1
|
Di Fiore R, Suleiman S, Drago-Ferrante R, Subbannayya Y, Suleiman S, Vasileva-Slaveva M, Yordanov A, Pentimalli F, Giordano A, Calleja-Agius J. The Role of FBXW7 in Gynecologic Malignancies. Cells 2023; 12:1415. [PMID: 37408248 DOI: 10.3390/cells12101415] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/28/2023] [Accepted: 05/15/2023] [Indexed: 07/07/2023] Open
Abstract
The F-Box and WD Repeat Domain Containing 7 (FBXW7) protein has been shown to regulate cellular growth and act as a tumor suppressor. This protein, also known as FBW7, hCDC4, SEL10 or hAGO, is encoded by the gene FBXW7. It is a crucial component of the Skp1-Cullin1-F-box (SCF) complex, which is a ubiquitin ligase. This complex aids in the degradation of many oncoproteins, such as cyclin E, c-JUN, c-MYC, NOTCH, and MCL1, via the ubiquitin-proteasome system (UPS). The FBXW7 gene is commonly mutated or deleted in numerous types of cancer, including gynecologic cancers (GCs). Such FBXW7 mutations are linked to a poor prognosis due to increased treatment resistance. Hence, detection of the FBXW7 mutation may possibly be an appropriate diagnostic and prognostic biomarker that plays a central role in determining suitable individualized management. Recent studies also suggest that, under specific circumstances, FBXW7 may act as an oncogene. There is mounting evidence indicating that the aberrant expression of FBXW7 is involved in the development of GCs. The aim of this review is to give an update on the role of FBXW7 as a potential biomarker and also as a therapeutic target for novel treatments, particularly in the management of GCs.
Collapse
Affiliation(s)
- Riccardo Di Fiore
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD 2080 Msida, Malta
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
| | - Sherif Suleiman
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD 2080 Msida, Malta
| | | | - Yashwanth Subbannayya
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Sarah Suleiman
- Whipps Cross Hospital, Barts Health NHS Trust, Leytonstone, London E11 1NR, UK
| | - Mariela Vasileva-Slaveva
- Department of Breast Surgery, "Dr. Shterev" Hospital, 1330 Sofia, Bulgaria
- Research Institute, Medical University Pleven, 5800 Pleven, Bulgaria
- Bulgarian Breast and Gynecological Cancer Association, 1784 Sofia, Bulgaria
| | - Angel Yordanov
- Department of Gynecological Oncology, Medical University Pleven, 5800 Pleven, Bulgaria
| | - Francesca Pentimalli
- Department of Medicine and Surgery, LUM University "Giuseppe DeGennaro", 70010 Casamassima, Italy
| | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Jean Calleja-Agius
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD 2080 Msida, Malta
| |
Collapse
|
2
|
Tsubaki M, Takeda T, Koumoto Y, Usami T, Matsuda T, Seki S, Sakai K, Nishio K, Nishida S. Activation of ERK1/2 by MOS and TPL2 leads to dasatinib resistance in chronic myeloid leukaemia cells. Cell Prolif 2023:e13420. [PMID: 36847709 DOI: 10.1111/cpr.13420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/21/2023] [Accepted: 01/27/2023] [Indexed: 03/01/2023] Open
Abstract
The development of BCR::ABL1 tyrosine kinase inhibitors (TKIs), such as dasatinib, has dramatically improved survival in cases of chronic myeloid leukaemia (CML). However, the development of resistance to BCR::ABL1 TKIs is a clinical problem. BCR::ABL1 TKI resistance is known to have BCR::ABL1-dependent or BCR::ABL1-independent mechanisms, but the mechanism of BCR::ABL1 independence is not well understood. In the present study, we investigated the mechanism of BCR::ABL1-independent dasatinib resistance. The expression and activation level of genes or proteins were evaluated using array CGH, real time PCR, or western blot analysis. Gene expression was modulated using siRNA-mediated knockdown. Cell survival was assessed by using trypan blue dye method. We found that dasatinib-resistant K562/DR and KU812/DR cells did not harbour a BCR::ABL1 mutation but had elevated expression and/or activation of MOS, TPL2 and ERK1/2. In addition, MOS siRNA, TPL2 siRNA and trametinib resensitized dasatinib-resistant cells to dasatinib. Moreover, expression levels of MOS in dasatinib non-responder patients with CML were higher than those in dasatinib responders, and the expression of TPL2 tended to increase in dasatinib non-responder patients compared with that in responder patients. Our results indicate that activation of ERK1/2 by elevated MOS and TPL2 expression is involved in dasatinib resistance, and inhibition of these proteins overcomes dasatinib resistance. Therefore, MOS, TPL2 and ERK1/2 inhibitors may be therapeutically useful for treating BCR::ABL1-independent dasatinib-resistant CML.
Collapse
Affiliation(s)
- Masanobu Tsubaki
- Division of Pharmacotherapy, Kindai University School of Pharmacy, Higashi-Osaka, Osaka, Japan
| | - Tomoya Takeda
- Division of Pharmacotherapy, Kindai University School of Pharmacy, Higashi-Osaka, Osaka, Japan
| | - Yuuichi Koumoto
- Division of Pharmacotherapy, Kindai University School of Pharmacy, Higashi-Osaka, Osaka, Japan
| | - Takehiro Usami
- Division of Pharmacotherapy, Kindai University School of Pharmacy, Higashi-Osaka, Osaka, Japan
| | - Takuya Matsuda
- Division of Pharmacotherapy, Kindai University School of Pharmacy, Higashi-Osaka, Osaka, Japan
| | - Shiori Seki
- Division of Pharmacotherapy, Kindai University School of Pharmacy, Higashi-Osaka, Osaka, Japan
| | - Kazuko Sakai
- Department of Genome Biology, Kindai University School of Medicine, Osakasayama, Osaka, Japan
| | - Kazuto Nishio
- Department of Genome Biology, Kindai University School of Medicine, Osakasayama, Osaka, Japan
| | - Shozo Nishida
- Division of Pharmacotherapy, Kindai University School of Pharmacy, Higashi-Osaka, Osaka, Japan
| |
Collapse
|
3
|
Targeted-sequence of normal urothelium and tumor of patients with non-muscle invasive bladder cancer. Sci Rep 2022; 12:16642. [PMID: 36198773 PMCID: PMC9535027 DOI: 10.1038/s41598-022-21158-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 09/23/2022] [Indexed: 11/14/2022] Open
Abstract
During tumorigenesis, certain tissues are colonized by mutant clones with oncogenic driver mutations as precancer lesions. These mutations can facilitate clonal expansion and may contribute to malignant transformation. The molecular features of low-grade non-muscle invasive bladder cancer (NMIBC) and high-grade bladder cancer are so distinct that they are thought to follow different evolutionary tumorigenesis pathways. Although NMIBC accounts for most bladder tumors, the somatic mutation patterns in “precancer” urothelium of patients with NMIBC remain unclear. Here, we analyzed specimens of normal urothelium and bladder tumors from patients with low-grade and high-grade NMIBC and investigated the genomic evolution of the cancer. Somatic mutations were analyzed using 50 oncogene-targeted sequences and droplet digital polymerase chain reaction for TERT promoter mutations. Somatic mutations in TERT promoter, FGFR3, and CDKN2A were characteristically identified in the normal urothelium of patients with NMIBC. These mutations, consistently identified in both tumor and normal specimens, likely affect clonal expansion during the malignant transformation of NMIBC. Though larger samples and comprehensive study are warranted to confirm our results, the difference in mutational landscape of the precancerous urothelium of patients with bladder cancer could offer deeper understandings of genomic evolution in bladder tumorigenesis.
Collapse
|
4
|
Kaibori M, Sakai K, Matsushima H, Kosaka H, Matsui K, De Velasco MA, Sekimoto M, Nishio K. Patients with polyclonal hepatocellular carcinoma are at a high risk of early recurrence and have a poor recurrence-free survival period. Hepatol Int 2022; 16:135-147. [PMID: 34973129 PMCID: PMC8843910 DOI: 10.1007/s12072-021-10278-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/12/2021] [Indexed: 12/24/2022]
Abstract
Background/purpose of the study Tumor heterogeneity based on copy number variations is associated with the evolution of cancer and its clinical grade. Clonal composition (CC) represents the number of clones based on the distribution of B-allele frequency (BAF) obtained from a genome-wide single nucleotide polymorphism (SNP) array. A higher CC number represents a high degree of heterogeneity. We hypothesized and evaluated that the CC number in hepatocellular carcinoma (HCC) tissues might be associated with the clinical outcomes of patients. Methods Somatic mutation, whole transcriptome, and CC number based on copy number variations of 36 frozen tissue samples of operably resected HCC tissues were analyzed by targeted deep sequencing, transcriptome analysis, and SNP array. Results The samples were classified into the heterogeneous tumors as poly-CC (n = 26) and the homogeneous tumors as mono-CC (n = 8). The patients with poly-CC had a higher rate of early recurrence and a significantly shorter recurrence-free survival period than the mono-CC patients (7.0 months vs. not reached, p = 0.0084). No differences in pathogenic non-synonymous mutations, such as TP53, were observed between the two groups when targeted deep sequencing was applied. A transcriptome analysis showed that cell cycle-related pathways were enriched in the poly-CC tumors, compared to the mono-CC tumors. Poly-CC HCC is highly proliferative and has a high risk of early recurrence. Conclusion CC is a possible candidate biomarker for predicting the risk of early postoperative recurrence and warrants further investigation. Supplementary Information The online version contains supplementary material available at 10.1007/s12072-021-10278-4.
Collapse
Affiliation(s)
- Masaki Kaibori
- Department of Surgery, Hirakata Hospital, Kansai Medical University, Hirakata, Osaka, Japan
| | - Kazuko Sakai
- Department of Genome Biology, Faculty of Medicine, Kindai University, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Hideyuki Matsushima
- Department of Surgery, Hirakata Hospital, Kansai Medical University, Hirakata, Osaka, Japan
| | - Hisashi Kosaka
- Department of Surgery, Hirakata Hospital, Kansai Medical University, Hirakata, Osaka, Japan
| | - Kosuke Matsui
- Department of Surgery, Hirakata Hospital, Kansai Medical University, Hirakata, Osaka, Japan
| | - Marco A De Velasco
- Department of Genome Biology, Faculty of Medicine, Kindai University, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Mitsugu Sekimoto
- Department of Surgery, Hirakata Hospital, Kansai Medical University, Hirakata, Osaka, Japan
| | - Kazuto Nishio
- Department of Genome Biology, Faculty of Medicine, Kindai University, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka, 589-8511, Japan.
| |
Collapse
|
5
|
Guo T, Dong X, Xie S, Zhang L, Zeng P, Zhang L. Cellular Mechanism of Gene Mutations and Potential Therapeutic Targets in Ovarian Cancer. Cancer Manag Res 2021; 13:3081-3100. [PMID: 33854378 PMCID: PMC8041604 DOI: 10.2147/cmar.s292992] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/19/2021] [Indexed: 02/05/2023] Open
Abstract
Ovarian cancer is a common and complex malignancy with poor prognostic outcome. Most women with ovarian cancer are diagnosed with advanced stage disease due to a lack of effective detection strategies in the early stage. Traditional treatment with cytoreductive surgery and platinum-based combination chemotherapy has not significantly improved prognosis and 5-year survival rates are still extremely poor. Therefore, novel treatment strategies are needed to improve the treatment of ovarian cancer patients. Recent advances of next generation sequencing technologies have both confirmed previous known mutated genes and discovered novel candidate genes in ovarian cancer. In this review, we illustrate recent advances in identifying ovarian cancer gene mutations, including those of TP53, BRCA1/2, PIK3CA, and KRAS genes. In addition, we discuss advances in targeting therapies for ovarian cancer based on these mutated genes in ovarian cancer. Further, we associate between detection of mutation genes by liquid biopsy and the potential early diagnostic value in ovarian cancer.
Collapse
Affiliation(s)
- Tao Guo
- Department of Gynecology and Obstetrics, West China Second Hospital, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Xue Dong
- Department of Gynecology, Cheng Du Shang Jin Nan Fu Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Shanli Xie
- First People's Hospital of Guangyuan, Guangyuan, Sichuan, 628000, People's Republic of China
| | - Ling Zhang
- Department of Gynecology and Obstetrics, Guangyuan Central Hospital, Guangyuan, Sichuan, 628000, People's Republic of China
| | - Peibin Zeng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Lin Zhang
- Department of Forensic Biology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China
| |
Collapse
|
6
|
Xu F, Li J, Ni M, Cheng J, Zhao H, Wang S, Zhou X, Wu X. FBW7 suppresses ovarian cancer development by targeting the N 6-methyladenosine binding protein YTHDF2. Mol Cancer 2021; 20:45. [PMID: 33658012 PMCID: PMC7927415 DOI: 10.1186/s12943-021-01340-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 02/23/2021] [Indexed: 12/14/2022] Open
Abstract
Background The tumor suppressor FBW7 is the substrate recognition component of the SCF E3-ubiquitin ligase complex that mediates proteolytic degradation of various oncogenic proteins. However, the role of FBW7 in ovarian cancer progression remains inadequately understood. Methods IP-MASS, co-IP, immunohistochemistry, and western blotting were used to identify the potential substrate of FBW7 in ovarian cancer. The biological effects of FBW7 were investigated using in vitro and in vivo models. LC/MS was used to detect the m6A levels in ovarian cancer tissues. MeRIP-Seq and RNA-Seq were used to assess the downstream targets of YTHDF2. Results We unveil that FBW7 is markedly down-regulated in ovarian cancer tissues and its high expression is associated with favorable prognosis and elevated m6A modification levels. Consistently, ectopic FBW7 inhibits ovarian cancer cell survival and proliferation in vitro and in vivo, while ablation of FBW7 empowers propagation of ovarian cancer cells. In addition, the m6A reader protein, YTHDF2, is identified as a novel substrate for FBW7. FBW7 counteracts the tumor-promoting effect of YTHDF2 by inducing proteasomal degradation of the latter in ovarian cancer. Furthermore, YTHDF2 globally regulates the turnover of m6A-modified mRNAs, including the pro-apoptotic gene BMF. Conclusions Our study has demonstrated that FBW7 suppresses tumor growth and progression via antagonizing YTHDF2-mediated BMF mRNA decay in ovarian cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s12943-021-01340-8.
Collapse
Affiliation(s)
- Fei Xu
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Jiajia Li
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Mengdong Ni
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Jingyi Cheng
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Haiyun Zhao
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Shanshan Wang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.,Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Xiang Zhou
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China. .,Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
| | - Xiaohua Wu
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| |
Collapse
|
7
|
Chao J, Bedell V, Lee J, Li MS, Chu P, Yuan YC, Zhao D, Klempner SJ, Lin RJ. Association Between Spatial Heterogeneity Within Nonmetastatic Gastroesophageal Adenocarcinomas and Survival. JAMA Netw Open 2020; 3:e203652. [PMID: 32338752 PMCID: PMC7186861 DOI: 10.1001/jamanetworkopen.2020.3652] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
IMPORTANCE Intratumoral heterogeneity has been recognized as a significant barrier in successfully developing targetable biomarkers for gastroesophageal adenocarcinoma (GEA) and may affect neoadjuvant precision medicine approaches. OBJECTIVE To describe intratumoral spatial heterogeneity of tumor cell populations in nonmetastatic GEA and its association with survival. DESIGN, SETTING, AND PARTICIPANTS This case series retrospectively identified 41 patients with GEA who underwent up-front surgical resection at a tertiary referral cancer center from January 1, 1989, through December 31, 2013. Survival was calculated from date of surgery to date of death through June 1, 2017. Data were analyzed from June 2, 2017, to March 1, 2019. MAIN OUTCOMES AND MEASURES Overall survival, intratumoral clonal composition determined by genomic single-nucleotide variation array and bioinformatic analysis, and intercellular tumoral distances determined by multiprobe fluorescence in situ hybridization. RESULTS Among the 41 patients included in the analysis (22 men [54%]; mean [SD] age, 63 [12] years), a high proportion (19 [46%]) presented with tumors possessing high intratumoral heterogeneity. Kaplan-Meier analysis demonstrated that cases with an intratumoral clonal composition count of at least 2 exhibited worse survival compared with cases with a clonal composition count of 0 to 1 (univariate hazard ratio, 3.92; 95% CI, 1.27-12.08; P = .02). This finding remained significant on multivariate analysis controlling for stage, Lauren histologic subtype, receipt of adjuvant therapy, and age (multivariate hazard ratio, 4.55; 95% CI, 1.09-19.04; P = .04). Multiprobe fluorescence in situ hybridization demonstrated intratumoral clonal populations coexisting at submillimeter distances with differing relevant oncogenic copy number alterations, such as EGFR, JAK2, FGFR2, MET, CCND1, KRAS, MYC, PIK3CA, CD274, and PDCD1LG2. CONCLUSIONS AND RELEVANCE This study found that spatial intratumoral heterogeneity of oncogenic copy number alterations exists before metastatic dissemination, and increased heterogeneity was associated with worse outcomes in resected GEA. Baseline heterogeneity illustrates the challenges in GEA targeted therapy. Further study may offer insight into strategies on combinatorial and/or sequential targeted and immunotherapeutic approaches.
Collapse
Affiliation(s)
- Joseph Chao
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Victoria Bedell
- Cytogenetics Core, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Jeeyun Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Min Sierra Li
- Department of Biostatistics, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Peiguo Chu
- Department of Pathology, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Yate-Ching Yuan
- Bioinformatics Core, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Dan Zhao
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Samuel J. Klempner
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston
- Harvard Medical School, Boston, Massachusetts
| | - Ren-Jang Lin
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California
| |
Collapse
|
8
|
Bokhari Y, Alhareeri A, Arodz T. QuaDMutNetEx: a method for detecting cancer driver genes with low mutation frequency. BMC Bioinformatics 2020; 21:122. [PMID: 32293263 PMCID: PMC7092414 DOI: 10.1186/s12859-020-3449-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 03/10/2020] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Cancer is caused by genetic mutations, but not all somatic mutations in human DNA drive the emergence or growth of cancers. While many frequently-mutated cancer driver genes have already been identified and are being utilized for diagnostic, prognostic, or therapeutic purposes, identifying driver genes that harbor mutations occurring with low frequency in human cancers is an ongoing endeavor. Typically, mutations that do not confer growth advantage to tumors - passenger mutations - dominate the mutation landscape of tumor cell genome, making identification of low-frequency driver mutations a challenge. The leading approach for discovering new putative driver genes involves analyzing patterns of mutations in large cohorts of patients and using statistical methods to discriminate driver from passenger mutations. RESULTS We propose a novel cancer driver gene detection method, QuaDMutNetEx. QuaDMutNetEx discovers cancer drivers with low mutation frequency by giving preference to genes encoding proteins that are connected in human protein-protein interaction networks, and that at the same time show low deviation from the mutual exclusivity pattern that characterizes driver mutations occurring in the same pathway or functional gene group across a cohort of cancer samples. CONCLUSIONS Evaluation of QuaDMutNetEx on four different tumor sample datasets show that the proposed method finds biologically-connected sets of low-frequency driver genes, including many genes that are not found if the network connectivity information is not considered. Improved quality and interpretability of the discovered putative driver gene sets compared to existing methods shows that QuaDMutNetEx is a valuable new tool for detecting driver genes. QuaDMutNetEx is available for download from https://github.com/bokhariy/QuaDMutNetExunder the GNU GPLv3 license.
Collapse
Affiliation(s)
- Yahya Bokhari
- Department of Computer Science, College of Engineering, Virginia Commonwealth University, 401 W. Main St., Richmond, VA 23284, USA
- Department of Biostatistics and Bioinformatics, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Areej Alhareeri
- College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Tomasz Arodz
- Department of Computer Science, College of Engineering, Virginia Commonwealth University, 401 W. Main St., Richmond, VA 23284, USA.
| |
Collapse
|
9
|
Intratumor heterogeneity and homologous recombination deficiency of high-grade serous ovarian cancer are associated with prognosis and molecular subtype and change in treatment course. Gynecol Oncol 2020; 156:415-422. [DOI: 10.1016/j.ygyno.2019.11.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 11/02/2019] [Accepted: 11/08/2019] [Indexed: 01/19/2023]
|
10
|
Martins PR, Machado CMT, Coxir SA, de Oliveira AJ, Moreira TB, Campos LS, Alcântara R, de Paula SOC, de Oliveira Salles PG, Gollob KJ, Magalhães WCS. Cervical cancer patients that respond to chemoradiation therapy display an intense tumor infiltrating immune profile before treatment. Exp Mol Pathol 2019; 111:104314. [DOI: 10.1016/j.yexmp.2019.104314] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 09/13/2019] [Accepted: 09/18/2019] [Indexed: 02/07/2023]
|
11
|
Wang HL, Liu PF, Yue J, Jiang WH, Cui YL, Ren H, Wang H, Zhuang Y, Liu Y, Jiang D, Dong Q, Zhang H, Mi JH, Xu ZM, Tian CJ, Zhang ZZ, Wang XW, Su MN, Lu W. Somatic gene mutation signatures predict cancer type and prognosis in multiple cancers with pan-cancer 1000 gene panel. Cancer Lett 2019; 470:181-190. [PMID: 31765737 DOI: 10.1016/j.canlet.2019.11.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/12/2019] [Accepted: 11/18/2019] [Indexed: 02/07/2023]
Abstract
Most cancers are caused by somatic mutations. Some common mutations in the same cancer type can form a "signature" to specifically predict the prognosis or to distinguish it from other cancers. In this study, 710 somatic cell mutations were identified in 142 cases, including digestive, lung and urogenital cancers, and the digestive cancers were further divided into liver, stomach, intestinal, esophageal and cardia cancer. The above mutations were located in 166 genes. In addition, a group of high-frequency mutation genes with specific characteristics were screened to form predictive signatures for each cancer. Verification using TCGA suggested that the signatures could predict the stages, progression-free survival, and overall survival of digestive, intestinal, and liver cancers (P < 0.05). The validation cases further confirmed the predictive role of digestive and liver cancers signatures in diagnosis and prognosis. Overall, this study established predictive signatures for different cancer systems and their subtypes. These findings enable a better understanding in cancer genome, and contribute to the personalized diagnosis and treatment.
Collapse
Affiliation(s)
- Hai-Long Wang
- Department of Oncology, Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital, Tianjin, China
| | - Peng-Fei Liu
- Department of Oncology, Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital, Tianjin, China
| | - Jie Yue
- Department of Esophageal Oncology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Wen-Hua Jiang
- Department of Radiotherapy, Tianjin Medical University Second Hospital, Tianjin, China
| | - Yun-Long Cui
- Department of Hepatobiliary Oncology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - He Ren
- Department of Pathology, Center of Tumour Immunology and Cytotherapy, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.
| | - Han Wang
- Department of Applied Statistics, College of Science, Hebei University of Technology, Tianjin, China
| | - Yan Zhuang
- Department of Colorectal Oncology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Yong Liu
- Department of Gastric Oncology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Da Jiang
- Department of Medical Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Qian Dong
- Department of Medical Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Hui Zhang
- Division of Biostatistics, Department of Prevebtive Medicine, Northwestern University Feinberg School of Medicine, Chicago, USA
| | - Jia-Hui Mi
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, China
| | - Zan-Mei Xu
- Tianjin Marvel Medical Laboratory, Tianjin Marvelbio Technology Co.,Ltd, Tianjin, China
| | - Cai-Juan Tian
- Tianjin Marvel Medical Laboratory, Tianjin Marvelbio Technology Co.,Ltd, Tianjin, China
| | - Zhen-Zhen Zhang
- Tianjin Marvel Medical Laboratory, Tianjin Marvelbio Technology Co.,Ltd, Tianjin, China
| | - Xiao-Wei Wang
- Tianjin Marvel Medical Laboratory, Tianjin Marvelbio Technology Co.,Ltd, Tianjin, China
| | - Mei-Na Su
- Tianjin Marvel Medical Laboratory, Tianjin Marvelbio Technology Co.,Ltd, Tianjin, China
| | - Wei Lu
- Department of Hepatobiliary Oncology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.
| |
Collapse
|
12
|
Wang D, Yang L, Yu W, Zhang Y. Investigational fibroblast growth factor receptor 2 antagonists in early phase clinical trials to treat solid tumors. Expert Opin Investig Drugs 2019; 28:903-916. [PMID: 31560229 DOI: 10.1080/13543784.2019.1672655] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: Fibroblast growth factor receptor 2 (FGFR2) is a highly conserved transmembrane tyrosine kinase receptor. FGFR2 dysregulation occurs in numerous human solid tumors and overexpression is closely associated with tumor progression. FGFR2 has recently been reported as a therapeutic target for cancer. Several targeted therapies are being investigated to disrupt FGFR2 activity; these include multi-target tyrosine kinase inhibitors (TKIs), pan-FGFR targeted TKIs and FGFR2 monoclonal antibodies. Areas: This review examines FGFR2 regulation and function in cancer and its potential as a target for cancer treatment. Expert opinion: Highly specific FGFR2 blockers have not yet been developed and moreover, resistance to FGFR2-targeted therapies is a challenge. More sophisticated patient selection strategies would help improve FGFR2-targeted therapies and combination therapy is considered the most promising approach for cancer patients with FGFR2 alterations.
Collapse
Affiliation(s)
- Dan Wang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , P.R. China.,Cancer Center, The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , P.R. China.,Henan Key Laboratory for Tumor Immunology and Biotherapy , Zhengzhou , Henan , P.R. China
| | - Li Yang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , P.R. China.,Cancer Center, The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , P.R. China.,Henan Key Laboratory for Tumor Immunology and Biotherapy , Zhengzhou , Henan , P.R. China
| | - Weina Yu
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , P.R. China.,Cancer Center, The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , P.R. China.,Henan Key Laboratory for Tumor Immunology and Biotherapy , Zhengzhou , Henan , P.R. China
| | - Yi Zhang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , P.R. China.,Cancer Center, The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , P.R. China.,Henan Key Laboratory for Tumor Immunology and Biotherapy , Zhengzhou , Henan , P.R. China.,School of Life Sciences, Zhengzhou University , Zhengzhou , Henan , P.R. China
| |
Collapse
|
13
|
Abstract
BACKGROUND Forkhead box P3 (Foxp3) plays important roles in the development and pathogensis of cancer. To investigate the association of 3 polymorphisms of Foxp3 (rs3761548, rs 3761549 and rs2280883) and cancer risk, an updated meta-analysis was performed. METHODS Around 11 studies including 4344 cancer patients and 4665 healthy controls were selected for this meta-analysis. There were nine studies with 3783 cases and 4096 controls for rs3761548, 4 studies with 1669 cases and 1613 controls for rs3761549 and 4 studies with 1821 cases and 1799 controls for rs2280883. Odds radios (ORs) and 95% confidence intervals (CIs) were used to evaluate the cancer risk. RESULTS Meta-analysis showed that rs3761548 was associated with an increased cancer risk in the overall population under the recessive model (AA vs CA + CC: OR = 1.45, 95%CI = 1.03-2.02, P = .03). No association was found between rs3761549, rs2280883 polymorphisms, and cancer susceptibility in the overall population. Nonetheless, in the genotyping methods subgroup analysis of rs2280883, a lower risk of cancer was found in studies using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) under the allelic model (C vs T: OR = 0.70, 95%CI = 0.52-0.95, P = .02), heterozygote model (TC vs TT: OR = 0.60, 95%CI = 0.41-0.87, P = .008) and dominant model (CC + TC vs TT: OR = 0.63, 95%CI = 0.45-0.90, P = .01). In the subgroup analysis by cancer types showed C allele or TC carriers were insusceptible to cancer under 3 genetic models (C vs T: OR = 0.78, 95%CI = 0.64-0.95, P = .01; TC vs TT: OR = 0.50, 95%CI = 0.32-0.79, P = .003; CC + TC vs TT: OR = 0.64, 95%CI = 0.51-0.82, P < .001). CONCLUSION Our results suggest that rs3761548 polymorphism is associated with cancer risk.
Collapse
|
14
|
Rotolo F, Zhu CQ, Brambilla E, Graziano SL, Olaussen K, Le-Chevalier T, Pignon JP, Kratzke R, Soria JC, Shepherd FA, Seymour L, Michiels S, Tsao MS. Genome-wide copy number analyses of samples from LACE-Bio project identify novel prognostic and predictive markers in early stage non-small cell lung cancer. Transl Lung Cancer Res 2018; 7:416-427. [PMID: 30050779 DOI: 10.21037/tlcr.2018.05.01] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Background Adjuvant chemotherapy (ACT) provides modest benefit in resected non-small cell lung cancer (NSCLC) patients. Genome-wide studies have identified gene copy number aberrations (CNA), but their prognostic implication is unknown. Methods DNA from 1,013 FFPE tumor samples from three pivotal multicenter randomized trials (ACT vs. control) in the LACE-Bio consortium (median follow-up: 5.2 years) was successfully extracted, profiled using a molecular inversion probe SNP assay, normalized relative to a pool of normal tissues and segmented. Minimally recurrent regions were identified. P values were adjusted to control the false discovery rate (Q values). Results A total of 976 samples successfully profiled, 414 (42%) adenocarcinoma (ADC), 430 (44%) squamous cell carcinoma (SCC) and 132 (14%) other NSCLC; 710 (73%) males. We identified 431 recurrent regions, with on average 51 gains and 43 losses; 253 regions (59%) were ≤3 Mb. Most frequent gains (up to 48%) were on chr1, 3q, 5p, 6p, 8q, 22q; most frequent losses (up to 40%) on chr3p, 8p, 9p. CNA frequency of 195 regions was significantly different (Q≤0.05) between ADC and SCC. Fourteen regions (7p11-12, 9p21, 18q12, and 19p11-13) were associated with disease-free survival (DFS) (univariate P≤0.005, Q<0.142), with poorer DFS for losses of regions including CDKN2A/B [hazard ratio (HR) for 2-fold lower CN: 1.5 (95% CI: 1.2-1.9), P<0.001, Q=0.020] and STK11 [HR =2.4 (1.3-4.3), P=0.005, Q=0.15]. Chromosomal instability was associated with poorer DFS (HR =1.5, P=0.015), OS (HR =1.2, P=0.189) and lung-cancer specific survival (HR =1.7, P=0.003). Conclusions These large-scale genome-wide analyses of gene CNA provide new candidate prognostic markers for stage I-III NSCLC.
Collapse
Affiliation(s)
- Federico Rotolo
- Gustave Roussy, Université Paris-Saclay, Service de Biostatistique et d'Epidémiologie, Villejuif, France.,Université Paris-Saclay, Univ. Paris-Sud, UVSQ, CESP, INSERM, Villejuif, France.,Ligue Nationale Contre le Cancer Meta-Analysis Platform, Gustave Roussy, Villejuif, France
| | - Chang-Qi Zhu
- University Health Network, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Elisabeth Brambilla
- Department of Pathology, Institut Albert Bonniot, Hopital Albert Michallon, Grenoble, France
| | | | - Ken Olaussen
- INSERM U981, Université Paris-Sud, Université Paris-Saclay and Gustave Roussy Cancer Campus, Villejuif, France
| | | | - Jean-Pierre Pignon
- Gustave Roussy, Université Paris-Saclay, Service de Biostatistique et d'Epidémiologie, Villejuif, France.,Université Paris-Saclay, Univ. Paris-Sud, UVSQ, CESP, INSERM, Villejuif, France.,Ligue Nationale Contre le Cancer Meta-Analysis Platform, Gustave Roussy, Villejuif, France
| | - Robert Kratzke
- Department of Medical Oncology, University of Minnesota, Minneapolis, MN, USA
| | - Jean-Charles Soria
- INSERM U981, Université Paris-Sud, Université Paris-Saclay and Gustave Roussy Cancer Campus, Villejuif, France.,Department of Medical Oncology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Frances A Shepherd
- University Health Network, Princess Margaret Cancer Centre, Toronto, ON, Canada.,Department of Medicine, Division of Medical Oncology, University of Toronto, Toronto, ON, Canada
| | - Lesley Seymour
- Canadian Cancer Trials Group and Queen's University, Kingston, ON, Canada
| | - Stefan Michiels
- Gustave Roussy, Université Paris-Saclay, Service de Biostatistique et d'Epidémiologie, Villejuif, France.,Université Paris-Saclay, Univ. Paris-Sud, UVSQ, CESP, INSERM, Villejuif, France.,Ligue Nationale Contre le Cancer Meta-Analysis Platform, Gustave Roussy, Villejuif, France
| | - Ming-Sound Tsao
- University Health Network, Princess Margaret Cancer Centre, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
15
|
Garziera M, Cecchin E, Canzonieri V, Sorio R, Giorda G, Scalone S, De Mattia E, Roncato R, Gagno S, Poletto E, Romanato L, Sartor F, Polesel J, Toffoli G. Identification of Novel Somatic TP53 Mutations in Patients with High-Grade Serous Ovarian Cancer (HGSOC) Using Next-Generation Sequencing (NGS). Int J Mol Sci 2018; 19:ijms19051510. [PMID: 29783665 PMCID: PMC5983728 DOI: 10.3390/ijms19051510] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 04/26/2018] [Accepted: 05/16/2018] [Indexed: 02/07/2023] Open
Abstract
Somatic mutations in TP53 are a hallmark of high-grade serous ovarian cancer (HGSOC), although their prognostic and predictive value as markers is not well defined. Next-generation sequencing (NGS) can identify novel mutations with high sensitivity, that may be repurposed as potential druggable anti-cancer targets and aid in therapeutic decisions. Here, a commercial NGS cancer panel comprising 26 genes, including TP53, was used to identify new genetic markers of platinum resistance and patient prognosis in a retrospective set of patients diagnosed with epithelial ovarian cancer. Six novel TP53 somatic mutations in untreated tumors from six distinct patients diagnosed with HGSOC were identified: TP53 c.728_739delTGGGCGGCATGA (p.Met243_Met247del, in-frame insertion or deletion (INDEL); TP53 c.795_809delGGGACGGAACAGCTT (p.Gly266_Phe270del, in-frame INDEL); TP53 c.826_827GC>AT (p.Ala276Ile, missense); TP53 c.1022insT (p.Arg342Profs*5, frameshift INDEL); TP53 c.1180delT (p.Ter394Aspfs*28, frameshift INDEL); and TP53 c.573insT (p.Gln192Serfs*17, frameshift INDEL). Novel TP53 variants were validated by classical sequencing methods and their impact on protein expression in tumors explored by immunohistochemistry. Further insights into the potential functional effect of the mutations were obtained by different in silico approaches, bioinformatics tools, and structural modeling. This discovery of previously unreported TP53 somatic mutations provides an opportunity to translate NGS technology into personalized medicine and identify new potential targets for therapeutic applications.
Collapse
Affiliation(s)
- Marica Garziera
- Experimental and Clinical Pharmacology Unit, CRO Aviano-National Cancer Institute, IRCCS, via F. Gallini 2, 33081 Aviano (PN), Italy.
| | - Erika Cecchin
- Experimental and Clinical Pharmacology Unit, CRO Aviano-National Cancer Institute, IRCCS, via F. Gallini 2, 33081 Aviano (PN), Italy.
| | - Vincenzo Canzonieri
- Pathology Unit, CRO Aviano-National Cancer Institute, IRCCS, via F. Gallini 2, 33081 Aviano (PN), Italy.
| | - Roberto Sorio
- Medical Oncology Unit C, CRO Aviano-National Cancer Institute, IRCCS, via F. Gallini 2, 33081 Aviano (PN), Italy.
| | - Giorgio Giorda
- Gynecological Oncology Unit, CRO Aviano-National Cancer Institute, IRCCS, via F. Gallini 2, 33081 Aviano (PN), Italy.
| | - Simona Scalone
- Medical Oncology Unit C, CRO Aviano-National Cancer Institute, IRCCS, via F. Gallini 2, 33081 Aviano (PN), Italy.
| | - Elena De Mattia
- Experimental and Clinical Pharmacology Unit, CRO Aviano-National Cancer Institute, IRCCS, via F. Gallini 2, 33081 Aviano (PN), Italy.
| | - Rossana Roncato
- Experimental and Clinical Pharmacology Unit, CRO Aviano-National Cancer Institute, IRCCS, via F. Gallini 2, 33081 Aviano (PN), Italy.
| | - Sara Gagno
- Experimental and Clinical Pharmacology Unit, CRO Aviano-National Cancer Institute, IRCCS, via F. Gallini 2, 33081 Aviano (PN), Italy.
| | - Elena Poletto
- Medical Oncology Department, Azienda Sanitaria Universitaria Integrata di Udine, via Pozzuolo 330, 33100 Udine (UD), Italy.
| | - Loredana Romanato
- Experimental and Clinical Pharmacology Unit, CRO Aviano-National Cancer Institute, IRCCS, via F. Gallini 2, 33081 Aviano (PN), Italy.
| | - Franca Sartor
- Experimental and Clinical Pharmacology Unit, CRO Aviano-National Cancer Institute, IRCCS, via F. Gallini 2, 33081 Aviano (PN), Italy.
| | - Jerry Polesel
- Unit of Cancer Epidemiology, CRO Aviano-National Cancer Institute, IRCCS, via F. Gallini 2, 33081 Aviano (PN), Italy.
| | - Giuseppe Toffoli
- Experimental and Clinical Pharmacology Unit, CRO Aviano-National Cancer Institute, IRCCS, via F. Gallini 2, 33081 Aviano (PN), Italy.
| |
Collapse
|