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Iñiguez-Muñoz S, Llinàs-Arias P, Ensenyat-Mendez M, Bedoya-López AF, Orozco JIJ, Cortés J, Roy A, Forsberg-Nilsson K, DiNome ML, Marzese DM. Hidden secrets of the cancer genome: unlocking the impact of non-coding mutations in gene regulatory elements. Cell Mol Life Sci 2024; 81:274. [PMID: 38902506 DOI: 10.1007/s00018-024-05314-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 12/07/2023] [Accepted: 06/06/2024] [Indexed: 06/22/2024]
Abstract
Discoveries in the field of genomics have revealed that non-coding genomic regions are not merely "junk DNA", but rather comprise critical elements involved in gene expression. These gene regulatory elements (GREs) include enhancers, insulators, silencers, and gene promoters. Notably, new evidence shows how mutations within these regions substantially influence gene expression programs, especially in the context of cancer. Advances in high-throughput sequencing technologies have accelerated the identification of somatic and germline single nucleotide mutations in non-coding genomic regions. This review provides an overview of somatic and germline non-coding single nucleotide alterations affecting transcription factor binding sites in GREs, specifically involved in cancer biology. It also summarizes the technologies available for exploring GREs and the challenges associated with studying and characterizing non-coding single nucleotide mutations. Understanding the role of GRE alterations in cancer is essential for improving diagnostic and prognostic capabilities in the precision medicine era, leading to enhanced patient-centered clinical outcomes.
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Affiliation(s)
- Sandra Iñiguez-Muñoz
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Pere Llinàs-Arias
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Miquel Ensenyat-Mendez
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Andrés F Bedoya-López
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Javier I J Orozco
- Saint John's Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Javier Cortés
- International Breast Cancer Center (IBCC), Pangaea Oncology, Quiron Group, 08017, Barcelona, Spain
- Medica Scientia Innovation Research SL (MEDSIR), 08018, Barcelona, Spain
- Faculty of Biomedical and Health Sciences, Department of Medicine, Universidad Europea de Madrid, 28670, Madrid, Spain
| | - Ananya Roy
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- University of Nottingham Biodiscovery Institute, Nottingham, UK
| | - Maggie L DiNome
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Diego M Marzese
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain.
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA.
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2
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Khan SU, Ullah Z, Shaukat H, Unab S, Jannat S, Ali W, Ali A, Irfan M, Khan MF, Cervantes-Villagrana RD. TP53 and its Regulatory Genes as Prognosis of Cutaneous Melanoma. Cancer Inform 2023; 22:11769351231177267. [PMID: 37667731 PMCID: PMC10475268 DOI: 10.1177/11769351231177267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 05/03/2023] [Indexed: 09/06/2023] Open
Abstract
The present study was the first comprehensive investigation of genetic mutation and expression levels of the p53 signaling genes in cutaneous melanoma through various genetic databases providing large datasets. The mutational landscape of p53 and its signaling genes was higher than expected, with TP53 followed by CDKN2A being the most mutated gene in cutaneous melanoma. Furthermore, the expression analysis showed that TP53, MDM2, CDKN2A, and TP53BP1 were overexpressed, while MDM4 and CDKN2B were under-expressed in cutaneous melanoma. Overall, TCGA data revealed that among all the other p53 signaling proteins, CDKN2A was significantly higher in both sun and non-sun-exposed healthy tissues than in melanoma. Likewise, MDM4 and TP53BP1 expressions were markedly greater in non-sun-exposed healthy tissues compared to other groups. However, CDKN2B expression was higher in the sun-exposed healthy tissues than in other tissues. In addition, various genes were expressed significantly differently among males and females. In addition, CDKN2A was highly expressed in the SK-MEL-30 skin cancer cell line, whereas, Immune cell type expression analysis revealed that the MDM4 was highly expressed in naïve B-cells. Furthermore, all six genes were significantly overexpressed in extraordinarily overweight or obese tumor tissues compared to healthy tissues. MDM2 expression and tumor stage were closely related. There were differences in gene expression across patient age groups and positive nodal status. TP53 showed a positive correlation with B cells, MDM2 with CD8+T cells, macrophages and neutrophils, and MDM4 with neutrophils. CDKN2A/B had a non-significant correlation with all six types of immune cells. However, TP53BP1 was positively correlated with all five types of immune cells except B cells. Only TP53, MDM2, and CDKN2A had a role in cutaneous melanoma-specific tumor immunity. All TP53 and its regulating genes may be predictive for prognosis. The results of the present study need to be validated through future screening, in vivo, and in vitro studies.
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Affiliation(s)
- Safir Ullah Khan
- Department of Cell Biology, Center for Research and Advanced Studies, National Polytechnic Institute, Mexico City, Mexico
| | - Zahid Ullah
- Department of Software Engineering, Abasyn University Peshawar, Peshawar, Pakistan
| | - Hadia Shaukat
- Department of Zoology, Women University of Swabi, Swabi, Khyber Pakhtunkhwa, Pakistan
| | - Sheeza Unab
- Department of Zoology, University of Mianwali, Mianwali, Pakistan
| | - Saba Jannat
- Department of Zoology, Women University of Swabi, Swabi, Khyber Pakhtunkhwa, Pakistan
| | - Waqar Ali
- Biochemical and Biotechnological Sciences Università degli studi della Campania Luigi Vanvitelli, Caserta, Campania, Italy
| | - Amir Ali
- Nanosciences and Nanotechnology Program, Center for Research and Advanced Studies, National Polytechnic Institute, Mexico City, Mexico
| | - Muhammad Irfan
- Department of Zoology, Wildlife and Fisheries, Pir Mehr Ali Shah Arid Agriculture University Rawalpindi, Punjab, Pakistan
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Rojano E, Seoane P, Ranea JAG, Perkins JR. Regulatory variants: from detection to predicting impact. Brief Bioinform 2019; 20:1639-1654. [PMID: 29893792 PMCID: PMC6917219 DOI: 10.1093/bib/bby039] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/18/2018] [Indexed: 02/01/2023] Open
Abstract
Variants within non-coding genomic regions can greatly affect disease. In recent years, increasing focus has been given to these variants, and how they can alter regulatory elements, such as enhancers, transcription factor binding sites and DNA methylation regions. Such variants can be considered regulatory variants. Concurrently, much effort has been put into establishing international consortia to undertake large projects aimed at discovering regulatory elements in different tissues, cell lines and organisms, and probing the effects of genetic variants on regulation by measuring gene expression. Here, we describe methods and techniques for discovering disease-associated non-coding variants using sequencing technologies. We then explain the computational procedures that can be used for annotating these variants using the information from the aforementioned projects, and prediction of their putative effects, including potential pathogenicity, based on rule-based and machine learning approaches. We provide the details of techniques to validate these predictions, by mapping chromatin-chromatin and chromatin-protein interactions, and introduce Clustered Regularly Interspaced Short Palindromic Repeats-Associated Protein 9 (CRISPR-Cas9) technology, which has already been used in this field and is likely to have a big impact on its future evolution. We also give examples of regulatory variants associated with multiple complex diseases. This review is aimed at bioinformaticians interested in the characterization of regulatory variants, molecular biologists and geneticists interested in understanding more about the nature and potential role of such variants from a functional point of views, and clinicians who may wish to learn about variants in non-coding genomic regions associated with a given disease and find out what to do next to uncover how they impact on the underlying mechanisms.
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Affiliation(s)
- Elena Rojano
- Department of Molecular Biology and Biochemistry, University of Malaga (UMA), 29010 Malaga, Spain
| | - Pedro Seoane
- Department of Molecular Biology and Biochemistry, University of Malaga (UMA), 29010 Malaga, Spain
| | - Juan A G Ranea
- CIBER de Enfermedades Raras, ISCIII, Madrid, Spain and Department of Molecular Biology and Biochemistry, University of Malaga (UMA), 29010 Malaga, Spain
| | - James R Perkins
- Research laboratory, IBIMA-Regional University Hospital of Malaga, UMA, Malaga 29009, Spain
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4
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Chang YC, Fong Y, Tsai EM, Chang YG, Chou HL, Wu CY, Teng YN, Liu TC, Yuan SS, Chiu CC. Exogenous C₈-Ceramide Induces Apoptosis by Overproduction of ROS and the Switch of Superoxide Dismutases SOD1 to SOD2 in Human Lung Cancer Cells. Int J Mol Sci 2018; 19:ijms19103010. [PMID: 30279365 PMCID: PMC6213533 DOI: 10.3390/ijms19103010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/25/2018] [Accepted: 09/27/2018] [Indexed: 02/07/2023] Open
Abstract
Ceramides, abundant sphingolipids on the cell membrane, can act as signaling molecules to regulate cellular functions including cell viability. Exogenous ceramide has been shown to exert potent anti-proliferative effects against cancer cells, but little is known about how it affects reactive oxygen species (ROS) in lung cancer cells. In this study, we investigated the effect of N-octanoyl-D-erythro-sphingosine (C₈-ceramide) on human non-small-cell lung cancer H1299 cells. Flow cytometry-based assays indicated that C₈-ceramide increased the level of endogenous ROS in H1299 cells. Interestingly, the ratio of superoxide dismutases (SODs) SOD1 and SOD2 seem to be regulated by C₈-ceramide treatment. Furthermore, the accumulation of cell cycle G1 phase and apoptotic populations in C₈-ceramide-treated H1299 cells was observed. The results of the Western blot showed that C₈-ceramide causes a dramatically increased protein level of cyclin D1, a critical regulator of cell cycle G1/S transition. These results suggest that C₈-ceramide acts as a potent chemotherapeutic agent and may increase the endogenous ROS level by regulating the switch of SOD1 and SOD2, causing the anti-proliferation, and consequently triggering the apoptosis of NSCLC H1299 cells. Accordingly, our works may give a promising strategy for lung cancer treatment in the future.
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Affiliation(s)
- Yuli C Chang
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
| | - Yao Fong
- Chest Surgery, Chi-Mei Medical Center, Yung Kang City, Tainan 901, Taiwan.
| | - Eing-Mei Tsai
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
- Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan.
| | - Ya-Gin Chang
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
| | - Han Lin Chou
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
| | - Chang-Yi Wu
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung 804, Taiwan;.
| | - Yen-Ni Teng
- Department of Biological Sciences and Technology, National University of Tainan, Tainan 700, Taiwan.
| | - Ta-Chih Liu
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
- Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan.
| | - Shyng-Shiou Yuan
- Translational Research Center, Cancer Center, Department of Medical Research, Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
| | - Chien-Chih Chiu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung 804, Taiwan;.
- Translational Research Center, Cancer Center, Department of Medical Research, Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
- Research Center for Environment Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
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5
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Deng N, Zhou H, Fan H, Yuan Y. Single nucleotide polymorphisms and cancer susceptibility. Oncotarget 2017; 8:110635-110649. [PMID: 29299175 PMCID: PMC5746410 DOI: 10.18632/oncotarget.22372] [Citation(s) in RCA: 190] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/03/2017] [Indexed: 12/12/2022] Open
Abstract
A large number of genes associated with various cancer types contain single nucleotide polymorphisms (SNPs). SNPs are located in gene promoters, exons, introns as well as 5'- and 3'- untranslated regions (UTRs) and affect gene expression by different mechanisms. These mechanisms depend on the role of the genetic elements in which the individual SNPs are located. Moreover, alterations in epigenetic regulation due to gene polymorphisms add to the complexity underlying cancer susceptibility related to SNPs. In this systematic review, we discuss the various genetic and epigenetic mechanisms involved in determining cancer susceptibility related to various SNPs located in different genetic elements. We also discuss the diagnostic potential of these SNPs and the focus for future studies.
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Affiliation(s)
- Na Deng
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China.,Department of Hematology, The Fourth Affiliated Hospital of China Medical University, Shenyang 110001, China
| | - Heng Zhou
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China
| | - Hua Fan
- Department of Hematology, The Fourth Affiliated Hospital of China Medical University, Shenyang 110001, China
| | - Yuan Yuan
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China.,National Clinical Research Center for Digestive Diseases, Xi'an 110001, China
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6
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Wang L, Zhang P, Molkentine DP, Chen C, Molkentine JM, Piao H, Raju U, Zhang J, Valdecanas DR, Tailor RC, Thames HD, Buchholz TA, Chen J, Ma L, Mason KA, Ang KK, Meyn RE, Skinner HD. TRIP12 as a mediator of human papillomavirus/p16-related radiation enhancement effects. Oncogene 2016; 36:820-828. [PMID: 27425591 DOI: 10.1038/onc.2016.250] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 05/16/2016] [Accepted: 06/03/2016] [Indexed: 12/21/2022]
Abstract
Patients with human papillomavirus (HPV)-positive head and neck squamous cell carcinoma (HNSCC) have better responses to radiotherapy and higher overall survival rates than do patients with HPV-negative HNSCC, but the mechanisms underlying this phenomenon are unknown. p16 is used as a surrogate marker for HPV infection. Our goal was to examine the role of p16 in HPV-related favorable treatment outcomes and to investigate the mechanisms by which p16 may regulate radiosensitivity. HNSCC cells and xenografts (HPV/p16-positive and -negative) were used. p16-overexpressing and small hairpin RNA-knockdown cells were generated, and the effect of p16 on radiosensitivity was determined by clonogenic cell survival and tumor growth delay assays. DNA double-strand breaks (DSBs) were assessed by immunofluorescence analysis of 53BP1 foci; DSB levels were determined by neutral comet assay; western blotting was used to evaluate protein changes; changes in protein half-life were tested with a cycloheximide assay; gene expression was examined by real-time polymerase chain reaction; and data from The Cancer Genome Atlas HNSCC project were analyzed. p16 overexpression led to downregulation of TRIP12, which in turn led to increased RNF168 levels, repressed DNA damage repair (DDR), increased 53BP1 foci and enhanced radioresponsiveness. Inhibition of TRIP12 expression further led to radiosensitization, and overexpression of TRIP12 was associated with poor survival in patients with HPV-positive HNSCC. These findings reveal that p16 participates in radiosensitization through influencing DDR and support the rationale of blocking TRIP12 to improve radiotherapy outcomes.
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Affiliation(s)
- L Wang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - P Zhang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - D P Molkentine
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - C Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - J M Molkentine
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - H Piao
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - U Raju
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - J Zhang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - D R Valdecanas
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - R C Tailor
- Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - H D Thames
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - T A Buchholz
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - J Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - L Ma
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - K A Mason
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - K-K Ang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - R E Meyn
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - H D Skinner
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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7
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Bandaru S, Ponnala D, Lakkaraju C, Bhukya CK, Shaheen U, Nayarisseri A. Identification of High Affinity Non-Peptidic Small Molecule Inhibitors of MDM2-p53 Interactions through Structure-Based Virtual Screening Strategies. Asian Pac J Cancer Prev 2015; 16:3759-65. [DOI: 10.7314/apjcp.2015.16.9.3759] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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