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Gissi DB, Suàrez-Fernandez C, Rossi R, Vitali F, Marzi Manfroni A, Gabusi A, Morandi L, Balbi T, Montebugnoli L, Foschini MP, Tarsitano A. Direct healthcare costs of oral cancer: A retrospective study from a tertiary care center. J Craniomaxillofac Surg 2024; 52:630-635. [PMID: 38582671 DOI: 10.1016/j.jcms.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/19/2023] [Accepted: 03/05/2024] [Indexed: 04/08/2024] Open
Abstract
The aim of this study was to retrospectively evaluate the direct costs of OSCC treatment and postsurgical surveillance in a tertiary hospital in northeast Italy. Sixty-three consecutive patients surgically treated for primitive OSCC at S. Orsola Hospital in Bologna (Italy) between January 2018 and January 2020 were analyzed. Billing records of the Emilia Romagna healthcare system and institutional costs were used to derive specific costs for the following clinical categories: operating theatre costs, intensive and ordinary hospitalization, radiotherapy, chemotherapy, postsurgical complications, visits, and examinations during the follow-up period. The study population comprised 17 OSCC patients classified at stage I, 14 at stage II, eight at stage III, and 24 at stage IV. The estimated mean total direct cost for OSCC treatment and postsurgical surveillance was €26 338.48 per patient (stage I: €10 733, stage II: €19 642.9, stage III: €30 361.4, stage IV: €39 957.2). An advanced diagnosis (stages III and IV), complex surgical procedure, and loco-regional recurrences resulted in variables that were significantly associated with a higher cost of OSCC treatment and postsurgical surveillance. Redirection of funds used for OSCC treatment to screening measures may be an effective strategy to improve overall health outcomes and optimize national health resources.
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Affiliation(s)
- Davide Bartolomeo Gissi
- Department of Biomedical and Neuromotor Sciences, Section of Oral Sciences, University of Bologna, Bologna, Italy.
| | - Carlota Suàrez-Fernandez
- Department of Surgery and Medical-Surgical Specialities, School of Medicine and Health Sciences, University of Oviedo, Oviedo, Spain
| | - Roberto Rossi
- Department of Biomedical and Neuromotor Sciences, Section of Oral Sciences, University of Bologna, Bologna, Italy
| | - Francesco Vitali
- Oral and Maxillofacial Surgery Unit, IRCCS Azienda Ospedaliero-Universitaria, Bologna, Italy; Department of Biomedical and Neuromotor Sciences, Section of Maxillofacial Surgery at Policlinico S. Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Alice Marzi Manfroni
- Oral and Maxillofacial Surgery Unit, IRCCS Azienda Ospedaliero-Universitaria, Bologna, Italy; Department of Biomedical and Neuromotor Sciences, Section of Maxillofacial Surgery at Policlinico S. Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Andrea Gabusi
- Department of Biomedical and Neuromotor Sciences, Section of Oral Sciences, University of Bologna, Bologna, Italy
| | - Luca Morandi
- Functional and Molecular Neuroimaging Unit, Bellaria Hospital, Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy; IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Tiziana Balbi
- Unit of Anatomic Pathology, S. Orsola Hospital, IRCCS Azienda Ospedaliero-Universitaria, Bologna, Italy
| | - Lucio Montebugnoli
- Department of Biomedical and Neuromotor Sciences, Section of Oral Sciences, University of Bologna, Bologna, Italy
| | - Maria Pia Foschini
- Department of Biomedical and Neuromotor Sciences, Section of Anatomic Pathology at Bellaria Hospital, University of Bologna, Bologna, Italy
| | - Achille Tarsitano
- Oral and Maxillofacial Surgery Unit, IRCCS Azienda Ospedaliero-Universitaria, Bologna, Italy; Department of Biomedical and Neuromotor Sciences, Section of Maxillofacial Surgery at Policlinico S. Orsola-Malpighi, University of Bologna, Bologna, Italy
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Inchanalkar M, Srivatsa S, Ambatipudi S, Bhosale PG, Patil A, Schäffer AA, Beerenwinkel N, Mahimkar MB. Genome-wide DNA methylation profiling of HPV-negative leukoplakia and gingivobuccal complex cancers. Clin Epigenetics 2023; 15:93. [PMID: 37245006 DOI: 10.1186/s13148-023-01510-z] [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: 09/13/2022] [Accepted: 05/21/2023] [Indexed: 05/29/2023] Open
Abstract
BACKGROUND Gingivobuccal complex oral squamous cell carcinoma (GBC-OSCC) is an aggressive malignancy with high mortality often preceded by premalignant lesions, including leukoplakia. Previous studies have reported genomic drivers in OSCC, but much remains to be elucidated about DNA methylation patterns across different stages of oral carcinogenesis. RESULTS There is a serious lack of biomarkers and clinical application of biomarkers for early detection and prognosis of gingivobuccal complex cancers. Hence, in search of novel biomarkers, we measured genome-wide DNA methylation in 22 normal oral tissues, 22 leukoplakia, and 74 GBC-OSCC tissue samples. Both leukoplakia and GBC-OSCC had distinct methylation profiles as compared to normal oral tissue samples. Aberrant DNA methylation increases during the different stages of oral carcinogenesis, from premalignant lesions to carcinoma. We identified 846 and 5111 differentially methylated promoters in leukoplakia and GBC-OSCC, respectively, with a sizable fraction shared between the two sets. Further, we identified potential biomarkers from integrative analysis in gingivobuccal complex cancers and validated them in an independent cohort. Integration of genome, epigenome, and transcriptome data revealed candidate genes with gene expression synergistically regulated by copy number and DNA methylation changes. Regularised Cox regression identified 32 genes associated with patient survival. In an independent set of samples, we validated eight genes (FAT1, GLDC, HOXB13, CST7, CYB5A, MLLT11, GHR, LY75) from the integrative analysis and 30 genes from previously published reports. Bisulfite pyrosequencing validated GLDC (P = 0.036), HOXB13 (P < 0.0001) promoter hypermethylation, and FAT1 (P < 0.0001) hypomethylation in GBC-OSCC compared to normal controls. CONCLUSIONS Our findings identified methylation signatures associated with leukoplakia and gingivobuccal complex cancers. The integrative analysis in GBC-OSCC identified putative biomarkers that enhance existing knowledge of oral carcinogenesis and may potentially help in risk stratification and prognosis of GBC-OSCC.
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Affiliation(s)
- Mayuri Inchanalkar
- Mahimkar Lab, Cancer Research Institute (CRI), Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Center, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Sumana Srivatsa
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Srikant Ambatipudi
- Mahimkar Lab, Cancer Research Institute (CRI), Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Center, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Achutha Menon Centre for Health Science Studies, Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram, Kerala, India
| | - Priyanka G Bhosale
- Mahimkar Lab, Cancer Research Institute (CRI), Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Center, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Centre for Gene Therapy and Regenerative Medicine, Guy's Hospital, King's College London, Tower Wing, London, UK
| | - Asawari Patil
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
- Department of Pathology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai, India
| | - Alejandro A Schäffer
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, and National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Manoj B Mahimkar
- Mahimkar Lab, Cancer Research Institute (CRI), Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Center, Kharghar, Navi Mumbai, Maharashtra, 410210, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India.
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3
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Dholariya S, Singh RD, Sonagra A, Yadav D, Vajaria BN, Parchwani D. Integrating Cutting-Edge Methods to Oral Cancer Screening, Analysis, and Prognosis. Crit Rev Oncog 2023; 28:11-44. [PMID: 37830214 DOI: 10.1615/critrevoncog.2023047772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Oral cancer (OC) has become a significant barrier to health worldwide due to its high morbidity and mortality rates. OC is among the most prevalent types of cancer that affect the head and neck region, and the overall survival rate at 5 years is still around 50%. Moreover, it is a multifactorial malignancy instigated by genetic and epigenetic variabilities, and molecular heterogeneity makes it a complex malignancy. Oral potentially malignant disorders (OPMDs) are often the first warning signs of OC, although it is challenging to predict which cases will develop into malignancies. Visual oral examination and histological examination are still the standard initial steps in diagnosing oral lesions; however, these approaches have limitations that might lead to late diagnosis of OC or missed diagnosis of OPMDs in high-risk individuals. The objective of this review is to present a comprehensive overview of the currently used novel techniques viz., liquid biopsy, next-generation sequencing (NGS), microarray, nanotechnology, lab-on-a-chip (LOC) or microfluidics, and artificial intelligence (AI) for the clinical diagnostics and management of this malignancy. The potential of these novel techniques in expanding OC diagnostics and clinical management is also reviewed.
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Affiliation(s)
- Sagar Dholariya
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), Rajkot, Gujarat, India
| | - Ragini D Singh
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), Rajkot, Gujarat, India
| | - Amit Sonagra
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), Rajkot, Gujarat, India
| | | | | | - Deepak Parchwani
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), Rajkot, Gujarat, India
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Tian X, Shi C, Liu S, Zhao C, Wang X, Cao Y. Methylation related genes are associated with prognosis of patients with head and neck squamous cell carcinoma via altering tumor immune microenvironment. J Dent Sci 2023; 18:57-64. [PMID: 36643267 PMCID: PMC9831828 DOI: 10.1016/j.jds.2022.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/12/2022] [Indexed: 01/18/2023] Open
Abstract
Background/purpose Analysis of methylomes may enable prognostic stratification in patients with head and neck squamous cell carcinoma (HNSCC). This study aimed to identify methylation-related differentially expressed genes (mrDEGs), and to assess their efficacy in predicting patients' survival, tumor immune microenvironment alterations and immune checkpoints in patients with HNSCC. Materials and methods The methylome and transcriptome data of 528 HNSCC and 50 normal samples from TCGA database were used as training cohort. We identified mrDEGs and constituted a risk score model using Kaplan-Meier analysis and multivariate Cox regression. The prognostic efficacy of the risk score was validated in GSE65858 and GSE41613. We determined the enrichment of previously defined biological processes of mrDEGs. We separated the HNSCC patients into low-risk and high-risk groups and compared their immune cell infiltration and immune checkpoints' expressions. Results The risk score model was constituted by nine prognostic mrDEGs, including LIMD2, SYCP2, EPHX3, UCLH1, STC2, PRAME, SLC7A4, PLOD2, and ACADL. The risk score was a significant prognostic factor both in training (P < 0.001) and validation dataset (GSE65858: P = 0.008; GSE41613 = 0.015). The prognostic mrDEGs were enriched in multiple immune-associated pathways. Effector immune cells were increased in low-risk patients, including CD8+ T cells, activated CD4+ T cells, and plasma cells, whereas tumor associated M2 macrophages were recruited in the high-risk group. Expressions of immune checkpoints were generally higher in low-risk patients, including CTLA-4, PD-1 and LAG3. Conclusion The mrDEGs can stratify HNSCC patients' prognosis, which correlates with alterations in tumor immune infiltrations and immune checkpoints.
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Affiliation(s)
- Xudong Tian
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, China,Department of Head and Neck Oncology, West China College of Stomatology, Sichuan University, Chengdu, China
| | - Congyu Shi
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, China,Department of Head and Neck Oncology, West China College of Stomatology, Sichuan University, Chengdu, China
| | - Shan Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, China,Department of Head and Neck Oncology, West China College of Stomatology, Sichuan University, Chengdu, China
| | - Chengzhi Zhao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, China,Department of Oral and Maxillofacial Surgery, West China College of Stomatology, Sichuan University, Chengdu, China
| | - Xiaoyi Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, China,Department of Head and Neck Oncology, West China College of Stomatology, Sichuan University, Chengdu, China
| | - Yubin Cao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Sichuan University, Chengdu, China,Department of Oral and Maxillofacial Surgery, West China College of Stomatology, Sichuan University, Chengdu, China,Corresponding author. State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Head and Neck Oncology, West China College of Stomatology, Sichuan University, No. 14, 3rd Section of Ren Min Nan Rd, Chengdu, 610041, China.,
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Köhnke T, Liu X, Haubner S, Bücklein V, Hänel G, Krupka C, Solis-Mezarino V, Herzog F, Subklewe M. Integrated multiomic approach for identification of novel immunotherapeutic targets in AML. Biomark Res 2022; 10:43. [PMID: 35681175 PMCID: PMC9185890 DOI: 10.1186/s40364-022-00390-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/01/2022] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Immunotherapy of acute myeloid leukemia has experienced considerable advances, however novel target antigens continue to be sought after. To this end, unbiased approaches for surface protein detection are limited and integration with other data types, such as gene expression and somatic mutational burden, are poorly utilized. The Cell Surface Capture technology provides an unbiased, discovery-driven approach to map the surface proteins on cells of interest. Yet, direct utilization of primary patient samples has been limited by the considerable number of viable cells needed. METHODS Here, we optimized the Cell Surface Capture protocol to enable direct interrogation of primary patient samples and applied our optimized protocol to a set of samples from patients with acute myeloid leukemia (AML) to generate the AML surfaceome. We then further curated this AML surfaceome to exclude antigens expressed on healthy tissues and integrated mutational burden data from hematologic cancers to further enrich for targets which are likely to be essential to leukemia biology. Finally, we validated our findings in a separate cohort of AML patient samples. RESULTS Our protocol modifications allowed us to double the yield in identified proteins and increased the specificity from 54 to 80.4% compared to previous approaches. Using primary AML patient samples, we were able to identify a total of 621 surface proteins comprising the AML surfaceome. We integrated this data with gene expression and mutational burden data to curate a set of robust putative target antigens. Seventy-six proteins were selected as potential candidates for further investigation of which we validated the most promising novel candidate markers, and identified CD148, ITGA4 and Integrin beta-7 as promising targets in AML. Integrin beta-7 showed the most promising combination of expression in patient AML samples, and low or absent expression on healthy hematopoietic tissue. CONCLUSION Taken together, we demonstrate the feasibility of a highly optimized surfaceome detection method to interrogate the entire AML surfaceome directly from primary patient samples and integrate this data with gene expression and mutational burden data to achieve a robust, multiomic target identification platform. This approach has the potential to accelerate the unbiased target identification for immunotherapy of AML.
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Affiliation(s)
- Thomas Köhnke
- Department of Medicine III, University Hospital, LMU Munich, Marchioninistr 15, 81377, Munich, Germany.,Laboratory for Translational Cancer Immunology, Gene Center Munich, LMU Munich, Munich, Germany
| | - Xilong Liu
- Laboratory for Translational Cancer Immunology, Gene Center Munich, LMU Munich, Munich, Germany
| | - Sascha Haubner
- Department of Medicine III, University Hospital, LMU Munich, Marchioninistr 15, 81377, Munich, Germany.,Laboratory for Translational Cancer Immunology, Gene Center Munich, LMU Munich, Munich, Germany
| | - Veit Bücklein
- Department of Medicine III, University Hospital, LMU Munich, Marchioninistr 15, 81377, Munich, Germany.,Laboratory for Translational Cancer Immunology, Gene Center Munich, LMU Munich, Munich, Germany
| | - Gerulf Hänel
- Department of Medicine III, University Hospital, LMU Munich, Marchioninistr 15, 81377, Munich, Germany.,Laboratory for Translational Cancer Immunology, Gene Center Munich, LMU Munich, Munich, Germany
| | - Christina Krupka
- Laboratory for Translational Cancer Immunology, Gene Center Munich, LMU Munich, Munich, Germany
| | | | - Franz Herzog
- Department of Biochemistry, Gene Center, LMU Munich, Munich, Germany
| | - Marion Subklewe
- Department of Medicine III, University Hospital, LMU Munich, Marchioninistr 15, 81377, Munich, Germany. .,Laboratory for Translational Cancer Immunology, Gene Center Munich, LMU Munich, Munich, Germany. .,German Cancer Consortium (DKTK), Heidelberg, Germany. .,German Cancer Research Center (DKFZ), Heidelberg, Germany.
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6
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Gabusi A, Gissi DB, Grillini S, Stefanini M, Tarsitano A, Marchetti C, Foschini MP, Montebugnoli L, Morandi L. Shared epigenetic alterations between oral cancer and periodontitis: a preliminary study. Oral Dis 2022. [PMID: 35567390 DOI: 10.1111/odi.14251] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 04/13/2022] [Accepted: 05/11/2022] [Indexed: 11/28/2022]
Abstract
INTRODUCTION We recently developed a non-invasive sampling procedure for oral squamous cell carcinoma (OSCC) detection based on DNA methylation analysis of a panel of 13 genes. Oral cancer, as well as acute and chronic inflammatory diseases, may influence the methylation level of several genes in the oral cavity. In the present study, we evaluated the presence of periodontal disease(PD) and the methylation status using our 13-gene panel. METHODS Oral brushing specimens were collected from three different patient groups: 23 gingival OSCC patients, 15 patients affected by PD, and 15 healthy volunteers lacking evidence of PD. DNA methylation analysis was performed and each sample was determined to be positive or negative based on a predefined cut-off value. RESULTS Positive results were found for 23/23 OSCC patients, 3/15 PD patients and 0/15 samples from healthy volunteers. The GP1BB and MIR193 genes in the PD group exhibited mean methylation levels similar to OSCC patients. ZAP70 showed different methylation levels among three groups. CONCLUSION Preliminary data identified shared epigenetic alterations between PD and OSCC patients in two inflammatory genes(GP1BB and MIR193). This study may help identify potential links between the two diseases and serve as a starting point for future research focused on pathogenesis.
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Affiliation(s)
- Andrea Gabusi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy
| | - Davide B Gissi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy
| | - Sara Grillini
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy
| | - Martina Stefanini
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy
| | - Achille Tarsitano
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy.,Oral and Maxillo-facial Surgery Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna
| | - Claudio Marchetti
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy.,Oral and Maxillo-facial Surgery Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna
| | - Maria Pia Foschini
- Section of Anatomic Pathology at Bellaria Hospital, Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Lucio Montebugnoli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy
| | - Luca Morandi
- Functional MR Unit, IRCCS Istituto delle Scienze Neurologiche di Bologna, Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy.,IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
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7
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miRNA-Mediated Low Expression of EPHX3 Is Associated with Poor Prognosis and Tumor Immune Infiltration in Head and Neck Squamous Cell Carcinomas. JOURNAL OF ONCOLOGY 2022; 2022:7633720. [PMID: 35401746 PMCID: PMC8993555 DOI: 10.1155/2022/7633720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/10/2022] [Accepted: 03/20/2022] [Indexed: 11/17/2022]
Abstract
The aim of this study was to explore the regulatory role of epoxide hydrolase 3 (EPHX3) in head and neck squamous cell carcinoma (HNSCC) and to analyze its bioinformatic function, as well as, to screen and predict the miRNAs that can regulate EPHX3 expression in HNSCC. We examined the expression profile and prognostic potential of EPHX3 in TCGA and GTEX databases and performed functional enrichment analysis of EPHX3 using string database. Subsequently, we analyzed the regulatory role of miRNAs on EPHX3, including expression analysis, correlation analysis, and survival analysis. In addition, we also used TIMER to investigate the relationship among EPHX3 expression level, immune checkpoints, and immune infiltration in HNSCC. The results of data analysis after TGCA showed that EPHX3 is a key regulator of tumorigenesis in 13 cancers and can be used as a marker of poor prognosis in HNSCC patients. Bioinformatics analysis revealed that miR-4713-3p is a key miRNA of EPHX3 in HNSCC. Together, our findings indicate that EPHX3 exerts its anticancer effects by suppressing tumor immune checkpoint expression and immune cell infiltration. Overall, our data uncovered miRNA-mediated EPHX3 downregulation as a contributor to poor HNSCC prognosis and reduced tumor immune infiltration.
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Viet CT, Zhang X, Xu K, Yu G, Asam K, Thomas CM, Callahan NF, Doan C, Walker PC, Nguyen K, Kidd SC, Lee SC, Grandhi A, Allen CT, Young S, Melville JC, Shum JW, Viet DT, Herford AS, Roden DF, Gonzalez ML, Zhong JF, Aouizerat BE. Brush swab as a noninvasive surrogate for tissue biopsies in epigenomic profiling of oral cancer. Biomark Res 2021; 9:90. [PMID: 34930473 PMCID: PMC8686381 DOI: 10.1186/s40364-021-00349-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/28/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Oral squamous cell carcinoma (OSCC) has poor survival rates. There is a pressing need to develop more precise risk assessment methods to tailor clinical treatment. Epigenome-wide association studies in OSCC have not produced a viable biomarker. These studies have relied on methylation array platforms, which are limited in their ability to profile the methylome. In this study, we use MethylCap-Seq (MC-Seq), a comprehensive methylation quantification technique, and brush swab samples, to develop a noninvasive, readily translatable approach to profile the methylome in OSCC patients. METHODS Three OSCC patients underwent collection of cancer and contralateral normal tissue and brush swab biopsies, totaling 4 samples for each patient. Epigenome-wide DNA methylation quantification was performed using the SureSelectXT Methyl-Seq platform. DNA quality and methylation site resolution were compared between brush swab and tissue samples. Correlation and methylation value difference were determined for brush swabs vs. tissues for each respective patient and site (i.e., cancer or normal). Correlations were calculated between cancer and normal tissues and brush swab samples for each patient to determine the robustness of DNA methylation marks using brush swabs in clinical biomarker studies. RESULTS There were no significant differences in DNA yield between tissue and brush swab samples. Mapping efficiency exceeded 90% across all samples, with no differences between tissue and brush swabs. The average number of CpG sites with at least 10x depth of coverage was 2,716,674 for brush swabs and 2,903,261 for tissues. Matched tissue and brush swabs had excellent correlation (r = 0.913 for cancer samples and r = 0.951 for normal samples). The methylation profile of the top 1000 CpGs was significantly different between cancer and normal samples (mean p-value = 0.00021) but not different between tissues and brush swabs (mean p-value = 0.11). CONCLUSIONS Our results demonstrate that MC-Seq is an efficient platform for epigenome profiling in cancer biomarker studies, with broader methylome coverage than array-based platforms. Brush swab biopsy provides adequate DNA yield for MC-Seq, and taken together, our findings set the stage for development of a non-invasive methylome quantification technique for oral cancer with high translational potential.
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Affiliation(s)
- Chi T Viet
- Department of Oral and Maxillofacial Surgery, Loma Linda University School of Dentistry, Loma Linda, CA, USA.
| | - Xinyu Zhang
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- VA Connecticut Healthcare System, West Haven, CT, USA
| | - Ke Xu
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- VA Connecticut Healthcare System, West Haven, CT, USA
| | - Gary Yu
- New York University Rory Meyers College of Nursing, New York, NY, USA
| | - Kesava Asam
- Department of Oral and Maxillofacial Surgery, New York University College of Dentistry, New York, NY, USA
- Bluestone Center for Clinical Research, New York University College of Dentistry, New York, NY, USA
| | - Carissa M Thomas
- Department of Otolaryngology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nicholas F Callahan
- Department of Oral and Maxillofacial Surgery, University of Illinois Chicago, College of Dentistry, Chicago, IL, USA
| | - Coleen Doan
- Department of Oral and Maxillofacial Surgery, Loma Linda University School of Dentistry, Loma Linda, CA, USA
| | - Paul C Walker
- Department of Otolaryngology, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Khanh Nguyen
- Department of Otolaryngology, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Stephanie C Kidd
- Department of Otolaryngology, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Steve C Lee
- Department of Otolaryngology, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Anupama Grandhi
- Department of Oral and Maxillofacial Surgery, Loma Linda University School of Dentistry, Loma Linda, CA, USA
| | - Clint T Allen
- Section on Translational Tumor Immunology, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Simon Young
- Department of Oral, Head and Neck Oncology and Microvascular Reconstructive Surgery, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - James C Melville
- Department of Oral, Head and Neck Oncology and Microvascular Reconstructive Surgery, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jonathan W Shum
- Department of Oral, Head and Neck Oncology and Microvascular Reconstructive Surgery, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, USA
| | | | - Alan S Herford
- Department of Oral and Maxillofacial Surgery, Loma Linda University School of Dentistry, Loma Linda, CA, USA
| | - Dylan F Roden
- Department of Otolaryngology, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Manuel L Gonzalez
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jiang F Zhong
- Department of Basic Sciences, Loma Linda University, School of Medicine, Loma Linda, CA, USA
| | - Bradley E Aouizerat
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- VA Connecticut Healthcare System, West Haven, CT, USA
- New York University Rory Meyers College of Nursing, New York, NY, USA
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Head and Neck Cancers Are Not Alike When Tarred with the Same Brush: An Epigenetic Perspective from the Cancerization Field to Prognosis. Cancers (Basel) 2021; 13:cancers13225630. [PMID: 34830785 PMCID: PMC8616074 DOI: 10.3390/cancers13225630] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/30/2021] [Accepted: 11/02/2021] [Indexed: 12/26/2022] Open
Abstract
Simple Summary Squamous cell carcinomas affect different head and neck subsites and, although these tumors arise from the same epithelial lining and share risk factors, they differ in terms of clinical behavior and molecular carcinogenesis mechanisms. Differences between HPV-negative and HPV-positive tumors are those most frequently explored, but further data suggest that the molecular heterogeneity observed among head and neck subsites may go beyond HPV infection. In this review, we explore how alterations of DNA methylation and microRNA expression contribute to head and neck squamous cell carcinoma (HNSCC) development and progression. The association of these epigenetic alterations with risk factor exposure, early carcinogenesis steps, transformation risk, and prognosis are described. Finally, we discuss the potential application of the use of epigenetic biomarkers in HNSCC. Abstract Head and neck squamous cell carcinomas (HNSCC) are among the ten most frequent types of cancer worldwide and, despite all efforts, are still diagnosed at late stages and show poor overall survival. Furthermore, HNSCC patients often experience relapses and the development of second primary tumors, as a consequence of the field cancerization process. Therefore, a better comprehension of the molecular mechanisms involved in HNSCC development and progression may enable diagnosis anticipation and provide valuable tools for prediction of prognosis and response to therapy. However, the different biological behavior of these tumors depending on the affected anatomical site and risk factor exposure, as well as the high genetic heterogeneity observed in HNSCC are major obstacles in this pursue. In this context, epigenetic alterations have been shown to be common in HNSCC, to discriminate the tumor anatomical subsites, to be responsive to risk factor exposure, and show promising results in biomarker development. Based on this, this review brings together the current knowledge on alterations of DNA methylation and microRNA expression in HNSCC natural history, focusing on how they contribute to each step of the process and on their applicability as biomarkers of exposure, HNSCC development, progression, and response to therapy.
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Bononi G, Tuccinardi T, Rizzolio F, Granchi C. α/β-Hydrolase Domain (ABHD) Inhibitors as New Potential Therapeutic Options against Lipid-Related Diseases. J Med Chem 2021; 64:9759-9785. [PMID: 34213320 PMCID: PMC8389839 DOI: 10.1021/acs.jmedchem.1c00624] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Much of the experimental evidence in the literature has linked altered lipid metabolism to severe diseases such as cancer, obesity, cardiovascular pathologies, diabetes, and neurodegenerative diseases. Therefore, targeting key effectors of the dysregulated lipid metabolism may represent an effective strategy to counteract these pathological conditions. In this context, α/β-hydrolase domain (ABHD) enzymes represent an important and diversified family of proteins, which are involved in the complex environment of lipid signaling, metabolism, and regulation. Moreover, some members of the ABHD family play an important role in the endocannabinoid system, being designated to terminate the signaling of the key endocannabinoid regulator 2-arachidonoylglycerol. This Perspective summarizes the research progress in the development of ABHD inhibitors and modulators: design strategies, structure-activity relationships, action mechanisms, and biological studies of the main ABHD ligands will be highlighted.
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Affiliation(s)
- Giulia Bononi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Tiziano Tuccinardi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Flavio Rizzolio
- Pathology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy.,Department of Molecular Sciences and Nanosystems, Ca' Foscari University, 30123 Venezia, Italy
| | - Carlotta Granchi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
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Sorroche BP, Talukdar FR, Lima SCS, Melendez ME, de Carvalho AC, de Almeida GC, De Marchi P, Lopes M, Ribeiro Pinto LF, Carvalho AL, Herceg Z, Arantes LMRB. DNA Methylation Markers from Negative Surgical Margins Can Predict Recurrence of Oral Squamous Cell Carcinoma. Cancers (Basel) 2021; 13:2915. [PMID: 34207933 PMCID: PMC8230600 DOI: 10.3390/cancers13122915] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/21/2021] [Accepted: 05/27/2021] [Indexed: 12/02/2022] Open
Abstract
The identification of molecular markers in negative surgical margins of oral squamous cell carcinoma (OSCC) might help in identifying residual molecular aberrations, and potentially improve the prediction of prognosis. We performed an Infinium MethylationEPIC BeadChip array on 32 negative surgical margins stratified based on the status of tumor recurrence in order to identify recurrence-specific aberrant DNA methylation (DNAme) markers. We identified 2512 recurrence-associated Differentially Methylated Positions (DMPs) and 392 Differentially Methylated Regions (DMRs) which were enriched in cell signaling and cancer-related pathways. A set of 14-CpG markers was able to discriminate recurrent and non-recurrent cases with high specificity and sensitivity rates (AUC 0.98, p = 3 × 10-6; CI: 0.95-1). A risk score based on the 14-CpG marker panel was applied, with cases classified within higher risk scores exhibiting poorer survival. The results were replicated using tumor-adjacent normal HNSCC samples from The Cancer Genome Atlas (TCGA). We identified residual DNAme aberrations in the negative surgical margins of OSCC patients, which could be informative for patient management by improving therapeutic intervention. This study proposes a novel DNAme-based 14-CpG marker panel as a promising predictor for tumor recurrence, which might contribute to improved decision-making for the personalized treatment of OSCC cases.
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Affiliation(s)
- Bruna Pereira Sorroche
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, SP, Brazil; (B.P.S.); (M.E.M.); (A.C.d.C.); (A.L.C.)
| | | | - Sheila Coelho Soares Lima
- Molecular Carcinogenesis Program, Brazilian National Cancer Institute, Rio de Janeiro 20231-050, RJ, Brazil; (S.C.S.L.); (M.L.); (L.F.R.P.)
| | - Matias Eliseo Melendez
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, SP, Brazil; (B.P.S.); (M.E.M.); (A.C.d.C.); (A.L.C.)
| | - Ana Carolina de Carvalho
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, SP, Brazil; (B.P.S.); (M.E.M.); (A.C.d.C.); (A.L.C.)
| | | | - Pedro De Marchi
- Medical Oncology Department, Barretos Cancer Hospital, Barretos 14784-400, SP, Brazil;
- Oncoclínicas, Rio de Janeiro 22250-905, RJ, Brazil
| | - Monique Lopes
- Molecular Carcinogenesis Program, Brazilian National Cancer Institute, Rio de Janeiro 20231-050, RJ, Brazil; (S.C.S.L.); (M.L.); (L.F.R.P.)
| | - Luis Felipe Ribeiro Pinto
- Molecular Carcinogenesis Program, Brazilian National Cancer Institute, Rio de Janeiro 20231-050, RJ, Brazil; (S.C.S.L.); (M.L.); (L.F.R.P.)
| | - André Lopes Carvalho
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, SP, Brazil; (B.P.S.); (M.E.M.); (A.C.d.C.); (A.L.C.)
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer, 69008 Lyon, France;
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