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Stecklein SR, Barlow W, Pusztai L, Timms K, Kennedy R, Logan GE, Seitz R, Badve S, Gökmen-Polar Y, Porter P, Linden H, Tripathy D, Hortobagyi GN, Godwin AK, Thompson A, Hayes DF, Sharma P. Dual Prognostic Classification of Triple-Negative Breast Cancer by DNA Damage Immune Response and Homologous Recombination Deficiency. JCO Precis Oncol 2023; 7:e2300197. [PMID: 37972336 PMCID: PMC10681491 DOI: 10.1200/po.23.00197] [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: 04/24/2023] [Revised: 07/12/2023] [Accepted: 09/11/2023] [Indexed: 11/19/2023] Open
Abstract
PURPOSE Triple-negative breast cancer (TNBC) is a heterogeneous disease. We previously showed that homologous recombination deficiency (HRD) and the DNA damage immune response (DDIR) signature are prognostic in TNBC. We hypothesized that these biomarkers reflect related but not completely interdependent biological processes, that their combined use would be prognostic, and that simultaneous assessment of the immunologic microenvironment and susceptibility to DNA damaging therapies might be able to identify subgroups with distinct therapeutic vulnerabilities. METHODS We analyzed the dual DDIR/HRD classification in 341 patients with TNBC treated with adjuvant anthracycline-based chemotherapy on the SWOG S9313 trial and corroborated our findings in The Cancer Genome Atlas breast cancer data set. RESULTS DDIR/HRD classification is highly prognostic in TNBC and identifies biologically and immunologically distinct subgroups. Immune-enriched DDIR+/HRD+ TNBCs have the most favorable prognosis, and DDIR+/HRD- and DDIR-/HRD+ TNBCs have favorable intermediate prognosis, despite the latter being immune-depleted. DDIR-/HRD- TNBCs have the worst prognosis and represent an internally heterogeneous group of immune-depleted chemoresistant tumors. CONCLUSION Our findings propose DDIR/HRD classification as a potentially clinically relevant approach to categorize tumors on the basis of therapeutic vulnerabilities.
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Affiliation(s)
| | | | | | | | - Richard Kennedy
- Almac Diagnostic Services, Craigavon, Northern Ireland, United Kingdom
- Patrick G Johnston Centre for Cancer Research, Queen's University of Belfast, Belfast, United Kingdom
| | - Gemma E. Logan
- Almac Diagnostic Services, Craigavon, Northern Ireland, United Kingdom
| | | | - Sunil Badve
- Emory University School of Medicine, Atlanta, GA
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Ohira T, Yoshimura K, Kugoh H. Human artificial chromosome carrying 3p21.3-p22.2 region suppresses hTERT transcription in oral cancer cells. Chromosome Res 2023; 31:17. [PMID: 37353691 PMCID: PMC10289923 DOI: 10.1007/s10577-023-09726-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/24/2023] [Accepted: 06/06/2023] [Indexed: 06/25/2023]
Abstract
Telomerase is a ribonucleoprotein ribonucleic enzyme that elongates telomere repeat sequences at the ends of chromosomes and contributes to cellular immortalization. The catalytic component of telomerase, human telomerase reverse transcriptase (hTERT), has been observed to be reactivated in immortalized cells. Notably, most cancer cells have been found to have active hTERT mRNA transcription, resulting in continuous cell division, which is crucial for malignant transformation. Therefore, discovering mechanisms underlying the regulation of hTERT transcription is an attractive target for cancer-specific treatments.Loss of heterozygosity (LOH) of chromosome 3p21.3 has been frequently observed in human oral squamous cell carcinoma (OSCC). Moreover, we previously reported that HSC3 OSCC microcell hybrid clones with an introduced human chromosome 3 (HSC3#3) showed inhibition of hTERT transcription compared with the parental HSC3 cells. This study examined whether hTERT transcription regulators are present in the 3p21.3 region. We constructed a human artificial chromosome (HAC) vector (3p21.3-HAC) with only the 3p21.3-p22.2 region and performed functional analysis using the 3p21.3-HAC. HSC3 microcell hybrid clones with an introduced 3p21.3-HAC exhibited significant suppression of hTERT transcription, similar to the microcell hybrid clones with an intact chromosome 3. In contrast, HSC3 clones with truncated chromosome 3 with deletion of the 3p21.3 region (3delp21.3) showed no effect on hTERT expression levels. These results provide direct evidence that hTERT suppressor gene(s) were retained in the 3p21.3 region, suggesting that the presence of regulatory factors that control telomerase enzyme activity may be involved in the development of OSCC.
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Affiliation(s)
- Takahito Ohira
- Department of Chromosome Biomedical Engineering, Tottori University, 86 Nishi-Cho, Yonago, Tottori, 683-8503, Japan
- Chromosome Engineering Research Center, Tottori University, 86 Nishi-Cho, Yonago, Tottori, 683-8503, Japan
| | - Kaho Yoshimura
- Department of Chromosome Biomedical Engineering, Tottori University, 86 Nishi-Cho, Yonago, Tottori, 683-8503, Japan
| | - Hiroyuki Kugoh
- Department of Chromosome Biomedical Engineering, Tottori University, 86 Nishi-Cho, Yonago, Tottori, 683-8503, Japan.
- Chromosome Engineering Research Center, Tottori University, 86 Nishi-Cho, Yonago, Tottori, 683-8503, Japan.
- Division of Genome and Cellular Function, Department of Molecular and Cellular Biology, Tottori University, 86 Nishi-Cho, Yonago, Tottori, 683-8503, Japan.
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Du X, Zhao Z, Zhao X, Wang H, Jiang L, Tang W. Risk signature identification and NPRL2 affects sunitinib sensitivity in clear cell renal cell carcinoma. Biochem Biophys Res Commun 2023; 663:122-131. [PMID: 37121122 DOI: 10.1016/j.bbrc.2023.04.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/09/2023] [Accepted: 04/19/2023] [Indexed: 05/02/2023]
Abstract
Tumor suppressor genes (TSGs) play a crucial role in tumorigenesis and drug resistance. We analyzed the subtypes of clear cell renal cell carcinoma (ccRCC) mediated by 8 genes contained in the 3p21.3 tumor suppressor gene cluster and their effects on TME cell infiltration based on the TCGA database. The risk score model was established by principal component analysis. The hub gene NPRL2 was selected by protein-protein interactions (PPI) analysis. The effect of NPRL2 on sunitinib sensitivity of ccRCC was verified by using CCK-8, colony formation assay, wound healing assay, transwell assay and xenograft tumor model. Changes in protein expression were detected by Western blotting. We found that 8 TSGs were all differentially expressed in ccRCC samples, which could divide ccRCC into two subtypes. The constructed risk score model could predict the prognosis and drug sensitivity of ccRCC patients, and was an independent prognostic factor for ccRCC. Over-expression of NPRL2 promoted apoptosis, inhibited EMT, decreased the phosphorylation of the PI3K/AKT/mTOR signaling pathway to inhibit its activity, and promoted the sensitivity of sunitinib to ccRCC cells. Collectively, our findings increased the understanding of TSGs in ccRCC, suggesting that NPRL2 as a TSG could enhance sunitinib sensitivity to ccRCC cells.
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Affiliation(s)
- Xiaoyi Du
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhipeng Zhao
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xin Zhao
- Department of Urology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Hexi Wang
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Li Jiang
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Wei Tang
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
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Lu J, Fu LM, Cao Y, Fang Y, Cao JZ, Pan YH, Cen JJ, Liang YP, Chen ZH, Wei JH, Huang Y, Mumin MA, Xu QH, Wang YH, Zhu JQ, Liang H, Wang Z, Deng Q, Chen W, Jin XH, Liu ZP, Luo JH. LZTFL1 inhibits kidney tumor cell growth by destabilizing AKT through ZNRF1-mediated ubiquitin proteosome pathway. Oncogene 2023; 42:1543-1557. [PMID: 36966254 PMCID: PMC10039360 DOI: 10.1038/s41388-023-02666-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 03/01/2023] [Accepted: 03/10/2023] [Indexed: 03/27/2023]
Abstract
LZTFL1 is a tumor suppressor located in chromosomal region 3p21.3 that is deleted frequently and early in various cancer types including the kidney cancer. However, its role in kidney tumorigenesis remains unknown. Here we hypothesized a tumor suppressive function of LZTFL1 in clear cell renal cell carcinoma (ccRCC) and its mechanism of action based on extensive bioinformatics analysis of patients' tumor data and validated it using both gain- and loss-functional studies in kidney tumor cell lines and patient-derive xenograft (PDX) model systems. Our studies indicated that LZTFL1 inhibits kidney tumor cell proliferation by destabilizing AKT through ZNRF1-mediated ubiquitin proteosome pathway and inducing cell cycle arrest at G1. Clinically, we found that LZTFL1 is frequently deleted in ccRCC. Downregulation of LZTFL1 is associated with a poor ccRCC outcome and may be used as prognostic maker. Furthermore, we show that overexpression of LZTFL1 in PDX via lentiviral delivery suppressed PDX growth, suggesting that re-expression of LZTFL1 may be a therapeutic strategy against ccRCC.
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Affiliation(s)
- Jun Lu
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
- Departments of Internal Medicine and Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Liang-Min Fu
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Yun Cao
- Department of Pathology, Sun Yat-sen University Cancer Center of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Yong Fang
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Jia-Zheng Cao
- Department of Urology, Jiangmen Central Hospital, Jiangmen, Guangdong Province, People's Republic of China
| | - Yi-Hui Pan
- Department of Urology, The First People's Hospital of Changzhou, Changzhou, Jiangsu, People's Republic of China
| | - Jun-Jie Cen
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
- Departments of Internal Medicine and Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yan-Ping Liang
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
- Departments of Internal Medicine and Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Zhen-Hua Chen
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
- Departments of Internal Medicine and Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jin-Huan Wei
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Yong Huang
- Department of Emergency, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Mukhtar Adan Mumin
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Quan-Hui Xu
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Ying-Han Wang
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Jiang-Quan Zhu
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Hui Liang
- Department of Urology, Affiliated Longhua People's Hospital, Southern Medical University, Shenzhen, Guangdong Province, People's Republic of China
| | - Zhu Wang
- Department of Urology, Affiliated Longhua People's Hospital, Southern Medical University, Shenzhen, Guangdong Province, People's Republic of China
| | - Qiong Deng
- Department of Urology, Affiliated Longhua People's Hospital, Southern Medical University, Shenzhen, Guangdong Province, People's Republic of China
| | - Wei Chen
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Xiao-Han Jin
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China.
| | - Zhi-Ping Liu
- Departments of Internal Medicine and Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Jun-Hang Luo
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China.
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[Detection of DNA methylation of HYAL2 gene for differentiating malignant from benign thyroid tumors]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2022; 42:123-129. [PMID: 35249879 PMCID: PMC8901399 DOI: 10.12122/j.issn.1673-4254.2022.01.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
OBJECTIVE To assess the value of DNA methylation level of HYAL2 gene as a molecular marker for differential diagnosis of malignant and benign thyroid tumors. METHODS DNA methylation of HYAL2 gene in tissue specimens of 190 patients with papillary thyroid cancer (PTC) and 190 age- and gender-matched patients with benign thyroid tumors was examined by mass spectrometry, and the protein expression of HYAL2 was detected immunohistochemically for another 55 pairs of patients. Logistic regression analysis was performed to calculate the odds ratio (OR) and evaluate the correlation of per 10% reduction in DNA methylation with PTC. Receiver operating characteristic (ROC) curve analysis was performed and the area under curve (AUC) was calculated to assess the predictive value of alterations in HYAL2 methylation. RESULTS Hypomethylation of HYAL2_CpG_3 was significantly correlated with early-stage PTC (OR=1.51, P=0.001), even in stage I cancer (OR=1.42, P=0.007). Age-stratified analysis revealed a significantly stronger correlation between increased HYAL2_CpG_ 3 methylation and early-stage PTC in patients below 50 years than in those older than 50 years (OR: 1.89 vs 1.37, P < 0.05); ROC analysis also showed a larger AUC of 0.787 in younger patients. The results of immunohistochemistry showed that patients with PTC had significantly higher protein expressions of HYAL2 than patients with benign tumors. CONCLUSION The alterations of DNA methylation level of HYAL2 gene is significantly correlated with early-stage PTC, suggesting the value of DNA methylation level as a potential biomarker for differentiation of malignant from benign thyroid tumors.
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Sun S, Kong Q, Cai Z, Wang M, Zhao H, Zhao C. circ‑Grm1 promotes pulmonary artery smooth muscle cell proliferation and migration via suppression of GRM1 expression by FUS. Int J Mol Med 2021; 48:202. [PMID: 34528696 PMCID: PMC8480385 DOI: 10.3892/ijmm.2021.5035] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/02/2021] [Indexed: 01/15/2023] Open
Abstract
Pulmonary arterial hypertension is a progressive and fatal disease. Recent studies suggest that circular RNA (circRNAs/circs) can regulate various biological processes, including cell proliferation. Therefore, it is possible that circRNA may have important roles in pulmonary artery smooth muscle cell proliferation in hypoxic pulmonary hypertension (HPH). The aim of the present study was to determine the role and mechanism of circRNA‑glutamate metabotropic receptor 1 (circ‑Grm1; mmu_circ_0001907) in pulmonary artery smooth muscle cell (PASMC) proliferation and migration in HPH. High‑throughput transcriptome sequencing was used to screen circRNAs and targeted genes involved in HPH. Cell Counting Kit‑8 (CCK‑8), 5‑ethynyl‑2‑deoxyuridine and wound healing assays were employed to assess cell viability and migration. Reverse transcription‑quantitative PCR and western blotting were used to detect target gene expression in different groups. Bioinformatical approaches were used to predict the interaction probabilities of circ‑Grm1 and Grm1 with FUS RNA binding protein (FUS). The interactions of circ‑Grm1, Grm1 and FUS were evaluated using RNA silencing and RNA immunoprecipitation assays. The results demonstrated that circ‑Grm1 was upregulated in hypoxic PASMCs. Further experiments revealed that the knockdown of circ‑Grm1 could suppress the proliferation and migration of hypoxic PASMCs. Transcriptome sequencing revealed that Grm1 could be the target gene of circ‑Grm1. It was found that circ‑Grm1 could competitively bind to FUS and consequently downregulate Grm1. Moreover, Grm1 could inhibit the function of circ‑Grm1 by promoting the proliferative and migratory abilities of hypoxic PASMCs. The results also demonstrated that circ‑Grm1 influenced the biological functions of PASMCs via the Rap1/ERK pathway by regulating Grm1. Overall, the current results suggested that circ‑Grm1 was associated with HPH and promoted the proliferation and migration of PASMCs via suppression of Grm1 expression through FUS.
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Affiliation(s)
- Shijing Sun
- Department of Pediatrics, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
- Department of Pediatrics, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, Shandong 266034, P.R. China
| | - Qingyu Kong
- Department of Pediatrics, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Zhifeng Cai
- Department of Pediatrics, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Minmin Wang
- Department of Pediatrics, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Haizhao Zhao
- Department of Pediatrics, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Cuifen Zhao
- Department of Pediatrics, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
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Fang L, Shi L, Wang W, Chen Q, Rao X. Identifying key genes and small molecule compounds for nasopharyngeal carcinoma by various bioinformatic analysis. Medicine (Baltimore) 2021; 100:e27257. [PMID: 34664875 PMCID: PMC8448020 DOI: 10.1097/md.0000000000027257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 08/30/2021] [Indexed: 12/24/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC) is one of the most prevalent head and neck cancer in southeast Asia. It is necessary to proceed further studies on the mechanism of occurrence and development of NPC.In this study, we employed the microarray dataset GSE12452 and GSE53819 including 28 normal samples and 49 nasopharyngeal carcinoma samples downloaded from the Gene Expression Omnibus(GEO) to analysis. R software, STRING, CMap, and various databases were used to screen differentially expressed genes (DEGs), construct the protein-protein interaction (PPI) network, and proceed small molecule compounds analysis, among others.Totally, 424 DEGs were selected from the dataset. DEGs were mainly enriched in extracellular matrix organization, cilium organization, PI3K-Akt signaling pathway, collagen-containing extracellular matrix, and extracellular matrix-receptor interaction, among others. Top 10 upregulated and top 10 downregulated hub genes were identified as hub DEGs. Piperlongumine, apigenin, menadione, 1,4-chrysenequinone, and chrysin were identified as potential drugs to prevent and treat NPC. Besides, the effect of genes CDK1, CDC45, RSPH4A, and ZMYND10 on survival of NPC was validated in GEPIA database.The data revealed novel aberrantly expressed genes and pathways in NPC by bioinformatics analysis, potentially providing novel insights for the molecular mechanisms governing NPC progression. Although further studies needed, the results demonstrated that the expression levels of CDK1, CDC45, RSPH4A, and ZMYND10 probably affected survival of NPC patients.
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Affiliation(s)
- Lucheng Fang
- First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, Zhejiang Province, China
| | - Licai Shi
- First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, Zhejiang Province, China
| | - Wen Wang
- First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, Zhejiang Province, China
| | - Qinjuan Chen
- Second Affiliated Hospital of Wenzhou Medical University, Wenzhou City, Zhejiang Province, China
| | - Xingwang Rao
- First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, Zhejiang Province, China
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Convergent evolution of a genomic rearrangement may explain cancer resistance in hystrico- and sciuromorpha rodents. NPJ Aging Mech Dis 2021; 7:20. [PMID: 34471123 PMCID: PMC8410860 DOI: 10.1038/s41514-021-00072-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 06/21/2021] [Indexed: 11/09/2022] Open
Abstract
The rodents of hystricomorpha and sciuromorpha suborders exhibit remarkably lower incidence of cancer. The underlying genetic basis remains obscure. We report a convergent evolutionary split of human 3p21.31, a locus hosting a large number of tumour-suppressor genes (TSGs) and frequently deleted in several tumour types, in hystrico- and sciuromorphs. Analysis of 34 vertebrate genomes revealed that the synteny of 3p21.31 cluster is functionally and evolutionarily constrained in most placental mammals, but exhibit large genomic interruptions independently in hystricomorphs and sciuromorphs, owing to relaxation of underlying constraints. Hystrico- and sciuromorphs, therefore, escape from pro-tumorigenic co-deletion of several TSGs in cis. The split 3p21.31 sub-clusters gained proximity to proto-oncogene clusters from elsewhere, which might further nullify pro-tumorigenic impact of copy number variations due to co-deletion or co-amplification of genes with opposing effects. The split of 3p21.31 locus coincided with the accelerated rate of its gene expression and the body mass evolution of ancestral hystrico- and sciuromorphs. The genes near breakpoints were associated with the traits specific to hystrico- and sciuromorphs, implying adaptive significance. We conclude that the convergently evolved chromosomal interruptions of evolutionarily constrained 3p21.31 cluster might have impacted evolution of cancer resistance, body mass variation and ecological adaptations in hystrico- and sciuromorphs.
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Human chromosome 3p21.3 carries TERT transcriptional regulators in pancreatic cancer. Sci Rep 2021; 11:15355. [PMID: 34321527 PMCID: PMC8319171 DOI: 10.1038/s41598-021-94711-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/15/2021] [Indexed: 11/23/2022] Open
Abstract
Frequent loss of heterozygosity (LOH) on the short arm of human chromosome 3 (3p) region has been found in pancreatic cancer (PC), which suggests the likely presence of tumor suppressor genes in this region. However, the functional significance of LOH in this region in the development of PC has not been clearly defined. The human telomerase reverse transcriptase gene (hTERT) contributes to unlimited proliferative and tumorigenicity of malignant tumors. We previously demonstrated that hTERT expression was suppressed by the introduction of human chromosome 3 in several cancer cell lines. To examine the functional role of putative TERT suppressor genes on chromosome 3 in PC, we introduced an intact human chromosome 3 into the human PK9 and murine LTPA PC cell lines using microcell-mediated chromosome transfer. PK9 microcell hybrids with an introduced human chromosome 3 showed significant morphological changes and rapid growth arrest. Intriguingly, microcell hybrid clones of LTPA cells with an introduced human chromosome 3 (LTPA#3) showed suppression of mTert transcription, cell proliferation, and invasion compared with LTPA#4 cells containing human chromosome 4 and parental LTPA cells. Additionally, the promoter activity of mTert was downregulated in LTPA#3. Furthermore, we confirmed that TERT regulatory gene(s) are present in the 3p21.3 region by transfer of truncated chromosomes at arbitrary regions. These results provide important information on the functional significance of the LOH at 3p for development and progression of PC.
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Wang C, Wu Y, Liu Y, Pan F, Zeng H, Li X, Yu L. Tumor Suppressor Effect of RBMS3 in Breast Cancer. Technol Cancer Res Treat 2021; 20:15330338211004921. [PMID: 33910421 PMCID: PMC8107673 DOI: 10.1177/15330338211004921] [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: 11/15/2022] Open
Abstract
Background: RBMS3 (RNA-binding motif, single-stranded-intervacting protein 3) acts as a tumor-suppressive gene in a number of human cancers, however, its role in breast cancer is not fully understood. This study aimed to investigate the expression and clinicopathological significance of RBMS3 in breast cancer. Methods: A total of 998 breast cancer tissue samples in The Cancer Genome Atlas (TCGA) database with survival outcomes were divided into high RBMS3 expression and low expression groups using the median as the cutoff. Clinicopathological characteristics and prognosis were compared between the 2 groups. Results: TCGA showed that RBMS3 mRNA was downregulated in breast cancer tissues, and RBMS3 downregulation was correlated with poor prognosis. Immunohistochemistry staining of 127 paraffin-embedded breast cancer tissues showed that RBMS3 protein was localized in the cytoplasm and nucleus; however, nuclear staining was present in 90.0% of normal breast tissues but only 28.3% of breast cancer tissues. Decreased RBMS3 protein expression was significantly correlated with estrogen receptor (ER)-negative status and death at final follow-up. Patients with lower RBMS3 protein expression had substantially shorter survival than those with higher RBMS3 expression. Univariate and multivariate analysis indicated that the combination of RBMS3 expression and ER status (a variable designated as “cofactor”) was an independent prognostic factor in patients with breast cancer (hazard ratio [HR] = 0.420, 95% confidence interval [CI]: 0.223-0.791, P = 0.007). Conclusion: RBMS3 downregulation was correlated with poor prognosis in breast cancer patients, and the combination of RBMS3 expression and ER status was an independent prognostic factor.
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Affiliation(s)
- Chunyang Wang
- Zhujiang New Town Dental Clinic, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Yidan Wu
- Diagnosis and Treatment Center of Breast Disease, Shantou Central Hospital, Shantou, Guangdong, China
| | - Yunqi Liu
- Department of Cardiac Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Fushun Pan
- Department of Medical Ultrasonics, Institute of Diagnostic and Interventional Ultrasound, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Huijuan Zeng
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiaoxi Li
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Liang Yu
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
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Chen CH, Lin YJ, Lin YY, Lin CH, Feng LY, Chang IYF, Wei KC, Huang CY. Glioblastoma Primary Cells Retain the Most Copy Number Alterations That Predict Poor Survival in Glioma Patients. Front Oncol 2021; 11:621432. [PMID: 33981597 PMCID: PMC8108987 DOI: 10.3389/fonc.2021.621432] [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: 10/26/2020] [Accepted: 04/06/2021] [Indexed: 11/16/2022] Open
Abstract
Gliomas are solid tumors that originate from glial cells in the brain or spine and account for 74.6% of malignant primary central nervous system tumors worldwide. As patient-derived primary cells are important tools for drug screening and new therapy development in glioma, we aim to understand the genomic similarity of the primary cells to their parental tumors by comparing their whole-genome copy number variations and expression profile of glioma clinicopathologic factors. We found that the primary cells from grade II/III gliomas lost most of the gene copy number alterations (CNAs), which were mainly located on chromosome 1p and 19q in their parental tumors. The glioblastoma (GBM) primary cells preserved 83.7% of the gene CNAs in the parental GBM tumors, including chromosome 7 gain and 10q loss. The CNA gains of LINC00226 and ADAM6 and the chromosome 16p11 loss were reconstituted in primary cells from both grade II/III gliomas and GBMs. Interestingly, we found these CNAs were correlated to overall survival (OS) in glioma patients using the Merged Cohort LGG and GBM dataset from cBioPortal. The gene CNAs preserved in glioma primary cells often predicted poor survival, whereas the gene CNAs lost in grade II/III primary cells were mainly associated to better prognosis in glioma patients. Glioma prognostic factors that predict better survival, such as IDH mutations and 1p/19q codeletion in grade II/III gliomas, were lost in their primary cells, whereas methylated MGMT promoters as well as TERT promoter mutations were preserved in GBM primary cells while lost in grade II/III primary cells. Our results suggest that GBM primary cells tend to preserve CNAs in their parental tumors, and these CNAs are correlated to poor OS and predict worse prognosis in glioma patients.
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Affiliation(s)
- Chia-Hua Chen
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Department of Neurosurgery, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Ya-Jui Lin
- Department of Neurosurgery, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan.,The Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - You-Yu Lin
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chang-Hung Lin
- Department of Neurosurgery, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan.,Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Li-Ying Feng
- School of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Neurosurgery, New Taipei Municipal TuCheng Hospital, New Taipei City, Taiwan
| | - Ian Yi-Feng Chang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Department of Neurosurgery, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Kuo-Chen Wei
- Department of Neurosurgery, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan.,School of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Neurosurgery, New Taipei Municipal TuCheng Hospital, New Taipei City, Taiwan
| | - Chiung-Yin Huang
- School of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Neurosurgery, New Taipei Municipal TuCheng Hospital, New Taipei City, Taiwan
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12
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Chhabra R, Rockfield S, Guergues J, Nadeau OW, Hill R, Stevens SM, Nanjundan M. Global miRNA/proteomic analyses identify miRNAs at 14q32 and 3p21, which contribute to features of chronic iron-exposed fallopian tube epithelial cells. Sci Rep 2021; 11:6270. [PMID: 33737539 PMCID: PMC7973504 DOI: 10.1038/s41598-021-85342-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 03/01/2021] [Indexed: 02/06/2023] Open
Abstract
Malignant transformation of fallopian tube secretory epithelial cells (FTSECs) is a key contributing event to the development of high-grade serous ovarian carcinoma (HGSOC). Our recent findings implicate oncogenic transformative events in chronic iron-exposed FTSECs, including increased expression of oncogenic mediators, increased telomerase transcripts, and increased growth/migratory potential. Herein, we extend these studies by implementing an integrated transcriptomic and mass spectrometry-based proteomics approach to identify global miRNA and protein alterations, for which we also investigate a subset of these targets to iron-induced functional alterations. Proteomic analysis identified > 4500 proteins, of which 243 targets were differentially expressed. Sixty-five differentially expressed miRNAs were identified, of which 35 were associated with the “top” proteomic molecules (> fourfold change) identified by Ingenuity Pathway Analysis. Twenty of these 35 miRNAs are at the 14q32 locus (encoding a cluster of 54 miRNAs) with potential to be regulated by DNA methylation and histone deacetylation. At 14q32, miR-432-5p and miR-127-3p were ~ 100-fold downregulated whereas miR-138-5p was 16-fold downregulated at 3p21 in chronic iron-exposed FTSECs. Combinatorial treatment with methyltransferase and deacetylation inhibitors reversed expression of these miRNAs, suggesting chronic iron exposure alters miRNA expression via epigenetic alterations. In addition, PAX8, an important target in HGSOC and a potential miRNA target (from IPA) was epigenetically deregulated in iron-exposed FTSECs. However, both PAX8 and ALDH1A2 (another IPA-predicted target) were experimentally identified to be independently regulated by these miRNAs although TERT RNA was partially regulated by miR-138-5p. Interestingly, overexpression of miR-432-5p diminished cell numbers induced by long-term iron exposure in FTSECs. Collectively, our global profiling approaches uncovered patterns of miRNA and proteomic alterations that may be regulated by genome-wide epigenetic alterations and contribute to functional alterations induced by chronic iron exposure in FTSECs. This study may provide a platform to identify future biomarkers for early ovarian cancer detection and new targets for therapy.
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Affiliation(s)
- Ravneet Chhabra
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, 33620, USA
| | - Stephanie Rockfield
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, 33620, USA.,Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jennifer Guergues
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, 33620, USA.,Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, VT, 05446, USA
| | - Owen W Nadeau
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, VT, 05446, USA
| | - Robert Hill
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, 33620, USA
| | - Stanley M Stevens
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, 33620, USA.,Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, VT, 05446, USA
| | - Meera Nanjundan
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, 33620, USA.
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13
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Abstract
Post-translational modifications of cellular substrates with ubiquitin and ubiquitin-like proteins (UBLs), including ubiquitin, SUMOs, and neural precursor cell-expressed developmentally downregulated protein 8, play a central role in regulating many aspects of cell biology. The UBL conjugation cascade is initiated by a family of ATP-dependent enzymes termed E1 activating enzymes and executed by the downstream E2-conjugating enzymes and E3 ligases. Despite their druggability and their key position at the apex of the cascade, pharmacologic modulation of E1s with potent and selective drugs has remained elusive until 2009. Among the eight E1 enzymes identified so far, those initiating ubiquitylation (UBA1), SUMOylation (SAE), and neddylation (NAE) are the most characterized and are implicated in various aspects of cancer biology. To date, over 40 inhibitors have been reported to target UBA1, SAE, and NAE, including the NAE inhibitor pevonedistat, evaluated in more than 30 clinical trials. In this Review, we discuss E1 enzymes, the rationale for their therapeutic targeting in cancer, and their different inhibitors, with emphasis on the pharmacologic properties of adenosine sulfamates and their unique mechanism of action, termed substrate-assisted inhibition. Moreover, we highlight other less-characterized E1s-UBA6, UBA7, UBA4, UBA5, and autophagy-related protein 7-and the opportunities for targeting these enzymes in cancer. SIGNIFICANCE STATEMENT: The clinical successes of proteasome inhibitors in cancer therapy and the emerging resistance to these agents have prompted the exploration of other signaling nodes in the ubiquitin-proteasome system including E1 enzymes. Therefore, it is crucial to understand the biology of different E1 enzymes, their roles in cancer, and how to translate this knowledge into novel therapeutic strategies with potential implications in cancer treatment.
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Affiliation(s)
- Samir H Barghout
- Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada (S.H.B., A.D.S.); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (S.H.B., A.D.S.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Tanta University, Tanta, Egypt (S.H.B.)
| | - Aaron D Schimmer
- Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada (S.H.B., A.D.S.); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (S.H.B., A.D.S.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Tanta University, Tanta, Egypt (S.H.B.)
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14
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Yin Q, Yang X, Li L, Xu T, Zhou W, Gu W, Ma F, Yang R. The Association Between Breast Cancer and Blood-Based Methylation of S100P and HYAL2 in the Chinese Population. Front Genet 2020; 11:977. [PMID: 33005177 PMCID: PMC7485126 DOI: 10.3389/fgene.2020.00977] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/03/2020] [Indexed: 02/05/2023] Open
Abstract
Previous work has shown that DNA methylation in peripheral blood may be associated with malignancy; however, these studies have mainly been conducted within Caucasian populations. Here, we investigated the association between blood-based methylation of S100 calcium-binding protein P gene (S100P) and hyaluronoglucosaminidase 2 gene (HYAL2) and breast cancer (BC) via mass spectrometry in two independent case-control studies of the Chinese population with a total of 351 BC cases and 427 cancer-free female controls. In Study I, in which subjects had an average of 45 years, hypomethylation of S100P showed a protective effect for women ≤45 years (six out of nine CpG sites, p < 0.05) but not for women >45 years. In contrast, hypomethylation of HAYL2 was not correlated with BC in women ≤45 years but was a risk factor for women >45 years (three out of four CpG sites, p < 0.05). We proposed an age-dependent correlation between BC and methylation of S100P and HYAL2 and performed further validation in Study II with older subjects (average age = 52.5 years), where hypomethylation of both S100P and HYAL2 was a risk factor for BC (p < 0.05 for 10 CpG sites) as reported in Caucasians who develop BC around 55 years old. Together with the observation that Chinese cancer-free females having variant basal methylation levels comparing to Caucasians, we assumed that blood-based methylation might be modified by ethnic background, hormone status, and lifestyle. Here, we highlighted that the epigenetic biomarkers warrant validations when its application in variant ethnic groups is considered.
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Affiliation(s)
- Qiming Yin
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xiaoqin Yang
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Lixi Li
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Tian Xu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Wenjie Zhou
- Chengdu Shang Jin Nan Fu Hospital, West China Hospital, Sichuan University, Chengdu, China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Fei Ma
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Rongxi Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
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15
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The Melanoma and Breast Cancer Association: An Overview of their 'Second Primary Cancers' and the Epidemiological, Genetic and Biological correlations. Crit Rev Oncol Hematol 2020; 152:102989. [PMID: 32485529 DOI: 10.1016/j.critrevonc.2020.102989] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/22/2020] [Accepted: 05/14/2020] [Indexed: 12/18/2022] Open
Abstract
This study reviews the relevant epidemiological studies associating cutaneous melanoma and breast carcinomas and provides an overview of the possible genetic, biological and bias factors that underpin this relationship. Standardised incidence ratio (SIR) for primary cutaneous melanoma after breast carcinoma ranged from 1.16 to 5.13 and ranged from 1.03 to 4.10 for primary breast carcinoma after cutaneous melanoma. Epidemiological studies highlight age, gender and use of radiotherapy and chemotherapy as potential risk factors for second primary cancers (SPCs). Mutations in BRCA2, CDKN2A, CDK4 and BAP1 may partly underlie any SPC association. The impact of socio-cultural factors and surveillance bias may be attributed to the findings of SPC partially or entirely. In conclusion, this study has highlighted the association between breast carcinoma and melanoma and identified various factors for further research and the optimised management of patients with both cancers.
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16
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Sharma A, Liu H, Tobar-Tosse F, Noll A, Chand Dakal T, Li H, Holz FG, Loeffler KU, Herwig-Carl MC. Genome organization in proximity to the BAP1 locus appears to play a pivotal role in a variety of cancers. Cancer Sci 2020; 111:1385-1391. [PMID: 31957195 PMCID: PMC7156870 DOI: 10.1111/cas.14319] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/26/2019] [Accepted: 01/09/2020] [Indexed: 12/12/2022] Open
Abstract
Cancer studies primarily focus on the characterization of the key driver genes and the underlying pathways. However, the contribution of other cancer-associated genes located in the genomic neighborhood of the driver genes could help to understand further aspects of cancer progression. Given the frequent involvement of chromosome 3 in multiple human cancers, in particular in the form of the prognostically highly relevant monosomy 3 in uveal melanoma (UM), we investigated the cumulative impact of cancer-associated genes on chromosome 3. Our analysis showed that these genes are enriched with repetitive elements with genes surrounded by distinctive repeats (MIR, hAT-Charlie, ERVL-MaLR, LINE-2, and simple/low complexity) in the promoter being more precisely associated with cancer-related pathways than the ones with major transposable elements (SINE/Alu and LINE-1). Additionally, these genes showed strong intrachromosomal chromatin interactions in 3D nuclear organization. Further investigations revealed a genomic hotspot in the vicinity of BAP1 locus, which is affected in 27 types of different cancers and contains abundant noncoding RNAs that are often expressed in a tissue-specific manner. The cross-species comparison of these cancer-associated genes revealed mostly a shared synteny in closer primates. However, near to the BAP1 locus signs of chromosomal inversions were observed during the course of evolution. To our knowledge, this is the first study to characterize the entire genomic neighborhood of cancer-associated genes located on any single chromosome. Based on our results, we hypothesize that monosomy of chromosome 3 will have important clinical and molecular consequences in the respective diseases and in particular in UM.
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Affiliation(s)
- Amit Sharma
- Department of Ophthalmology, University Hospital Bonn, Bonn, Germany
| | - Hongde Liu
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, China
| | | | - Angela Noll
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Tikam Chand Dakal
- Department of Biotechnology, Mohanlal Sukhadia University Udaipur, Udaipur, India
| | - Huamei Li
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, China
| | - Frank G Holz
- Department of Ophthalmology, University Hospital Bonn, Bonn, Germany
| | - Karin U Loeffler
- Department of Ophthalmology, University Hospital Bonn, Bonn, Germany
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17
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The Role of RASSF1 Methylation in Lung Carcinoma. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1255:99-108. [PMID: 32949393 DOI: 10.1007/978-981-15-4494-1_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Lung carcinoma is the most frequently diagnosed malignant neoplasms and mainly consists of small-cell lung carcinoma (SCLC) and non-small-cell lung carcinoma (NSCLC). Large number of lung carcinoma patients have poor outcomes due to the late diagnosis and the limited therapeutic options. Previous attempts have proved that the evolution of lung carcinoma is a multistep molecular aberration which various genetic or epigenetic alterations may be take part in. Among these molecular aberrations, the inactivation of tumor suppressor gene has been widely observed in all types of carcinoma including lung carcinoma. As a vital inactivated mechanism, DNA methylation of tumor suppressor gene is frequently found in lung cancer. To gain exhaustive comprehension of the carcinogenesis of lung carcinoma, we summarize our current knowledge on DNA methylation of RASSF1 (RAS-Association Domain Family 1) and its clinical significance in lung carcinoma.
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18
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Wang Y, Dan L, Li Q, Li L, Zhong L, Shao B, Yu F, He S, Tian S, He J, Xiao Q, Putti TC, He X, Feng Y, Lin Y, Xiang T. ZMYND10, an epigenetically regulated tumor suppressor, exerts tumor-suppressive functions via miR145-5p/NEDD9 axis in breast cancer. Clin Epigenetics 2019; 11:184. [PMID: 31801619 PMCID: PMC6894283 DOI: 10.1186/s13148-019-0785-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 11/24/2019] [Indexed: 02/07/2023] Open
Abstract
Background Recent studies suggested that ZMYND10 is a potential tumor suppressor gene in multiple tumor types. However, the mechanism by which ZMYND10 inhibits breast cancer remains unclear. Here, we investigated the role and mechanism of ZMYND10 in breast cancer inhibition. Results ZMYND10 was dramatically reduced in multiple breast cancer cell lines and tissues, which was associated with promoter hypermethylation. Ectopic expression of ZMYND10 in silenced breast cancer cells induced cell apoptosis while suppressed cell growth, cell migration and invasion in vitro, and xenograft tumor growth in vivo. Furthermore, molecular mechanism studies indicated that ZMYND10 enhances expression of miR145-5p, which suppresses the expression of NEDD9 protein through directly targeting the 3'-untranslated region of NEDD9 mRNA. Conclusions Results from this study show that ZMYND10 suppresses breast cancer tumorigenicity by inhibiting the miR145-5p/NEDD9 signaling pathway. This novel discovered signaling pathway may be a valid target for small molecules that might help to develop new therapies to better inhibit the breast cancer metastasis.
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Affiliation(s)
- Yan Wang
- Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Liangying Dan
- Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,The People's Hospital of Tongliang District, Chongqing, China
| | - Qianqian Li
- Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lili Li
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Translational Oncology, Sir YK Pao Center for Cancer, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Lan Zhong
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Translational Oncology, Sir YK Pao Center for Cancer, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Bianfei Shao
- Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Fang Yu
- Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Sanxiu He
- Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shaorong Tian
- Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jin He
- Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qian Xiao
- Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Thomas C Putti
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Xiaoqian He
- Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yixiao Feng
- Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yong Lin
- Molecular Biology and Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Tingxiu Xiang
- Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
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19
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Dawson RE, Nieto Guil AF, Robertson LJ, Piltz SG, Hughes JN, Thomas PQ. Functional screening of GATOR1 complex variants reveals a role for mTORC1 deregulation in FCD and focal epilepsy. Neurobiol Dis 2019; 134:104640. [PMID: 31639411 DOI: 10.1016/j.nbd.2019.104640] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 10/07/2019] [Accepted: 10/13/2019] [Indexed: 12/20/2022] Open
Abstract
Mutations in the GAP activity toward RAGs 1 (GATOR1) complex genes (DEPDC5, NPRL2 and NPRL3) have been associated with focal epilepsy and focal cortical dysplasia (FCD). GATOR1 functions as an inhibitor of the mTORC1 signalling pathway, indicating that the downstream effects of mTORC1 deregulation underpin the disease. However, the vast majority of putative disease-causing variants have not been functionally assessed for mTORC1 repression activity. Here, we develop a novel in vitro functional assay that enables rapid assessment of GATOR1-gene variants. Surprisingly, of the 17 variants tested, we show that only six showed significantly impaired mTORC1 inhibition. To further investigate variant function in vivo, we generated a conditional Depdc5 mouse which modelled a 'second-hit' mechanism of disease. Generation of Depdc5 null 'clones' in the embryonic brain resulted in mTORC1 hyperactivity and modelled epilepsy and FCD symptoms including large dysmorphic neurons, defective migration and lower seizure thresholds. Using this model, we validated DEPDC5 variant F164del to be loss-of-function. We also show that Q542P is not functionally compromised in vivo, consistent with our in vitro findings. Overall, our data show that mTORC1 deregulation is the central pathological mechanism for GATOR1 variants and also indicates that a significant proportion of putative disease variants are pathologically inert, highlighting the importance of GATOR1 variant functional assessment.
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Affiliation(s)
- Ruby E Dawson
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia.
| | - Alvaro F Nieto Guil
- School of Medicine, University of Adelaide, Adelaide, SA 5005, Australia; Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia.
| | - Louise J Robertson
- School of Medicine, University of Adelaide, Adelaide, SA 5005, Australia; Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia.
| | - Sandra G Piltz
- School of Medicine, University of Adelaide, Adelaide, SA 5005, Australia; Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia.
| | - James N Hughes
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia.
| | - Paul Q Thomas
- School of Medicine, University of Adelaide, Adelaide, SA 5005, Australia; Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; Precision Medicine Theme, South Australia Health and Medical Research Institute, Adelaide, SA 5000, Australia.
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20
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Garikipati VNS, Verma SK, Cheng Z, Liang D, Truongcao MM, Cimini M, Yue Y, Huang G, Wang C, Benedict C, Tang Y, Mallaredy V, Ibetti J, Grisanti L, Schumacher SM, Gao E, Rajan S, Wilusz JE, Goukassian D, Houser SR, Koch WJ, Kishore R. Circular RNA CircFndc3b modulates cardiac repair after myocardial infarction via FUS/VEGF-A axis. Nat Commun 2019; 10:4317. [PMID: 31541092 PMCID: PMC6754461 DOI: 10.1038/s41467-019-11777-7] [Citation(s) in RCA: 265] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 07/30/2019] [Indexed: 02/08/2023] Open
Abstract
Circular RNAs are generated from many protein-coding genes, but their role in cardiovascular health and disease states remains unknown. Here we report identification of circRNA transcripts that are differentially expressed in post myocardial infarction (MI) mouse hearts including circFndc3b which is significantly down-regulated in the post-MI hearts. Notably, the human circFndc3b ortholog is also significantly down-regulated in cardiac tissues of ischemic cardiomyopathy patients. Overexpression of circFndc3b in cardiac endothelial cells increases vascular endothelial growth factor-A expression and enhances their angiogenic activity and reduces cardiomyocytes and endothelial cell apoptosis. Adeno-associated virus 9 -mediated cardiac overexpression of circFndc3b in post-MI hearts reduces cardiomyocyte apoptosis, enhances neovascularization and improves left ventricular functions. Mechanistically, circFndc3b interacts with the RNA binding protein Fused in Sarcoma to regulate VEGF expression and signaling. These findings highlight a physiological role for circRNAs in cardiac repair and indicate that modulation of circFndc3b expression may represent a potential strategy to promote cardiac function and remodeling after MI. Circular RNAs (circRNAs) are non-coding RNAs generated from pre-mRNAs of coding genes by the splicing machinery whose function in the heart is poorly understood. Here the authors show that AAV-mediated delivery of the circRNA circFndc3b prevents cardiomyocyte apoptosis, enhances angiogenesis, and attenuates LV dysfunction post-MI in mice by regulating FUS-VEGF-A signalling.
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Affiliation(s)
| | - Suresh Kumar Verma
- Division of Cardiovascular Diseases, Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Zhongjian Cheng
- Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Dongming Liang
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - May M Truongcao
- Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Maria Cimini
- Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Yujia Yue
- Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Grace Huang
- Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Chunlin Wang
- Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Cindy Benedict
- Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Yan Tang
- Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Vandana Mallaredy
- Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Jessica Ibetti
- Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Laurel Grisanti
- Department of Biomedical Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Sarah M Schumacher
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, 44195, USA
| | - Erhe Gao
- Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Sudarsan Rajan
- Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Jeremy E Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - David Goukassian
- Zena & Michael A. Weiner Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Steven R Houser
- Cardiovascular Research Center and Department of Physiology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Walter J Koch
- Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA.,Department of Pharmacology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Raj Kishore
- Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA. .,Department of Pharmacology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA.
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21
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Wei Q, Chen Y, Gu YF, Zhao W. Molecular Characterization and Functional Analysis of Leucine Zipper Transcription Factor Like 1 in Zebrafish ( Danio rerio). Front Physiol 2019; 10:801. [PMID: 31293455 PMCID: PMC6603235 DOI: 10.3389/fphys.2019.00801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/06/2019] [Indexed: 11/13/2022] Open
Abstract
Leucine zipper transcription factor like 1 (LZTFL1) is a member of the Bardet-Biedl syndrome gene family. LZTFL1-null mice show the phenotype of obesity, retinal degeneration, and abnormal cilia development. Functionally, LZTFL1 serves as a tumor suppressor and a negative regulator in the hedgehog signaling pathways. The biological function of mammalian LZTFL1 is partially addressed, but data on other model organisms are limited. Zebrafish (Danio rerio) is widely considered as a powerful model to understand the functions of genes implicated in obesity, disease, and cancer. In this study, LZTFL1 homologs were identified in zebrafish (zebrafish LZTFL1). The full-length cDNA of zebrafish LZTFL1 contained 897 bps encoding 298 amino acids. Zebrafish LZTFL1 displayed conserved domains of coil-coil and leucine zipper domain. PCR results showed that zebrafish LZTFL1 was widely distributed in various tissues. Western blot analysis further revealed that zebrafish LZTFL1 was detected to be ectopically expressed in HeLa cells with correct molecular weight. Fluorescence images showed as well that zebrafish LZTFL1 was localized in the cytoplasm. Furthermore, luciferase reporter assay indicated zebrafish LZTFL1 served as a negative regulator in the hedgehog signaling pathway. These data supported that zebrafish was a good model for understanding the biological roles of LZTFL1.
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Affiliation(s)
- Qun Wei
- Department of Surgical Oncology, Institute of Clinical Medicine, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yongxia Chen
- Department of Surgical Oncology, Institute of Clinical Medicine, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yi-Feng Gu
- Department of Surgical Oncology, Institute of Clinical Medicine, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Wenhe Zhao
- Department of Surgical Oncology, Institute of Clinical Medicine, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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22
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Calanca N, Paschoal AP, Munhoz ÉP, Galindo LT, Barbosa BM, Caldeira JRF, Oliveira RA, Cavalli LR, Rogatto SR, Rainho CA. The long non-coding RNA ANRASSF1 in the regulation of alternative protein-coding transcripts RASSF1A and RASSF1C in human breast cancer cells: implications to epigenetic therapy. Epigenetics 2019; 14:741-750. [PMID: 31062660 DOI: 10.1080/15592294.2019.1615355] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Alternative protein-coding transcripts of the RASSF1 gene have been associated with dual functions in human cancer: while RASSF1C isoform has oncogenic properties, RASSF1A is a tumour suppressor frequently silenced by hypermethylation. Recently, the antisense long non-coding RNA RASSF1 (ANRASSF1) was implicated in a locus-specific mechanism for the RASSF1A epigenetic repression mediated by PRC2 (Polycomb Repressive Complex 2). Here, we evaluated the methylation patterns of the promoter regions of RASSF1A and RASSF1C and the expression levels of these RASSF1 transcripts in breast cancer and breast cancer cell lines. As expected, RASSF1C remained unmethylated and RASSF1A was hypermethylated at high frequencies in 75 primary breast cancers, and also in a panel of three mammary epithelial cells (MEC) and 10 breast cancer cell lines (BCC). Although RASSF1C was expressed in all cell lines, only two of them expressed the transcript RASSF1A. ANRASSF1 expression levels were increased in six BCCs. In vitro induced demethylation with 5-Aza-2'-deoxicytydine (5-Aza-dC) resulted in up-regulation of RASSF1A and an inverse correlation with ANRASSF1 relative abundance in BCCs. However, increased levels of both transcripts were observed in two MECs (184A1 and MCF10A) after treatment with 5-Aza-dC. Overall, these findings indicate that ANRASSF1 is differentially expressed in MECs and BCCs. The lncRNA ANRASSF1 provides new perspectives as a therapeutic target for locus-specific regulation of RASSF1A.
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Affiliation(s)
- Naiade Calanca
- a Department of Genetics, Institute of Biosciences , São Paulo State University (Unesp) , Botucatu , Brazil
| | - Ana Paula Paschoal
- a Department of Genetics, Institute of Biosciences , São Paulo State University (Unesp) , Botucatu , Brazil
| | - Érika Prando Munhoz
- a Department of Genetics, Institute of Biosciences , São Paulo State University (Unesp) , Botucatu , Brazil
| | - Layla Testa Galindo
- a Department of Genetics, Institute of Biosciences , São Paulo State University (Unesp) , Botucatu , Brazil
| | - Barbara Mitsuyasu Barbosa
- a Department of Genetics, Institute of Biosciences , São Paulo State University (Unesp) , Botucatu , Brazil
| | | | - Rogério Antonio Oliveira
- c Department of Biostatistics, Institute of Biosciences , São Paulo State University (Unesp) , Botucatu , Brazil
| | - Luciane Regina Cavalli
- d Department of Oncology , Georgetown University Medical Center , Washington , DC , USA.,e Faculdades Pequeno Préncipe e Instituto de Pesquisa Pelé Pequeno Príncipe , , Curitiba , Brazil
| | - Silvia Regina Rogatto
- f Department of Clinical Genetics , University Hospital, Institute of Regional Health Research, University of Southern Denmark Vejle , Denmark
| | - Cláudia Aparecida Rainho
- a Department of Genetics, Institute of Biosciences , São Paulo State University (Unesp) , Botucatu , Brazil
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23
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Pećina-Šlaus N, Kafka A, Gotovac Jerčić K, Logara M, Bukovac A, Bakarić R, Borovečki F. Comparable Genomic Copy Number Aberrations Differ across Astrocytoma Malignancy Grades. Int J Mol Sci 2019; 20:ijms20051251. [PMID: 30871102 PMCID: PMC6429132 DOI: 10.3390/ijms20051251] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/04/2019] [Accepted: 03/06/2019] [Indexed: 01/13/2023] Open
Abstract
A collection of intracranial astrocytomas of different malignancy grades was analyzed for copy number aberrations (CNA) in order to identify regions that are driving cancer pathogenesis. Astrocytomas were analyzed by Array Comparative Genomic Hybridization (aCGH) and bioinformatics utilizing a Bioconductor package, Genomic Identification of Significant Targets in Cancer (GISTIC) 2.0.23 and DAVID software. Altogether, 1438 CNA were found of which losses prevailed. On our total sample, significant deletions affected 14 chromosomal regions, out of which deletions at 17p13.2, 9p21.3, 13q12.11, 22q12.3 remained significant even at 0.05 q-value. When divided into malignancy groups, the regions identified as significantly deleted in high grades were: 9p21.3; 17p13.2; 10q24.2; 14q21.3; 1p36.11 and 13q12.11, while amplified were: 3q28; 12q13.3 and 21q22.3. Low grades comprised significant deletions at 3p14.3; 11p15.4; 15q15.1; 16q22.1; 20q11.22 and 22q12.3 indicating their involvement in early stages of tumorigenesis. Significantly enriched pathways were: PI3K-Akt, Cytokine-cytokine receptor, the nucleotide-binding oligomerization domain (NOD)–like receptor, Jak-STAT, retinoic acid-inducible gene (RIG)-I-like receptor and Toll-like receptor pathways. HPV and herpex simplex infection and inflammation pathways were also represented. The present study brings new data to astrocytoma research amplifying the wide spectrum of changes that could help us identify the regions critical for tumorigenesis.
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Affiliation(s)
- Nives Pećina-Šlaus
- Laboratory of Neurooncology, Croatian Institute for Brain Research, School of Medicine University of Zagreb, Šalata 12, 10000 Zagreb, Croatia.
- Department of Biology, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia.
| | - Anja Kafka
- Laboratory of Neurooncology, Croatian Institute for Brain Research, School of Medicine University of Zagreb, Šalata 12, 10000 Zagreb, Croatia.
- Department of Biology, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia.
| | - Kristina Gotovac Jerčić
- Department for Functional Genomics, Center for Translational and Clinical Research, University of Zagreb, School of Medicine and University Hospital Center Zagreb, Šalata 2, 10000 Zagreb, Croatia.
| | | | - Anja Bukovac
- Laboratory of Neurooncology, Croatian Institute for Brain Research, School of Medicine University of Zagreb, Šalata 12, 10000 Zagreb, Croatia.
- Department of Biology, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia.
| | | | - Fran Borovečki
- Department for Functional Genomics, Center for Translational and Clinical Research, University of Zagreb, School of Medicine and University Hospital Center Zagreb, Šalata 2, 10000 Zagreb, Croatia.
- Department of Neurology, University Hospital Center Zagreb, Kišpatićeva 12, 10000 Zagreb, Croatia.
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24
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BAP1 expression is prognostic in breast and uveal melanoma but not colon cancer and is highly positively correlated with RBM15B and USP19. PLoS One 2019; 14:e0211507. [PMID: 30716094 PMCID: PMC6361507 DOI: 10.1371/journal.pone.0211507] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 01/15/2019] [Indexed: 12/25/2022] Open
Abstract
BAP1 is a tumor suppressor gene important to the development and prognosis of many cancers, especially uveal melanoma (UM). Its role in more common cancers such as breast and colon cancer is largely unknown. We collected the transcriptome profiling data sets from the TCGA uveal melanoma (TCGA-UVM), breast cancer (TCGA-BRCA), and colon cancer (TCGA-COAD) projects to analyze the expression of BAP1. We found that patients with UM and breast cancer, but not colon cancer, who died had a lower level of BAP1 gene expression compared to surviving patients. Importantly, in breast cancer patients, the lowest BAP1 expression levels corresponded to the dead young patients (age at diagnosis < 46). Since the number of cases in TCGA-BRCA was much higher than TCGA-UVM, we obtained highly correlated genes with BAP1 in invasive breast carcinomas. Then, we tested if these genes are also highly correlated with BAP1 in UM and colon cancer. We found that BAP1 is highly positively correlated with RBM15B and USP19 expression in invasive breast carcinoma, UM, and colon adenocarcinoma. All three genes are located in close proximity on the 3p21 tumor suppressor region that is commonly altered in many cancers.
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25
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Saeed K, Ojamies P, Pellinen T, Eldfors S, Turkki R, Lundin J, Järvinen P, Nisen H, Taari K, Af Hällström TM, Rannikko A, Mirtti T, Kallioniemi O, Östling P. Clonal heterogeneity influences drug responsiveness in renal cancer assessed by ex vivo drug testing of multiple patient-derived cancer cells. Int J Cancer 2018; 144:1356-1366. [PMID: 30125350 DOI: 10.1002/ijc.31815] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 07/13/2018] [Accepted: 07/26/2018] [Indexed: 12/28/2022]
Abstract
Renal cell cancer (RCC) has become a prototype example of the extensive intratumor heterogeneity and clonal evolution of human cancers. However, there is little direct evidence on how the genetic heterogeneity impacts on drug response profiles of the cancer cells. Our goal was to determine how genomic clonal evolution impacts drug responses. Finding from our study could help to define the challenge that clonal evolution poses on cancer therapy. We established multiple patient-derived cells (PDCs) from different tumor regions of four RCC patients, verified their clonal relationship to each other and to the uncultured tumor tissue by genome sequencing. Furthermore, comprehensive drug-sensitivity testing with 460 oncological drugs was performed on all PDC clones. The PDCs retained many cancer-specific copy number alterations and mutations in driver genes such as VHL, PBRM1, PIK3C2A, KMD5C and TSC2 genes. The drug testing highlighted vulnerability in the PDCs toward approved RCC drugs, such as the mTOR-inhibitor temsirolimus, but also novel sensitivities were uncovered. The individual PDC clones from different tumor regions in a patient showed distinct drug-response profiles, suggesting that genomic heterogeneity contributes to the variability in drug responses. Studies of multiple PDCs from a patient with cancer are informative for elucidating cancer heterogeneity and for the determination on how the genomic evolution is manifested in cancer drug responsiveness. This approach could facilitate tailoring of drugs and drug combinations to individual patients.
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Affiliation(s)
- Khalid Saeed
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Poojitha Ojamies
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Teijo Pellinen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Samuli Eldfors
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Riku Turkki
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Johan Lundin
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Petrus Järvinen
- Department of Urology, Helsinki University Hospital, Helsinki, Finland
| | - Harry Nisen
- Department of Urology, Helsinki University Hospital, Helsinki, Finland
| | - Kimmo Taari
- Department of Urology, Helsinki University Hospital, Helsinki, Finland
| | - Taija M Af Hällström
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,AstraZeneca, Espoo, Finland
| | - Antti Rannikko
- Department of Urology, Helsinki University Hospital, Helsinki, Finland
| | - Tuomas Mirtti
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,Department of Pathology, HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Olli Kallioniemi
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,Department of Oncology and Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Päivi Östling
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,Department of Oncology and Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
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26
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Kordiak J, Czarnecka KH, Pastuszak-Lewandoska D, Antczak A, Migdalska-Sęk M, Nawrot E, Domańska-Senderowska D, Kiszałkiewicz J, Brzeziańska-Lasota E. Small suitability of the DLEC1, MLH1 and TUSC4 mRNA expression analysis as potential prognostic or differentiating markers for NSCLC patients in the Polish population. J Genet 2018; 96:227-234. [PMID: 28674222 DOI: 10.1007/s12041-017-0770-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
According to the latest data, lung cancer is one of the most common cancer worldwide, men contributing nearly 21.2% and women 8.6% of all diagnosed cancers. Late detection of tumour drastically reduces the chance for a cure. Thus, it is important to search for candidate biomarkers for screening of early stage nonsmall cell lung carcinoma (NSCLC). Tumour suppressor genes, DLEC1, TUSC4 and MLH1, localized on 3p21 are recognized to play a role in NSCLC carcinogenesis. The aim of this study was to assess the relationship between the DLEC1, TUSC4 and MLH1 mRNA expression, and clinical features of NSCLC patients, tobacco addiction, and tumour histopathological characteristics. The DLEC1, TUSC4 and MLH1 expression was analysed in lung tumour tissue samples obtained from 69 patients diagnosed with NSCLC: squamous cell carcinoma (n = 34), adenocarcinoma (n = 24), large cell carcinoma (n = 5), carcinoma adenosquamosum (n = 5). A decreased gene expression (RQ < 0.7) was observed for DLEC1 in 60.9% of tumour samples, for MLH1 in 50.7% and for TUSC4 in 26% of NSCLC samples. DLEC1 was decreased in more aggressive subtypes: large cell carcinoma and adenocarcinoma-squamous cell carcinoma. The simultaneous downregulation of two of the studied genes, DLEC1 andMLH1,was observed in 30.4% of NSCLCsamples, highlighting the importance of these two genes in lung carcinogenesis. We found no correlation between the DLEC1, TUSC4 and MLH1 gene expression and NSCLC patient characteristics (gender, age and smoking) or cancer histopathology. No significant differences in the gene expression among NSCLC subtypes indicate the weakness of DLEC1, TUSC4 and MLH1 expression analysis as potential differentiating markers of NSCLC subtypes in the Polish population.
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Affiliation(s)
- Jacek Kordiak
- Department of Chest Surgery, General and Oncological Surgery, University Hospital No. 2, Medical University of Lodz, 133 Żeromskiego Str., 90-549 Lodz, Poland.
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27
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Abstract
Most members of the poly(ADP-ribose)polymerase family, PARP family, have a catalytic activity that involves the transfer of ADP-ribose from a beta-NAD+-molecule to protein acceptors. It was recently discovered by Talhaoui et al. that DNA-dependent PARP1 and PARP2 can also modify DNA. Here, we demonstrate that DNA-dependent PARP3 can modify DNA and form a specific primed structure for further use by the repair proteins. We demonstrated that gapped DNA that was ADP-ribosylated by PARP3 could be ligated to double-stranded DNA by DNA ligases. Moreover, this ADP-ribosylated DNA could serve as a primed DNA substrate for PAR chain elongation by the purified proteins PARP1 and PARP2 as well as by cell-free extracts. We suggest that this ADP-ribose modification can be involved in cellular pathways that are important for cell survival in the process of double-strand break formation.
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Affiliation(s)
- E A Belousova
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), SB RAS, Lavrentiev Av. 8, Novosibirsk, 630090, Russia
| | - А A Ishchenko
- Groupe Réparation de l'ADN, Equipe Labellisée par la Ligue Nationale Contre le Cancer, CNRS UMR8200, Univ. Paris-Sud, Université Paris-Saclay, F-94805, Villejuif, France.,Gustave Roussy, Université Paris-Saclay, F-94805, Villejuif, France
| | - O I Lavrik
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), SB RAS, Lavrentiev Av. 8, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Pirogov Str. 2, Novosibirsk, 630090, Russia.
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28
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Valdés-Mora F, Locke WJ, Bandrés E, Gallego-Ortega D, Cejas P, García-Cabezas MA, Colino-Sanguino Y, Feliú J, Del Pulgar TG, Lacal JC. Clinical relevance of the transcriptional signature regulated by CDC42 in colorectal cancer. Oncotarget 2018; 8:26755-26770. [PMID: 28460460 PMCID: PMC5432295 DOI: 10.18632/oncotarget.15815] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 02/20/2017] [Indexed: 01/29/2023] Open
Abstract
CDC42 is an oncogenic Rho GTPase overexpressed in colorectal cancer (CRC). Although CDC42 has been shown to regulate gene transcription, the specific molecular mechanisms regulating the oncogenic ability of CDC42 remain unknown. Here, we have characterized the transcriptional networks governed by CDC42 in the CRC SW620 cell line using gene expression analysis. Our results establish that several cancer-related signaling pathways, including cell migration and cell proliferation, are regulated by CDC42. This transcriptional signature was validated in two large cohorts of CRC patients and its clinical relevance was also studied. We demonstrate that three CDC42-regulated genes offered a better prognostic value when combined with CDC42 compared to CDC42 alone. In particular, the concordant overexpression of CDC42 and silencing of the putative tumor suppressor gene CACNA2D2 dramatically improved the prognostic value. The CACNA2D2/CDC42 prognostic classifier was further validated in a third CRC cohort as well as in vitro and in vivo CRC models. Altogether, we show that CDC42 has an active oncogenic role in CRC via the transcriptional regulation of multiple cancer-related pathways and that CDC42-mediated silencing of CACNA2D2 is clinically relevant. Our results further support the use of CDC42 specific inhibitors for the treatment of the most aggressive types of CRC.
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Affiliation(s)
- Fatima Valdés-Mora
- Histone Variants Group, Epigenetics Research Program, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, New South Wales, Australia
| | - Warwick J Locke
- Epigenetics Research Program, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Eva Bandrés
- Immunology Unit, Department of Haematology, Complejo Hospitalario de Navarra, Navarra Health Service, Pamplona, Spain
| | - David Gallego-Ortega
- St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, New South Wales, Australia.,Tumour Development Group, The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Paloma Cejas
- Laboratorio de Oncología Translacional, Servicio de Oncología Médica, IdiPAZ, Madrid, Spain
| | | | - Yolanda Colino-Sanguino
- Histone Variants Group, Epigenetics Research Program, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, New South Wales, Australia
| | - Jaime Feliú
- Laboratorio de Oncología Translacional, Servicio de Oncología Médica, IdiPAZ, Madrid, Spain.,Servicio de Oncología Médica, IdiPAZ, CIBERONC, Madrid, Spain
| | | | - Juan Carlos Lacal
- Laboratorio de Oncología Translacional, Servicio de Oncología Médica, IdiPAZ, Madrid, Spain
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29
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Li L, Xu J, Qiu G, Ying J, Du Z, Xiang T, Wong KY, Srivastava G, Zhu XF, Mok TS, Chan ATC, Chan FKL, Ambinder RF, Tao Q. Epigenomic characterization of a p53-regulated 3p22.2 tumor suppressor that inhibits STAT3 phosphorylation via protein docking and is frequently methylated in esophageal and other carcinomas. Am J Cancer Res 2018; 8:61-77. [PMID: 29290793 PMCID: PMC5743460 DOI: 10.7150/thno.20893] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 09/15/2017] [Indexed: 12/13/2022] Open
Abstract
Rationale: Oncogenic STAT3 signaling activation and 3p22-21.3 locus alteration are common in multiple tumors, especially carcinomas of the nasopharynx, esophagus and lung. Whether these two events are linked remains unclear. Our CpG methylome analysis identified a 3p22.2 gene, DLEC1, as a methylated target in esophageal squamous cell (ESCC), nasopharyngeal (NPC) and lung carcinomas. Thus, we further characterized its epigenetic abnormalities and functions. Methods: CpG methylomes were established by methylated DNA immunoprecipitation. Promoter methylation was analyzed by methylation-specific PCR and bisulfite genomic sequencing. DLEC1 expression and clinical significance were analyzed using TCGA database. DLEC1 functions were analyzed by transfections followed by various cell biology assays. Protein-protein interaction was assessed by docking, Western blot and immunoprecipitation analyses. Results: We defined the DLEC1 promoter within a CpG island and p53-regulated. DLEC1 was frequently downregulated in ESCC, lung and NPC cell lines and primary tumors, but was readily expressed in normal tissues and immortalized normal epithelial cells, with mutations rarely detected. DLEC1 methylation was frequently detected in ESCC tumors and correlated with lymph node metastasis, tumor recurrence and progression, with DLEC1 as the most frequently methylated among the established 3p22.2 tumor suppressors (RASSF1A, PLCD1 and ZMYND10/BLU). DLEC1 inhibits carcinoma cell growth through inducing cell cycle arrest and apoptosis, and also suppresses cell metastasis by reversing epithelial-mesenchymal transition (EMT) and cell stemness. Moreover, DLEC1 represses oncogenic signaling including JAK/STAT3, MAPK/ERK, Wnt/β-catenin and AKT pathways in multiple carcinoma types. Particularly, DLEC1 inhibits IL-6-induced STAT3 phosphorylation in a dose-dependent manner. DLEC1 contains three YXXQ motifs and forms a protein complex with STAT3 via protein docking, which blocks STAT3-JAK2 interaction and STAT3 phosphorylation. IL-6 stimulation enhances the binding of DLEC1 with STAT3, which diminishes their interaction with JAK2 and further leads to decreased STAT3 phosphorylation. The YXXQ motifs of DLEC1 are crucial for its inhibition of STAT3 phosphorylation, and disruption of these motifs restores STAT3 phosphorylation through abolishing DLEC1 binding to STAT3. Conclusions: Our study demonstrates, for the first time, predominant epigenetic silencing of DLEC1 in ESCC, and a novel mechanistic link of epigenetic DLEC1 disruption with oncogenic STAT3 signaling in multiple carcinomas.
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30
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Franch-Expósito S, Esteban-Jurado C, Garre P, Quintanilla I, Duran-Sanchon S, Díaz-Gay M, Bonjoch L, Cuatrecasas M, Samper E, Muñoz J, Ocaña T, Carballal S, López-Cerón M, Castells A, Vila-Casadesús M, Derdak S, Laurie S, Beltran S, Carvajal J, Bujanda L, Ruiz-Ponte C, Camps J, Gironella M, Lozano JJ, Balaguer F, Cubiella J, Caldés T, Castellví-Bel S. Rare germline copy number variants in colorectal cancer predisposition characterized by exome sequencing analysis. J Genet Genomics 2017; 45:41-45. [PMID: 29396139 DOI: 10.1016/j.jgg.2017.12.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 11/24/2017] [Accepted: 12/18/2017] [Indexed: 01/11/2023]
Affiliation(s)
- Sebastià Franch-Expósito
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Clara Esteban-Jurado
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Pilar Garre
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, Health Research Institute of the Hospital Clínico San Carlos, Madrid 28040, Spain
| | - Isabel Quintanilla
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Saray Duran-Sanchon
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Marcos Díaz-Gay
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Laia Bonjoch
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Miriam Cuatrecasas
- Department of Pathology, Hospital Clinic de Barcelona, Barcelona 08036, Spain
| | - Esther Samper
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Jenifer Muñoz
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Teresa Ocaña
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Sabela Carballal
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - María López-Cerón
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Antoni Castells
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | | | - Maria Vila-Casadesús
- Bioinformatics Platform, CIBER of Hepatic and Digestive Diseases, Barcelona 08036, Spain
| | - Sophia Derdak
- National Center of Genomic Analysis, Science Park of Barcelona, Barcelona 08028, Spain
| | - Steven Laurie
- National Center of Genomic Analysis, Science Park of Barcelona, Barcelona 08028, Spain
| | - Sergi Beltran
- National Center of Genomic Analysis, Science Park of Barcelona, Barcelona 08028, Spain
| | - Jaime Carvajal
- Andalusian Developmental Biology Institute, CSIC-Pablo de Olavide University-Andalusian Regional Government, Sevilla 41013, Spain
| | - Luis Bujanda
- Gastroenterology Department, Hospital Donostia-Biodonostia Institute, CIBER of Hepatic and Digestive Diseases, University of the Basque Country (UPV/EHU), San Sebastián 20080, Spain
| | - Clara Ruiz-Ponte
- Galician Public Foundation of Genomic Medicine (FPGMX), CIBER of Rare Diseases, Genomics Medicine Group, Hospital Clínico Universitario, University of Santiago de Compostela, Santiago de Compostela 15706, Spain
| | - Jordi Camps
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Meritxell Gironella
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Juan José Lozano
- Bioinformatics Platform, CIBER of Hepatic and Digestive Diseases, Barcelona 08036, Spain
| | - Francesc Balaguer
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain
| | - Joaquín Cubiella
- Gastroenterology Department, Complexo Hospitalario Universitario de Ourense, Ourense Biomedical Research Institute, Ourense 32005, Spain
| | - Trinidad Caldés
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, Health Research Institute of the Hospital Clínico San Carlos, Madrid 28040, Spain
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic de Barcelona, August Pi i Sunyer Biomedical Research Institute, CIBER of Hepatic and Digestive Diseases, University of Barcelona, Barcelona 08036, Spain.
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31
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Role of ESCRT component HD-PTP/ PTPN23 in cancer. Biochem Soc Trans 2017; 45:845-854. [PMID: 28620046 DOI: 10.1042/bst20160332] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 03/29/2017] [Accepted: 04/07/2017] [Indexed: 12/11/2022]
Abstract
Sustained cellular signalling originated from the receptors located at the plasma membrane is widely associated with cancer susceptibility. Endosomal sorting and degradation of the cell surface receptors is therefore crucial to preventing chronic downstream signalling and tumorigenesis. Since the Endosomal Sorting Complexes Required for Transport (ESCRT) controls these processes, ESCRT components were proposed to act as tumour suppressor genes. However, the bona fide role of ESCRT components in tumorigenesis has not been clearly demonstrated. The ESCRT member HD-PTP/PTPN23 was recently identified as a novel haplo-insufficient tumour suppressor in vitro and in vivo, in mice and humans. In this mini-review, we outline the role of the ESCRT components in cancer and summarize the functions of HD-PTP/PTPN23 in tumorigenesis.
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32
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Zhou J, Huang Z, Wang Z, Liu S, Grandien A, Ernberg I, He Z, Zhang X. Tumor suppressor BLU promotes TRAIL-induced apoptosis by downregulating NF-κB signaling in nasopharyngeal carcinoma. Oncotarget 2017; 8:43853-43865. [PMID: 28029652 PMCID: PMC5546445 DOI: 10.18632/oncotarget.14126] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 11/19/2016] [Indexed: 12/17/2022] Open
Abstract
A putative tumor suppressor BLU mapped on the chromosomal 3p21 region, is frequently lost in human tumors including nasopharyngeal carcinoma (NPC). To explore the underlying mechanism of tumor suppression by BLU, its potential to promote apoptosis induced by TRAIL, an effector molecule elaborated by natural killer-T (NKT) cells was investigated. BLU was re-expressed in NPC-derived HNE1 cells by recombinant adenoviral infection and the cells were challenged with recombinant TRAIL. The growth inhibition of BLU was assayed and apoptosis was examined by flow cytometry-based tetramethylrhodamine ethyl ester (TMRE) and annexin V staining, cleavage of pro-caspase-8 and poly ADP ribose polymerase (PARP). The modulation of NF-κB pathway by BLU was evaluated by the reporter activity and estimation of the level of the molecules involved such as IKKalpha, p65 NF-κB, as well as NF-κB induced anti-apoptotic factors cFLIPL and cIAP2. The expression of BLU exerted in vitro and in vivo growth inhibitory effect and promoted TRAIL-induced apoptosis. This phenomenon was validated by FACS-based assays of mitochondrial membrane potential (BLU vs. Vector 87.8% ± 7.7% and 72.1%±6.7% at 6h exposure to TRAIL) and phosphatidylserine turnover (BLU vs. vector: 28.7%±2.9% and 22.6%±2.5%), as well as, enhanced caspapse-8 cleavage. Similar with the findings that BLU promotes chemotherapeutic agent-induced apoptosis, it also augmented death receptor-induced pathway through NF-κB pathway inhibition. In conclusion, BLU suppressed tumor formation by strengthening the antitumor immunity.
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Affiliation(s)
- Jiahui Zhou
- Department of Pathophysiology and China-America Cancer Research Institute, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, Guangdong, China
| | - Zunnan Huang
- Department of Pathophysiology and China-America Cancer Research Institute, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, Guangdong, China
| | - Ziyou Wang
- Department of Pathophysiology and China-America Cancer Research Institute, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, Guangdong, China
| | - Shumin Liu
- Department of Pathophysiology and China-America Cancer Research Institute, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, Guangdong, China
| | - Alf Grandien
- Center for Haematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ingemar Ernberg
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Zhiwei He
- Department of Pathophysiology and China-America Cancer Research Institute, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, Guangdong, China
| | - Xiangning Zhang
- Department of Pathophysiology and China-America Cancer Research Institute, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, Guangdong, China
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33
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Schott S, Yang R, Stöcker S, Canzian F, Giese N, Bugert P, Bergmann F, Strobel O, Hackert T, Sohn C, Burwinkel B. HYAL2 methylation in peripheral blood as a potential marker for the detection of pancreatic cancer: a case control study. Oncotarget 2017; 8:67614-67625. [PMID: 28978057 PMCID: PMC5620197 DOI: 10.18632/oncotarget.18757] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 05/23/2017] [Indexed: 12/27/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy which is mostly diagnosed in advanced and inoperable stages though surgery remains the only curable therapeutic approach. Early detection markers are urgently needed to improve diagnosis. Altered hyaluronoglucosaminidase 2 gene (HYAL2) DNA methylation in peripheral blood is known to be associated with malignancy at early stage but has not been evaluated in PDAC patients. This study evaluates the association between blood-based HYAL2 methylation and PDAC by a case-control study with 191 controls and 82 PDAC patients. Decreased methylation of all four investigated HYAL2 methylation sites showed highly significant association with PDAC (odds ratio (ORs) per −10% methylation ranging from 2.03 to 12.74, depending on the specific CpG site, p < 0.0001 for all). HYAL2 methylation sites were also distinguishable between stage I&II PDAC (61 subjects) and controls (ORs per-10% methylation from 3.17 - 23.04, p < 0.0001 for all). Thus, HYAL2 methylation level enabled a very good discrimination of PDAC cases from healthy controls (area under curve (AUC) = 0.92, 95% Confidence interval (C.I.): 0.88 - 0.96), and was also powerful for the detection of PDAC at stage I&II (AUC = 0.93, 95% C.I.: 0.89 - 0.98). Moreover, the blood-based HYAL2 methylation pattern was similar among PDAC patients with differential clinical characteristics, and showed no correlation with the overall survival of PDAC patients. Our study reveals a strong association between decreased HYAL2 methylation in peripheral blood and PDAC, and provides a promising blood-based marker for the detection of PDAC.
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Affiliation(s)
- Sarah Schott
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, 69120 Heidelberg, Germany.,Department of Gynecology and Obstetrics, University Women's Clinic, 69120 Heidelberg, Germany.,German Cancer Consortium (DKTK), NCT Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Rongxi Yang
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, 69120 Heidelberg, Germany.,Department of Gynecology and Obstetrics, University Women's Clinic, 69120 Heidelberg, Germany.,Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Sarah Stöcker
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, 69120 Heidelberg, Germany.,Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Federico Canzian
- Genomic Epidemiology Group (C055), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Nathalia Giese
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Peter Bugert
- Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, University of Heidelberg, German Red Cross Blood Service Baden-Württemberg - Hessen, 68167 Mannheim, Germany
| | - Frank Bergmann
- Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Oliver Strobel
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Thilo Hackert
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Christof Sohn
- Department of Gynecology and Obstetrics, University Women's Clinic, 69120 Heidelberg, Germany
| | - Barbara Burwinkel
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, 69120 Heidelberg, Germany.,Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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34
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Martinelli G, Mancini M, De Benedittis C, Rondoni M, Papayannidis C, Manfrini M, Meggendorfer M, Calogero R, Guadagnuolo V, Fontana MC, Bavaro L, Padella A, Zago E, Pagano L, Zanotti R, Scaffidi L, Specchia G, Albano F, Merante S, Elena C, Savini P, Gangemi D, Tosi P, Ciceri F, Poletti G, Riccioni L, Morigi F, Delledonne M, Haferlach T, Cavo M, Valent P, Soverini S. SETD2 and histone H3 lysine 36 methylation deficiency in advanced systemic mastocytosis. Leukemia 2017; 32:139-148. [PMID: 28663576 PMCID: PMC5770597 DOI: 10.1038/leu.2017.183] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 05/16/2017] [Accepted: 05/26/2017] [Indexed: 12/23/2022]
Abstract
The molecular basis of advanced systemic mastocytosis (SM) is not fully understood and despite novel therapies the prognosis remains dismal. Exome sequencing of an index-patient with mast cell leukemia (MCL) uncovered biallelic loss-of-function mutations in the SETD2 histone methyltransferase gene. Copy-neutral loss-of-heterozygosity at 3p21.3 (where SETD2 maps) was subsequently found in SM patients and prompted us to undertake an in-depth analysis of SETD2 copy number, mutation status, transcript expression and methylation levels, as well as functional studies in the HMC-1 cell line and in a validation cohort of 57 additional cases with SM, including MCL, aggressive SM and indolent SM. Reduced or no SETD2 protein expression—and consequently, H3K36 trimethylation—was found in all cases and inversely correlated with disease aggressiveness. Proteasome inhibition rescued SETD2 expression and H3K36 trimethylation and resulted in marked accumulation of ubiquitinated SETD2 in SETD2-deficient patients but not in patients with near-normal SETD2 expression. Bortezomib and, to a lesser extent, AZD1775 alone or in combination with midostaurin induced apoptosis and reduced clonogenic growth of HMC-1 cells and of neoplastic mast cells from advanced SM patients. Our findings may have implications for prognostication of SM patients and for the development of improved treatment approaches in advanced SM.
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Affiliation(s)
- G Martinelli
- Department of Experimental, Diagnostic and Specialty Medicine, Hematology/Oncology 'L. e A. Seràgnoli', University of Bologna, Bologna, Italy
| | - M Mancini
- Department of Experimental, Diagnostic and Specialty Medicine, Hematology/Oncology 'L. e A. Seràgnoli', University of Bologna, Bologna, Italy
| | - C De Benedittis
- Department of Experimental, Diagnostic and Specialty Medicine, Hematology/Oncology 'L. e A. Seràgnoli', University of Bologna, Bologna, Italy
| | - M Rondoni
- Ospedale Santa Maria delle Croci, Ravenna, Italy
| | - C Papayannidis
- Department of Experimental, Diagnostic and Specialty Medicine, Hematology/Oncology 'L. e A. Seràgnoli', University of Bologna, Bologna, Italy
| | - M Manfrini
- Department of Experimental, Diagnostic and Specialty Medicine, Hematology/Oncology 'L. e A. Seràgnoli', University of Bologna, Bologna, Italy
| | | | - R Calogero
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - V Guadagnuolo
- Department of Experimental, Diagnostic and Specialty Medicine, Hematology/Oncology 'L. e A. Seràgnoli', University of Bologna, Bologna, Italy
| | - M C Fontana
- Department of Experimental, Diagnostic and Specialty Medicine, Hematology/Oncology 'L. e A. Seràgnoli', University of Bologna, Bologna, Italy
| | - L Bavaro
- Department of Experimental, Diagnostic and Specialty Medicine, Hematology/Oncology 'L. e A. Seràgnoli', University of Bologna, Bologna, Italy
| | - A Padella
- Department of Experimental, Diagnostic and Specialty Medicine, Hematology/Oncology 'L. e A. Seràgnoli', University of Bologna, Bologna, Italy
| | - E Zago
- Personal Genomics, University of Verona, Verona, Italy.,Department of Biotechnologies, University of Verona, Verona, Italy
| | - L Pagano
- Institute of Hematology, Catholic University S. Cuore, Rome, Italy
| | - R Zanotti
- Section of Hematology, Department of Medicine, Azienda Ospedaliera Universitaria Integrata di Verona, Verona, Italy.,Multidisciplinary Outpatients Clinics for Mastocytosis (GISM), Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - L Scaffidi
- Section of Hematology, Department of Medicine, Azienda Ospedaliera Universitaria Integrata di Verona, Verona, Italy.,Multidisciplinary Outpatients Clinics for Mastocytosis (GISM), Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - G Specchia
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, Bari, Italy
| | - F Albano
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, Bari, Italy
| | - S Merante
- Department of Oncology-Hematology, Hematology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - C Elena
- Department of Oncology-Hematology, Hematology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - P Savini
- Department of Internal Medicine, Faenza Hospital, Faenza, Italy
| | | | - P Tosi
- Hematology Unit, Rimini, Italy
| | - F Ciceri
- University Vita-Salute San Raffaele, Milan, Italy.,IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - G Poletti
- Department of Clinical Pathology, Centro Servizi Pievesestina, AUSL Romagna, Pievesestina di Cesena, Italy
| | - L Riccioni
- Unit of Anatomic Pathology, 'M. Bufalini' Hospital, Cesena, Italy
| | - F Morigi
- Unit of Anatomic Pathology, 'M. Bufalini' Hospital, Cesena, Italy
| | - M Delledonne
- Personal Genomics, University of Verona, Verona, Italy.,Department of Biotechnologies, University of Verona, Verona, Italy
| | - T Haferlach
- MLL Munich Leukemia Laboratory, Munich, Germany
| | - M Cavo
- Department of Experimental, Diagnostic and Specialty Medicine, Hematology/Oncology 'L. e A. Seràgnoli', University of Bologna, Bologna, Italy
| | - P Valent
- Department of Medicine I, Division of Hematology and Hemostaseology and Ludwig Boltzmann Cluster Oncology, Medical University of Vienna, Vienna, Austria
| | - S Soverini
- Department of Experimental, Diagnostic and Specialty Medicine, Hematology/Oncology 'L. e A. Seràgnoli', University of Bologna, Bologna, Italy
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35
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Zhou J, Chen C, Li HF, Hu YJ, Xie HL. Revealing radiotherapy- and chemoradiation-induced pathway dynamics in glioblastoma by analyzing multiple differential networks. Mol Med Rep 2017; 16:696-702. [PMID: 28560382 PMCID: PMC5482131 DOI: 10.3892/mmr.2017.6641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 03/02/2017] [Indexed: 02/02/2023] Open
Abstract
The progression of glioblastoma (GBM) is driven by dynamic alterations in the activity and connectivity of gene pathways. Revealing these dynamic events is necessary in order to understand the pathological mechanisms of, and develop effective treatments for, GBM. The present study aimed to investigate dynamic alterations in pathway activity and connectivity across radiotherapy and chemoradiation conditions in GBM, and to give system-level insights into molecular mechanisms for GBM therapy. A total of two differential co-expression networks (DCNs) were constructed using Pearson correlation coefficient analysis and one sided t-tests, based on gene expression profiles and protein-protein interaction networks, one for each condition. Subsequently, shared differential modules across DCNs were detected via significance analysis for candidate modules, which were obtained according to seed selection, module search by seed expansion and refinement of searched modules. As condition-specific differential modules mediate differential biological processes, the module connectivity dynamic score (MCDS) was implemented to explore dynamic alterations among them. Based on DCNs with 287 nodes and 1,052 edges, a total of 28 seed genes and seven candidate modules were identified. Following significance analysis, five shared differential modules were identified in total. Dynamic alterations among these differential modules were identified using the MCDS, and one module with significant dynamic alterations was identified, termed the dynamic module. The present study revealed the dynamic alterations of shared differential modules, identified one dynamic module between the radiotherapy and chemoradiation conditions, and demonstrated that pathway dynamics may applied to the study of the pathogenesis and therapy of GBM.
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Affiliation(s)
- Jia Zhou
- Department of Geratology, Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang 310007, P.R. China
| | - Chao Chen
- Department of Radiotherapy, Zhejiang Provincial Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang 310006, P.R. China
| | - Hua-Feng Li
- Department of Radiotherapy, Zhejiang Provincial Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang 310006, P.R. China
| | - Yu-Jie Hu
- Department of Radiotherapy, Zhejiang Provincial Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang 310006, P.R. China
| | - Hong-Ling Xie
- Department of Radiotherapy, Zhejiang Provincial Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang 310006, P.R. China
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36
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Abstract
The majority of kidney cancers are associated with mutations in the von Hippel-Lindau gene and a small proportion are associated with infrequent mutations in other well characterized tumour-suppressor genes. In the past 15 years, efforts to uncover other key genes involved in renal cancer have identified many genes that are dysregulated or silenced via epigenetic mechanisms, mainly through methylation of promoter CpG islands or dysregulation of specific microRNAs. In addition, the advent of next-generation sequencing has led to the identification of several novel genes that are mutated in renal cancer, such as PBRM1, BAP1 and SETD2, which are all involved in histone modification and nucleosome and chromatin remodelling. In this Review, we discuss how altered DNA methylation, microRNA dysregulation and mutations in histone-modifying enzymes disrupt cellular pathways in renal cancers.
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Affiliation(s)
- Mark R Morris
- Brain Tumour Research Centre, Wolverhampton School of Sciences, University of Wolverhampton, Wulfruna Street, Wolverhampton WV1 1LY, UK
| | - Farida Latif
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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37
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High-density array-CGH with targeted NGS unmask multiple noncontiguous minute deletions on chromosome 3p21 in mesothelioma. Proc Natl Acad Sci U S A 2016; 113:13432-13437. [PMID: 27834213 DOI: 10.1073/pnas.1612074113] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We used a custom-made comparative genomic hybridization array (aCGH; average probe interval 254 bp) to screen 33 malignant mesothelioma (MM) biopsies for somatic copy number loss throughout the 3p21 region (10.7 Mb) that harbors 251 genes, including BRCA1 (breast cancer 1)-associated protein 1 (BAP1), the most commonly mutated gene in MM. We identified frequent minute biallelic deletions (<3 kb) in 46 of 251 genes: four were cancer-associated genes: SETD2 (SET domain-containing protein 2) (7 of 33), BAP1 (8 of 33), PBRM1 (polybromo 1) (3 of 33), and SMARCC1 (switch/sucrose nonfermentable- SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily c, member 1) (2 of 33). These four genes were further investigated by targeted next-generation sequencing (tNGS), which revealed sequence-level mutations causing biallelic inactivation. Combined high-density aCGH and tNGS revealed biallelic gene inactivation in SETD2 (9 of 33, 27%), BAP1 (16 of 33, 48%), PBRM1 (5 of 33, 15%), and SMARCC1 (2 of 33, 6%). The incidence of genetic alterations detected is much higher than reported in the literature because minute deletions are not detected by NGS or commercial aCGH. Many of these minute deletions were not contiguous, but rather alternated with segments showing oscillating copy number changes along the 3p21 region. In summary, we found that in MM: (i) multiple minute simultaneous biallelic deletions are frequent in chromosome 3p21, where they occur as distinct events involving multiple genes; (ii) in addition to BAP1, mutations of SETD2, PBRM1, and SMARCC1 are frequent in MM; and (iii) our results suggest that high-density aCGH combined with tNGS provides a more precise estimate of the frequency and types of genes inactivated in human cancer than approaches based exclusively on NGS strategy.
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38
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Su Y, Fang H, Jiang F. Integrating DNA methylation and microRNA biomarkers in sputum for lung cancer detection. Clin Epigenetics 2016; 8:109. [PMID: 27777637 PMCID: PMC5070138 DOI: 10.1186/s13148-016-0275-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 10/05/2016] [Indexed: 02/02/2023] Open
Abstract
Background Abnormal microRNA (miRNA) expressions and promoter methylation of genes detected in sputum may provide biomarkers for non-small lung cancer (NSCLC). Here, we evaluate the individual and combined analysis of the two classes of sputum molecular biomarkers for NSCLC detection. Results We analyze expression of 3 miRNAs (miR-21, miR-31, and miR-210) and methylation of 3 genes (RASSF1A, PRDM14, and 3OST2), which were previously identified as potential biomarkers for NSCLC, in sputum of a set of 117 stage I NSCLC patients and 174 cancer-free smokers. The results are validated in a different set of 144 stage I NSCLC patients and 171 controls. The panel of 3 miRNA biomarkers has 81.5 % sensitivity and 85.9 % specificity; the panel of 3 methylation biomarkers displays 82.9 % sensitivity and 76.4 % specificity for NSCLC detection. Integrated analysis of 2 miRNAs (miR-31 and miR-210) and 2 genes (RASSF1A and 3OST2) yields higher sensitivity (87.3 %) and specificity (90.3 %) compared with the individual panels of the biomarkers (P < 0.05). Combined analysis of all the 3 miRNAs and 3 genes does not have performance superior to that of the panel of 2 miRNAs and 2 genes (P > 0.05). The performance of combined use of the two classes of biomarkers was confirmed in the validation set. Conclusions The integration of two different classes of biomarkers synergistically improves both the sensitivity and the specificity for the early detection of NSCLC. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0275-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yun Su
- Department of Surgery, Jiangsu Province Hospital of Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023 China
| | - HongBin Fang
- Department of Epidemiology, University of Maryland School of Medicine, Baltimore, MD USA
| | - Feng Jiang
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD USA
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39
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Chromosomal abnormalities in hepatic cysts point to novel polycystic liver disease genes. Eur J Hum Genet 2016; 24:1707-1714. [PMID: 27552964 DOI: 10.1038/ejhg.2016.97] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 06/22/2016] [Accepted: 06/28/2016] [Indexed: 12/27/2022] Open
Abstract
Autosomal dominant polycystic liver disease (ADPLD) is caused by variants in PRKCSH, SEC63, and LRP5, whereas autosomal dominant polycystic kidney disease is caused by variants in PKD1 and PKD2. Liver cyst development in these disorders is explained by somatic loss-of-heterozygosity (LOH) of the wild-type allele in the developing cyst. We hypothesize that we can use this mechanism to identify novel disease genes that reside in LOH regions. In this study, we aim to map abnormal genomic regions using high-density SNP microarrays to find novel PLD genes. We collected 46 cysts from 23 patients with polycystic or sporadic hepatic cysts, and analyzed DNA from those cysts using high-resolution microarray (n=24) or Sanger sequencing (n=22). We here focused on regions of homozygosity on the autosomes (>3.0 Mb) and large CNVs (>1.0 Mb). We found frequent LOH in PRKCSH (22/29) and PKD1/PKD2 (2/3) cysts of patients with known heterozygous germline variants in the respective genes. In the total cohort, 12/23 patients harbored abnormalities outside of familiar areas. In individual ADPLD cases, we identified germline events: a 2q13 complex rearrangement resulting in BUB1 haploinsufficiency, a 47XXX karyotype, chromosome 9q copy-number loss, and LOH on chromosome 3p. The latter region was overlapping with an LOH region identified in two other cysts. Unique germline and somatic abnormalities occur frequently in and outside of known genes underlying cysts. Each liver cyst has a unique genetic makeup. LOH driver gene BUB1 may imply germline causes of genetic instability in PLD.
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40
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Zhou Y, Huang H, Zhang K, Ding X, Jia L, Yu L, Zhu G, Guo J. miRNA-216 and miRNA-499 target cyb561d2 in zebrafish in response to fipronil exposure. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2016; 45:98-107. [PMID: 27267425 DOI: 10.1016/j.etap.2016.05.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 05/15/2016] [Accepted: 05/21/2016] [Indexed: 06/06/2023]
Abstract
MicroRNA (miRNA) can regulate the expression of its target gene by mediating mRNA cleavage or by translational repression at a post-transcriptional level. Usually, one miRNA may regulate many genes as its targets, while one gene may also be targeted by many miRNAs. We previously demonstrated that cyb561d2, whose protein product is involved in cell defense, and chemical stress, is targeted by miR-155 in adult zebrafish (Danio rerio) when exposed to fipronil (5-amino-1-[2,6-dichloro-4-(trifluoromethyl) phenyl]-4-[(trifluoromethyl) sulphinyl]-1H-pyrazole-3-carbonitrile). Microcosm Targets prediction showed that the cyb561d2 gene is also highly possibly targeted by miR-194a, miR-216b, miR-429, and miR-499. These interactions need to be further validated experimentally. In this study, we evaluated the effects of fipronil on miR-194a, miR-216b, miR-429, miR-499 and cyb561d2 in zebrafish and investigated whether these four miRNAs could regulate the expression of cyb561d2 in both mRNA and protein levels. The expression of cyb561d2 was upregulated in both mRNA and protein level in a dose-dependent manner upon stimulation of fipronil, and miR-216b and miR-499 were downregulated concurrently, whereas there was no significant changes were observed in the expression level of miR-194a and miR-429. The dual luciferase report assay demonstrated that miR-216b and miR-499 interacted with cyb561d2 3'-untranslated regions (3'-UTR), miR-194a and miR-429 did not stimulate degradation of cyb561d2 mRNA. The expression of cyb561d2 was reduced in both mRNA and protein level when ZF4 cells were transfected with miR-499 mimic, whereas expression level of both mRNA and protein was increased when endogenous miR-499 was inhibited by transfection with miR-499 inhibitor. Likewise, the mRNA and protein level of cyb561d2 was affected by treatment with the mimics and the inhibitor of miR-216b. In contrast, when ZF4 cells were transfected with a mimic of miR-194a or miR-429, the expression of cyb561d2 mRNA was not significantly changed. As a result, cyb561d2 is targeted by miR-155, miR-216b and miR-499 upon fipronil exposure, and miR-194a and miR-429 can not target cyb561d2. The expression pattern of these 3 miRNAs presents novel fipronil responses that could be used as a toxicological biomarker.
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Affiliation(s)
- Yongyong Zhou
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China
| | - Hannian Huang
- Department of Applied Engineering, Zhejiang Economic & Trade Polytechnic, Hangzhou 310018, People's Republic of China
| | - Kai Zhang
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China
| | - Xianfeng Ding
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China
| | - Longlue Jia
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China
| | - Liang Yu
- Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310029, People's Republic of China
| | - Guonian Zhu
- Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310029, People's Republic of China
| | - Jiangfeng Guo
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China.
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Mitochondria, calcium, and tumor suppressor Fus1: At the crossroad of cancer, inflammation, and autoimmunity. Oncotarget 2016; 6:20754-72. [PMID: 26246474 PMCID: PMC4673227 DOI: 10.18632/oncotarget.4537] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/27/2015] [Indexed: 12/12/2022] Open
Abstract
Mitochondria present a unique set of key intracellular functions such as ATP synthesis, production of reactive oxygen species (ROS) and Ca2+ buffering. Mitochondria both encode and decode Ca2+ signals and these interrelated functions have a direct impact on cell signaling and metabolism. High proliferative potential is a key energy-demanding feature shared by cancer cells and activated T lymphocytes. Switch of a metabolic state mediated by alterations in mitochondrial homeostasis plays a fundamental role in maintenance of the proliferative state. Recent studies show that tumor suppressors have the ability to affect mitochondrial homeostasis controlling both cancer and autoimmunity. Herein, we discuss established and putative mechanisms of calcium–dependent regulation of both T cell and tumor cell activities. We use the mitochondrial protein Fus1 as a case of tumor suppressor that controls immune response and tumor growth via maintenance of mitochondrial homeostasis. We focus on the regulation of mitochondrial Ca2+ handling as a key function of Fus1 and highlight the mechanisms of a crosstalk between Ca2+ accumulation and mitochondrial homeostasis. Given the important role of Ca2+ signaling, mitochondrial Ca2+ transport and ROS production in the activation of NFAT and NF-κB transcription factors, we outline the importance of Fus1 activities in this context.
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Pastuszak-Lewandoska D, Kordiak J, Antczak A, Migdalska-Sęk M, Czarnecka KH, Górski P, Nawrot E, Kiszałkiewicz JM, Domańska-Senderowska D, Brzeziańska-Lasota E. Expression level and methylation status of three tumor suppressor genes, DLEC1, ITGA9 and MLH1, in non-small cell lung cancer. Med Oncol 2016; 33:75. [DOI: 10.1007/s12032-016-0791-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 06/04/2016] [Indexed: 11/30/2022]
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Youssef G, Wallace WAH, Dagleish MP, Cousens C, Griffiths DJ. Ovine pulmonary adenocarcinoma: a large animal model for human lung cancer. ILAR J 2016; 56:99-115. [PMID: 25991702 DOI: 10.1093/ilar/ilv014] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Lung cancer is the leading cause of cancer deaths worldwide. Recent progress in understanding the molecular pathogenesis of this disease has resulted in novel therapeutic strategies targeting specific groups of patients. Further studies are required to provide additional advances in diagnosis and treatment. Animal models are valuable tools for studying oncogenesis in lung cancer, particularly during the early stages of disease where tissues are rarely available from human cases. Mice have traditionally been used for studying lung cancer in vivo, and a variety of spontaneous and transgenic models are available. However, it is recognized that other species may also be informative for studies of cancer. Ovine pulmonary adenocarcinoma (OPA) is a naturally occurring lung cancer of sheep caused by retrovirus infection and has several features in common with adenocarcinoma of humans, including a similar histological appearance and activation of common cell signaling pathways. Additionally, the size and organization of human lungs are much closer to those of sheep lungs than to those of mice, which facilitates experimental approaches in sheep that are not available in mice. Thus OPA presents opportunities for studying lung tumor development that can complement conventional murine models. Here we describe the potential applications of OPA as a model for human lung adenocarcinoma with an emphasis on the various in vivo and in vitro experimental systems available.
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Affiliation(s)
- Gehad Youssef
- Gehad Youssef, BSc, is a research scientist at the Moredun Research Institute, Edinburgh, UK. William A. H. Wallace, MBChB(Hons), PhD, FRCPE, FRCPath, is a consultant pathologist at the Royal Infirmary of Edinburgh and Honorary Reader in Pathology, Edinburgh University, UK; Mark P. Dagleish BVM&S, PhD, MRCVS, FRCPath, is Head of Pathology at the Moredun Research Institute, Edinburgh, UK. Chris Cousens, PhD, is a senior research scientist at the Moredun Research Institute, Edinburgh, UK, and David J. Griffiths, PhD, is a principal research scientist at the Moredun Research Institute, Edinburgh, UK
| | - William A H Wallace
- Gehad Youssef, BSc, is a research scientist at the Moredun Research Institute, Edinburgh, UK. William A. H. Wallace, MBChB(Hons), PhD, FRCPE, FRCPath, is a consultant pathologist at the Royal Infirmary of Edinburgh and Honorary Reader in Pathology, Edinburgh University, UK; Mark P. Dagleish BVM&S, PhD, MRCVS, FRCPath, is Head of Pathology at the Moredun Research Institute, Edinburgh, UK. Chris Cousens, PhD, is a senior research scientist at the Moredun Research Institute, Edinburgh, UK, and David J. Griffiths, PhD, is a principal research scientist at the Moredun Research Institute, Edinburgh, UK
| | - Mark P Dagleish
- Gehad Youssef, BSc, is a research scientist at the Moredun Research Institute, Edinburgh, UK. William A. H. Wallace, MBChB(Hons), PhD, FRCPE, FRCPath, is a consultant pathologist at the Royal Infirmary of Edinburgh and Honorary Reader in Pathology, Edinburgh University, UK; Mark P. Dagleish BVM&S, PhD, MRCVS, FRCPath, is Head of Pathology at the Moredun Research Institute, Edinburgh, UK. Chris Cousens, PhD, is a senior research scientist at the Moredun Research Institute, Edinburgh, UK, and David J. Griffiths, PhD, is a principal research scientist at the Moredun Research Institute, Edinburgh, UK
| | - Chris Cousens
- Gehad Youssef, BSc, is a research scientist at the Moredun Research Institute, Edinburgh, UK. William A. H. Wallace, MBChB(Hons), PhD, FRCPE, FRCPath, is a consultant pathologist at the Royal Infirmary of Edinburgh and Honorary Reader in Pathology, Edinburgh University, UK; Mark P. Dagleish BVM&S, PhD, MRCVS, FRCPath, is Head of Pathology at the Moredun Research Institute, Edinburgh, UK. Chris Cousens, PhD, is a senior research scientist at the Moredun Research Institute, Edinburgh, UK, and David J. Griffiths, PhD, is a principal research scientist at the Moredun Research Institute, Edinburgh, UK
| | - David J Griffiths
- Gehad Youssef, BSc, is a research scientist at the Moredun Research Institute, Edinburgh, UK. William A. H. Wallace, MBChB(Hons), PhD, FRCPE, FRCPath, is a consultant pathologist at the Royal Infirmary of Edinburgh and Honorary Reader in Pathology, Edinburgh University, UK; Mark P. Dagleish BVM&S, PhD, MRCVS, FRCPath, is Head of Pathology at the Moredun Research Institute, Edinburgh, UK. Chris Cousens, PhD, is a senior research scientist at the Moredun Research Institute, Edinburgh, UK, and David J. Griffiths, PhD, is a principal research scientist at the Moredun Research Institute, Edinburgh, UK
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Yan W, Scoumanne A, Jung YS, Xu E, Zhang J, Zhang Y, Ren C, Sun P, Chen X. Mice deficient in poly(C)-binding protein 4 are susceptible to spontaneous tumors through increased expression of ZFP871 that targets p53 for degradation. Genes Dev 2016; 30:522-34. [PMID: 26915821 PMCID: PMC4782047 DOI: 10.1101/gad.271890.115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/26/2016] [Indexed: 01/06/2023]
Abstract
Poly(C)-binding protein 4 (PCBP4), also called MCG10 and a target of p53, plays a role in the cell cycle and is implicated in lung tumor suppression. Here, we found that PCBP4-deficient mice are prone to lung adenocarcinoma, lymphoma, and kidney tumor and that PCBP4-deficient mouse embryo fibroblasts (MEFs) exhibit enhanced cell proliferation but decreased cellular senescence. We also found that p53 expression is markedly reduced in PCBP4-deficient MEFs and mouse tissues, suggesting that PCBP4 in turn regulates p53 expression. To determine how PCBP4 regulates p53 expression, PCBP4 targets were identified by RNA immunoprecipitation followed by RNA sequencing (RNA-seq). We found that the transcript encoding ZFP871 (zinc finger protein 871; also called ZNF709 in humans) interacts with and is regulated by PCBP4 via mRNA stability. Additionally, we found that ZFP871 physically interacts with p53 and MDM2 proteins. Consistently, ectopic expression of ZFP871 decreases-whereas knockdown of ZFP871 increases-p53 protein stability through a proteasome-dependent degradation pathway. Moreover, loss of ZFP871 reverses the reduction of p53 expression by lack of PCBP4, and thus increased expression of ZFP871 is responsible for decreased expression of p53 in the PCBP4-deficient MEFs and mouse tissues. Interestingly, we found that, like PCBP4, ZFP871 is also regulated by DNA damage and p53. Finally, we showed that knockdown of ZFP871 markedly enhances p53 expression, leading to growth suppression and apoptosis in a p53-dependent manner. Thus, the p53-PCBP4-ZFP871 axis represents a novel feedback loop in the p53 pathway. Together, we hypothesize that PCBP4 is a potential tissue-specific tumor suppressor and that ZFP871 is part of MDM2 and possibly other ubiquitin E3 ligases that target p53 for degradation.
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Affiliation(s)
- Wensheng Yan
- Comparative Oncology Laboratory, School of Veterinary Medicine, School of Medicine, University of California at Davis, Davis, California 95616, USA
| | - Ariane Scoumanne
- Comparative Oncology Laboratory, School of Veterinary Medicine, School of Medicine, University of California at Davis, Davis, California 95616, USA
| | - Yong-Sam Jung
- Comparative Oncology Laboratory, School of Veterinary Medicine, School of Medicine, University of California at Davis, Davis, California 95616, USA
| | - Enshun Xu
- Comparative Oncology Laboratory, School of Veterinary Medicine, School of Medicine, University of California at Davis, Davis, California 95616, USA
| | - Jin Zhang
- Comparative Oncology Laboratory, School of Veterinary Medicine, School of Medicine, University of California at Davis, Davis, California 95616, USA
| | - Yanhong Zhang
- Comparative Oncology Laboratory, School of Veterinary Medicine, School of Medicine, University of California at Davis, Davis, California 95616, USA
| | - Cong Ren
- Comparative Oncology Laboratory, School of Veterinary Medicine, School of Medicine, University of California at Davis, Davis, California 95616, USA
| | - Pei Sun
- Comparative Oncology Laboratory, School of Veterinary Medicine, School of Medicine, University of California at Davis, Davis, California 95616, USA
| | - Xinbin Chen
- Comparative Oncology Laboratory, School of Veterinary Medicine, School of Medicine, University of California at Davis, Davis, California 95616, USA
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Expression and DNA methylation alterations of seven cancer-associated 3p genes and their predicted regulator miRNAs (miR-129-2, miR-9-1) in breast and ovarian cancers. Gene 2015; 576:483-91. [PMID: 26519551 DOI: 10.1016/j.gene.2015.10.059] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 10/14/2015] [Accepted: 10/25/2015] [Indexed: 01/05/2023]
Abstract
The methylation of promoter CpG islands and interactions between microRNAs (miRNAs) and messenger RNAs (mRNAs) of target genes are considered two crucial epigenetic mechanisms for inducing gene and pathway deregulation in tumors. Here, the expression levels of seven cancer-associated 3p genes (RASSF1(isoform A), RARB(isoform 2), SEMA3B, RHOA, GPX1, NKIRAS1, and CHL1) and their predicted regulator miRNAs (miR-129-2, miR-9-1) were analyzed in breast (BC, 40 samples) and ovarian (OC, 14 samples) cancers using RT-PCR and qPCR. We first revealed a negative correlation between the level of the miR-129-2 precursor and RASSF1(A) and GPX1 mRNA levels in BC (Spearman's correlation coefficient (rs) was − 0.26 in both cases). Similar results were observed for the miR-129-2 precursor and the RASSF1(A), GPX1, RARB(2), and CHL1 genes in OC (rs was in the range − 0.48 to − 0.54). Using methylation-specific PCR, a significant correlation was shown between promoter hypermethylation and the down-regulation of the RASSF1(A), GPX1, RARB(2), SEMA3B, MIR-129-2, and MIR-9-1 genes in BC (rs = 0.41 to 0.75) and of the RASSF1(A) gene in OC (rs = 0.67). We first demonstrated a high hypermethylation frequency of MIR-129-2 and SEMA3B (up to 45 to 48%) in both BC (69 samples) and OC (41 samples). Moreover, we observed a positive correlation between the hypermethylation of MIR-129-2 and the up-regulation of the RASSF1(A) and GPX1 genes in BC (rs = 0.38 and 0.42, respectively). QPCR analysis of the expression of RASSF1(A) and mature miR-129-2 in additional BC sample set (24 samples) revealed a negative correlation between them (rs = − 0.41) that strengthened the results obtained during the analysis of miR-129-2 precursor level. In summary, the obtained data indicate the involvement of methylation in the down-regulation of the studied coding and miRNA genes and suggest the involvement of miR-129-2 in the deregulation of RASSF1(A) via a direct interaction or/and mediators in common pathways (according to KEGG, Gene Ontology (FDR < 0.01), and GeneCards data) in the examined gynecological tumors.
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The TORC1 effector kinase Npr1 fine tunes the inherent activity of the Mep2 ammonium transport protein. Nat Commun 2015; 5:3101. [PMID: 24476960 DOI: 10.1038/ncomms4101] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 12/13/2013] [Indexed: 12/30/2022] Open
Abstract
The TORC1 complex controls cell growth upon integrating nutritional signals including amino-acid availability. TORC1 notably adapts the plasma membrane protein content by regulating arrestin-mediated endocytosis of amino-acid transporters. Here we demonstrate that TORC1 further fine tunes the inherent activity of the ammonium transport protein, Mep2, a yeast homologue of mammalian Rhesus factors, independently of arrestin-mediated endocytosis. The TORC1 effector kinase Npr1 and the upstream TORC1 regulator Npr2 control Mep2 transport activity by phospho-silencing a carboxy-terminal autoinhibitory domain. Under poor nitrogen supply, Npr1 enables Mep2 S457 phosphorylation and thus ammonium transport activity. Supplementation of the preferred nitrogen source glutamine leads to Mep2 inactivation and instant S457 dephosphorylation via plasma membrane Psr1 and Psr2 redundant phosphatases. This study underscores that TORC1 also adjusts nutrient permeability to regulate cell growth in a fast and flexible response to environmental perturbation, establishing a hierarchy in the transporters to be degraded, inactivated or maintained active at the plasma membrane.
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Sakai N, Saito Y, Fujiwara Y, Shiraki T, Imanishi Y, Koshimizu TA, Shibata K. Identification of protein arginine N-methyltransferase 5 (PRMT5) as a novel interacting protein with the tumor suppressor protein RASSF1A. Biochem Biophys Res Commun 2015; 467:778-84. [PMID: 26482848 DOI: 10.1016/j.bbrc.2015.10.065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 10/12/2015] [Indexed: 01/05/2023]
Abstract
The candidate tumor suppressor gene RASSF1A (Ras-association domain family 1, isoform A) is inactivated in many types of adult and childhood cancers. However, the mechanisms by which RASSF1A exerts tumor suppressive functions have yet to be elucidated. In this report, we sought to identify candidate proteins that interact with RASSF1A using proteomic screening. Using peptide mass fingerprinting, we identified protein arginine N-methyltransferase 5 (PRMT5), a type II protein arginine N-methyltransferase that monomethylates and symmetrically dimethylates arginine residues, as a novel protein that interacts with RASSF1A. The association between the two proteins was confirmed by co-immunoprecipitation and immunofluorescence staining. Co-expressing RASSF1A and PRMT5 led to a redistribution of PRMT5 from the cytosol to stabilized microtubules, where RASSF1A and PRMT5 became co-localized. Our results demonstrate that PRMT5 translocates to bundled microtubules on stabilization by RASSF1A expression. Our results show that the tumor suppressor RASSF1A interacts with PRMT5 in vivo and in vitro. Notably, this is the first demonstration of RASSF1A-dependent microtubule recruitment of PRMT5, suggesting a novel role for RASSF1A in the anchoring of cytosolic PRMT5 to microtubules.
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Affiliation(s)
- Nobuya Sakai
- Division of Functional Genomics, Faculty of Pharmaceutical Science, Himeji Dokkyo University, Hyogo 670-0896, Japan
| | - Yumiko Saito
- Division of Functional Genomics, Faculty of Pharmaceutical Science, Himeji Dokkyo University, Hyogo 670-0896, Japan
| | - Yoko Fujiwara
- Division of Molecular Pharmacology, Department of Pharmacology, Jichi Medical University, Tochigi 329-0498, Japan
| | - Takashi Shiraki
- Division of Functional Genomics, Faculty of Pharmaceutical Science, Himeji Dokkyo University, Hyogo 670-0896, Japan
| | - Yorihisa Imanishi
- Division of Head and Neck Surgery, Department of Otorhinolaryngology, School of Medicine, Keio University, Tokyo 160-8582, Japan
| | - Taka-aki Koshimizu
- Division of Molecular Pharmacology, Department of Pharmacology, Jichi Medical University, Tochigi 329-0498, Japan
| | - Katsushi Shibata
- Division of Functional Genomics, Faculty of Pharmaceutical Science, Himeji Dokkyo University, Hyogo 670-0896, Japan.
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Nawaz I, Hu LF, Du ZM, Moumad K, Ignatyev I, Pavlova TV, Kashuba V, Almgren M, Zabarovsky ER, Ernberg I. Integrin α9 gene promoter is hypermethylated and downregulated in nasopharyngeal carcinoma. Oncotarget 2015; 6:31493-507. [PMID: 26372814 PMCID: PMC4741620 DOI: 10.18632/oncotarget.5154] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 08/27/2015] [Indexed: 02/07/2023] Open
Abstract
Epigenetic silencing of tumor suppressor genes (TSGs) by promoter methylation can be an early event in the multi-step process of carcinogenesis. Human chromosome 3 contains clusters of TSGs involved in many cancer types including nasopharyngeal carcinoma (NPC), the most common cancer in Southern China. Among ten candidate TSGs identified in chromosome 3 using NotI microarray, ITGA9 and WNT7A could be validated. 5'-aza-2' deoxycytidine treatment restored the expression of ITGA9 and WNT7A in two NPC cell lines. Immunostaining showed strong expression of these genes in the membrane and cytoplasm of adjacent control nasopharyngeal epithelium cells, while they were weakly expressed in NPC tumor cells. The ITGA9 promoter showed marked differentially methylation between tumor and control tissue, whereas no differentially methylation could be detected for the WNT7A promoter. The expression level of ITGA9 in NPC tumors was downregulated 4.9-fold, compared to the expression in control. ITGA9 methylation was detected by methylation specific PCR (MSP) in 56% of EBV positive NPC-cases with 100% specificity. Taken together, this suggests that ITGA9 might be a TSG in NPC that is involved in tumor cell biology. The possibility of using ITGA9 methylation as a marker for early detection of NPC should further be explored.
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Affiliation(s)
- Imran Nawaz
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Microbiology, Faculty of Life Sciences, University of Balochistan, Quetta, Pakistan
| | - Li-Fu Hu
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Zi-Ming Du
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- State Key Laboratory of Oncology in South China, and Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
| | - Khalid Moumad
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Oncovirology Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Ilya Ignatyev
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Tatiana V. Pavlova
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Vladimir Kashuba
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Malin Almgren
- Department Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Centre for Molecular Medicine, Stockholm, Sweden
| | - Eugene R. Zabarovsky
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical & Experimental Medicine, Division of Cell Biology, Linköping University, Linköping, Sweden
| | - Ingemar Ernberg
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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Huang N, Cheng S, Mi X, Tian Q, Huang Q, Wang F, Xu Z, Xie Z, Chen J, Cheng Y. Downregulation of nitrogen permease regulator like-2 activates PDK1-AKT1 and contributes to the malignant growth of glioma cells. Mol Carcinog 2015; 55:1613-1626. [PMID: 26455908 DOI: 10.1002/mc.22413] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 08/20/2015] [Accepted: 08/31/2015] [Indexed: 12/24/2022]
Affiliation(s)
- Ning Huang
- Department of Neurosurgery; The Second Affiliated Hospital of Chongqing Medical University; Chongqing China
| | - Si Cheng
- Department of Orthopaedics; The First Affiliated Hospital of Chongqing Medical University; Chongqing China
| | - Xiujuan Mi
- Department of neurology; The First Affiliated Hospital of Chongqing Medical University; Chongqing China
- Chongqing Key Laboratory of Neurology; Chongqing China
| | - Qin Tian
- Department of Neurosurgery; The Second Affiliated Hospital of Chongqing Medical University; Chongqing China
- Institute of Life Sciences; Chongqing Medical University; Chongqing China
| | - Qin Huang
- Department of Neurosurgery; The Second Affiliated Hospital of Chongqing Medical University; Chongqing China
| | - Feng Wang
- Department of Neurosurgery; The Second Affiliated Hospital of Chongqing Medical University; Chongqing China
| | - Zongye Xu
- Department of Neurosurgery; The Second Affiliated Hospital of Chongqing Medical University; Chongqing China
| | - Zongyi Xie
- Department of Neurosurgery; The Second Affiliated Hospital of Chongqing Medical University; Chongqing China
| | - Jin Chen
- Department of Neurosurgery; The Second Affiliated Hospital of Chongqing Medical University; Chongqing China
| | - Yuan Cheng
- Department of Neurosurgery; The Second Affiliated Hospital of Chongqing Medical University; Chongqing China
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50
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Dmitriev AA, Rosenberg EE, Krasnov GS, Gerashchenko GV, Gordiyuk VV, Pavlova TV, Kudryavtseva AV, Beniaminov AD, Belova AA, Bondarenko YN, Danilets RO, Glukhov AI, Kondratov AG, Alexeyenko A, Alekseev BY, Klein G, Senchenko VN, Kashuba VI. Identification of Novel Epigenetic Markers of Prostate Cancer by NotI-Microarray Analysis. DISEASE MARKERS 2015; 2015:241301. [PMID: 26491211 PMCID: PMC4602334 DOI: 10.1155/2015/241301] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 07/11/2015] [Accepted: 07/14/2015] [Indexed: 12/30/2022]
Abstract
A significant need for reliable and accurate cancer diagnostics and prognosis compels the search for novel biomarkers that would be able to discriminate between indolent and aggressive tumors at the early stages of disease. The aim of this work was identification of potential diagnostic biomarkers for characterization of different types of prostate tumors. NotI-microarrays with 180 clones associated with chromosome 3 genes/loci were applied to determine genetic and epigenetic alterations in 33 prostate tumors. For 88 clones, aberrations were detected in more than 10% of tumors. The major types of alterations were DNA methylation and/or deletions. Frequent methylation of the discovered loci was confirmed by bisulfite sequencing on selective sampling of genes: FGF12, GATA2, and LMCD1. Three genes (BHLHE40, BCL6, and ITGA9) were tested for expression level alterations using qPCR, and downregulation associated with hypermethylation was shown in the majority of tumors. Based on these data, we proposed the set of potential biomarkers for detection of prostate cancer and discrimination between prostate tumors with different malignancy and aggressiveness: BHLHE40, FOXP1, LOC285205, ITGA9, CTDSPL, FGF12, LOC440944/SETD5, VHL, CLCN2, OSBPL10/ZNF860, LMCD1, FAM19A4, CAND2, MAP4, KY, and LRRC58. Moreover, we probabilistically estimated putative functional relations between the genes within each set using the network enrichment analysis.
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Affiliation(s)
- Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- P.A. Herzen Moscow Cancer Research Institute, Ministry of Healthcare of the Russian Federation, Moscow 125284, Russia
| | - Eugenia E. Rosenberg
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kiev 03680, Ukraine
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Ganna V. Gerashchenko
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kiev 03680, Ukraine
| | - Vasily V. Gordiyuk
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kiev 03680, Ukraine
| | - Tatiana V. Pavlova
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, 17177 Stockholm, Sweden
| | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Artemy D. Beniaminov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Anastasia A. Belova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Yuriy N. Bondarenko
- Institute of Urology, National Academy of Medical Sciences of Ukraine, Kiev 04053, Ukraine
| | - Rostislav O. Danilets
- Institute of Urology, National Academy of Medical Sciences of Ukraine, Kiev 04053, Ukraine
| | - Alexander I. Glukhov
- Department of Molecular Biology, Kurchatov NBIC Centre NRC “Kurchatov Institute”, Moscow 123182, Russia
| | - Aleksandr G. Kondratov
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kiev 03680, Ukraine
| | - Andrey Alexeyenko
- Bioinformatics Infrastructure for Life Sciences, Science for Life Laboratory, Karolinska Institute, 17177 Stockholm, Sweden
| | - Boris Y. Alekseev
- P.A. Herzen Moscow Cancer Research Institute, Ministry of Healthcare of the Russian Federation, Moscow 125284, Russia
| | - George Klein
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, 17177 Stockholm, Sweden
| | - Vera N. Senchenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Vladimir I. Kashuba
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kiev 03680, Ukraine
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, 17177 Stockholm, Sweden
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