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Li Y, Meng F, Sui C, Wang Y, Cheng D. CircRNA hsa_circ_0001627 aggravates cervical cancer progression through upregulation of FNDC3B and activating PI3K/mTOR signaling pathway. J Cell Commun Signal 2023; 17:627-638. [PMID: 36357650 PMCID: PMC10409949 DOI: 10.1007/s12079-022-00696-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/01/2022] [Indexed: 11/12/2022] Open
Abstract
Circular RNAs (CircRNAs) are key regulators in the development and progression of human cancers. However, the biological roles and mechanisms of circRNAs in gastric cancer (GC) remain largely unknown. Analyzing circRNA microarray dataset (GSE102686) and clinical specimens, a novel circRNA termed hsa_circ_0001627, was identified and it was highly expressed in CC cancerous tissues and cells, and was associated with poor clinical outcomes. Functionally, hsa_circ_0001627 silencing impaired the malignant progression of CC cells and the growth of CC xenografts in nude mice. Mechanistically, hsa_circ_0001627 acted as a miR-1225-5p sponge, thus indirectly regulating FNDC3B and leading to the activation of PI3K/mTOR signaling pathway. Collectively, the present study indicates that hsa_circ_0001627 regulates miR-1225-5p/FNDC3B/PI3K/mTOR axis and functions as an oncogene in CC progression, suggesting the potential therapeutic use of hsa_circ_0001627 in CC treatment.
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Affiliation(s)
- Yan Li
- Department of Biotherapy, Cancer Research Institute, The First Hospital of China Medical University, 110001, Shenyang, Liaoning, China
| | - Fandong Meng
- Department of Biotherapy, Cancer Research Institute, The First Hospital of China Medical University, 110001, Shenyang, Liaoning, China
| | - Chengguang Sui
- Department of Biotherapy, Cancer Research Institute, The First Hospital of China Medical University, 110001, Shenyang, Liaoning, China
| | - Yang Wang
- Department of Biotherapy, Cancer Research Institute, The First Hospital of China Medical University, 110001, Shenyang, Liaoning, China
| | - Dali Cheng
- Department of Gynaecology and Obstetrics, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Heping District, 110000, Shenyang, Liaoning, China.
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2
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Vellichirammal NN, Tan YD, Xiao P, Eudy J, Shats O, Kelly D, Desler M, Cowan K, Guda C. The mutational landscape of a US Midwestern breast cancer cohort reveals subtype-specific cancer drivers and prognostic markers. Hum Genomics 2023; 17:64. [PMID: 37454130 PMCID: PMC10349437 DOI: 10.1186/s40246-023-00511-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 07/11/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND Female breast cancer remains the second leading cause of cancer-related death in the USA. The heterogeneity in the tumor morphology across the cohort and within patients can lead to unpredictable therapy resistance, metastasis, and clinical outcome. Hence, supplementing classic pathological markers with intrinsic tumor molecular markers can help identify novel molecular subtypes and the discovery of actionable biomarkers. METHODS We conducted a large multi-institutional genomic analysis of paired normal and tumor samples from breast cancer patients to profile the complex genomic architecture of breast tumors. Long-term patient follow-up, therapeutic regimens, and treatment response for this cohort are documented using the Breast Cancer Collaborative Registry. The majority of the patients in this study were at tumor stage 1 (51.4%) and stage 2 (36.3%) at the time of diagnosis. Whole-exome sequencing data from 554 patients were used for mutational profiling and identifying cancer drivers. RESULTS We identified 54 tumors having at least 1000 mutations and 185 tumors with less than 100 mutations. Tumor mutational burden varied across the classified subtypes, and the top ten mutated genes include MUC4, MUC16, PIK3CA, TTN, TP53, NBPF10, NBPF1, CDC27, AHNAK2, and MUC2. Patients were classified based on seven biological and tumor-specific parameters, including grade, stage, hormone receptor status, histological subtype, Ki67 expression, lymph node status, race, and mutational profiles compared across different subtypes. Mutual exclusion of mutations in PIK3CA and TP53 was pronounced across different tumor grades. Cancer drivers specific to each subtype include TP53, PIK3CA, CDC27, CDH1, STK39, CBFB, MAP3K1, and GATA3, and mutations associated with patient survival were identified in our cohort. CONCLUSIONS This extensive study has revealed tumor burden, driver genes, co-occurrence, mutual exclusivity, and survival effects of mutations on a US Midwestern breast cancer cohort, paving the way for developing personalized therapeutic strategies.
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Affiliation(s)
| | - Yuan-De Tan
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Peng Xiao
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - James Eudy
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Oleg Shats
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, USA
| | - David Kelly
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, USA
| | - Michelle Desler
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, USA
| | - Kenneth Cowan
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, USA
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
- Center for Biomedical Informatics Research and Innovation, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, USA.
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3
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Hong B, Zhang X, Du X, Yang D, Hu Z, Zhang X, Zhang N. Exploring the Potential Driver Gene Mutations That Promote Renal Cancer Cell Metastasis and Implantation Based on Circulating Tumor Cells Culture. Diagnostics (Basel) 2023; 13:diagnostics13111855. [PMID: 37296706 DOI: 10.3390/diagnostics13111855] [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: 04/13/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Studies have shown that the circulating tumor cell (CTC) is a necessary condition for the invasion and distant metastasis of renal cell carcimona (RCC). However, few CTCs-related gene mutations have been developed which could promote the metastasis and implantation of RCC. The objective of this study is to explore the potential driver gene mutations that promote RCC metastasis and implantation based on CTCs culture. Fifteen patients with primary mRCC and three healthy subjects were included, and peripheral blood was obtained. After the preparation of synthetic biological scaffolds, peripheral blood CTCs were cultured. Successful cultured CTCs were applied to construct CTCs-derived xenograft (CDX) models, followed by DNA extraction, whole exome sequencing (WES) and bioinformatics analysis. Synthetic biological scaffolds were constructed based on previously applied techniques, and peripheral blood CTCs culture was successfully performed. We then constructed CDX models and performed WES, and explored the potential driver gene mutations that may promote RCC metastasis and implantation. Bioinformatics analysis showed that KAZN and POU6F2 may be closely related to the prognosis of RCC. We successfully performed the culture of peripheral blood CTCs and, on this basis we initially explored the potential driver mutations for the metastasis and implantation of RCC.
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Affiliation(s)
- Baoan Hong
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Urology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Xuezhou Zhang
- Department of Urology, Beijing Anzhen Hospital, Capital Medical University, Beijing 100029, China
| | - Xin Du
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Urology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Dazhi Yang
- Acrogenic Biotechnologies INC, Rockville, MD 20850, USA
| | - Zhiyuan Hu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Xiuli Zhang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Ning Zhang
- Department of Urology, Beijing Anzhen Hospital, Capital Medical University, Beijing 100029, China
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4
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Ji H, Li K, Jiang W, Li J, Zhang JA, Zhu X. MRVI1 and NTRK3 Are Potential Tumor Suppressor Genes Commonly Inactivated by DNA Methylation in Cervical Cancer. Front Oncol 2022; 11:802068. [PMID: 35141152 PMCID: PMC8818726 DOI: 10.3389/fonc.2021.802068] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/24/2021] [Indexed: 11/13/2022] Open
Abstract
The abnormally methylated tumor suppressor genes (TSGs) associated with cervical cancer are unclear. DNA methylation data, RNA-seq expression profiles, and overall survival data were downloaded from TCGA CESC database. DMGs and DEGs were obtained through CHAMP and DESeq packages, respectively. TSGs were downloaded from TSGene 2.0. Candidate hypermethylated/down-regulated TSGs were further evaluated and pyrosequencing was used to confirm their difference in methylation levels of selected TSGs in cervical cancer patients. A total of 25946 differentially methylated CpGs corresponding to 2686 hypermethylated genes and 4898 hypomethylated genes between cervical cancer and adjacent normal cervical tissues were found in this study. Besides, 693 DEGs (109 up-regulated and 584 down-regulated) were discovered in cervical cancer tissues. Then, 192 hypermethylated/down-regulated genes were obtained in cervical cancer compared to adjacent tissues. Interestingly, 26 TSGs were found in hypermethylated/down-regulated genes. Among these genes, low expression of MRVI1 and NTRK3 was associated with poor overall survival in cervical cancer. Moreover, GEO data showed that MRVI1 and NTRK3 were significantly decreased in cervical cancer tissues. The expression levels of MRVI1 and NTRK3 were negatively correlated with the methylation levels of their promoter CpG sites. Additionally, elevated methylation levels of MRVI1 and NTRK3 promoter were further verified in cervical cancer tissues by pyrosequencing experiments. Finally, the ROC results showed that the promoter methylation levels of MRVI1 and NTRK3 had the ability to discriminate cervical cancer from healthy samples. The study contributes to our understanding of the roles of MRVI1 and NTRK3 in cervical cancer.
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Affiliation(s)
- Huihui Ji
- Center of Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Kehan Li
- Center of Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Wenxiao Jiang
- Center of Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jingwei Li
- Department of Obstetrics and Gynecology, Taizhou Woman and Children’s Hospital of Wenzhou Medical University, Taizhou, China
| | - Jian-an Zhang
- Center of Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xueqiong Zhu
- Center of Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Department of Obstetrics and Gynecology, Taizhou Woman and Children’s Hospital of Wenzhou Medical University, Taizhou, China
- *Correspondence: Xueqiong Zhu,
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5
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Li L, Chen S, Tang Y, Wu J, He Y, Qiu L. Oncogene or tumor suppressor gene: An integrated pan-cancer analysis of NBPF1. Front Endocrinol (Lausanne) 2022; 13:950326. [PMID: 36060966 PMCID: PMC9428449 DOI: 10.3389/fendo.2022.950326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
Neuroblastoma breakpoint family, member 1 (NBPF1), appears to be a double-edged sword with regard to its role in carcinogenesis. On the one hand, the tumor-suppressing functions of NBPF1 have been definitively observed in neuroblastoma, prostate cancer, cutaneous squamous cell carcinoma, and cervical cancer. On the other hand, there is evidence that NBPF1 regulates the colony formation, invasion, and maintenance of liver cancer cells and hence functions as an oncogene. The roles of NBPF1 are strictly dependent on the biological context and type of organization. However, a systematic pan-cancer analysis has thus far not been undertaken, and the significance of NBPF1 in the occurrence and progression of many malignancies is uncertain. In this paper, bioinformatics techniques were employed to analyze NBPF1 expression across different cancers and investigate the relationship between NBPF1 and clinical features, prognosis, genetic alteration, and tumor immune microenvironment, respectively. Our results show that NBPF1 is variably expressed in distinct tumor tissues and is also closely linked to clinical outcomes. In particular, compared to other tumor types, there was a strong negative correlation between NBPF1 expression and various components of the tumor microenvironment in adrenocortical carcinoma (ACC). We thus developed an NBPF1-derived immune risk model based on NBPF1-related immune genes; ACC patients with a high-risk score tended to have a poorer prognosis, accompanied by immune hyporesponsiveness. NBPF1 can be used as a prognostic biomarker for multiple cancers. Moreover, anti-NBPF1 immunotherapy may be suitable for treating ACC patients.
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Affiliation(s)
- Lei Li
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, China
| | - Sen Chen
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, School of Biology and Engineering, Guizhou Medical University, Guiyang, China
| | - Yueming Tang
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, China
| | - Jie Wu
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, China
- *Correspondence: Jie Wu, ; Yangzhige He, ; Ling Qiu,
| | - Yangzhige He
- Department of Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- *Correspondence: Jie Wu, ; Yangzhige He, ; Ling Qiu,
| | - Ling Qiu
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, China
- *Correspondence: Jie Wu, ; Yangzhige He, ; Ling Qiu,
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6
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Pathogenesis of Penile Squamous Cell Carcinoma: Molecular Update and Systematic Review. Int J Mol Sci 2021; 23:ijms23010251. [PMID: 35008677 PMCID: PMC8745288 DOI: 10.3390/ijms23010251] [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: 11/30/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 12/22/2022] Open
Abstract
Penile squamous cell carcinoma (PSCC) is a rare but aggressive neoplasm with dual pathogenesis (human papillomavirus (HPV)-associated and HPV-independent). The development of targeted treatment is hindered by poor knowledge of the molecular landscape of PSCC. We performed a thorough review of genetic alterations of PSCC focused on somatic mutations and/or copy number alterations. A total of seven articles have been identified which, overall, include 268 PSCC. However, the series are heterogeneous regarding methodologies employed for DNA sequencing and HPV detection together with HPV prevalence, and include, in general, a limited number of cases, which results in markedly different findings. Reported top-ranked mutations involve TP53, CDKN2A, FAT1, NOTCH-1 and PIK3CA. Numerical alterations involve gains in MYC and EGFR, as well as amplifications in HPV integration loci. A few genes including TP53, CDKN2A, PIK3CA and CCND1 harbor both somatic mutations and copy number alterations. Notch, RTK-RAS and Hippo pathways are frequently deregulated. Nevertheless, the relevance of the identified alterations, their role in signaling pathways or their association with HPV status remain elusive. Combined targeting of different pathways might represent a valid therapeutic approach in PSCC. This work calls for large-scale sequencing studies with robust HPV testing to improve the genomic understanding of PSCC.
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7
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Molecular Landscape of Vulvar Squamous Cell Carcinoma. Int J Mol Sci 2021; 22:ijms22137069. [PMID: 34209172 PMCID: PMC8269046 DOI: 10.3390/ijms22137069] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 02/06/2023] Open
Abstract
Vulvar squamous cell carcinoma (VSCC) is a rare malignancy with dual pathogenesis, Human papillomavirus (HPV)-associated and HPV-independent, with a poorly explored molecular landscape. We aimed to summarize the findings of the series analyzing molecular hallmarks of this neoplasm. In January 2021, we conducted a comprehensive literature search using Pubmed Medline and Scopus to identify publications focused on genomic profiling of VSCC. Observational studies, including both prospective and retrospective designs, evaluating molecular alterations in VSCC were deemed eligible. A total of 14 studies analyzing 749 VSCC were identified. The study series were heterogeneous in HPV testing and sequencing strategies, included small sets of tumors and cancer genes, and commonly lacked survival analysis. Only one extensive targeted next-generation sequencing-based study comprised a large cohort of 280 VSCC. The mutated genes, their number, and frequencies were highly variable between the series. Overall, TP53 and CDKN2A, followed by PIK3CA, HRAS, and PTEN, were the most frequently studied and mutated genes. Mutations involved in the PI3K/AKT/mTOR pathway, including TP53, HRAS, KRAS, and PIK3CA, have been consistently reported across the studies. However, the role of individual mutations or pathways in the development of VSCC remains unclear. In conclusion, heterogeneity and the small sample size of available molecular series contribute to a limited view of the molecular landscape of VSCC. Large-scale genome- or exome-wide studies with robust HPV testing are necessary to improve the molecular characterization of VSCC.
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8
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Molecular characterization of vulvar squamous cell cancer: High time to gain ground. Gynecol Oncol 2021; 158:519-520. [PMID: 32912480 DOI: 10.1016/j.ygyno.2020.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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NBPF1 independently determine the risk stratification and prognosis of patients with neuroblastoma. Genomics 2020; 112:3951-3957. [DOI: 10.1016/j.ygeno.2020.06.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 06/22/2020] [Indexed: 02/07/2023]
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10
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Prieske K, Alawi M, Oliveira-Ferrer L, Jaeger A, Eylmann K, Burandt E, Schmalfeldt B, Joosse SA, Woelber L. Genomic characterization of vulvar squamous cell carcinoma. Gynecol Oncol 2020; 158:547-554. [PMID: 32591094 DOI: 10.1016/j.ygyno.2020.06.482] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/08/2020] [Indexed: 11/25/2022]
Abstract
BACKGROUND Despite increasing incidence, vulvar squamous cell carcinoma (VSCC) is still a rare disease. Until now, two etiological pathways have been described: a high-risk human papillomavirus (HPV)-dependent route and an HPV-independent pathway often associated with lichen sclerosus. To date, therapeutic strategies in VSCC are not influenced by molecular pathological information and therapeutic options for advanced or recurrent disease are limited. METHODS Whole exome sequencing of DNA, isolated from 34 VSCC samples and matched normal tissue for each individual was performed on an Illumina HiSeq4000. Short variant discovery was carried out using BWA mem and FreeBayes. Variants were annotated using ANNOVAR. RESULTS FIGO stages were: IB (n = 7), II (n = 11), III (n = 8), and IVA (n = 3), (n = 5 unknown). TP53 missense mutations were most commonly detected with 56% (19/34). 12/34 (35.3%) samples were HPV positive (all HPV16), HPV positivity and TP53 mutations were mutually exclusive (p < .0001). Additionally, we observed mutations in known cancer relevant genes, like NBPF1 (n = 7), MACF1 (n = 5), SYNE2 (n = 5), DOCK2 (n = 4), KMT2D (n = 4), MAP2 (n = 4), NACA (n = 4), PIK3CA (n = 4), SYNE1 (n = 4), FBWX7 (n = 3), MSH6 (n = 3), NSD1 (n = 3), POLE (n = 3), TSC2, (n = 3) and CDKN2A (n = 2), but at considerably lower frequencies. For the total cohort 1848 cancer related mutations were detected (median of 54.4 per sample). CONCLUSIONS The key mutation in HPV negative vulvar carcinoma affects TP53. While a multitude of cancer related mutations was detected in various samples, only few mutations recur and/or affect concurrent signaling pathways.
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Affiliation(s)
- Katharina Prieske
- Department of Gynaecology and Gynaecologic Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Malik Alawi
- Bioinformatics Core Facility, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Leticia Oliveira-Ferrer
- Department of Gynaecology and Gynaecologic Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna Jaeger
- Department of Gynaecology and Gynaecologic Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kathrin Eylmann
- Department of Gynaecology and Gynaecologic Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Eike Burandt
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Barbara Schmalfeldt
- Department of Gynaecology and Gynaecologic Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Simon A Joosse
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Linn Woelber
- Department of Gynaecology and Gynaecologic Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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11
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Jiang N, Dai Q, Su X, Fu J, Feng X, Peng J. Role of PI3K/AKT pathway in cancer: the framework of malignant behavior. Mol Biol Rep 2020; 47:4587-4629. [PMID: 32333246 PMCID: PMC7295848 DOI: 10.1007/s11033-020-05435-1] [Citation(s) in RCA: 308] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/03/2020] [Indexed: 12/12/2022]
Abstract
Given that the PI3K/AKT pathway has manifested its compelling influence on multiple cellular process, we further review the roles of hyperactivation of PI3K/AKT pathway in various human cancers. We state the abnormalities of PI3K/AKT pathway in different cancers, which are closely related with tumorigenesis, proliferation, growth, apoptosis, invasion, metastasis, epithelial-mesenchymal transition, stem-like phenotype, immune microenvironment and drug resistance of cancer cells. In addition, we investigated the current clinical trials of inhibitors against PI3K/AKT pathway in cancers and found that the clinical efficacy of these inhibitors as monotherapy has so far been limited despite of the promising preclinical activity, which means combinations of targeted therapy may achieve better efficacies in cancers. In short, we hope to feature PI3K/AKT pathway in cancers to the clinic and bring the new promising to patients for targeted therapies.
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Affiliation(s)
- Ningni Jiang
- Department of Pathology, The Third Affiliated Hospital of Guangzhou Medical University, 63 Duobao Road, Guangzhou, 510150 China
- The Third Clinical School of Guangzhou Medical University, Guangzhou, 510150 China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, 510150 China
| | - Qijie Dai
- Department of Pathology, The Third Affiliated Hospital of Guangzhou Medical University, 63 Duobao Road, Guangzhou, 510150 China
- The Third Clinical School of Guangzhou Medical University, Guangzhou, 510150 China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, 510150 China
| | - Xiaorui Su
- Department of Pathology, The Third Affiliated Hospital of Guangzhou Medical University, 63 Duobao Road, Guangzhou, 510150 China
- The Third Clinical School of Guangzhou Medical University, Guangzhou, 510150 China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, 510150 China
| | - Jianjiang Fu
- Department of Pathology, The Third Affiliated Hospital of Guangzhou Medical University, 63 Duobao Road, Guangzhou, 510150 China
- The Third Clinical School of Guangzhou Medical University, Guangzhou, 510150 China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, 510150 China
| | - Xuancheng Feng
- Department of Pathology, The Third Affiliated Hospital of Guangzhou Medical University, 63 Duobao Road, Guangzhou, 510150 China
- The Third Clinical School of Guangzhou Medical University, Guangzhou, 510150 China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, 510150 China
| | - Juan Peng
- Department of Pathology, The Third Affiliated Hospital of Guangzhou Medical University, 63 Duobao Road, Guangzhou, 510150 China
- The Third Clinical School of Guangzhou Medical University, Guangzhou, 510150 China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, 510150 China
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
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12
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Ma R, Jing C, Zhang Y, Cao H, Liu S, Wang Z, Chen D, Zhang J, Wu Y, Wu J, Feng J. The somatic mutation landscape of Chinese Colorectal Cancer. J Cancer 2020; 11:1038-1046. [PMID: 31956350 PMCID: PMC6959081 DOI: 10.7150/jca.37017] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 10/27/2019] [Indexed: 01/01/2023] Open
Abstract
Colorectal cancer (CRC) is the fifth leading cause of cancer-related death in China. The incidence of Chinese CRC has increased dramatically with the changes of dietary and lifestyle. However, the genetic landscape of Chinese colorectal cancer mutation is still poorly understood. In this study, we have performed whole exome-sequencing analysis of 63 CRC cases. We found that Chinese CRC were hypermutated, which were enriched in ECM-receptor interaction, antigen processing and presentation, and focal adhesion. Analysis with clinical characteristics indicated that the deficiency of CRC driver gene, FCGBP and NBPF1 conferred CRC development and was showed worse survival rates, which could be the novel regulators and, diagnostic and prognostic biomarkers for Chinese CRC. Taken together, the application of whole exome-sequencing unveiled previously unsuspected somatic mutation landscape in Chinese CRCs, which may expand the understanding of disease mechanisms and provide an alternative personalized treatment for Chinese CRC patients.
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Affiliation(s)
- Rong Ma
- Clinical Cancer Research Center, Jiangsu Cancer Hospital &Jiangsu Institute of Cancer Research &The Affiliated Cancer Hospital of Nanjing Medical University, China
| | - Changwen Jing
- Clinical Cancer Research Center, Jiangsu Cancer Hospital &Jiangsu Institute of Cancer Research &The Affiliated Cancer Hospital of Nanjing Medical University, China
| | - Yuan Zhang
- Clinical Cancer Research Center, Jiangsu Cancer Hospital &Jiangsu Institute of Cancer Research &The Affiliated Cancer Hospital of Nanjing Medical University, China
| | - Haixia Cao
- Clinical Cancer Research Center, Jiangsu Cancer Hospital &Jiangsu Institute of Cancer Research &The Affiliated Cancer Hospital of Nanjing Medical University, China
| | - Siwen Liu
- Clinical Cancer Research Center, Jiangsu Cancer Hospital &Jiangsu Institute of Cancer Research &The Affiliated Cancer Hospital of Nanjing Medical University, China
| | - Zhuo Wang
- Clinical Cancer Research Center, Jiangsu Cancer Hospital &Jiangsu Institute of Cancer Research &The Affiliated Cancer Hospital of Nanjing Medical University, China
| | - Dan Chen
- Clinical Cancer Research Center, Jiangsu Cancer Hospital &Jiangsu Institute of Cancer Research &The Affiliated Cancer Hospital of Nanjing Medical University, China
| | - Junying Zhang
- Clinical Cancer Research Center, Jiangsu Cancer Hospital &Jiangsu Institute of Cancer Research &The Affiliated Cancer Hospital of Nanjing Medical University, China
| | - Yang Wu
- Clinical Cancer Research Center, Jiangsu Cancer Hospital &Jiangsu Institute of Cancer Research &The Affiliated Cancer Hospital of Nanjing Medical University, China
| | - Jianzhong Wu
- Clinical Cancer Research Center, Jiangsu Cancer Hospital &Jiangsu Institute of Cancer Research &The Affiliated Cancer Hospital of Nanjing Medical University, China
| | - Jifeng Feng
- Department of Chemotherapy, Jiangsu Cancer Hospital &Jiangsu Institute of Cancer Research &The Affiliated Cancer Hospital of Nanjing Medical University, China
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13
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Dash S, Kinney NA, Varghese RT, Garner HR, Feng WC, Anandakrishnan R. Differentiating between cancer and normal tissue samples using multi-hit combinations of genetic mutations. Sci Rep 2019; 9:1005. [PMID: 30700767 PMCID: PMC6353925 DOI: 10.1038/s41598-018-37835-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 12/14/2018] [Indexed: 01/06/2023] Open
Abstract
Cancer is known to result from a combination of a small number of genetic defects. However, the specific combinations of mutations responsible for the vast majority of cancers have not been identified. Current computational approaches focus on identifying driver genes and mutations. Although individually these mutations can increase the risk of cancer they do not result in cancer without additional mutations. We present a fundamentally different approach for identifying the cause of individual instances of cancer: we search for combinations of genes with carcinogenic mutations (multi-hit combinations) instead of individual driver genes or mutations. We developed an algorithm that identified a set of multi-hit combinations that differentiate between tumor and normal tissue samples with 91% sensitivity (95% Confidence Interval (CI) = 89-92%) and 93% specificity (95% CI = 91-94%) on average for seventeen cancer types. We then present an approach based on mutational profile that can be used to distinguish between driver and passenger mutations within these genes. These combinations, with experimental validation, can aid in better diagnosis, provide insights into the etiology of cancer, and provide a rational basis for designing targeted combination therapies.
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Affiliation(s)
- Sajal Dash
- Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
| | - Nicholas A Kinney
- Biomedical Sciences, Edward Via College of Osteopathic Medicine, Blacksburg, VA, USA
- Gibbs Cancer Center and Research Institute, Spartanburg, SC, USA
| | - Robin T Varghese
- Biomedical Sciences, Edward Via College of Osteopathic Medicine, Blacksburg, VA, USA
- Gibbs Cancer Center and Research Institute, Spartanburg, SC, USA
| | - Harold R Garner
- Biomedical Sciences, Edward Via College of Osteopathic Medicine, Blacksburg, VA, USA
- Gibbs Cancer Center and Research Institute, Spartanburg, SC, USA
| | - Wu-Chun Feng
- Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
- Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Ramu Anandakrishnan
- Biomedical Sciences, Edward Via College of Osteopathic Medicine, Blacksburg, VA, USA.
- Gibbs Cancer Center and Research Institute, Spartanburg, SC, USA.
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14
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Down-regulation of HPGD by miR-146b-3p promotes cervical cancer cell proliferation, migration and anchorage-independent growth through activation of STAT3 and AKT pathways. Cell Death Dis 2018; 9:1055. [PMID: 30333561 PMCID: PMC6192999 DOI: 10.1038/s41419-018-1059-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
While the application of early screening and HPV vaccines has reduced the incidence and mortality rates of cervical cancer, it remains the third most common carcinoma and fourth leading cause of cancer-associated death among women worldwide. The precise mechanisms underlying progression of cervical cancer are not fully understood at present. Here, we detected significant down-regulation of 15-hydroxyprostaglandin dehydrogenase (HPGD) in cervical cancer tissues. Overexpression of HPGD inhibited cervical cancer cell proliferation, migration and anchorage-independent growth to a significant extent. To clarify the mechanisms underlying HPGD down-regulation in cervical cancer, miRNA microarray, bioinformatics and luciferase reporter analyses were performed. HPGD was identified as a direct target of miR-146b-3p displaying up-regulation in cervical cancer tissues. Similar to the effects of HPGD overexpression, down-regulation of miR-146b-3p strongly suppressed proliferation, migration and anchorage-independent growth of cervical cancer cells. Furthermore, HPGD negatively regulated activities of STAT3 and AKT that promote cervical cancer cell proliferation. Notably, HPV oncogenes E6 and E7 were determined as potential contributory factors to these alterations. Our results collectively suggest that the HPGD/miR-146b-3p axis plays a significant role in cervical cancer and may serve as a potentially effective therapeutic target.
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15
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Sa JK, Lee IH, Hong SD, Kong DS, Nam DH. Genomic and transcriptomic characterization of skull base chordoma. Oncotarget 2018; 8:1321-1328. [PMID: 27901492 PMCID: PMC5352057 DOI: 10.18632/oncotarget.13616] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 11/08/2016] [Indexed: 11/25/2022] Open
Abstract
Skull base chordoma is a primary rare malignant bone-origin tumor showing relatively slow growth pattern and locally destructive lesions, which can only be characterized by histologic components. There is no available prognostic or therapeutic biomarker to predict clinical outcome or treatment response and the molecular mechanisms underlying chordoma development still remain unexplored. Therefore, we sought out to identify novel somatic variations that are associated with chordoma progression and potentially employed as therapeutic targets. Thirteen skull base chordomas were subjected for whole-exome and/or whole-transcriptome sequencing. In process, we have identified chromosomal aberration in 1p, 7, 10, 13 and 17q, high frequency of functional germline SNP of the T gene, rs2305089 (P = 0.0038) and several recurrent alterations including MUC4, NBPF1, NPIPB15 mutations and novel gene fusion of SAMD5-SASH1 for the first time in skull base chordoma.
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Affiliation(s)
- Jason K Sa
- Graduate School of Health Science & Technology, Samsung Advanced Institute for Health Science & Technology (SAIHST), Sungkyunkwan University, Seoul, Korea.,Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea.,Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Korea
| | - In-Hee Lee
- Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea.,Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Korea
| | - Sang Duk Hong
- Department of Otorhinolaryngology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Doo-Sik Kong
- Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea.,Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Korea.,Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Do-Hyun Nam
- Graduate School of Health Science & Technology, Samsung Advanced Institute for Health Science & Technology (SAIHST), Sungkyunkwan University, Seoul, Korea.,Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea.,Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Korea.,Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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