 AA cases. STAT3 clones can be found not only in known LGL concomitant cases, but in a small proportion of unsuspected ones (7% AA and 2.5% MDS). In STAT3-mutated AA patients, an interesting trend toward better responses of immunosuppressive therapy and an association with the presence of human leukocyte antigen-DR15 were found. MDSs harboring a STAT3 mutant clone showed a lower degree of bone marrow cellularity and a higher frequency of developing chromosome 7 abnormalities. STAT3-mutant LGL clones may facilitate a persistently dysregulated autoimmune activation, responsible for the primary induction of bone marrow failure in a subset of AA and MDS patients.
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