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Kurtović M, Piteša N, Bartoniček N, Ozretić P, Musani V, Čonkaš J, Petrić T, King C, Sabol M. RNA-seq and ChIP-seq Identification of Unique and Overlapping Targets of GLI Transcription Factors in Melanoma Cell Lines. Cancers (Basel) 2022; 14:cancers14184540. [PMID: 36139698 PMCID: PMC9497141 DOI: 10.3390/cancers14184540] [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] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/05/2022] [Accepted: 09/14/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Despite significant progress in therapy, melanoma still has a rising incidence worldwide, and novel treatment strategies are needed. Recently, researchers have recognized the involvement of the Hedgehog-GLI (HH-GLI) signaling pathway in melanoma and its consistent crosstalk with the MAPK pathway. In order to further investigate the link between the two pathways and to find new target genes that could be considered for combination therapy, we set out to find transcriptional targets of all three GLI proteins in melanoma. METHODS We performed RNA sequencing on three melanoma cell lines (CHL-1, A375, and MEL224) with overexpressed GLI1, GLI2, and GLI3 and combined them with the results of ChIP-sequencing on endogenous GLI1, GLI2, and GLI3 proteins. After combining these results, 21 targets were selected for validation by qPCR. RESULTS RNA-seq revealed a total of 808 differentially expressed genes (DEGs) for GLI1, 941 DEGs for GLI2, and 58 DEGs for GLI3. ChIP-seq identified 527 genes that contained GLI1 binding sites in their promoters, 1103 for GLI2 and 553 for GLI3. A total of 15 of these targets were validated in the tested cell lines, 6 of which were detected by both RNA-seq and ChIP-seq. CONCLUSIONS Our study provides insight into the unique and overlapping transcriptional output of the GLI proteins in melanoma. We suggest that our findings could provide new potential targets to consider while designing melanoma-targeted therapy.
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Affiliation(s)
- Matea Kurtović
- Division of Molecular Medicine, Ruđer Bošković Institute, 10 000 Zagreb, Croatia
| | - Nikolina Piteša
- Division of Molecular Medicine, Ruđer Bošković Institute, 10 000 Zagreb, Croatia
| | - Nenad Bartoniček
- The Garvan Institute of Medical Research, 384 Victoria St., Darlinghurst, NSW 2010, Australia
- The Kinghorn Centre for Clinical Genomics, 370 Victoria St., Darlinghurst, NSW 2010, Australia
| | - Petar Ozretić
- Division of Molecular Medicine, Ruđer Bošković Institute, 10 000 Zagreb, Croatia
| | - Vesna Musani
- Division of Molecular Medicine, Ruđer Bošković Institute, 10 000 Zagreb, Croatia
| | - Josipa Čonkaš
- Division of Molecular Medicine, Ruđer Bošković Institute, 10 000 Zagreb, Croatia
| | - Tina Petrić
- Division of Molecular Medicine, Ruđer Bošković Institute, 10 000 Zagreb, Croatia
| | - Cecile King
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia
| | - Maja Sabol
- Division of Molecular Medicine, Ruđer Bošković Institute, 10 000 Zagreb, Croatia
- Correspondence:
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Young LC, Rodriguez-Viciana P. MRAS: A Close but Understudied Member of the RAS Family. Cold Spring Harb Perspect Med 2018; 8:cshperspect.a033621. [PMID: 29311130 DOI: 10.1101/cshperspect.a033621] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
MRAS is the closest relative to the classical RAS oncoproteins and shares most regulatory and effector interactions. However, it also has unique functions, including its ability to function as a phosphatase regulatory subunit when in complex with SHOC2 and protein phosphatase 1 (PP1). This phosphatase complex regulates a crucial step in the activation cycle of RAF kinases and provides a key coordinate input required for efficient ERK pathway activation and transformation by RAS. MRAS mutations rarely occur in cancer but deregulated expression may play a role in tumorigenesis in some settings. Activating mutations in MRAS (as well as SHOC2 and PP1) do occur in the RASopathy Noonan syndrome, underscoring a key role for MRAS within the RAS-ERK pathway. MRAS also has unique roles in cell migration and differentiation and has properties consistent with a key role in the regulation of cell polarity. Further investigations should shed light on what remains a relatively understudied RAS family member.
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Affiliation(s)
- Lucy C Young
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California 94158
| | - Pablo Rodriguez-Viciana
- UCL Cancer Institute, Paul O'Gorman Building, University College London, London WC1E 6BT, United Kingdom
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Yasumoto M, Sakamoto E, Ogasawara S, Isobe T, Kizaki J, Sumi A, Kusano H, Akiba J, Torimura T, Akagi Y, Itadani H, Kobayashi T, Hasako S, Kumazaki M, Mizuarai S, Oie S, Yano H. Muscle RAS oncogene homolog (MRAS) recurrent mutation in Borrmann type IV gastric cancer. Cancer Med 2016; 6:235-244. [PMID: 27891760 PMCID: PMC5269692 DOI: 10.1002/cam4.959] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 10/12/2016] [Accepted: 10/14/2016] [Indexed: 12/21/2022] Open
Abstract
The prognosis of patients with Borrmann type IV gastric cancer (Type IV) is extremely poor. Thus, there is an urgent need to elucidate the molecular mechanisms underlying the oncogenesis of Type IV and to identify new therapeutic targets. Although previous studies using whole-exome and whole-genome sequencing have elucidated genomic alterations in gastric cancer, none has focused on comprehensive genetic analysis of Type IV. To discover cancer-relevant genes in Type IV, we performed whole-exome sequencing and genome-wide copy number analysis on 13 patients with Type IV. Exome sequencing identified 178 somatic mutations in protein-coding sequences or at splice sites. Among the mutations, we found a mutation in muscle RAS oncogene homolog (MRAS), which is predicted to cause molecular dysfunction. MRAS belongs to the Ras subgroup of small G proteins, which includes the prototypic RAS oncogenes. We analyzed an additional 46 Type IV samples to investigate the frequency of MRAS mutation. There were eight nonsynonymous mutations (mutation frequency, 17%), showing that MRAS is recurrently mutated in Type IV. Copy number analysis identified six focal amplifications and one homozygous deletion, including insulin-like growth factor 1 receptor (IGF1R) amplification. The samples with IGF1R amplification had remarkably higher IGF1R mRNA and protein expression levels compared with the other samples. This is the first report of MRAS recurrent mutation in human tumor samples. Our results suggest that MRAS mutation and IGF1R amplification could drive tumorigenesis of Type IV and could be new therapeutic targets.
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Affiliation(s)
- Makiko Yasumoto
- Department of Pathology, Kurume University School of Medicine, Kurume, Japan.,Division of Gastroenterology, Department of Medicine, Kurume University School of Medicine Kurume, Kurume, Japan
| | - Etsuko Sakamoto
- Discovery and Preclinical Research Division, Taiho Pharmaceutical Co., Ltd., Tsukuba, Japan
| | - Sachiko Ogasawara
- Department of Pathology, Kurume University School of Medicine, Kurume, Japan
| | - Taro Isobe
- Department of Surgery, Kurume General Hospital, Kurume, Japan
| | - Junya Kizaki
- Department of Surgery, Kurume General Hospital, Kurume, Japan
| | - Akiko Sumi
- Department of Pathology, Kurume University School of Medicine, Kurume, Japan.,Department of Radiology, Kurume University School of Medicine, Kurume, Japan
| | - Hironori Kusano
- Department of Pathology, Kurume University School of Medicine, Kurume, Japan
| | - Jun Akiba
- Department of Pathology, Kurume University School of Medicine, Kurume, Japan
| | - Takuji Torimura
- Division of Gastroenterology, Department of Medicine, Kurume University School of Medicine Kurume, Kurume, Japan
| | - Yoshito Akagi
- Department of Surgery, Kurume General Hospital, Kurume, Japan
| | - Hiraku Itadani
- Discovery and Preclinical Research Division, Taiho Pharmaceutical Co., Ltd., Tsukuba, Japan
| | - Tsutomu Kobayashi
- Discovery and Preclinical Research Division, Taiho Pharmaceutical Co., Ltd., Tsukuba, Japan
| | - Shinichi Hasako
- Discovery and Preclinical Research Division, Taiho Pharmaceutical Co., Ltd., Tsukuba, Japan
| | - Masafumi Kumazaki
- Discovery and Preclinical Research Division, Taiho Pharmaceutical Co., Ltd., Tsukuba, Japan
| | - Shinji Mizuarai
- Discovery and Preclinical Research Division, Taiho Pharmaceutical Co., Ltd., Tsukuba, Japan
| | - Shinji Oie
- Discovery and Preclinical Research Division, Taiho Pharmaceutical Co., Ltd., Tsukuba, Japan
| | - Hirohisa Yano
- Department of Pathology, Kurume University School of Medicine, Kurume, Japan
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Alshahid M, Wakil SM, Al-Najai M, Muiya NP, Elhawari S, Gueco D, Andres E, Hagos S, Mazhar N, Meyer BF, Dzimiri N. New susceptibility locus for obesity and dyslipidaemia on chromosome 3q22.3. Hum Genomics 2013; 7:15. [PMID: 23738802 PMCID: PMC3681549 DOI: 10.1186/1479-7364-7-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 05/13/2013] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The muscle Ras (MRAS) gene resides on chromosome 3q22.3 and encodes a member of the membrane-associated Ras small GTPase proteins, which function as signal transducers in multiple processes including cell growth and differentiation. Its role in cardiovascular disease is not fully understood yet. In a preliminary study in heterozygous familial hypercholesterolaemia, we identified a locus linking the early onset of coronary artery disease (CAD) to chromosome 3q.22 and elected to sequence the MRAS gene using the MegaBACE DNA analysis system. In the present study, we investigated the association of seven single-nucleotide polymorphisms (SNPs) at this locus with CAD and its dyslipidaemia-related risk traits in 4,650 Saudi angiographed individuals using TaqMan assays by the Applied Biosystems real-time Prism 7900HT Sequence Detection System. RESULTS Among the studied SNPs, rs6782181 (p = 0.017) and rs9818870T (p = 0.009) were associated with CAD following adjustment for sex, age and other confounding risk factors. The rs6782181_GG also conferred risk for obesity (1,764 cases vs. 2,586 controls) [1.16(1.03-1.30); p = 0.017], hypercholesterolaemia (1,686 vs. 2,744) [1.23(1.02-1.47); p = 0.019], hypertriglyceridaemia (1,155 vs. 3,496) [1.29(1.01-1.45); p = 0.043] and low high-density lipoprotein-cholesterol (lHDL-chol) levels (1,935 vs. 2,401) [1.15(1.02-1.30); p = 0.023] after adjustment. Additionally, rs253662_(CT+TT) [1.16(1.01-1.32); p = 0.030] was associated with lHDL-chol levels. Interestingly, rs253662 (p = 0.014) and rs6782181 (p = 0.019) were protective against acquiring high low-density lipoprotein-cholesterol (hLDL-chol) levels (p = 0.014), while rs1720819 showed similar effects against CAD (p < 0.0001). More importantly, a 7-mer haplotype, ACCTGAC (χ2 = 7.66; p = 0.0056), constructed from the studied SNPs, its 6-mer derivative CCTGAC (χ2 = 6.90; p = 0.0086) and several other shorter derivatives conferred risk for obesity. hLDL-chol was weakly linked to CTAA (χ2 = 3.79; p = 0.052) and CCT (χ2 = 4.32; p = 0.038), while several other haplotypes were protective against both obesity and hLDL-chol level. CONCLUSION Our results demonstrate that the genomic locus for the MRAS gene confers risk for CAD, obesity and dyslipidaemia and point to the possible involvement of other genes or regulatory elements at this locus, rather than changes in the M-Ras protein function, in these events.
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Affiliation(s)
- Maie Alshahid
- King Faisal Heart Institute, MBC-16, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Salma M Wakil
- Genetics Department, MBC-03, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Mohammed Al-Najai
- Genetics Department, MBC-03, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Nzioka P Muiya
- Genetics Department, MBC-03, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Samar Elhawari
- Genetics Department, MBC-03, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Daisy Gueco
- Genetics Department, MBC-03, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Editha Andres
- Genetics Department, MBC-03, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Samia Hagos
- Genetics Department, MBC-03, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Nejat Mazhar
- Genetics Department, MBC-03, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Brian F Meyer
- King Faisal Heart Institute, MBC-16, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Nduna Dzimiri
- Genetics Department, MBC-03, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
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