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Jian Y, Chen Q, Al-Danakh A, Xu Z, Xu C, Sun X, Yu X, Yang D, Wang S. Identification and validation of sialyltransferase ST3Gal5 in bladder cancer through bioinformatics and experimental analysis. Int Immunopharmacol 2024; 138:112569. [PMID: 38959540 DOI: 10.1016/j.intimp.2024.112569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/12/2024] [Accepted: 06/24/2024] [Indexed: 07/05/2024]
Abstract
BACKGROUND Bladder cancer (BLCA) is one of the top ten most common cancers in the world. Aberrant sialylation is a common feature in tumorigenesis and tumor immunity. This study seeks to explore the potential impact of sialyltransferase ST3Gal5 on BLCA. METHODS Initially, glycosyltransferase-related DEGs (GRDEGs) were identified using multiple bioinformatics approaches in TCGA-BLCA cohort and validated using GEO databases. Clinical prognosis integration facilitated the determination of ST3Gal5 as an independent prognostic factor in BLCA, employing univariate and multivariate Cox regression analyses. Immune cell infiltration was assessed via CIBERSORT and ssGSEA analyses, while HLA and immune checkpoint genes' levels, along with drug sensitivity, were evaluated in low- and high-ST3Gal5 groups. The TIDE and IPS scores were used to gauge the immune checkpoint blockade (ICB) response. Furthermore, functional experiments, both in vivo and in vitro, were conducted to elucidate the biological roles of ST3Gal5. RESULTS In agreement with bioinformatics findings, ST3Gal5 expression was down-regulated in BLCA tissues and cells, correlating with poorer prognostic outcomes. The StromalScore, ImmuneScore, and ESTIMATEScore were significantly elevated in low-ST3Gal5 group. Moreover, the levels of HLA and immune checkpoint genes were upregulated in low-ST3Gal5 group. Down-regulated ST3Gal5 promoted the proliferation, migration, and invasion of BLCA cells in vivo and in vitro. CONCLUSION Our findings demonstrated that low ST3Gal5 level promoted tumorigenesis and progression of BLCA, implying its potential as a predictive biomarker and therapeutic target.
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Affiliation(s)
- Yuli Jian
- Department of Urology, First Affiliated Hospital of Dalian Medical University, Dalian Medical University, Dalian 116011, China; Liaoning Provincial Core Lab of Glycobiology and Glycoengineering, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Qiwei Chen
- Department of Urology, First Affiliated Hospital of Dalian Medical University, Dalian Medical University, Dalian 116011, China; Zhongda Hospital, Medical School, Advanced Institute for Life and Health, Southeast University, Nanjing 210096, China
| | - Abdullah Al-Danakh
- Department of Urology, First Affiliated Hospital of Dalian Medical University, Dalian Medical University, Dalian 116011, China
| | - Zhongyang Xu
- Liaoning Provincial Core Lab of Glycobiology and Glycoengineering, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Chunyan Xu
- Liaoning Provincial Core Lab of Glycobiology and Glycoengineering, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Xiaoxin Sun
- Liaoning Provincial Core Lab of Glycobiology and Glycoengineering, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Xiao Yu
- Department of Pathology and Forensic Medicine, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Deyong Yang
- Department of Urology, First Affiliated Hospital of Dalian Medical University, Dalian Medical University, Dalian 116011, China.
| | - Shujing Wang
- Liaoning Provincial Core Lab of Glycobiology and Glycoengineering, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China.
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Almutairy AF, Alhamed AS, Grant SG, Falso MJ, Day BW, Simmons CR, Latimer JJ. Cancer-specific alterations in nuclear matrix proteins determined by multi-omics analyses of ductal carcinoma in situ. Front Oncol 2024; 14:1406946. [PMID: 39165691 PMCID: PMC11333849 DOI: 10.3389/fonc.2024.1406946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/20/2024] [Indexed: 08/22/2024] Open
Abstract
Introduction Breast cancer (BC) is the most common cancer affecting women in the United States. Ductal carcinoma in situ (DCIS) is the earliest identifiable pre-invasive BC lesion. Estimates show that 14 to 50% of DCIS cases progress to invasive BC. Methods Our objective was to identify nuclear matrix proteins (NMP) with specifically altered expression in DCIS and later stages of BC compared to non-diseased breast reduction mammoplasty and a contralateral breast explant culture using mass spectrometry and RNA sequencing to accurately identify aggressive DCIS. Results Sixty NMPs were significantly differentially expressed between the DCIS and non-diseased breast epithelium in an isogenic contralateral pair of patient-derived extended explants. Ten of the sixty showed significant mRNA expression level differences that matched the protein expression. These 10 proteins were similarly expressed in non-diseased breast reduction cells. Three NMPs (RPL7A, RPL11, RPL31) were significantly upregulated in DCIS and all other BC stages compared to the matching contralateral breast culture and an unrelated non-diseased breast reduction culture. RNA sequencing analyses showed that these three genes were increasingly upregulated with BC progression. Finally, we identified three NMPs (AHNAK, CDC37 and DNAJB1) that were significantly downregulated in DCIS and all other BC stages compared to the isogenically matched contralateral culture and the non-diseased breast reduction culture using both proteomics and RNA sequencing techniques. Discussion These genes should form the basis of, or contribute to, a molecular diagnostic panel that could identify DCIS lesions likely to be indolent and therefore not requiring aggressive treatment.
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Affiliation(s)
- Ali F. Almutairy
- Department of Pharmacology and Toxicology, College of Pharmacy, Qassim University, Buraidah, Saudi Arabia
- Department of Pharmaceutical Sciences, Barry and Judy Silverman College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL, United States
- AutoNation Institute for Breast Cancer Research and Care, Nova Southeastern University, Fort Lauderdale, FL, United States
| | - Abdullah S. Alhamed
- Department of Pharmaceutical Sciences, Barry and Judy Silverman College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL, United States
- AutoNation Institute for Breast Cancer Research and Care, Nova Southeastern University, Fort Lauderdale, FL, United States
- Pharmacology Department, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Stephen G. Grant
- AutoNation Institute for Breast Cancer Research and Care, Nova Southeastern University, Fort Lauderdale, FL, United States
- Department of Public Health, Dr. Kiran C. Patel College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, United States
- Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Miranda J. Falso
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Billy W. Day
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, United States
| | - Colton R. Simmons
- Department of Pharmaceutical Sciences, Barry and Judy Silverman College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL, United States
- AutoNation Institute for Breast Cancer Research and Care, Nova Southeastern University, Fort Lauderdale, FL, United States
| | - Jean J. Latimer
- Department of Pharmaceutical Sciences, Barry and Judy Silverman College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL, United States
- AutoNation Institute for Breast Cancer Research and Care, Nova Southeastern University, Fort Lauderdale, FL, United States
- Department of Obstetrics and Gynecology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
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Almutairy A, Alhamed A, Grant SG, Sarachine Falso MJ, Day BW, Simmons CR, Latimer JJ. Cancer-Specific Alterations in Nuclear Matrix Proteins Determined by Multi-omics Analyses of Ductal Carcinoma in Situ. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580215. [PMID: 38405693 PMCID: PMC10888842 DOI: 10.1101/2024.02.13.580215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Breast cancer (BC) is the most common cancer affecting women in the United States. Ductal carcinoma in situ (DCIS) is the earliest identifiable pre-invasive BC lesion. Estimates show that 14 to 50% of DCIS cases progress to invasive BC. Our objective was to identify nuclear matrix proteins (NMP) with specifically altered expression in DCIS and later stages of BC compared to non-diseased breast reduction mammoplasty and a contralateral breast explant using mass spectrometry and RNA sequencing to accurately identify aggressive DCIS. Sixty NMPs were significantly differentially expressed between the DCIS and non-diseased breast epithelium in an isogenic contralateral pair of patient-derived extended explants. Ten of the sixty showed significant mRNA expression level differences that matched the protein expression. These 10 proteins were similarly expressed in non-diseased breast reduction cells. Three NMPs (RPL7A, RPL11, RPL31) were significantly upregulated in DCIS and all other BC stages compared to the matching contralateral breast culture and an unrelated non-diseased breast reduction culture. RNA sequencing analyses showed that these three genes were upregulated increasingly with BC progression. Finally, we identified three NMPs (AHNAK, CDC37 and DNAJB1) that were significantly downregulated in DCIS and all other BC stages compared to the isogenically matched contralateral culture and the non-diseased breast reduction culture using both proteomics and RNA sequencing techniques.
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Horie M, Takagane K, Itoh G, Kuriyama S, Yanagihara K, Yashiro M, Umakoshi M, Goto A, Arita J, Tanaka M. Exosomes secreted by ST3GAL5 high cancer cells promote peritoneal dissemination by establishing a premetastatic microenvironment. Mol Oncol 2024; 18:21-43. [PMID: 37716915 PMCID: PMC10766203 DOI: 10.1002/1878-0261.13524] [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: 03/26/2023] [Revised: 08/29/2023] [Accepted: 09/15/2023] [Indexed: 09/18/2023] Open
Abstract
Peritoneal dissemination of cancer affects patient survival. The behavior of peritoneal mesothelial cells (PMCs) and immune cells influences the establishment of a microenvironment that promotes cancer cell metastasis in the peritoneum. Here, we investigated the roles of lactosylceramide alpha-2,3-sialyltransferase (ST3G5; also known as ST3GAL5 and GM3 synthase) in the exosome-mediated premetastatic niche in peritoneal milky spots (MSs). Exosomes secreted from ST3G5high cancer cells (ST3G5high -cExos) were found to contain high levels of hypoxia-inducible factor 1-alpha (HIF1α) and accumulated in MSs via uptake in macrophages (MΦs) owing to increased expression of sialic acid-binding Ig-like lectin 1 (CD169; also known as SIGLEC1). ST3G5high -cExos induced pro-inflammatory cytokines and glucose metabolic changes in MΦs, and the interaction of these MΦs with PMCs promoted mesothelial-mesenchymal transition (MMT) in PMCs, thereby generating αSMA+ myofibroblasts. ST3G5high -cExos also increased the expression of immune checkpoint molecules and T-cell exhaustion in MSs, which accelerated metastasis to the omentum. These events were prevented following ST3G5 depletion in cancer cells. Mechanistically, ST3G5high -cExos upregulated chemokines, including CC-chemokine ligand 5 (CCL5), in recipient MΦs and dendritic cells (DCs), which induced MMT and immunosuppression via activation of signal transducer and activator of transcription 3 (STAT3). Maraviroc, a C-C chemokine receptor type 5 (CCR5) antagonist, prevented ST3G5high -cExo-mediated MMT, T-cell suppression, and metastasis in MSs. Our results suggest ST3G5 as a suitable therapeutic target for preventing cExo-mediated peritoneal dissemination.
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Affiliation(s)
- Misato Horie
- Department of Molecular Medicine and BiochemistryAkita University Graduate School of MedicineJapan
- Department of Gastroenterological SurgeryAkita University Graduate School of MedicineJapan
| | - Kurara Takagane
- Department of Molecular Medicine and BiochemistryAkita University Graduate School of MedicineJapan
| | - Go Itoh
- Department of Molecular Medicine and BiochemistryAkita University Graduate School of MedicineJapan
| | - Sei Kuriyama
- Department of Molecular Medicine and BiochemistryAkita University Graduate School of MedicineJapan
| | - Kazuyoshi Yanagihara
- Division of Rare Cancer ResearchNational Cancer Center Research InstituteTokyoJapan
| | - Masakazu Yashiro
- Department of Molecular Oncology and TherapeuticsOsaka Metropolitan University Graduate School of MedicineJapan
| | - Michinobu Umakoshi
- Department of Cellular and Organ PathologyAkita University Graduate School of MedicineJapan
| | - Akiteru Goto
- Department of Cellular and Organ PathologyAkita University Graduate School of MedicineJapan
| | - Junichi Arita
- Department of Gastroenterological SurgeryAkita University Graduate School of MedicineJapan
| | - Masamitsu Tanaka
- Department of Molecular Medicine and BiochemistryAkita University Graduate School of MedicineJapan
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5
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Friedlová N, Zavadil Kokáš F, Hupp TR, Vojtěšek B, Nekulová M. IFITM protein regulation and functions: Far beyond the fight against viruses. Front Immunol 2022; 13:1042368. [PMID: 36466909 PMCID: PMC9716219 DOI: 10.3389/fimmu.2022.1042368] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/27/2022] [Indexed: 07/30/2023] Open
Abstract
Interferons (IFNs) are important cytokines that regulate immune responses through the activation of hundreds of genes, including interferon-induced transmembrane proteins (IFITMs). This evolutionarily conserved protein family includes five functionally active homologs in humans. Despite the high sequence homology, IFITMs vary in expression, subcellular localization and function. The initially described adhesive and antiproliferative or pro-oncogenic functions of IFITM proteins were diluted by the discovery of their antiviral properties. The large set of viruses that is inhibited by these proteins is constantly expanding, as are the possible mechanisms of action. In addition to their beneficial antiviral effects, IFITM proteins are often upregulated in a broad spectrum of cancers. IFITM proteins have been linked to most hallmarks of cancer, including tumor cell proliferation, therapeutic resistance, angiogenesis, invasion, and metastasis. Recent studies have described the involvement of IFITM proteins in antitumor immunity. This review summarizes various levels of IFITM protein regulation and the physiological and pathological functions of these proteins, with an emphasis on tumorigenesis and antitumor immunity.
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Affiliation(s)
- Nela Friedlová
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Filip Zavadil Kokáš
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czechia
| | - Ted R. Hupp
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czechia
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Bořivoj Vojtěšek
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czechia
| | - Marta Nekulová
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czechia
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Bang J, Kang D, Jung J, Yoo TJ, Shim MS, Gladyshev VN, Tsuji PA, Hatfield DL, Kim JH, Lee BJ. SEPHS1: Its evolution, function and roles in development and diseases. Arch Biochem Biophys 2022; 730:109426. [PMID: 36202216 PMCID: PMC9648052 DOI: 10.1016/j.abb.2022.109426] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 11/25/2022]
Abstract
Selenophosphate synthetase (SEPHS) was originally discovered in prokaryotes as an enzyme that catalyzes selenophosphate synthesis using inorganic selenium and ATP as substrates. However, in contrast to prokaryotes, two paralogs, SEPHS1 and SEPHS2, occur in many eukaryotes. Prokaryotic SEPHS, also known as SelD, contains either cysteine (Cys) or selenocysteine (Sec) in the catalytic domain. In eukaryotes, only SEPHS2 carries out selenophosphate synthesis and contains Sec at the active site. However, SEPHS1 contains amino acids other than Sec or Cys at the catalytic position. Phylogenetic analysis of SEPHSs reveals that the ancestral SEPHS contains both selenophosphate synthesis and another unknown activity, and that SEPHS1 lost the selenophosphate synthesis activity. The three-dimensional structure of SEPHS1 suggests that its homodimer is unable to form selenophosphate, but retains ATPase activity to produce ADP and inorganic phosphate. The most prominent function of SEPHS1 is that it is implicated in the regulation of cellular redox homeostasis. Deficiency of SEPHS1 leads to the disturbance in the expression of genes involved in redox homeostasis. Different types of reactive oxygen species (ROS) are accumulated in response to SEPHS deficiency depending on cell or tissue types. The accumulation of ROS causes pleiotropic effects such as growth retardation, apoptosis, DNA damage, and embryonic lethality. SEPHS1 deficiency in mouse embryos affects retinoic signaling and other related signaling pathways depending on the embryonal stage until the embryo dies at E11.5. Dysregulated SEPHS1 is associated with the pathogenesis of various diseases including cancer, Crohn's disease, and osteoarthritis.
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Affiliation(s)
- Jeyoung Bang
- Interdisciplinary Program in Bioinformatics, College of Natural Sciences, Seoul National University, Seoul, South Korea
| | - Donghyun Kang
- School of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul, South Korea
| | - Jisu Jung
- School of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul, South Korea
| | - Tack-Jin Yoo
- School of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul, South Korea
| | - Myoung Sup Shim
- Department of Ophthalmology, Duke Eye Center, Duke University, Durham, NC, USA
| | - Vadim N Gladyshev
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Petra A Tsuji
- Department of Biological Sciences, Towson University, 8000 York Rd., Towson, MD, USA
| | - Dolph L Hatfield
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jin-Hong Kim
- School of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul, South Korea.
| | - Byeong Jae Lee
- Interdisciplinary Program in Bioinformatics, College of Natural Sciences, Seoul National University, Seoul, South Korea; School of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul, South Korea.
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Cui HY, Wei W, Qian MR, Tian RF, Fu X, Li HW, Nan G, Yang T, Lin P, Chen X, Zhu YM, Wang B, Sun XX, Dou JH, Jiang JL, Li L, Wang SJ, Chen ZN. PDGFA-associated protein 1 is a novel target of c-Myc and contributes to colorectal cancer initiation and progression. Cancer Commun (Lond) 2022; 42:750-767. [PMID: 35716012 PMCID: PMC9395323 DOI: 10.1002/cac2.12322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/26/2022] [Accepted: 06/06/2022] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The mechanism underlying colorectal cancer (CRC) initiation and progression remains elusive, and overall survival is far from satisfactory. Previous studies have shown that PDGFA-associated protein 1 (PDAP1) is upregulated in several cancers including CRC. Here, we aimed to identify the cause and consequence of PDAP1 dysregulation in CRC and evaluate its role as a potential therapeutic target. METHODS Multi-omics data analysis was performed to identify potential key players in CRC initiation and progression. Immunohistochemistry (IHC) staining was applied to determine the expression pattern of PDAP1 in CRC tissues. Pdap1 conditional knockout mice were used to establish colitis and CRC mouse models. RNA sequencing, a phosphoprotein antibody array, western blotting, histological analysis, 5-bromo-2'-deoxyuridine (BrdU) incorporation assay, and interactome analysis were applied to identify the underlying mechanisms of PDAP1. A human patient-derived xenograft (PDX) model was used to assess the potential of PDAP1 as a therapeutic target. RESULTS PDAP1 was identified as a potential key player in CRC development using multi-omics data analysis. PDAP1 was overexpressed in CRC cells and correlated with reduced overall survival. Further investigation showed that PDAP1 was critical for the regulation of cell proliferation, migration, invasion, and metastasis. Significantly, depletion of Pdap1 in intestinal epithelial cells impaired mucosal restitution in dextran sulfate sodium salt-induced colitis and inhibited tumor initiation and growth in colitis-associated cancers. Mechanistic studies showed that c-Myc directly transactivated PDAP1, which contributed to the high PDAP1 expression in CRC cells. PDAP1 interacted with the juxtamembrane domain of epidermal growth factor receptor (EGFR) and facilitated EGFR-mitogen-activated protein kinase (MAPK) signaling activation, which resulted in FOS-related antigen 1 (FRA-1) expression, thereby facilitating CRC progression. Notably, silencing of PDAP1 could hinder the growth of patient-derived xenografts that sustain high PDAP1 levels. CONCLUSIONS PDAP1 facilitates mucosal restitution and carcinogenesis in colitis-associated cancer. c-Myc-driven upregulation of PDAP1 promotes proliferation, migration, invasion, and metastasis of CRC cells via the EGFR-MAPK-FRA-1 signaling axis. These findings indicated that PDAP1 inhibition is warranted for CRC patients with PDAP1 overexpression.
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Affiliation(s)
- Hong-Yong Cui
- National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, P. R. China
| | - Wei Wei
- National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, P. R. China
| | - Mei-Rui Qian
- National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, P. R. China
| | - Ruo-Fei Tian
- National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, P. R. China
| | - Xin Fu
- National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, P. R. China
| | - Hong-Wei Li
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi, 710032, P. R. China
| | - Gang Nan
- National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, P. R. China
| | - Ting Yang
- National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, P. R. China.,Department of Clinical Medicine, Medical College of Yan'an University, Yan'an, Shaanxi, 716000, P. R. China
| | - Peng Lin
- National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, P. R. China
| | - Xi Chen
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, Shaanxi, 710127, P. R. China
| | - Yu-Meng Zhu
- National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, P. R. China
| | - Bin Wang
- National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, P. R. China
| | - Xiu-Xuan Sun
- National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, P. R. China
| | - Jian-Hua Dou
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi, 710032, P. R. China
| | - Jian-Li Jiang
- National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, P. R. China
| | - Ling Li
- National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, P. R. China
| | - Shi-Jie Wang
- National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, P. R. China
| | - Zhi-Nan Chen
- National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, P. R. China
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Chirichella M, Bianchi N, Džafo E, Foli E, Gualdrini F, Kenyon A, Natoli G, Monticelli S. RFX transcription factors control a miR-150/PDAP1 axis that restrains the proliferation of human T cells. PLoS Biol 2022; 20:e3001538. [PMID: 35143476 PMCID: PMC8865640 DOI: 10.1371/journal.pbio.3001538] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 02/23/2022] [Accepted: 01/13/2022] [Indexed: 01/11/2023] Open
Abstract
Within the immune system, microRNAs (miRNAs) exert key regulatory functions. However, what are the mRNA targets regulated by miRNAs and how miRNAs are transcriptionally regulated themselves remain for the most part unknown. We found that in primary human memory T helper lymphocytes, miR-150 was the most abundantly expressed miRNA, and its expression decreased drastically upon activation, suggesting regulatory roles. Constitutive MIR150 gene expression required the RFX family of transcription factors, and its activation-induced down-regulation was linked to their reduced expression. By performing miRNA pull-down and sequencing experiments, we identified PDGFA-associated protein 1 (PDAP1) as one main target of miR-150 in human T lymphocytes. PDAP1 acted as an RNA-binding protein (RBP), and its CRISPR/Cas-9–mediated deletion revealed that it prominently contributed to the regulation of T-cell proliferation. Overall, using an integrated approach involving quantitative analysis, unbiased genomics, and genome editing, we identified RFX factors, miR-150, and the PDAP1 RBP as the components of a regulatory axis that restrains proliferation of primary human T lymphocytes. MicroRNAs exert key regulatory functions in the immune system, but their targets are largely unknown. This study shows that the ability of primary human T lymphocytes to proliferate in response to T cell receptor activation is modulated by a network comprising miR-150, transcription factors of the RFX family, and the RNA-binding protein PDAP1.
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Affiliation(s)
- Michele Chirichella
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Niccolò Bianchi
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Emina Džafo
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Elena Foli
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Francesco Gualdrini
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Milan, Italy
- Humanitas University, Milan, Italy
| | - Amy Kenyon
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Milan, Italy
| | - Gioacchino Natoli
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Milan, Italy
- Humanitas University, Milan, Italy
| | - Silvia Monticelli
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
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9
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Bonilla B, Brown AJ, Hengel SR, Rapchak KS, Mitchell D, Pressimone CA, Fagunloye AA, Luong TT, Russell RA, Vyas RK, Mertz TM, Zaher HS, Mosammaparast N, Malc EP, Mieczkowski PA, Roberts SA, Bernstein KA. The Shu complex prevents mutagenesis and cytotoxicity of single-strand specific alkylation lesions. eLife 2021; 10:68080. [PMID: 34723799 PMCID: PMC8610418 DOI: 10.7554/elife.68080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 10/29/2021] [Indexed: 12/31/2022] Open
Abstract
Three-methyl cytosine (3meC) are toxic DNA lesions, blocking base pairing. Bacteria and humans express members of the AlkB enzymes family, which directly remove 3meC. However, other organisms, including budding yeast, lack this class of enzymes. It remains an unanswered evolutionary question as to how yeast repairs 3meC, particularly in single-stranded DNA. The yeast Shu complex, a conserved homologous recombination factor, aids in preventing replication-associated mutagenesis from DNA base damaging agents such as methyl methanesulfonate (MMS). We found that MMS-treated Shu complex-deficient cells exhibit a genome-wide increase in A:T and G:C substitutions mutations. The G:C substitutions displayed transcriptional and replicational asymmetries consistent with mutations resulting from 3meC. Ectopic expression of a human AlkB homolog in Shu-deficient yeast rescues MMS-induced growth defects and increased mutagenesis. Thus, our work identifies a novel homologous recombination-based mechanism mediated by the Shu complex for coping with alkylation adducts.
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Affiliation(s)
- Braulio Bonilla
- Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, United States
| | - Alexander J Brown
- Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, United States
| | - Sarah R Hengel
- Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, United States
| | - Kyle S Rapchak
- Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, United States
| | - Debra Mitchell
- Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, United States
| | - Catherine A Pressimone
- Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, United States
| | - Adeola A Fagunloye
- Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, United States
| | - Thong T Luong
- Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, United States
| | - Reagan A Russell
- University of Pittsburgh School of Medicine, Pittsburgh, United States
| | - Rudri K Vyas
- Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, United States
| | - Tony M Mertz
- Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, United States
| | - Hani S Zaher
- Biology, Washington University in St Louis, St. Louis, United States
| | | | - Ewa P Malc
- Genetics, University of North Carolina Chapel Hill, Chapel Hill, United States
| | - Piotr A Mieczkowski
- Genetics, University of North Carolina Chapel Hill, Chapel Hill, United States
| | - Steven A Roberts
- Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, United States
| | - Kara A Bernstein
- Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, United States
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10
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Yang F, Cai S, Ling L, Zhang H, Tao L, Wang Q. Identification of a Five-Gene Prognostic Model and Its Potential Drug Repurposing in Colorectal Cancer Based on TCGA, GTEx and GEO Databases. Front Genet 2021; 11:622659. [PMID: 33537062 PMCID: PMC7848190 DOI: 10.3389/fgene.2020.622659] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/18/2020] [Indexed: 12/18/2022] Open
Abstract
Colorectal cancer (CRC) is a major cause of cancer deaths worldwide. Unfortunately, many CRC patients are still being diagnosed at an advanced stage of the cancer, and the 5-year survival rate is only ~30%. Effective prognostic markers of CRC are therefore urgently needed. To address this issue, we performed a detailed bioinformatics analysis based on the Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), and Gene Expression Omnibus (GEO) databases to identify prognostic biomarkers for CRC, which in turn help in exploring potential drug-repurposing. We identified five hub genes (PGM2, PODXL, RHNO1, SCD, and SEPHS1), which had good performance in survival prediction and might be involved in CRC through three key pathways (“Cell cycle,” “Purine metabolism,” and “Spliceosome” KEGG pathways) identified by a KEGG pathway enrichment analysis. What is more, we performed a co-expression analysis between five hub genes and transcription factors to explore the upstream regulatory region. Furthermore, we screened the potential drug-repurposing for the five hub genes in CRC according to the Binding DB and ZINC15 databases. Taking together, we constructed a five-gene signature to predict overall survival of CRC and found the potential drug-repurposing, which may improve the outcome of CRC in the future.
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Affiliation(s)
- Feng Yang
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Shaoyi Cai
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Li Ling
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Haiji Zhang
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Liang Tao
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Qin Wang
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
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11
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Xu B, Liu D, Wang Z, Tian R, Zuo Y. Multi-substrate selectivity based on key loops and non-homologous domains: new insight into ALKBH family. Cell Mol Life Sci 2021; 78:129-141. [PMID: 32642789 PMCID: PMC11072825 DOI: 10.1007/s00018-020-03594-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/24/2020] [Accepted: 07/03/2020] [Indexed: 12/16/2022]
Abstract
AlkB homologs (ALKBH) are a family of specific demethylases that depend on Fe2+ and α-ketoglutarate to catalyze demethylation on different substrates, including ssDNA, dsDNA, mRNA, tRNA, and proteins. Previous studies have made great progress in determining the sequence, structure, and molecular mechanism of the ALKBH family. Here, we first review the multi-substrate selectivity of the ALKBH demethylase family from the perspective of sequence and structural evolution. The construction of the phylogenetic tree and the comparison of key loops and non-homologous domains indicate that the paralogs with close evolutionary relationship have similar domain compositions. The structures show that the lack and variations of four key loops change the shape of clefts to cause the differences in substrate affinity, and non-homologous domains may be related to the compatibility of multiple substrates. We anticipate that the new insights into selectivity determinants of the ALKBH family are useful for understanding the demethylation mechanisms.
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Affiliation(s)
- Baofang Xu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Dongyang Liu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zerong Wang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Ruixia Tian
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yongchun Zuo
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
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12
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Genomic profile and immune contexture in colorectal cancer-relevance for prognosis and immunotherapy. Clin Exp Med 2020; 21:195-204. [PMID: 32720224 DOI: 10.1007/s10238-020-00649-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 07/17/2020] [Indexed: 12/12/2022]
Abstract
Colorectal cancer (CRC) is one of the leading cancers in both genders. TNM staging system is still the most commonly used tumor classification and prognostic system. The disadvantage of TNM is that the prognostic information it provides is incomplete, and patients with the same histological tumor stages may differ significantly in the clinical outcome. Therefore, the identification of new prognostic parameters is crucial. The carcinogenic process that gives rise to an individual tumor is unique and tumor microenviroment should be taken into consideration. In CRC, T-cell infiltration is not homogenous, and recent studies are mostly focusing on memory T-cells and CD8 cells in predicting disease-free survival (DFS) and overall survival (OS). It seems that DFS and OS are not only dependent on microsatellite instable or stable status but mostly on the levels of expression of the immune signatures. Also, patients with high infiltration of cytotoxic and memory cells have significantly better outcome. This review consolidates current knowledge and recent research about importance of immune-cell-associated proteins, specific gene profiles of immune cells and immunotherapy in CRC. We also discussed cell-specific signatures in cancer treatment.
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13
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Yan K, Yang Y, Zhang Y, Zhao W, Liao L. Normalization Method Utilizing Endogenous Proteins for Quantitative Proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1380-1388. [PMID: 32268065 DOI: 10.1021/jasms.0c00012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We developed a normalization method utilizing the expression levels of a panel of endogenous proteins as normalization standards (EPNS herein). We tested the validity of the method using two sets of tandem mass tag (TMT)-labeled data and found that this normalization method effectively reduced global intensity bias at the protein level. The coefficient of variation (CV) of the overall median was reduced by 55% and 82% on average, compared to the reduction by 72% and 86% after normalization using the upper quartile. Furthermore, we used differential protein expression analysis and statistical learning to identify biomarkers for colorectal cancer from a CPTAC data set. The expression changes of a panel of proteins, including NUP205, GTPBP4, CNN2, GNL3, and S100A11, all of which highly correlate with colorectal cancer. Applying these five proteins as model features, random forest modeling obtained prediction results with the maximum AUC of 0.9998 using EPNS-normalized data, comparing favorably to the AUC of 0.9739 using the raw data. Thus, the normalization method based on EPNS reduced the global intensity bias and is applicable for quantitative proteomic analysis.
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Affiliation(s)
- Kai Yan
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yueying Yang
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yunpeng Zhang
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Wanbing Zhao
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Lujian Liao
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China
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14
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Michel M, Homan EJ, Wiita E, Pedersen K, Almlöf I, Gustavsson AL, Lundbäck T, Helleday T, Warpman Berglund U. In silico Druggability Assessment of the NUDIX Hydrolase Protein Family as a Workflow for Target Prioritization. Front Chem 2020; 8:443. [PMID: 32548091 PMCID: PMC7274155 DOI: 10.3389/fchem.2020.00443] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 04/28/2020] [Indexed: 01/13/2023] Open
Abstract
Computational chemistry has now been widely accepted as a useful tool for shortening lead times in early drug discovery. When selecting new potential drug targets, it is important to assess the likelihood of finding suitable starting points for lead generation before pursuing costly high-throughput screening campaigns. By exploiting available high-resolution crystal structures, an in silico druggability assessment can facilitate the decision of whether, and in cases where several protein family members exist, which of these to pursue experimentally. Many of the algorithms and software suites commonly applied for in silico druggability assessment are complex, technically challenging and not always user-friendly. Here we applied the intuitive open access servers of DoGSite, FTMap and CryptoSite to comprehensively predict ligand binding pockets, druggability scores and conformationally active regions of the NUDIX protein family. In parallel we analyzed potential ligand binding sites, their druggability and pocket parameter using Schrödinger's SiteMap. Then an in silico docking cascade of a subset of the ZINC FragNow library using the Glide docking program was performed to assess identified pockets for large-scale small-molecule binding. Subsequently, this initial dual ranking of druggable sites within the NUDIX protein family was benchmarked against experimental hit rates obtained both in-house and by others from traditional biochemical and fragment screening campaigns. The observed correlation suggests that the presented user-friendly workflow of a dual parallel in silico druggability assessment is applicable as a standalone method for decision on target prioritization and exclusion in future screening campaigns.
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Affiliation(s)
- Maurice Michel
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Evert J Homan
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Elisée Wiita
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Kia Pedersen
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Ingrid Almlöf
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Anna-Lena Gustavsson
- Chemical Biology Consortium Sweden (CBCS), Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Thomas Lundbäck
- Chemical Biology Consortium Sweden (CBCS), Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.,Department of Oncology and Metabolism, Sheffield Cancer Centre, University of Sheffield, Sheffield, United Kingdom
| | - Ulrika Warpman Berglund
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
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15
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Marcinkowski M, Pilžys T, Garbicz D, Steciuk J, Zugaj D, Mielecki D, Sarnowski TJ, Grzesiuk E. Human and Arabidopsis alpha-ketoglutarate-dependent dioxygenase homolog proteins-New players in important regulatory processes. IUBMB Life 2020; 72:1126-1144. [PMID: 32207231 DOI: 10.1002/iub.2276] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 02/20/2020] [Accepted: 03/08/2020] [Indexed: 12/31/2022]
Abstract
The family of AlkB homolog (ALKBH) proteins, the homologs of Escherichia coli AlkB 2-oxoglutarate (2OG), and Fe(II)-dependent dioxygenase are involved in a number of important regulatory processes in eukaryotic cells including repair of alkylation lesions in DNA, RNA, and nucleoprotein complexes. There are nine human and thirteen Arabidopsis thaliana ALKBH proteins described, which exhibit diversified functions. Among them, human ALKBH5 and FaT mass and Obesity-associated (FTO) protein and Arabidopsis ALKBH9B and ALKBH10B have been recognized as N6 methyladenine (N6 meA) demethylases, the most abundant posttranscriptional modification in mRNA. The FTO protein is reported to be associated with obesity and type 2 diabetes, and involved in multiple other processes, while ALKBH5 is induced by hypoxia. Arabidopsis ALKBH9B is an N6 meA demethylase influencing plant susceptibility to viral infections via m6 A/A ratio control in viral RNA. ALKBH10B has been discovered to be a functional Arabidopsis homolog of FTO; thus, it is also an RNA N6 meA demethylase involved in plant flowering and several other regulatory processes including control of metabolism. High-throughput mass spectrometry showed multiple sites of human ALKBH phosphorylation. In the case of FTO, the type of modified residue decides about the further processing of the protein. This modification may result in subsequent protein ubiquitination and proteolysis, or in the blocking of these processes. However, the impact of phosphorylation on the other ALKBH function and their downstream pathways remains nearly unexplored in both human and Arabidopsis. Therefore, the investigation of evolutionarily conserved functions of ALKBH proteins and their regulatory impact on important cellular processes is clearly called for.
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Affiliation(s)
- Michał Marcinkowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Tomaš Pilžys
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Damian Garbicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jaroslaw Steciuk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Dorota Zugaj
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Damian Mielecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Tomasz J Sarnowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Elżbieta Grzesiuk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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16
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Dietary phytochemicals as the potential protectors against carcinogenesis and their role in cancer chemoprevention. Clin Exp Med 2020; 20:173-190. [PMID: 32016615 DOI: 10.1007/s10238-020-00611-w] [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: 11/22/2019] [Accepted: 01/27/2020] [Indexed: 02/06/2023]
Abstract
Health-threatening consequences of carcinogen exposure are mediated via occurrence of electrophiles or reactive oxygen species. As a result, the accumulation of biomolecular damage leads to the cancer initiation, promotion or progression. Accordingly, there is an association between lifestyle factors including inappropriate diet or carcinogen formation during food processing, mainstream, second or third-hand tobacco smoke and other environmental or occupational carcinogens and malignant transformation. Nevertheless, increasing evidence supports the protective effects of naturally occurring phytochemicals against carcinogen exposure as well as carcinogenesis in general. Isolated phytochemicals or their mixtures present in the whole plant food demonstrate efficacy against malignancy induced by carcinogens widely spread in our environment. Phytochemicals also minimize the generation of carcinogenic substances during the processing of meat and meat products. Based on numerous data, selected phytochemicals or plant foods should be highly recommended to become a stable and regular part of the diet as the protectors against carcinogenesis.
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17
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Koliadenko V, Wilanowski T. Additional functions of selected proteins involved in DNA repair. Free Radic Biol Med 2020; 146:1-15. [PMID: 31639437 DOI: 10.1016/j.freeradbiomed.2019.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/16/2019] [Accepted: 10/16/2019] [Indexed: 12/30/2022]
Abstract
Protein moonlighting is a phenomenon in which a single polypeptide chain can perform a number of different unrelated functions. Here we present our analysis of moonlighting in the case of selected DNA repair proteins which include G:T mismatch-specific thymine DNA glycosylase (TDG), methyl-CpG-binding domain protein 4 (MBD4), apurinic/apyrimidinic endonuclease 1 (APE1), AlkB homologs, poly (ADP-ribose) polymerase 1 (PARP-1) and single-strand selective monofunctional uracil DNA glycosylase 1 (SMUG1). Most of their additional functions are not accidental and clear patterns are emerging. Participation in RNA metabolism is not surprising as bases occurring in RNA are the same or very similar to those in DNA. Other common additional function involves regulation of transcription. This is not unexpected as these proteins bind to specific DNA regions for DNA repair, hence they can also be recruited to regulate transcription. Participation in demethylation and replication of DNA appears logical as well. Some of the multifunctional DNA repair proteins play major roles in many diseases, including cancer. However, their moonlighting might prove a major difficulty in the development of new therapies because it will not be trivial to target a single protein function without affecting its other functions that are not related to the disease.
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Affiliation(s)
- Vlada Koliadenko
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096, Warsaw, Poland
| | - Tomasz Wilanowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096, Warsaw, Poland.
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18
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Mohan M, Akula D, Dhillon A, Goyal A, Anindya R. Human RAD51 paralogue RAD51C fosters repair of alkylated DNA by interacting with the ALKBH3 demethylase. Nucleic Acids Res 2019; 47:11729-11745. [PMID: 31642493 PMCID: PMC7145530 DOI: 10.1093/nar/gkz938] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/02/2019] [Accepted: 10/09/2019] [Indexed: 12/31/2022] Open
Abstract
The integrity of our DNA is challenged daily by a variety of chemicals that cause DNA base alkylation. DNA alkylation repair is an essential cellular defence mechanism to prevent the cytotoxicity or mutagenesis from DNA alkylating chemicals. Human oxidative demethylase ALKBH3 is a central component of alkylation repair, especially from single-stranded DNA. However, the molecular mechanism of ALKBH3-mediated damage recognition and repair is less understood. We report that ALKBH3 has a direct protein-protein interaction with human RAD51 paralogue RAD51C. We also provide evidence that RAD51C-ALKBH3 interaction stimulates ALKBH3-mediated repair of methyl-adduct located within 3'-tailed DNA, which serves as a substrate for the RAD51 recombinase. We further show that the lack of RAD51C-ALKBH3 interaction affects ALKBH3 function in vitro and in vivo. Our data provide a molecular mechanism underlying upstream events of alkyl adduct recognition and repair by ALKBH3.
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Affiliation(s)
- Monisha Mohan
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy 502285, India
| | - Deepa Akula
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy 502285, India
| | - Arun Dhillon
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Roy Anindya
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy 502285, India
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19
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Shi M, Wang ZS, Huang LY, Dong JJ, Zheng XQ, Lu JL, Liang YR, Ye JH. Utilization of albumin fraction from defatted rice bran to stabilize and deliver (-)-epigallocatechin gallate. Food Chem 2019; 311:125894. [PMID: 31787396 DOI: 10.1016/j.foodchem.2019.125894] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 11/09/2019] [Accepted: 11/11/2019] [Indexed: 01/09/2023]
Abstract
This work aims to use defatted rice bran albumin (RBA) for delivering epigallocatechin gallate (EGCg). The mode of RBA particle size shifted from 142 nm to 164 nm upon interaction with EGCg. Hydrophobic interaction is the major force between EGCg and RBA resulted in the formation of EGCg-RBA complex based on fluorescence quenching. Upon incorporation into RBA, the recovery of EGCg in pH 7.4 phosphate buffer was elevated by 2 folds. The recovery of EGCg in EGCg-RBA was 18.9% after 2 h intestinal digestion, being higher than 7.6% of native EGCg. The pretreatments of HT-29 cells with EGCg, RBA and EGCg-RBA significantly repressed the transcriptional activation of mitogen-activated protein kinase 14, nuclear transcription factor-κB, and activators of transcription 3 as stimulated with interleukin-1β afterwards, leading to attenuated expressions of corresponding downstream genes. Antioxidant ability importantly functioned in anti-inflammation. RBA is a promising vehicle with inherent anti-inflammatory property for stabilizing and delivering EGCg.
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Affiliation(s)
- Meng Shi
- Tea Research Institute, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310013, China
| | - Ze-Shi Wang
- Tea Research Institute, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310013, China
| | - Long-Yue Huang
- Tea Research Institute, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310013, China
| | - Jun-Jie Dong
- Zhejiang Camel Transworld (Organic Food) Co., Ltd., 16 Chachang Road, Yuhang District, Hangzhou 310000, China
| | - Xin-Qiang Zheng
- Tea Research Institute, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310013, China
| | - Jian-Liang Lu
- Tea Research Institute, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310013, China
| | - Yue-Rong Liang
- Tea Research Institute, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310013, China.
| | - Jian-Hui Ye
- Tea Research Institute, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310013, China.
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20
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Pilžys T, Marcinkowski M, Kukwa W, Garbicz D, Dylewska M, Ferenc K, Mieczkowski A, Kukwa A, Migacz E, Wołosz D, Mielecki D, Klungland A, Piwowarski J, Poznański J, Grzesiuk E. ALKBH overexpression in head and neck cancer: potential target for novel anticancer therapy. Sci Rep 2019; 9:13249. [PMID: 31519943 PMCID: PMC6744417 DOI: 10.1038/s41598-019-49550-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 08/27/2019] [Indexed: 01/12/2023] Open
Abstract
The nine identified human homologues of E. coli AlkB 2-oxoglutarate (2OG) and Fe(II)-dependent dioxygenase, ALKBH1-8 and FTO, display different substrate specificities and diverse biological functions. Here we discovered the combined overexpression of members of the ALKBH family in head and neck squamous cell carcinomas (HNSCC). We found direct correlation of ALKBH3 and FTO expression with primary HNSCC tumor size. We observed unidentified thus far cytoplasmic localization of ALKBH2 and 5 in HNSCC, suggesting abnormal role(s) of ALKBH proteins in cancer. Further, high expression of ALKBHs was observed not only in HNSCC, but also in several cancerous cell lines and silencing ALKBH expression in HeLa cancer cells resulted in dramatically decreased survival. Considering the discovered impact of high expression of ALKBH proteins on HNSCC development, we screened for ALKBH blockers among newly synthetized anthraquinone derivatives and demonstrated their potential to support standard anticancer therapy.
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Affiliation(s)
- Tomaš Pilžys
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Michał Marcinkowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Wojciech Kukwa
- Department of Otolaryngology, Medical University of Warsaw, Warsaw, Poland
| | - Damian Garbicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Małgorzata Dylewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Karolina Ferenc
- Veterinary Research Centre and Center for Biomedical Research, Department of Large Animal Diseases with the Clinic, Faculty of Veterinary Medicine, Warsaw University of Life Sciences, Warsaw, Poland
| | - Adam Mieczkowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Andrzej Kukwa
- Department of Otolaryngology, Medical University of Warsaw, Warsaw, Poland
| | - Ewa Migacz
- Department of Otolaryngology, Medical University of Warsaw, Warsaw, Poland
| | - Dominika Wołosz
- Department of Pathology, Medical University of Warsaw, Warsaw, Poland
| | - Damian Mielecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Jan Piwowarski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
| | - Elżbieta Grzesiuk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
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Zhao H, He Y, Li H, Zhu A, Ye Y, Liu G, Zhao C, Zhang X. The opposite role of alternatively spliced isoforms of LINC00477 in gastric cancer. Cancer Manag Res 2019; 11:4569-4576. [PMID: 31191018 PMCID: PMC6529032 DOI: 10.2147/cmar.s202430] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 04/09/2019] [Indexed: 12/11/2022] Open
Abstract
Background: Aberrant transcript alternative splicing is an important regulatory process closely connected with oncogenesis. Purpose: The objective of this study was to determine the phenotype and function of a novel long noncoding RNA (lncRNA) LINC00477 in gastric cancer. Patients and methods: The gastric cancer samples of 140 from Oncomine database and 17 from our own hospital, as well as three gastric cancer cell lines MKN-45, AGS and KATO III were used in this study. The expression of the spliced isoforms of LINC00477 were tested. The tumor effects of LINC00477 on gastric cancer were investigated in vitro and in vivo. The mechanism of LINC00477 interacted with aconitase 1 (ACO1) was further examined by RIP and pull down assay. Results: The overall expression of LINC00477 was reduced in gastric cancers compared to normal gastric tissues. The isoform 1 of LINC00477 was down-regulated while the isoform 2 was up-regulated in gastric cancer cells. The opposite role of isoforms 1 and 2 in the proliferation and migration of cancer cells in vitro and in vivo was observed. Furthermore, isoform 1 of LINC00477 was determined to interact with ACO1 and suppress the conversion ability from citrate to isocitrate by ACO1. Conclusion: we presented the important roles of the spliced isoforms of long noncoding RNA, LINC00477 in gastric carcinogenesis.
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Affiliation(s)
- Hongchao Zhao
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Yuanhang He
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Haohao Li
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Ali Zhu
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Yanwei Ye
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Guanghui Liu
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Chunlin Zhao
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Xiefu Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
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22
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Jiang Z, You Q, Zhang X. Medicinal chemistry of metal chelating fragments in metalloenzyme active sites: A perspective. Eur J Med Chem 2019; 165:172-197. [PMID: 30684796 DOI: 10.1016/j.ejmech.2019.01.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 12/22/2018] [Accepted: 01/08/2019] [Indexed: 12/25/2022]
Abstract
Numerous metal-containing enzymes (metalloenzymes) have been considered as drug targets related to diseases such as cancers, diabetes, anemia, AIDS, malaria, bacterial infection, fibrosis, and neurodegenerative diseases. Inhibitors of the metalloenzymes have been developed independently, most of which are mimics of substrates of the corresponding enzymes. However, little attention has been paid to the interactions between inhibitors and active site metal ions. This review is focused on different metal binding fragments and their chelating properties in the metal-containing active binding pockets of metalloenzymes. We have enumerated over one hundred of inhibitors targeting various metalloenzymes and identified over ten kinds of fragments with different binding patterns. Furthermore, we have investigated the inhibitors that are undergoing clinical evaluation in order to help looking for more potential scaffolds bearing metal binding fragments. This review will provide deep insights for the rational design of novel inhibitors targeting the metal-containing binding sites of specific proteins.
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Affiliation(s)
- Zhensheng Jiang
- Sate Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qidong You
- Sate Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Xiaojin Zhang
- Sate Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Chemistry, School of Science, China Pharmaceutical University, Nanjing, 211198, China.
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23
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Alteber Z, Sharbi-Yunger A, Pevsner-Fischer M, Blat D, Roitman L, Tzehoval E, Elinav E, Eisenbach L. The anti-inflammatory IFITM genes ameliorate colitis and partially protect from tumorigenesis by changing immunity and microbiota. Immunol Cell Biol 2018; 96:284-297. [PMID: 29356071 DOI: 10.1111/imcb.12000] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 12/04/2017] [Accepted: 12/06/2017] [Indexed: 12/19/2022]
Abstract
Inflammation plays pivotal roles in different stages of tumor development. Screening for predisposing genetic abnormalities and understanding the roles these genes play in the crosstalk between immune and cancer cells will provide new targets for cancer therapy and prevention. The interferon inducible transmembrane (IFITM) genes are involved in pathogenesis of the gastro-intestinal tract. We aimed at delineating the role of IFITM3 in colonic epithelial homeostasis, inflammation and colitis-associated tumorigenesis using IFITM3-deficient mice. Chemical induction of colitis in IFITM3-deficient mice results in significantly increased clinical signs of inflammation and induction of invasive tumorigenesis. Bone marrow transplantation showed that cells of the hematopoietic system are responsible for colitis deterioration. In these mice, impaired cytokine expression skewed inflammatory response toward pathogenic Th17 with reduced expression of the anti-inflammatory cytokine IL10 during the recovery phase. Intriguingly, mice lacking the entire IFITM locus developed spontaneous chronic colitis from the age of 14 weeks. Sequencing the 16S rRNA of naïve mice lacking IFITM3 gene, or the entire locus containing five IFITM genes, revealed these mice had significant bacterial differences from their wild-type littermates. Our novel results provide strong evidence for the essential role of IFITM genes in ameliorating colitis and colitis-associated tumorigenesis.
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Affiliation(s)
- Zoya Alteber
- Department of Immunology, The Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Adi Sharbi-Yunger
- Department of Immunology, The Weizmann Institute of Science, Rehovot, 76100, Israel
| | | | - Dan Blat
- Department of Immunology, The Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Lior Roitman
- Department of Immunology, The Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Esther Tzehoval
- Department of Immunology, The Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Eran Elinav
- Department of Immunology, The Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Lea Eisenbach
- Department of Immunology, The Weizmann Institute of Science, Rehovot, 76100, Israel
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24
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Kang X, Wang F, Lan X, Li X, Zheng S, Lv Z, Zhuang Y, Zhao Y, Zhou S. Lentivirus-mediated shRNA Targeting CNN2 Inhibits Hepatocarcinoma in Vitro and in Vivo. Int J Med Sci 2018; 15:69-76. [PMID: 29333089 PMCID: PMC5765741 DOI: 10.7150/ijms.21113] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Accepted: 09/11/2017] [Indexed: 01/12/2023] Open
Abstract
Objective: Hepatocellular carcinoma (HCC) is one of the most common malignant tumors with a high rate of mortality. Our previous study shows the expression of calponin 2 (CNN2) is up-regulated in hepatocellular carcinoma tissues, especially in metastatic ones. To better understand the role of CNN2 in HCC, RNA interference (RNAi) was used to explore its role in tumor growth and metastasis. Methods: Lentivirus-mediated CNN2-shRNA was transfected into SK-hep-1 cells, and the efficacy of CNN2 expression, cell migration, invasion, proliferation and cell cycles were evaluated by quantitative real-time polymerase chain reaction (qRT-PCR), Western blot (WB), Transwell assay, methyl thiazol tetrazolium assay and flow cytometry, respectively. SK-hep-1 cells transfected with Lentivirus-CNN2 shRNA were xenografted in Balb/C nude mice to explore the effect of CNN2-shRNA in tumor growth. Xenograft tumor tissues were examined for their histopathology, cell apoptosis, the expression of total protein and their corresponding phosphorylated protein of MEK1/2, ERK1/2, AKT, by hematoxylin and eosin stain (H & E staining), TUNEL assay, immunohistochemical technique, respectively. Results: Our research shows it is evident that CNN2 shRNA can effectively down-regulate the expressions of CNN2 mRNA and protein, inhibit cell proliferations, arrest cell cycles at the S phase and reduce cell migration and invasion. SK-hep-1 cells with CNN2 down-regulation have markedly attenuated tumor growth in nude mice. Xenograft tumor tissues have displayed typical tumor characteristics and no apoptosis is detected in shRNA group or in control group. No metastatic tumor was found in any group of nude mice. With CNN2 protein down-regulation, the protein of pMEK1/2 and pERK1/2 are effectively down-regulated, except pAKT, AKT, MEK1/2 and ERK1/2. Conclusions: CNN2 plays an important role in tumor growth and metastasis, possibly through MEK1/2-ERK1/2 signaling pathway. Our study illustrate that CNN2 might be a potential target in HCC molecular target therapy.
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Affiliation(s)
- Xueqing Kang
- Department of Biochemistry and Molecular Biology, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, the Guangxi Zhuang Autonomous Region, China
| | - Feng Wang
- Department of Biochemistry and Molecular Biology, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, the Guangxi Zhuang Autonomous Region, China
| | - Xiuwan Lan
- Department of Biochemistry and Molecular Biology, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, the Guangxi Zhuang Autonomous Region, China
| | - Xiaolong Li
- Department of Biochemistry and Molecular Biology, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, the Guangxi Zhuang Autonomous Region, China
| | - Shunxin Zheng
- Department of Biochemistry and Molecular Biology, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, the Guangxi Zhuang Autonomous Region, China
| | - Zhilue Lv
- Department of Biochemistry and Molecular Biology, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, the Guangxi Zhuang Autonomous Region, China
| | - Yuan Zhuang
- Department of Biochemistry and Molecular Biology, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, the Guangxi Zhuang Autonomous Region, China
| | - Yongxiang Zhao
- Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, the Guangxi Zhuang Autonomous Region, China
| | - Sufang Zhou
- Department of Biochemistry and Molecular Biology, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, the Guangxi Zhuang Autonomous Region, China
- Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, the Guangxi Zhuang Autonomous Region, China
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25
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Abstract
Tumor-associated gangliosides play important roles in regulation of signal transduction induced by growth-factor receptors including EGFR, FGFR, HGF and PDGFR in a specific microdomain called glycosynapse in the cancer cell membranes, and in interaction with glycan recognition molecules involved in cell adhesion and immune regulation including selectins and siglecs. As the genes involved in the synthesis and degradation of tumor-associated gangliosides were identified, biological functions became clearer from the experimental results employing forced overexpression and/or knockdown/knockout of the genes. Studies on the regulatory mechanisms for their expression also achieved great advancements. Epigenetic silencing of glycan-related genes is a dominant mechanism in glycan alteration at early stages of carcinogenesis. Development of hypoxia resistance involving activation of a transcription factor HIF, and acquisition of cancer stem cell-like characteristics through epithelial-mesenchymal transition are important mechanisms for glycan modulations in the later stages of cancer progression. In the initial stages of studies, the gangliosides which specifically appear in cancers attracted attention under the name of tumor-associated gangliosides. However, it became apparent that not only the cancer-associated gangliosides but also the normal gangliosides present in nonmalignant cells and tissues perform important biological functions, and some of them tend to disappear in cancer cells resulting in the loss of the physiological functions, and this sometimes facilitates progression of cancers.
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26
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Carreras-Puigvert J, Zitnik M, Jemth AS, Carter M, Unterlass JE, Hallström B, Loseva O, Karem Z, Calderón-Montaño JM, Lindskog C, Edqvist PH, Matuszewski DJ, Ait Blal H, Berntsson RPA, Häggblad M, Martens U, Studham M, Lundgren B, Wählby C, Sonnhammer ELL, Lundberg E, Stenmark P, Zupan B, Helleday T. A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family. Nat Commun 2017; 8:1541. [PMID: 29142246 PMCID: PMC5688067 DOI: 10.1038/s41467-017-01642-w] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 10/06/2017] [Indexed: 01/04/2023] Open
Abstract
The NUDIX enzymes are involved in cellular metabolism and homeostasis, as well as mRNA processing. Although highly conserved throughout all organisms, their biological roles and biochemical redundancies remain largely unclear. To address this, we globally resolve their individual properties and inter-relationships. We purify 18 of the human NUDIX proteins and screen 52 substrates, providing a substrate redundancy map. Using crystal structures, we generate sequence alignment analyses revealing four major structural classes. To a certain extent, their substrate preference redundancies correlate with structural classes, thus linking structure and activity relationships. To elucidate interdependence among the NUDIX hydrolases, we pairwise deplete them generating an epistatic interaction map, evaluate cell cycle perturbations upon knockdown in normal and cancer cells, and analyse their protein and mRNA expression in normal and cancer tissues. Using a novel FUSION algorithm, we integrate all data creating a comprehensive NUDIX enzyme profile map, which will prove fundamental to understanding their biological functionality.
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Affiliation(s)
- Jordi Carreras-Puigvert
- Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Molecular Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 171 65, Sweden.
| | - Marinka Zitnik
- Faculty of Computer and Information Science, University of Ljubljana, SI-1000, Ljubljana, Slovenia
- Department of Computer Science, Stanford University, Palo Alto, CA, 94305, USA
| | - Ann-Sofie Jemth
- Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Molecular Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 171 65, Sweden
| | - Megan Carter
- Department of Biochemistry and Biophysics, Stockholm University, 106 91, Stockholm, Sweden
| | - Judith E Unterlass
- Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Molecular Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 171 65, Sweden
| | - Björn Hallström
- Cell Profiling-Affinity Proteomics, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, 17165, Sweden
| | - Olga Loseva
- Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Molecular Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 171 65, Sweden
| | - Zhir Karem
- Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Molecular Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 171 65, Sweden
| | - José Manuel Calderón-Montaño
- Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Molecular Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 171 65, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, 751 85, Uppsala, Sweden
| | - Per-Henrik Edqvist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, 751 85, Uppsala, Sweden
| | - Damian J Matuszewski
- Centre for Image Analysis and Science for Life Laboratory, Uppsala University, Uppsala, 751 05, Sweden
| | - Hammou Ait Blal
- Cell Profiling-Affinity Proteomics, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, 17165, Sweden
| | - Ronnie P A Berntsson
- Department of Biochemistry and Biophysics, Stockholm University, 106 91, Stockholm, Sweden
| | - Maria Häggblad
- Biochemical and Cellular Screening Facility, Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, 171 65, Sweden
| | - Ulf Martens
- Biochemical and Cellular Screening Facility, Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, 171 65, Sweden
| | - Matthew Studham
- Stockholm Bioinformatics Center, Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, 171 21, Solna, Sweden
| | - Bo Lundgren
- Biochemical and Cellular Screening Facility, Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, 171 65, Sweden
| | - Carolina Wählby
- Centre for Image Analysis and Science for Life Laboratory, Uppsala University, Uppsala, 751 05, Sweden
| | - Erik L L Sonnhammer
- Stockholm Bioinformatics Center, Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, 171 21, Solna, Sweden
| | - Emma Lundberg
- Cell Profiling-Affinity Proteomics, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, 17165, Sweden
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, 106 91, Stockholm, Sweden
| | - Blaz Zupan
- Faculty of Computer and Information Science, University of Ljubljana, SI-1000, Ljubljana, Slovenia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Thomas Helleday
- Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Molecular Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 171 65, Sweden.
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van der Wekken AJ, Kuiper JL, Saber A, Terpstra MM, Wei J, Hiltermann TJN, Thunnissen E, Heideman DAM, Timens W, Schuuring E, Kok K, Smit EF, van den Berg A, Groen HJM. Overall survival in EGFR mutated non-small-cell lung cancer patients treated with afatinib after EGFR TKI and resistant mechanisms upon disease progression. PLoS One 2017; 12:e0182885. [PMID: 28854272 PMCID: PMC5576694 DOI: 10.1371/journal.pone.0182885] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 07/26/2017] [Indexed: 11/24/2022] Open
Abstract
PURPOSE To determine survival in afatinib-treated patients after treatment with first-generation EGFR tyrosine kinase inhibitors (TKIs) and to study resistance mechanisms in afatinib-resistant tumors. METHODS Characteristics and survival of patients treated with afatinib after resistance to erlotinib or gefitinib in two large Dutch centers were collected. Whole exome sequencing (WES) and pathway analysis was performed on available pre- and post-afatinib tumor biopsies and normal tissue. RESULTS A total of 38 patients were treated with afatinib. T790M mutations were identified in 22/29 (76%) pre-afatinib treatment tumor samples. No difference in median progression-free-survival (2.8 months (95% CI 2.3-3.3) and 2.7 months (95% CI 0.9-4.6), p = 0.55) and median overall-survival (8.8 months (95% CI 4.2-13.4) and 3.6 months (95% CI 2.3-5.0), p = 0.14) were observed in T790M+ patients compared to T790M- mutations. Somatic mutations in TP53, ADAMTS2, CNN2 and multiple genes in the Wnt and PI3K-AKT pathway were observed in post-afatinib tumors of six afatinib-responding and in one non-responding patient. No new EGFR mutations were found in the post-afatinib samples of the six responding patients. Further analyses of post-afatinib progressive tumors revealed 28 resistant specific mutations in six genes (HLA-DRB1, AQP7, FAM198A, SEC31A, CNTLN, and ESX1) in three afatinib responding patients. No known EGFR-TKI resistant-associated copy number gains were acquired in the post-afatinib samples. CONCLUSION No differences in survival were observed in patients with EGFR-T790M treated with afatinib compared to those without T790M. Tumors from patients who had progressive disease during afatinib treatment were enriched for mutations in genes involved in Wnt and PI3K-AKT pathways.
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Affiliation(s)
- A. J. van der Wekken
- Department of Pulmonary Diseases, University of Groningen, University Medical Centre Groningen, Groningen, Netherlands
| | - J. L. Kuiper
- Department of Pulmonary Diseases, VU University Medical Centre, Amsterdam, Netherlands
| | - A. Saber
- Department of Pathology and Medical Biology, Groningen, University of Groningen, Groningen, Netherlands
| | - M. M. Terpstra
- University of Groningen, Department of Genetics, Groningen, Netherlands
| | - J. Wei
- University of Groningen, Department of Genetics, Groningen, Netherlands
| | - T. J. N. Hiltermann
- Department of Pulmonary Diseases, University of Groningen, University Medical Centre Groningen, Groningen, Netherlands
| | - E. Thunnissen
- Department of Pathology, VU University Medical Centre, Amsterdam, Netherlands
| | - D. A. M. Heideman
- Department of Pathology, VU University Medical Centre, Amsterdam, Netherlands
| | - W. Timens
- Department of Pathology and Medical Biology, Groningen, University of Groningen, Groningen, Netherlands
| | - E. Schuuring
- Department of Pathology and Medical Biology, Groningen, University of Groningen, Groningen, Netherlands
| | - K. Kok
- University of Groningen, Department of Genetics, Groningen, Netherlands
| | - E. F. Smit
- Department of Pulmonary Diseases, VU University Medical Centre, Amsterdam, Netherlands
- Department of Thoracic Oncology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - A. van den Berg
- Department of Pathology and Medical Biology, Groningen, University of Groningen, Groningen, Netherlands
| | - H. J. M. Groen
- Department of Pulmonary Diseases, University of Groningen, University Medical Centre Groningen, Groningen, Netherlands
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28
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Stefansson OA, Hermanowicz S, van der Horst J, Hilmarsdottir H, Staszczak Z, Jonasson JG, Tryggvadottir L, Gudjonsson T, Sigurdsson S. CpG promoter methylation of the ALKBH3 alkylation repair gene in breast cancer. BMC Cancer 2017; 17:469. [PMID: 28679371 PMCID: PMC5498885 DOI: 10.1186/s12885-017-3453-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 06/26/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND DNA repair of alkylation damage is defective in various cancers. This occurs through somatically acquired inactivation of the MGMT gene in various cancer types, including breast cancers. In addition to MGMT, the two E. coli AlkB homologs ALKBH2 and ALKBH3 have also been linked to direct reversal of alkylation damage. However, it is currently unknown whether ALKBH2 or ALKBH3 are found inactivated in cancer. METHODS Methylome datasets (GSE52865, GSE20713, GSE69914), available through Omnibus, were used to determine whether ALKBH2 or ALKBH3 are found inactivated by CpG promoter methylation. TCGA dataset enabled us to then assess the impact of CpG promoter methylation on mRNA expression for both ALKBH2 and ALKBH3. DNA methylation analysis for the ALKBH3 promoter region was carried out by pyrosequencing (PyroMark Q24) in 265 primary breast tumours and 30 proximal normal breast tissue samples along with 8 breast-derived cell lines. ALKBH3 mRNA and protein expression were analysed in cell lines using RT-PCR and Western blotting, respectively. DNA alkylation damage assay was carried out in cell lines based on immunofluorescence and confocal imaging. Data on clinical parameters and survival outcomes in patients were obtained and assessed in relation to ALKBH3 promoter methylation. RESULTS The ALKBH3 gene, but not ALKBH2, undergoes CpG promoter methylation and transcriptional silencing in breast cancer. We developed a quantitative alkylation DNA damage assay based on immunofluorescence and confocal imaging revealing higher levels of alkylation damage in association with epigenetic inactivation of the ALKBH3 gene (P = 0.029). In our cohort of 265 primary breast cancer, we found 72 cases showing aberrantly high CpG promoter methylation over the ALKBH3 promoter (27%; 72 out of 265). We further show that increasingly higher degree of ALKBH3 promoter methylation is associated with reduced breast-cancer specific survival times in patients. In this analysis, ALKBH3 promoter methylation at >20% CpG methylation was found to be statistically significantly associated with reduced survival (HR = 2.3; P = 0.012). By thresholding at the clinically relevant CpG methylation level (>20%), we find the incidence of ALKBH3 promoter methylation to be 5% (13 out of 265). CONCLUSIONS ALKBH3 is a novel addition to the catalogue of DNA repair genes found inactivated in breast cancer. Our results underscore a link between defective alkylation repair and breast cancer which, additionally, is found in association with poor disease outcome.
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Affiliation(s)
- Olafur Andri Stefansson
- Cancer Research Laboratory, Biomedical Center, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
| | - Stefan Hermanowicz
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
- Department of Biochemistry and Molecular Biology, Biomedical Center, Vatnsmyrarvegur 16 (5th floor), 101 Reykjavik, Iceland
| | - Jasper van der Horst
- Cancer Research Laboratory, Biomedical Center, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
| | - Holmfridur Hilmarsdottir
- Cancer Research Laboratory, Biomedical Center, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
| | - Zuzanna Staszczak
- Cancer Research Laboratory, Biomedical Center, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
| | - Jon Gunnlaugur Jonasson
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
- Icelandic Cancer Registry, Skogarhlid 8, Reykjavik, Iceland
- Department of Pathology, Landspitali University Hospital, Reykjavik, Iceland
| | - Laufey Tryggvadottir
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
- Icelandic Cancer Registry, Skogarhlid 8, Reykjavik, Iceland
| | - Thorkell Gudjonsson
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
- Department of Biochemistry and Molecular Biology, Biomedical Center, Vatnsmyrarvegur 16 (5th floor), 101 Reykjavik, Iceland
| | - Stefan Sigurdsson
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16 (4th floor), 101 Reykjavik, Iceland
- Department of Biochemistry and Molecular Biology, Biomedical Center, Vatnsmyrarvegur 16 (5th floor), 101 Reykjavik, Iceland
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Hu J, Xie W, Shang L, Yang X, Li Q, Xu M, Dou J, Zhou Y, Niu W, Wu Y. Knockdown of calponin 2 suppressed cell growth in gastric cancer cells. Tumour Biol 2017; 39:1010428317706455. [PMID: 28714360 DOI: 10.1177/1010428317706455] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Calponin family members are actin filament-associated regulatory proteins with distinct expression patterns. Previous studies on CNN2 (calponin 2) have demonstrated that CNN2 is expressed in a broad range of tissues and cell types, exhibiting potential regulatory roles in a number of cellular activities, including cell proliferation, cell migration, and platelet adhesion. In this work, we found that both messenger RNA and protein expression levels of CNN2 were remarkably upregulated in 60%-70% of gastric cancer tissues by comparison with those of neighboring non-tumorous mucosa. By utilizing specific shCNN2 (small hairpin RNA targeting CNN2), the potential role of CNN2 in regulating AGS gastric cancer cell growth was then further investigated. AGS cells infected with shCNN2 exhibited significantly decreased cell growth ability by comparison with control cells in vitro. Moreover, while there was no obvious difference in cell cycle distribution between two groups, enhanced cell apoptosis was detected in cells with reduced CNN2 expression. Consistently, caspase 3/7 activity was also remarkably activated upon shCNN2 lentivirus infection. Taken together, our results demonstrated that knockdown of endogenous CNN2 in AGS cells could significantly activate cell apoptosis pathway and therefore suppress cell growth in vitro. The deletion of CNN2 might be a potential therapeutic approach to inhibit aggressive growth of gastric cancer.
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Affiliation(s)
- Jianwei Hu
- 1 Endoscopy Center and Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, P.R. China
| | - Wenjuan Xie
- 2 State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, P.R. China
| | - Lingyue Shang
- 2 State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, P.R. China
| | - Xi Yang
- 2 State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, P.R. China
| | - Quanlin Li
- 1 Endoscopy Center and Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, P.R. China
| | - Meidong Xu
- 1 Endoscopy Center and Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, P.R. China
| | - Jianming Dou
- 2 State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, P.R. China
| | - Yiren Zhou
- 2 State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, P.R. China
| | - Weixin Niu
- 1 Endoscopy Center and Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, P.R. China
| | - Yanhua Wu
- 2 State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, P.R. China
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Walker AR, Silvestrov P, Müller TA, Podolsky RH, Dyson G, Hausinger RP, Cisneros GA. ALKBH7 Variant Related to Prostate Cancer Exhibits Altered Substrate Binding. PLoS Comput Biol 2017; 13:e1005345. [PMID: 28231280 PMCID: PMC5322872 DOI: 10.1371/journal.pcbi.1005345] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 01/04/2017] [Indexed: 11/18/2022] Open
Abstract
The search for prostate cancer biomarkers has received increased attention and several DNA repair related enzymes have been linked to this dysfunction. Here we report a targeted search for single nucleotide polymorphisms (SNPs) and functional impact characterization of human ALKBH family dioxygenases related to prostate cancer. Our results uncovered a SNP of ALKBH7, rs7540, which is associated with prostate cancer disease in a statistically significantly manner in two separate cohorts, and maintained in African American men. Comparisons of molecular dynamics (MD) simulations on the wild-type and variant protein structures indicate that the resulting alteration in the enzyme induces a significant structural change that reduces ALKBH7’s ability to bind its cosubstrate. Experimental spectroscopy studies with purified proteins validate our MD predictions and corroborate the conclusion that this cancer-associated mutation affects productive cosubstrate binding in ALKBH7. Improvements in personalized DNA sequencing have led to an increased interest in targeted biomarkers for therapeutic and diagnostic purposes. In this work, we report on a new biomarker for prostate cancer found through a targeted search for single nucleotide polymorphisms (SNPs) of the genes encoding human ALKBH family dioxygenases. Our results uncovered rs7540, which leads to a missense mutation in ALKBH7. Comparative molecular dynamics simulations on the wild type and SNP variant of the protein show that the mutation elicits a structural change that dramatically decreases ALKBH7’s affinity for its cosubstrate. This prediction is confirmed by experimental UV-Vis spectroscopy. Taken together, these results give important insights into a novel prostate-cancer related SNP and its impact on the structure and function of ALKBH7.
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Affiliation(s)
- Alice R. Walker
- Department of Chemistry, Wayne State University, Detroit, MI, United States of America
| | - Pavel Silvestrov
- Department of Chemistry, Wayne State University, Detroit, MI, United States of America
| | - Tina A. Müller
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States of America
| | - Robert H. Podolsky
- Wayne State University Department of Family Medicine and Public Health Sciences, Wayne State University, Detroit, MI, United States of America
| | - Gregory Dyson
- Karmanos Cancer Institute, Wayne State University, Detroit, MI, United States of America
| | - Robert P. Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States of America
| | - Gerardo Andrés Cisneros
- Department of Chemistry, Wayne State University, Detroit, MI, United States of America
- * E-mail:
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Selenophosphate synthetase 1 is an essential protein with roles in regulation of redox homoeostasis in mammals. Biochem J 2016; 473:2141-54. [PMID: 27208177 DOI: 10.1042/bcj20160393] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 05/16/2016] [Indexed: 12/23/2022]
Abstract
Selenophosphate synthetase (SPS) was initially detected in bacteria and was shown to synthesize selenophosphate, the active selenium donor. However, mammals have two SPS paralogues, which are designated SPS1 and SPS2. Although it is known that SPS2 catalyses the synthesis of selenophosphate, the function of SPS1 remains largely unclear. To examine the role of SPS1 in mammals, we generated a Sps1-knockout mouse and found that systemic SPS1 deficiency led to embryos that were clearly underdeveloped by embryonic day (E)8.5 and virtually resorbed by E14.5. The knockout of Sps1 in the liver preserved viability, but significantly affected the expression of a large number of mRNAs involved in cancer, embryonic development and the glutathione system. Particularly notable was the extreme deficiency of glutaredoxin 1 (GLRX1) and glutathione transferase Omega 1 (GSTO1). To assess these phenotypes at the cellular level, we targeted the removal of SPS1 in F9 cells, a mouse embryonal carcinoma (EC) cell line, which affected the glutathione system proteins and accordingly led to the accumulation of hydrogen peroxide in the cell. Furthermore, we found that several malignant characteristics of SPS1-deficient F9 cells were reversed, suggesting that SPS1 played a role in supporting and/or sustaining cancer. In addition, the overexpression of mouse or human GLRX1 led to a reversal of observed increases in reactive oxygen species (ROS) in the F9 SPS1/GLRX1-deficient cells and resulted in levels that were similar to those in F9 SPS1-sufficient cells. The results suggested that SPS1 is an essential mammalian enzyme with roles in regulating redox homoeostasis and controlling cell growth.
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32
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iTRAQ-based quantitative proteomic analysis of esophageal squamous cell carcinoma. Tumour Biol 2015; 37:1909-18. [DOI: 10.1007/s13277-015-3840-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 07/24/2015] [Indexed: 01/09/2023] Open
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Ji T, Ma F, Huo L, Guo X, Chen B, Zhou Q. Calponin-h2 is upregulated in the tissues and plasma of patients with breast cancer. Mol Med Rep 2015; 12:2886-92. [PMID: 25976781 DOI: 10.3892/mmr.2015.3782] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 04/04/2015] [Indexed: 11/06/2022] Open
Abstract
Increasing evidence has demonstrated that changes in plasma nuclear matrix proteins are specific markers of cancer. Furthermore, proteomic analysis has revealed that calponin-h2 is upregulated in human breast cancer tissue, but is absent in healthy and benign controls. However, the roles of levels of plasma calponin-h2 in the diagnosis of breast cancer and its association with clinicopathological parameters remain to be elucidated. In the present study, the plasma levels of calponin-h2 in patients with breast cancer, benign breast disease and in healthy controls were examined using an enzyme-linked immunosorbent assay. The expression levels of calponin-h2 in invasive breast cancer and normal breast tissues were measured using immunohistochemistry. Statistical analyses examined the association between the levels of plasma calponin-h2 and clinicopathological parameters. The results demonstrated that the plasma level of calponin-h2 in breast cancer was significantly higher than those in the healthy control and benign breast disease groups (P<0.05). The combination of calponin-h2, carcinoembryonic antigen, carbohydrate antigen 15-3 improved the diagnosis of breast cancer. The plasma levels of calponin-h2 PR-breast cancers was significantly higher, compared with PR+ breast cancers (P=0.033), and the plasma levels of calponin-h2 in patients with breast cancer aged >50 years was significantly higher than in patients ≤ 50 years of age (P=0.001). No association was found between the level of plasma calponin-h2 and other clinicopathological parameters of breast cancer. Taken together, these results indicated that calponin-h2 may be a useful marker of breast cancer.
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Affiliation(s)
- Tianxing Ji
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510260, P.R. China
| | - Feifei Ma
- Department of VIP Obstetrics, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510260, P.R. China
| | - Leijun Huo
- Department of Pathology, Guangdong Women and Children Hospital, Guangzhou, Guangdong 511442, P.R. China
| | - Xuguang Guo
- Department of Clinical Laboratory, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510140, P.R. China
| | - Bo Chen
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510260, P.R. China
| | - Qiang Zhou
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510260, P.R. China
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Ougland R, Rognes T, Klungland A, Larsen E. Non-homologous functions of the AlkB homologs. J Mol Cell Biol 2015; 7:494-504. [PMID: 26003568 DOI: 10.1093/jmcb/mjv029] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 02/26/2015] [Indexed: 12/22/2022] Open
Abstract
The DNA repair enzyme AlkB was identified in E. coli more than three decades ago. Since then, nine mammalian homologs, all members of the superfamily of alpha-ketoglutarate and Fe(II)-dependent dioxygenases, have been identified (designated ALKBH1-8 and FTO). While E. coli AlkB serves as a DNA repair enzyme, only two mammalian homologs have been confirmed to repair DNA in vivo. The other mammalian homologs have remarkably diverse substrate specificities and biological functions. Substrates recognized by the different AlkB homologs comprise erroneous methyl- and etheno adducts in DNA, unique wobble uridine modifications in certain tRNAs, methylated adenines in mRNA, and methylated lysines on proteins. The phenotypes of organisms lacking or overexpressing individual AlkB homologs include obesity, severe sensitivity to inflammation, infertility, growth retardation, and multiple malformations. Here we review the present knowledge of the mammalian AlkB homologs and their implications for human disease and development.
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Affiliation(s)
- Rune Ougland
- Clinic for Diagnostics and Intervention and Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, 0027 Oslo, Norway Department of Anesthesiology, Division of Emergencies and Critical Care, Oslo University Hospital, The Norwegian Radium Hospital, 0310 Oslo, Norway
| | - Torbjørn Rognes
- Clinic for Diagnostics and Intervention and Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, 0027 Oslo, Norway Department of Informatics, University of Oslo, 0316 Oslo, Norway
| | - Arne Klungland
- Clinic for Diagnostics and Intervention and Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, 0027 Oslo, Norway Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, Norway
| | - Elisabeth Larsen
- Clinic for Diagnostics and Intervention and Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, 0027 Oslo, Norway
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Müller TA, Hausinger RP. AlkB and Its Homologues – DNA Repair and Beyond. 2-OXOGLUTARATE-DEPENDENT OXYGENASES 2015. [DOI: 10.1039/9781782621959-00246] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
AlkB is an Fe(ii)/2-oxoglutarate-dependent dioxygenase that is part of the adaptive response to alkylating agents in Escherichia coli. AlkB hydroxylates a wide variety of alkylated DNA bases producing unstable intermediates which decompose to restore the non-alkylated bases. Homologues exist in other bacteria, metazoa (e.g. nine in humans), plants and viruses, but not in archaea, with many catalysing the same oxidative demethylation reactions as for AlkB. The mammalian enzymes Alkbh2 and Alkbh3 catalyse direct DNA repair, Alkbh5 and FTO (Alkbh9) are RNA demethylases, and Alkbh8 is used to synthesize a tRNA, while the remaining mammalian homologues have alternative functions. Alkbh1 is an apurinic/apyrimidinic lyase in addition to exhibiting demethylase activities, but no clear role for the Alkbh1 protein has emerged. Alkbh4 is involved in cell division and potentially demethylates actin, whereas the mitochondrial homologue Alkbh7 has a role in obesity; however, no enzymatic activity has been linked to Alkbh4 or Alkbh7. Here, we discuss AlkB as the ‘archetype’ of this class of hydroxylases, compare it to Alkbh2 and Alkbh3, and then briefly review the diverse (and largely unknown) functions of Alkbh1, Alkbh4, Alkbh6 and Alkbh7. Alkbh5, Alkbh8 and Alkbh9 (FTO) are described separately.
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Affiliation(s)
- Tina A. Müller
- Department of Microbiology and Molecular Genetics, Michigan State University East Lansing MI 48824 USA
| | - Robert P. Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University East Lansing MI 48824 USA
- Department of Biochemistry and Molecular Biology, Michigan State University East Lansing MI 48824 USA
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36
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Hung FH, Chiu HW, Chang YC. Revealing pathway maps of renal cell carcinoma by gene expression change. Comput Biol Med 2014; 51:111-21. [DOI: 10.1016/j.compbiomed.2014.04.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 04/24/2014] [Accepted: 04/28/2014] [Indexed: 11/29/2022]
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Affiliation(s)
- Guanqun Zheng
- Department of Chemistry and
Institute for Biophysical Dynamics, The
University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United
States
| | - Ye Fu
- Department of Chemistry and
Institute for Biophysical Dynamics, The
University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United
States
| | - Chuan He
- Department of Chemistry and
Institute for Biophysical Dynamics, The
University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United
States
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38
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Affiliation(s)
- Guanqun Zheng
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago , 929 East 57th Street, Chicago, Illinois 60637, United States
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39
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Ruder EH, Berndt SI, Gilsing AMJ, Graubard BI, Burdett L, Hayes RB, Weissfeld JL, Ferrucci LM, Sinha R, Cross AJ. Dietary iron, iron homeostatic gene polymorphisms and the risk of advanced colorectal adenoma and cancer. Carcinogenesis 2014; 35:1276-83. [PMID: 24536049 DOI: 10.1093/carcin/bgu028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Dietary iron intake and variation in iron homeostasis genes may affect colorectal neoplasia risk. We conducted two nested case-control studies within the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial: one of advanced colorectal adenoma (1205 cases; 1387 controls) and one of colorectal cancer (370 cases; 401 controls). Iron intake was estimated with a food frequency questionnaire and genotyping was performed for 21 genes. Unconditional logistic regression was used to estimate odds ratio (OR) and 95% confidence intervals (95% CIs) for colorectal neoplasia risk within quartiles of intake. Several single nucleotide polymorphisms (SNPs) modified the association between iron intake and the risk of adenoma or cancer. Dietary iron was positively associated with colorectal adenoma among three SNPs of HEPHL1, including carriers of the AA genotype at rs7946162 (ORQ4-Q1 = 2.22, 95% CI 1.15-4.27, Ptrend = 0.03; Pinteraction = 0.10), the TT genotype at rs2460063 (ORQ4-Q1 = 2.39, 95% CI 1.26-4.54, Ptrend = 0.02; Pinteraction = 0.04) and the GG genotype at rs7127348 (ORQ4-Q1 = 2.40, 95% CI 1.23-4.67, Ptrend = 0.02; Pinteraction = 0.09). Heme iron was positively associated with colorectal cancer among those with GG genotypes for ACO1 rs10970985 (ORQ4-Q 1 = 2.45, 95% CI 3.40-8.06, Ptrend = 0.004; Pinteraction = 0.05). However, none of the associations were statistically significant after adjustment for multiple comparisons. Future studies should target the specific genes and SNPs for which the association was significant prior to multiple comparison correction.
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Affiliation(s)
- Elizabeth H Ruder
- School of Health and Rehabilitation Sciences, University of Pittsburgh, 4051 Forbes Tower, Pittsburgh, PA 15260, USA,
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Anne M J Gilsing
- Department of Epidemiology, School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Barry I Graubard
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Laurie Burdett
- Core Genotyping Facility, National Cancer Institute, SAIC-Frederick, Inc., Gaithersburg, MD 20892, USA
| | - Richard B Hayes
- Division of Epidemiology, Department of Environmental Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Joel L Weissfeld
- University of Pittsburgh Medical Center Cancer Pavilion, Pittsburgh, PA 15232, USA and
| | | | - Rashmi Sinha
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Amanda J Cross
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
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Kovářová D, Plachý J, Kosla J, Trejbalová K, Čermák V, Hejnar J. Downregulation of HOPX Controls Metastatic Behavior in Sarcoma Cells and Identifies Genes Associated with Metastasis. Mol Cancer Res 2013; 11:1235-47. [DOI: 10.1158/1541-7786.mcr-12-0687] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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41
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Marimuthu A, Subbannayya Y, Sahasrabuddhe NA, Balakrishnan L, Syed N, Sekhar NR, Katte TV, Pinto SM, Srikanth SM, Kumar P, Pawar H, Kashyap MK, Maharudraiah J, Ashktorab H, Smoot DT, Ramaswamy G, Kumar RV, Cheng Y, Meltzer SJ, Roa JC, Chaerkady R, Prasad TK, Harsha HC, Chatterjee A, Pandey A. SILAC-based quantitative proteomic analysis of gastric cancer secretome. Proteomics Clin Appl 2013; 7:355-66. [PMID: 23161554 PMCID: PMC3804263 DOI: 10.1002/prca.201200069] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 09/24/2012] [Accepted: 10/25/2012] [Indexed: 02/05/2023]
Abstract
PURPOSE Gastric cancer is a commonly occurring cancer in Asia and one of the leading causes of cancer deaths. However, there is no reliable blood-based screening test for this cancer. Identifying proteins secreted from tumor cells could lead to the discovery of clinically useful biomarkers for early detection of gastric cancer. EXPERIMENTAL DESIGN A SILAC-based quantitative proteomic approach was employed to identify secreted proteins that were differentially expressed between neoplastic and non-neoplastic gastric epithelial cells. Proteins from the secretome were subjected to SDS-PAGE and SCX-based fractionation, followed by mass spectrometric analysis on an LTQ-Orbitrap Velos mass spectrometer. Immunohistochemical labeling was employed to validate a subset of candidates using tissue microarrays. RESULTS We identified 2205 proteins in the gastric cancer secretome of which 263 proteins were overexpressed greater than fourfold in gastric cancer-derived cell lines as compared to non-neoplastic gastric epithelial cells. Three candidate proteins, proprotein convertase subtilisin/kexin type 9 (PCSK9), lectin mannose binding 2 (LMAN2), and PDGFA-associated protein 1 (PDAP1) were validated by immunohistochemical labeling. CONCLUSIONS AND CLINICAL RELEVANCE We report here the largest cancer secretome described to date. The novel biomarkers identified in the current study are excellent candidates for further testing as early detection biomarkers for gastric adenocarcinoma.
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Affiliation(s)
- Arivusudar Marimuthu
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Yashwanth Subbannayya
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Rajiv Gandhi University of Health Sciences, Bangalore 560041, India
- Department of Biochemistry, Kidwai Memorial Institute of Oncology, Bangalore, 560066, India
| | - Nandini A. Sahasrabuddhe
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | - Lavanya Balakrishnan
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Department of Biotechnology, Kuvempu University, Shankaraghatta 577 451, India
| | - Nazia Syed
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry-605014, India
| | - Nirujogi Raja Sekhar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Teesta V. Katte
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Sneha M. Pinto
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | - Srinivas M. Srikanth
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Praveen Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Harsh Pawar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Rajiv Gandhi University of Health Sciences, Bangalore 560041, India
| | - Manoj K. Kashyap
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Jagadeesha Maharudraiah
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | - Hassan Ashktorab
- Department of Medicine, Howard University, Washington DC 20060, USA
| | - Duane T Smoot
- Department of Medicine, Meharry Medical College, Nashville 37208, Tennessee, USA
| | - Girija Ramaswamy
- Rajiv Gandhi University of Health Sciences, Bangalore 560041, India
- Department of Biochemistry, Kidwai Memorial Institute of Oncology, Bangalore, 560066, India
| | - Rekha V. Kumar
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, 560066, India
| | - Yulan Cheng
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Stephen J Meltzer
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Juan Carlos Roa
- Department of Pathology, Universidad de La Frontera, Temuco, Chile
| | - Raghothama Chaerkady
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205 Maryland, USA
| | - T.S. Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
- Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - H. C. Harsha
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Akhilesh Pandey
- Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205 Maryland, USA
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205 Maryland, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA
- To whom correspondence should be addressed: Akhilesh Pandey M.D., Ph.D., McKusick-Nathans Institute of Genetic Medicine, 733 N. Broadway, BRB 527, Johns Hopkins University, Baltimore, MD 21205. Tel.: 410-502-6662; Fax: 410-502-7544;
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Johannessen TCA, Prestegarden L, Grudic A, Hegi ME, Tysnes BB, Bjerkvig R. The DNA repair protein ALKBH2 mediates temozolomide resistance in human glioblastoma cells. Neuro Oncol 2012; 15:269-78. [PMID: 23258843 DOI: 10.1093/neuonc/nos301] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
INTRODUCTION Glioblastoma multiforme (GBM; World Health Organization astrocytoma grade IV) is the most frequent and most malignant primary brain tumor in adults. Despite multimodal therapy, all such tumors practically recur during the course of therapy, causing a median survival of only 14.6 months in patients with newly diagnosed GBM. The present study was aimed at examining the expression of the DNA repair protein AlkB homolog 2 (ALKBH2) in human GBM and determining whether it could promote resistance to temozolomide chemotherapy. METHODS ALKBH2 expression in GBM cell lines and in human GBM was determined by quantitative real-time PCR (qRT-PCR) and gene expression analysis, respectively. Drug sensitivity was assessed in GBM cells overexpressing ALKBH2 and in cells in which ALKBH2 expression was silenced by small-interfering (si)RNA. ALKBH2 expression following activation of the p53 pathway was examined by western blotting and qRT-PCR. RESULTS ALKBH2 was abundantly expressed in established GBM cell lines and human GBM, and temozolomide exposure increased cellular ALKBH2 expression levels. Overexpression of ALKBH2 in the U87 and U251 GBM cell lines enhanced resistance to the methylating agents temozolomide and methyl methanesulfonate but not to the nonmethylating agent doxorubicin. Conversely, siRNA-mediated knockdown of ALKBH2 increased sensitivity of GBM cells to temozolomide and methyl methanesulfonate but not to doxorubicin or cisplatin. Nongenotoxic activation of the p53 pathway by the selective murine double minute 2 antagonist nutlin-3 caused a significant decrease in cellular ALKBH2 transcription levels. CONCLUSION Our findings identify ALKBH2 as a novel mediator of temozolomide resistance in human GBM cells. Furthermore, we place ALKBH2 into a new cellular context by showing its regulation by the p53 pathway.
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TAKESHITA NOBUYOSHI, MORI MIKITO, KANO MASAYUKI, HOSHINO ISAMU, AKUTSU YASUNORI, HANARI NAOYUKI, YONEYAMA YASUO, IKEDA NORIMASA, ISOZAKI YUKA, MARUYAMA TETSUROU, AKANUMA NAOKI, MIYAZAWA YUKIMASA, MATSUBARA HISAHIRO. miR-203 inhibits the migration and invasion of esophageal squamous cell carcinoma by regulating LASP1. Int J Oncol 2012; 41:1653-61. [DOI: 10.3892/ijo.2012.1614] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Accepted: 08/06/2012] [Indexed: 11/05/2022] Open
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Yamato I, Sho M, Shimada K, Hotta K, Ueda Y, Yasuda S, Shigi N, Konishi N, Tsujikawa K, Nakajima Y. PCA-1/ALKBH3 contributes to pancreatic cancer by supporting apoptotic resistance and angiogenesis. Cancer Res 2012; 72:4829-39. [PMID: 22826605 DOI: 10.1158/0008-5472.can-12-0328] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The PCA-1/ALKBH3 gene implicated in DNA repair is expressed in several human malignancies but its precise contributions to cancer remain mainly unknown. In this study, we have determined its functions and clinical importance in pancreatic cancer. PCA-1/ALKBH3 functions in proliferation, apoptosis and angiogenesis were evaluated in human pancreatic cancer cells in vitro and in vivo. Further, PCA-1/ALKBH3 expression in 116 patients with pancreatic cancer was evaluated by immunohistochemistry. siRNA-mediated silencing of PCA-1/ALKBH3 expression induced apoptosis and suppressed cell proliferation. Conversely, overexpression of PCA-1/ALKBH3 increased anchorage-independent growth and invasiveness. In addition, PCA-1/ALKBH3 silencing downregulated VEGF expression and inhibited angiogenesis in vivo. Furthermore, immunohistochemical analysis showed that PCA-1/ALKBH3 expression was abundant in pancreatic cancer tissues, where it correlated with advanced tumor status, pathological stage and VEGF intensity. Importantly, patients with low positivity of PCA-1/ALKBH3 expression had improved postoperative prognosis compared with those with high positivity. Our results establish PCA-1/ALKBH3 as important gene in pancreatic cancer with potential utility as a therapeutic target in this fatal disease.
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Affiliation(s)
- Ichiro Yamato
- Department of Surgery, Nara Medical University, Kashihara, Nara, Japan
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Almiñana C, Fazeli A. Exploring the application of high-throughput genomics technologies in the field of maternal-embryo communication. Theriogenology 2012; 77:717-37. [PMID: 22217573 DOI: 10.1016/j.theriogenology.2011.11.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 08/30/2011] [Accepted: 09/02/2011] [Indexed: 01/23/2023]
Abstract
Deciphering the complex molecular dialogue between the maternal tract and embryo is crucial to increasing our understanding of pregnancy failure, infertility problems and in the modulation of embryo development, which has consequences through adulthood. High-throughput genomic technologies have been applied to look for a holistic view of the molecular interactions occurring during this dialogue. Among these technologies, microarrays have been widely used, being one of the most popular tools in maternal-embryo communication. Today, next generation sequencing technologies are dwarfing the capabilities of microarrays. The application of these new technologies has broadened to almost all areas of genomics research, because of their massive sequencing capacity. We review the current status of high-throughput genomic technologies and their application to maternal-embryo communication research. We also survey next generation technologies and their huge potential in many research areas. Given the diversity of unanswered questions in the field of maternal-embryo communication and the wide range of possibilities that these technologies offer, here we discuss future perspectives on the use of these technologies to enhance maternal-embryo research.
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Affiliation(s)
- Carmen Almiñana
- Academic Unit of Reproductive and Development Medicine, University of Sheffield, Sheffield, UK.
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