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Wang MD, Li HT, Peng LX, Mei Y, Zheng LS, Li CZ, Meng DF, Lang YH, Xu L, Peng XS, Liu ZJ, Xie DH, Guo LL, Ma MG, Ding LY, Huang BJ, Cao Y, Qian CN. TSPAN1 inhibits metastasis of nasopharyngeal carcinoma via suppressing NF-kB signaling. Cancer Gene Ther 2024; 31:454-463. [PMID: 38135697 DOI: 10.1038/s41417-023-00716-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023]
Abstract
Nasopharyngeal carcinoma (NPC) originates in the epithelial cells of the nasopharynx and is a common malignant tumor in southern China and Southeast Asia. Metastasis of NPC remains the main cause of death for NPC patients even though the tumor is sensitive to radiotherapy and chemotherapy. Here, we found that the transmembrane protein tetraspanin1 (TSPAN1) potently inhibited the in vitro migration and invasion, as well as, the in vivo metastasis of NPC cells via interacting with the IKBB protein. In addition, TSPAN1 was essential in preventing the overactivation of the NF-kB pathway in TSPAN1 overexpressing NPC cells. Furthermore, reduced TSPAN1 expression was associated with NPC metastasis and the poor prognosis of NPC patients. These results uncovered the suppressive role of TSPAN1 against NF-kB signaling in NPC cells for preventing NPC metastasis. Its therapeutic value warrants further investigation.
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Affiliation(s)
- Ming-Dian Wang
- Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, P. R. China
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Hui-Ting Li
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
- Department of Anesthesiology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Li-Xia Peng
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Yan Mei
- Department of Pathology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, P. R. China
| | - Li-Sheng Zheng
- Department of Pathology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, P. R. China
| | - Chang-Zhi Li
- Medical School, Pingdingshan University, Pingdingshan, Henan Province, 467021, P. R. China
| | - Dong-Fang Meng
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, P. R. China
| | - Yan-Hong Lang
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Liang Xu
- Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, P. R. China
| | - Xing-Si Peng
- Department of radiation oncology, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510120, P. R. China
| | - Zhi-Jie Liu
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
- Department of Radiotherapy, Affiliated Dongguan Hospital, Southern Medical University (Dongguan People's Hospital), Dongguan, Guangdong, China
| | - De-Huan Xie
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Ling-Ling Guo
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Mao-Guang Ma
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, P.R. China
| | - Liu-Yan Ding
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Bi-Jun Huang
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Yun Cao
- Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, P. R. China.
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China.
| | - Chao-Nan Qian
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China.
- Guangzhou Concord Cancer Center, Guangzhou, 510060, P. R. China.
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2
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Elsner F, Hoffmann M, Fahrioglu‐Yamaci R, Czyz Z, Feliciello G, Mederer T, Polzer B, Treitschke S, Rümmele P, Weber F, Wiesinger H, Robold T, Sziklavari Z, Sienel W, Hofmann H, Klein CA. Disseminated cancer cells detected by immunocytology in lymph nodes of
NSCLC
patients are highly prognostic and undergo parallel molecular evolution. J Pathol 2022; 258:250-263. [DOI: 10.1002/path.5996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/20/2022] [Accepted: 07/28/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Felix Elsner
- Chair of Experimental Medicine and Therapy Research University of Regensburg Regensburg Germany
- Institute of Pathology University of Regensburg Regensburg Germany
- Institute of Pathology University Hospital Erlangen Erlangen Germany
| | - Martin Hoffmann
- Division of Personalized Tumour Therapy Fraunhofer ITEM‐R Regensburg Germany
| | - Rezan Fahrioglu‐Yamaci
- Chair of Experimental Medicine and Therapy Research University of Regensburg Regensburg Germany
| | - Zbigniew Czyz
- Chair of Experimental Medicine and Therapy Research University of Regensburg Regensburg Germany
| | | | - Tobias Mederer
- Chair of Experimental Medicine and Therapy Research University of Regensburg Regensburg Germany
| | - Bernhard Polzer
- Division of Personalized Tumour Therapy Fraunhofer ITEM‐R Regensburg Germany
| | - Steffi Treitschke
- Division of Personalized Tumour Therapy Fraunhofer ITEM‐R Regensburg Germany
| | - Petra Rümmele
- Institute of Pathology University of Regensburg Regensburg Germany
- Institute of Pathology University Hospital Erlangen Erlangen Germany
| | - Florian Weber
- Institute of Pathology University of Regensburg Regensburg Germany
| | | | - Tobias Robold
- Department of Thoracic Surgery University Hospital Regensburg Regensburg Germany
| | - Zsolt Sziklavari
- Department of Thoracic Surgery Krankenhaus Barmherzige Brüder Regensburg Regensburg Germany
- Department of Thoracic Surgery Klinikum Coburg, Coburg Germany
| | - Wulf Sienel
- Department of Thoracic Surgery University of Munich Grosshadern Campus, Munich Germany
| | - Hans‐Stefan Hofmann
- Department of Thoracic Surgery University Hospital Regensburg Regensburg Germany
- Department of Thoracic Surgery Krankenhaus Barmherzige Brüder Regensburg Regensburg Germany
| | - Christoph A. Klein
- Chair of Experimental Medicine and Therapy Research University of Regensburg Regensburg Germany
- Division of Personalized Tumour Therapy Fraunhofer ITEM‐R Regensburg Germany
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Graf RP, Eskander R, Brueggeman L, Stupack DG. Association of Copy Number Variation Signature and Survival in Patients With Serous Ovarian Cancer. JAMA Netw Open 2021; 4:e2114162. [PMID: 34181012 PMCID: PMC8239953 DOI: 10.1001/jamanetworkopen.2021.14162] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
IMPORTANCE Tailoring therapeutic regimens to individual patients with ovarian cancer is informed by severity of disease using a variety of clinicopathologic indicators. Although DNA repair variations are increasingly used for therapy selection in ovarian cancer, molecular features are not widely used for general assessment of patient prognosis and disease severity. OBJECTIVE To distill a highly dynamic characteristic, signature of copy number variations (CNV), into a risk score that could be easily validated analytically or repurposed for use given existing US Food and Drug Administration (FDA)-approved multigene assays. DESIGN, SETTING, AND PARTICIPANTS This genetic association study used the Cancer Genome Atlas Ovarian Cancer database to assess for genome-wide survival associations agnostic to gene function. Regions enriched for significant associations were compared to associations from scrambled data. CNV associations were condensed into a risk score, which was internally validated using bootstrapping. The participants were patients with serous ovarian cancer (stages I-IV) diagnosed from 1992 to 2013. Statistical analysis was performed from April to July 2020. MAIN OUTCOMES AND MEASURES Overall survival (OS). RESULTS Among 564 patients with serous ovarian cancer, the mean (SD) age was 59.7 (11.5) years; 34 (6%) identified as Black or African American. A total of 13 genome regions, comprising 14 alterations, were identified as significantly risk associated. Composite risk score was independent of total CNV burden, total mutational burden, BRCA status, and open-source genome-wide DNA repair deficiency signatures. Binned terciles yielded high-, standard-, and low-risk groups with respective median OS estimates of 2.9 (95% CI, 2.3-3.2) years, 4.1 (95% CI, 3.7-4.8) years, and 5.7 (95% CI, 4.7-7.4) years, respectively (P < .001). Associated 5-year survival estimates in each tercile were 15% (95% CI, 10%-22%), 36% (95% CI, 29%-46%), and 53% (95% CI, 45%-62%). The risk score had more discriminatory ability to prognosticate OS than age, clinical stage, grade, and race combined, and was strongly additive to significant clinical features (P < .001). Simulated adaptation of FDA-approved assays showed similar performance. Gene ontology analyses of identified regions showed an enrichment for regulatory miRNAs and protein kinase regulators. CONCLUSIONS AND RELEVANCE This study found that a CNV-based risk score is independent to and stronger than current or near-future ovarian cancer genomic biomarkers to prognosticate OS. CNV regions identified were not strongly associated with canonical ovarian cancer biological pathways, identifying candidates for future mechanistic investigations. External validation of the CNV risk score, especially in concert with more extensive clinical features, could be pursued via existing FDA-approved assays.
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Affiliation(s)
- Ryon P. Graf
- Moores Cancer Center, University of California, San Diego
- Now at Foundation Medicine Inc, Cambridge, Massachusetts
| | - Ramez Eskander
- Moores Cancer Center, University of California, San Diego
| | - Leo Brueggeman
- Interdisciplinary Genetics Program, University of Iowa, Iowa City
- Medical Scientist Training Program, University of Iowa, Iowa City
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4
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Su CT, Urban Z. LTBP4 in Health and Disease. Genes (Basel) 2021; 12:genes12060795. [PMID: 34071145 PMCID: PMC8224675 DOI: 10.3390/genes12060795] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/14/2021] [Accepted: 05/21/2021] [Indexed: 12/20/2022] Open
Abstract
Latent transforming growth factor β (TGFβ)-binding protein (LTBP) 4, a member of the LTBP family, shows structural homology with fibrillins. Both these protein types are characterized by calcium-binding epidermal growth factor-like repeats interspersed with 8-cysteine domains. Based on its domain composition and distribution, LTBP4 is thought to adopt an extended structure, facilitating the linear deposition of tropoelastin onto microfibrils. In humans, mutations in LTBP4 result in autosomal recessive cutis laxa type 1C, characterized by redundant skin, pulmonary emphysema, and valvular heart disease. LTBP4 is an essential regulator of TGFβ signaling and is related to development, immunity, injury repair, and diseases, playing a central role in regulating inflammation, fibrosis, and cancer progression. In this review, we focus on medical disorders or diseases that may be manipulated by LTBP4 in order to enhance the understanding of this protein.
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Affiliation(s)
- Chi-Ting Su
- Department of Internal Medicine, Renal Division, National Taiwan University Hospital Yunlin Branch, Douliu 640, Taiwan;
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Medicine, National Taiwan University Cancer Center Hospital, Taipei 106, Taiwan
| | - Zsolt Urban
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Correspondence: ; Tel.: +1-412-648-8269
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5
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Karlsson IK, Ericsson M, Wang Y, Jylhävä J, Hägg S, Dahl Aslan AK, Reynolds CA, Pedersen NL. Epigenome-wide association study of level and change in cognitive abilities from midlife through late life. Clin Epigenetics 2021; 13:85. [PMID: 33883019 PMCID: PMC8061224 DOI: 10.1186/s13148-021-01075-9] [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: 01/27/2021] [Accepted: 04/12/2021] [Indexed: 11/18/2022] Open
Abstract
Background Epigenetic mechanisms are important in aging and may be involved in late-life changes in cognitive abilities. We conducted an epigenome-wide association study of leukocyte DNA methylation in relation to level and change in cognitive abilities, from midlife through late life in 535 Swedish twins.
Results Methylation levels were measured with the Infinium Human Methylation 450 K or Infinium MethylationEPIC array, and all sites passing quality control on both arrays were selected for analysis (n = 250,816). Empirical Bayes estimates of individual intercept (age 65), linear, and quadratic change were obtained from latent growth curve models of cognitive traits and used as outcomes in linear regression models. Significant sites (p < 2.4 × 10–7) were followed up in between-within twin pair models adjusting for familial confounding and full-growth modeling. We identified six significant associations between DNA methylation and level of cognitive abilities at age 65: cg18064256 (PPP1R13L) with processing speed and spatial ability; cg04549090 (NRXN3) with spatial ability; cg09988380 (POGZ), cg25651129 (-), and cg08011941 (ENTPD8) with working memory. The genes are involved in neuroinflammation, neuropsychiatric disorders, and ATP metabolism. Within-pair associations were approximately half that of between-pair associations across all sites. In full-growth curve models, associations between DNA methylation and cognitive level at age 65 were of small effect sizes, and associations between DNA methylation and longitudinal change in cognitive abilities of very small effect sizes. Conclusions Leukocyte DNA methylation was associated with level, but not change in cognitive abilities. The associations were substantially attenuated in within-pair analyses, indicating they are influenced in part by genetic factors. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01075-9.
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Affiliation(s)
- Ida K Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden. .,Institute of Gerontology and Aging Research Network - Jönköping (ARN-J), School of Health and Welfare, Jönköping University, Jönköping, Sweden.
| | - Malin Ericsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Yunzhang Wang
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Juulia Jylhävä
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Sara Hägg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Anna K Dahl Aslan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Institute of Gerontology and Aging Research Network - Jönköping (ARN-J), School of Health and Welfare, Jönköping University, Jönköping, Sweden.,Department of Health Sciences, School of Health Sciences and Welfare, University of Skövde, Skövde, Sweden
| | | | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Department of Psychology, University of Southern California, Los Angeles, CA, USA
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6
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Roles of acyl-CoA synthetase long-chain family member 5 and colony stimulating factor 2 in inhibition of palmitic or stearic acids in lung cancer cell proliferation and metabolism. Cell Biol Toxicol 2020; 37:15-34. [PMID: 32347412 DOI: 10.1007/s10565-020-09520-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 02/28/2020] [Indexed: 02/07/2023]
Abstract
Lung cancer is a heterogeneous and complex disease with the highest incidence and mortality rate. The present study aims at defining the lung cancer phenome specificity of lipidomic profiles, screening target lipid-dependent transcriptional alternations, identifying target lipid-associated target genes, and exploring molecular mechanisms. Lung cancer-specific and lung cancer subtype-specific target lipids palmitic acid (C16:0) and stearic acid (C18:0) were found as target lipids by integrating clinical phenomics, lipidomics, and transcriptomics and exhibited antiproliferative effects in sensitive cells. The metabolism-associated gene ACSL5 or inflammation-associated gene CCL3 was identified in lung adenocarcinoma or small lung cancer cells, respectively. C16:0 or C18:0 could upregulate ACSL5 or CSF2 expression in a time- and dose-dependent pattern, and the deletion of both genes led to the insensitivity of cells. Target lipids increased the expression of PDK4 gene in different patterns and inhibited cell proliferation through alterations of intracellular energy. Thus, our data provide a new strategy to investigate the trans-points between clinical and phenomics and lipidomics and target lipid-associated molecular mechanisms to benefit from the discovery of new therapies.
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7
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Xue H, Huang H, Wang Y, An G, Zhang M, Xu L, Lin Y. Molecular cytogenetic identification of small supernumerary marker chromosomes using chromosome microarray analysis. Mol Cytogenet 2019; 12:13. [PMID: 30911334 PMCID: PMC6416931 DOI: 10.1186/s13039-019-0425-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 02/27/2019] [Indexed: 12/18/2022] Open
Abstract
Background This study aimed to evaluate the feasibility of chromosomal microarray analysis (CMA) in detecting the origin and structure of small supernumerary marker chromosomes (sSMCs) in prenatal and postnatal cases and to clarify sSMC-related genotype-phenotype correlations. Results Thirty-three cases carrying sSMCs were identified by banding cytogenetics. Of these cases, twenty-nine were first characterized by CMA and only two by FISH. The remaining two cases were excluded for their refusal to accept further examination. The chromosomal origins of twenty-two cases were successfully identified, in which pathogenetic copy number variations (PCNVs) were found in sixteen cases, four cases showed variants of uncertain significance (VOUS), one case showed benign CNVs, and one case showed probable PCNVs. For the nine cases with negative CMA results, only one of them contained centromere heterochromatin likely due to its normal phenotype, whereas reasons for the remaining eight cases were uncertain. We also found that CMA results indicating pathogenic abnormalities further affect the rate of pregnancy termination. Conclusions This study showed that CMA combined with cytogenetic analysis is particularly effective in identifying sSMCs. However, in order to establish sSMC-related genotype-phenotype correlations, the inclusion of more sSMC cases will be necessary in future studies.
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Affiliation(s)
- Huili Xue
- Fujian Provincial Key Laboratory for Prenatal diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, affiliated hospital of Fujian Medical University, Fuzhou, 350001 Fujian China
| | - Hailong Huang
- Fujian Provincial Key Laboratory for Prenatal diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, affiliated hospital of Fujian Medical University, Fuzhou, 350001 Fujian China
| | - Yan Wang
- Fujian Provincial Key Laboratory for Prenatal diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, affiliated hospital of Fujian Medical University, Fuzhou, 350001 Fujian China
| | - Gang An
- Fujian Provincial Key Laboratory for Prenatal diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, affiliated hospital of Fujian Medical University, Fuzhou, 350001 Fujian China
| | - Min Zhang
- Fujian Provincial Key Laboratory for Prenatal diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, affiliated hospital of Fujian Medical University, Fuzhou, 350001 Fujian China
| | - Liangpu Xu
- Fujian Provincial Key Laboratory for Prenatal diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, affiliated hospital of Fujian Medical University, Fuzhou, 350001 Fujian China
| | - Yuan Lin
- Fujian Provincial Key Laboratory for Prenatal diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, affiliated hospital of Fujian Medical University, Fuzhou, 350001 Fujian China
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8
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Zhu J, Luo JZ, Li CB. Correlations of an Insertion/Deletion Polymorphism (rs10680577) in the RERT-lncRNA with the Susceptibility, Clinicopathological Features, and Prognosis of Lung Cancer. Biochem Genet 2018; 57:147-158. [PMID: 30073577 DOI: 10.1007/s10528-018-9883-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 07/24/2018] [Indexed: 12/13/2022]
Abstract
The aim of this study was to investigate the correlations of an Ins/Del polymorphism (rs10680577) in the RERT-lncRNA with the susceptibility, clinicopathological features, and prognosis of lung cancer. A total of 376 patients with lung cancer and 419 healthy subjects were enrolled in this study. The genotype of rs10680577 was performed using polymerase chain reaction (PCR) followed by polyacrylamide gel electrophoresis. Quantitative real-time PCR was used to measure RERT-lncRNA and EGLN2 expressions. Subjects with Del allele of rs10680577 exhibited an elevated risk of lung cancer. The expressions of RERT-lncRNA and EGLN2 in tumor tissues were higher than adjacent normal tissues, manifesting a positive correlation. Compared to patients with Ins/Ins genotype carriers, those with Ins/Del + Del/Del genotype carriers had upregulated expressions of RERT-lncRNA and EGLN2. Moreover, Ins/Del + Del/Del genotype and expressions of RERT-lncRNA and EGLN2 were associated with age, smoking habits, and TNM stage in lung cancer patients. Besides, patients with Ins/Ins genotype of rs10680577 had a longer OS than those with Ins/Del + Del/Del genotype carriers, and patients with lower expressions of RERT-lncRNA and EGLN2 presented a shorter OS than those with higher expressions. COX multivariate analysis demonstrated that Ins/Del + Del/Del genotype and higher expressions of RERT lncRNA and EGLN2 were risk factors affecting the prognosis of lung cancer. The Ins/Del polymorphism (rs10680577) in RERT-lncRNA was correlated with the risk, major clinicopathological features, and prognosis of lung cancer patients, and the patients with Ins/Del + Del/Del genotype carriers had higher expressions of RERT-lncRNA and EGLN2 than those with Ins/Ins carriers.
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Affiliation(s)
- Jing Zhu
- Department of Laboratory Medicine, Jingzhou Central Hospital, The Second Clinical Medical College, Yangtze University, Jingzhou, 434020, Hubei, China
| | - Jin-Zhu Luo
- Department of Laboratory Medicine, Jingzhou Central Hospital, The Second Clinical Medical College, Yangtze University, Jingzhou, 434020, Hubei, China
| | - Cheng-Bin Li
- Department of Laboratory Medicine, Jingzhou Central Hospital, The Second Clinical Medical College, Yangtze University, Jingzhou, 434020, Hubei, China.
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9
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Backes C, Ludwig N, Leidinger P, Huwer H, Tenzer S, Fehlmann T, Franke A, Meese E, Lenhof HP, Keller A. Paired proteomics, transcriptomics and miRNomics in non-small cell lung cancers: known and novel signaling cascades. Oncotarget 2018; 7:71514-71525. [PMID: 27588394 PMCID: PMC5342097 DOI: 10.18632/oncotarget.11723] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 08/01/2016] [Indexed: 12/14/2022] Open
Abstract
High-throughput omics analyses are applied to elucidate molecular pathogenic mechanisms in cancer. Given restricted cohort sizes and contrasting large feature sets paired multi-omics analysis supports discovery of true positive deregulated signaling cascades. For lung cancer patients we measured from the same tissue biopsies proteomic- (6,183 proteins), transcriptomic- (34,687 genes) and miRNomic data (2,549 miRNAs). To minimize inter-individual variations case and control lung biopsies have been gathered from the same individuals.Considering single omics entities, 15 of 2,549 miRNAs (0.6%), 752 of 34,687 genes (2.2%) and 141 of 6,183 proteins (2.3%) were significantly deregulated. Multivariate analysis also revealed that effects in miRNA were smaller compared to genes and proteins indicating that expression changes of miRNAs might also have limited impact of pathogenicity. However, a new algorithm for modeling the complex mutual interactions of miRNAs and their target genes facilitated precise prediction of deregulation in cancer genes (92.3% accuracy, p=0.007). Lastly, deregulation of genes in cancer matched deregulation of proteins coded by the genes in 80% of cases.The resulting interaction network, which is based on quantitative analysis of the abundance of miRNAs, mRNAs and proteins each taken from the same lung cancer tissue and from the same autologous normal lung tissue confirms molecular pathological changes and further contributes to the discovery of altered signaling cascades in lung cancer.
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Affiliation(s)
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University, Germany
| | | | | | - Stefan Tenzer
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, Germany
| | | | - Eckart Meese
- Department of Human Genetics, Saarland University, Germany
| | | | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, Germany
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10
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Kim DW, Kim KC, Kim KB, Dunn CT, Park KS. Transcriptional deregulation underlying the pathogenesis of small cell lung cancer. Transl Lung Cancer Res 2018. [PMID: 29535909 DOI: 10.21037/tlcr.2017.10.07] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The discovery of recurrent alterations in genes encoding transcription regulators and chromatin modifiers is one of the most important recent developments in the study of the small cell lung cancer (SCLC) genome. With advances in models and analytical methods, the field of SCLC biology has seen remarkable progress in understanding the deregulated transcription networks linked to the tumor development and malignant progression. This review will discuss recent discoveries on the roles of RB and P53 family of tumor suppressors and MYC family of oncogenes in tumor initiation and development. It will also describe the roles of lineage-specific factors in neuroendocrine (NE) cell differentiation and homeostasis and the roles of epigenetic alterations driven by changes in NFIB and chromatin modifiers in malignant progression and chemoresistance. These recent findings have led to a model of transcriptional network in which multiple pathways converge on regulatory regions of crucial genes linked to tumor development. Validation of this model and characterization of target genes will provide critical insights into the biology of SCLC and novel strategies for tumor intervention.
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Affiliation(s)
- Dong-Wook Kim
- Department of Microbiology, Immunology, and Cancer Biology, The University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, USA
| | - Keun-Cheol Kim
- Department of Microbiology, Immunology, and Cancer Biology, The University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, USA.,Department of Biological Sciences, Kangwon National University, Chuncheon, Korea
| | - Kee-Beom Kim
- Department of Microbiology, Immunology, and Cancer Biology, The University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, USA
| | - Colin T Dunn
- Department of Microbiology, Immunology, and Cancer Biology, The University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, USA
| | - Kwon-Sik Park
- Department of Microbiology, Immunology, and Cancer Biology, The University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, USA
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11
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Marquez-Vilendrer SB, Thompson K, Lu L, Reisman D. Mechanism of BRG1 silencing in primary cancers. Oncotarget 2018; 7:56153-56169. [PMID: 27486753 PMCID: PMC5302903 DOI: 10.18632/oncotarget.10593] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/19/2016] [Indexed: 11/25/2022] Open
Abstract
BRG1 (SMARCA4) is a documented tumor suppressor and a key subunit of the SWI/SNF chromatin remodeling complex that is silenced in many cancer types. Studies have shown that BRG1 is mutated in cancer-derived cell lines, which led to the assertion that BRG1 is also mutated in primary human tumors. However, the sequencing of BRG1-deficient tumors has revealed a paucity of mutations; hence, the cause of BRG1 silencing in tumors remains an enigma. We conducted immunohistochemistry (IHC) on a number of tumor microarrays to characterize the frequency of BRG1 loss in different tumor types. We also analyzed BRG1-deficient tumors by sequencing the genomic DNA and the mRNA. We then tested if BRG1 expression could be induced in BRG1-negative cell lines (i.e., that lack mutations in BRG1) after the application of several different epigenetic agents, including drugs that inhibit the AKT pathway. We found that a subset of BRG1-negative cell lines also demonstrated aberrant splicing of BRG1, and in at least 30% of BRG1-deficient tumors, BRG1 expression appeared to be suppressed due to aberrant BRG1 splicing. As the majority of BRG1-deficient tumors lack mutations or splicing defects that could drive BRG1 loss of expression, this suggests that other mechanisms underlie BRG1 silencing. To this end, we analyzed 3 BRG1-deficient nonmutated cancer cell lines and found that BRG1 was inducible in these cell lines upon inhibition of the AKT pathway. We show that the loss of BRG1 is associated with the loss of E-cadherin and up-regulation of Vimentin in primary tumors, which explains why BRG1 loss is associated with a poor prognosis in multiple tumor types.
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Affiliation(s)
| | - Kenneth Thompson
- Division of Hematology/Oncology, Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Li Lu
- Department of Pathology, University of Florida, Gainesville, Florida, USA
| | - David Reisman
- Division of Hematology/Oncology, Department of Medicine, University of Florida, Gainesville, Florida, USA
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12
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Cohen AS, Khalil FK, Welsh EA, Schabath MB, Enkemann SA, Davis A, Zhou JM, Boulware DC, Kim J, Haura EB, Morse DL. Cell-surface marker discovery for lung cancer. Oncotarget 2017; 8:113373-113402. [PMID: 29371917 PMCID: PMC5768334 DOI: 10.18632/oncotarget.23009] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/11/2017] [Indexed: 12/15/2022] Open
Abstract
Lung cancer is the leading cause of cancer deaths in the United States. Novel lung cancer targeted therapeutic and molecular imaging agents are needed to improve outcomes and enable personalized care. Since these agents typically cannot cross the plasma membrane while carrying cytotoxic payload or imaging contrast, discovery of cell-surface targets is a necessary initial step. Herein, we report the discovery and characterization of lung cancer cell-surface markers for use in development of targeted agents. To identify putative cell-surface markers, existing microarray gene expression data from patient specimens were analyzed to select markers with differential expression in lung cancer compared to normal lung. Greater than 200 putative cell-surface markers were identified as being overexpressed in lung cancers. Ten cell-surface markers (CA9, CA12, CXorf61, DSG3, FAT2, GPR87, KISS1R, LYPD3, SLC7A11 and TMPRSS4) were selected based on differential mRNA expression in lung tumors vs. non-neoplastic lung samples and other normal tissues, and other considerations involving known biology and targeting moieties. Protein expression was confirmed by immunohistochemistry (IHC) staining and scoring of patient tumor and normal tissue samples. As further validation, marker expression was determined in lung cancer cell lines using microarray data and Kaplan–Meier survival analyses were performed for each of the markers using patient clinical data. High expression for six of the markers (CA9, CA12, CXorf61, GPR87, LYPD3, and SLC7A11) was significantly associated with worse survival. These markers should be useful for the development of novel targeted imaging probes or therapeutics for use in personalized care of lung cancer patients.
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Affiliation(s)
- Allison S Cohen
- Department of Cancer Imaging and Metabolism, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Farah K Khalil
- Department of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Eric A Welsh
- Biomedical Informatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Steven A Enkemann
- Molecular Genomics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Andrea Davis
- Department of Cancer Imaging and Metabolism, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Jun-Min Zhou
- Biostatistics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - David C Boulware
- Biostatistics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Jongphil Kim
- Department of Biostatistics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.,Department of Oncologic Sciences, College of Medicine, University of South Florida, Tampa, FL, USA
| | - Eric B Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - David L Morse
- Department of Cancer Imaging and Metabolism, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.,Department of Oncologic Sciences, College of Medicine, University of South Florida, Tampa, FL, USA.,Department of Physics, College of Arts and Sciences, University of South Florida, Tampa, FL, USA
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13
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Hou W, Yin J, Vogel U, Sun Z, Liang D. 19p13.3-GADD45B common variants and 19q13.3-PPP1R13L and 19q13.3-CD3EAP in lung cancer risk among Chinese. Chem Biol Interact 2017; 277:74-78. [PMID: 28870783 DOI: 10.1016/j.cbi.2017.08.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 08/29/2017] [Accepted: 08/30/2017] [Indexed: 01/29/2023]
Abstract
Lung cancer is the most common cause of cancer-related mortality worldwide. The GADD45 gene family plays important roles in a variety of the responses to cell injury including cell cycle checkpoints, apoptosis, DNA repair and anti-tumor immunity. The 19p13.3-GADD45B encoded protein product is involved in apoptosis and inhibiting tumor growth. To evaluate the association of 19p13.3-GADD45B common variants and lung cancer risk, the present study containing 544 Chinese lung cancer cases and 550 cancer-free controls was conducted. Three htSNPs (haplotype-tagging single nucleotide polymorphism) (rs7354, rs14384, and rs3783501) covering 95% of the common haplotype diversity in 19p13.3-GADD45B and interaction of 19p13.3-GADD45B and 19q13.3-PPP1R13L and 19q13.3-CD3EAP variants and smoking-duration were explored. Genotype and allele frequencies and haplotype distributions of the 19p13.3-GADD45B 3 htSNPs were not associated with lung cancer risk after adjustment for smoking status. 19p13.3-GADD45B rs7354 was associated with lung cancer risk among ≤20 (years) smokers [C/A-A/A versus CC, OR (95% CI) = 3.20 (1.11-9.20), P = 0.025] in a dominant model stratified by smoking duration. MDR (multifactor dimensionality reduction) analyses showed that smoking history as main effect and three-way models (smoking duration, 19p13.3-GADD45B rs3783501, 19q13.3-CD3EAP rs967591) (P = 0.001-0.002) indicated statistically significant association with lung cancer risk. The study identified evidence implicating DNA damage response genes on chromosome 19 in etiology of smoke-exposed lung cancer. In conclusion, our findings demonstrate that 19p13.3-GADD45B rs7354 variant and interaction between 19p13.3-GADD45B rs3783501 and 19q13.3-CD3EAP rs967591 may play a role in association with smoke-exposed lung cancer among Chinese. 19p13.3-GADD45B variants should be further evaluated in large prospective studies with molecular pathological annotations of lung cancer.
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Affiliation(s)
- Wei Hou
- Key Laboratory of Environment and Population Health of Liaoning Education Ministry (Shenyang Medical College), Shenyang 110034, Liaoning Province, People's Republic of China; Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing 100142, People's Republic of China
| | - Jiaoyang Yin
- Key Laboratory of Environment and Population Health of Liaoning Education Ministry (Shenyang Medical College), Shenyang 110034, Liaoning Province, People's Republic of China.
| | - Ulla Vogel
- National Research Centre for the Working Environment, Lerso Parkalle 105, DK-2100 Copenhagen O, Denmark
| | - Zhenxiang Sun
- Key Laboratory of Environment and Population Health of Liaoning Education Ministry (Shenyang Medical College), Shenyang 110034, Liaoning Province, People's Republic of China
| | - Duohong Liang
- Key Laboratory of Environment and Population Health of Liaoning Education Ministry (Shenyang Medical College), Shenyang 110034, Liaoning Province, People's Republic of China
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14
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Han W, Zhang Z, He B, Xu Y, Zhang J, Cao W. Integrated analysis of long non-coding RNAs in human gastric cancer: An in silico study. PLoS One 2017; 12:e0183517. [PMID: 28841672 PMCID: PMC5571953 DOI: 10.1371/journal.pone.0183517] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 08/04/2017] [Indexed: 02/04/2023] Open
Abstract
Accumulating evidence highlights the important role of long non-coding RNAs (lncRNAs) in a large number of biological processes. However, the knowledge of genome scale expression of lncRNAs and their potential biological function in gastric cancer is still lacking. Using RNA-seq data from 420 gastric cancer patients in The Cancer Genome Atlas (TCGA), we identified 1,294 lncRNAs differentially expressed in gastric cancer compared with adjacent normal tissues. We also found 247 lncRNAs differentially expressed between intestinal subtype and diffuse subtype. Survival analysis revealed 33 lncRNAs independently associated with patient overall survival, of which 6 lncRNAs were validated in the internal validation set. There were 181 differentially expressed lncRNAs located in the recurrent somatic copy number alterations (SCNAs) regions and their correlations between copy number and RNA expression level were also analyzed. In addition, we inferred the function of lncRNAs by construction of a co-expression network for mRNAs and lncRNAs. Together, this study presented an integrative analysis of lncRNAs in gastric cancer and provided a valuable resource for further functional research of lncRNAs in gastric cancer.
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Affiliation(s)
- Weiwei Han
- Department of Gastroenterology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Zhenyu Zhang
- Department of Gastroenterology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Bangshun He
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yijun Xu
- Department of Gastroenterology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Jun Zhang
- Department of Gastroenterology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Weijun Cao
- Department of Gastroenterology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
- * E-mail:
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15
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Critical roles of mucin-1 in sensitivity of lung cancer cells to tumor necrosis factor-alpha and dexamethasone. Cell Biol Toxicol 2017; 33:361-371. [DOI: 10.1007/s10565-017-9393-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 04/18/2017] [Indexed: 12/16/2022]
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16
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Lu J, Liu Q, Wang L, Tu W, Chu H, Ding W, Jiang S, Ma Y, Shi X, Pu W, Zhou X, Jin L, Wang J, Wu W. Increased expression of latent TGF-β-binding protein 4 affects the fibrotic process in scleroderma by TGF-β/SMAD signaling. J Transl Med 2017; 97:591-601. [PMID: 28263294 DOI: 10.1038/labinvest.2017.20] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 01/03/2017] [Accepted: 01/13/2017] [Indexed: 01/06/2023] Open
Abstract
Scleroderma is a fibrosis-related disorder characterized by cutaneous and internal organ fibrosis, and excessive collagen deposition in extracellular matrix (ECM) is a major cause of fibrosis. Transforming growth factor-β (TGF-β)/SMAD signaling has a central role in the pathogenesis of fibrosis by inducing abnormal collagen accumulation in ECM, and latent TGF-β-binding protein 4 (LTBP-4) affects the secretion of latent TGF-β to ECM. A previous study indicated that bleomycin (BLM) treatment increased LTBP-4 expression in lung fibroblasts of Thy-1 knockout mice with lung fibrosis, and LTBP-4 further promoted TGF-β bioavailability as well as SMAD3 phosphorylation. However, the expression and function of LTBP-4 in human scleroderma remain unclear. We aimed to investigate the potential role of LTBP-4 in scleroderma through clinical, in vivo and in vitro studies. LTBP-4 and TGF-β expressions were significantly upregulated in systemic scleroderma (SSc) patients' plasma compared with normal controls (LTBP-4, 1,215±100.2 vs 542.8±41.7 ng/ml, P<0.0001; TGF-β, 1.5±0.2 vs 0.7±0.1 ng/ml, P=0.0031), while no significant difference was found between localized scleroderma (LSc) and normal controls. The plasma concentrations of LTBP-4 and TGF-β were even higher in SSc patients with lung fibrosis (LTBP-4, 1462± 137.3 vs 892.8±113.4 ng/ml, P=0.0037; TGF-β, 2.0±0.4 vs 0.9±0.2 ng/ml, P=0.0212) and esophagus involvement (1390±134.4 vs 940.7±127.0 ng/ml, P=0.0269; TGF-β, 1.9±0.3 vs 0.9±0.2 ng/ml, P=0.0426). The area under receiver operating characteristics (ROC) curve of LTBP-4 was 0.86. Immunohistochemistry measurement also demonstrated a higher LTBP-4 expression in sclerotic skin tissue of LSc and SSc compared with normal controls. More positive fibroblasts were also found in BLM-induced scleroderma mouse model than the saline-treated group. In in vitro studies, knockdown of LTBP-4 in SSc skin fibroblasts prominently reduced downstream COL1A1, COL1A2, and COL3A1 mRNA level by 84%, 82%, and 43%, respectively, and other fibrosis-related genes' expression were also decreased. Furthermore, extracellular TGF-β level and the SMAD2/3 phosphorylation were inhibited through LTBP-4 knockdown treatment, suggesting that the knockdown of LTBP-4 reduced the collagen expression through TGF-β/SMAD signaling pathway. Taken together, these data suggest that LTBP-4 affects fibrotic process in scleroderma, and the high expression of LTBP-4 in SSc plasma may serve as a clinical biomarker in diagnosing this disease. In addition, this study also lays the theoretical foundation for targeting LTBP-4 as treatment of scleroderma.
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Affiliation(s)
- Jiaying Lu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Qingmei Liu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Lei Wang
- Division of Rheumatology, Shanghai TCM-integrated Hospital, Shanghai, China
| | - Wenzhen Tu
- Division of Rheumatology, Shanghai TCM-integrated Hospital, Shanghai, China
| | - Haiyan Chu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Weifeng Ding
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Shuai Jiang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Yanyun Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiangguang Shi
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Weilin Pu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiaodong Zhou
- University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, China
| | - Wenyu Wu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
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17
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Kakizaki F, Sonoshita M, Miyoshi H, Itatani Y, Ito S, Kawada K, Sakai Y, Taketo MM. Expression of metastasis suppressor gene AES driven by a Yin Yang (YY) element in a CpG island promoter and transcription factor YY2. Cancer Sci 2017; 107:1622-1631. [PMID: 27561171 PMCID: PMC5132282 DOI: 10.1111/cas.13063] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 08/21/2016] [Accepted: 08/23/2016] [Indexed: 01/25/2023] Open
Abstract
We recently found that the product of the AES gene functions as a metastasis suppressor of colorectal cancer (CRC) in both humans and mice. Expression of amino‐terminal enhancer of split (AES) protein is significantly decreased in liver metastatic lesions compared with primary colon tumors. To investigate its downregulation mechanism in metastases, we searched for transcriptional regulators of AES in human CRC and found that its expression is reduced mainly by transcriptional dysregulation and, in some cases, by additional haploidization of its coding gene. The AES promoter‐enhancer is in a typical CpG island, and contains a Yin‐Yang transcription factor recognition sequence (YY element). In human epithelial cells of normal colon and primary tumors, transcription factor YY2, a member of the YY family, binds directly to the YY element, and stimulates expression of AES. In a transplantation mouse model of liver metastases, however, expression of Yy2 (and therefore of Aes) is downregulated. In human CRC metastases to the liver, the levels of AES protein are correlated with those of YY2. In addition, we noticed copy‐number reduction for the AES coding gene in chromosome 19p13.3 in 12% (5/42) of human CRC cell lines. We excluded other mechanisms such as point or indel mutations in the coding or regulatory regions of the AES gene, CpG methylation in the AES promoter enhancer, expression of microRNAs, and chromatin histone modifications. These results indicate that Aes may belong to a novel family of metastasis suppressors with a CpG‐island promoter enhancer, and it is regulated transcriptionally.
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Affiliation(s)
- Fumihiko Kakizaki
- Department of Pharmacology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Division of Experimental Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiro Sonoshita
- Department of Pharmacology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Hiroyuki Miyoshi
- Division of Experimental Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Gastrointestinal Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshiro Itatani
- Department of Pharmacology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Gastrointestinal Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Shinji Ito
- Medical Research Support Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kenji Kawada
- Gastrointestinal Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshiharu Sakai
- Gastrointestinal Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - M Mark Taketo
- Department of Pharmacology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Division of Experimental Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Gastrointestinal Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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18
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19
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Zhang Y, Wang DC, Shi L, Zhu B, Min Z, Jin J. Genome analyses identify the genetic modification of lung cancer subtypes. Semin Cancer Biol 2017; 42:20-30. [DOI: 10.1016/j.semcancer.2016.11.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 11/08/2016] [Indexed: 12/15/2022]
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20
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Wang DC, Wang X. Tomorrow's genome medicine in lung cancer. Semin Cancer Biol 2016; 42:39-43. [PMID: 27840277 DOI: 10.1016/j.semcancer.2016.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 11/08/2016] [Indexed: 02/03/2023]
Abstract
Tomorrow's genome medicine in lung cancer should focus more on the homogeneity and heterogeneity of lung cancer which play an important role in the development of drug resistance, genetic complexity, as well as confusion and difficulty of early diagnosis and therapy. Chromosome positioning and repositioning may contribute to the sensitivity of lung cancer cells to therapy, the heterogeneity associated with drug resistance, and the mechanism of lung carcinogenesis. The CCCTC-binding factor plays critical roles in genome topology and function, increased risk of carcinogenicity, and potential of lung cancer-specific mediations. Chromosome reposition in lung cancer can be regulated by CCCTC binding factor. Single-cell gene sequencing, as part of genome medicine, was paid special attention in lung cancer to understand mechanical phenotypes, single-cell biology, heterogeneity, and chromosome positioning and function of single lung cancer cells. We at first propose to develop an intelligent single-cell robot of human cells to integrate together systems information of molecules, genes, proteins, organelles, membranes, architectures, signals, and functions. It can be a powerful automatic system to assist clinicians in the decision-making, molecular understanding, risk analyzing, and prognosis predicting.
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Affiliation(s)
- Diane C Wang
- Zhongshan Hospital Institute of Clinical Science, Fudan University, Shanghai Institute of Clinical Bioinformatics, Shanghai, China
| | - Xiangdong Wang
- Zhongshan Hospital Institute of Clinical Science, Fudan University, Shanghai Institute of Clinical Bioinformatics, Shanghai, China.
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21
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Hou J, Zhang Y, Zhu Z. Gene heterogeneity in metastasis of colorectal cancer to the lung. Semin Cell Dev Biol 2016; 64:58-64. [PMID: 27590223 DOI: 10.1016/j.semcdb.2016.08.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 08/30/2016] [Indexed: 12/21/2022]
Abstract
Colorectal cancer (CRC) as a heterogeneous disease, is one of the most common and serious cancers with high metastases and mortality. Lung is one of the most common sites of CRC metastases with high heterogeneity between cells, pathways, or molecules. The present review will focus on potential roles of gene heterogeneity in KRAS pathway in the development of CRC metastasis to lung and clinical therapies, which would lead to better understanding of the metastatic control and benefit to the treatment of metastases. KRAS is the central relay for pathways originating at the epidermal growth factor receptor (EGFR) family. KRAS mutation exists in about 40% CRC, associated with higher cumulative incidence of CRC lung metastasis, and acts as an independent predictor of metastasis to lung. Mutations in KRAS can lead to poor response of patients to panitumumab, and inferior progression-free survival. However, most patients with KRAS wild-type tumors still do not respond, which indicates other mutations. Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) mutation was associated with lung metastases in metastatic colorectal cancer. PIK3CA mutation in exon 20 was found to be correlated with patient survival in the metastatic setting after the treatment with cetuximab and chemotherapy. The heterogeneity of KRAS pathway was found in the phosphatase and tensin homologue deleted on chromosome ten loss, disheveled binding antagonist of beta catenin 2 overexpression and increased dual-specificity protein phosphatase 4 expression of CRC lung metastasis.
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Affiliation(s)
- Jiayun Hou
- Zhongshan Hospital Institute of Clinical Science, Fudan University, Shanghai Institute of Clinical Bioinformatics, Biomedical Research Center, Shanghai, China
| | - Yong Zhang
- Zhongshan Hospital Institute of Clinical Science, Fudan University, Shanghai Institute of Clinical Bioinformatics, Biomedical Research Center, Shanghai, China.
| | - Zhitu Zhu
- Jinzhou Hospital of Jinzhou Medical University, JinZhou, China.
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22
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Wang DC, Wang X. Systems heterogeneity: An integrative way to understand cancer heterogeneity. Semin Cell Dev Biol 2016; 64:1-4. [PMID: 27552921 DOI: 10.1016/j.semcdb.2016.08.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 08/19/2016] [Indexed: 12/14/2022]
Abstract
The concept of systems heterogeneity was firstly coined and explained in the Special Issue, as a new alternative to understand the importance and complexity of heterogeneity in cancer. Systems heterogeneity can offer a full image of heterogeneity at multi-dimensional functions and multi-omics by integrating gene or protein expression, epigenetics, sequencing, phosphorylation, transcription, pathway, or interaction. The Special Issue starts with the roles of epigenetics in the initiation and development of cancer heterogeneity through the interaction between permanent genetic mutations and dynamic epigenetic alterations. Cell heterogeneity was defined as the difference in biological function and phenotypes between cells in the same organ/tissue or in different organs, as well as various challenges, as exampled in telocytes. The single cell heterogeneity has the value of identifying diagnostic biomarkers and therapeutic targets and clinical potential of single cell systems heterogeneity in clinical oncology. A number of signaling pathways and factors contribute to the development of systems heterogeneity. Proteomic heterogeneity can change the strategy and thinking of drug discovery and development by understanding the interactions between proteins or proteins with drugs in order to optimize drug efficacy and safety. The association of cancer heterogeneity with cancer cell evolution and metastasis was also overviewed as a new alternative for diagnostic biomarkers and therapeutic targets in clinical application.
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Affiliation(s)
- Diane Catherine Wang
- Minghang Hospital of Fudan University, Shanghai Medical College, Shanghai, China
| | - Xiangdong Wang
- Minghang Hospital of Fudan University, Shanghai Medical College, Shanghai, China.
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23
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Wang X. CBT profiles of cabozantinib approved for advanced renal cell carcinomas. Cell Biol Toxicol 2016; 32:259-61. [DOI: 10.1007/s10565-016-9349-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 06/30/2016] [Indexed: 12/27/2022]
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24
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Geles KG, Zhong W, O'Brien SK, Baxter M, Loreth C, Pallares D, Damelin M. Upregulation of RNA Processing Factors in Poorly Differentiated Lung Cancer Cells. Transl Oncol 2016; 9:89-98. [PMID: 27084424 PMCID: PMC4833891 DOI: 10.1016/j.tranon.2016.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 01/11/2016] [Accepted: 01/19/2016] [Indexed: 12/22/2022] Open
Abstract
Intratumoral heterogeneity in non–small cell lung cancer (NSCLC) has been appreciated at the histological and cellular levels, but the association of less differentiated pathology with poor clinical outcome is not understood at the molecular level. Gene expression profiling of intact human tumors fails to reveal the molecular nature of functionally distinct epithelial cell subpopulations, in particular the tumor cells that fuel tumor growth, metastasis, and disease relapse. We generated primary serum-free cultures of NSCLC and then exposed them to conditions known to promote differentiation: the air-liquid interface (ALI) and serum. The transcriptional network of the primary cultures was associated with stem cells, indicating a poorly differentiated state, and worse overall survival of NSCLC patients. Strikingly, the overexpression of RNA splicing and processing factors was a prominent feature of the poorly differentiated cells and was also observed in clinical datasets. A genome-wide analysis of splice isoform expression revealed many alternative splicing events that were specific to the differentiation state of the cells, including an unexpectedly high frequency of events on chromosome 19. The poorly differentiated cells exhibited alternative splicing in many genes associated with tumor progression, as exemplified by the preferential expression of the short isoform of telomeric repeat-binding factor 1 (TERF1), also known as Pin2. Our findings demonstrate the utility of the ALI method for probing the molecular mechanisms that underlie NSCLC pathogenesis and provide novel insight into posttranscriptional mechanisms in poorly differentiated lung cancer cells.
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Affiliation(s)
- Kenneth G Geles
- Pfizer Inc., Oncology-Rinat Research & Development, 401 N. Middletown Rd., Pearl River, NY 10965 USA
| | - Wenyan Zhong
- Pfizer Inc., Oncology-Rinat Research & Development, 401 N. Middletown Rd., Pearl River, NY 10965 USA
| | - Siobhan K O'Brien
- Pfizer Inc., Oncology-Rinat Research & Development, 401 N. Middletown Rd., Pearl River, NY 10965 USA
| | - Michelle Baxter
- Pfizer Inc., Oncology-Rinat Research & Development, 401 N. Middletown Rd., Pearl River, NY 10965 USA
| | - Christine Loreth
- Pfizer Inc., Oncology-Rinat Research & Development, 401 N. Middletown Rd., Pearl River, NY 10965 USA
| | | | - Marc Damelin
- Pfizer Inc., Oncology-Rinat Research & Development, 401 N. Middletown Rd., Pearl River, NY 10965 USA.
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