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Bai F, Liu X, Zhang X, Mao Z, Wen H, Ma J, Pei XH. p18INK4C and BRCA1 inhibit follicular cell proliferation and dedifferentiation in thyroid cancer. Cell Cycle 2023; 22:1637-1653. [PMID: 37345432 PMCID: PMC10361144 DOI: 10.1080/15384101.2023.2225938] [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: 09/09/2022] [Revised: 04/13/2023] [Accepted: 06/09/2023] [Indexed: 06/23/2023] Open
Abstract
Only 3% of thyroid cancers are medullary thyroid carcinomas (MTCs), the rest are follicular epithelial cell derived non-MTCs (NMTCs). A dysfunctional INK4-CDK4-RB pathway is detected in most of NMTCs. DNA repair defects and genome instability are associated with NMTC dedifferentiation and aggressiveness. Whether inactivation of the INK4-CDK4-RB pathway induces NMTCs and how differentiation of NMTC cells is controlled remain elusive. In this study, we generated p18Ink4c and Brca1 singly and doubly deficient mice as well as p16Ink4a and Brca1 singly and doubly deficient mice. By using these mice and human thyroid carcinoma cell lines, we discovered that loss of p18Ink4c, not p16Ink4a, in mice stimulated follicular cell proliferation and induced NMTCs. Depletion of Brca1 alone or both p16Ink4a and Brca1 did not induce thyroid tumor. Depletion of Brca1 in p18Ink4c null mice results in poorly differentiated and aggressive NMTCs with epithelial-mesenchymal transition (EMT) features and enhanced DNA damage. Knockdown of BRCA1 in thyroid carcinoma cells activated EMT and promoted tumorigenesis whereas overexpression of BRCA1 inhibited EMT. BRCA1 and EMT marker expression were inversely related in human thyroid cancers. Our finding, for the first time, demonstrates that inactivation of INK4-CDK4-RB pathway induces NMTCs and that Brca1 deficiency promotes dedifferentiation of NMTC cells. These results suggest that BRCA1 and p18INK4C collaboratively suppress thyroid tumorigenesis and progression and CDK4 inhibitors will be effective for treatment of INK4-inactivated or cyclin D-overexpressed thyroid carcinomas.
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Affiliation(s)
- Feng Bai
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, the First Affiliated Hospital, Shenzhen University Health Science Center, Shenzhen, China
- Department of Pathology, Shenzhen University Health Science Center, Shenzhen, China
- Dewitt Daughtry Family Department of Surgery, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Xiong Liu
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, the First Affiliated Hospital, Shenzhen University Health Science Center, Shenzhen, China
- Department of Anatomy and Histology, Shenzhen University Health Science Center, Shenzhen, China
| | - Xu Zhang
- Department of Pathology, School of Basic Medicine, Lanzhou University, Lanzhou, China
| | - Zhuo Mao
- Department of Physiology, Shenzhen University Health Science Center, Shenzhen, China
| | - He Wen
- Department of Biochemistry and Molecular Biology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, China
| | - Jinshan Ma
- Dewitt Daughtry Family Department of Surgery, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
- Department of Thoracic Surgery, Xinjiang Uigur Autonomous Region People’s Hospital, Xinjiang, China
| | - Xin-Hai Pei
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, the First Affiliated Hospital, Shenzhen University Health Science Center, Shenzhen, China
- Dewitt Daughtry Family Department of Surgery, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
- Department of Anatomy and Histology, Shenzhen University Health Science Center, Shenzhen, China
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2
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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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3
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Lenoir M, Martín R, Torres-Maravilla E, Chadi S, González-Dávila P, Sokol H, Langella P, Chain F, Bermúdez-Humarán LG. Butyrate mediates anti-inflammatory effects of Faecalibacterium prausnitzii in intestinal epithelial cells through Dact3. Gut Microbes 2020; 12:1-16. [PMID: 33054518 PMCID: PMC7567499 DOI: 10.1080/19490976.2020.1826748] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The commensal bacterium Faecalibacterium prausnitzii plays a key role in inflammatory bowel disease (IBD) pathogenesis and serves as a general health biomarker in humans. However, the host molecular mechanisms that underlie its anti-inflammatory effects remain unknown. In this study we performed a transcriptomic approach on human intestinal epithelial cells (HT-29) stimulated with TNF-α and exposed to F. prausnitzii culture supernatant (SN) in order to determine the impact of this commensal bacterium on intestinal epithelial cells. Moreover, modulation of the most upregulated gene after F. prausnitzii SN contact was validated both in vitro and in vivo. Our results showed that F. prausnitzii SN upregulates the expression of Dact3, a gene linked to the Wnt/JNK pathway. Interestingly, when we silenced Dact3 expression, the effect of F. prausnitzii SN was lost. Butyrate was identified as the F. prausnitzii effector responsible for Dact3 modulation. Dact3 upregulation was also validated in vivo in both healthy and inflamed mice treated with either F. prausnitzii SN or the live bacteria, respectively. Finally, we demonstrated by colon transcriptomics that gut microbiota directly influences Dact3 expression. This study provides new clues about the host molecular mechanisms involved in the anti-inflammatory effects of the beneficial commensal bacterium F. prausnitzii.
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Affiliation(s)
- Marion Lenoir
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Rebeca Martín
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | | | - Sead Chadi
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | | | - Harry Sokol
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France,Sorbonne Universités, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology department, F-75012Paris, France
| | - Philippe Langella
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Florian Chain
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Luis G. Bermúdez-Humarán
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France,CONTACT Luis G. Bermúdez-Humarán Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350Jouy-en-Josas, France
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4
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Bonjoch L, Franch-Expósito S, Garre P, Belhadj S, Muñoz J, Arnau-Collell C, Díaz-Gay M, Gratacós-Mulleras A, Raimondi G, Esteban-Jurado C, Soares de Lima Y, Herrera-Pariente C, Cuatrecasas M, Ocaña T, Castells A, Fillat C, Capellá G, Balaguer F, Caldés T, Valle L, Castellví-Bel S. Germline Mutations in FAF1 Are Associated With Hereditary Colorectal Cancer. Gastroenterology 2020; 159:227-240.e7. [PMID: 32179092 DOI: 10.1053/j.gastro.2020.03.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 02/19/2020] [Accepted: 03/08/2020] [Indexed: 01/03/2023]
Abstract
BACKGROUND & AIMS A significant proportion of colorectal cancer (CRC) cases have familial aggregation but little is known about the genetic factors that contribute to these cases. We performed an exhaustive functional characterization of genetic variants associated with familial CRC. METHODS We performed whole-exome sequencing analyses of 75 patients from 40 families with a history of CRC (including early-onset cases) of an unknown germline basis (discovery cohort). We also sequenced specific genes in DNA from an external replication cohort of 473 families, including 488 patients with colorectal tumors that had normal expression of mismatch repair proteins (validation cohort). We disrupted the Fas-associated factor 1 gene (FAF1) in DLD-1 CRC cells using CRISPR/Cas9 gene editing; some cells were transfected with plasmids that express FAF1 missense variants. Cells were analyzed by immunoblots, quantitative real-time polymerase chain reaction, and functional assays monitoring apoptosis, proliferation, and assays for Wnt signaling or nuclear factor (NF)-kappa-B activity. RESULTS We identified predicted pathogenic variant in the FAF1 gene (c.1111G>A; p.Asp371Asn) in the discovery cohort; it was present in 4 patients of the same family. We identified a second variant in FAF1 in the validation cohort (c.254G>C; p.Arg85Pro). Both variants encoded unstable FAF1 proteins. Expression of these variants in CRC cells caused them to become resistant to apoptosis, accumulate beta-catenin in the cytoplasm, and translocate NF-kappa-B to the nucleus. CONCLUSIONS In whole-exome sequencing analyses of patients from families with a history of CRC, we identified variants in FAF1 that associate with development of CRC. These variants encode unstable forms of FAF1 that increase resistance of CRC cells to apoptosis and increase activity of beta-catenin and NF-kappa-B.
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Affiliation(s)
- Laia Bonjoch
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Sebastià Franch-Expósito
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Pilar Garre
- Molecular Oncology Laboratory, Centro Investigación Biomédica en Red de Cáncer (CIBERONC). Hospital Clínico San Carlos. Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Sami Belhadj
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Jenifer Muñoz
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Coral Arnau-Collell
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Marcos Díaz-Gay
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Anna Gratacós-Mulleras
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Giulia Raimondi
- Gene Therapy and Cancer, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Universitat de Barcelona, Barcelona, Spain
| | - Clara Esteban-Jurado
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Yasmin Soares de Lima
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Cristina Herrera-Pariente
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Miriam Cuatrecasas
- Pathology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD) and Tumor Bank-Biobank, Hospital Clínic, Barcelona, Spain
| | - Teresa Ocaña
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Antoni Castells
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Cristina Fillat
- Gene Therapy and Cancer, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Universitat de Barcelona, Barcelona, Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Francesc Balaguer
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Trinidad Caldés
- Molecular Oncology Laboratory, Centro Investigación Biomédica en Red de Cáncer (CIBERONC). Hospital Clínico San Carlos. Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Sergi Castellví-Bel
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.
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5
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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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Guo M, Peng Y, Gao A, Du C, Herman JG. Epigenetic heterogeneity in cancer. Biomark Res 2019; 7:23. [PMID: 31695915 PMCID: PMC6824025 DOI: 10.1186/s40364-019-0174-y] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 10/10/2019] [Indexed: 12/15/2022] Open
Abstract
Phenotypic and functional heterogeneity is one of the hallmarks of human cancers. Tumor genotype variations among tumors within different patients are known as interpatient heterogeneity, and variability among multiple tumors of the same type arising in the same patient is referred to as intra-patient heterogeneity. Subpopulations of cancer cells with distinct phenotypic and molecular features within a tumor are called intratumor heterogeneity (ITH). Since Nowell proposed the clonal evolution of tumor cell populations in 1976, tumor heterogeneity, especially ITH, was actively studied. Research has focused on the genetic basis of cancer, particularly mutational activation of oncogenes or inactivation of tumor-suppressor genes (TSGs). The phenomenon of ITH is commonly explained by Darwinian-like clonal evolution of a single tumor. Despite the monoclonal origin of most cancers, new clones arise during tumor progression due to the continuous acquisition of mutations. It is clear that disruption of the "epigenetic machinery" plays an important role in cancer development. Aberrant epigenetic changes occur more frequently than gene mutations in human cancers. The epigenome is at the intersection of the environment and genome. Epigenetic dysregulation occurs in the earliest stage of cancer. The current trend of epigenetic therapy is to use epigenetic drugs to reverse and/or delay future resistance to cancer therapies. A majority of cancer therapies fail to achieve durable responses, which is often attributed to ITH. Epigenetic therapy may reverse drug resistance in heterogeneous cancer. Complete understanding of genetic and epigenetic heterogeneity may assist in designing combinations of targeted therapies based on molecular information extracted from individual tumors.
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Affiliation(s)
- Mingzhou Guo
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, 40 Daxue Road, Zhengzhou, Henan 450052 China
| | - Yaojun Peng
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - Aiai Gao
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - Chen Du
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - James G Herman
- 3The Hillman Cancer Center, University of Pittsburgh Cancer Institute, 5117 Centre Ave., Pittsburgh, PA 15213 USA
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7
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Yan HX, Du J, Fu J, Huang W, Jia LM, Ping P, Zhao L, Song YQ, Jia XM, Dou JT, Mu YM, Wang FL, Tian W, Lyu ZH. Microarray-based differential expression profiling of long noncoding RNAs and messenger RNAs in formalin-fixed paraffin-embedded human papillary thyroid carcinoma samples. Transl Cancer Res 2019; 8:439-451. [PMID: 35116776 PMCID: PMC8797411 DOI: 10.21037/tcr.2019.02.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 01/17/2019] [Indexed: 11/06/2022]
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) can regulate the expression of genes at almost every level. The altered expression of lncRNAs was observed in many kinds of cancers. Until recently, few studies have focused on the function of lncRNAs in the context of papillary thyroid carcinoma (PTC). METHODS In the current study, we collected seven PTC and nodular goiter tissue samples and explored mRNA and lncRNA expression patterns in these samples by microarray. RESULTS We observed aberrant expression of 94 lncRNAs and 99 mRNAs in the seven PTC samples as compared to the nodular goiter tissue [fold change (FC) ≥2.0; P<0.01]. To confirm these microarray results, quantitative polymerase chain reaction (q-PCR) was performed to assess the expression of three randomly selected differentially expressed mRNAs and lncRNAs, confirming our microarray findings significantly. We then performed gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) analyses to systematically characterize the twelve significantly differential genes. A co-expression analysis revealed that the lncRNAs n382996, n342483, and n409114 were closely related to the regulation of MT1G, MT1H, and MT1F. CONCLUSIONS In the present study a string of novel lncRNAs associated with PTC were identified. Further study of these lncRNAs should be performed to identify novel target molecules which may improve diagnosis and treatment of PTC.
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Affiliation(s)
- Hui-Xian Yan
- Department and Key Laboratory of Endocrinology and Metabolism, PLA General Hospital, Beijing 100853, China.,Department of Endocrinology, Beijing Haidian Hospital, Beijing Haidian Section of Peking University Third Hospital, Beijing 100080, China
| | - Jin Du
- Department and Key Laboratory of Endocrinology and Metabolism, PLA General Hospital, Beijing 100853, China
| | - Jing Fu
- Department of Pathology, Beijing Haidian Hospital, Beijing Haidian Section of Peking University Third Hospital, Beijing 100080, China
| | - Wei Huang
- Department of Endocrinology, Beijing Haidian Hospital, Beijing Haidian Section of Peking University Third Hospital, Beijing 100080, China
| | - Li-Meng Jia
- Department of General Surgery, Beijing Haidian Hospital, Beijing Haidian Section of Peking University Third Hospital, Beijing 100080, China
| | - Pang Ping
- Department and Key Laboratory of Endocrinology and Metabolism, PLA General Hospital, Beijing 100853, China.,Department of Endocrinology, Hainan Branch of PLA General Hospital, Sanya 572013, China
| | - Ling Zhao
- Department and Key Laboratory of Endocrinology and Metabolism, PLA General Hospital, Beijing 100853, China
| | - Ye-Qiong Song
- Department and Key Laboratory of Endocrinology and Metabolism, PLA General Hospital, Beijing 100853, China
| | - Xiao-Meng Jia
- Department and Key Laboratory of Endocrinology and Metabolism, PLA General Hospital, Beijing 100853, China
| | - Jing-Tao Dou
- Department and Key Laboratory of Endocrinology and Metabolism, PLA General Hospital, Beijing 100853, China
| | - Yi-Ming Mu
- Department and Key Laboratory of Endocrinology and Metabolism, PLA General Hospital, Beijing 100853, China
| | - Fu-Lin Wang
- Department of Pathology, PLA General Hospital, Beijing 100853, China
| | - Wen Tian
- Department of General Surgery, PLA General Hospital, Beijing 100853, China
| | - Zhao-Hui Lyu
- Department and Key Laboratory of Endocrinology and Metabolism, PLA General Hospital, Beijing 100853, China
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8
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Sandler JE, Huang H, Zhao N, Wu W, Liu F, Ma S, Udelsman R, Zhang Y. Germline Variants in DNA Repair Genes, Diagnostic Radiation, and Risk of Thyroid Cancer. Cancer Epidemiol Biomarkers Prev 2017; 27:285-294. [PMID: 29263185 DOI: 10.1158/1055-9965.epi-17-0319] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 06/27/2017] [Accepted: 12/15/2017] [Indexed: 01/30/2023] Open
Abstract
Background: Radiation exposure is a well-documented risk factor for thyroid cancer; diagnostic imaging represents an increasing source of exposure. Germline variations in DNA repair genes could increase risk of developing thyroid cancer following diagnostic radiation exposure. No studies have directly tested for interaction between germline mutations and radiation exposure.Methods: Using data and DNA samples from a Connecticut population-based case-control study performed in 2010 to 2011, we genotyped 440 cases of incident thyroid cancer and 465 population-based controls for 296 SNPs in 52 DNA repair genes. We used multivariate unconditional logistic regression models to estimate associations between each SNP and thyroid cancer risk, as well as to directly estimate the genotype-environment interaction between each SNP and ionizing radiation.Results: Three SNPs were associated with increased risk of thyroid cancer and with thyroid microcarcinoma: HUS rs2708896, HUS rs10951937, and MGMT rs12769288. No SNPs were associated with increased risk of larger tumor (>10 mm) in the additive model. The gene-environment interaction analysis yielded 24 SNPs with Pinteraction < 0.05 for all thyroid cancer, 12 SNPs with Pinteraction < 0.05 for thyroid microcarcinoma, and 5 SNPs with Pinteraction < 0.05 for larger tumors.Conclusions: Germline variants in DNA repair genes are associated with thyroid cancer risk and are differentially associated with thyroid microcarcinoma and large tumor size. Our study provides the first evidence that germline genetic variations modify the association between diagnostic radiation and thyroid cancer risk.Impact: Thyroid microcarcinoma may represent a distinct subset of thyroid cancer. The effect of diagnostic radiation on thyroid cancer risk varies by germline polymorphism. Cancer Epidemiol Biomarkers Prev; 27(3); 285-94. ©2017 AACR.
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Affiliation(s)
| | - Huang Huang
- Department of Surgery, Yale School of Medicine, New Haven, Connecticut
| | - Nan Zhao
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut
| | - Weiwei Wu
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut.,School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Fangfang Liu
- The 302 Military Hospital, Beijing, China.,Department of Surgery, Yale School of Medicine, New Haven, Connecticut
| | - Shuangge Ma
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut
| | - Robert Udelsman
- Endocrine Neoplasia Institute, Miami Cancer Center, Miami, Florida
| | - Yawei Zhang
- Department of Surgery, Yale School of Medicine, New Haven, Connecticut. .,Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut
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9
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Wu C, Zhang D. Identification of early-stage lung adenocarcinoma prognostic signatures based on statistical modeling. Cancer Biomark 2017; 18:117-123. [PMID: 27935544 DOI: 10.3233/cbm-151368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BACKGROUND Current staging methods are lack of precision in predicting prognosis of early-stage lung adenocarcinomas. OBJECTIVE We aimed to develop a gene expression signature to identify high- and low-risk groups of patients. METHODS We used the Bayesian Model Averaging algorithm to analyze the DNA microarray data from 442 lung adenocarcinoma patients from three independent cohorts, one of which was used for training. RESULTS The patients were assigned to either high- or low-risk groups based on the calculated risk scores based on the identified 25-gene signature. The prognostic power was evaluated using Kaplan-Meier analysis and the log-rank test. The testing sets were divided into two distinct groups with log-rank test p-values of 0.00601 and 0.0274 respectively. CONCLUSIONS Our results show that the prognostic models could successfully predict patients' outcome and serve as biomarkers for early-stage lung adenocarcinoma overall survival analysis.
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Affiliation(s)
- Chunxiao Wu
- Department of Thoracic Surgery, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China.,Department of Thoracic Surgery, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Donglei Zhang
- Department of Thoracic Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201112, China.,Department of Thoracic Surgery, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
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10
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Yang M, Tian J, Guo X, Yang Y, Guan R, Qiu M, Li Y, Sun X, Zhen Y, Zhang Y, Chen C, Li Y, Fang H. Long noncoding RNA are aberrantly expressed in human papillary thyroid carcinoma. Oncol Lett 2016; 12:544-552. [PMID: 27347178 PMCID: PMC4906702 DOI: 10.3892/ol.2016.4653] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 05/19/2016] [Indexed: 12/20/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have emerged as key regulatory molecules at almost every level of gene expression regulation. The altered expression of lncRNAs is a characteristic of numerous types of cancer, and lncRNAs have been demonstrated to promote the development, invasion and metastasis of tumors through various mechanisms. However, the role of lncRNAs in papillary thyroid carcinoma (PTC) remain unclear. In the present study, differentially expressed lncRNAs and mRNAs were detected by human lncRNA microarray in three pairs of PTC and adjacent noncancerous samples. The microarray results revealed that 675 lncRNAs and 751 mRNAs were abnormally expressed in the three PTC samples compared with adjacent noncancerous samples (fold change ≥2.0; P<0.05). To validate the microarray results, 8 differentially expressed lncRNAs were randomly selected for quantitative polymerase chain reaction (qPCR). The results of qPCR were consistent with the microarray data; the 8 lncRNAs had an aberrant expression in the PTC samples compared with the adjacent noncancerous samples. Gene ontology and pathway analysis indicated that there were 7 downregulated pathways and 29 upregulated pathways in PTC. LncRNA classification and subgroup analysis revealed 7 pairs of enhancer-like lncRNA-mRNA, 9 pairs of antisense lncRNA-mRNA and 45 pairs of lncRNA-mRNA were differentially expressed between PTC and their paired noncancerous samples. In conclusion, the present study identified a series of novel PTC-associated lncRNAs. Further study with these lncRNAs is instrumental for the identification of novel target molecules that could lead to improved diagnosis and treatment for PTC.
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Affiliation(s)
- Meiliu Yang
- Department of Internal Medicine, Hebei Medical University, Shijiazhuang, Hebei 050017, P.R. China
| | - Jinli Tian
- Department of Endocrinology, Tangshan Workers' Hospital, Tangshan, Hebei 063000, P.R. China
| | - Xin Guo
- Department of Endocrinology, Tangshan Workers' Hospital, Tangshan, Hebei 063000, P.R. China
| | - Ying Yang
- Department of Internal Medicine, Hebei Medical University, Shijiazhuang, Hebei 050017, P.R. China
| | - Ruhua Guan
- Department of Medicine, Hebei United University, Tangshan, Hebei 063000, P.R. China
| | - Mingyue Qiu
- Department of Internal Medicine, Hebei Medical University, Shijiazhuang, Hebei 050017, P.R. China
| | - Yukai Li
- Department of Internal Medicine, Hebei Medical University, Shijiazhuang, Hebei 050017, P.R. China
| | - Xueling Sun
- Department of Endocrinology, Tangshan Workers' Hospital, Tangshan, Hebei 063000, P.R. China
| | - Yanfeng Zhen
- Department of Endocrinology, Tangshan Workers' Hospital, Tangshan, Hebei 063000, P.R. China
| | - Yazhong Zhang
- Department of Endocrinology, Tangshan Workers' Hospital, Tangshan, Hebei 063000, P.R. China
| | - Chunyou Chen
- Department of Endocrinology, Tangshan Workers' Hospital, Tangshan, Hebei 063000, P.R. China
| | - Yanbing Li
- Department of Endocrinology, Tangshan Workers' Hospital, Tangshan, Hebei 063000, P.R. China
| | - Hui Fang
- Department of Internal Medicine, Hebei Medical University, Shijiazhuang, Hebei 050017, P.R. China; Department of Endocrinology, Tangshan Workers' Hospital, Tangshan, Hebei 063000, P.R. China
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11
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Sigurdson AJ, Brenner AV, Roach JA, Goudeva L, Müller JA, Nerlich K, Reiners C, Schwab R, Pfeiffer L, Waldenberger M, Braganza M, Xu L, Sturgis EM, Yeager M, Chanock SJ, Pfeiffer RM, Abend M, Port M. Selected single-nucleotide polymorphisms in FOXE1, SERPINA5, FTO, EVPL, TICAM1 and SCARB1 are associated with papillary and follicular thyroid cancer risk: replication study in a German population. Carcinogenesis 2016; 37:677-684. [PMID: 27207655 DOI: 10.1093/carcin/bgw047] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 04/15/2016] [Indexed: 01/08/2023] Open
Abstract
Several single-nucleotide polymorphisms (SNPs) have been associated with papillary and follicular thyroid cancer (PTC and FTC, respectively) risk, but few have replicated. After analyzing 17525 tag SNPs in 1129 candidate genes, we found associations with PTC risk in SERPINA5, FTO, HEMGN (near FOXE1) and other genes. Here, we report results from a replication effort in a large independent PTC/FTC case-control study conducted in Germany. We evaluated the best tagging SNPs from our previous PTC study and additionally included SNPs in or near FOXE1 and NKX2-1 genes, known susceptibility loci for thyroid cancer. We genotyped 422 PTC and 130 FTC cases and 752 controls recruited from three German clinical centers. We used polytomous logistic regression to simultaneously estimate PTC and FTC associations for 79 SNPs based on log-additive models. We assessed effect modification by body mass index (BMI), gender and age for all SNPs, and selected SNP by SNP interactions. We confirmed associations with PTC and SNPs in FOXE1/HEMGN, SERPINA5 (rs2069974), FTO (rs8047395), EVPL (rs2071194), TICAM1 (rs8120) and SCARB1 (rs11057820) genes. We found associations with SNPs in FOXE1, SERPINA5, FTO, TICAM1 and HSPA6 and FTC. We found two significant interactions between FTO (rs8047395) and BMI (P = 0.0321) and between TICAM1 (rs8120) and FOXE1 (rs10984377) (P = 0.0006). Besides the known associations with FOXE1 SNPs, we confirmed additional PTC SNP associations reported previously. We also found several new associations with FTC risk and noteworthy interactions. We conclude that multiple variants and host factors might interact in complex ways to increase risk of PTC and FTC.
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Affiliation(s)
| | | | | | | | - Jörg A Müller
- Department of Nuclear Medicine, Hannover Medical School, Hannover, Germany
| | - Kai Nerlich
- Department of Nuclear Medicine, University Hospital Würzburg, Würzburg, Germany
| | - Christoph Reiners
- Department of Nuclear Medicine, University Hospital Würzburg, Würzburg, Germany
| | - Robert Schwab
- Department of Surgery, Federal Armed Forces Hospital, Koblenz, Germany
| | - Liliane Pfeiffer
- Research Unit of Molecular Epidemiology and.,Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology and.,Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | | | - Li Xu
- Department of Head and Neck Surgery, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Erich M Sturgis
- Department of Head and Neck Surgery, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | | | | | - Ruth M Pfeiffer
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael Abend
- Bundeswehr Institute of Radiobiology, University of Ulm, Neuherbergstr. 11, Munich 80937, Germany and
| | - Matthias Port
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
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12
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Franz A, Pirson PA, Pilger D, Halder S, Achuthankutty D, Kashkar H, Ramadan K, Hoppe T. Chromatin-associated degradation is defined by UBXN-3/FAF1 to safeguard DNA replication fork progression. Nat Commun 2016; 7:10612. [PMID: 26842564 PMCID: PMC4743000 DOI: 10.1038/ncomms10612] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 01/05/2016] [Indexed: 01/10/2023] Open
Abstract
The coordinated activity of DNA replication factors is a highly dynamic process that involves ubiquitin-dependent regulation. In this context, the ubiquitin-directed ATPase CDC-48/p97 recently emerged as a key regulator of chromatin-associated degradation in several of the DNA metabolic pathways that assure genome integrity. However, the spatiotemporal control of distinct CDC-48/p97 substrates in the chromatin environment remained unclear. Here, we report that progression of the DNA replication fork is coordinated by UBXN-3/FAF1. UBXN-3/FAF1 binds to the licensing factor CDT-1 and additional ubiquitylated proteins, thus promoting CDC-48/p97-dependent turnover and disassembly of DNA replication factor complexes. Consequently, inactivation of UBXN-3/FAF1 stabilizes CDT-1 and CDC-45/GINS on chromatin, causing severe defects in replication fork dynamics accompanied by pronounced replication stress and eventually resulting in genome instability. Our work identifies a critical substrate selection module of CDC-48/p97 required for chromatin-associated protein degradation in both Caenorhabditis elegans and humans, which is relevant to oncogenesis and aging. Cdc48/p97 is a key component of the ubiquitin-proteasome system, acting as a ubiquitin-directed segregase to regulate multiple cellular functions. Here the authors identify UBXN-3/FAF1 as a crucial regulator of chromatin-associated protein degradation that recruits Cdc48/p97 to DNA replication forks.
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Affiliation(s)
- André Franz
- Institute for Genetics and CECAD Research Center, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Paul A Pirson
- Institute for Genetics and CECAD Research Center, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Domenic Pilger
- Institute for Genetics and CECAD Research Center, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany.,Department of Oncology, University of Oxford, Cancer Research UK/Medical Research Council Oxford, Institute for Radiation Oncology, Old Road Campus Research Building, OX3 7DQ Oxford, UK
| | - Swagata Halder
- Department of Oncology, University of Oxford, Cancer Research UK/Medical Research Council Oxford, Institute for Radiation Oncology, Old Road Campus Research Building, OX3 7DQ Oxford, UK
| | - Divya Achuthankutty
- Department of Oncology, University of Oxford, Cancer Research UK/Medical Research Council Oxford, Institute for Radiation Oncology, Old Road Campus Research Building, OX3 7DQ Oxford, UK
| | - Hamid Kashkar
- Centre for Molecular Medicine Cologne and Institute for Medical Microbiology, Immunology and Hygiene at CECAD Research Center, University Hospital of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Kristijan Ramadan
- Department of Oncology, University of Oxford, Cancer Research UK/Medical Research Council Oxford, Institute for Radiation Oncology, Old Road Campus Research Building, OX3 7DQ Oxford, UK
| | - Thorsten Hoppe
- Institute for Genetics and CECAD Research Center, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
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13
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Figlioli G, Elisei R, Romei C, Melaiu O, Cipollini M, Bambi F, Chen B, Köhler A, Cristaudo A, Hemminki K, Gemignani F, Försti A, Landi S. A Comprehensive Meta-analysis of Case-Control Association Studies to Evaluate Polymorphisms Associated with the Risk of Differentiated Thyroid Carcinoma. Cancer Epidemiol Biomarkers Prev 2016; 25:700-13. [PMID: 26843521 DOI: 10.1158/1055-9965.epi-15-0652] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 01/23/2016] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Linkage analyses and association studies suggested that inherited genetic variations play a role in the development of differentiated thyroid carcinoma (DTC). METHODS We combined the results from a genome-wide association study (GWAS) performed by our group and from published studies on DTC. With a first approach, we evaluated whether a SNP published as associated with the risk of DTC could replicate in our GWAS (using FDR as adjustment for multiple comparisons). With the second approach, meta-analyses were performed between literature and GWAS when both sources suggested an association, increasing the statistical power of the analysis. RESULTS rs1799814 (CYP1A1), rs1121980 (FTO), and 3 SNPs within 9q22 (rs965513, rs7048394, and rs894673) replicated the associations described in the literature. In addition, the meta-analyses between literature and GWAS revealed 10 more SNPs within 9q22, six within FTO, two within SOD1, and single variations within HUS1, WDR3, UGT2B7, ALOX12, TICAM1, ATG16L1, HDAC4, PIK3CA, SULF1, IL11RA, VEGFA, and 1p31.3, 2q35, 8p12, and 14q13. CONCLUSION This analysis confirmed several published risk loci that could be involved in DTC predisposition. IMPACT These findings provide evidence for the role of germline variants in DTC etiology and are consistent with a polygenic model of the disease. Cancer Epidemiol Biomarkers Prev; 25(4); 700-13. ©2016 AACR.
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Affiliation(s)
- Gisella Figlioli
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany. Department of Biology, University of Pisa, Pisa, Italy
| | - Rossella Elisei
- Department of Endocrinology and Metabolism, University of Pisa, Pisa, Italy
| | - Cristina Romei
- Department of Endocrinology and Metabolism, University of Pisa, Pisa, Italy
| | | | | | - Franco Bambi
- Blood Centre, Azienda Ospedaliero Universitaria A. Meyer, Firenze, Italy
| | - Bowang Chen
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Aleksandra Köhler
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany. II Medizinische Klinik, Gastrologie, Onkologie und Palliativmedizin, St.Agnes-Hospital Bocholt, Bocholt, Germany
| | - Alfonso Cristaudo
- Department of Endocrinology and Metabolism, University of Pisa, Pisa, Italy
| | - Kari Hemminki
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany. Center for Primary Health Care Research, Clinical Research Center, Lund University, Malmö, Sweden
| | | | - Asta Försti
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany. Center for Primary Health Care Research, Clinical Research Center, Lund University, Malmö, Sweden.
| | - Stefano Landi
- Department of Biology, University of Pisa, Pisa, Italy.
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14
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Liefke R, Windhof-Jaidhauser IM, Gaedcke J, Salinas-Riester G, Wu F, Ghadimi M, Dango S. The oxidative demethylase ALKBH3 marks hyperactive gene promoters in human cancer cells. Genome Med 2015. [PMID: 26221185 PMCID: PMC4517488 DOI: 10.1186/s13073-015-0180-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Background The oxidative DNA demethylase ALKBH3 targets single-stranded DNA (ssDNA) in order to perform DNA alkylation damage repair. ALKBH3 becomes upregulated during tumorigenesis and is necessary for proliferation. However, the underlying molecular mechanism remains to be understood. Methods To further elucidate the function of ALKBH3 in cancer, we performed ChIP-seq to investigate the genomic binding pattern of endogenous ALKBH3 in PC3 prostate cancer cells coupled with microarray experiments to examine the expression effects of ALKBH3 depletion. Results We demonstrate that ALKBH3 binds to transcription associated locations, such as places of promoter-proximal paused RNA polymerase II and enhancers. Strikingly, ALKBH3 strongly binds to the transcription initiation sites of a small number of highly active gene promoters. These promoters are characterized by high levels of transcriptional regulators, including transcription factors, the Mediator complex, cohesin, histone modifiers, and active histone marks. Gene expression analysis showed that ALKBH3 does not directly influence the transcription of its target genes, but its depletion induces an upregulation of ALKBH3 non-bound inflammatory genes. Conclusions The genomic binding pattern of ALKBH3 revealed a putative novel hyperactive promoter type. Further, we propose that ALKBH3 is an intrinsic DNA repair protein that suppresses transcription associated DNA damage at highly expressed genes and thereby plays a role to maintain genomic integrity in ALKBH3-overexpressing cancer cells. These results raise the possibility that ALKBH3 may be a potential target for inhibiting cancer progression. Electronic supplementary material The online version of this article (doi:10.1186/s13073-015-0180-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Robert Liefke
- Division of Newborn Medicine and Program in Epigenetics, Department of Medicine, Boston Children's Hospital, Boston, MA 02115 USA ; Department of Cell Biology, Harvard Medical School, Boston, MA 02115 USA
| | | | - Jochen Gaedcke
- University Medical Center, Department of General-, and Visceral Surgery, D-37075 Göttingen, Germany
| | | | - Feizhen Wu
- Epigenetics Laboratory, Institute of Biomedical Sciences, Fudan University, Shanghai, 200032 China
| | - Michael Ghadimi
- University Medical Center, Department of General-, and Visceral Surgery, D-37075 Göttingen, Germany
| | - Sebastian Dango
- University Medical Center, Department of General-, and Visceral Surgery, D-37075 Göttingen, Germany ; Division of Newborn Medicine and Program in Epigenetics, Department of Medicine, Boston Children's Hospital, Boston, MA 02115 USA ; Department of Cell Biology, Harvard Medical School, Boston, MA 02115 USA
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15
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Hotta K, Sho M, Fujimoto K, Shimada K, Yamato I, Anai S, Harada H, Tsujikawa K, Konishi N, Shinohara N, Nakajima Y. Clinical significance and therapeutic potential of prostate cancer antigen-1/ALKBH3 in human renal cell carcinoma. Oncol Rep 2015; 34:648-54. [PMID: 26035443 DOI: 10.3892/or.2015.4017] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 04/14/2015] [Indexed: 11/06/2022] Open
Abstract
Prostate cancer antigen-1 (PCA-1)/ALKBH3 has been recently identified in human prostate cancer and its expression is correlated with disease progression and prognosis. However, the precise role and function of PCA-1/ALKBH3 in human malignancies are largely unknown. In the present study, we investigated the clinical significance and therapeutic potential of PCA-1/ALKBH3 in renal cell carcinoma (RCC). PCA-1/ALKBH3 expression was examined by immunohistochemistry in 101 RCC patients who underwent radical or partial nephrectomy. Its expression was positively correlated with advanced pathological T- and M-factors and TNM stage (T, P<0.05; M, P<0.01; TNM, P<0.01, respectively). In the prognostic analysis, PCA-1/ALKBH3-negative patients with RCC had a significantly better prognosis than PCA-1/ALKBH3-positive patients (5-year survival rate, 92.9 vs. 75.9%, respectively; P<0.05). Next, the therapeutic potential of targeting PCA-1/ALKBH3 was further evaluated by small interfering RNA method using a human RCC cell line (CAKI-1). We found that PCA-1/ALKBH3 knockdown significantly inhibited the growth of CAKI-1 cells compared with the control (P<0.001). Furthermore, knockdown of PCA-1 induced apoptosis in CAKI-1 cells, as assessed by poly(ADP-ribose) polymerase-cleavage assays. We demonstrated for the first time that PCA-1/ALKBH3 expression has a significant prognostic impact on patient prognosis in RCC. Furthermore, its knockdown has a therapeutic efficacy on RCC. Taken together, both our clinical and experimental data strongly suggest that PCA-1/ALKBH3 may be functionally important and a novel molecular target for human RCC.
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Affiliation(s)
- Kiyohiko Hotta
- Department of Surgery, Nara Medical University, Kashihara, Nara, Japan
| | - Masayuki Sho
- Department of Surgery, Nara Medical University, Kashihara, Nara, Japan
| | - Kiyohide Fujimoto
- Department of Urology, Nara Medical University, Kashihara, Nara, Japan
| | - Keiji Shimada
- Department of Pathology, Nara Medical University, Kashihara, Nara, Japan
| | - Ichiro Yamato
- Department of Surgery, Nara Medical University, Kashihara, Nara, Japan
| | - Satoshi Anai
- Department of Urology, Nara Medical University, Kashihara, Nara, Japan
| | - Hiroshi Harada
- Kidney Transplant Surgery, Sapporo City General Hospital, Sapporo, Japan
| | - Kazutake Tsujikawa
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Noboru Konishi
- Department of Pathology, Nara Medical University, Kashihara, Nara, Japan
| | - Nobuo Shinohara
- Department of Renal and Genitourinary Surgery, Hokkaido University Graduate School of Medicine, Sapporo, Japan
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16
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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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17
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Nagy R, Ringel MD. Genetic predisposition for nonmedullary thyroid cancer. HORMONES & CANCER 2015; 6:13-20. [PMID: 25338077 PMCID: PMC10355960 DOI: 10.1007/s12672-014-0205-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 10/15/2014] [Indexed: 10/24/2022]
Abstract
Nonmedullary thyroid cancer (NMTC) can be sporadic or can occur as a component cancer as part of several well-described hereditary cancer syndromes. NMTC, particularly papillary thyroid cancer, also can occur by itself in families and is often termed familial NMTC or familial papillary thyroid cancer. The occurrence of NMTC in families, along with extensive population-based evidence from patients with sporadic thyroid cancer, together suggest that NMTC has a strong genetic component, only a small proportion of which has been characterized to date. Advances in genetic and genomic technology have rapidly advanced our understanding of the complex nature of NMTC susceptibility, although much remains to be explained. Herein, we describe the current state of knowledge, starting with a brief review of hereditary syndromic causes and moving on to describe recent data using modern genomic approaches to identifying genes involved in the predisposition to NMTC.
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Affiliation(s)
- Rebecca Nagy
- Divison of Human Genetics, The Ohio State University College of Medicine and Arthur G. James Comprehensive Cancer Center and Richard G. Solove Research Institute, Columbus, OH 43210 USA
- Division of Endocrinology, Diabetes, and Metabolism, Department of Internal Medicine, The Ohio State University College of Medicine and Arthur G. James Comprehensive Cancer Center and Richard G. Solove Research Institute, Columbus, OH 43210 USA
- Department of Internal Medicine, Division of Human Genetics, The Ohio State University Wexner Medical Center, 2001 Polaris Parkway, Columbus, OH 43240 USA
| | - Matthew D. Ringel
- Divison of Human Genetics, The Ohio State University College of Medicine and Arthur G. James Comprehensive Cancer Center and Richard G. Solove Research Institute, Columbus, OH 43210 USA
- Division of Endocrinology, Diabetes, and Metabolism, Department of Internal Medicine, The Ohio State University College of Medicine and Arthur G. James Comprehensive Cancer Center and Richard G. Solove Research Institute, Columbus, OH 43210 USA
- Department of Internal Medicine, Division of Endocrinology, Metabolism and Diabetes, The Ohio State University Wexner Medical Center, 1581 Dodd Drive; McCampbell Hall room 565, Columbus, OH 43210 USA
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18
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Song CM, Kwon TK, Park BL, Ji YB, Tae K. Single nucleotide polymorphisms of ataxia telangiectasia mutated and the risk of papillary thyroid carcinoma. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2015; 56:70-76. [PMID: 25196645 DOI: 10.1002/em.21898] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 08/20/2014] [Indexed: 06/03/2023]
Abstract
Genetic factors associated with susceptibility to papillary thyroid carcinoma (PTC) are not well known. We evaluated the association between single nucleotide polymorphisms (SNPs) of ataxia telangiectasia mutated (ATM) and the risk of PTC. A total of 437 histologically confirmed PTC cases and 184 cancer-free controls without thyroid nodules were recruited. Genotypes with respect to five ATM SNPs (rs189037, rs664677, rs373759, rs664143, and rs4585) were determined by the TaqMan assay, and odds ratios and 95% confidence intervals were obtained by logistic regression analysis. Linkage disequilibria and haplotypes were examined from the genotype data. When evaluated separately the genotype distributions of the five ATM SNPs were similar in the PTC cases and controls. Three ATM SNPs (rs373759, rs664143, and rs4585) were found to be in strong linkage disequilibrium (D' = 1.00, P < 0.001). When the three haplotypes (C-A-G), (T-G-T), and (C-G-T) of these three ATM SNP sites were analyzed, ATM haplotype (C-G-T) +/- was associated with a lower risk of PTC than ATM haplotype (C-G-T) -/- (P = 0.03) after adjusting for age and gender. Our results suggest that genetic polymorphisms of ATM may play an important role in the development of thyroid cancer in the Korean population.
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Affiliation(s)
- Chang Myeon Song
- Department of Otolaryngology-Head and Neck Surgery, College of Medicine, Hanyang University, Seoul, Korea
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Wu FF, He XF, Shen HW, Qin GJ. Association between the XRCC1 polymorphisms and thyroid cancer risk: a meta-analysis from case-control studies. PLoS One 2014; 9:e87764. [PMID: 25211472 PMCID: PMC4161346 DOI: 10.1371/journal.pone.0087764] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 12/01/2013] [Indexed: 12/17/2022] Open
Abstract
Background The previous published data on the association between the X-ray repair cross-conplementation group 1 (XRCC1) polymorphisms and thyroid cancer risk remained controversial. Hence, we performed a meta-analysis on all available studies that provided 1729 cases and 3774 controls (from 11 studies) for XRCC1 Arg399Gln, 1040 cases and 2487 controls for Arg194Trp (from 7 studies), and 1432 cases and 3356 controls for Arg280His (from 8 studies). Methodology/Principal Findings PubMed, CNKI, and EMBASE database were searched to identify relevant studies. Overall, no significant association was found between XRCC1 Arg399Gln (recessive model: OR = 0.95, 95% CI = 0.77–1.15; dominant model: OR = 0.89, 95% CI = 0.75–1.05; homozygote model: OR = 0.92, 95% CI = 0.69–1.23; Heterozygote model: OR = 0.91, 95% CI = 0.80–1.03; additive model: OR = 0.93, 95% CI = 0.81–1.07), Arg194Trp (recessive model: OR = 1.41, 95% CI = 0.62–3.23; dominant model: OR = 1.01, 95% CI = 0.77–1.34; homozygote model: OR = 1.42, 95% CI = 0.55–3.67; Heterozygote model: OR = 1.03, 95% CI = 0.85–1.26; additive model: OR = 1.08, 95% CI = 0.81–1.42), and Arg280His (recessive model: OR = 1.08, 95% CI = 0.56–2.10; dominant model: OR = 1.01, 95% CI = 0.84–1.22; homozygote model: OR = 1.00, 95% CI = 0.51–1.96; Heterozygote model: OR = 1.04, 95% CI = 0.75–1.42; additive model: OR = 1.03, 95% CI = 0.86–1.23) and thyroid cancer risk when all the eligible studies were pooled into the meta-analysis. In the further stratified and sensitivity analyses, significant association was still not found in these three genetic polymorphisms. Conclusions/Significance In summary, this meta-analysis indicates that XRCC1 Arg399Gln, Arg280His, and Arg194Trp are not associated with thyroid cancer.
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Affiliation(s)
- Fei-Fei Wu
- Department of Endocrinology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiao-Feng He
- Department of Research, Peace Hospital of Changzhi Medical College, Changzhi, China
| | - Hu-Wei Shen
- Department of Endocrinology, Peace Hospital of Changzhi Medical College, Changzhi, China
| | - Gui-Jun Qin
- Department of Endocrinology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- * E-mail:
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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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21
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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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Salomaa S, Prise KM, Atkinson MJ, Wojcik A, Auvinen A, Grosche B, Sabatier L, Jourdain JR, Salminen E, Baatout S, Kulka U, Rabus H, Blanchardon E, Averbeck D, Weiss W. State of the art in research into the risk of low dose radiation exposure--findings of the fourth MELODI workshop. JOURNAL OF RADIOLOGICAL PROTECTION : OFFICIAL JOURNAL OF THE SOCIETY FOR RADIOLOGICAL PROTECTION 2013; 33:589-603. [PMID: 23803528 DOI: 10.1088/0952-4746/33/3/589] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The fourth workshop of the Multidisciplinary European Low Dose Initiative (MELODI) was organised by STUK-Radiation and Nuclear Safety Authority of Finland. It took place from 12 to 14 September 2012 in Helsinki, Finland. The meeting was attended by 179 scientists and professionals engaged in radiation research and radiation protection. We summarise the major scientific findings of the workshop and the recommendations for updating the MELODI Strategic Research Agenda and Road Map for future low dose research activities.
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Affiliation(s)
- Sisko Salomaa
- STUK-Radiation and Nuclear Safety Authority, PO Box 14, 00881 Helsinki, Finland.
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Chen HS, Pfeiffer RM, Zhang S. A powerful method for combining P-values in genomic studies. Genet Epidemiol 2013; 37:814-9. [PMID: 23959976 DOI: 10.1002/gepi.21755] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 06/25/2013] [Accepted: 07/11/2013] [Indexed: 11/10/2022]
Abstract
After genetic regions have been identified in genomewide association studies (GWAS), investigators often follow up with more targeted investigations of specific regions. These investigations typically are based on single nucleotide polymorphisms (SNPs) with dense coverage of a region. Methods are thus needed to test the hypothesis of any association in given genetic regions. Several approaches for combining P-values obtained from testing individual SNP hypothesis tests are available. We recently proposed a sequential procedure for testing the global null hypothesis of no association in a region. When this global null hypothesis is rejected, this method provides a list of significant hypotheses and has weak control of the family-wise error rate. In this paper, we devise a permutation-based version of the test that accounts for correlations of tests based on SNPs in the same genetic region. Based on simulated data, the method has correct control of the type I error rate and higher or comparable power to other tests.
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Affiliation(s)
- Huann-Sheng Chen
- Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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Bao Y, Jiang L, Zhou JY, Zou JJ, Zheng JY, Chen XF, Liu ZM, Shi YQ. XRCC1 gene polymorphisms and the risk of differentiated thyroid carcinoma (DTC): a meta-analysis of case-control studies. PLoS One 2013; 8:e64851. [PMID: 23717668 PMCID: PMC3661468 DOI: 10.1371/journal.pone.0064851] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 04/18/2013] [Indexed: 12/15/2022] Open
Abstract
Background Previous studies investigating the association between X-ray repair cross-complementing group 1 (XRCC1) polymorphisms and thyroid cancer risk have yielded inconsistent results. This meta-analysis was performed to derive a more precise estimation of the relationship between three XRCC1 polymorphisms and thyroid cancer risk. Methods/Principal Findings PubMed and EMBASE database were systematically searched to identify relevant studies. 10 publications were selected for this meta-analysis, including 11 studies for Arg399Gln polymorphism (1726 cases and 3774 controls), 7 studies for Arg194Trp polymorphism (1037 cases and 2487 controls) and 8 studies for Arg280His polymorphism (1432 cases and 3356 controls). The results in total population did not show any significant association between these three polymorphisms and the risk of DTC for all genetic models. However, when stratified by ethnicity, the results showed that Arg280His polymorphism was associated with an increased risk of DTC among Caucasians (Arg/His vs. Arg/Arg: OR = 1.45, 95% CI = 1.09–1.93; dominant model: OR = 1.43, 95% CI = 1.08–1.89; additive model: OR = 1.38, 95% CI = 1.05–1.80), whereas individuals carrying Arg/His genotype have a significantly reduced risk of DTC among Asians (Arg/His vs. Arg/Arg: OR = 0.71, 95% CI = 0.51–0.98). We also detected that 399Gln variant allele carriers might presented an overall decreased risk of DTC in mixed population. Furthermore, subgroup analyses by histological subtype revealed that Arg194Trp polymorphism was significantly associated with reduced risk for papillary thyroid carcinoma (PTC) (dominant model: OR = 0.71, 95% CI = 0.50–0.99). Conclusions This meta-analysis suggests that Arg280His polymorphism might contribute to the susceptibility of DTC among Caucasians, whereas it might provide protective effects in Asians against the risk of DTC. Additionally, our results support the protective role of Arg194Trp polymorphism in developing PTC, and show evidence of an association between Arg399Gln polymorphism and decreased risk of DTC in mixed population.
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Affiliation(s)
- Yi Bao
- Department of Endocrinology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Lei Jiang
- Department of Neurosurgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Jue-Yu Zhou
- Institute of Genetic Engineering, Southern Medical University, Guangzhou, China
- * E-mail: (JYZ); (YQS)
| | - Jun-Jie Zou
- Department of Endocrinology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Jiao-Yang Zheng
- Department of Endocrinology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Xiang-Fang Chen
- Department of Endocrinology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Zhi-Min Liu
- Department of Endocrinology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Yong-Quan Shi
- Department of Endocrinology, Changzheng Hospital, Second Military Medical University, Shanghai, China
- * E-mail: (JYZ); (YQS)
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ICAD deficiency in human colon cancer and predisposition to colon tumorigenesis: linkage to apoptosis resistance and genomic instability. PLoS One 2013; 8:e57871. [PMID: 23451280 PMCID: PMC3579889 DOI: 10.1371/journal.pone.0057871] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 01/29/2013] [Indexed: 12/31/2022] Open
Abstract
We previously showed that DNA fragmentation factor, which comprises a caspase-3-activated DNase (CAD) and its inhibitor (ICAD), may influence the rate of cell death by generating PARP-1-activating DNA breaks. Here we tested the hypothesis that ICAD-deficient colon epithelial cells exhibiting resistance to death stimuli may accumulate additional genetic modifications, leading to a tumorigenic phenotype. We show that ICAD deficiency may be associated with colon malignancy in humans. Indeed, an examination of ICAD expression using immunohistochemistry in an array of both colon cancer and normal tissues revealed that ICAD expression levels were severely compromised in the cancerous tissues. Upon DNA damage caused by a low dose of irradiation, ICAD cells acquire a tumorigenic phenotype. Colon epithelial cells derived from ICAD mice showed a significant resistance to death induced by the colon carcinogen dimethylhydrazine in vitro and in mice. Such resistance was associated with a decrease in PARP-1 activation. In an animal model of dimethylhydrazine-induced colon tumorigenesis, ICAD−/− mice developed significantly higher numbers of tumors with markedly larger sizes than the wild-type counterparts. Interestingly, the phenotype of the ICAD−/− mice was not associated with a significant increase in the precancerous aberrant crypt foci suggesting a potential link to tumor progression rather than initiation. More importantly, ICAD deficiency was associated with severe genomic instability as assessed by array comparative genomic hybridization. Such genomic instability consisted most prominently of amplifications but with sizable deletions as compared to the wild-type counterparts affecting several cancer-related genes including RAF-1, GSN, LMO3, and Fzd6 independently of p53. Altogether, our results present a viable case for the involvement of ICAD deficiency in colon carcinogenesis and show that apoptosis and genomic instability may comprise the means by which such deficiency may contribute to the process of increasing susceptibility to carcinogen-induced tumorigenesis.
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Sonu IS, Blonski W, Lin MV, Lewis J, Aberra F, Lichtenstein GR. Papillary thyroid cancer and inflammatory bowel disease: Is there a relationship? World J Gastroenterol 2013; 19:1079-84. [PMID: 23467027 PMCID: PMC3581995 DOI: 10.3748/wjg.v19.i7.1079] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Revised: 09/28/2012] [Accepted: 10/22/2012] [Indexed: 02/06/2023] Open
Abstract
AIM: To formally study age of diagnosis of papillary thyroid cancer (PTC) in inflammatory bowel disease (IBD) patients and evaluate the prevalence of PTC in IBD patients compared to a control population.
METHODS: We were interested in testing the hypothesis that patients with IBD are more likely to be diagnosed with PTC than a control population. A retrospective cohort analysis was performed using the University of Pennsylvania Health System’s electronic database. Outpatients from 1998-2009 were included in the search, and patients in the cohort were selected based on ICD-9 codes. Inclusion criteria included the diagnosis of Crohn’s disease (CD) or ulcerative colitis (UC) and the concurrent diagnosis of thyroid cancer in comparison to a control population. Using these methods 912 patients with CD and 1774 with UC were compared to 1638 diverticulitis and 19 447 asthma controls. Statistics were performed using corrected chi-square analysis. The primary outcome for this study was the diagnosis of PTC. Approval to conduct this study was obtained by the Institutional Review Board at the University of Pennsylvania.
RESULTS: The mean age was 47.5 years (range: 18-102 years) and 66% patients were female. An analysis of variance model was used to compare the age of PTC diagnosis between the CD, UC, asthma and diverticulitis groups, and a statistically significant difference in age at PTC diagnosis was noted across all groups (F = 6.35, df = 3, P = 0.0006). The age of PTC diagnosis in CD patients was statistically significantly lower than UC, asthma, and diverticulitis patients (average PTC diagnosis age for CD 25, UC 49, asthma 45, diverticulitis 63). After covarying for sex and age in 2009, the difference in age at PTC diagnosis remained statistically significant (F = 4.13, df = 3, P = 0.0089). A total of 86 patients were diagnosed with PTC. Nine patients (0.5%) with UC were diagnosed with PTC. Patients with UC were not shown to be more likely to develop PTC [odds ratio (OR): 1.544, 95%CI 0.767-3.108] compared to asthma controls. Four patients (0.4%) with CD were diagnosed with PTC. Patients with CD were not shown to be more likely to develop PTC (OR: 1.334, 95%CI 0.485-3.672) compared to a control population with asthma. Nine patients (0.5%) with a history of diverticulitis were diagnosed with PTC. Patients with diverticulitis were not shown to be more likely to develop PTC (OR: 1.673, 95%CI 0.831-3.368) compared to asthma controls. Patients with CD or UC were not less likely to develop PTC compared to those with diverticulitis (CD OR: 0.80, 95%CI 0.25-2.60; UC OR: 0.92, 95%CI 0.37-2.33). None of the patients used immunosuppressant medications prior to the diagnosis of PTC (azathioprine, 6-mercaptopurine, and methotrexate).
CONCLUSION: There is a significant difference in age of diagnosis of PTC in patients with CD compared to patients with UC and the control populations studied.
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27
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Almeida A. Genetic determinants of neuronal vulnerability to apoptosis. Cell Mol Life Sci 2013; 70:71-88. [PMID: 22695677 PMCID: PMC11113535 DOI: 10.1007/s00018-012-1029-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 04/22/2012] [Accepted: 05/07/2012] [Indexed: 12/18/2022]
Abstract
Apoptosis is a common mode of cell death that contributes to neuronal loss associated with neurodegeneration. Single-nucleotide polymorphisms (SNPs) in chromosomal DNA are contributing factors dictating natural susceptibility of humans to disease. Here, the most common SNPs affecting neuronal vulnerability to apoptosis are reviewed in the context of neurological disorders. Polymorphic variants in genes encoding apoptotic proteins, either from the extrinsic (FAS, TNF-α, CASP8) or the intrinsic (BAX, BCL2, CASP3, CASP9) pathways could be highly valuable in the diagnosis of neurodegenerative diseases and stroke. Interestingly, the Arg72Pro SNP in TP53, the gene encoding tumor suppressor p53, was recently revealed a biomarker of poor prognosis in stroke due to its ability to modulate neuronal apoptotic death. Search for new SNPs responsible for genetic variability to apoptosis will ensure the implementation of novel diagnostic and prognostic tools, as well as therapeutic strategies against neurological diseases.
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Affiliation(s)
- Angeles Almeida
- Instituto de Investigación Biomédica de Salamanca, Hospital Universitario de Salamanca, 37007, Salamanca, Spain.
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Kitahara CM, Neta G, Pfeiffer RM, Kwon D, Xu L, Freedman ND, Hutchinson AA, Chanock SJ, Sturgis EM, Sigurdson AJ, Brenner AV. Common obesity-related genetic variants and papillary thyroid cancer risk. Cancer Epidemiol Biomarkers Prev 2012; 21:2268-71. [PMID: 23064004 PMCID: PMC3518668 DOI: 10.1158/1055-9965.epi-12-0790] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Epidemiologic studies have shown consistent associations between obesity and increased thyroid cancer risk, but, to date, no studies have investigated the relationship between thyroid cancer risk and obesity-related single-nucleotide polymorphisms (SNP). METHODS We evaluated 575 tag SNPs in 23 obesity-related gene regions in a case-control study of 341 incident papillary thyroid cancer (PTC) cases and 444 controls of European ancestry. Logistic regression models, adjusted for attained age, year of birth, and sex were used to calculate ORs and 95% confidence intervals (CI) with SNP genotypes, coded as 0, 1, and 2 and modeled continuously to calculate P(trend). RESULTS Nine of 10 top-ranking SNPs (P(trend) < 0.01) were located in the FTO (fat mass and obesity associated) gene region, whereas the other was located in INSR (insulin receptor). None of the associations were significant after correcting for multiple testing. CONCLUSIONS Our data do not support an important role of obesity-related genetic polymorphisms in determining the risk of PTC. IMPACT Factors other than selected genetic polymorphisms may be responsible for the observed associations between obesity and increased PTC risk.
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Affiliation(s)
- Cari M Kitahara
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, EPS 7056, 6120 Executive Blvd, Rockville, MD 20852, USA.
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Cho SH, Kim SK, Kwon E, Park HJ, Kwon KH, Chung JH. Polymorphism ofIGF1RIs Associated with Papillary Thyroid Carcinoma in a Korean Population. J Interferon Cytokine Res 2012; 32:401-6. [DOI: 10.1089/jir.2011.0084] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Se Hee Cho
- Department of Physiology, College of Liberal Arts, University of Minnesota, Minneapolis, Minnesota
| | - Su Kang Kim
- Department of Pharmacology and Kohwang Medical Research Institute, School of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Eri Kwon
- Department of Pharmacology and Kohwang Medical Research Institute, School of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Hae Jeong Park
- Department of Pharmacology and Kohwang Medical Research Institute, School of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Kee Hwan Kwon
- Department of Otorhinolaryngology-Head and Neck Surgery, Ilsong Memorial Institute of Head and Neck Cancer, Hallym University College of Medicine, Seoul, Republic of Korea
| | - Joo-Ho Chung
- Department of Pharmacology and Kohwang Medical Research Institute, School of Medicine, Kyung Hee University, Seoul, Republic of Korea
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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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Neta G, Yu CL, Brenner A, Gu F, Hutchinson A, Pfeiffer R, Sturgis EM, Xu L, Linet MS, Alexander BH, Chanock S, Sigurdson AJ. Common genetic variants in the 8q24 region and risk of papillary thyroid cancer. Laryngoscope 2012; 122:1040-2. [PMID: 22275265 PMCID: PMC3408055 DOI: 10.1002/lary.23209] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 12/08/2011] [Accepted: 12/22/2011] [Indexed: 01/08/2023]
Abstract
OBJECTIVES/HYPOTHESIS Single nucleotide polymorphisms (SNPs) in the 8q24 chromosomal region identified from genome-wide scans have been associated with the risk of several cancers, including breast (rs1562430), prostate (rs1447295), and colon (rs6983267). A genome-wide scan in 26 families with papillary thyroid cancer (PTC) also found susceptibility loci in 8q24, supporting a closer evaluation of this chromosomal region in relation to the risk of sporadic PTC. STUDY DESIGN Case-control study. METHODS We evaluated 157 tag SNPs in the 8q24 chromosomal region between 120.91 Mb and 128.78 Mb (including rs1562430, rs1447295, and rs6983267) in a case-control study of 344 PTC cases and 452 age and gender frequency-matched controls. We used logistic regression to estimate odds ratios and compute P values of linear trend for PTC with genotypes of interest. To account for multiple comparisons, we applied the false discovery rate (FDR) method. RESULTS We did not find a significant association between rs1562430, rs1447295, or rs6983267 and PTC risk. We found that one SNP (rs4733616) was associated with PTC risk at P = .003, and 12 other SNPs were associated with PTC risk at P < .05. However, no SNPs remained significant after FDR correction. CONCLUSIONS Our findings do not support a strong association between SNPs in the 8q24 chromosomal region and risk of sporadic PTC, but several SNPs with small effects might exist.
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Affiliation(s)
- Gila Neta
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA.
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Schonfeld SJ, Neta G, Sturgis EM, Pfeiffer RM, Hutchinson AA, Xu L, Wheeler W, Guénel P, Rajaraman P, de Vathaire F, Ron E, Tucker MA, Chanock SJ, Sigurdson AJ, Brenner AV. Common genetic variants in sex hormone pathway genes and papillary thyroid cancer risk. Thyroid 2012; 22:151-6. [PMID: 22224819 PMCID: PMC3271376 DOI: 10.1089/thy.2011.0309] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
BACKGROUND Hormonal differences are hypothesized to contribute to the approximately ≥2-fold higher thyroid cancer incidence rates among women compared with men worldwide. Although thyroid cancer cells express estrogen receptors and estrogen has a proliferative effect on papillary thyroid cancer (PTC) cells in vitro, epidemiologic studies have not found clear associations between thyroid cancer and female hormonal factors. We hypothesized that polymorphic variation in hormone pathway genes is associated with the risk of developing papillary thyroid cancer. METHODS We evaluated the association between PTC and 1151 tag single nucleotide polymorphisms (SNPs) in 58 candidate gene regions involved in sex hormone synthesis and metabolism, gonadotropins, and prolactin in a case-control study of 344 PTC cases and 452 controls, frequency matched on age and sex. Odds ratios and p-values for the linear trend for the association between each SNP genotype and PTC risk were estimated using unconditional logistic regression. SNPs in the same gene region or pathway were aggregated using adaptive rank-truncated product methods to obtain gene region-specific or pathway-specific p-values. To account for multiple comparisons, we applied the false discovery rate method. RESULTS Seven SNPs had p-values for linear trend <0.01, including four in the CYP19A1 gene, but none of the SNPs remained significant after correction for multiple comparisons. Results were similar when restricting the dataset to women. p-values for examined gene regions and for all genes combined were ≥0.09. CONCLUSIONS Based on these results, SNPs in selected hormone pathway genes do not appear to be strongly related to PTC risk. This observation is in accord with the lack of consistent associations between hormonal factors and PTC risk in epidemiologic studies.
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Affiliation(s)
- Sara J Schonfeld
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892-7238, USA.
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