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Nalawansha DA, Mangano K, den Besten W, Potts PR. TAC-tics for Leveraging Proximity Biology in Drug Discovery. Chembiochem 2024; 25:e202300712. [PMID: 38015747 DOI: 10.1002/cbic.202300712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 11/30/2023]
Abstract
Chemically induced proximity (CIP) refers to co-opting naturally occurring biological pathways using synthetic molecules to recruit neosubstrates that are not normally encountered or to enhance the affinity of naturally occurring interactions. Leveraging proximity biology through CIPs has become a rapidly evolving field and has garnered considerable interest in basic research and drug discovery. PROteolysis TArgeting Chimera (PROTAC) is a well-established CIP modality that induces the proximity between a target protein and an E3 ubiquitin ligase, causing target protein degradation via the ubiquitin-proteasome system. Inspired by PROTACs, several other induced proximity modalities have emerged to modulate both proteins and RNA over recent years. In this review, we summarize the critical advances and opportunities in the field, focusing on protein degraders, RNA degraders and non-degrader modalities such as post-translational modification (PTM) and protein-protein interaction (PPI) modulators. We envision that these emerging proximity-based drug modalities will be valuable resources for both biological research and therapeutic discovery in the future.
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Affiliation(s)
| | - Kyle Mangano
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Willem den Besten
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Patrick Ryan Potts
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
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2
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Li X, Zuo H, Zhang L, Sun Q, Xin Y, Zhang L. Validating HMMR Expression and Its Prognostic Significance in Lung Adenocarcinoma Based on Data Mining and Bioinformatics Methods. Front Oncol 2021; 11:720302. [PMID: 34527588 PMCID: PMC8435795 DOI: 10.3389/fonc.2021.720302] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/10/2021] [Indexed: 12/25/2022] Open
Abstract
Hyaluronic acid-mediated motility receptor (HMMR), a tumor-related gene, plays a vital role in the occurrence and progression of various cancers. This research is aimed to reveal the effect of HMMR in lung adenocarcinoma (LUAD). We first obtained the gene expression profiles and clinical data of patients with LUAD from The Cancer Genome Atlas (TCGA) database. Then, based on the TCGA cohort, the HMMR expression difference between LUAD tissues and nontumor tissues was detected and verified with public tissue microarrays (TMAs), clinical LUAD specimen cohort, and Gene Expression Omnibus (GEO) cohort. Logistic regression analysis and chi-square test were adopted to study the correlation between HMMR expression and clinicopathological parameters. The effect of HMMR expression on survival was evaluated by Kaplan–Meier survival analysis and using the Cox regression model. Furthermore, Gene Set Enrichment Analysis (GSEA) was utilized to screen out signaling pathways related to LUAD and the co-expression analysis was employed to build the protein–protein interaction (PPI) network. The HMMR expression level in LUAD tissues was dramatically higher than that in nontumor tissues. Logistic regression analysis and chi-square test demonstrated that the high HMMR expression in LUAD has relation with gender, pathological stage, T classification, lymph node metastasis, and distant metastasis. The Kaplan–Meier curve suggested a poor prognosis for LUAD patients with high HMMR expression. Multivariate analysis implied that the high HMMR expression was a vital independent predictor of poor overall survival (OS). GSEA indicated that a total of 15 signaling pathways were enriched in samples with the high HMMR expression phenotype. The PPI network gave 10 genes co-expressed with HMMR. HMMR may be an oncogene in LUAD and is expected to become a potential prognostic indicator and therapeutic target for LUAD.
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Affiliation(s)
- Xia Li
- First Clinical College, Xuzhou Medical University, Xuzhou, China.,Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Haiwei Zuo
- School of Medical Information & Engineering, Xuzhou Medical University, Xuzhou, China
| | - Li Zhang
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
| | - Qiuwen Sun
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, China
| | - Yong Xin
- Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.,Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Longzhen Zhang
- Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.,Cancer Institute, Xuzhou Medical University, Xuzhou, China
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D'Souza AM, Cast A, Kumbaji M, Rivas M, Gulati R, Johnston M, Smithrud D, Geller J, Timchenko N. Small Molecule Cjoc42 Improves Chemo-Sensitivity and Increases Levels of Tumor Suppressor Proteins in Hepatoblastoma Cells and in Mice by Inhibiting Oncogene Gankyrin. Front Pharmacol 2021; 12:580722. [PMID: 33746747 PMCID: PMC7969996 DOI: 10.3389/fphar.2021.580722] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 01/18/2021] [Indexed: 12/31/2022] Open
Abstract
Objective: Relapsed hepatoblastoma (HBL) and upfront hepatocellular carcinoma (HCC) are notoriously chemoresistant tumors associated with poor outcomes. Gankyrin (Gank) is a known oncogene that is overexpressed in pediatric liver cancer and implicated in chemo-resistance. The goal of this study was to evaluate if the Gank-tumor suppressor axis is activated in chemoresistant hepatoblastoma patients and examine if an inhibitor of Gank, Cjoc42, might improve the chemosensitivity of cancer cells. Methods: Expression of Gank and its downstream targets were examined in fresh human HBL samples using immunostaining, QRT-PCR, and Western Blot. Cancer cells, Huh6 (human HBL) and Hepa1c1c7 (mouse HCC) were treated with Cjoc42 and with Cjoc42 in combination with cisplatin or doxorubicin. Cell proliferation, apoptosis, and chemoresistance were examined. To examine activities of Cjoc42 in vivo, mice were treated with different doses of Cjoc42, and biological activities of Gank and cytotoxicity of Cjoc42 were tested. Results: Elevation of Gank and Gank-mediated elimination of TSPs are observed in patients with minimal necrosis after chemotherapy and relapsed disease. The treatment of Huh6 and Hepa1c1c7 with Cjoc42 was not cytotoxic; however, in combination with cisplatin or doxorubicin, Cjoc42 caused a significant increase in cytotoxicity compared to chemotherapy alone with increased apoptosis. Examination of Cjoc42 in WT mice showed that Cjoc42 is well tolerated without systemic toxicity, and levels of tumor suppressors CUGBP1, Rb, p53, C/EBPα, and HNF4α are increased by blocking their Gank-dependent degradation. Conclusions: Our work shows that Cjoc42 might be a promising adjunct to chemotherapy for the treatment of severe pediatric liver cancer and presents mechanisms by which Cjoc42 increases chemo-sensitivity.
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Affiliation(s)
- Amber M D'Souza
- Departments of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, Hematology and Oncology, University of Illinois College of Medicine, Peoria, IL, United States
| | - Ashley Cast
- Departments of Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Meenasri Kumbaji
- Departments of Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Maria Rivas
- Departments of Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Ruhi Gulati
- Departments of Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Michael Johnston
- Departments of Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Surgery, University of Cincinnati, Cincinnati, OH, United States
| | - David Smithrud
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, United States
| | - James Geller
- Departments of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Nikolai Timchenko
- Departments of Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Surgery, University of Cincinnati, Cincinnati, OH, United States
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4
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Identification and Verification of Molecular Subtypes with Enhanced Immune Infiltration Based on m6A Regulators in Cutaneous Melanoma. BIOMED RESEARCH INTERNATIONAL 2021; 2021:2769689. [PMID: 33490266 PMCID: PMC7801086 DOI: 10.1155/2021/2769689] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 11/13/2020] [Accepted: 12/22/2020] [Indexed: 02/08/2023]
Abstract
Background As the most aggressive type of skin cancer, cutaneous melanoma (CM) is experiencing a rapidly rising mortality in recent years. Exploring potential prognostic biomarkers or mechanisms of disease progression therefore has a great significance for CM. The purpose of this study was to identify genetic markers and prognostic performance of N6-methyladenosine (m6A) regulators in CM. Method Gene expression profiles, copy number variation (CNV), and single nucleotide polymorphism (SNP) data of patients were obtained from The Cancer Genome Atlas (TCGA) database. Results Genomic variation and association analysis of gene expressions revealed a high degree of genomic variation in the presence of m6A-regulated genes. m6A patients with high-frequency genomic variants in the regulatory gene tended to develop a worse prognosis (p < 0.01). Unsupervised cluster analysis of the expression profiles of m6A-regulated genes identified three clinically distinct molecular subtypes, including degradation-enhanced subgroup and immune-enhanced subgroup, with significant prognostic differences (p = 0.046). A novel prognostic signature, which was established according to m6A-related characteristic genes identified through genome-wide expression spectrum, could effectively identify samples with poor prognosis and enhanced immune infiltration, and the effectiveness was also verified in the dataset of the chip. Conclusion We identified genetic changes in the m6A regulatory gene in CM and related survival outcomes. The findings of this study provide new insights into the epigenetic understanding of m6A in CM.
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Wu X, Liu G, Liu R, He J, Wang G, Zhang H, Liu T, Bai J, Cheng N, Qiu J. Expression of ubiquitin-conjugating enzyme E2T in colorectal cancers and clinical implications. Oncol Lett 2020; 20:275. [PMID: 33014154 PMCID: PMC7520753 DOI: 10.3892/ol.2020.12138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 08/13/2020] [Indexed: 01/05/2023] Open
Abstract
Ubiquitin-conjugating enzyme E2T (UBE2T) plays a significant role in carcinogenesis. Previous studies have demonstrated that UBE2T promotes the development and progression of numerous types of cancer. However, the association between UBE2T expression and colorectal cancer (CRC) remains unclear. In the present study, UBE2T protein expression was examined in the tissues of patients with CRC via immunohistochemistry. In addition, UBE2T expression data and corresponding clinical information were obtained from The Cancer Genome Atlas (TCGA). In the clinical samples, the associations between UBE2T expression and clinicopathological factors were evaluated by the χ2 or Fisher's exact tests. In TCGA data, associations between UBE2T expression and clinical characteristics were evaluated using a logistic regression model. Overall survival was analyzed using Kaplan-Meier and Cox regression analyses. Reverse transcription-quantitative PCR (RT-qPCR) and western blotting assays were used to examine UBE2T expression in normal and CRC cell lines. Gene set enrichment analysis (GSEA) was performed on the dataset from TCGA. UBE2T protein was highly expressed in the cytoplasm of tumor cells in 29/50 clinical samples, whereas in the adjacent normal tissues, it was only highly expressed in 2/50 samples. Furthermore, UBE2T expression was associated with the N classification (P<0.001), clinical TNM stage (P<0.001) and histological grade of tumors (P=0.010). Survival analysis showed an association between high UBE2T expression and poor survival rate in patients with CRC (P=0.002). Cox regression analysis also revealed that UBE2T expression was an independent prognostic factor for these patients (P=0.006). RT-qPCR and western blotting showed that UBE2T was expressed in CRC cell lines at higher levels than that in a normal colon cell line. Analysis of TCGA data revealed that UBE2T was highly expressed in tumor samples compared with normal samples, but was not associated with prognosis. GSEA showed that high expression of UBE2T was associated with the Kyoto Encyclopedia of Genes and Genomes pathways ‘cell cycle’, ‘oxidative phosphorylation’, ‘DNA replication’, ‘p53 signaling pathway’, ‘ubiquitin mediated proteolysis’ and ‘pentose phosphate pathway’. These results indicate that UBE2T may play an important role in the progression of CRC and serve as a potential prognostic factor during the treatment of cancer.
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Affiliation(s)
- Xiangtian Wu
- Department of General Surgery, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi 710061, P.R. China
| | - Gang Liu
- Department of Emergency Surgery, East Hospital, Tongji University, Shanghai 200120, P.R. China
| | - Ruiting Liu
- Department of General Surgery, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi 710061, P.R. China
| | - Jing He
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Guorong Wang
- Department of General Surgery, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi 710061, P.R. China
| | - Haibao Zhang
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710000, P.R. China
| | - Tianjie Liu
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710000, P.R. China
| | - Jirong Bai
- Department of Pathology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Ning Cheng
- Department of General Surgery, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi 710061, P.R. China
| | - Jian Qiu
- Department of General Surgery, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi 710061, P.R. China
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Rusinek D, Pfeifer A, Cieslicka M, Kowalska M, Pawlaczek A, Krajewska J, Szpak-Ulczok S, Tyszkiewicz T, Halczok M, Czarniecka A, Zembala-Nozynska E, Chekan M, Lamch R, Handkiewicz-Junak D, Ledwon A, Paliczka-Cieslik E, Kropinska A, Jarzab B, Oczko-Wojciechowska M. TERT Promoter Mutations and Their Impact on Gene Expression Profile in Papillary Thyroid Carcinoma. Cancers (Basel) 2020; 12:E1597. [PMID: 32560331 PMCID: PMC7352936 DOI: 10.3390/cancers12061597] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/11/2020] [Accepted: 06/15/2020] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Telomerase reverse transcriptase promoter (TERTp) mutations are related to a worse prognosis in various malignancies, including papillary thyroid carcinoma (PTC). Since mechanisms responsible for the poorer outcome of TERTp(+) patients are still unknown, searching for molecular consequences of TERTp mutations in PTC was the aim of our study. METHODS The studied cohort consisted of 54 PTCs, among them 24 cases with distant metastases. BRAF V600E, RAS, and TERTp mutational status was evaluated in all cases. Differences in gene expression profile between TERTp(+) and TERTp(-) PTCs were examined using microarrays. The evaluation of signaling pathways and gene ontology was based on the Gene Set Enrichment Analysis. RESULTS Fifty-nine percent (32/54) of analyzed PTCs were positive for at least one mutation: 27 were BRAF(+), among them eight were TERTp(+), and 1 NRAS(+), whereas five other samples harbored RAS mutations. Expression of four genes significantly differed in BRAF(+)TERTp(+) and BRAF(+)TERTp(-) PTCs. Deregulation of pathways involved in key cell processes was observed. CONCLUSIONS TERTp mutations are related to higher PTC aggressiveness. CRABP2 gene was validated as associated with TERTp mutations. However, its potential use in diagnostics or risk stratification in PTC patients needs further studies.
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Affiliation(s)
- Dagmara Rusinek
- Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (A.P.); (M.C.); (M.K.); (A.P.); (T.T.); (M.H.); (M.O.-W.)
| | - Aleksandra Pfeifer
- Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (A.P.); (M.C.); (M.K.); (A.P.); (T.T.); (M.H.); (M.O.-W.)
| | - Marta Cieslicka
- Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (A.P.); (M.C.); (M.K.); (A.P.); (T.T.); (M.H.); (M.O.-W.)
| | - Malgorzata Kowalska
- Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (A.P.); (M.C.); (M.K.); (A.P.); (T.T.); (M.H.); (M.O.-W.)
| | - Agnieszka Pawlaczek
- Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (A.P.); (M.C.); (M.K.); (A.P.); (T.T.); (M.H.); (M.O.-W.)
| | - Jolanta Krajewska
- Department of Nuclear Medicine and Endocrine Oncology, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (J.K.); (S.S.-U.); (D.H.-J.); (A.L.); (E.P.-C.); (A.K.); (B.J.)
| | - Sylwia Szpak-Ulczok
- Department of Nuclear Medicine and Endocrine Oncology, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (J.K.); (S.S.-U.); (D.H.-J.); (A.L.); (E.P.-C.); (A.K.); (B.J.)
| | - Tomasz Tyszkiewicz
- Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (A.P.); (M.C.); (M.K.); (A.P.); (T.T.); (M.H.); (M.O.-W.)
| | - Monika Halczok
- Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (A.P.); (M.C.); (M.K.); (A.P.); (T.T.); (M.H.); (M.O.-W.)
| | - Agnieszka Czarniecka
- Department of Oncological and Reconstructive Surgery, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland;
| | - Ewa Zembala-Nozynska
- Tumor Pathology Department, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (E.Z.-N.); (M.C.); (R.L.)
| | - Mykola Chekan
- Tumor Pathology Department, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (E.Z.-N.); (M.C.); (R.L.)
| | - Roman Lamch
- Tumor Pathology Department, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (E.Z.-N.); (M.C.); (R.L.)
| | - Daria Handkiewicz-Junak
- Department of Nuclear Medicine and Endocrine Oncology, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (J.K.); (S.S.-U.); (D.H.-J.); (A.L.); (E.P.-C.); (A.K.); (B.J.)
| | - Aleksandra Ledwon
- Department of Nuclear Medicine and Endocrine Oncology, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (J.K.); (S.S.-U.); (D.H.-J.); (A.L.); (E.P.-C.); (A.K.); (B.J.)
| | - Ewa Paliczka-Cieslik
- Department of Nuclear Medicine and Endocrine Oncology, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (J.K.); (S.S.-U.); (D.H.-J.); (A.L.); (E.P.-C.); (A.K.); (B.J.)
| | - Aleksandra Kropinska
- Department of Nuclear Medicine and Endocrine Oncology, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (J.K.); (S.S.-U.); (D.H.-J.); (A.L.); (E.P.-C.); (A.K.); (B.J.)
| | - Barbara Jarzab
- Department of Nuclear Medicine and Endocrine Oncology, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (J.K.); (S.S.-U.); (D.H.-J.); (A.L.); (E.P.-C.); (A.K.); (B.J.)
| | - Malgorzata Oczko-Wojciechowska
- Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland; (A.P.); (M.C.); (M.K.); (A.P.); (T.T.); (M.H.); (M.O.-W.)
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Shao X, Lv N, Liao J, Long J, Xue R, Ai N, Xu D, Fan X. Copy number variation is highly correlated with differential gene expression: a pan-cancer study. BMC MEDICAL GENETICS 2019; 20:175. [PMID: 31706287 PMCID: PMC6842483 DOI: 10.1186/s12881-019-0909-5] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 10/15/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND Cancer is a heterogeneous disease with many genetic variations. Lines of evidence have shown copy number variations (CNVs) of certain genes are involved in development and progression of many cancers through the alterations of their gene expression levels on individual or several cancer types. However, it is not quite clear whether the correlation will be a general phenomenon across multiple cancer types. METHODS In this study we applied a bioinformatics approach integrating CNV and differential gene expression mathematically across 1025 cell lines and 9159 patient samples to detect their potential relationship. RESULTS Our results showed there is a close correlation between CNV and differential gene expression and the copy number displayed a positive linear influence on gene expression for the majority of genes, indicating that genetic variation generated a direct effect on gene transcriptional level. Another independent dataset is utilized to revalidate the relationship between copy number and expression level. Further analysis show genes with general positive linear influence on gene expression are clustered in certain disease-related pathways, which suggests the involvement of CNV in pathophysiology of diseases. CONCLUSIONS This study shows the close correlation between CNV and differential gene expression revealing the qualitative relationship between genetic variation and its downstream effect, especially for oncogenes and tumor suppressor genes. It is of a critical importance to elucidate the relationship between copy number variation and gene expression for prevention, diagnosis and treatment of cancer.
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Affiliation(s)
- Xin Shao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ning Lv
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jie Liao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jinbo Long
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Rui Xue
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ni Ai
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Donghang Xu
- Department of Pharmacy, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009, China.
| | - Xiaohui Fan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
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Chakravorty D, Banerjee K, Mapder T, Saha S. In silico modeling of phosphorylation dependent and independent c-Myc degradation. BMC Bioinformatics 2019; 20:230. [PMID: 31068129 PMCID: PMC6505206 DOI: 10.1186/s12859-019-2846-x] [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: 04/09/2019] [Accepted: 04/24/2019] [Indexed: 12/24/2022] Open
Abstract
Background c-Myc plays an important role in cell proliferation, cell growth and in differentiation, making it a key regulator for carcinogenesis and pluripotency. Tight control of c-myc turnover is required by ubiquitin-mediated degradation. This is achieved in the system by two F-box proteins Skp2 and FBXW7. Results Dynamic modelling technique was used to build two exclusive models for phosphorylation dependent degradation of Myc by FBXW7 (Model 1) and phosphorylation independent degradation by Skp2 (Model 2). Sensitivity analysis performed on these two models revealed that these models were corroborating experimental studies. It was also seen that Model 1 was more robust and perhaps more efficient in degrading c-Myc. These results questioned the existence of the two models in the system and to answer the question a combined model was hypothesised which had a decision making switch. The combined model had both Skp2 and FBXW7 mediated degradation where again the latter played a more important role. This model was able to achieve the lowest levels of ubiquitylated Myc and therefore functioned most efficiently in degradation of Myc. Conclusion In this report, c-Myc degradation by two F-box proteins was mathematically evaluated based on the importance of c-Myc turnover. The study was performed in a homeostatic system and therefore, prompts the exploration of c-Myc degradation in cancer state and in pluripotent state. Electronic supplementary material The online version of this article (10.1186/s12859-019-2846-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Tarunendu Mapder
- ARC CoE for Mathematical and Statistical Frontiers, School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia.
| | - Sudipto Saha
- Bioinformatics Centre, Bose Institute, Kolkata, India.
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9
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Park S, Lim J, Kim JR, Cho S. Inhibitory effects of resveratrol on hepatitis B virus X protein-induced hepatocellular carcinoma. J Vet Sci 2018; 18:419-429. [PMID: 28385009 PMCID: PMC5746434 DOI: 10.4142/jvs.2017.18.4.419] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 01/11/2017] [Accepted: 02/07/2017] [Indexed: 12/27/2022] Open
Abstract
Liver cancer occurs very frequently worldwide and hepatocellular carcinoma (HCC) accounts for more than 80% of total primary liver cancer cases. In this study, the anticarcinogenic effects of resveratrol against hepatitis B virus (HBV)-induced HCC were investigated by using HBV X-protein-overexpressing Huh7 (Huh7-HBx) human hepatoma cells. MTT assay showed that resveratrol decreased cell viability. Fluorescence-activated cell-sorter analysis showed that resveratrol induced G1 cell cycle arrest without increasing the sub-G1 phase cell population. Therefore, we evaluated its effect on regulation of cyclin D1, which is critically involved in G1/S transition. Resveratrol lowered cyclin D1 transcription. Western blot analysis of the effects of resveratrol on upstream cyclin D1 transcriptional signaling, extracellular signal-related kinase (ERK), p90RSK, Akt, and p70S6K revealed inhibition of Akt but not the ERK signaling pathway. Collectively, the results indicate that resveratrol inhibits Huh7-HBx proliferation by decreasing cyclin D1 expression through blockade of Akt signaling. We investigated the anticarcinogenic effect and mechanism of resveratrol in xenograft model mice implanted with Huh7-HBx cells. Intraperitoneal resveratrol injection reduced tumor size in the mice. Expression of survivin was reduced, but cyclin D1 was not affected. The results demonstrate that resveratrol treatment may help manage HBV-induced HCC by regulating survivin.
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Affiliation(s)
- Seungmo Park
- BK21 PLUS Program for Creative Veterinary Science Research, Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.,Institute of Laboratory Animal Resources, Seoul National University, Seoul 08826, Korea
| | - Jihae Lim
- College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Jong Rhan Kim
- Advanced Institutes of Convergence Technology, Seoul National University, Seoul 08826, Korea
| | - Seongbeom Cho
- BK21 PLUS Program for Creative Veterinary Science Research, Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
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10
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Rainger J, Pehlivan D, Johansson S, Bengani H, Sanchez-Pulido L, Williamson KA, Ture M, Barker H, Rosendahl K, Spranger J, Horn D, Meynert A, Floyd JAB, Prescott T, Anderson CA, Rainger JK, Karaca E, Gonzaga-Jauregui C, Jhangiani S, Muzny DM, Seawright A, Soares DC, Kharbanda M, Murday V, Finch A, Gibbs RA, van Heyningen V, Taylor MS, Yakut T, Knappskog PM, Hurles ME, Ponting CP, Lupski JR, Houge G, FitzPatrick DR. Monoallelic and biallelic mutations in MAB21L2 cause a spectrum of major eye malformations. Am J Hum Genet 2014; 94:915-23. [PMID: 24906020 PMCID: PMC4121478 DOI: 10.1016/j.ajhg.2014.05.005] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 05/13/2014] [Indexed: 11/28/2022] Open
Abstract
We identified four different missense mutations in the single-exon gene MAB21L2 in eight individuals with bilateral eye malformations from five unrelated families via three independent exome sequencing projects. Three mutational events altered the same amino acid (Arg51), and two were identical de novo mutations (c.151C>T [p.Arg51Cys]) in unrelated children with bilateral anophthalmia, intellectual disability, and rhizomelic skeletal dysplasia. c.152G>A (p.Arg51His) segregated with autosomal-dominant bilateral colobomatous microphthalmia in a large multiplex family. The fourth heterozygous mutation (c.145G>A [p.Glu49Lys]) affected an amino acid within two residues of Arg51 in an adult male with bilateral colobomata. In a fifth family, a homozygous mutation (c.740G>A [p.Arg247Gln]) altering a different region of the protein was identified in two male siblings with bilateral retinal colobomata. In mouse embryos, Mab21l2 showed strong expression in the developing eye, pharyngeal arches, and limb bud. As predicted by structural homology, wild-type MAB21L2 bound single-stranded RNA, whereas this activity was lost in all altered forms of the protein. MAB21L2 had no detectable nucleotidyltransferase activity in vitro, and its function remains unknown. Induced expression of wild-type MAB21L2 in human embryonic kidney 293 cells increased phospho-ERK (pERK1/2) signaling. Compared to the wild-type and p.Arg247Gln proteins, the proteins with the Glu49 and Arg51 variants had increased stability. Abnormal persistence of pERK1/2 signaling in MAB21L2-expressing cells during development is a plausible pathogenic mechanism for the heterozygous mutations. The phenotype associated with the homozygous mutation might be a consequence of complete loss of MAB21L2 RNA binding, although the cellular function of this interaction remains unknown.
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Affiliation(s)
- Joe Rainger
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, 604B, Houston, TX 77030, USA
| | - Stefan Johansson
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Jonas Liesvei 65, 5021 Bergen, Norway; Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
| | - Hemant Bengani
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - Luis Sanchez-Pulido
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, UK
| | - Kathleen A Williamson
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - Mehmet Ture
- Department of Medical Genetics, University of Uludag, 16120 Bursa, Turkey
| | - Heather Barker
- Edinburgh Cancer Research Centre, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - Karen Rosendahl
- Paediatric Radiology Department, Haukeland University Hospital, 5021 Bergen, Norway
| | | | - Denise Horn
- Institut für Medizinische Genetik, Charité Campus Virchow-Klinikum, 13353 Berlin, Germany
| | - Alison Meynert
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - James A B Floyd
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Trine Prescott
- Medical Genetics, Oslo University Hospital, 0424 Oslo, Norway
| | - Carl A Anderson
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Jacqueline K Rainger
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, 604B, Houston, TX 77030, USA
| | - Claudia Gonzaga-Jauregui
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, 604B, Houston, TX 77030, USA
| | - Shalini Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS BCM225, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS BCM225, Houston, TX 77030, USA
| | - Anne Seawright
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - Dinesh C Soares
- Centre for Genomics and Experimental Medicine, Medical Research Council Institute Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - Mira Kharbanda
- Clinical Genetics, Southern General Hospital, Glasgow G51 4TF, UK
| | - Victoria Murday
- Clinical Genetics, Southern General Hospital, Glasgow G51 4TF, UK
| | - Andrew Finch
- Edinburgh Cancer Research Centre, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, 604B, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS BCM225, Houston, TX 77030, USA
| | - Veronica van Heyningen
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - Martin S Taylor
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - Tahsin Yakut
- Department of Medical Genetics, University of Uludag, 16120 Bursa, Turkey
| | - Per M Knappskog
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Jonas Liesvei 65, 5021 Bergen, Norway; Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Chris P Ponting
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, UK
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, 604B, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS BCM225, Houston, TX 77030, USA
| | - Gunnar Houge
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Jonas Liesvei 65, 5021 Bergen, Norway
| | - David R FitzPatrick
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK.
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11
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Calcagno DQ, Freitas VM, Leal MF, de Souza CRT, Demachki S, Montenegro R, Assumpção PP, Khayat AS, Smith MDAC, dos Santos AKCR, Burbano RR. MYC, FBXW7 and TP53 copy number variation and expression in gastric cancer. BMC Gastroenterol 2013; 13:141. [PMID: 24053468 PMCID: PMC3851138 DOI: 10.1186/1471-230x-13-141] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 09/10/2013] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND MYC deregulation is a common event in gastric carcinogenesis, usually as a consequence of gene amplification, chromosomal translocations, or posttranslational mechanisms. FBXW7 is a p53-controlled tumor-suppressor that plays a role in the regulation of cell cycle exit and reentry via MYC degradation. METHODS We evaluated MYC, FBXW7, and TP53 copy number, mRNA levels, and protein expression in gastric cancer and paired non-neoplastic specimens from 33 patients and also in gastric adenocarcinoma cell lines. We also determined the invasion potential of the gastric cancer cell lines. RESULTS MYC amplification was observed in 51.5% of gastric tumor samples. Deletion of one copy of FBXW7 and TP53 was observed in 45.5% and 21.2% of gastric tumors, respectively. MYC mRNA expression was significantly higher in tumors than in non-neoplastic samples. FBXW7 and TP53 mRNA expression was markedly lower in tumors than in paired non-neoplastic specimens. Moreover, deregulated MYC and FBXW7 mRNA expression was associated with the presence of lymph node metastasis and tumor stage III-IV. Additionally, MYC immunostaining was more frequently observed in intestinal-type than diffuse-type gastric cancers and was associated with MYC mRNA expression. In vitro studies showed that increased MYC and reduced FBXW7 expression is associated with a more invasive phenotype in gastric cancer cell lines. This result encouraged us to investigate the activity of the gelatinases MMP-2 and MMP-9 in both cell lines. Both gelatinases are synthesized predominantly by stromal cells rather than cancer cells, and it has been proposed that both contribute to cancer progression. We observed a significant increase in MMP-9 activity in ACP02 compared with ACP03 cells. These results confirmed that ACP02 cells have greater invasion capability than ACP03 cells. CONCLUSION In conclusion, FBXW7 and MYC mRNA may play a role in aggressive biologic behavior of gastric cancer cells and may be a useful indicator of poor prognosis. Furthermore, MYC is a candidate target for new therapies against gastric cancer.
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Affiliation(s)
- Danielle Queiroz Calcagno
- Laboratório de Citogenética Humana, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brasil.
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12
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Cepeda D, Ng HF, Sharifi HR, Mahmoudi S, Cerrato VS, Fredlund E, Magnusson K, Nilsson H, Malyukova A, Rantala J, Klevebring D, Viñals F, Bhaskaran N, Zakaria SM, Rahmanto AS, Grotegut S, Nielsen ML, Szigyarto CAK, Sun D, Lerner M, Navani S, Widschwendter M, Uhlén M, Jirström K, Pontén F, Wohlschlegel J, Grandér D, Spruck C, Larsson LG, Sangfelt O. CDK-mediated activation of the SCF(FBXO) (28) ubiquitin ligase promotes MYC-driven transcription and tumourigenesis and predicts poor survival in breast cancer. EMBO Mol Med 2013; 5:1067-86. [PMID: 23776131 PMCID: PMC3721474 DOI: 10.1002/emmm.201202341] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 05/09/2013] [Accepted: 05/10/2013] [Indexed: 12/12/2022] Open
Abstract
SCF (Skp1/Cul1/F-box) ubiquitin ligases act as master regulators of cellular homeostasis by targeting key proteins for ubiquitylation. Here, we identified a hitherto uncharacterized F-box protein, FBXO28 that controls MYC-dependent transcription by non-proteolytic ubiquitylation. SCFFBXO28 activity and stability are regulated during the cell cycle by CDK1/2-mediated phosphorylation of FBXO28, which is required for its efficient ubiquitylation of MYC and downsteam enhancement of the MYC pathway. Depletion of FBXO28 or overexpression of an F-box mutant unable to support MYC ubiquitylation results in an impairment of MYC-driven transcription, transformation and tumourigenesis. Finally, in human breast cancer, high FBXO28 expression and phosphorylation are strong and independent predictors of poor outcome. In conclusion, our data suggest that SCFFBXO28 plays an important role in transmitting CDK activity to MYC function during the cell cycle, emphasizing the CDK-FBXO28-MYC axis as a potential molecular drug target in MYC-driven cancers, including breast cancer.
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Affiliation(s)
- Diana Cepeda
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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13
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Mori T, Ikeda DD, Fukushima T, Takenoshita S, Kochi H. NIRF constitutes a nodal point in the cell cycle network and is a candidate tumor suppressor. Cell Cycle 2011; 10:3284-99. [PMID: 21952639 DOI: 10.4161/cc.10.19.17176] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In biological networks, a small number of "hub" proteins play critical roles in the network integrity and functions. The cell cycle network orchestrates versatile cellular functions through interactions between many signaling modules, whose defects impair diverse cellular processes, often leading to cancer. However, the network architecture and molecular basis that ensure proper coordination between distinct modules are unclear. Here, we show that the ubiquitin ligase NIRF (also known as UHRF2), which induces G1 arrest, interacts with multiple cell cycle proteins including cyclins (A2, B1, D1 and E1), p53 and pRB, and ubiquitinates cyclins D1 and E1. Consistent with its versatility, a bioinformatic network analysis demonstrated that NIRF is an intermodular hub protein that is responsible for the coordination of multiple network modules. Notably, intermodular hubs are frequently associated with oncogenesis. Indeed, we detected loss of heterozygosity of the NIRF gene in several kinds of tumors. When a cancer outlier profile analysis was applied to the Oncomine database, loss of the NIRF gene was found at statistically significant levels in diverse tumors. Importantly, a recurrent microdeletion targeting NIRF was observed in non-small cell lung carcinoma. Furthermore, NIRF is immediately adjacent to the single nucleotide polymorphism rs719725, which is reportedly associated with the risk of colorectal cancer. These observations suggest that NIRF occupies a prominent position within the cell cycle network, and is a strong candidate for a tumor suppressor whose aberration contributes to the pathogenesis of diverse malignancies.
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Affiliation(s)
- Tsutomu Mori
- Department of Human Lifesciences, Fukushima Medical University School of Nursing, Fukushima, Japan.
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14
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Anwar A, Norris DA, Fujita M. Ubiquitin proteasomal pathway mediated degradation of p53 in melanoma. Arch Biochem Biophys 2010; 508:198-203. [PMID: 21167122 DOI: 10.1016/j.abb.2010.12.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 12/09/2010] [Accepted: 12/10/2010] [Indexed: 01/19/2023]
Abstract
Ubiquitin proteasomal pathway (UPP) is the principle mechanism for protein catabolism and affects cellular processes critical for survival and proliferation. Levels of tumor suppressor protein p53 are very low in cells due to its rapid turnover by UPP-mediated degradation. While p53 is mutated in human cancers, most human melanomas maintain wild-type conformation. In this study, to investigate the effects of UPP inhibitor invitro and in vivo, we used a genetically-engineered mouse model (GEMM) that has the same genetic alterations as those of human melanomas. Melanoma cells were established from mouse tumors and named 8B20 cells. Treatment of 8B20 cells with the UPP inhibitors, MG132 and clasto-lactacystin-β-lactone, led to an increase in levels of p53 while treatment with non-proteasomal inhibitors did not alter p53 levels. UPP inhibitors induced formation of heavy molecular weight ubiquitinated proteins, a hallmark of UPP inhibition, and p53-specific poly-ubiquitinated products in 8B20 cells. To further decipher the mechanism of p53 stabilization, we investigated half-life of p53 in cells treated with cycloheximide to block de novo protein synthesis. Treatment of 8B20 cells with MG132 led to an increase in the half-life of p53. Further analysis revealed that p53 stabilization was not mediated by phosphorylation of Ser-15 and Ser-20 residues. In vivo studies showed that MG132 induced p53 overexpression and reduced tumor growth, suggesting an important role of p53 stabilization in controlling melanoma. Taken together, our studies provide a proof of principle for using a GEMM to address the mechanisms of action and efficacy of melanoma treatment.
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Affiliation(s)
- Adil Anwar
- Department of Dermatology, University of Colorado Denver, Aurora, CO 80045, USA.
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15
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Sales G, Coppe A, Bisognin A, Biasiolo M, Bortoluzzi S, Romualdi C. MAGIA, a web-based tool for miRNA and Genes Integrated Analysis. Nucleic Acids Res 2010; 38:W352-9. [PMID: 20484379 PMCID: PMC2896126 DOI: 10.1093/nar/gkq423] [Citation(s) in RCA: 133] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MAGIA (miRNA and genes integrated analysis) is a novel web tool for the integrative analysis of target predictions, miRNA and gene expression data. MAGIA is divided into two parts: the query section allows the user to retrieve and browse updated miRNA target predictions computed with a number of different algorithms (PITA, miRanda and Target Scan) and Boolean combinations thereof. The analysis section comprises a multistep procedure for (i) direct integration through different functional measures (parametric and non-parametric correlation indexes, a variational Bayesian model, mutual information and a meta-analysis approach based on P-value combination) of mRNA and miRNA expression data, (ii) construction of bipartite regulatory network of the best miRNA and mRNA putative interactions and (iii) retrieval of information available in several public databases of genes, miRNAs and diseases and via scientific literature text-mining. MAGIA is freely available for Academic users at http://gencomp.bio.unipd.it/magia.
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Affiliation(s)
- Gabriele Sales
- Department of Biology, University of Padua, via U. Bassi 58/B, 35121 Padova, Italy
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16
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Tan Y, Sangfelt O, Spruck C. The Fbxw7/hCdc4 tumor suppressor in human cancer. Cancer Lett 2008; 271:1-12. [PMID: 18541364 DOI: 10.1016/j.canlet.2008.04.036] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2008] [Revised: 04/23/2008] [Accepted: 04/23/2008] [Indexed: 12/11/2022]
Abstract
Fbxw7/hCdc4 is a member of the F-box family of proteins, which function as interchangeable substrate recognition components of the SCF ubiquitin ligases. SCF(Fbxw7/hCdc4) targets several important oncoproteins including c-Myc, c-Jun, cyclin E1, and Notch, for ubiquitin-dependent proteolysis. Recent studies have shown that FBXW7/hCDC4 is mutated in a variety of human tumor types, suggesting that it is a general tumor suppressor in human cancer. Alteration of Fbxw7/hCdc4 function is linked to defects in differentiation, cellular proliferation, and genetic instability. In this review, we summarize what is known about Fbxw7/hCdc4-mediated degradation in the regulation of cellular proliferation and discuss how alteration of its function contributes to human tumorigenesis.
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Affiliation(s)
- YingMeei Tan
- Department of Tumor Cell Biology, Sidney Kimmel Cancer Center, San Diego, CA 92121, USA
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17
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Handra-Luca A, Ruhin B, Lesty C, Fouret P. P27, SKP2, and extra-cellular signal-related kinase signalling in human salivary gland mucoepidermoid carcinoma. Oral Oncol 2006; 42:1005-10. [PMID: 16757206 DOI: 10.1016/j.oraloncology.2005.12.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2005] [Accepted: 12/13/2005] [Indexed: 10/24/2022]
Abstract
Extra-cellular signal-related kinase (ERK) can modulate P27 in several ways. ERK is phosphorylated in a subset of salivary gland mucoepidermoid carcinoma (MEC). We determined immunohistochemical expression of P27, SKP2, cyclin A, Ki67, phospho-RB, and phospho-ERK in 43 MEC. SKP2 correlated with tumour size, microscopic grade, and a worse prognosis. Cyclin A and Ki67 also predicted prognosis, and were correlated with SKP2. P27 did not predict prognosis. P27 had no inverse relationship with SKP2, and correlated with neither Ki67 nor cyclin A. Instead, P27 high expressers had higher levels of phospho-ERK and phospho-RB. When highly expressed, P27 co-localized with cyclin D1 in the nuclei. Relationships of P27 with ERK and RB and its nuclear co-localization with cyclin D1 favour the hypothesis that P27 is in complexes with cyclin D1. This may explain why P27 in contrast to SKP2 and cyclin A does not correlate with tumour cell proliferation and prognosis.
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Affiliation(s)
- Adriana Handra-Luca
- Service d'Anatomie Pathologique, AP-HP Hôpital Jean Verdier and Université Paris 13/Nord, France
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18
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Cho CH, Seo M, Lee YI, Kim SY, Youn HD, Juhnn YS. Dibutyryl cAMP stimulates the proliferation of SH-SY5Y human neuroblastoma cells by up-regulating Skp2 protein. J Cancer Res Clin Oncol 2006; 133:135-44. [PMID: 17004068 DOI: 10.1007/s00432-006-0153-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2006] [Accepted: 08/02/2006] [Indexed: 01/19/2023]
Abstract
PURPOSE We previously found that the proliferation of SH-SY5Y neuroblastoma cells is stimulated when cAMP is up-regulated by stable expression of stimulatory G protein. Therefore, this study was performed to investigate the mechanism whereby cAMP stimulates the proliferation of SH-SY5Y cells. METHODS To investigate the effect of cAMP on cellular proliferation, SH-SY5Y neuroblastoma cells were treated with dibutyryl cAMP (dbcAMP), and then cell growth, thymidine incorporation and cell cycle phase distribution were analyzed. The expression and the activity of the molecules that regulate cell cycle progression were monitored by Western blot, RT-PCR, and kinase activity assay. RESULTS Treatment with dbcAMP produced a biphasic effect on cellular proliferation; especially treatment with low concentration of dbcAMP (0.5 mM) showed a higher cellular proliferation rate and promoted G1/S transition in cell cycle. The dbcAMP (0.5 mM) treatment increased CDK2 activity, and it significantly decreased p27Kip1 expression with a decreased half-life of p27Kip1 protein. Moreover, dbcAMP (0.5 mM) increased the protein level and the stability of Skp2 with a concomitant decrease in its ubiquitination. CONCLUSIONS cAMP up-regulates Skp2 protein by reducing its degradation probably through decreasing the ubiquitination of Skp2, which might result in accelerated degradation of p27Kip1, increase in CDK2 activity, and stimulation of SH-SY5Y cell proliferation in sequence.
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Affiliation(s)
- Chin-Ho Cho
- Department of Biochemistry and Molecular Biology, Laboratory of Cellular Signaling, Cancer Research Institute, Seoul National University College of Medicine, 28 Yongon-dong, Jongno-gu, Seoul, 110-799, South Korea
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19
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Hann SR. Role of post-translational modifications in regulating c-Myc proteolysis, transcriptional activity and biological function. Semin Cancer Biol 2006; 16:288-302. [PMID: 16938463 DOI: 10.1016/j.semcancer.2006.08.004] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The Myc proteins play a central role in cellular proliferation, differentiation, apoptosis and tumorigenesis. Although it is clear that multiple molecular mechanisms mediate these functions, it is unclear how individual mechanisms contribute and if different mechanisms work in concert or separately in mediating the diverse biological functions of c-Myc. Similarly, the role of post-translational modifications in regulating c-Myc molecular and biological properties has remained uncertain, despite over 20 years of research. In particular, phosphorylation of the N-terminal transcriptional regulatory domain has been shown to have a variety of consequences ranging from dramatic effects on apoptosis, tumorigenesis and c-Myc proteolysis to negligible effects on cellular transformation and transcriptional activity. This review attempts to provide a comprehensive and critical evaluation of the accumulated evidence to address the complex and controversial issues surrounding the role of post-translational modifications in c-Myc function, focusing on phosphorylation and ubiquitination of the N-terminal transcriptional regulatory domain. An overall model emerges that suggests phosphorylation and ubiquitination play critical roles in cell cycle progression, cell growth, apoptosis and tumorigenesis that are mediated by phosphorylation-dependent transcriptional activation of distinct sets of target genes and synchronized proteolysis.
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Affiliation(s)
- Stephen R Hann
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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20
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Romanenko AM, Kinoshita A, Wanibuchi H, Wei M, Zaparin WK, Vinnichenko WI, Vozianov AF, Fukushima S. Involvement of ubiquitination and sumoylation in bladder lesions induced by persistent long-term low dose ionizing radiation in humans. J Urol 2006; 175:739-43. [PMID: 16407042 DOI: 10.1016/s0022-5347(05)00172-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2005] [Indexed: 11/18/2022]
Abstract
PURPOSE We determined whether ubiquitination and sumoylation processes are up-regulated in bladder urothelium by chronic, long-term, persistent low doses of ionizing radiation in male patients with benign prostate hyperplasia and females with chronic cystitis living more than 19 years in 137Cs contaminated areas after the Chernobyl accident in Ukraine. MATERIALS AND METHODS Bladder urothelial biopsies from 45 patients were subjected to histopathological and immunohistochemical study of Ub, SUMO1, SUMO E2 conjugating enzyme Ubc9, and the cell cycle inhibitors p53 and p27(Kip1). RESULTS Of 25 group 1 patients from radio contaminated areas chronic proliferative atypical cystitis (Chernobyl cystitis), featuring multiple foci of dysplasia, and carcinoma in situ were observed in 23 (92%) and 19 (76%), respectively, in addition to 1 small pTa grade 1 urothelial carcinoma. Chronic cystitis with areas of dysplasia and urothelial hyperplasia were detected in 2 (10%) and 3 (15%), respectively of the 20 patients in control group 2 from clean (without radio contamination) areas of Ukraine. Greatly increased levels of Ub, SUMO1, Ubc9 and p53 as well as decreased levels of p27(Kip1) were evident in patients in group 1 compared to those in group 2 (all p <0.001). CONCLUSIONS These findings support the hypothesis that up-regulated ubiquitination and sumoylation processes might be an adaptive response to unscheduled proteolysis of aberrant p53 and p27(Kip1) cell cycle regulators occurring with long-term low dose rate ionizing radiation exposure with a possible contribution to urothelial carcinogenesis.
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Affiliation(s)
- Alina M Romanenko
- Department of Pathology, Institute of Urology, Academy of Medical Sciences of Ukraine, Ukraine
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21
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Laman H, Funes JM, Ye H, Henderson S, Galinanes-Garcia L, Hara E, Knowles P, McDonald N, Boshoff C. Transforming activity of Fbxo7 is mediated specifically through regulation of cyclin D/cdk6. EMBO J 2005; 24:3104-16. [PMID: 16096642 PMCID: PMC1201355 DOI: 10.1038/sj.emboj.7600775] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2005] [Accepted: 07/18/2005] [Indexed: 12/19/2022] Open
Abstract
D cyclins (D1, D2 and D3) and their catalytic subunits (cyclin-dependent kinases cdk4 and cdk6) have a facilitating, but nonessential, role in cell cycle entry. Tissue-specific functions for D-type cyclins and cdks have been reported; however, the biochemical properties of these kinases are indistinguishable. We report that an F box protein, Fbxo7, interacted with cellular and viral D cyclins and distinguished among the cdks that bind D-type cyclins, specifically binding cdk6, in vitro and in vivo. Fbxo7 specifically regulated D cyclin/cdk6 complexes: Fbxo7 knockdown decreased cdk6 association with cyclin and its overexpression increased D cyclin/cdk6 activity and E2F activity. Fbxo7 interacted with p27, but its enhancement of cyclin D/cdk6 activity was p21/p27 independent. Fbxo7 overexpression transformed murine fibroblasts, rendering them tumorigenic in athymic nude mice. Transformed phenotypes were dependent on cdk6, as knockdown of cdk6 reversed them. Fbxo7 was highly expressed in epithelial tumors, but not in normal tissues, suggesting that it may have a proto-oncogenic role in human cancers.
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Affiliation(s)
- Heike Laman
- Cancer Research UK, Viral Oncology Group, Wolfson Institute for Biomedical Research, University College London, London, UK.
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22
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Farràs R, Bossis G, Andermarcher E, Jariel-Encontre I, Piechaczyk M. Mechanisms of delivery of ubiquitylated proteins to the proteasome: new target for anti-cancer therapy? Crit Rev Oncol Hematol 2005; 54:31-51. [PMID: 15780906 DOI: 10.1016/j.critrevonc.2004.11.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2004] [Indexed: 02/04/2023] Open
Abstract
The proteasome is the main proteolytic machinery of the cell. It is responsible for the basal turnover of many intracellular polypeptides, the elimination of abnormal proteins and the generation of the vast majority of peptides presented by class I major histocompatibility complex molecules. Proteasomal proteolysis is also involved in the control of virtually all cellular functions and major decisions through the spatially and timely regulated destruction of essential cell regulators. Therefore, the elucidation of its molecular mechanisms is crucial for the full understanding of the physiology of cells and whole organisms. Conversely, it is increasingly clear that proteasomal degradation is either altered in numerous pathological situations, including many cancers and diseases resulting from aberrant cell differentiation, or instrumental for the development of these pathologies. This, consequently, makes it an attractive target for therapeutical intervention. There is ample evidence that most cell proteins must be polyubiquitylated prior to proteasomal degradation. If the structure and the mode of functioning of the proteasome, as well as the enzymology of ubiquitylation, are relatively well understood, how substrates are delivered to and recognized by the proteolytic machine has remained mysterious till recently. The recent literature indicates that the mechanisms involved are multiple, complex and exquisitely regulated and provides new potential targets for anti-cancer pharmacological intervention.
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Affiliation(s)
- Rosa Farràs
- Institute of Molecular Genetics of Montpellier (IGMM), UMR 5535-IFR122, CNRS, Montpellier Cedex 05, France
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23
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Butz N, Ruetz S, Natt F, Hall J, Weiler J, Mestan J, Ducarre M, Grossenbacher R, Hauser P, Kempf D, Hofmann F. The human ubiquitin-conjugating enzyme Cdc34 controls cellular proliferation through regulation of p27Kip1 protein levels. Exp Cell Res 2005; 303:482-93. [PMID: 15652359 DOI: 10.1016/j.yexcr.2004.10.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2004] [Revised: 10/12/2004] [Indexed: 11/18/2022]
Abstract
Ubiquitin-mediated degradation of the cyclin-dependent kinase inhibitor p27Kip1 was shown to be required for the activation of key cyclin-dependent kinases, thereby triggering the onset of DNA replication and cell cycle progression. Although the SCFSkp2 ubiquitin ligase has been reported to mediate p27Kip1 degradation, the nature of the human ubiquitin-conjugating enzyme involved in this process has not yet been determined at the cellular level. Here, we show that antisense oligonucleotides targeting the human ubiquitin-conjugating enzyme Cdc34 downregulate its expression, inhibit the degradation of p27Kip1, and prevent cellular proliferation. Elevation of p27Kip1 protein level is found to be the sole requirement for the inhibition of cellular proliferation induced upon downregulation of Cdc34. Indeed, reducing the expression of p27Kip1 with a specific antisense oligonucleotide is sufficient to reverse the anti-proliferative phenotype elicited by the Cdc34 antisense. Furthermore, downregulation of Cdc34 is found to specifically increase the abundance of the SCFSkp2) ubiquitin ligase substrate p27Kip1, but has no concomitant effect on the level of IkBalpha and beta-catenin, which are known substrates of a closely related SCF ligase.
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Affiliation(s)
- Nicole Butz
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Disease Area Oncology, CH-4002 Basel, Switzerland
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24
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Liang M, Liang YY, Wrighton K, Ungermannova D, Wang XP, Brunicardi FC, Liu X, Feng XH, Lin X. Ubiquitination and proteolysis of cancer-derived Smad4 mutants by SCFSkp2. Mol Cell Biol 2004; 24:7524-37. [PMID: 15314162 PMCID: PMC506984 DOI: 10.1128/mcb.24.17.7524-7537.2004] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Smad4/DPC4, a common signal transducer in transforming growth factor beta (TGF-beta) signaling, is frequently inactivated in human cancer. Although the ubiquitin-proteasome pathway has been established as one mechanism of inactivating Smad4 in cancer, the specific ubiquitin E3 ligase for ubiquitination-mediated proteolysis of Smad4 cancer mutants remains unclear. In this report, we identified the SCFSkp2 complex as candidate Smad4-interacting proteins in an antibody array-based screen and further elucidated the functions of SCFSkp2 in mediating the metabolic instability of cancer-derived Smad4 mutants. We found that Skp2, the F-box component of SCFSkp2, physically interacted with Smad4 at the physiological levels. Several cancer-derived unstable mutants exhibited significantly increased binding to Skp2, which led to their increased ubiquitination and accelerated proteolysis. These results suggest an important role for the SCFSkp2 complex in switching cancer mutants of Smad4 to undergo polyubiquitination-dependent degradation.
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Affiliation(s)
- Min Liang
- Department of Molecular & Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Room 137D, Houston, TX 77030, USA
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