1
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Ariffin NS. Increased RUNX1 mutations in breast cancer disease progression. Pathol Res Pract 2024; 254:155076. [PMID: 38219493 DOI: 10.1016/j.prp.2023.155076] [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: 09/07/2023] [Revised: 12/29/2023] [Accepted: 12/30/2023] [Indexed: 01/16/2024]
Abstract
Despite advances in screening, therapy and surveillance, breast cancer remains threatening to women. Worst, patients suffer from side effects of treatments and cancer cells become resistant. The emergence of RUNX1 in breast cancer has put it in a spotlight due to its roles in the disease progression. It also plays important roles in normal mammary glands such as for cell growth, proliferation, migration and stemness. However, mutations in the RUNX1 gene have changed the regulation of these phenotypes and the full spectrum of its implications in breast cancer patients is unknown. In this study therefore, the pattern of RUNX1 mutations in breast cancer patients was examined to understand its fundamental impacts on the disease. The perturbation of RUNX1 and its mutations in breast cancer was elucidated through different studies reported in cBioPortal in the past ten years. From our analyses, the majority of RUNX1 mutations were found in the primary breast cancer, with women constituted most of the mutations, especially on the left side of the breast. Similarly, increased number of mutations was observed in ER-positive breast cancer patients and this was also the case at the early stage of the disease development. The level of RUNX1 mutations also increased gradually as patients got older and the peak was highest in the patients of 60-70 years old. Altogether, these data indicated that the mutated RUNX1 gene contributed to the progression of breast cancer and understanding of its regulatory mechanisms is crucial to therapeutically target this gene in the future.
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Affiliation(s)
- Nur Syamimi Ariffin
- Department of Pharmacology and Pharmaceutical Chemistry, Faculty of Pharmacy, Universiti Teknologi MARA, 42300 Bandar Puncak Alam, Selangor, Malaysia.
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2
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He J, Ding Y, Lin H, Liu X, Chen X, Shen W, Zhou S, Feng C, Wang M, Xia J, He N. Differential genome-wide associated variants and enriched pathways of ECG parameters among people with versus without HIV. AIDS 2023; 37:1871-1882. [PMID: 37418550 PMCID: PMC10481915 DOI: 10.1097/qad.0000000000003647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 07/09/2023]
Abstract
OBJECTIVES People with HIV (PWH) are more likely to develop ECG abnormalities. Substantial evidence exists for genetic contribution to ECG parameters among general population. However, whether and how would host genome associate with ECG parameters among PWH is unclear. Our research aims to analyze and compare genetic variants, mapped genes, and enriched pathways of ECG parameters among PWH and HIV-negative controls. DESIGN A cross-sectional study. METHOD We performed a large original genome-wide association study (GWAS) of ECG parameters among PWH ( n = 1730) and HIV-negative controls ( n = 3746). Genome-wide interaction analyses were also conducted. RESULTS A total of 18 novel variants were detected among PWH, six for PR interval including rs76345397 at ATL2 , 11 for QRS duration including rs10483994 at KCNK10 and rs2478830 at JCAD , and one for QTc interval (rs9815364). Among HIV-negative controls, we identified variants located at previously reported ECG-related genes ( SCN5A , CNOT1 ). Genetic variants had a significant interaction with HIV infection ( P < 5 × 10 -8 ), implying that HIV infection and host genome might jointly influence ECG parameters. Mapped genes for PR interval and QRS duration among PWH were enriched in the biological process of viral genome replication and host response to virus, respectively, whereas enriched pathways for PR interval among HIV-negative controls were in the cellular component of voltage-gated sodium channel complex. CONCLUSION The present GWAS indicated a distinctive impact of host genome on quantitative ECG parameters among PWH. Different from HIV-negative controls, host genome might influence the cardiac electrical activity by interfering with HIV viral infection, production, and latency among PWH.
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Affiliation(s)
- Jiayu He
- Department of Epidemiology, School of Public Health, and Key Laboratory of Public Health Safety of Ministry of Education
- Yi-Wu Research Institute
- Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai
| | - Yingying Ding
- Department of Epidemiology, School of Public Health, and Key Laboratory of Public Health Safety of Ministry of Education
- Yi-Wu Research Institute
| | - Haijiang Lin
- Department of Epidemiology, School of Public Health, and Key Laboratory of Public Health Safety of Ministry of Education
- Taizhou City Center for Disease Control and Prevention, Zhejiang Province, China
| | - Xing Liu
- Department of Epidemiology, School of Public Health, and Key Laboratory of Public Health Safety of Ministry of Education
- Yi-Wu Research Institute
| | - Xiaoxiao Chen
- Department of Epidemiology, School of Public Health, and Key Laboratory of Public Health Safety of Ministry of Education
- Taizhou City Center for Disease Control and Prevention, Zhejiang Province, China
| | - Weiwei Shen
- Taizhou City Center for Disease Control and Prevention, Zhejiang Province, China
| | - Sujuan Zhou
- Department of Epidemiology, School of Public Health, and Key Laboratory of Public Health Safety of Ministry of Education
- Yi-Wu Research Institute
- Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai
| | - Cheng Feng
- Department of Epidemiology, School of Public Health, and Key Laboratory of Public Health Safety of Ministry of Education
- Yi-Wu Research Institute
| | - Miaochen Wang
- Department of Epidemiology, School of Public Health, and Key Laboratory of Public Health Safety of Ministry of Education
- Yi-Wu Research Institute
| | - Jingjing Xia
- Department of Epidemiology, School of Public Health, and Key Laboratory of Public Health Safety of Ministry of Education
- Yi-Wu Research Institute
| | - Na He
- Department of Epidemiology, School of Public Health, and Key Laboratory of Public Health Safety of Ministry of Education
- Yi-Wu Research Institute
- Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai
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3
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Li L, Tianrui K, Chunlei L, Zhendong Q, Xiaoyan C, Wenhong D. HYDIN mutation status as a potential predictor of immune checkpoint inhibitor efficacy in melanoma. Aging (Albany NY) 2023; 15:7997-8012. [PMID: 37595251 PMCID: PMC10496993 DOI: 10.18632/aging.204925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 07/10/2023] [Indexed: 08/20/2023]
Abstract
BACKGROUND The advent of immune checkpoint inhibitors (ICIs) has altered the outlook for cancer treatment. The estimation of predictive biomarkers could contribute to maximizing the benefits from ICIs treatment. Here, we explored the association between HYDIN mutations (HYDIN-MUT) in melanoma and ICIs efficacy. METHODS Clinical data and sequencing data from published studies were utilized to assess the association between HYDIN-MUT and the efficacy of ICIs treatment in melanoma patients. RESULTS Compared to other tumor types, HYDIN (36.14%) has the highest mutation rate in melanoma patients. In the anti-PD-1 treated cohort (n = 254), the HYDIN-MUT patients had a longer OS after ICIs treatment than the HYDIN wild-type (HYDIN-WT) patients (HR = 0.590 [95% CI, 0.410-0.847], P = 0.004); the objective response rate (ORR) and durable clinical benefit (DCB) were increased in patients with HYDIN-MUT (ORR = 46.25, DCB = 56.00%) compared to patients with HYDIN-WT (ORR = 30.99%, DCB = 42.76%) (ORR: P = 0.019; DCB: P = 0.060). In the anti-CTLA4 treated cohort (n = 174), HYDIN-MUT patients achieved significantly longer OS than HYDIN-WT patients (HR = 0.549 [95% CI, 0.366-0.823], P = 0.003); the proportion of ORR and DCB in HYDIN-MUT patients was significantly higher than that in HYDIN-WT patients (ORR 40.54% vs. 14.42%, P = 0.031; DCB 45.76% vs. 22.22%, P = 0.002). Further gene set enrichment analysis demonstrated that DNA repair and anti-tumor immunity were significantly enhanced in HYDIN-MUT patients. CONCLUSIONS HYDIN mutations are a potential predictive biomarker of ICIs efficacy in melanoma patients.
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Affiliation(s)
- Liu Li
- Department of General Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Kuang Tianrui
- Department of General Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Li Chunlei
- Department of General Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Qiu Zhendong
- Department of General Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Chen Xiaoyan
- Department of General Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Deng Wenhong
- Department of General Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
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4
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Battistella E, Vakalopoulou M, Sun R, Estienne T, Lerousseau M, Nikolaev S, Andres EA, Carre A, Niyoteka S, Robert C, Paragios N, Deutsch E. COMBING: Clustering in Oncology for Mathematical and Biological Identification of Novel Gene Signatures. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:3317-3331. [PMID: 34714749 DOI: 10.1109/tcbb.2021.3123910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Precision medicine is a paradigm shift in healthcare relying heavily on genomics data. However, the complexity of biological interactions, the large number of genes as well as the lack of comparisons on the analysis of data, remain a tremendous bottleneck regarding clinical adoption. In this paper, we introduce a novel, automatic and unsupervised framework to discover low-dimensional gene biomarkers. Our method is based on the LP-Stability algorithm, a high dimensional center-based unsupervised clustering algorithm. It offers modularity as concerns metric functions and scalability, while being able to automatically determine the best number of clusters. Our evaluation includes both mathematical and biological criteria to define a quantitative metric. The recovered signature is applied to a variety of biological tasks, including screening of biological pathways and functions, and characterization relevance on tumor types and subtypes. Quantitative comparisons among different distance metrics, commonly used clustering methods and a referential gene signature used in the literature, confirm state of the art performance of our approach. In particular, our signature, based on 27 genes, reports at least 30 times better mathematical significance (average Dunn's Index) and 25% better biological significance (average Enrichment in Protein-Protein Interaction) than those produced by other referential clustering methods. Finally, our signature reports promising results on distinguishing immune inflammatory and immune desert tumors, while reporting a high balanced accuracy of 92% on tumor types classification and averaged balanced accuracy of 68% on tumor subtypes classification, which represents, respectively 7% and 9% higher performance compared to the referential signature.
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5
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BenAyed-Guerfali D, Kifagi C, BenKridis-Rejeb W, Ammous-Boukhris N, Ayedi W, Khanfir A, Daoud J, Mokdad-Gargouri R. The Identification by Exome Sequencing of Candidate Genes in BRCA-Negative Tunisian Patients at a High Risk of Hereditary Breast/Ovarian Cancer. Genes (Basel) 2022; 13:genes13081296. [PMID: 35893033 PMCID: PMC9331434 DOI: 10.3390/genes13081296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/16/2022] [Accepted: 07/19/2022] [Indexed: 12/24/2022] Open
Abstract
(1) Background: Germline variants in BRCA1/BRCA2 genes explain about 20% of hereditary breast/ovarian cancer (HBOC) cases. In the present paper, we aim to identify genetic determinants in BRCA-negative families from the South of Tunisia. (2) Methods: Exome Sequencing (ES) was performed on the lymphocyte DNA of patients negative for BRCA mutations from each Tunisian family with a high risk of HBOC. (3) Results: We focus on the canonical genes associated with HBOC and identified missense variants in DNA damage response genes, such as ATM, RAD52, and RAD54; however, no variants in PALB2, Chek2, and TP53 genes were found. To identify novel candidate genes, we selected variants harboring a loss of function and identified 17 stop-gain and 11 frameshift variants in genes not commonly known to be predisposed to HBOC. Then, we focus on rare and high-impact genes shared by at least 3 unrelated patients from each family and selected 16 gene variants. Through combined data analysis from MCODE with gene ontology and KEGG pathways, a short list of eight candidate genes (ATM, EP300, LAMA1, LAMC2, TNNI3, MYLK, COL11A2, and LAMB3) was created. The impact of the 24 selected genes on survival was analyzed using the TCGA data resulting in a selection of five candidate genes (EP300, KMT2C, RHPN2, HSPG2, and CCR3) that showed a significant association with survival. (4) Conclusions: We identify novel candidate genes predisposed to HBOC that need to be validated in larger cohorts and investigated by analyzing the co-segregation of selected variants in affected families and the locus-specific loss of heterozygosity to highlight their relevance for HBOC risk.
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Affiliation(s)
- Dorra BenAyed-Guerfali
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, Sfax 3038, Tunisia; (D.B.-G.); (C.K.); (N.A.-B.); (W.A.)
| | - Chamseddine Kifagi
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, Sfax 3038, Tunisia; (D.B.-G.); (C.K.); (N.A.-B.); (W.A.)
| | - Wala BenKridis-Rejeb
- Department of Medical Oncology, Habib Bourguiba Hospital, Sfax 3002, Tunisia; (W.B.-R.); (A.K.)
| | - Nihel Ammous-Boukhris
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, Sfax 3038, Tunisia; (D.B.-G.); (C.K.); (N.A.-B.); (W.A.)
| | - Wajdi Ayedi
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, Sfax 3038, Tunisia; (D.B.-G.); (C.K.); (N.A.-B.); (W.A.)
| | - Afef Khanfir
- Department of Medical Oncology, Habib Bourguiba Hospital, Sfax 3002, Tunisia; (W.B.-R.); (A.K.)
| | - Jamel Daoud
- Department of Radiotherapy, Habib Bourguiba Hospital, Sfax 3002, Tunisia;
| | - Raja Mokdad-Gargouri
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, Sfax 3038, Tunisia; (D.B.-G.); (C.K.); (N.A.-B.); (W.A.)
- Correspondence: ; Tel./Fax: +216-748-744-49
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6
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Sun J, Liu Z, Quan J, Li L, Zhao G, Lu J. RNA-seq Analysis Reveals Alternative Splicing Under Heat Stress in Rainbow Trout (Oncorhynchus mykiss). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:5-17. [PMID: 34787764 DOI: 10.1007/s10126-021-10082-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 11/03/2021] [Indexed: 06/13/2023]
Abstract
Rainbow trout (Oncorhynchus mykiss) is one of the most economically important cold-water farmed species in the world, and transcriptomic studies in response to heat stress have been conducted and will be studied in depth. Alternative splicing (AS), a post-transcriptional regulatory process that regulates gene expression and increases proteomic diversity, is still poorly understood in rainbow trout under heat stress. In the present study, 18,623 alternative splicing events were identified from 9936 genes using RNA transcriptome sequencing technology (RNA-Seq) and genomic information. A total of 2731 differential alternative splicing (DAS) events were found among 2179 differentially expressed genes (DEGs). Gene ontology analysis revealed that the DEGs were mainly enriched in cellular metabolic process, cell part, and organic cyclic compound binding under heat stress. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis displayed that the DEGs were enriched for 39 pathways, and some key pathways, such as lysine degradation, are involved in the regulation of heat stress in liver tissues of rainbow trout. The results were validated by qRT-PCR, confirming reliability of our bioinformatics analysis.
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Affiliation(s)
- Jun Sun
- College of Animal Science & Technology, Gansu Province, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou, 730070, People's Republic of China
| | - Zhe Liu
- College of Animal Science & Technology, Gansu Province, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou, 730070, People's Republic of China.
| | - Jinqiang Quan
- College of Animal Science & Technology, Gansu Province, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou, 730070, People's Republic of China
| | - Lanlan Li
- College of Animal Science & Technology, Gansu Province, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou, 730070, People's Republic of China
| | - Guiyan Zhao
- College of Animal Science & Technology, Gansu Province, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou, 730070, People's Republic of China
| | - Junhao Lu
- College of Animal Science & Technology, Gansu Province, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou, 730070, People's Republic of China
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7
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Zhu W, Zhang J, Yuan X, Liu X, Zhang Z, Mao Y, Feng Y, Yue A, Sun J, Wen C, Xu J, Shen Y, Che Y, Du J. Whole-exome sequencing reveals novel candidate single nucleotide variations for preventing adverse effects of levonorgestrel implantation. Pharmacogenomics 2021; 22:1185-1199. [PMID: 34783250 DOI: 10.2217/pgs-2021-0105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To identify novel genes associated with adverse effects of levonorgestrel (LNG) implants based on comparative whole-exome sequencing. Materials & methods: A cohort comprising 104 participants, including 52 controls and 52 women with LNG-related adverse effects, was recruited. Seven cases and eight controls were selected for whole-exome sequencing. We verified 13 single nucleotide variations (SNVs) related with integrin-mediated signaling pathway and cell proliferation using the MassARRAY platform. Results: Finally, we screened 49 cases and 52 controls for analyses. Two SNVs (rs7255721 and rs1042522) were located in ADAMTS10 and TP53, respectively, and significantly different between two groups. These two SNVs lead to changes in protein structure and physicochemical parameters. Conclusion: Here, we defined two pathogenic mutations related to adverse LNG effects.
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Affiliation(s)
- Weiqiang Zhu
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical & Pharmaceutical Technologies), Medical School, Fudan University, Shanghai 200032, China
| | - Junxian Zhang
- Department of Family Planning, Maternal & Child Health Care Hospital of Xinjiang Uygur Autonomous Region, Xinjiang 830001, China
| | - Xuelian Yuan
- Hami Central Hospital, Xinjiang Medical University, Xinjiang 830099, China
| | - Xiaoli Liu
- Chongqing Health Center for Women & Children, Chongqing 400010, China
| | - Zhaofeng Zhang
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical & Pharmaceutical Technologies), Medical School, Fudan University, Shanghai 200032, China
| | - Yanyan Mao
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical & Pharmaceutical Technologies), Medical School, Fudan University, Shanghai 200032, China
| | - Ying Feng
- Department of Family Planning, Maternal & Child Health Care Hospital of Xinjiang Uygur Autonomous Region, Xinjiang 830001, China
| | - Ailing Yue
- Hami Central Hospital, Xinjiang Medical University, Xinjiang 830099, China
| | - Junjie Sun
- Chongqing Health Center for Women & Children, Chongqing 400010, China
| | - Chuan Wen
- Hami Central Hospital, Xinjiang Medical University, Xinjiang 830099, China
| | - Jianhua Xu
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical & Pharmaceutical Technologies), Medical School, Fudan University, Shanghai 200032, China
| | - Yupei Shen
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical & Pharmaceutical Technologies), Medical School, Fudan University, Shanghai 200032, China
| | - Yan Che
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical & Pharmaceutical Technologies), Medical School, Fudan University, Shanghai 200032, China
| | - Jing Du
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical & Pharmaceutical Technologies), Medical School, Fudan University, Shanghai 200032, China
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8
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Zhang B, Li Y, Yang L, Chen Y. A Four-Gene-Based Risk Score With High Prognostic Value in Gastric Cancer. Front Oncol 2021; 11:584213. [PMID: 34540650 PMCID: PMC8443773 DOI: 10.3389/fonc.2021.584213] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 08/06/2021] [Indexed: 11/13/2022] Open
Abstract
Background Gastric adenocarcinoma is an important contributor to cancer mortality and morbidity. This study aimed to explore the prognostic value of mutation patterns in gastric adenocarcinoma. Materials and Methods We extracted somatic mutation data for 437 gastric adenocarcinoma samples from The Cancer Genome Atlas (TCGA) Stomach Adenocarcinoma (STAD) cohort. Kaplan-Meier survival in the R package maftools was used to analyze associations between mutations and survival. Multivariate Cox proportional model was used to establish risk formula. A four-gene-based risk score was developed to predict the overall survival of patients with gastric adenocarcinoma. We used the Tianjin cohort dataset with survival information to further evaluate the clinical value of this mutation signature. Results Forty-five survival-related mutated genes were identified and verified, most of which were co-occurring in their mutation pattern and co-occurring with MLH3 and polymerase ϵ (POLE) mutations. Gastric adenocarcinoma samples with the 45 mutated genes had a significantly higher mutation count. Four-gene [UTRN, MUC16, coiled-coil domain-containing protein 178 (CCDC178), and HYDIN] mutation status was used to build a prognostic risk score that could be translated into the clinical setting. The association between the four-gene-based signature and overall survival remained statistically significant after controlling for age, sex, TNM stage, and POLE mutation status in the multivariate model [hazard ratio (HR), 1.88; 95% CI, 1.33-2.7; p < 0.001]. The prognostic significance of the four-gene-based risk score identified in TCGA cohort was validated in the Tianjin cohort. Conclusion A four-mutated gene risk formula was developed that correlated with the overall survival of patients with gastric adenocarcinoma using a multivariable Cox regression model. In two independent genomic datasets from TCGA and Tianjin cohorts, low risk scores were associated with higher tumor mutation loads and improved outcome in patients with gastric adenocarcinoma. This finding may have implications for prognostic prediction and therapeutic guidance for gastric adenocarcinoma.
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Affiliation(s)
- Bingdong Zhang
- Department of Gastrointestinal Surgery & Department of Clinical Nutrition, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Yuerui Li
- Geriatric Cardiology Department of The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese People's Liberation Army of China General Hospital, Beijing, China
| | - Liu Yang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, School of Medicine, Tsinghua University, Beijing, China
| | - Yongbing Chen
- Department of Gastrointestinal Surgery & Department of Clinical Nutrition, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
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9
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Zhang YF, Wang YX, Zhang N, Lin ZH, Wang LR, Feng Y, Pan Q, Wang L. Prognostic alternative splicing regulatory network of RBM25 in hepatocellular carcinoma. Bioengineered 2021; 12:1202-1211. [PMID: 33830865 PMCID: PMC8806338 DOI: 10.1080/21655979.2021.1908812] [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] [Indexed: 01/20/2023] Open
Abstract
RNA-binding motif protein 25 (RBM25) is a poorly characterized RNA-binding protein that is involved in several biological processes and regulates the proliferation and metastasis of tumor cells. The regulatory role of RBM25 in hepatocellular carcinoma (HCC) is unknown. Here, RBM25 expression and outcomes in HCC patients were evaluated using The Cancer Genome Atlas database. RBM25 was overexpressed in HCC patients compared with the healthy group. The high expression of RBM25 in tumor tissues was significantly related to poor overall survival (P<0.001). Overexpression of RBM25 significantly contributed to poorer survival in male patients and N0 stage patients (P<0.001). Spearman analysis and weighted gene co-expression network analysis identified 694 RBM25-related genes. Protein-protein interaction network analysis revealed the Cluster with the highest score, which positively correlated with RBM25. CDCA5 and INCENP were identified as the core functional genes related to RBM25. The overexpression of CDCA5 and INCENP in HCC patients was examined using the Human Protein Atlas database. The findings collectively indicated that RBM25 may interact with CDCA5 and INCENP to regulate HCC. Our detailed characterization of RBM25 protein interactions and related core functional genes provides a basis for further studies aimed at identifying molecular regulatory pathways or splicing events.
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Affiliation(s)
- Yong-Fa Zhang
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi-Xiu Wang
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ning- Zhang
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhen-Hai Lin
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Long-Rong Wang
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yun Feng
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qi Pan
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lu Wang
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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10
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Yim HE, Kim JH, Ahn MS, Jung Y, Roh J, Park SH, Kim TG, Choi JH, Kang SY. Clinicopathological and Molecular Analysis of 45 Cases of Pure Mucinous Breast Cancer. Front Oncol 2021; 10:558760. [PMID: 33732635 PMCID: PMC7956951 DOI: 10.3389/fonc.2020.558760] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 12/30/2020] [Indexed: 11/16/2022] Open
Abstract
Pure mucinous breast carcinoma (PMBC) is characterized by clusters of tumor cells floating in abundant extracellular mucin and can be classified into paucicellular (Type A) and hypercellular (Type B) subtypes. However, the clinicopathological and genomic differences between these two subtypes have not been well characterized. We retrospectively investigated the clinicopathologic features of 45 cases of surgically removed PMBC (31 Type A and 14 Type B). We also performed whole-exome sequencing (WES) in eight cases of PMBC. We found that Type B PMBC occurs at an older age and shows more aggressive clinical behavior than Type A. WES analysis revealed that HYDIN was the most frequently mutated gene in both types of PMBC. Although Type B PMBC showed a tendency toward more frequent genetic alterations, there were no statistically significant differences between the two subtypes in single nucleotide variants or insertions or deletions of bases associated with moderate or high effects. Our results provide additional evidence that PMBCs are clinicopathologically and genetically heterogeneous and lack pathognomonic genetic alterations. Further, Type B PMBC is more frequently associated with lymph node metastasis than Type A.
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Affiliation(s)
- Hyun Ee Yim
- Department of Pathology, Ajou University School of Medicine, Suwon, South Korea
| | - Jang-Hee Kim
- Department of Pathology, Ajou University School of Medicine, Suwon, South Korea
| | - Mi Sun Ahn
- Department of Hematology-Oncology, Ajou University School of Medicine, Suwon, South Korea
| | - Yongsik Jung
- Department of Surgery, Ajou University School of Medicine, Suwon, South Korea
| | - Jin Roh
- Department of Pathology, Ajou University School of Medicine, Suwon, South Korea
| | - So Hyun Park
- Department of Pathology, Ajou University School of Medicine, Suwon, South Korea
| | - Tae-Gyu Kim
- Department of Pathology, Ajou University School of Medicine, Suwon, South Korea
| | - Jin-Hyuk Choi
- Department of Hematology-Oncology, Ajou University School of Medicine, Suwon, South Korea
| | - Seok Yun Kang
- Department of Hematology-Oncology, Ajou University School of Medicine, Suwon, South Korea
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11
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Midha MK, Huang YF, Yang HH, Fan TC, Chang NC, Chen TH, Wang YT, Kuo WH, Chang KJ, Shen CY, Yu AL, Chiu KP, Chen CJ. Comprehensive Cohort Analysis of Mutational Spectrum in Early Onset Breast Cancer Patients. Cancers (Basel) 2020; 12:E2089. [PMID: 32731431 PMCID: PMC7464007 DOI: 10.3390/cancers12082089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 12/13/2022] Open
Abstract
Early onset breast cancer (EOBC), diagnosed at age ~40 or younger, is associated with a poorer prognosis and higher mortality rate compared to breast cancer diagnosed at age 50 or older. EOBC poses a serious threat to public health and requires in-depth investigation. We studied a cohort comprising 90 Taiwanese female patients, aiming to unravel the underlying mechanisms of EOBC etiopathogenesis. Sequence data generated by whole-exome sequencing (WES) and whole-genome sequencing (WGS) from white blood cell (WBC)-tumor pairs were analyzed to identify somatic missense mutations, copy number variations (CNVs) and germline missense mutations. Similar to regular breast cancer, the key somatic mutation-susceptibility genes of EOBC include TP53 (40% prevalence), PIK3CA (37%), GATA3 (17%) and KMT2C (17%), which are frequently reported in breast cancer; however, the structural protein-coding genes MUC17 (19%), FLG (16%) and NEBL (11%) show a significantly higher prevalence in EOBC. Furthermore, the top 2 genes harboring EOBC germline mutations, MUC16 (19%) and KRT18 (19%), encode structural proteins. Compared to conventional breast cancer, an unexpectedly higher number of EOBC susceptibility genes encode structural proteins. We suspect that mutations in structural proteins may increase physical permeability to environmental hormones and carcinogens and cause breast cancer to occur at a young age.
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Affiliation(s)
- Mohit K. Midha
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan; (M.K.M.); (Y.-F.H.); (T.-H.C.); (C.-J.C.)
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 112, Taiwan
| | - Yu-Feng Huang
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan; (M.K.M.); (Y.-F.H.); (T.-H.C.); (C.-J.C.)
| | - Hsiao-Hsiang Yang
- Department of Medical Research, Hsinchu Mackay Memorial Hospital, Hsinchu 300, Taiwan;
| | - Tan-Chi Fan
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou and Chang Gung University, No. 5, Fu-Shin St., Kuei Shang, Taoyuan 333, Taiwan; (T.-C.F.); (N.-C.C.); (A.L.Y.)
| | - Nai-Chuan Chang
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou and Chang Gung University, No. 5, Fu-Shin St., Kuei Shang, Taoyuan 333, Taiwan; (T.-C.F.); (N.-C.C.); (A.L.Y.)
| | - Tzu-Han Chen
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan; (M.K.M.); (Y.-F.H.); (T.-H.C.); (C.-J.C.)
| | - Yu-Tai Wang
- National Center for High-Performance Computing, Hsinchu Science Park, Hsinchu 300, Taiwan;
| | - Wen-Hung Kuo
- Department of Surgery, National Taiwan University Hospital, Taipei 100, Taiwan; (W.-H.K.); (K.-J.C.)
| | - King-Jen Chang
- Department of Surgery, National Taiwan University Hospital, Taipei 100, Taiwan; (W.-H.K.); (K.-J.C.)
| | - Chen-Yang Shen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan;
| | - Alice L. Yu
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou and Chang Gung University, No. 5, Fu-Shin St., Kuei Shang, Taoyuan 333, Taiwan; (T.-C.F.); (N.-C.C.); (A.L.Y.)
- Department of Pediatrics, University of California in San Diego, San Diego, CA 92161, USA
| | - Kuo-Ping Chiu
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan; (M.K.M.); (Y.-F.H.); (T.-H.C.); (C.-J.C.)
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 112, Taiwan
- Department of Life Sciences, College of Life Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Chien-Jen Chen
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan; (M.K.M.); (Y.-F.H.); (T.-H.C.); (C.-J.C.)
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12
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Nassar A, Abouelhoda M, Mansour O, Loutfy SA, Hafez MM, Gomaa M, Bahnassy A, El-Din Youssef AS, Lotfy MM, Ismail H, Ahmed OS, Abou-Bakr AAE, Zekri ARN. Targeted next generation sequencing identifies somatic mutations in a cohort of Egyptian breast cancer patients. J Adv Res 2020; 24:149-157. [PMID: 32322420 PMCID: PMC7167517 DOI: 10.1016/j.jare.2020.04.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/17/2020] [Accepted: 04/01/2020] [Indexed: 02/07/2023] Open
Abstract
Breast cancer (BC) incidence is progressively increasing in Egypt. However, there is insufficient knowledge of the acquired somatic mutations in Egyptian BC patients which limit our understanding of its progression. To the best of our knowledge, this is the first Egyptian cohort to sequence a multiple-gene panel of cancer related genes on BC patients. Four hundred and nine cancer related genes were sequenced in 46 fresh breast tumors of Egyptian BC patients to identify somatic mutations and their frequencies. TP53 and PIK3CA were the most top two frequently mutated genes. We detected 15 different somatic mutations in TP53 and 8 different ones in PIK3CA, each in 27 samples (58.7%). According to Clinvar database; we found 19 pathogenic somatic mutations: 7 in Tp53, 5 in PIK3CA, and single variants of VHL, STK11, AKT1, KRAS, IDH2, PTEN and ERBB2. We also identified 5 variants with uncertain significance (4 in TP53 and 1 in CEBPA) and 4 variants with conflicting interpretations of pathogenicity (2 in TP53 and 1 in each of APC and JAK3). Moreover, one drug response variant (p.P72R) in TP53 was detected in 8 samples. Furthermore, four novel variants were identified in JAK2, MTOR, KIT and EPHB. Further analysis, by Ingenuity Variant Analysis software (IVA), showed that PI3K/AKT signaling is altered in greater than 50% of Egyptian BC patients which implicates PI3K/AKT signaling as a therapeutic target. In this cohort, we shed the light on the most frequently detected somatic mutations and the most altered pathway in Egyptian BC patients.
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Affiliation(s)
- Auhood Nassar
- Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | | | - Osman Mansour
- Medical Oncology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Samah A. Loutfy
- Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Mohamed M. Hafez
- Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - M. Gomaa
- Radiology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Abeer Bahnassy
- Pathology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | | | - Mai M. Lotfy
- Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Hoda Ismail
- Pathology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Ola S. Ahmed
- Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | | | - Abdel-Rahman N. Zekri
- Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
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13
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Trapani V, Wolf FI. Dysregulation of Mg2+ homeostasis contributes to acquisition of cancer hallmarks. Cell Calcium 2019; 83:102078. [DOI: 10.1016/j.ceca.2019.102078] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/26/2019] [Accepted: 08/23/2019] [Indexed: 02/06/2023]
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14
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Wong KK, Banham AH, Yaacob NS, Nur Husna SM. The oncogenic roles of TRPM ion channels in cancer. J Cell Physiol 2019; 234:14556-14573. [PMID: 30710353 DOI: 10.1002/jcp.28168] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 01/10/2019] [Indexed: 01/24/2023]
Abstract
Transient receptor potential (TRP) proteins are a diverse family of ion channels present in multiple types of tissues. They function as gatekeepers for responses to sensory stimuli including temperature, vision, taste, and pain through their activities in conducting ion fluxes. The TRPM (melastatin) subfamily consists of eight members (i.e., TRPM1-8), which collectively regulate fluxes of various types of cations such as K+ , Na+ , Ca2+ , and Mg2+ . Growing evidence in the past two decades indicates that TRPM ion channels, their isoforms, or long noncoding RNAs encoded within the locus may be oncogenes involved in the regulation of cancer cell growth, proliferation, autophagy, invasion, and epithelial-mesenchymal transition, and their significant association with poor clinical outcomes of cancer patients. In this review, we describe and discuss recent findings implicating TRPM channels in different malignancies, their functions, mechanisms, and signaling pathways involved in cancers, as well as summarizing their normal physiological functions and the availability of ion channel pharmacological inhibitors.
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Affiliation(s)
- Kah Keng Wong
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Alison H Banham
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Nik Soriani Yaacob
- Department of Chemical Pathology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan, Malaysia
| | - Siti Muhamad Nur Husna
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
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15
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Snezhkina AV, Lukyanova EN, Fedorova MS, Kalinin DV, Melnikova NV, Stepanov OA, Kiseleva MV, Kaprin AD, Pudova EA, Kudryavtseva AV. Novel Genes Associated with the Development of Carotid Paragangliomas. Mol Biol 2019. [DOI: 10.1134/s0026893319040137] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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16
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Ai K, Jia Y, Li J, Wang C, Wang Y. Systematic analysis of multigene predictors in gastric cancer exploiting gene expression signature. J Cell Biochem 2019; 120:8069-8077. [PMID: 30426570 DOI: 10.1002/jcb.28085] [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] [Received: 10/09/2018] [Accepted: 10/29/2018] [Indexed: 01/24/2023]
Abstract
Gastric cancer (GC) is the second most common cause of cancer death worldwide but could be more curable if diagnosed at an earlier stage. At present, the capability to predict the efficaciousness of molecular diagnosis for GC for each patient remains elusive. The purpose of this study was to identify tumor biomarkers through systems analysis of multigene predictors exploiting the available data resource. In this study, we investigated the top 10% overexpressed genes in GC from five data sets of the Oncomine platform, with 265 GC samples versus 174 normal gastric mucosa samples. Sixteen candidate genes were identified as predictors of GC, of which 14 genes were verified through the comparison of expression levels in specimens from normal (chronic gastritis, 21 samples) and GC groups (38 samples). In addition, unique molecular portraits of diffuse adenocarcinoma (DA), intestinal adenocarcinoma (IA), and mixed adenocarcinoma (MA) were studied through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis, where DA showed higher extracellular matrix alteration while IA and MA showed higher cell-cycle alteration than other types. We also found that the elevated expressions of genes during GC progression were independent of gene mutations, and high core-binding factor subunit β expression is correlated with a high overall survival rate in GC patients. Our research may provide an efficient clinical diagnosis of GC at an early stage with high accuracy and thus help improve the overall survival rate through early therapeutic interventions.
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Affiliation(s)
- Kuankuan Ai
- Department of Gastroenterology, Affiliated Hospital of Jining Medical College, Jining, China
| | - Yanli Jia
- Department of Gastroenterology, Yanzhou Hospital of Affiliated Hospital of Jining Medical College, Yanzhou, China
| | - Jin Li
- Department of Gastroenterology, Heze Municipal Hospital, Heze, China
| | - Chong Wang
- Department of Endocrinology, Heze Municipal Hospital, Heze, China
| | - Yan Wang
- Department of Gastroenterology, Affiliated Hospital of Jining Medical College, Jining, China
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17
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Ge Y, Schuster MB, Pundhir S, Rapin N, Bagger FO, Sidiropoulos N, Hashem N, Porse BT. The splicing factor RBM25 controls MYC activity in acute myeloid leukemia. Nat Commun 2019; 10:172. [PMID: 30635567 PMCID: PMC6329799 DOI: 10.1038/s41467-018-08076-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 12/07/2018] [Indexed: 11/09/2022] Open
Abstract
Cancer sequencing studies have implicated regulators of pre-mRNA splicing as important disease determinants in acute myeloid leukemia (AML), but the underlying mechanisms have remained elusive. We hypothesized that "non-mutated" splicing regulators may also play a role in AML biology and therefore conducted an in vivo shRNA screen in a mouse model of CEBPA mutant AML. This has led to the identification of the splicing regulator RBM25 as a novel tumor suppressor. In multiple human leukemic cell lines, knockdown of RBM25 promotes proliferation and decreases apoptosis. Mechanistically, we show that RBM25 controls the splicing of key genes, including those encoding the apoptotic regulator BCL-X and the MYC inhibitor BIN1. This mechanism is also operative in human AML patients where low RBM25 levels are associated with high MYC activity and poor outcome. Thus, we demonstrate that RBM25 acts as a regulator of MYC activity and sensitizes cells to increased MYC levels.
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Affiliation(s)
- Ying Ge
- The Finsen Laboratory, Rigshospitalet, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Mikkel Bruhn Schuster
- The Finsen Laboratory, Rigshospitalet, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Sachin Pundhir
- The Finsen Laboratory, Rigshospitalet, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Nicolas Rapin
- The Finsen Laboratory, Rigshospitalet, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Frederik Otzen Bagger
- The Finsen Laboratory, Rigshospitalet, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Nikos Sidiropoulos
- The Finsen Laboratory, Rigshospitalet, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Nadia Hashem
- The Finsen Laboratory, Rigshospitalet, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Bo Torben Porse
- The Finsen Laboratory, Rigshospitalet, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark. .,Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark. .,Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.
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18
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Gara SK, Lack J, Zhang L, Harris E, Cam M, Kebebew E. Metastatic adrenocortical carcinoma displays higher mutation rate and tumor heterogeneity than primary tumors. Nat Commun 2018; 9:4172. [PMID: 30301885 PMCID: PMC6178360 DOI: 10.1038/s41467-018-06366-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 08/15/2018] [Indexed: 12/21/2022] Open
Abstract
Adrenocortical cancer (ACC) is a rare cancer with poor prognosis and high mortality due to metastatic disease. All reported genetic alterations have been in primary ACC, and it is unknown if there is molecular heterogeneity in ACC. Here, we report the genetic changes associated with metastatic ACC compared to primary ACCs and tumor heterogeneity. We performed whole-exome sequencing of 33 metastatic tumors. The overall mutation rate (per megabase) in metastatic tumors was 2.8-fold higher than primary ACC tumor samples. We found tumor heterogeneity among different metastatic sites in ACC and discovered recurrent mutations in several novel genes. We observed 37–57% overlap in genes that are mutated among different metastatic sites within the same patient. We also identified new therapeutic targets in recurrent and metastatic ACC not previously described in primary ACCs. Adrenocortical cancer (ACC) is a rarely diagnosed and aggressive cancer whose metastatic form has been scarcely studied. Here, the authors study primary and metastatic ACC to investigate genomic heterogeneity, discovering higher mutation rates in metastatic lesions and novel recurrent mutations.
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Affiliation(s)
- Sudheer Kumar Gara
- Endocrine Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Justin Lack
- Center for Cancer Research, Collaborative Bioinformatics Resource, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lisa Zhang
- Endocrine Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Emerson Harris
- Endocrine Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Margaret Cam
- Center for Cancer Research, Collaborative Bioinformatics Resource, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Electron Kebebew
- Endocrine Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA. .,Department of Surgery and Stanford Cancer Institute, Stanford University, Stanford, CA, 94305, USA.
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19
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Giménez-Mascarell P, Schirrmacher CE, Martínez-Cruz LA, Müller D. Novel Aspects of Renal Magnesium Homeostasis. Front Pediatr 2018; 6:77. [PMID: 29686978 PMCID: PMC5900390 DOI: 10.3389/fped.2018.00077] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 03/13/2018] [Indexed: 12/29/2022] Open
Abstract
Magnesium (Mg2+) is indispensable for several vital functions, such as neurotransmission, cardiac conductance, blood glucose, blood pressure regulation, and proper function of more than 300 enzymes. Thus, Mg2+ homeostasis is subject to tight regulation. Besides the fast and immediate regulation of plasma Mg2+, a major part of Mg2+ homeostasis is realized by a concerted action of epithelial molecular structures that tightly control intestinal uptake and renal absorption. This mechanism is provided by a combination of para- and transcellular pathways. Whereas the first pathway provides the organism with a maximal amount of vital substances by a minimal energy expenditure, the latter enables controlling and fine-tuning by means of local and regional regulatory systems and also, hormonal control. The paracellular pathway is driven by an electrochemical gradient and realized in principal by the tight junction (TJ), a supramolecular organization of membrane-bound proteins and their adaptor and scaffolding proteins. TJ determinants are claudins (CLDN), a family of membrane spanning proteins that generate a barrier or a pore between two adjacent epithelial cells. Many insights into molecular mechanisms of Mg2+ handling have been achieved by the identification of alterations and mutations in human genes which cause disorders of paracellular Mg2+ pathways (CLDN10, CLDN14, CLDN16, CLDN19). Also, in the distal convoluted tubule, a basolateral protein, CNNM2, causes if mutated, familial dominant and also recessive renal Mg2+ wasting, albeit its true function has not been clarified yet, but is assumed to play a key role in the transcellular pathway. Moreover, mutations in human genes that are involved in regulating these proteins directly or indirectly cause, if mutated human diseases, mostly in combination with comorbidities as diabetes, cystic renal disease, or metabolic abnormalities. Generation and characterization of animal models harboring the corresponding mutations have further contributed to the elucidation of physiology and pathophysiology of Mg2+ disorders. Finally, high-end crystallization techniques allow understanding of Mg2+ handling in more detail. As this field is rapidly growing, we describe here the principles of physiology and pathophysiology of epithelial transport of renal Mg2+ homeostasis with emphasis on recently identified mechanisms involved.
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Affiliation(s)
| | - Carlotta Else Schirrmacher
- Department of Pediatric Gastroenterology, Nephrology and Metabolism, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Dominik Müller
- Department of Pediatric Gastroenterology, Nephrology and Metabolism, Charité - Universitätsmedizin Berlin, Berlin, Germany
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20
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Meißner T, Mark A, Williams C, Berdel WE, Wiebe S, Kerkhoff A, Wardelmann E, Gaiser T, Müller-Tidow C, Rosenstiel P, Arnold N, Leyland-Jones B, Franke A, Stanulla M, Forster M. Metastatic triple-negative breast cancer patient with TP53 tumor mutation experienced 11 months progression-free survival on bortezomib monotherapy without adverse events after ending standard treatments with grade 3 adverse events. Cold Spring Harb Mol Case Stud 2017; 3:mcs.a001677. [PMID: 28679691 PMCID: PMC5495034 DOI: 10.1101/mcs.a001677] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Accepted: 04/24/2017] [Indexed: 01/02/2023] Open
Abstract
A triple-negative breast cancer patient had no hereditary BRCA1, BRCA2, or TP53 risk variants. After exhaustion of standard treatments, she underwent experimental treatments and whole-exome sequencing of tumor, blood, and a metastasis. Well-tolerated experimental bortezomib monotherapy was administered for a progression-free period of 11 mo. After progression, treatments were changed and the exome data were evaluated, expanded with RNA and exome sequencing of a late-stage metastasis. In the final stage, eribulin alone and in combination with anthracyclines were administered. While suffering from grade 3 adverse events, skin metastases progressed. She lived 51 mo after initial diagnosis.Toxicity from anthracyclines and cisplatin may have been due to associated germline variants CBR3 C4Y and V224M and GSTP1 I105V, respectively. Somatic mutations predicted or reported as pathogenic were detected in 38 genes in tumor tissues. All tumor samples harbored the heterozygous TP53 Y220C variant, known to destabilize p53 and down-regulate p53-mediated apoptosis. The success of bortezomib may be explained by the previously reported up-regulation of caspase-mediated apoptosis, which is p53-independent. Phylogenetic analysis of blood, primary tumor, and two metastases inferred an ancestral tumor cell with 12 expressed tumor mutations from which all three tumors may have evolved.Although our first urgent analysis could only include 40 genes, postmortem analysis uncovered the aggressiveness and suggested experimental therapies including 16 actionable targets, partly validated by immunohistochemistry. Exome and transcriptome analyses yielded comprehensive therapy-relevant information and should be considered for patients at first diagnosis.
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Affiliation(s)
- Tobias Meißner
- Department of Molecular and Experimental Medicine, Avera Cancer Institute, La Jolla, California 92037, USA
| | - Adam Mark
- Department of Molecular and Experimental Medicine, Avera Cancer Institute, La Jolla, California 92037, USA
| | - Casey Williams
- Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, South Dakota 57105, USA
| | - Wolfgang E Berdel
- Department of Medicine A, Hematology and Oncology, University Hospital Muenster, D-48149 Muenster, Germany
| | - Stephanie Wiebe
- Department of Medicine A, Hematology and Oncology, University Hospital Muenster, D-48149 Muenster, Germany
| | - Andrea Kerkhoff
- Department of Medicine A, Hematology and Oncology, University Hospital Muenster, D-48149 Muenster, Germany
| | - Eva Wardelmann
- Gerhard-Domagk-Institute of Pathology, University Hospital Muenster, D-48149 Muenster, Germany
| | - Timo Gaiser
- Institute of Pathology Mannheim, University Hospital Mannheim, D-68167 Mannheim, Germany
| | - Carsten Müller-Tidow
- Department of Medicine IV, Hematology and Oncology, University Hospital of Halle (Saale), D-06120 Halle, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Schleswig-Holstein, D-24105 Kiel, Germany
| | - Norbert Arnold
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Schleswig-Holstein, D-24105 Kiel, Germany.,Department of Gynaecology and Obstetrics, University Hospital of Schleswig-Holstein, Christian-Albrechts-University of Kiel, D-24105 Kiel, Germany
| | - Brian Leyland-Jones
- Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, South Dakota 57105, USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Schleswig-Holstein, D-24105 Kiel, Germany
| | - Martin Stanulla
- Department of Pediatric Haematology and Oncology, Hannover Medical School, D-30625 Hannover, Germany
| | - Michael Forster
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Schleswig-Holstein, D-24105 Kiel, Germany
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