1
|
Gupta I, Badrzadeh F, Tsentalovich Y, Gaykalova DA. Connecting the dots: investigating the link between environmental, genetic, and epigenetic influences in metabolomic alterations in oral squamous cell carcinoma. J Exp Clin Cancer Res 2024; 43:239. [PMID: 39169426 PMCID: PMC11337877 DOI: 10.1186/s13046-024-03141-5] [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: 05/20/2024] [Accepted: 07/28/2024] [Indexed: 08/23/2024] Open
Abstract
Oral squamous cell carcinoma (OSCC) accounts for around 90% of all oral cancers and is the eighth most common cancer worldwide. Despite progress in managing OSCC, the overall prognosis remains poor, with a survival rate of around 50-60%, largely due to tumor size and recurrence. The challenges of late-stage diagnosis and limitations in current methods emphasize the urgent need for less invasive techniques to enable early detection and treatment, crucial for improving outcomes in this aggressive form of oral cancer. Research is currently aimed at unraveling tumor-specific metabolite profiles to identify candidate biomarkers as well as discover underlying pathways involved in the onset and progression of cancer that could be used as new targets for diagnostic and therapeutic purposes. Metabolomics is an advanced technological approach to identify metabolites in different sample types (biological fluids and tissues). Since OSCC promotes metabolic reprogramming influenced by a combination of genetic predisposition and environmental factors, including tobacco and alcohol consumption, and viral infections, the identification of distinct metabolites through screening may aid in the diagnosis of this condition. Moreover, studies have shown the use of metabolites during the catalysis of epigenetic modification, indicating a link between epigenetics and metabolism. In this review, we will focus on the link between environmental, genetic, and epigenetic influences in metabolomic alterations in OSCC. In addition, we will discuss therapeutic targets of tumor metabolism, which may prevent oral tumor growth, metastasis, and drug resistance.
Collapse
Affiliation(s)
- Ishita Gupta
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Otorhinolaryngology-Head and Neck Surgery, Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical Center, Baltimore, MD, USA
| | - Fariba Badrzadeh
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Otorhinolaryngology-Head and Neck Surgery, Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical Center, Baltimore, MD, USA
| | - Yuri Tsentalovich
- International tomography center CB RAS, Institutskaya str. 3a, Novosibirsk, 630090, Russia
| | - Daria A Gaykalova
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
- Department of Otorhinolaryngology-Head and Neck Surgery, Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical Center, Baltimore, MD, USA.
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.
- Institute for Genome Sciences, 670 West Baltimore Street, Baltimore, MD, 21201, USA.
| |
Collapse
|
2
|
Wang K, Zhu W, Huang W, Huang K, Luo H, Long L, Yi B. TRIM Expression in HNSCC: Exploring the Link Between Ubiquitination, Immune Infiltration, and Signaling Pathways Through Bioinformatics. Int J Gen Med 2024; 17:2389-2405. [PMID: 38808201 PMCID: PMC11132118 DOI: 10.2147/ijgm.s463286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 05/13/2024] [Indexed: 05/30/2024] Open
Abstract
Objective Ubiquitination is an important post-translational modification. However, the significance of the TRIM family of E3 ubiquitin ligases in head and neck squamous cell carcinoma (HNSCC) has not been determined. In this study, the roles of TRIM E3 ubiquitin ligases in lymphovascular invasion in head and neck squamous cell carcinoma (HNSCC) were evaluated. Materials and Methods TRIM expression and related parameters were obtained from UbiBrowser2.0, UALCAN, TIMER, TISIDB, LinkedOmics, STRING, and GeneMANIA databases. Immunohistochemistry was used to confirm their expression. Results TRIM2, TRIM11, TRIM28, and TRIM56 were upregulated in HNSCC with lymphovascular invasion. TRIM expression was strongly associated with immune infiltration, including key treatment targets, like PD-1 and CTL4. Co-expressed genes and possible ubiquitination substrates included tumor-related factors. The TRIMs had predicted roles in ubiquitination-related pathways and vital signaling pathways, eg, MAPK, PI3K-Akt, and JAK-STAT signaling pathways. Conclusion Ubiquitination mediated by four TRIMs might be involved in the regulation of tumor immunity, laying the foundation for future studies of the roles of the TRIM family on the prediction and personalized medicine in HNSCC. The four TRIMs might exert oncogenic effects by promoting lymphovascular invasion in HNSCC.
Collapse
Affiliation(s)
- Kun Wang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
| | - Wei Zhu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
| | - Wei Huang
- Research Center of Carcinogenesis and Targeted Therapy, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
| | - Kangkang Huang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
| | - Huidan Luo
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
| | - Lu Long
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
| | - Bin Yi
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People’s Republic of China
| |
Collapse
|
3
|
Gil-Martín E, Ramos E, López-Muñoz F, Egea J, Romero A. Potential of melatonin to reverse epigenetic aberrations in oral cancer: new findings. EXCLI JOURNAL 2023; 22:1280-1310. [PMID: 38234969 PMCID: PMC10792176 DOI: 10.17179/excli2023-6624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/22/2023] [Indexed: 01/19/2024]
Abstract
It is now an accepted principle that epigenetic alterations cause cellular dyshomeostasis and functional changes, both of which are essential for the initiation and completion of the tumor cycle. Oral carcinogenesis is no exception in this regard, as most of the tumors in the different subsites of the oral cavity arise from the cross-reaction between (epi)genetic inheritance and the huge challenge of environmental stressors. Currently, the biochemical machinery is put at the service of the tumor program, halting the cell cycle, triggering uncontrolled proliferation, driving angiogenesis and resistance to apoptosis, until the archetypes of the tumor phenotype are reached. Melatonin has the ability to dynamically affect the epigenetic code. It has become accepted that melatonin can reverse (epi)genetic aberrations present in oral and other cancers, suggesting the possibility of enhancing the oncostatic capacity of standard multimodal treatments by incorporating this indolamine as an adjuvant. First steps in this direction confirm the potential of melatonin as a countermeasure to mitigate the detrimental side effects of conventional first-line radiochemotherapy. This single effect could produce synergies of extraordinary clinical importance, allowing doses to be increased and treatments not to be interrupted, ultimately improving patients' quality of life and prognosis. Motivated by the urgency of improving the medical management of oral cancer, many authors advocate moving from in vitro and preclinical research, where the bulk of melatonin cancer research is concentrated, to systematic randomized clinical trials on large cohorts. Recognizing the challenge to improve the clinical management of cancer, our motivation is to encourage comprehensive and robust research to reveal the clinical potential of melatonin in oral cancer control. To improve the outcome and quality of life of patients with oral cancer, here we provide the latest evidence of the oncolytic activity that melatonin can achieve by manipulating epigenetic patterns in oronasopharyngeal tissue.
Collapse
Affiliation(s)
- Emilio Gil-Martín
- Department of Biochemistry, Genetics and Immunology, Faculty of Biology, University of Vigo, 36310 Vigo, Spain
| | - Eva Ramos
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain
| | - Francisco López-Muñoz
- Faculty of Health, Camilo José Cela University of Madrid (UCJC), 28692 Madrid, Spain
- Neuropsychopharmacology Unit, Hospital 12 de Octubre Research Institute, 28041 Madrid, Spain
| | - Javier Egea
- Unidad de Investigación, Hospital Santa Cristina, Instituto de Investigación Sanitaria Princesa (IIS-IP), 28006 Madrid, Spain
| | - Alejandro Romero
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain
| |
Collapse
|
4
|
Lai TY, Ko YC, Chen YL, Lin SF. The Way to Malignant Transformation: Can Epigenetic Alterations Be Used to Diagnose Early-Stage Head and Neck Cancer? Biomedicines 2023; 11:1717. [PMID: 37371812 DOI: 10.3390/biomedicines11061717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/05/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Identifying and treating tumors early is the key to secondary prevention in cancer control. At present, prevention of oral cancer is still challenging because the molecular drivers responsible for malignant transformation of the 11 clinically defined oral potentially malignant disorders are still unknown. In this review, we focused on studies that elucidate the epigenetic alterations demarcating malignant and nonmalignant epigenomes and prioritized findings from clinical samples. Head and neck included, the genomes of many cancer types are largely hypomethylated and accompanied by focal hypermethylation on certain specific regions. We revisited prior studies that demonstrated that sufficient uptake of folate, the primary dietary methyl donor, is associated with oral cancer reduction. As epigenetically driven phenotypic plasticity, a newly recognized hallmark of cancer, has been linked to tumor initiation, cell fate determination, and drug resistance, we discussed prior findings that might be associated with this hallmark, including gene clusters (11q13.3, 19q13.43, 20q11.2, 22q11-13) with great potential for oral cancer biomarkers, and successful examples in screening early-stage nasopharyngeal carcinoma. Although one-size-fits-all approaches have been shown to be ineffective in most cancer therapies, the rapid development of epigenome sequencing methods raises the possibility that this nonmutagenic approach may be an exception. Only time will tell.
Collapse
Affiliation(s)
- Ting-Yu Lai
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Ying-Chieh Ko
- National Institute of Cancer Research, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Yu-Lian Chen
- National Institute of Cancer Research, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Su-Fang Lin
- National Institute of Cancer Research, National Health Research Institutes, Miaoli 35053, Taiwan
| |
Collapse
|
5
|
Patini R, Cordaro M, Marchesini D, Scilla F, Gioco G, Rupe C, D'Agostino MA, Lajolo C. Is Systemic Immunosuppression a Risk Factor for Oral Cancer? A Systematic Review and Meta-Analysis. Cancers (Basel) 2023; 15:3077. [PMID: 37370688 DOI: 10.3390/cancers15123077] [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: 04/30/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
Even if the relationship between immunosuppression and increased incidence of systemic cancers is well known, there is less awareness about the risk of developing oral cancer in immunosuppressed patients. The aim of this review was to evaluate the association between immunosuppression and the development of oral cancer. Two authors independently and, in duplicate, conducted a systematic literature review of international journals and electronic databases (MEDLINE via OVID, Scopus, and Web of Science) from their inception to 28 April 2023. The assessment of risk of bias and overall quality of evidence was performed using the Newcastle-Ottawa Scale and GRADE system. A total of 2843 articles was identified, of which 44 met the inclusion criteria and were included in either the qualitative or quantitative analysis. The methodological quality of the included studies was generally high or moderate. The quantitative analysis of the studies revealed that immunosuppression should be considered a risk factor for the development of oral cancer, with a percentage of increased risk ranging from 0.2% to 1% (95% CI: 0.2% to 1.4%). In conclusion, the results suggest that a constant and accurate follow-up should be reserved for all immunosuppressed patients as a crucial strategy to intercept lesions that have an increased potential to evolve into oral cancer.
Collapse
Affiliation(s)
- Romeo Patini
- Department of Head, Neck and Sense Organs, School of Dentistry, Catholic University of Sacred Heart, Fondazione Policlinico Universitario "A. Gemelli"-IRCCS Rome, 00135 Rome, Italy
| | - Massimo Cordaro
- Department of Head, Neck and Sense Organs, School of Dentistry, Catholic University of Sacred Heart, Fondazione Policlinico Universitario "A. Gemelli"-IRCCS Rome, 00135 Rome, Italy
| | - Denise Marchesini
- Department of Head, Neck and Sense Organs, School of Dentistry, Catholic University of Sacred Heart, Fondazione Policlinico Universitario "A. Gemelli"-IRCCS Rome, 00135 Rome, Italy
| | - Francesco Scilla
- Department of Head, Neck and Sense Organs, School of Dentistry, Catholic University of Sacred Heart, Fondazione Policlinico Universitario "A. Gemelli"-IRCCS Rome, 00135 Rome, Italy
| | - Gioele Gioco
- Department of Head, Neck and Sense Organs, School of Dentistry, Catholic University of Sacred Heart, Fondazione Policlinico Universitario "A. Gemelli"-IRCCS Rome, 00135 Rome, Italy
| | - Cosimo Rupe
- Department of Head, Neck and Sense Organs, School of Dentistry, Catholic University of Sacred Heart, Fondazione Policlinico Universitario "A. Gemelli"-IRCCS Rome, 00135 Rome, Italy
| | - Maria Antonietta D'Agostino
- Department of Geriatric and Orthopedic Sciences, Catholic University of Sacred Heart, Fondazione Policlinico Universitario "A. Gemelli"-IRCCS Rome, 00135 Rome, Italy
| | - Carlo Lajolo
- Department of Head, Neck and Sense Organs, School of Dentistry, Catholic University of Sacred Heart, Fondazione Policlinico Universitario "A. Gemelli"-IRCCS Rome, 00135 Rome, Italy
| |
Collapse
|
6
|
Vatsa PP, Jindal Y, Bhadwalkar J, Chamoli A, Upadhyay V, Mandoli A. Role of epigenetics in OSCC: an understanding above genetics. Med Oncol 2023; 40:122. [PMID: 36941511 DOI: 10.1007/s12032-023-01992-0] [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: 02/12/2023] [Accepted: 03/08/2023] [Indexed: 03/22/2023]
Abstract
Oral cavity cancer is categorized under head and neck cancer that frequently develops from squamous cells hence also known as oral squamous cell carcinoma (OSCC). Although molecular markers for oral cavity cancer are already known, epigenetic signatures for the same haven't been explored much. Epigenetic and genetic alterations were initially thought to be discrete mechanisms driving the tumour but the whole exome sequencing of various cancers has revealed the interdependency of epigenetics and genetic alterations. The reversible nature of these epigenetic changes makes them an alluring target for cancer therapeutics. The primary epigenetic alterations in cancer include DNA methylation and histone modifications. These alterations are useful for patient early detection and prognostication. This review summarizes the epigenetic perspective to understand the etiology, epigenetic biomarkers, and epi-drugs for better predictive diagnosis and treatment of OSCC.
Collapse
Affiliation(s)
- Priyanka P Vatsa
- Department of Biotechnology, NIPER-Ahmedabad, Opposite Air Force Station, Palaj, Gandhinagar, Gujarat, 382355, India
| | - Yogita Jindal
- Department of Biotechnology, NIPER-Ahmedabad, Opposite Air Force Station, Palaj, Gandhinagar, Gujarat, 382355, India
| | - Janhavi Bhadwalkar
- Department of Biotechnology, NIPER-Ahmedabad, Opposite Air Force Station, Palaj, Gandhinagar, Gujarat, 382355, India
| | - Ambika Chamoli
- Department of Biotechnology, NIPER-Ahmedabad, Opposite Air Force Station, Palaj, Gandhinagar, Gujarat, 382355, India
| | - Vinal Upadhyay
- Department of Biotechnology, NIPER-Ahmedabad, Opposite Air Force Station, Palaj, Gandhinagar, Gujarat, 382355, India
| | - Amit Mandoli
- Department of Biotechnology, NIPER-Ahmedabad, Opposite Air Force Station, Palaj, Gandhinagar, Gujarat, 382355, India.
| |
Collapse
|
7
|
Laskar SG, Chaukar D, Deshpande M, Chatterjee A, Sinha S, Chakraborty S, Agarwal JP, Gupta T, Budrukkar A, Murthy V, Pai P, Chaturvedi P, Pantvaidya G, Deshmukh A, Nair D, Nair S, Prabhash K, Swain M, Kumar A, Noronha V, Patil V, Joshi A, DCruz A. Oral cavity adjuvant therapy (OCAT) -a phase III, randomized controlled trial of surgery followed by conventional RT (5 fr/wk) versus concurrent CT-RT versus accelerated RT (6fr/wk) in locally advanced, resectable, squamous cell carcinoma of oral cavity. Eur J Cancer 2023; 181:179-187. [PMID: 36669426 DOI: 10.1016/j.ejca.2022.12.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/14/2022] [Accepted: 12/17/2022] [Indexed: 12/28/2022]
Abstract
BACKGROUND Limited data exists regarding the impact of intensification of adjuvant therapy in resected Oral Cavity Squamous Cell Carcinomas (OCSCC) with adverse prognostic features on histopathology. PATIENTS AND METHODS This was a three-arm phase III, randomised trial including patients with resected advanced OCSCC. Randomisation was done in a 1:1:1 ratio: Arm-A- standard adjuvant radiation therapy (RT) 60Gy/30 fractions over 6 weeks versus Arm-B-concurrent chemoradiation versus Arm-C-accelerated radiation therapy (6 d a week). The trial was powered to detect an absolute difference of 10% in 5-year Locoregional Control (LRC). RESULTS The trial was conducted between June 2005 and March 2013. Majority of the patients were males, had T3-T4 disease, had N2-N3 nodal status and had Extra-Capsular Extension (ECE) in nodes. The median follow-up was 95.9 months. There was no difference between the three arms (A versus B versus C) for 10-year locoregional control (LRC): 60.2% versus 61.4% versus 65.7%, p = 0.57; disease free survival (DFS): 37.4% versus 43.9% versus 39.6%, p = 0.40; or Overall Survival (OS): 39.7% versus 46.6% versus 40.4%, p = 0.40. There was no benefit of intensification with either modality in patients with any single adverse pathological factor. A benefit of intensification could be seen in patients with a combination of high-risk features: T3-T4 primary tumours with N2-N3 nodes along with ECE for DFS (Arm B versus Arm A HR) = 0.53, Arm C versus Arm A HR = 0.63) and OS (Arm B versus Arm A HR = 0.58, Arm C versus Arm A HR = 0.60). CONCLUSIONS All optimally resected OCSCC with adverse features did not benefit from intensification of adjuvant therapy. Only a cohort of patients with a combination of high-risk features are likely candidates for intensification. CLINICAL TRIAL REGISTRATION NCT00193843.
Collapse
Affiliation(s)
- Sarbani G Laskar
- Department of Radiation Oncology, Tata Memorial Centre, Homi Bhabha National Institute (HBNI), Mumbai, India.
| | - Devendra Chaukar
- Department of Head and Neck Surgery, Tata Memorial Centre, Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Mandar Deshpande
- Department of Surgical Oncology, Kokilaben Dhirubai Ambani Hospital, Mumbai, India
| | - Abhishek Chatterjee
- Department of Radiation Oncology, Tata Memorial Centre, Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Shwetabh Sinha
- Department of Radiation Oncology, Tata Memorial Centre, Homi Bhabha National Institute (HBNI), Mumbai, India
| | | | - Jai P Agarwal
- Department of Radiation Oncology, Tata Memorial Centre, Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Tejpal Gupta
- Department of Radiation Oncology, Tata Memorial Centre, Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Ashwini Budrukkar
- Department of Radiation Oncology, Tata Memorial Centre, Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Vedang Murthy
- Department of Radiation Oncology, Tata Memorial Centre, Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Prathamesh Pai
- Department of Head and Neck Surgery, Tata Memorial Centre, Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Pankaj Chaturvedi
- Department of Head and Neck Surgery, Tata Memorial Centre, Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Gouri Pantvaidya
- Department of Head and Neck Surgery, Tata Memorial Centre, Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Anuja Deshmukh
- Department of Head and Neck Surgery, Tata Memorial Centre, Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Deepa Nair
- Department of Head and Neck Surgery, Tata Memorial Centre, Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Sudhir Nair
- Department of Head and Neck Surgery, Tata Memorial Centre, Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Kumar Prabhash
- Department of Medical Oncology, Tata Memorial Centre, Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Monali Swain
- Department of Radiation Oncology, Tata Memorial Centre, Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Anuj Kumar
- Department of Radiation Oncology, Tata Memorial Centre, Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Vanita Noronha
- Department of Medical Oncology, Tata Memorial Centre, Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Vijay Patil
- Department of Medical Oncology, Tata Memorial Centre, Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Amit Joshi
- Department of Medical Oncology, Tata Memorial Centre, Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Anil DCruz
- Director Oncology Services and Head Neck Cancer Surgeon, Apollo Hospitals, Mumbai, India
| |
Collapse
|
8
|
Liu X, Chen J, Li J, Zeng Z, Jiang X, Gao Y, Huang Z, Wu Q, Gong Y, Xie C. Integrated analysis reveals common DNA methylation patterns of alcohol-associated cancers: A pan-cancer analysis. Front Genet 2023; 14:1032683. [PMID: 36861126 PMCID: PMC9968750 DOI: 10.3389/fgene.2023.1032683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 01/24/2023] [Indexed: 02/16/2023] Open
Abstract
Background: The role of alcohol in carcinogenesis has received increasing attention in recent years. Evidence shows its impacts on various aspects, including epigenetics alteration. The DNA methylation patterns underlying alcohol-associated cancers are not fully understood. Methods: We investigated the aberrant DNA methylation patterns in four alcohol-associated cancers based on the Illumina HumanMethylation450 BeadChip. Pearson coefficient correlations were identified between differential methylated CpG probes and annotated genes. Transcriptional factor motifs were enriched and clustered using MEME Suite, and a regulatory network was constructed. Results: In each cancer, differential methylated probes (DMPs) were identified, and 172 hypermethylated and 21 hypomethylated pan-cancer DMPs (PDMPs) were examined further. Annotated genes significantly regulated by PDMPs were investigated and enriched in transcriptional misregulation in cancers. The CpG island chr19:58220189-58220517 was hypermethylated in all four cancers and silenced in the transcription factor ZNF154. Various biological effects were exerted by 33 hypermethylated and seven hypomethylated transcriptional factor motifs grouped into five clusters. Eleven pan-cancer DMPs were identified to be associated with clinical outcomes in the four alcohol-associated cancers, which might provide a potential point of view for clinical outcome prediction. Conclusion: This study provides an integrated insight into DNA methylation patterns in alcohol-associated cancers and reveals the corresponding features, influences, and potential mechanisms.
Collapse
Affiliation(s)
- Xingyu Liu
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jiarui Chen
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jiali Li
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zihang Zeng
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xueping Jiang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yanping Gao
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhengrong Huang
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China,Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Qiuji Wu
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China,Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yan Gong
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China,Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China,*Correspondence: Yan Gong, ; Conghua Xie,
| | - Conghua Xie
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China,Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China,*Correspondence: Yan Gong, ; Conghua Xie,
| |
Collapse
|
9
|
Xu QS, Shen ZZ, Yuan LQ. Identification and validation of a novel cuproptosis-related lncRNA signature for prognosis and immunotherapy of head and neck squamous cell carcinoma. Front Cell Dev Biol 2022; 10:968590. [DOI: 10.3389/fcell.2022.968590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/28/2022] [Indexed: 11/18/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a highly prevalent and heterogeneous malignancy with a dismal overall survival rate. Nevertheless, the effective biomarkers remain ambiguous and merit further investigation. Cuproptosis is a novel defined pathway of programmed cell death that contributes to the progression of cancers. Meanwhile, long non-coding RNAs (lncRNAs) play a crucial role in the biological process of tumors. Nevertheless, the prognostic value of cuproptosis-related lncRNAs in HNSCC is still obscure. This study aimed to develop a new cuproptosis-related lncRNAs (CRLs) signature to estimate survival and tumor immunity in patients with HNSCC. Herein, 620 cuproptosis-related lncRNAs were identified from The Cancer Genome Atlas database through the co-expression method. To construct a risk model and validate the accuracy of the results, the samples were divided into two cohorts randomly and equally. Subsequently, a prognostic model based on five CRLs was constructed by the Cox regression analysis with the least absolute shrinkage and selection operator (LASSO) algorithm. In addition, the prognostic potential of the five-CRL signature was verified via Cox regression, survival analysis, the receiver operating characteristic (ROC) curve, nomogram, and clinicopathologic characteristics correlation analysis. Furthermore, we explored the associations between the signature risk score (RS) and immune landscape, somatic gene mutation, and drug sensitivity. Finally, we gathered six clinical samples and different HNSCC cell lines to validate our bioinformatics results. Overall, the proposed novel five-CRL signature can predict prognosis and assess the efficacy of immunotherapy and targeted therapies to prolong the survival of patients with HNSCC.
Collapse
|
10
|
Antra, Parashar P, Hungyo H, Jain A, Ahmad S, Tandon V. Unraveling molecular mechanisms of Head and neck cancer. Crit Rev Oncol Hematol 2022; 178:103778. [PMID: 35932993 DOI: 10.1016/j.critrevonc.2022.103778] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 03/02/2022] [Accepted: 08/01/2022] [Indexed: 12/24/2022] Open
Abstract
Malignancies that develop from mucosal epithelium of the upper aerodigestive tract are known as head and neck squamous cell carcinomas (HNSCC). Heterogeneity, late stage diagnosis and high recurrence rate are big hurdles in head and neck treatment regimen. Presently, the biomarkers available for diagnosis and prognosis of HNSCC are based on smoking as the major risk habit. This review shed light on the differential environment of HNSCC in smokeless tobacco consuming Indian patients. Frequent mutation in genes involved in DNA repair pathway (p53), cell proliferation (PIK3CA, HRAS) and cell death (CASP8, FADD) are common in western population. On the contrary, the genes involved in metastasis (MMPs, YAP1), lymphocyte proliferation (TNFRSF4, CD80), cell-cell adhesion (DCC, EDNRB), miRNA processing (DROSHA) and inflammatory responses (TLR9, IL-9) are mutated in Indian HNSCC patients. Gene ontology enrichment analysis highlighted that responses to chemical stimulus, immune pathways and stress pathways are highly enriched in Indian patients.
Collapse
Affiliation(s)
- Antra
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067
| | - Palak Parashar
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067
| | - Hungharla Hungyo
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067
| | - Anuja Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067
| | - Shandar Ahmad
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067
| | - Vibha Tandon
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067.
| |
Collapse
|
11
|
Prognostic and therapeutic prediction by screening signature combinations from transcriptome-methylome interactions in oral squamous cell carcinoma. Sci Rep 2022; 12:11400. [PMID: 35794182 PMCID: PMC9259703 DOI: 10.1038/s41598-022-15534-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/24/2022] [Indexed: 02/05/2023] Open
Abstract
DNA methylation pattern in oral squamous cell carcinoma (OSCC) remains poorly described. This study aimed to perform a genome-wide integrated analysis of the transcriptome and methylome and assess the efficacy of their prognostic signature model in patients with OSCC. We analyzed transcriptome and methylome data from 391 OSCC samples and 41 adjacent normal samples. A total of 8074 differentially expressed genes (DEGs) and 10,084 differentially expressed CpGs (DMCpGs) were identified. Then 241 DEGs with DMCpGs were identified. According to the prognostic analysis, the prognostic signature of methylation-related differentially expressed genes (mrDEGPS) was established. mrDEGPS consisted of seven prognostic methylation-related genes, including ESRRG, CCNA1, SLC20A1, COL6A6, FCGBP, CDKN2A, and ZNF43. mrDEGPS was a significant stratification factor of survival (P < 0.00001) irrespective of the clinical stage. The immune effector components, including B cells, CD4+ T cells, and CD8+ T cells, were decreased in the tumor environment of patients with high mrDEGPS. Immune checkpoint expressions, including CTLA-4, PD-1, LAG3, LGALS9, HAVCR2, and TIGHT, were comprehensively elevated (P < 0.001). The estimated half-maximal inhibitory concentration difference between low- and high-risk patients was inconsistent among chemotherapeutic drugs. In conclusion, the transcriptome–methylome interaction pattern in OSCC is complex. mrDEGPS can predict patient survival and responses to immunotherapy and chemotherapy and facilitate clinical decision-making in patients with OSCC.
Collapse
|
12
|
Mao P, Shen Y, Xu X, Zhong J. Comprehensive Analysis of the Immune Cell Infiltration Landscape and Immune-Related Methylation in Retinoblastoma. Front Genet 2022; 13:864473. [PMID: 35664300 PMCID: PMC9157546 DOI: 10.3389/fgene.2022.864473] [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: 01/28/2022] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
Retinoblastoma is a common pediatric intraocular cancer, originating from cone precursors. The development of immunotherapies can help eradicate the tumor without vision loss, which would largely improve the quality of life of patients with retinoblastoma. Investigation of the tumor immune microenvironment provides knowledge for developing novel immunotherapies in cancer. However, the immune cell infiltrative landscape of retinoblastoma is unknown. Here, we compared the relative expression of immune gene signatures among 59 patients with retinoblastoma. The patients were divided into two subgroups according to the 28 types of immune cell infiltration (ICI) scores. We found that a subgroup with high ICI scores had increased expression levels of late cone markers, while the other subgroup exhibited larger tumor size and metastasis propensity. Furthermore, hypermethylated genes in the high-ICI subgroup were associated with immune regulation in the tumor microenvironment, suggesting that DNA methylation may play a vital regulatory role in retinoblastoma immunity. Our study provides a comprehensive framework for the systemic analysis of the influences of epigenetic events on the tumor immune microenvironment. We anticipate that our assay can not only provide insights into tumor immune regulation but also open up the perspectives for the identification of novel immunotherapy targets for retinoblastoma.
Collapse
Affiliation(s)
- Peiyao Mao
- Shanghai Key Laboratory of Ocular Fundus Diseases, Department of Ophthalmology, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, National Clinical Research Center for Eye Diseases, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Shanghai, China
| | - Yinchen Shen
- Shanghai Key Laboratory of Ocular Fundus Diseases, Department of Ophthalmology, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, National Clinical Research Center for Eye Diseases, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Shanghai, China
| | - Xun Xu
- Shanghai Key Laboratory of Ocular Fundus Diseases, Department of Ophthalmology, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, National Clinical Research Center for Eye Diseases, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Shanghai, China
| | - Jiawei Zhong
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| |
Collapse
|
13
|
Molecular Research on Oral Diseases and Related Biomaterials: A Journey from Oral Cell Models to Advanced Regenerative Perspectives. Int J Mol Sci 2022; 23:ijms23095288. [PMID: 35563679 PMCID: PMC9105421 DOI: 10.3390/ijms23095288] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/28/2022] [Accepted: 05/04/2022] [Indexed: 02/05/2023] Open
Abstract
Oral diseases such as gingivitis, periodontitis, and oral cancer affect millions of people worldwide. Much research has been conducted to understand the pathogenetic mechanisms of these diseases and translate this knowledge into therapeutics. This review aims to take the reader on a journey from the initial molecular discoveries to complex regenerative issues in oral medicine. For this, a semi-systematic literature search was carried out in Medline and Web of Science databases to retrieve the primary literature describing oral cell models and biomaterial applications in oral regenerative medicine. First, an in vitro cell model of gingival keratinocytes is discussed, which illustrates patho- and physiologic principles in the context of oral epithelial homeostasis and carcinogenesis and represents a cellular tool to understand biomaterial-based approaches for periodontal tissue regeneration. Consequently, a layered gradient nonwoven (LGN) is described, which demonstrates that the key features of biomaterials serve as candidates for oral tissue regeneration. LGN supports proper tissue formation and obeys the important principles for molecular mechanotransduction. Furthermore, current biomaterial-based tissue regeneration trends, including polymer modifications, cell-based treatments, antimicrobial peptides and optogenetics, are introduced to represent the full spectrum of current approaches to oral disease mitigation and prevention. Altogether, this review is a foray through established and new concepts in oral regenerative medicine and illustrates the process of knowledge translation from basic molecular and cell biological research to future clinical applications.
Collapse
|
14
|
Zhao Y, Chen D, Yin J, Xie J, Sun CY, Lu M. Comprehensive Analysis of Tumor Immune Microenvironment Characteristics for the Prognostic Prediction and Immunotherapy of Oral Squamous Cell Carcinoma. Front Genet 2022; 13:788580. [PMID: 35464860 PMCID: PMC9024147 DOI: 10.3389/fgene.2022.788580] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/18/2022] [Indexed: 12/24/2022] Open
Abstract
Background: Oral squamous cell carcinoma (OSCC) is the most common cancer of oral and maxillofacial region. A recent clinical research has shown that tumor immune microenvironment (TIME)cells are closely related to immunotherapy sensitivity and OSCC prognosis. Nonetheless, a comprehensive analysis of TIME in OSCC has not been reported. Methods: Bioinformatics and computational algorithms were employed to determine the significance of TIME cells in 257 OSCC patients. TIME scores were measured by three TIME models, and then used to evaluate the prognosis of OSCC patients. Results: High TIME score was characterized by better prognosis in OSCC patients less than 60 years old, overexpression of immunotherapy targets (e.g., PD-1 and CLTA-4), and higher T-cell activity to inhibit tumor growth. Besides, poor prognosis was associated with low time score. Conclusion: TIME score exhibited potential as a prognostic biomarker and an indicator in predict immunotherapeutic outcomes. Through the understanding of TIME model, this study can provide a better scheme for immunotherapy as the effective treatment of OSCC patients in the future.
Collapse
Affiliation(s)
- Yijie Zhao
- Department of Oral and Maxillofacial Surgery, Shanghai Stomatological Hospital, Fudan University, Shanghai, China
| | - Dongyi Chen
- Department of Prosthodontics, School and Hospital of Stomatology, Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - Junhao Yin
- Department of Oral Surgery, Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian Xie
- Department of Prosthodontics, School and Hospital of Stomatology, Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - Chun-yu Sun
- Department of Oral Surgery, Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Mengmeng Lu
- Department of Oral and Maxillofacial Surgery, Shanghai Stomatological Hospital, Fudan University, Shanghai, China
- *Correspondence: Mengmeng Lu,
| |
Collapse
|
15
|
The World of Oral Cancer and Its Risk Factors Viewed from the Aspect of MicroRNA Expression Patterns. Genes (Basel) 2022; 13:genes13040594. [PMID: 35456400 PMCID: PMC9027895 DOI: 10.3390/genes13040594] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/17/2022] [Accepted: 03/23/2022] [Indexed: 01/27/2023] Open
Abstract
Oral cancer is one of the leading causes of death worldwide, with a reported 5-year survival rate of around 50% after treatment. Epigenetic modifications are considered to have a key role in oral carcinogenesis due to histone modifications, aberrant DNA methylation, and altered expression of miRNAs. MicroRNAs (miRNAs) are small non-coding RNAs that have a key role in cancer development by regulating signaling pathways involved in carcinogenesis. MiRNA deregulation identified in oral cancer has led to the idea of using them as potential biomarkers for early diagnosis, prognosis, and the development of novel therapeutic strategies. In recent years, a key role has been observed for risk factors in preventing and treating this malignancy. The purpose of this review is to summarize the recent knowledge about the altered mechanisms of oral cancer due to risk factors and the role of miRNAs in these mechanisms.
Collapse
|
16
|
On the Cutting Edge of Oral Cancer Prevention: Finding Risk-Predictive Markers in Precancerous Lesions by Longitudinal Studies. Cells 2022; 11:cells11061033. [PMID: 35326482 PMCID: PMC8947091 DOI: 10.3390/cells11061033] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/11/2022] [Accepted: 03/13/2022] [Indexed: 02/06/2023] Open
Abstract
Early identification and management of precancerous lesions at high risk of developing cancers is the most effective and economical way to reduce the incidence, mortality, and morbidity of cancers as well as minimizing treatment-related complications, including pain, impaired functions, and disfiguration. Reliable cancer-risk-predictive markers play an important role in enabling evidence-based decision making as well as providing mechanistic insight into the malignant conversion of precancerous lesions. The focus of this article is to review updates on markers that may predict the risk of oral premalignant lesions (OPLs) in developing into oral squamous cell carcinomas (OSCCs), which can logically be discovered only by prospective or retrospective longitudinal studies that analyze pre-progression OPL samples with long-term follow-up outcomes. These risk-predictive markers are different from those that prognosticate the survival outcome of cancers after they have been diagnosed and treated, or those that differentiate between different lesion types and stages. Up-to-date knowledge on cancer-risk-predictive markers discovered by longitudinally followed studies will be reviewed. The goal of this endeavor is to use this information as a starting point to address some key challenges limiting our progress in this area in the hope of achieving effective translation of research discoveries into new clinical interventions.
Collapse
|
17
|
Liu X, Chen J, Li J, Zeng Z, Jiang X, Gao Y, Huang Z, Wu Q, Gong Y, Xie C. Comprehensive analysis reveals common DNA methylation patterns of tobacco-associated cancers: A pan-cancer analysis. Gene 2021; 804:145900. [PMID: 34400279 DOI: 10.1016/j.gene.2021.145900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 12/14/2022]
Abstract
The role of tobacco in carcinogenesis has received increasing attention across a number of disciplines in recent years. Accumulating evidences reveal that tobacco consumption affects various epigenetic modifications, especially DNA methylation. However, the genetic modifications of methylation patterns involved in tobacco-attributable cancers remain poorly understood. In this manuscript, aberrant DNA methylation patterns were investigated in 9 tobacco-attributable cancers. Differential methylated probes (DMPs) were identified in each cancer type and a total of 2,392 hyper- and 736 hypomethylated pan-cancer DMPs (PDMPs) were screened out for further analysis. PDMP-associated genes were mostly enriched in metabolism-associated pathways, suggesting the potential roles of methylation alternation in reprogramming cancer cell metabolism. Hypomethylated PDMPs cg12422154, cg02772121 and cg06051311 constituted an enhancer region, significantly downregulating TRIM15, TRIM26 and RPP21, which serve as epigenetically therapeutic biomarkers. Forty-three hypermethylated and 13 hypomethylated transcription factor motifs were clustered into 6 groups, and exhibited various biological functions. Forty-nine PDMPs were reported to be associated with prognosis, providing effective tools to predict clinical outcomes. In summary, our studies revealed the characteristics, influences and potential mechanisms of DNA methylation patterns of tobacco-attributable cancer.
Collapse
Affiliation(s)
- Xingyu Liu
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jiarui Chen
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jiali Li
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zihang Zeng
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xueping Jiang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yanping Gao
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhengrong Huang
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China; Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Qiuji Wu
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China; Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yan Gong
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China; Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China.
| | - Conghua Xie
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China; Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China.
| |
Collapse
|
18
|
Shenoy SR, Dey B. Funding for cancer research by an Indian funding agency, DBT. J Biosci 2021. [DOI: 10.1007/s12038-020-00121-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
19
|
Porcuna J, Mínguez-Martínez J, Ricote M. The PPARα and PPARγ Epigenetic Landscape in Cancer and Immune and Metabolic Disorders. Int J Mol Sci 2021; 22:ijms221910573. [PMID: 34638914 PMCID: PMC8508752 DOI: 10.3390/ijms221910573] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 02/07/2023] Open
Abstract
Peroxisome proliferator-activated receptors (PPARs) are ligand-modulated nuclear receptors that play pivotal roles in nutrient sensing, metabolism, and lipid-related processes. Correct control of their target genes requires tight regulation of the expression of different PPAR isoforms in each tissue, and the dysregulation of PPAR-dependent transcriptional programs is linked to disorders, such as metabolic and immune diseases or cancer. Several PPAR regulators and PPAR-regulated factors are epigenetic effectors, including non-coding RNAs, epigenetic enzymes, histone modifiers, and DNA methyltransferases. In this review, we examine advances in PPARα and PPARγ-related epigenetic regulation in metabolic disorders, including obesity and diabetes, immune disorders, such as sclerosis and lupus, and a variety of cancers, providing new insights into the possible therapeutic exploitation of PPAR epigenetic modulation.
Collapse
|
20
|
Li G, Raffield L, Logue M, Miller MW, Santos HP, O’Shea TM, Fry RC, Li Y. CUE: CpG impUtation ensemble for DNA methylation levels across the human methylation450 (HM450) and EPIC (HM850) BeadChip platforms. Epigenetics 2021; 16:851-861. [PMID: 33016200 PMCID: PMC8330997 DOI: 10.1080/15592294.2020.1827716] [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: 05/20/2020] [Revised: 08/08/2020] [Accepted: 09/09/2020] [Indexed: 10/23/2022] Open
Abstract
DNA methylation at CpG dinucleotides is one of the most extensively studied epigenetic marks. With technological advancements, geneticists can profile DNA methylation with multiple reliable approaches. However, profiling platforms can differ substantially in the CpGs they assess, consequently hindering integrated analysis across platforms. Here, we present CpG impUtation Ensemble (CUE), which leverages multiple classical statistical and modern machine learning methods, to impute from the Illumina HumanMethylation450 (HM450) BeadChip to the Illumina HumanMethylationEPIC (HM850) BeadChip. Data were analysed from two population cohorts with methylation measured both by HM450 and HM850: the Extremely Low Gestational Age Newborns (ELGAN) study (n = 127, placenta) and the VA Boston Posttraumatic Stress Disorder (PTSD) genetics repository (n = 144, whole blood). Cross-validation results show that CUE achieves the lowest predicted root-mean-square error (RMSE) (0.026 in PTSD) and the highest accuracy (99.97% in PTSD) compared with five individual methods tested, including k-nearest-neighbours, logistic regression, penalized functional regression, random forest, and XGBoost. Finally, among all 339,033 HM850-only CpG sites shared between ELGAN and PTSD, CUE successfully imputed 289,604 (85.4%) sites, where success was defined as RMSE < 0.05 and accuracy >95% in PTSD. In summary, CUE is a valuable tool for imputing CpG methylation from the HM450 to HM850 platform.
Collapse
Affiliation(s)
- Gang Li
- Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Laura Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Mark Logue
- National Center for PTSD: Behavioral Sciences Division at VA Boston Healthcare System, Boston, MA, USA
- Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
- Biomedical Genetics, Boston University School of Medicine, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Mark W. Miller
- National Center for PTSD: Behavioral Sciences Division at VA Boston Healthcare System, Boston, MA, USA
- Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - Hudson P. Santos
- School of Nursing, University of North Carolina, Chapel Hill, NC, USA
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - T. Michael O’Shea
- Department of Pediatrics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Rebecca C. Fry
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
| |
Collapse
|
21
|
Yang A, Zhou Y, Kong Y, Wei X, Ye F, Zhang L, Zhong X, Li M, Lu S, An X, Xiao W. Identification and Validation of Immune-Related Methylation Clusters for Predicting Immune Activity and Prognosis in Breast Cancer. Front Immunol 2021; 12:704557. [PMID: 34276701 PMCID: PMC8278823 DOI: 10.3389/fimmu.2021.704557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 06/16/2021] [Indexed: 11/13/2022] Open
Abstract
The role of DNA methylation of breast cancer-infiltrating immune cells has not been fully explored. We conducted a cohort-based retrospective study analyzing the genome-wide immune-related DNA methylation of 1057 breast cancer patients from the TCGA cohort and GSE72308 cohort. Based on patients' overall survival (OS), a prognostic risk score system using 18 immune-related methylation genes (IRMGs) was established and further validated in an independent cohort. Kaplan-Meier analysis showed a clear separation of OS between the low- and high-risk groups. Patients in the low-risk group had a higher immune score and stromal score compared with the high-risk group. Moreover, the characteristics based on 18-IRMGs signature were related to the tumor immune microenvironment and affected the abundance of tumor-infiltrating immune cells. Consistently, the 18-IRMGs signatures showed similar influences on immune modulation and survival in another external validation cohort (GSE72308). In conclusion, the proposed 18-IRMGs signature could be a potential marker for breast cancer prognostication.
Collapse
Affiliation(s)
- Anli Yang
- Department of Breast Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ying Zhou
- Department of Infectious Diseases and Endemic Disease Control, Haizhu District Center for Disease Control and Prevention, Guangzhou, China
| | - Yanan Kong
- Department of Breast Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiaoli Wei
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Feng Ye
- Department of Breast Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Lijuan Zhang
- Department of Breast Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xian Zhong
- Department of Ultrasound, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Mingyue Li
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Shilin Lu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xin An
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Weikai Xiao
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| |
Collapse
|
22
|
Yang Z, Yan G, Zheng L, Gu W, Liu F, Chen W, Cui X, Wang Y, Yang Y, Chen X, Fu Y, Xu X. YKT6, as a potential predictor of prognosis and immunotherapy response for oral squamous cell carcinoma, is related to cell invasion, metastasis, and CD8+ T cell infiltration. Oncoimmunology 2021; 10:1938890. [PMID: 34221701 PMCID: PMC8224202 DOI: 10.1080/2162402x.2021.1938890] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Metastasis and immune suppression account for the poor prognosis of oral squamous cell carcinoma (OSCC). YKT6 is a member of the soluble NSF attachment protein receptor (SNARE) family, and the effect of YKT6 in OSCC remains elusive. The purpose of this study was to explore promising prognostic and immune therapeutic candidate biomarkers for OSCC and to understand the expression pattern, prognostic value, immune effects, and biological functions of YKT6. Genes correlated with tumor metastasis and CD8 + T cell levels were identified by weighted gene coexpression network analysis (WGCNA). Next, YKT6 was analyzed through differential expression, prognostic and machine learning analyses. The molecular and immune characteristics of YKT6 were analyzed in independent cohorts, clinical specimens, and in vitro. In addition, we investigated the role of YKT6 at the pan-cancer level. The results suggested that the red module in WGCNA, as a hub module, was associated with lymph node (LN) metastasis and CD8 + T cell infiltration. Upregulation of YKT6 was found in OSCC and linked to adverse prognosis. A nomogram model containing YKT6 expression and tumor stage was constructed for clinical practice. The aggressive and immune-inhibitory phenotypes showed YKT6 overexpression, and the effect of YKT6 on OSCC cell invasion and metastasis in vitro was observed. Moreover, the low expression of YKT6 was correlated with high CD8 + T cell levels and potential immunotherapy response in OSCC. Similar results were found at the pan-cancer level. In total, YKT6 is a promising candidate biomarker for prognosis, molecular, and immune characteristics in OSCC.
Collapse
Affiliation(s)
- Zongcheng Yang
- Department of Implantology, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, Shandong, People's Republic of China
| | - Guangxing Yan
- Department of Oral Pathology, School and Hospital of Stomatology, Jilin University, Changchun, People's Republic of China
| | - Lixin Zheng
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Shandong University, Jinan, Shandong, People's Republic of China
| | - Wenchao Gu
- Department of Diagnostic Radiology and Nuclear Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Fen Liu
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Shandong University, Jinan, Shandong, People's Republic of China
| | - Wei Chen
- Department of Implantology, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, Shandong, People's Republic of China
| | - Xiujie Cui
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Shandong University, Jinan, Shandong, People's Republic of China
| | - Yue Wang
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Shandong University, Jinan, Shandong, People's Republic of China
| | - Yaling Yang
- Department of Pediatrics, The First Hospital of Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Xiyan Chen
- Department of Stomatology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Yue Fu
- Department of Physiology & Pathophysiology, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Xin Xu
- Department of Implantology, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, Shandong, People's Republic of China
| |
Collapse
|
23
|
Genes and pathways monotonically dysregulated during progression from normal through leukoplakia to gingivo-buccal oral cancer. NPJ Genom Med 2021; 6:32. [PMID: 33980865 PMCID: PMC8115176 DOI: 10.1038/s41525-021-00195-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/19/2021] [Indexed: 01/17/2023] Open
Abstract
Oral squamous cell carcinoma of the gingivo-buccal region (OSCC-GB) accounts for the highest cancer morbidity and mortality among men in India. It has been observed that about one-third of individuals with oral leukoplakia, a dysplastic precancerous lesion in the oral cavity, progress to oral cancer. We aimed to identify systematic transcriptomic changes as a normal tissue in the oral cavity progresses to frank OSCC-GB. Seventy-two OSCC-GB patients, from multiple hospitals, were recruited, and transcriptome analysis of tumor and adjacent normal tissue (of all patients) and adjacent leukoplakia tissue (of a subset of 25 unselected patients with concomitant leukoplakia) was performed. We have identified many differences in the transcriptomic profiles between OSCC-GB and squamous cell carcinoma of the head and neck regions. Compared to the normal/precancerous tissue, significant enrichment of ECM−receptor interaction, PI3K-Akt signaling, cytokine−cytokine receptor interaction, focal adhesion, and cell cycle pathways were observed in OSCC-GB. Using gene set enrichment analysis, we identified a profound role of interferon receptor signaling in tumor growth by activating immune evasion mechanisms. The role of tumor-infiltrating immune cells further supported the growth and immunosuppressive mechanism of tumor tissues. Some immune evasion genes—CD274, CD80, and IDO1—were found to be activated even in the precancerous tissue. Taken together, our findings provide a clear insight into the sequential genetic dysregulation associated with progression to oral cancer. This insight provides a window to the development of predictive biomarkers and therapeutic targets for gingivo-buccal oral cancer.
Collapse
|
24
|
Gougousis S, Mouchtaropoulou E, Besli I, Vrochidis P, Skoumpas I, Constantinidis I. HPV-Related Oropharyngeal Cancer and Biomarkers Based on Epigenetics and Microbiome Profile. Front Cell Dev Biol 2021; 8:625330. [PMID: 33521000 PMCID: PMC7841258 DOI: 10.3389/fcell.2020.625330] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022] Open
Abstract
H uman papillomavirus (HPV) is considered the main cause of the increasing incidence rates of oropharyngeal squamous cell carcinoma (OPSCC), and soon, the global burden of HPV-related OPSCC is predicted to exceed that of cervical cancer. Moreover, a different molecular profile for HPV-related OPSCC has been described, opening new promising targeted therapies and immunotherapy approaches. Epigenetic and microbiome-based exploration of biomarkers has gained growing interest with a view to the primary oropharyngeal cancer (OPC) screening. Understanding the role of the epigenetic mechanism and the changes that occur during pathogenesis shows appreciable progress in recent years. The different methylation status of DNA and miRNAs demonstrates the value of possible biomarkers discriminating even in different stages of dysplasia. Through whole-genome bisulfite sequencing, differentially methylated regions (DMRs) hold the key to recover missing information. O n the other hand, the microbiota investigation signifies a new biomarker approach for the evaluation of OPC. Along with known cofactors playing a major role in microbiota differentiation, HPV-related cases must be explored further for better understanding. The dynamic approach of the shotgun metagenomic sequencing will robustly fill the gap especially in species/strain level and consequently to biomarker detection. The constantly growing incidence of HPV-related OPC should lead us in further investigation and understanding of the unique features of the disease, more accurate diagnostic methods, along with the development and implementation of new, targeted therapies. This paper comprehensively reviews the significance of biomarkers based on epigenetics and microbiome profile in the accuracy of the diagnosis of the HPV-related cancer in the oropharynx.
Collapse
Affiliation(s)
- Spyridon Gougousis
- GH "G. Papanikolaou," ENT, Head and Neck Department, Thessaloniki, Greece
| | | | - Ioanna Besli
- GH "G. Papanikolaou," ENT, Head and Neck Department, Thessaloniki, Greece
| | | | - Ioannis Skoumpas
- GH "G. Papanikolaou," ENT, Head and Neck Department, Thessaloniki, Greece
| | - Ioannis Constantinidis
- 1st Department of Otorhinolaryngology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| |
Collapse
|
25
|
Zhu J, Zhou Y, Zhu S, Li F, Xu J, Zhang L, Shu H. circRNA circ_102049 Implicates in Pancreatic Ductal Adenocarcinoma Progression through Activating CD80 by Targeting miR-455-3p. Mediators Inflamm 2021; 2021:8819990. [PMID: 33505218 PMCID: PMC7811564 DOI: 10.1155/2021/8819990] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/27/2020] [Accepted: 12/13/2020] [Indexed: 12/27/2022] Open
Abstract
Emerging evidence has shown that circular RNAs (circRNAs) and DNA methylation play important roles in the causation and progression of cancers. However, the roles of circRNAs and abnormal methylation genes in the tumorigenesis of pancreatic ductal adenocarcinoma (PDAC) are still largely unknown. Expression profiles of circRNA, gene methylation, and mRNA were downloaded from the GEO database, and differentially expressed genes were obtained via GEO2R, and a ceRNA network was constructed based on circRNA-miRNA pairs and miRNA-mRNA pairs. Inflammation-associated genes were collected from the GeneCards database. Then, functional enrichment analysis and protein-protein interaction (PPI) networks of inflammation-associated methylated expressed genes were investigated using Metascape and STRING databases, respectively, and visualized in Cytoscape. Hub genes of PPI networks were identified using the NetworkAnalyzer plugin. Also, we analyzed the methylation, protein expression levels, and prognostic value of hub genes in PDAC patients through the UALCAN, Human Protein Atlas (HPA), and Kaplan-Meier plotter databases, respectively. The circRNA_102049/miR-455-3p/CD80 axis was identified by the ceRNA network and hub genes. In vitro and in vivo experiments were performed to evaluate the functions of circRNA_102049. The regulatory mechanisms of circRNA_102049 and miR-455-3p were explored by RT-PCR, western blot, and dual-luciferase assays. In the present study, twelve hub genes (STAT1, CCND1, KRAS, CD80, ICAM1, ESR1, RAF1, RPS6KA2, KDM6B, TNRC6A, FOSB, and DNM1) were determined from the PPI networks. Additionally, the circRNA_102049 was upregulated in PDAC cell lines. Functionally, the knockdown of circRNA_102049 by siRNAs inhibited cell growth, inflammatory factors, and migratory and invasive potential and promoted cell apoptosis. Mechanistically, circRNA_102049 functioned as a sponge of miR-455-3p and partially reversed the effect of miR-455-3p and consequently upregulated CD80 expression. Our findings showed that circRNA_102049 and methylated hub genes play an important role in the proliferation, apoptosis, migration, invasion, and inflammatory response of PDAC, which might be selected as a promising prognostic marker and therapeutic target for PDAC.
Collapse
Affiliation(s)
- Jie Zhu
- Medical Laboratory, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Yong Zhou
- Medical Laboratory, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Shanshan Zhu
- Medical Laboratory, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Fei Li
- Medical Laboratory, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Jiajia Xu
- Medical Laboratory, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Liming Zhang
- Medical Laboratory, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Hairong Shu
- Department of Medical Service, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| |
Collapse
|
26
|
Mukhopadhyay S, Ghosh S, Das D, Arun P, Roy B, Biswas NK, Maitra A, Majumder PP. Application of Random Forest and data integration identifies three dysregulated genes and enrichment of Central Carbon Metabolism pathway in Oral Cancer. BMC Cancer 2020; 20:1219. [PMID: 33317464 PMCID: PMC7737291 DOI: 10.1186/s12885-020-07709-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 12/03/2020] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Studies of epigenomic alterations associated with diseases primarily focus on methylation profiles of promoter regions of genes, but not of other genomic regions. In our past work (Das et al. 2019) on patients suffering from gingivo-buccal oral cancer - the most prevalent form of cancer among males in India - we have also focused on promoter methylation changes and resultant impact on transcription profiles. Here, we have investigated alterations in non-promoter (gene-body) methylation profiles and have carried out an integrative analysis of gene-body methylation and transcriptomic data of oral cancer patients. METHODS Tumor and adjacent normal tissue samples were collected from 40 patients. Data on methylation in the non-promoter (gene-body) regions of genes and transcriptome profiles were generated and analyzed. Because of high dimensionality and highly correlated nature of these data, we have used Random Forest (RF) and other data-analytical methods. RESULTS Integrative analysis of non-promoter methylation and transcriptome data revealed significant methylation-driven alterations in some genes that also significantly impact on their transcription levels. These changes result in enrichment of the Central Carbon Metabolism (CCM) pathway, primarily by dysregulation of (a) NTRK3, which plays a dual role as an oncogene and a tumor suppressor; (b) SLC7A5 (LAT1) which is a transporter dedicated to essential amino acids, and is overexpressed in cancer cells to meet the increased demand for nutrients that include glucose and essential amino acids; and, (c) EGFR which has been earlier implicated in progression, recurrence, and stemness of oral cancer, but we provide evidence of epigenetic impact on overexpression of this gene for the first time. CONCLUSIONS In rapidly dividing cancer cells, metabolic reprogramming from normal cells takes place to enable enhanced proliferation. Here, we have identified that among oral cancer patients, genes in the CCM pathway - that plays a fundamental role in metabolic reprogramming - are significantly dysregulated because of perturbation of methylation in non-promoter regions of the genome. This result compliments our previous result that perturbation of promoter methylation results in significant changes in key genes that regulate the feedback process of DNA methylation for the maintenance of normal cell division.
Collapse
Affiliation(s)
| | - Sahana Ghosh
- National Institute of Biomedical Genomics, Kalyani, 741251, India
| | - Debodipta Das
- National Institute of Biomedical Genomics, Kalyani, 741251, India
| | - P Arun
- Tata Medical Centre, Kolkata, India
| | - Bidyut Roy
- Indian Statistical Institute, Kolkata, India
| | - Nidhan K Biswas
- National Institute of Biomedical Genomics, Kalyani, 741251, India
| | - Arindam Maitra
- National Institute of Biomedical Genomics, Kalyani, 741251, India
| | - Partha P Majumder
- National Institute of Biomedical Genomics, Kalyani, 741251, India. .,Indian Statistical Institute, Kolkata, India.
| |
Collapse
|
27
|
Marthong L, Ghosh S, Palodhi A, Imran M, Shunyu NB, Maitra A, Ghosh S. Whole Genome DNA Methylation and Gene Expression Profiling of Oropharyngeal Cancer Patients in North-Eastern India: Identification of Epigenetically Altered Gene Expression Reveals Potential Biomarkers. Front Genet 2020; 11:986. [PMID: 33133131 PMCID: PMC7578381 DOI: 10.3389/fgene.2020.00986] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 08/05/2020] [Indexed: 12/31/2022] Open
Abstract
Oropharyngeal cancer is a subtype of head and neck squamous cell carcinoma that is associated with unique risk exposures like consumption of smokeless tobacco and areca nut and is highly prevalent in the northeastern region of India, especially Meghalaya. However, the underlying epigenetic and transcriptomic changes in this cancer type is yet to be delineated. We have undertaken a study on genome wide somatic alterations in the DNA methylation and transcriptome in oropharyngeal cancer patients from this region using genome wide techniques in paired tumors and adjacent normal tissues. By using integrative approaches, we have identified 194 epigenetically silenced and 241 epigenetically overexpressed genes in the tumor tissue of these patients. Pathways that are significantly enriched by these genes include the pathways of immune systems, such as the interleukin signaling pathways and Toll-like receptor signaling pathway. Also, osteoclast differentiation pathway was found to be epigenetically upregulated. The pathways enriched by the epigenetically downregulated genes were found to be predominantly those involved in xenobiotic metabolism and keratinization. Two major transcription factors - SPI1 and RUNX1 were identified as epigenetically dysregulated, which further modulates 129 downstream genes. Comparison of our observations with the head and neck cancer data from TCGA revealed distinct DNA methylation and gene expression landscapes which might be specific for oropharyngeal cancer. HPV DNA sequences were not detected in any of the tumor samples in RNA-Seq data. The results obtained in this study might provide improved understanding of the disease.
Collapse
Affiliation(s)
- Lastborn Marthong
- Department of Zoology, North Eastern Hill University (NEHU), Shillong, India
| | - Sahana Ghosh
- National Institute of Biomedical Genomics (NIBMG), Kalyani, India
| | - Arindam Palodhi
- National Institute of Biomedical Genomics (NIBMG), Kalyani, India
| | - Mohamed Imran
- National Institute of Biomedical Genomics (NIBMG), Kalyani, India
| | - Neizekhotuo Brian Shunyu
- Department of Otorhinolaryngology (ENT), North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences (NEIGRIHMS), Shillong, India
| | - Arindam Maitra
- National Institute of Biomedical Genomics (NIBMG), Kalyani, India
| | - Srimoyee Ghosh
- Department of Zoology, North Eastern Hill University (NEHU), Shillong, India
| |
Collapse
|
28
|
Dompe C, Janowicz K, Hutchings G, Moncrieff L, Jankowski M, Nawrocki MJ, Józkowiak M, Mozdziak P, Petitte J, Shibli JA, Dyszkiewicz-Konwińska M, Bruska M, Piotrowska-Kempisty H, Kempisty B, Nowicki M. Epigenetic Research in Stem Cell Bioengineering-Anti-Cancer Therapy, Regenerative and Reconstructive Medicine in Human Clinical Trials. Cancers (Basel) 2020; 12:E1016. [PMID: 32326172 PMCID: PMC7226111 DOI: 10.3390/cancers12041016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 12/12/2022] Open
Abstract
The epigenome denotes all the information related to gene expression that is not contained in the DNA sequence but rather results from chemical changes to histones and DNA. Epigenetic modifications act in a cooperative way towards the regulation of gene expression, working at the transcriptional or post-transcriptional level, and play a key role in the determination of phenotypic variations in cells containing the same genotype. Epigenetic modifications are important considerations in relation to anti-cancer therapy and regenerative/reconstructive medicine. Moreover, a range of clinical trials have been performed, exploiting the potential of epigenetics in stem cell engineering towards application in disease treatments and diagnostics. Epigenetic studies will most likely be the basis of future cancer therapies, as epigenetic modifications play major roles in tumour formation, malignancy and metastasis. In fact, a large number of currently designed or tested clinical approaches, based on compounds regulating epigenetic pathways in various types of tumours, employ these mechanisms in stem cell bioengineering.
Collapse
Affiliation(s)
- Claudia Dompe
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (C.D.); (L.M.); (M.N.)
- The School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK; (K.J.); (G.H.)
| | - Krzysztof Janowicz
- The School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK; (K.J.); (G.H.)
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (M.J.); (M.J.N.); (M.D.-K.); (M.B.)
| | - Greg Hutchings
- The School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK; (K.J.); (G.H.)
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (M.J.); (M.J.N.); (M.D.-K.); (M.B.)
| | - Lisa Moncrieff
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (C.D.); (L.M.); (M.N.)
- The School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK; (K.J.); (G.H.)
| | - Maurycy Jankowski
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (M.J.); (M.J.N.); (M.D.-K.); (M.B.)
| | - Mariusz J. Nawrocki
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (M.J.); (M.J.N.); (M.D.-K.); (M.B.)
| | - Małgorzata Józkowiak
- Department of Toxicology, Poznan University of Medical Sciences, 61-631 Poznan, Poland; (M.J.); (H.P.-K.)
| | - Paul Mozdziak
- Physiology Graduate Program, North Carolina State University, Raleigh, NC 27695, USA;
| | - Jim Petitte
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC 27695, USA;
| | - Jamil A. Shibli
- Department of Periodontology and Oral Implantology, Dental Research Division, University of Guarulhos, São Paulo 07023-070, Brazil;
| | - Marta Dyszkiewicz-Konwińska
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (M.J.); (M.J.N.); (M.D.-K.); (M.B.)
- Department of Biomaterials and Experimental Dentistry, Poznan University of Medical Sciences, 61 701 Poznan, Poland
| | - Małgorzata Bruska
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (M.J.); (M.J.N.); (M.D.-K.); (M.B.)
| | - Hanna Piotrowska-Kempisty
- Department of Toxicology, Poznan University of Medical Sciences, 61-631 Poznan, Poland; (M.J.); (H.P.-K.)
| | - Bartosz Kempisty
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (C.D.); (L.M.); (M.N.)
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (M.J.); (M.J.N.); (M.D.-K.); (M.B.)
- Department of Obstetrics and Gynaecology, University Hospital and Masaryk University, 602 00 Brno, Czech Republic
- Department of Veterinary Surgery, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87 100 Torun, Poland
| | - Michał Nowicki
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (C.D.); (L.M.); (M.N.)
| |
Collapse
|