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Ahmadi M, Najari-Hanjani P, Ghaffarnia R, Ghaderian SMH, Mousavi P, Ghafouri-Fard S. The hsa-miR-3613-5p, a potential oncogene correlated with diagnostic and prognostic merits in kidney renal clear cell carcinoma. Pathol Res Pract 2023; 251:154903. [PMID: 37879147 DOI: 10.1016/j.prp.2023.154903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 10/14/2023] [Accepted: 10/20/2023] [Indexed: 10/27/2023]
Abstract
MicroRNA-3613 (hsa-miR-3613-5p), a biomarker with a dual role as an oncogenic or tumor suppressor, is associated with different types of cancer. This study aimed to determine the correlation between the hsa-miR-3613-5p gene expression and Kidney renal clear cell carcinoma (KIRC). Utilizing several bioinformatics tools, we examined the expression level and clinicopathological value of hsa-miR-3613-5p in patients with KIRC compared to normal tissues. Other bioinformatic measures, including survival analysis, diagnostic merit of hsa-miR-3613-5p, downstream target prediction, potential upstream lncRNAs, network construction, and functional enrichment analysis of hsa-miR-3613-5p, were performed. We observed that overexpression of hsa-miR-3613-5p in KIRC tissues had valuable diagnostic merit and was significantly correlated with the poor overall survival of KIRC patients. We also realized a correlation between abnormal expression of hsa-miR-3613-5p and several clinical parameters such as pathological stage, race, age, and histological grades in patients with KIRC. Moreover, we constructed the most potential regulatory network of hsa-miR-3613-5p in KIRC with 17 different axes, including four pseudogenes, two lncRNAs, and three mRNAs. Besides, we uncovered six variants in the mature form of hsa-miR-3613-5p. Finally, pathway enrichment analysis demonstrated that the top-ranked pathways for hsa-miR-3613-5p are cell cycle, cell adhesion molecules (CAMs), and hepatocellular carcinoma pathways. The present report suggests that the higher expression of hsa-miR-3613-5p is associated with the progression of KIRC. Therefore, it may be considered a valuable indicator for the early detection, risk stratification, and targeted treatment of patients with KIRC.
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Affiliation(s)
- Mohsen Ahmadi
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parisa Najari-Hanjani
- Department of Genetics, Faculty of Advanced Technologies in Medicine, Golestan University of Medical Science, Gorgan, Iran
| | - Roya Ghaffarnia
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Pegah Mousavi
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Li Y, Guo Y, Cheng Z, Tian C, Chen Y, Chen R, Yu F, Shi Y, Su F, Zhao S, Wang Z, Luo J, Tan H. Whole-exome sequencing of rectal neuroendocrine tumors. Endocr Relat Cancer 2023; 30:e220257. [PMID: 36645718 PMCID: PMC10450454 DOI: 10.1530/erc-22-0257] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 01/13/2023] [Indexed: 01/17/2023]
Abstract
The genetic characteristics of rectal neuroendocrine tumors (R-NETs) were poorly understood. Depicting the genetic characteristics may provide a biological basis for prognosis prediction and novel treatment development. Tissues of 18 R-NET patients were analyzed using whole-exome sequencing. The median tumor mutation burden (TMB) and microsatellite instability (MSI) were 1.15 Muts/MB (range, 0.03-23.28) and 0.36 (range, 0.00-10.97), respectively. Genes involved in P53 signaling, PI3K-AKT signaling, DNA damage repair, WNT signaling, etc. were frequently altered. Higher TMB (P = 0.078), higher CNV (P = 0.110), somatic mutation of CCDC168 (P = 0.049), HMCN1 (P = 0.040), MYO10 (P = 0.007), and amplification of ZC3H13 (P < 0.001) were associated with shorter OS. Potentially targetable gene alterations (PTGAs) were seen in 72% of the patients. FGFR1 amplification (22%) was the most common PTGA followed by BARD1 and BRCA2 mutation (each 17%). As for gene variations associated with the efficacy of immune checkpoint blockade (ICB), FAT1 alteration (39%) and PTEN depletion (28%) were commonly observed. In conclusion, frequently altered oncogenic pathways might contribute to the development and progression of R-NETs. Gene alterations significantly associated with prognosis might be potential novel targets. Targeted therapy might be a promising strategy as targetable alterations were prevalent in R-NETs. FAT1 alteration and PTEN depletion might be the main genetic alterations influencing the response to ICB besides overall low TMB and MSI in R-NETs.
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Affiliation(s)
- Yuanliang Li
- Department of Integrative Oncology, China-Japan Friendship Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Yiying Guo
- Department of Integrative Oncology, China-Japan Friendship Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zixuan Cheng
- Department of Integrative Oncology, China-Japan Friendship Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Chao Tian
- Department of Integrative Oncology, China-Japan Friendship Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Yingying Chen
- Department of Integrative Oncology, China-Japan Friendship Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Ruao Chen
- Department of Integrative Oncology, China-Japan Friendship Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Fuhuan Yu
- Department of Integrative Oncology, China-Japan Friendship Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Yanfen Shi
- Department of Pathology, China-Japan Friendship Hospital, Beijing, China
| | - Fei Su
- Department of Integrative Oncology, China-Japan Friendship Hospital, Beijing, China
| | - Shuhua Zhao
- Department of Biological Information Research, HaploX Biotechnology Co., Ltd, Shenzhen, Guangdong, China
| | - Zhizheng Wang
- Academic Department, HaploX Biotechnology, Co., Ltd, Shenzhen, Guangdong, China
| | - Jie Luo
- Department of Pathology, China-Japan Friendship Hospital, Beijing, China
| | - Huangying Tan
- Department of Integrative Oncology, China-Japan Friendship Hospital, Beijing University of Chinese Medicine, Beijing, China
- Department of Integrative Oncology, China-Japan Friendship Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Department of Integrative Oncology, China-Japan Friendship Hospital, Beijing, China
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Xiang S, Wei M, Zhao L, Lin A, Xiong Z. Integrated Analyses of the Expression and Prognostic Value of EPHB6 in Cervical Cancer and Its Correlation with Immune Infiltrates. JOURNAL OF ONCOLOGY 2023; 2023:2258906. [PMID: 37101747 PMCID: PMC10125771 DOI: 10.1155/2023/2258906] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/26/2022] [Accepted: 03/20/2023] [Indexed: 04/28/2023]
Abstract
Among women, cervical cancer (CC) ranks as the third most frequent form of carcinoma and the fourth greatest cancer-related cause of deaths. There is increasing evidence that points to the dysregulation of EPH receptor B6 (EPHB6) in various cancers. On the other hand, neither the expression nor the function of EPHB6 in CC has been researched. In the first part of this investigation, we analyzed the data from the TCGA and discovered that the level of EPHB6 was much lower in CC tissues than in normal cervical tissues. ROC assays revealed that high EPHB6 expression had an AUC value of 0.835 for CC. The survival study revealed that both the overall and disease-specific survivals in this condition were considerably lower among patients who had a low EPHB6 level compared to those who had a high EPHB6 level. It is important to note that the multivariate COX regression analysis indicated that the expression of EPHB6 was an independent predictive factor. In addition to this, the C-indexes and calibration plots of a nomogram derived from multivariate assays revealed an accurate prediction performance among patients with CC. Immune infiltration analysis indicated that the expression of EPHB6 was positively associated with the levels of Tcm, TReg, B cells, T cells, iDC, T helper cells, cytotoxic cells, and DC, while negatively associated with NK CD56bright cells and neutrophils. In summary, the downregulation of EPHB6 was strongly linked to a more aggressive clinical development of CC, suggesting its potential utility as a diagnostic and therapeutic target in CC.
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Affiliation(s)
- Siyang Xiang
- Department of Obstetrics and Gynecology, Chongqing Medical University, Chongqing, China
- Department of Gynaecology, The First People's Hospital of Chongqing Liangjiang New District, Chongqing, China
| | - Mei Wei
- Department of Obstetrics and Gynecology, Chongqing Medical University, Chongqing, China
- Department of Gynaecology, The First People's Hospital of Chongqing Liangjiang New District, Chongqing, China
| | - Limei Zhao
- Department of Gynaecology, The First People's Hospital of Chongqing Liangjiang New District, Chongqing, China
| | - Anping Lin
- Department of Obstetrics and Gynecology, Chongqing Medical University, Chongqing, China
| | - Zhengai Xiong
- Department of Obstetrics and Gynecology, Chongqing Medical University, Chongqing, China
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Husile H, Wu Z, Yang L, Cao Y, Wu Q. Identification of a HOXD13 variant in a Mongolian family with incomplete penetrance syndactyly by exon sequencing. BMC Med Genomics 2022; 15:210. [PMID: 36195906 PMCID: PMC9533607 DOI: 10.1186/s12920-022-01360-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/19/2022] [Indexed: 11/10/2022] Open
Abstract
Background Syndactyly (SD) refers to a deformity caused by the fusion and limb differentiation disorder of soft tissues and/or skeletons to varying extents between adjacent fingers (toes). The main features of this disease are phenotypic heterogeneity and genetic heterogeneity. In this study, we examined four generations of a Chinese Mongolian with different phenotypes of syndactylia and analysed and identified the pathogenic genetic variants of SD by exon sequencing. Methods The clinical phenotypes of patients were analysed, and the hands and feet were examined by X-ray. The pedigree was drawn, and the family data were analysed. Peripheral blood was collected from the family members, and genomic DNA was extracted. The candidate genes of SD were identified by exon sequencing, and the mutation sites of the captured candidate genes were amplified by PCR and verified by Sanger sequencing. Results The family has congenital syndactyly, which is an autosomal dominant disease. At present, this condition has been passed down for 4 generations and was identified in 9 patients, including 4 males and 5 females. Five patients, I2, II4, III5, III,7 and III10, had unilateral syndactyly, and four patients, III16, IV3, IV6 and IV7, had bilateral finger syndactyly. All of their toes were unaffected. The proband and the other patients in this family had a c.917G > A (p.R306Q) mutation, which is located at position 917 of the second exon of the HOXD13 gene. This mutation results in a change in the amino acid at position 306, in which arginine is changed to glutamine. This mutation cosegregates in unaffected individuals and affected patients in this family. Moreover, 201 Mongolian genome databases and a thousand human genome databases were referenced to further confirm that the pathogenic genetic variant that causes syndactyly in this family is found in HOXD13. Conclusion This study found that the mutation site of the pathogenic gene in this family was HOXD13, c.917G > A (p.R306Q). The phenotype of the family member III12 was normal, but this member was also a carrier of the pathogenic genetic variant. This indicates that the disease of this family has incomplete penetrance characteristics. Our results further enrich the expression profile of the HOXD13 gene. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01360-3.
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Affiliation(s)
- Husile Husile
- Affiliated Hospital of Inner Mongolia Minzu University, 028000, Tongliao, China.,Inner Mongolia Engineneering and Technical Research Center for personalized Medicine, 028000, Tongliao, China
| | - Zhifeng Wu
- Inner Mongolia Engineneering and Technical Research Center for personalized Medicine, 028000, Tongliao, China.,College of Life Sciences and Food Engineering, Inner Mongolia Minzu University, 028000, Tongliao, China
| | - Liqing Yang
- Affiliated Hospital of Inner Mongolia Minzu University, 028000, Tongliao, China.,Inner Mongolia Engineneering and Technical Research Center for personalized Medicine, 028000, Tongliao, China
| | - Yaning Cao
- School Of Life Sciences, Inner Mongolia University, 010000, Hohhot, China
| | - Qizhu Wu
- Affiliated Hospital of Inner Mongolia Minzu University, 028000, Tongliao, China. .,Inner Mongolia Engineneering and Technical Research Center for personalized Medicine, 028000, Tongliao, China.
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Ou H, Wang L, Xi Z, Shen H, Jiang Y, Zhou F, Liu Y, Zhou Y. MYO10 contributes to the malignant phenotypes of colorectal cancer via RACK1 by activating integrin/Src/FAK signaling. Cancer Sci 2022; 113:3838-3851. [PMID: 35912545 DOI: 10.1111/cas.15519] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/13/2022] [Accepted: 07/20/2022] [Indexed: 11/28/2022] Open
Abstract
Liver metastases still remain a major cause of colorectal cancer (CRC) patient death. MYO10 is upregulated in several tumor types, however, its significance and the underlying mechanism in CRC is not entirely clear. Here we found that MYO10 was highly expressed in CRC tumor tissues, especially in liver metastasis tissues. MYO10 knockout reduced CRC cell proliferation, invasion, and migration in vitro, and CRC metastasis in vivo. We identified RACK1 by LC-MS/MS and demonstrated that MYO10 interacts with and stabilizes RACK1. Mechanistically, MYO10 promotes CRC cell progression and metastasis via ubiquitination-mediated RACK1 degradation and integrin/Src/FAK signaling activation. Therefore, the MYO10/RACK1/integrin/Src/FAK axis may play an important role in CRC progression and metastasis.
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Affiliation(s)
- Haibin Ou
- Department of Radiation and Medical Oncology, Zhongnan Hospital, Wuhan University, Wuhan, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Lili Wang
- Department of Radiation and Medical Oncology, Zhongnan Hospital, Wuhan University, Wuhan, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Ziyao Xi
- Department of Radiation and Medical Oncology, Zhongnan Hospital, Wuhan University, Wuhan, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Hui Shen
- Department of Radiation and Medical Oncology, Zhongnan Hospital, Wuhan University, Wuhan, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Yaofei Jiang
- Department of Radiation and Medical Oncology, Zhongnan Hospital, Wuhan University, Wuhan, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Fuxiang Zhou
- Department of Radiation and Medical Oncology, Zhongnan Hospital, Wuhan University, Wuhan, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Yu Liu
- Department of Radiation and Medical Oncology, Zhongnan Hospital, Wuhan University, Wuhan, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Yunfeng Zhou
- Department of Radiation and Medical Oncology, Zhongnan Hospital, Wuhan University, Wuhan, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital, Wuhan University, Wuhan, China
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