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Zhang P, Tao C, Lu Y, Li P, Wang X, Dai Y, Xi Y, Shimura T, Li X, Fang J, Yang L, He D, Guo P. Epigenetic Reprogramming Potentiates ICAM1 Antibody Drug Conjugates in Preclinical Models of Melanoma. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400203. [PMID: 38874532 PMCID: PMC11321650 DOI: 10.1002/advs.202400203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 05/15/2024] [Indexed: 06/15/2024]
Abstract
Therapeutic benefits and underlying biomechanism(s) of antibody drug conjugates (ADC) in combination with other targeted therapeutics are largely unknown. Here, the synergy between ADC and epigenetic drug decitabine (DAC), a clinically approved DNA methylation inhibitor, in multiple preclinical models of melanoma specifically investigated. Mechanistically, the underlying biomechanisms of how DAC cooperatively worked with ICAM1 antibody conjugated DNA topoisomerase I inhibitor DXd (I1-DXd) is elucidated. DAC treatment significantly enhanced anti-tumor efficacy of I1-DXd by upregulating antigen expression, enhancing antibody internalization and potentiating tumor sensitivity by epigenetically reprogramming of melanoma. Meanwhile, I1-DXd/DAC combination also exerted regulatory effects on tumor microenvironment (TME) by enhancing tumor infiltration of innate and adaptive immune cells and improving penetration of ADCs with a boosted antitumor immunity. This study provides a rational ADC combination strategy for solid tumor treatment.
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Affiliation(s)
- Peng Zhang
- Department of Medical OncologyZhejiang Provincial People's HospitalHangzhouZhejiang310022China
- Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang ProvinceZhejiang Provincial People's HospitalPeople's Hospital of Hangzhou Medical CollegeHangzhouZhejiang310014China
- Hangzhou Institute of Medicine (HIM)Chinese Academy of SciencesHangzhouZhejiang310022China
| | - Changjuan Tao
- Department of Radiation OncologyThe Cancer Hospital of the University of Chinese Academy of SciencesZhejiang Cancer HospitalHangzhouZhejiang310022China
- Key Laboratory of Head and Neck Cancer Translational Research of Zhejiang ProvinceZhejiang Cancer HospitalHangzhouZhejiang310022China
| | - Ye Lu
- Hangzhou Institute of Medicine (HIM)Chinese Academy of SciencesHangzhouZhejiang310022China
| | - Peijing Li
- Department of Radiation OncologyThe Cancer Hospital of the University of Chinese Academy of SciencesZhejiang Cancer HospitalHangzhouZhejiang310022China
- Key Laboratory of Head and Neck Cancer Translational Research of Zhejiang ProvinceZhejiang Cancer HospitalHangzhouZhejiang310022China
| | - Xing Wang
- Department of Head and Neck SurgeryThe Cancer Hospital of the University of Chinese Academy of SciencesZhejiang Cancer HospitalHangzhouZhejiang310022China
| | - Yujie Dai
- MabPlex InternationalYantaiShandong264006China
| | - Yun Xi
- Department of PathologyThe Cancer Hospital of the University of Chinese Academy of SciencesZhejiang Cancer HospitalHangzhouZhejiang310022China
| | - Takaya Shimura
- Department of Gastroenterology and MetabolismNagoya City University Graduate School of Medical SciencesNagoya467–8601Japan
| | - Xinfang Li
- MabPlex InternationalYantaiShandong264006China
| | - Jianmin Fang
- School of Materials Science and EngineeringTianjin UniversityTianjin300072China
| | - Liu Yang
- Department of Medical OncologyZhejiang Provincial People's HospitalHangzhouZhejiang310022China
- Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang ProvinceZhejiang Provincial People's HospitalPeople's Hospital of Hangzhou Medical CollegeHangzhouZhejiang310014China
| | - Dawei He
- Department of UrologyChildren's Hospital of Chongqing Medical UniversityChongqingChina
| | - Peng Guo
- Hangzhou Institute of Medicine (HIM)Chinese Academy of SciencesHangzhouZhejiang310022China
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Fietz S, Diekmann E, de Vos L, Zarbl R, Hunecke A, Glosch AK, Färber M, Sirokay J, Hoffmann F, Fröhlich A, Franzen A, Strieth S, Landsberg J, Dietrich D. Circulating Cell-Free SHOX2 DNA Methylation Is a Predictive, Prognostic, and Monitoring Biomarker in Adjuvant and Palliative Anti-PD-1-Treated Melanoma. Clin Chem 2024; 70:516-527. [PMID: 38300881 DOI: 10.1093/clinchem/hvad230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 12/13/2023] [Indexed: 02/03/2024]
Abstract
BACKGROUND The majority of metastatic melanoma patients initially do not respond or acquire resistance to anti-programmed cell death 1 (PD-1) immunotherapy. Liquid biopsy biomarkers might provide useful early response information and allow for personalized treatment decisions. METHODS We prospectively assessed circulating cell-free SHOX2 DNA methylation (SHOX2 ccfDNAm) levels and their dynamic changes in blood plasma of melanoma patients by quantitative methylation-specific polymerase chain reaction. Patients were treated with either palliative (n = 42) or adjuvant (n = 55) anti-PD-1 immunotherapy. Moreover, we included n = 126 control patients without evidence of malignant disease. We analyzed SHOX2 ccfDNAm status prior to and 4 weeks after palliative treatment initiation with regard to outcome [objective response, progression-free survival (PFS), and overall survival (OS)]. In the adjuvant setting, we associated longitudinal SHOX2 ccfDNAm status with disease recurrence. RESULTS Sensitivity was 60% with 25/42 melanoma patients showing increased SHOX2 ccfDNAm levels, whereas specificity was 98% with 123/126 (P < 0.001) control patients having SHOX2 ccfDNAm levels below cut-off. Pretreatment SHOX2 ccfDNAm status did not correlate with outcome; however, SHOX2 ccfDNAm negativity 4 weeks after palliative treatment initiation was strongly associated with improved survival [PFS: hazard ratio (HR) = 0.25, P = 0.002; OS: HR = 0.12, P = 0.007]. Pretreatment positive patients who reached SHOX2 ccfDNAm clearance after 4 weeks of immunotherapy showed an exceptionally beneficial outcome. SHOX2 ccfDNAm testing allowed for an early detection of distant metastases in adjuvant-treated melanoma patients. CONCLUSIONS Our study suggests SHOX2 ccfDNAm to be an early predictor of outcome in anti-PD-1 treated melanoma patients. SHOX2 ccfDNAm testing may aid individualized treatment decision-making.
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Affiliation(s)
- Simon Fietz
- Department of Dermatology and Allergology, University Hospital Bonn, Bonn, Germany
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Eric Diekmann
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Luka de Vos
- Department of Dermatology and Allergology, University Hospital Bonn, Bonn, Germany
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Romina Zarbl
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Alina Hunecke
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Ann-Kathrin Glosch
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Moritz Färber
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Judith Sirokay
- Department of Dermatology and Allergology, University Hospital Bonn, Bonn, Germany
| | - Friederike Hoffmann
- Department of Dermatology and Allergology, University Hospital Bonn, Bonn, Germany
| | - Anne Fröhlich
- Department of Dermatology and Allergology, University Hospital Bonn, Bonn, Germany
| | - Alina Franzen
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Sebastian Strieth
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Jennifer Landsberg
- Department of Dermatology and Allergology, University Hospital Bonn, Bonn, Germany
| | - Dimo Dietrich
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
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Spiliopoulou P, Holanda Lopes CD, Spreafico A. Promising and Minimally Invasive Biomarkers: Targeting Melanoma. Cells 2023; 13:19. [PMID: 38201222 PMCID: PMC10777980 DOI: 10.3390/cells13010019] [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: 11/06/2023] [Revised: 11/29/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024] Open
Abstract
The therapeutic landscape of malignant melanoma has been radically reformed in recent years, with novel treatments emerging in both the field of cancer immunotherapy and signalling pathway inhibition. Large-scale tumour genomic characterization has accurately classified malignant melanoma into four different genomic subtypes so far. Despite this, only somatic mutations in BRAF oncogene, as assessed in tumour biopsies, has so far become a validated predictive biomarker of treatment with small molecule inhibitors. The biology of tumour evolution and heterogeneity has uncovered the current limitations associated with decoding genomic drivers based only on a single-site tumour biopsy. There is an urgent need to develop minimally invasive biomarkers that accurately reflect the real-time evolution of melanoma and that allow for streamlined collection, analysis, and interpretation. These will enable us to face challenges with tumour tissue attainment and process and will fulfil the vision of utilizing "liquid biopsy" to guide clinical decisions, in a manner akin to how it is used in the management of haematological malignancies. In this review, we will summarize the most recent published evidence on the role of minimally invasive biomarkers in melanoma, commenting on their future potential to lead to practice-changing discoveries.
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Affiliation(s)
- Pavlina Spiliopoulou
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada;
- School of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, UK
| | | | - Anna Spreafico
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada;
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Chatterjee K, Mal S, Ghosh M, Chattopadhyay NR, Roy SD, Chakraborty K, Mukherjee S, Aier M, Choudhuri T. Blood-based DNA methylation in advanced Nasopharyngeal Carcinoma exhibited distinct CpG methylation signature. Sci Rep 2023; 13:22086. [PMID: 38086861 PMCID: PMC10716134 DOI: 10.1038/s41598-023-45001-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 10/14/2023] [Indexed: 12/18/2023] Open
Abstract
The TNM staging system is currently used to detect cancer stages. Regardless, a small proportion of cancer patients recur even after therapy, suggesting more specific molecular tools are required to justify the stage-specific detection and prompt cancer diagnosis. Thus, we aimed to explore the blood-based DNA methylation signature of metastatic nasopharyngeal carcinoma (NPC) to establish a holistic methylation biomarker panel. For the identification of methylation signature, the EPIC BeadChip-based array was performed. Comparative analysis for identifying unique probes, validation, and functional studies was investigated by analyzing GEO and TCGA datasets. We observed 4093 differentially methylated probes (DMPs), 1232 hydroxymethylated probes, and 25 CpG islands. Gene expression study revealed both upregulated and downregulated genes. Correlation analysis suggested a positive (with a positive r, p ≤ 0.05) and negative (with a negative r, p ≤ 0.05) association with different cancers. TFBS analysis exhibited the binding site for many TFs. Furthermore, gene enrichment analysis indicated the involvement of those identified genes in biological pathways. However, blood-based DNA methylation data uncovered a distinct DNA methylation pattern, which might have an additive role in NPC progression by altering the TFs binding. Moreover, based on tissue-specificity, a variation of correlation between methylation and gene expression was noted in different cancers.
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Affiliation(s)
- Koustav Chatterjee
- Department of Biotechnology, Visva-Bharati, Santiniketan, Birbhum, West Bengal, India, 731235
| | - Sudipa Mal
- Department of Biotechnology, Visva-Bharati, Santiniketan, Birbhum, West Bengal, India, 731235
| | - Monalisha Ghosh
- Department of Biotechnology, Visva-Bharati, Santiniketan, Birbhum, West Bengal, India, 731235
| | | | - Sankar Deb Roy
- Department of Radiation Oncology, Eden Medical Center, Dimapur, Nagaland, India
| | - Koushik Chakraborty
- Department of Biotechnology, Visva-Bharati, Santiniketan, Birbhum, West Bengal, India, 731235
| | - Syamantak Mukherjee
- Department of Biotechnology, Visva-Bharati, Santiniketan, Birbhum, West Bengal, India, 731235
| | - Moatoshi Aier
- Department of Pathology, Eden Medical Center, Dimapur, Nagaland, India
| | - Tathagata Choudhuri
- Department of Biotechnology, Visva-Bharati, Santiniketan, Birbhum, West Bengal, India, 731235.
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Rubatto M, Borriello S, Sciamarrelli N, Pala V, Tonella L, Ribero S, Quaglino P. Exploring the role of epigenetic alterations and non-coding RNAs in melanoma pathogenesis and therapeutic strategies. Melanoma Res 2023; 33:462-474. [PMID: 37788101 DOI: 10.1097/cmr.0000000000000926] [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: 10/05/2023]
Abstract
Melanoma is a rare but highly lethal type of skin cancer whose incidence is increasing globally. Melanoma is characterized by high resistance to therapy and relapse. Despite significant advances in the treatment of metastatic melanoma, many patients experience progression due to resistance mechanisms. Epigenetic changes, including alterations in chromatin remodeling, DNA methylation, histone modifications, and non-coding RNA rearrangements, contribute to neoplastic transformation, metastasis, and drug resistance in melanoma. This review summarizes current research on epigenetic mechanisms in melanoma and their therapeutic potential. Specifically, we discuss the role of histone acetylation and methylation in gene expression regulation and melanoma pathobiology, as well as the promising results of HDAC inhibitors and DNMT inhibitors in clinical trials. We also examine the dysregulation of non-coding RNA, particularly miRNAs, and their potential as targets for melanoma therapy. Finally, we highlight the challenges of epigenetic therapies, such as the complexity of epigenetic mechanisms combined with immunotherapies and the need for combination therapies to overcome drug resistance. In conclusion, epigenetic changes may be reversible, and the use of combination therapy between traditional therapies and epigenetically targeted drugs could be a viable solution to reverse the increasing number of patients who develop treatment resistance or even prevent it. While several clinical trials are underway, the complexity of these mechanisms presents a significant challenge to the development of effective therapies. Further research is needed to fully understand the role of epigenetic mechanisms in melanoma and to develop more effective and targeted therapies.
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Affiliation(s)
- Marco Rubatto
- Department of Medical Sciences, Dermatologic Clinic, University of Turin Medical School, Turin, Italy
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Heft Neal ME, Walline HM, Haring CT. Circulating Tumor DNA in Human Papillomavirus-Mediated Oropharynx Cancer: Leveraging Early Data to Inform Future Directions. Cancer J 2023; 29:215-219. [PMID: 37471611 DOI: 10.1097/ppo.0000000000000670] [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: 07/22/2023]
Abstract
ABSTRACT Circulating tumor DNA (ctDNA) has become an area of intense study in many solid malignancies including head and neck cancer. This is of particular interest for human papillomavirus-mediated oropharyngeal squamous cell carcinoma as this cohort of patients has excellent survival and is undergoing current clinical trials aimed at treatment de-escalation. Recent studies have demonstrated the prognostic implications of pretreatment ctDNA and the utility of monitoring ctDNA during and posttreatment; however, there is a need for a more critical understanding of ctDNA as it is beginning to be incorporated into clinical trials. This review discusses the current state of ctDNA in oropharynx cancer focusing on ctDNA kinetics and minimal residual disease detection and ends with a discussion of future applications.
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Affiliation(s)
| | - Heather M Walline
- From the Department of Otolaryngology-Head and Neck Surgery, University of Michigan, Ann Arbor, MI
| | - Catherine T Haring
- Department of Otolaryngology-Head and Neck Surgery, The Ohio State University, Columbus, OH
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Song R, Liu F, Ping Y, Zhang Y, Wang L. Potential non-invasive biomarkers in tumor immune checkpoint inhibitor therapy: response and prognosis prediction. Biomark Res 2023; 11:57. [PMID: 37268978 DOI: 10.1186/s40364-023-00498-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/07/2023] [Indexed: 06/04/2023] Open
Abstract
Immune checkpoint inhibitors (ICIs) have dramatically enhanced the treatment outcomes for diverse malignancies. Yet, only 15-60% of patients respond significantly. Therefore, accurate responder identification and timely ICI administration are critical issues in tumor ICI therapy. Recent rapid developments at the intersection of oncology, immunology, biology, and computer science have provided an abundance of predictive biomarkers for ICI efficacy. These biomarkers can be invasive or non-invasive, depending on the specific sample collection method. Compared with invasive markers, a host of non-invasive markers have been confirmed to have superior availability and accuracy in ICI efficacy prediction. Considering the outstanding advantages of dynamic monitoring of the immunotherapy response and the potential for widespread clinical application, we review the recent research in this field with the aim of contributing to the identification of patients who may derive the greatest benefit from ICI therapy.
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Affiliation(s)
- Ruixia Song
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Henan Key Laboratory for Tumor Immunology and Biotherapy, Zhengzhou University, Zhengzhou, Henan, China
| | - Fengsen Liu
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Henan Key Laboratory for Tumor Immunology and Biotherapy, Zhengzhou University, Zhengzhou, Henan, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yu Ping
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yi Zhang
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
- Henan Key Laboratory for Tumor Immunology and Biotherapy, Zhengzhou University, Zhengzhou, Henan, China.
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China.
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou, Henan, China.
| | - Liping Wang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
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Huang CH, Han W, Wu YZ, Shen GL. Identification of aberrantly methylated differentially expressed genes and pro-tumorigenic role of KIF2C in melanoma. Front Genet 2022; 13:817656. [PMID: 35991567 PMCID: PMC9387026 DOI: 10.3389/fgene.2022.817656] [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: 11/18/2021] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Skin Cutaneous Melanoma (SKCM) is known as an aggressive malignant cancer, which could be directly derived from melanocytic nevi. However, the molecular mechanisms underlying the malignant transformation of melanocytes and melanoma tumor progression still remain unclear. Increasing research showed significant roles of epigenetic modifications, especially DNA methylation, in melanoma. This study focused on the identification and analysis of methylation-regulated differentially expressed genes (MeDEGs) between melanocytic nevus and malignant melanoma in genome-wide profiles.Methods: The gene expression profiling datasets (GSE3189 and GSE114445) and gene methylation profiling datasets (GSE86355 and GSE120878) were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) and differentially methylated genes (DMGs) were identified via GEO2R. MeDEGs were obtained by integrating the DEGs and DMGs. Then, a functional enrichment analysis of MeDEGs was performed. STRING and Cytoscape were used to describe the protein-protein interaction (PPI) network. Furthermore, survival analysis was implemented to select the prognostic hub genes. Next, we conducted gene set enrichment analysis (GSEA) of hub genes. To validate, SKCM cell culture and lentivirus infection was performed to reveal the expression and behavior pattern of KIF2C. Patients and specimens were collected and then immunohistochemistry (IHC) staining was conducted.Results: We identified 237 hypomethylated, upregulated genes and 182 hypermethylated, downregulated genes. Hypomethylation-upregulated genes were enriched in biological processes of the oxidation-reduction process, cell proliferation, cell division, phosphorylation, extracellular matrix disassembly and protein sumoylation. Pathway enrichment showed selenocompound metabolism, small cell lung cancer and lysosome. Hypermethylation-downregulated genes were enriched in biological processes of positive regulation of transcription from RNA polymerase II promoter, cell adhesion, cell proliferation, positive regulation of transcription, DNA-templated and angiogenesis. The most significantly enriched pathways involved the transcriptional misregulation in cancer, circadian rhythm, tight junction, protein digestion and absorption and Hippo signaling pathway. After PPI establishment and survival analysis, seven prognostic hub genes were CKS2, DTL, KIF2C, KPNA2, MYBL2, TPX2, and FBL. Moreover, the most involved hallmarks obtained by GSEA were E2F targets, G2M checkpoint and mitotic spindle. Importantly, among the 7 hub genes, we found that down-regulated level of KIF2C expression significantly inhibited the proliferative ability of SKCM cells and suppressed the metastasis capacity of SKCM cells.Conclusions: Our study identified potential aberrantly methylated-differentially expressed genes participating in the process of malignant transformation from nevus to melanoma tissues based on comprehensive genomic profiles. Transcription profiles of CKS2, DTL, KIF2C, KPNA2, MYBL2, TPX2, and FBL provided clues of aberrantly methylation-based biomarkers, which might improve the development of precision medicine. KIF2C plays a pro-tumorigenic role and potentially inhibited the proliferative ability in SKCM.
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Affiliation(s)
- Chun-Hui Huang
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
- Department of Surgery, Soochow University, Suzhou, China
| | - Wei Han
- Institute of Regenerative Biology and Medicine, Helmholtz Zentrum München, Munich, Germany
| | - Yi-Zhu Wu
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
- Department of Surgery, Soochow University, Suzhou, China
| | - Guo-Liang Shen
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
- Department of Surgery, Soochow University, Suzhou, China
- *Correspondence: Guo-Liang Shen,
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Dobre EG, Constantin C, Neagu M. Skin Cancer Research Goes Digital: Looking for Biomarkers within the Droplets. J Pers Med 2022; 12:jpm12071136. [PMID: 35887633 PMCID: PMC9323323 DOI: 10.3390/jpm12071136] [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: 06/02/2022] [Revised: 07/12/2022] [Accepted: 07/12/2022] [Indexed: 12/24/2022] Open
Abstract
Skin cancer, which includes the most frequent malignant non-melanoma carcinomas (basal cell carcinoma, BCC, and squamous cell carcinoma, SCC), along with the difficult to treat cutaneous melanoma (CM), pose important worldwide issues for the health care system. Despite the improved anti-cancer armamentarium and the latest scientific achievements, many skin cancer patients fail to respond to therapies, due to the remarkable heterogeneity of cutaneous tumors, calling for even more sophisticated biomarker discovery and patient monitoring approaches. Droplet digital polymerase chain reaction (ddPCR), a robust method for detecting and quantifying low-abundance nucleic acids, has recently emerged as a powerful technology for skin cancer analysis in tissue and liquid biopsies (LBs). The ddPCR method, being capable of analyzing various biological samples, has proved to be efficient in studying variations in gene sequences, including copy number variations (CNVs) and point mutations, DNA methylation, circulatory miRNome, and transcriptome dynamics. Moreover, ddPCR can be designed as a dynamic platform for individualized cancer detection and monitoring therapy efficacy. Here, we present the latest scientific studies applying ddPCR in dermato-oncology, highlighting the potential of this technology for skin cancer biomarker discovery and validation in the context of personalized medicine. The benefits and challenges associated with ddPCR implementation in the clinical setting, mainly when analyzing LBs, are also discussed.
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Affiliation(s)
- Elena-Georgiana Dobre
- Faculty of Biology, University of Bucharest, Splaiul Independentei 91–95, 050095 Bucharest, Romania;
- Correspondence:
| | - Carolina Constantin
- Immunology Department, “Victor Babes” National Institute of Pathology, 050096 Bucharest, Romania;
- Pathology Department, Colentina Clinical Hospital, 020125 Bucharest, Romania
| | - Monica Neagu
- Faculty of Biology, University of Bucharest, Splaiul Independentei 91–95, 050095 Bucharest, Romania;
- Immunology Department, “Victor Babes” National Institute of Pathology, 050096 Bucharest, Romania;
- Pathology Department, Colentina Clinical Hospital, 020125 Bucharest, Romania
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Promising Blood-Based Biomarkers for Melanoma: Recent Progress of Liquid Biopsy and Its Future Perspectives. Curr Treat Options Oncol 2022; 23:562-577. [PMID: 35298769 DOI: 10.1007/s11864-022-00948-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2021] [Indexed: 12/11/2022]
Abstract
OPINION STATEMENT Because the recent success of novel therapeutic approaches has dramatically changed the clinical management of melanoma, less invasive and repeatable monitoring tools that can predict the disease status, drug resistance, and the development of side effects are increasingly needed. As liquid biopsy has enabled us to diagnose and monitor disease status less invasively, substantial attention has been directed toward this technique, which is gaining importance as a diagnostic and/or prognostic tool. It is evident that microRNA, cell-free DNA, and circulating tumor cells obtained via liquid biopsy are promising diagnostic and prognostic tools for melanoma, and they also have utility for monitoring the disease status and predicting drug effects. Although current challenges exist for each biomarker, such as poor sensitivity and/or specificity and technical problems, recent technical advances have increasingly improved these aspects. For example, next-generation sequencing technology for detecting microRNAs or cell-free DNA enabled high-throughput analysis and provided significantly higher sensitivity. In particular, cancer personalized profiling by deep sequencing for quantifying cell-free DNA is a promising method for high-throughput analysis that provides real-time comprehensive data for patients at various disease stages. For wide clinical implementation, it is necessary to increase the sensitivity for the markers and standardize the assay procedures to make them reproducible, valid, and inexpensive; however, the broad clinical application of liquid biopsy could occur quickly. This review focuses on the significance of liquid biopsy, particularly related to the use of blood samples from patients with melanoma, and discusses its future perspectives.
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Aleotti V, Catoni C, Poggiana C, Rosato A, Facchinetti A, Scaini MC. Methylation Markers in Cutaneous Melanoma: Unravelling the Potential Utility of Their Tracking by Liquid Biopsy. Cancers (Basel) 2021; 13:6217. [PMID: 34944843 PMCID: PMC8699653 DOI: 10.3390/cancers13246217] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/02/2021] [Accepted: 12/08/2021] [Indexed: 01/19/2023] Open
Abstract
Malignant melanoma is the most serious, life-threatening form of all dermatologic diseases, with a poor prognosis in the presence of metastases and advanced disease. Despite recent advances in targeted therapy and immunotherapy, there is still a critical need for a better understanding of the fundamental mechanisms behind melanoma progression and resistance onset. Recent advances in genome-wide methylation methods have revealed that aberrant changes in the pattern of DNA methylation play an important role in many aspects of cancer progression, including cell proliferation and migration, evasion of cell death, invasion, and metastasization. The purpose of the current review was to gather evidence regarding the usefulness of DNA methylation tracking in liquid biopsy as a potential biomarker in melanoma. We investigated the key genes and signal transduction pathways that have been found to be altered epigenetically in melanoma. We then highlighted the circulating tumor components present in blood, including circulating melanoma cells (CMC), circulating tumor DNA (ctDNA), and tumor-derived extracellular vesicles (EVs), as a valuable source for identifying relevant aberrations in DNA methylation. Finally, we focused on DNA methylation signatures as a marker for tracking response to therapy and resistance, thus facilitating personalized medicine and decision-making in the treatment of melanoma patients.
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Affiliation(s)
- Valentina Aleotti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy; (V.A.); (C.C.); (A.F.); (M.C.S.)
| | - Cristina Catoni
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy; (V.A.); (C.C.); (A.F.); (M.C.S.)
| | - Cristina Poggiana
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy; (V.A.); (C.C.); (A.F.); (M.C.S.)
| | - Antonio Rosato
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy; (V.A.); (C.C.); (A.F.); (M.C.S.)
- Department of Surgery, Oncology and Gastroenterology, Oncology and Immunology Section, University of Padua, 35128 Padua, Italy
| | - Antonella Facchinetti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy; (V.A.); (C.C.); (A.F.); (M.C.S.)
- Department of Surgery, Oncology and Gastroenterology, Oncology and Immunology Section, University of Padua, 35128 Padua, Italy
| | - Maria Chiara Scaini
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy; (V.A.); (C.C.); (A.F.); (M.C.S.)
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Kamińska P, Buszka K, Zabel M, Nowicki M, Alix-Panabières C, Budna-Tukan J. Liquid Biopsy in Melanoma: Significance in Diagnostics, Prediction and Treatment Monitoring. Int J Mol Sci 2021; 22:9714. [PMID: 34575876 PMCID: PMC8468624 DOI: 10.3390/ijms22189714] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/25/2021] [Accepted: 09/06/2021] [Indexed: 02/06/2023] Open
Abstract
Liquid biopsy is a common term referring to circulating tumor cells and other biomarkers, such as circulating tumor DNA (ctDNA) or extracellular vesicles. Liquid biopsy presents a range of clinical advantages, such as the low invasiveness of the blood sample collection and continuous control of the tumor progression. In addition, this approach enables the mechanisms of drug resistance to be determined in various methods of cancer treatment, including immunotherapy. However, in the case of melanoma, the application of liquid biopsy in patient stratification and therapy needs further investigation. This review attempts to collect all of the relevant and recent information about circulating melanoma cells (CMCs) related to the context of malignant melanoma and immunotherapy. Furthermore, the biology of liquid biopsy analytes, including CMCs, ctDNA, mRNA and exosomes, as well as techniques for their detection and isolation, are also described. The available data support the notion that thoughtful selection of biomarkers and technologies for their detection can contribute to the development of precision medicine by increasing the efficacy of cancer diagnostics and treatment.
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Affiliation(s)
- Paula Kamińska
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (P.K.); (K.B.); (M.N.)
| | - Karolina Buszka
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (P.K.); (K.B.); (M.N.)
| | - Maciej Zabel
- Department of Anatomy and Histology, Collegium Medicum, University of Zielona Góra, 65-046 Zielona Góra, Poland;
| | - Michał Nowicki
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (P.K.); (K.B.); (M.N.)
| | - Catherine Alix-Panabières
- Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Centre of Montpellier, 34093 Montpellier, France;
- CREEC/CANECEV, MIVEGEC (CREES), University of Montpellier, CNRS, IRD, 34000 Montpellier, France
| | - Joanna Budna-Tukan
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (P.K.); (K.B.); (M.N.)
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Revythis A, Shah S, Kutka M, Moschetta M, Ozturk MA, Pappas-Gogos G, Ioannidou E, Sheriff M, Rassy E, Boussios S. Unraveling the Wide Spectrum of Melanoma Biomarkers. Diagnostics (Basel) 2021; 11:diagnostics11081341. [PMID: 34441278 PMCID: PMC8391989 DOI: 10.3390/diagnostics11081341] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 12/24/2022] Open
Abstract
The use of biomarkers in medicine has become essential in clinical practice in order to help with diagnosis, prognostication and prediction of treatment response. Since Alexander Breslow’s original report on “melanoma and prognostic values of thickness”, providing the first biomarker for melanoma, many promising new biomarkers have followed. These include serum markers, such as lactate dehydrogenase and S100 calcium-binding protein B. However, as our understanding of the DNA mutational profile progresses, new gene targets and proteins have been identified. These include point mutations, such as mutations of the BRAF gene and tumour suppressor gene tP53. At present, only a small number of the available biomarkers are being utilised, but this may soon change as more studies are published. The aim of this article is to provide a comprehensive review of melanoma biomarkers and their utility for current and, potentially, future clinical practice.
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Affiliation(s)
- Antonios Revythis
- Department of Medical Oncology, Medway NHS Foundation Trust, Windmill Road, Gillingham ME7 5NY, UK; (A.R.); (S.S.); (M.K.)
| | - Sidrah Shah
- Department of Medical Oncology, Medway NHS Foundation Trust, Windmill Road, Gillingham ME7 5NY, UK; (A.R.); (S.S.); (M.K.)
| | - Mikolaj Kutka
- Department of Medical Oncology, Medway NHS Foundation Trust, Windmill Road, Gillingham ME7 5NY, UK; (A.R.); (S.S.); (M.K.)
| | - Michele Moschetta
- CHUV, Lausanne University Hospital, Rue du Bugnon, 21 CH-1011 Lausanne, Switzerland;
| | - Mehmet Akif Ozturk
- Department of Internal Medicine, School of Medicine, Bahcesehir University, Istanbul 34353, Turkey;
| | - George Pappas-Gogos
- Department of Surgery, University Hospital of Ioannina, 45111 Ioannina, Greece;
| | - Evangelia Ioannidou
- Department of Paediatrics and Child Health, West Suffolk Hospital NHS Foundation Trust, Hardwick Lane, Bury St Edmunds IP33 2QZ, UK;
| | - Matin Sheriff
- Department of Urology, Medway NHS Foundation Trust, Windmill Road, Gillingham ME7 5NY, UK;
| | - Elie Rassy
- Department of Cancer Medicine, Gustave Roussy Institut, 94805 Villejuif, France;
| | - Stergios Boussios
- Department of Medical Oncology, Medway NHS Foundation Trust, Windmill Road, Gillingham ME7 5NY, UK; (A.R.); (S.S.); (M.K.)
- Faculty of Life Sciences & Medicine, School of Cancer & Pharmaceutical Sciences, King’s College London, London SE1 9RT, UK
- AELIA Organization, 9th Km Thessaloniki-Thermi, 57001 Thessaloniki, Greece
- Correspondence: or or
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14
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Palanca-Ballester C, Rodriguez-Casanova A, Torres S, Calabuig-Fariñas S, Exposito F, Serrano D, Redin E, Valencia K, Jantus-Lewintre E, Diaz-Lagares A, Montuenga L, Sandoval J, Calvo A. Cancer Epigenetic Biomarkers in Liquid Biopsy for High Incidence Malignancies. Cancers (Basel) 2021; 13:cancers13123016. [PMID: 34208598 PMCID: PMC8233712 DOI: 10.3390/cancers13123016] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 02/07/2023] Open
Abstract
Early alterations in cancer include the deregulation of epigenetic events such as changes in DNA methylation and abnormal levels of non-coding (nc)RNAs. Although these changes can be identified in tumors, alternative sources of samples may offer advantages over tissue biopsies. Because tumors shed DNA, RNA, and proteins, biological fluids containing these molecules can accurately reflect alterations found in cancer cells, not only coming from the primary tumor, but also from metastasis and from the tumor microenvironment (TME). Depending on the type of cancer, biological fluids encompass blood, urine, cerebrospinal fluid, and saliva, among others. Such samples are named with the general term "liquid biopsy" (LB). With the advent of ultrasensitive technologies during the last decade, the identification of actionable genetic alterations (i.e., mutations) in LB is a common practice to decide whether or not targeted therapy should be applied. Likewise, the analysis of global or specific epigenetic alterations may also be important as biomarkers for diagnosis, prognosis, and even for cancer drug response. Several commercial kits that assess the DNA promoter methylation of single genes or gene sets are available, with some of them being tested as biomarkers for diagnosis in clinical trials. From the tumors with highest incidence, we can stress the relevance of DNA methylation changes in the following genes found in LB: SHOX2 (for lung cancer); RASSF1A, RARB2, and GSTP1 (for lung, breast, genitourinary and colon cancers); and SEPT9 (for colon cancer). Moreover, multi-cancer high-throughput methylation-based tests are now commercially available. Increased levels of the microRNA miR21 and several miRNA- and long ncRNA-signatures can also be indicative biomarkers in LB. Therefore, epigenetic biomarkers are attractive and may have a clinical value in cancer. Nonetheless, validation, standardization, and demonstration of an added value over the common clinical practice are issues needed to be addressed in the transfer of this knowledge from "bench to bedside".
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Affiliation(s)
- Cora Palanca-Ballester
- Biomarkers and Precision Medicine (UBMP) and Epigenomics Unit, IIS, La Fe, 46026 Valencia, Spain;
| | - Aitor Rodriguez-Casanova
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, Spain; (A.R.-C.); (A.D.-L.)
- Roche-CHUS Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, Spain
| | - Susana Torres
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, 46014 Valencia, Spain
- TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, 46014 Valencia, Spain
| | - Silvia Calabuig-Fariñas
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, 46014 Valencia, Spain
- TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, 46014 Valencia, Spain
- Department of Pathology, Universitat de València, 46010 Valencia, Spain
| | - Francisco Exposito
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Diego Serrano
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Esther Redin
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Karmele Valencia
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Biochemistry and Genetics, School of Sciences, University of Navarra, 31008 Pamplona, Spain
| | - Eloisa Jantus-Lewintre
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, 46014 Valencia, Spain
- TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, 46014 Valencia, Spain
- Department of Biotechnology, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Angel Diaz-Lagares
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, Spain; (A.R.-C.); (A.D.-L.)
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
| | - Luis Montuenga
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Juan Sandoval
- Biomarkers and Precision Medicine (UBMP) and Epigenomics Unit, IIS, La Fe, 46026 Valencia, Spain;
- Correspondence: (J.S.); (A.C.)
| | - Alfonso Calvo
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
- Correspondence: (J.S.); (A.C.)
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Zheng Y, Sun H, Cong L, Liu C, Sun Q, Wu N, Cong X. Prognostic Value of ctDNA Mutation in Melanoma: A Meta-Analysis. JOURNAL OF ONCOLOGY 2021; 2021:6660571. [PMID: 34035810 PMCID: PMC8116156 DOI: 10.1155/2021/6660571] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 03/18/2021] [Accepted: 03/26/2021] [Indexed: 01/11/2023]
Abstract
PURPOSE Melanoma is the most aggressive form of skin cancer. Circulating tumor DNA (ctDNA) is a diagnostic and prognostic marker of melanoma. However, whether ctDNA mutations can independently predict survival remains controversial. This meta-analysis assessed the prognostic value of the presence or change in ctDNA mutations in melanoma patients. METHODS We identified studies from the PubMed, EMBASE, Web of Science, and Cochrane databases. We estimated the combined hazard ratios (HRs) for overall survival (OS) and progression-free survival (PFS) using either fixed-effect or random-effect models based on heterogeneity. RESULTS Sixteen studies including 1,781 patients were included. Both baseline and posttreatment detectable ctDNA were associated with poor OS (baseline detectable vs. undetectable, pooled HR = 1.97, 95% CI = 1.64-2.36, P < 0.00001; baseline undetectable vs. detectable, pooled HR = 0.19, 95% CI = 0.11-0.36, P < 0.00001; posttreatment detectable vs. undetectable, pooled HR = 2.36, 95% CI = 1.30-4.28, P=0.005). For PFS, baseline detectable ctDNA may be associated with adverse PFS (baseline detectable vs. undetectable, pooled HR = 1.41, 95% CI = 0.84-2.37, P=0.19; baseline undetectable vs. detectable, pooled HR = 0.43, 95% CI = 0.19-0.95, P=0.04) and baseline high ctDNA and increased ctDNA were significantly associated with adverse PFS (baseline high vs. low/undetectable, pooled HR = 3.29, 95% CI = 1.73-6.25, P=0.0003; increase vs. decrease, pooled HR = 4.48, 95% CI = 2.45-8.17, P < 0.00001). The baseline BRAFV600 ctDNA mutation-positive group was significantly associated with adverse OS compared with the baseline ctDNA-negative group (pooled HR = 1.90, 95% CI = 1.58-2.29, P < 0.00001). There were no significant differences in PFS between the baseline BRAFV600 ctDNA mutation-detectable group and the undetectable group (pooled HR = 1.02, 95% CI = 0.72-1.44, P=0.92). CONCLUSION The presence or elevation of ctDNA mutation or BRAFV600 ctDNA mutation was significantly associated with worse prognosis in melanoma patients.
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Affiliation(s)
- Yang Zheng
- Department of Dermatology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Hongyan Sun
- Biobank, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Lele Cong
- Department of Dermatology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Chenlu Liu
- Biobank, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Qian Sun
- Department of Dermatology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Nan Wu
- Department of Dermatology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Xianling Cong
- Department of Dermatology, China-Japan Union Hospital of Jilin University, Changchun, China
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16
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Emerging noninvasive methylation biomarkers of cancer prognosis and drug response prediction. Semin Cancer Biol 2021; 83:584-595. [PMID: 33757849 DOI: 10.1016/j.semcancer.2021.03.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/15/2021] [Accepted: 03/16/2021] [Indexed: 12/27/2022]
Abstract
Cancer is the second leading cause of death worldwide being responsible for 9.6 million deaths in 2018. Epigenetic alterations are key in directing the aberrant expression of tumor-associated genes that drive cellular malignant transformation and cancer progression. Among epigenetic alterations, DNA methylation is the most deeply studied one in relation to environmental exposure. Tissue biopsies have traditionally been the main procedure by which a small sample of body tissue is excised to confirm cancer diagnosis or to indicate the primary site when cancer has spread. In contrast, the analysis of circulating tumor-derived material, or tumor circulome, by means of liquid biopsy of peripheral blood, urine, saliva or sputum is a noninvasive, fast and reproducible alternative to tissue biopsy. Recently, the assessment of epigenetic alterations such as DNA methylation and hydroxymethylation in circulating free DNA has been proved possible. These marks can be associated to prognosis and response to a variety of treatments including chemotherapy, hormonotherapy or immunotherapy. Epigenetic biomarkers may offer some advantages over RNA or genetic biomarkers given their stability in bodily fluids and their high tissue-specificity. While many challenges are still ahead, the unique advantages of these types of biomarkers is urging the scientific community to persevere in their clinical validation and integration into reliable prediction models. This review aims at recapitulating the emerging noninvasive DNA methylated biomarkers of importance for prediction of prognosis and drug response in cancer.
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17
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Pinzani P, D'Argenio V, Del Re M, Pellegrini C, Cucchiara F, Salvianti F, Galbiati S. Updates on liquid biopsy: current trends and future perspectives for clinical application in solid tumors. Clin Chem Lab Med 2021; 59:1181-1200. [PMID: 33544478 DOI: 10.1515/cclm-2020-1685] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/20/2021] [Indexed: 01/19/2023]
Abstract
Despite advances in screening and therapeutics cancer continues to be one of the major causes of morbidity and mortality worldwide. The molecular profile of tumor is routinely assessed by surgical or bioptic samples, however, genotyping of tissue has inherent limitations: it represents a single snapshot in time and it is subjected to spatial selection bias owing to tumor heterogeneity. Liquid biopsy has emerged as a novel, non-invasive opportunity of detecting and monitoring cancer in several body fluids instead of tumor tissue. Circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), RNA (mRNA and microRNA), microvesicles, including exosomes and tumor "educated platelets" were recently identified as a source of genomic information in cancer patients which could reflect all subclones present in primary and metastatic lesions allowing sequential monitoring of disease evolution. In this review, we summarize the currently available information concerning liquid biopsy in breast cancer, colon cancer, lung cancer and melanoma. These promising issues still need to be standardized and harmonized across laboratories, before fully adopting liquid biopsy approaches into clinical practice.
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Affiliation(s)
- Pamela Pinzani
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Valeria D'Argenio
- Department of Human Sciences and Quality of Life Promotion, San Raffaele Open University, Rome, Italy.,CEINGE-Biotecnologie Avanzate, Naples, Italy
| | - Marzia Del Re
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Cristina Pellegrini
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Federico Cucchiara
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Francesca Salvianti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Silvia Galbiati
- Diabetes Research Institute, IRCCS Ospedale San Raffaele, Milan, Italy
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Abstract
Cell-free DNA (cfDNA) has the potential to enable non-invasive detection of disease states and progression. Beyond its sequence, cfDNA also represents the nucleosomal landscape of cell(s)-of-origin and captures the dynamics of the epigenome. In this review, we highlight the emergence of cfDNA epigenomic methods that assess disease beyond the scope of mutant tumour genotyping. Detection of tumour mutations is the gold standard for sequencing methods in clinical oncology. However, limitations inherent to mutation targeting in cfDNA, and the possibilities of uncovering molecular mechanisms underlying disease, have made epigenomics of cfDNA an exciting alternative. We discuss the epigenomic information revealed by cfDNA, and how epigenomic methods exploit cfDNA to detect and characterize cancer. Future applications of cfDNA epigenomic methods to act complementarily and orthogonally to current clinical practices has the potential to transform cancer management and improve cancer patient outcomes.
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Affiliation(s)
| | | | - Srinivas Ramachandran
- RNA Bioscience Initiative, and Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Mail Stop: 8101, 12801 East 17th Avenue L18–9102, Aurora, CO 80045, USA
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19
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Pradhan D, Jour G, Milton D, Vasudevaraja V, Tetzlaff MT, Nagarajan P, Curry JL, Ivan D, Long L, Ding Y, Ezhilarasan R, Sulman EP, Diab A, Hwu WJ, Prieto VG, Torres-Cabala CA, Aung PP. Aberrant DNA Methylation Predicts Melanoma-Specific Survival in Patients with Acral Melanoma. Cancers (Basel) 2019; 11:cancers11122031. [PMID: 31888295 PMCID: PMC6966546 DOI: 10.3390/cancers11122031] [Citation(s) in RCA: 10] [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: 10/21/2019] [Revised: 12/06/2019] [Accepted: 12/12/2019] [Indexed: 02/06/2023] Open
Abstract
Acral melanoma (AM) is a rare, aggressive type of cutaneous melanoma (CM) with a distinct genetic profile. We aimed to identify a methylome signature distinguishing primary acral lentiginous melanoma (PALM) from primary non-lentiginous AM (NALM), metastatic ALM (MALM), primary non-acral CM (PCM), and acral nevus (AN). A total of 22 PALM, nine NALM, 10 MALM, nine PCM, and three AN were subjected to genome-wide methylation analysis using the Illumina Infinium Methylation EPIC array interrogating 866,562 CpG sites. A prominent finding was that the methylation profiles of PALM and NALM were distinct. Four of the genes most differentially methylated between PALM and NALM or MALM were HHEX, DIPK2A, NELFB, and TEF. However, when primary AMs (PALM + NALM) were compared with MALM, IFITM1 and SIK3 were the most differentially methylated, highlighting their pivotal role in the metastatic potential of AMs. Patients with NALM had significantly worse disease-specific survival (DSS) than patients with PALM. Aberrant methylation was significantly associated with aggressive clinicopathologic parameters and worse DSS. Our study emphasizes the importance of distinguishing the two epigenetically distinct subtypes of AM. We also identified novel epigenetic prognostic biomarkers that may serve to risk-stratify patients with AM and may be leveraged for the development of targeted therapies.
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Affiliation(s)
- Dinesh Pradhan
- Department of Pathology, Section of Dermatopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (D.P.); (M.T.T.); (P.N.); (J.L.C.); (D.I.); (V.G.P.)
| | - George Jour
- Department of Pathology and Dermatology, NYU Langone Medical Center, New York, NY 10016, USA; (G.J.); (V.V.)
| | - Denái Milton
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Varshini Vasudevaraja
- Department of Pathology and Dermatology, NYU Langone Medical Center, New York, NY 10016, USA; (G.J.); (V.V.)
| | - Michael T. Tetzlaff
- Department of Pathology, Section of Dermatopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (D.P.); (M.T.T.); (P.N.); (J.L.C.); (D.I.); (V.G.P.)
- Department of Translational and Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Priyadharsini Nagarajan
- Department of Pathology, Section of Dermatopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (D.P.); (M.T.T.); (P.N.); (J.L.C.); (D.I.); (V.G.P.)
| | - Jonathan L. Curry
- Department of Pathology, Section of Dermatopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (D.P.); (M.T.T.); (P.N.); (J.L.C.); (D.I.); (V.G.P.)
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Doina Ivan
- Department of Pathology, Section of Dermatopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (D.P.); (M.T.T.); (P.N.); (J.L.C.); (D.I.); (V.G.P.)
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lihong Long
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Yingwen Ding
- Department of Radiation Oncology, NYU Langone School of Medicine, New York, NY 10016, USA; (Y.D.); (R.E.); (E.P.S.)
| | - Ravesanker Ezhilarasan
- Department of Radiation Oncology, NYU Langone School of Medicine, New York, NY 10016, USA; (Y.D.); (R.E.); (E.P.S.)
| | - Erik P. Sulman
- Department of Radiation Oncology, NYU Langone School of Medicine, New York, NY 10016, USA; (Y.D.); (R.E.); (E.P.S.)
| | - Adi Diab
- Department of Melanoma Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (A.D.); (W.-J.H.)
| | - Wen-Jen Hwu
- Department of Melanoma Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (A.D.); (W.-J.H.)
| | - Victor G. Prieto
- Department of Pathology, Section of Dermatopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (D.P.); (M.T.T.); (P.N.); (J.L.C.); (D.I.); (V.G.P.)
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Carlos Antonio Torres-Cabala
- Department of Pathology, Section of Dermatopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (D.P.); (M.T.T.); (P.N.); (J.L.C.); (D.I.); (V.G.P.)
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Correspondence: (C.A.T.-C.); (P.P.A.); Tel.: +713-752-2351 (C.A.T.-C.); +713-794-4951 (P.P.A.)
| | - Phyu P. Aung
- Department of Pathology, Section of Dermatopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (D.P.); (M.T.T.); (P.N.); (J.L.C.); (D.I.); (V.G.P.)
- Correspondence: (C.A.T.-C.); (P.P.A.); Tel.: +713-752-2351 (C.A.T.-C.); +713-794-4951 (P.P.A.)
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20
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Bhalla S, Kaur H, Dhall A, Raghava GPS. Prediction and Analysis of Skin Cancer Progression using Genomics Profiles of Patients. Sci Rep 2019; 9:15790. [PMID: 31673075 PMCID: PMC6823463 DOI: 10.1038/s41598-019-52134-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 10/07/2019] [Indexed: 02/07/2023] Open
Abstract
The metastatic Skin Cutaneous Melanoma (SKCM) has been associated with diminished survival rates and high mortality rates worldwide. Thus, segregating metastatic melanoma from the primary tumors is crucial to employ an optimal therapeutic strategy for the prolonged survival of patients. The SKCM mRNA, miRNA and methylation data of TCGA is comprehensively analysed to recognize key genomic features that can segregate metastatic and primary tumors. Further, machine learning models have been developed using selected features to distinguish the same. The Support Vector Classification with Weight (SVC-W) model developed using the expression of 17 mRNAs achieved Area under the Receiver Operating Characteristic (AUROC) curve of 0.95 and an accuracy of 89.47% on an independent validation dataset. This study reveals the genes C7, MMP3, KRT14, LOC642587, CASP7, S100A7 and miRNAs hsa-mir-205 and hsa-mir-203b as the key genomic features that may substantially contribute to the oncogenesis of melanoma. Our study also proposes genes ESM1, NFATC3, C7orf4, CDK14, ZNF827, and ZSWIM7 as novel putative markers for cutaneous melanoma metastasis. The major prediction models and analysis modules to predict metastatic and primary tumor samples of SKCM are available from a webserver, CancerSPP ( http://webs.iiitd.edu.in/raghava/cancerspp/ ).
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Affiliation(s)
- Sherry Bhalla
- Center for Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
- Centre for Systems Biology and Bioinformatics, Panjab University, Chandigarh, India
| | - Harpreet Kaur
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Anjali Dhall
- Center for Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Gajendra P S Raghava
- Center for Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India.
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21
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Donnelly D, Aung PP, Jour G. The "-OMICS" facet of melanoma: Heterogeneity of genomic, proteomic and metabolomic biomarkers. Semin Cancer Biol 2019; 59:165-174. [PMID: 31295564 DOI: 10.1016/j.semcancer.2019.06.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 01/23/2023]
Abstract
In the recent decade, cutting edge molecular and proteomic analysis platforms revolutionized biomarkers discovery in cancers. Melanoma is the prototype with over 51,100 biomarkers discovered and investigated thus far. These biomarkers include tissue based tumor cell and tumor microenvironment biomarkers and circulating biomarkers including tumor DNA (cf-DNA), mir-RNA, proteins and metabolites. These biomarkers provide invaluable information for diagnosis, prognosis and play an important role in prediction of treatment response. In this review, we summarize the most recent discoveries in each of these biomarker categories. We will discuss the challenges in their implementation and standardization and conclude with some perspectives in melanoma biomarker research.
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Affiliation(s)
- Douglas Donnelly
- The Ronald O. Perelman Department of Dermatology, New York University School of Medicine, New York, NY, United States; Interdisciplinary Melanoma Program, New York University School of Medicine, New York, NY, United States
| | - Phyu P Aung
- Department of Pathology, Section of Dermatopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - George Jour
- The Ronald O. Perelman Department of Dermatology, New York University School of Medicine, New York, NY, United States; Interdisciplinary Melanoma Program, New York University School of Medicine, New York, NY, United States; Department of Pathology, New York University School of Medicine, New York, NY, United States.
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22
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Bedin C, Crotti S, D'Angelo E, D'Aronco S, Pucciarelli S, Agostini M. Circulating Biomarkers for Response Prediction of Rectal Cancer to Neoadjuvant Chemoradiotherapy. Curr Med Chem 2019; 27:4274-4294. [PMID: 31060482 DOI: 10.2174/0929867326666190507084839] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 03/05/2019] [Accepted: 04/18/2019] [Indexed: 12/20/2022]
Abstract
Rectal cancer response to neoadjuvant Chemoradiotherapy (pCRT) is highly variable. In fact, it has been estimated that only about 21 % of patients show pathologic Complete Response (pCR) after therapy, while in most of the patients a partial or incomplete tumour regression is observed. Consequently, patients with a priori chemoradioresistant tumour should not receive the treatment, which is associated with substantial adverse effects and does not guarantee any clinical benefit. For Locally Advanced Rectal Cancer Patients (LARC), a standardized neoadjuvant treatment protocol is applied, the identification and the usefulness of prognostic or predictive biomarkers can improve the antitumoural treatment strategy, modifying the sequence, dose, and combination of radiotherapy, chemotherapy and surgical resection. For these reasons, a growing number of studies are actually focussed on the discovery and investigation of new predictive biomarkers of response to pCRT. In this review, we have selected the most recent literature (2012-2017) regarding the employment of blood-based biomarkers potentially predicting pCR in LARC patients and we have critically discussed them to highlight their real clinical benefit and the current limitations of the proposed methodological approaches.
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Affiliation(s)
- Chiara Bedin
- Nano-inspired Biomedicine Lab, Paediatric Research Institute-Città della Speranza, Padua, Italy
| | - Sara Crotti
- Nano-inspired Biomedicine Lab, Paediatric Research Institute-Città della Speranza, Padua, Italy
| | - Edoardo D'Angelo
- Nano-inspired Biomedicine Lab, Paediatric Research Institute-Città della Speranza, Padua, Italy
| | - Sara D'Aronco
- Nano-inspired Biomedicine Lab, Paediatric Research Institute-Città della Speranza, Padua, Italy,First Surgical Clinic Section, Department of Surgical, Oncological and Gastroenterological Science, University of
Padua, Padua, Italy
| | - Salvatore Pucciarelli
- First Surgical Clinic Section, Department of Surgical, Oncological and Gastroenterological Science, University of
Padua, Padua, Italy
| | - Marco Agostini
- Nano-inspired Biomedicine Lab, Paediatric Research Institute-Città della Speranza, Padua, Italy,First Surgical Clinic Section, Department of Surgical, Oncological and Gastroenterological Science, University of
Padua, Padua, Italy
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23
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Muluhngwi P, Valdes Jr R, Fernandez-Botran R, Burton E, Williams B, Linder MW. Cell-free DNA diagnostics: current and emerging applications in oncology. Pharmacogenomics 2019; 20:357-380. [DOI: 10.2217/pgs-2018-0174] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Liquid biopsy is a noninvasive dynamic approach for monitoring disease over time. It offers advantages including limited risks of blood sampling, opportunity for more frequent sampling, lower costs and theoretically non-biased sampling compared with tissue biopsy. There is a high degree of concordance between circulating tumor DNA mutations versus primary tumor mutations. Remote sampling of circulating tumor DNA can serve as viable option in clinical diagnostics. Here, we discuss the progress toward broad adoption of liquid biopsy as a diagnostic tool and discuss knowledge gaps that remain to be addressed.
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Affiliation(s)
- Penn Muluhngwi
- Department of Pathology & Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Roland Valdes Jr
- Department of Pathology & Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Rafael Fernandez-Botran
- Department of Pathology & Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Eric Burton
- Department of Neurology, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Brian Williams
- Department of Neurosurgery, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Mark W Linder
- Department of Pathology & Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
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24
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Potential clinical applications of circulating cell-free DNA in ovarian cancer patients. Expert Rev Mol Med 2018; 20:e6. [PMID: 30558693 DOI: 10.1017/erm.2018.5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Circulating cell-free DNA (cfDNA) consists of small fragments of DNA that circulate freely in the bloodstream. In cancer patients, a fraction of cfDNA is derived from tumour cells, therefore containing the same genetic and epigenetic alterations, and is termed circulating cell-free tumour DNA. The potential use of cfDNA, the so-called 'liquid biopsy', as a non-invasive cancer biomarker has recently received a lot of attention. The present review will focus on studies concerning the potential clinical applications of cfDNA in ovarian cancer patients.
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25
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Guo Y, Long J, Lei S. Promoter methylation as biomarkers for diagnosis of melanoma: A systematic review and meta-analysis. J Cell Physiol 2018; 234:7356-7367. [PMID: 30370527 DOI: 10.1002/jcp.27495] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 09/06/2018] [Indexed: 01/19/2023]
Abstract
Melanoma is one of the most common skin cancer that is characterized by rapid growth, early metastasis, high malignant, and mortality. Accumulating evidence demonstrated that promoter methylation of tumor-suppressor genes is implicated in the pathogenesis of melanoma. In the current study, we performed a meta-analysis to identify promising methylation biomarkers in the diagnosis of melanoma. We carried out a systematic literature search using Pubmed, Embase, and ISI web knowledge database and found that gene promoter methylation of 50 genes was reported to be associated with the risk of melanoma. Meta-analysis revealed that hypermethylation of claudin 11 (CLDN11; odds ratio [OR], 16.82; 95% confidence interval [CI], 1.97-143.29; p = 0.010), O-6-methylguanine-DNA methyltransferase (MGMT; OR, 5.59; 95% CI, 2.51-12.47; p < 0.0001), cyclin-dependent kinase inhibitor 2A (p16; OR, 6.57; 95% CI, 2.19-19.75; p = 0.0008), retinoic acid receptor β (RAR-β2; OR, 24.31; 95% CI, 4.58-129.01; p = 0.0002), and Ras association domain family member (RASSF1A; OR, 9.35; 95% CI, 4.73-18.45; p < 0.00001) was significantly higher in melanoma patients compared with controls. CLDN11 (OR, 14.52; 95% CI, 1.84-114.55; p = 0.01), MGMT (OR, 8.08; 95% CI, 1.84-35.46; p = 0.006), p16 (OR, 9.44; 95% CI, 2.68-33.29; p = 0.0005), and RASSF1A (OR, 7.72; 95% CI, 1.05-56.50; p = 0.04) hypermethylation was significantly increased in primary melanoma compared with controls. Methylation frequency of CLDN11 (OR, 25.56; 95% CI, 2.32-281.66; p = 0.008), MGMT (OR, 4.64; 95% CI, 1.98-10.90; p = 0.0004), p16 (OR, 4.31; 95% CI, 1.33-13.96; p = 0.01), and RASSF1A (OR, 10.10; 95% CI, 2.87-35.54; p = 0.0003) was significantly higher in metastasis melanoma compared with controls. These findings indicated that CLDN11, MGMT, p16, RAR-β2, and RASSF1A hypermethylation is a risk factor and a potential biomarker for melanoma. CLDN11, MGMT, p16, and RASSF1A promoter methylation may take part in the development of melanoma and become useful biomarkers in the early diagnosis of the disease.
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Affiliation(s)
- Yu Guo
- Department of Plastic Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Jianhong Long
- Department of Plastic Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Shaorong Lei
- Department of Plastic Surgery, Xiangya Hospital, Central South University, Changsha, China
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26
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Silva S, Danson S, Teare D, Taylor F, Bradford J, McDonagh AJG, Salawu A, Wells G, Burghel GJ, Brock I, Connley D, Cramp H, Hughes D, Tiffin N, Cox A. Genome-Wide Analysis of Circulating Cell-Free DNA Copy Number Detects Active Melanoma and Predicts Survival. Clin Chem 2018; 64:1338-1346. [DOI: 10.1373/clinchem.2018.290023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 06/05/2018] [Indexed: 12/13/2022]
Abstract
Abstract
BACKGROUND
A substantial number of melanoma patients develop local or metastatic recurrence, and early detection of these is vital to maximise benefit from new therapies such as inhibitors of BRAF and MEK, or immune checkpoints. This study explored the use of novel DNA copy-number profiles in circulating cell-free DNA (cfDNA) as a potential biomarker of active disease and survival.
PATIENTS AND METHODS
Melanoma patients were recruited from oncology and dermatology clinics in Sheffield, UK, and cfDNA was isolated from stored blood plasma. Using low-coverage whole-genome sequencing, we created copy-number profiles from cfDNA from 83 melanoma patients, 44 of whom had active disease. We used scoring algorithms to summarize copy-number aberrations and investigated their utility in multivariable logistic and Cox regression analyses.
RESULTS
The copy-number aberration score (CNAS) was a good discriminator of active disease (odds ratio, 3.1; 95% CI, 1.5–6.2; P = 0.002), and CNAS above or below the 75th percentile remained a significant discriminator in multivariable analysis for active disease (P = 0.019, with area under ROC curve of 0.90). Additionally, mortality was higher in those with CNASs above the 75th percentile than in those with lower scores (HR, 3.4; 95% CI, 1.5–7.9; P = 0.005), adjusting for stage of disease, disease status (active or resected), BRAF status, and cfDNA concentration.
CONCLUSIONS
This study demonstrates the potential of a de novo approach utilizing copy-number profiling of cfDNA as a biomarker of active disease and survival in melanoma. Longitudinal analysis of copy-number profiles as an early marker of relapsed disease is warranted.
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Affiliation(s)
- Shobha Silva
- Academic Unit of Clinical Oncology and Sheffield Experimental Cancer Medicine Centre, University of Sheffield, Sheffield, UK
| | - Sarah Danson
- Academic Unit of Clinical Oncology and Sheffield Experimental Cancer Medicine Centre, University of Sheffield, Sheffield, UK
| | - Dawn Teare
- School of Health and Related Research, University of Sheffield, Sheffield, UK
| | - Fiona Taylor
- Academic Unit of Clinical Oncology and Sheffield Experimental Cancer Medicine Centre, University of Sheffield, Sheffield, UK
| | - James Bradford
- Academic Unit of Molecular Oncology, Sheffield Medical School, University of Sheffield, Sheffield, UK
| | | | - Abdulazeez Salawu
- Academic Unit of Clinical Oncology and Sheffield Experimental Cancer Medicine Centre, University of Sheffield, Sheffield, UK
| | - Greg Wells
- Sheffield Genetic Diagnostics Group, Sheffield Children's NHS Foundation Trust, Western Bank Sheffield, UK
| | - George J Burghel
- The Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Ian Brock
- Academic Unit of Molecular Oncology, Sheffield Medical School, University of Sheffield, Sheffield, S10 2RX, UK
| | - Daniel Connley
- Academic Unit of Molecular Oncology, Sheffield Medical School, University of Sheffield, Sheffield, S10 2RX, UK
| | - Helen Cramp
- Academic Unit of Molecular Oncology, Sheffield Medical School, University of Sheffield, Sheffield, S10 2RX, UK
| | - David Hughes
- Department of Histopathology, Royal Hallamshire Hospital, Sheffield, UK
| | - Nick Tiffin
- Department of Histopathology, Royal Hallamshire Hospital, Sheffield, UK
| | - Angela Cox
- Academic Unit of Molecular Oncology, Sheffield Medical School, University of Sheffield, Sheffield, S10 2RX, UK
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27
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de Unamuno Bustos B, Murria Estal R, Pérez Simó G, Simarro Farinos J, Pujol Marco C, Navarro Mira M, Alegre de Miquel V, Ballester Sánchez R, Sabater Marco V, Llavador Ros M, Palanca Suela S, Botella Estrada R. Aberrant DNA methylation is associated with aggressive clinicopathological features and poor survival in cutaneous melanoma. Br J Dermatol 2018; 179:394-404. [PMID: 29278418 DOI: 10.1111/bjd.16254] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2017] [Indexed: 01/19/2023]
Abstract
BACKGROUND Promoter methylation of tumour suppressor genes (TSGs) has recently been implicated in the pathogenesis of several types of cancer. Regarding melanoma, over 100 genes that contribute to its pathogenesis have been identified to be aberrantly hypermethylated. OBJECTIVES This is a retrospective observational study that aims to analyse the prevalence of CpG island methylation in a series of primary melanomas, to identify the associations with the main clinicopathological features, and to explore the prognostic significance of methylation in melanoma survival. MATERIALS AND METHODS DNA methylation was analysed using methylation-specific multiplex ligation-dependent probe amplification in a series of 170 melanoma formalin-fixed paraffin-embedded tumour samples. The relationship between the methylation status, known somatic mutations and clinicopathological features was evaluated. Disease-free survival (DFS) and overall survival (OS) were displayed by the Kaplan-Meier method. RESULTS In the entire cohort, one or more genes were detected to be methylated in 55% of the patients. The most prevalent methylated genes were RARB 31%, PTEN 24%, APC 16%, CDH13 16%, ESR1 14%, CDKN2A 6% and RASSF1 5%. An association between aberrant methylation and aggressive clinicopathological features was observed (older age, increased Breslow thickness, presence of mitosis and ulceration, fast-growing melanomas, advancing stage and TERT mutations). Furthermore, Kaplan-Meier survival analysis showed a correlation of methylation and poorer DFS and OS. CONCLUSIONS Aberrant methylation of TSGs is a frequent event in melanoma. It is associated with aggressive clinicopathological features and poorer survival. Epigenetic alterations may represent a significant prognostic marker with utility in routine practice.
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Affiliation(s)
- B de Unamuno Bustos
- Department of Dermatology, Hospital Universitari i Politecnic La Fe, Valencia, Spain
| | - R Murria Estal
- Department of Molecular Biology Laboratory, Service of Clinical Analysis, Hospital Universitari i Politecnic La Fe, Valencia, Spain
| | - G Pérez Simó
- Department of Molecular Biology Laboratory, Service of Clinical Analysis, Hospital Universitari i Politecnic La Fe, Valencia, Spain
| | - J Simarro Farinos
- Department of Molecular Biology Laboratory, Service of Clinical Analysis, Hospital Universitari i Politecnic La Fe, Valencia, Spain
| | - C Pujol Marco
- Department of Dermatology, Hospital Universitari i Politecnic La Fe, Valencia, Spain
| | - M Navarro Mira
- Department of Dermatology, Hospital Universitari i Politecnic La Fe, Valencia, Spain
| | - V Alegre de Miquel
- Department of Dermatology, Hospital General Universitario de Valencia, Valencia, Spain
| | | | - V Sabater Marco
- Department of Pathology, Hospital General Universitario de Valencia, Valencia, Spain
| | - M Llavador Ros
- Department of Pathology, Hospital Universitari i Politecnic La Fe, Valencia, Spain
| | - S Palanca Suela
- Department of Molecular Biology Laboratory, Service of Clinical Analysis, Hospital Universitari i Politecnic La Fe, Valencia, Spain
| | - R Botella Estrada
- Department of Dermatology, Hospital Universitari i Politecnic La Fe, Valencia, Spain
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28
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Gaiser MR, von Bubnoff N, Gebhardt C, Utikal JS. Liquid Biopsy zur Überwachung von Melanompatienten. J Dtsch Dermatol Ges 2018; 16:405-416. [DOI: 10.1111/ddg.13461_g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/21/2017] [Indexed: 01/03/2023]
Affiliation(s)
- Maria Rita Gaiser
- Klinische Kooperationseinheit Klinische Kooperationseinheit Dermatoonkologie des Deutschen; Krebsforschungszentrums (DKFZ); Heidelberg Deutschland
- Klinik für Dermatologie, Venerologie und Allergologie, Universitätsmedizin Mannheim, Ruprecht-Karls-Universität Heidelberg; Mannheim Deutschland
| | - Nikolas von Bubnoff
- Klinik für Hämatologie; Onkologie und Stammzelltransplantation; Universitätsklinikum Freiburg; Deutschland
- Deutsches Konsortium für Translationale Krebsforschung (DKTK); Deutsches Krebsforschungszentrum (DKFZ); Heidelberg Deutschland
| | - Christoffer Gebhardt
- Klinische Kooperationseinheit Klinische Kooperationseinheit Dermatoonkologie des Deutschen; Krebsforschungszentrums (DKFZ); Heidelberg Deutschland
- Klinik für Dermatologie, Venerologie und Allergologie, Universitätsmedizin Mannheim, Ruprecht-Karls-Universität Heidelberg; Mannheim Deutschland
| | - Jochen Sven Utikal
- Klinische Kooperationseinheit Klinische Kooperationseinheit Dermatoonkologie des Deutschen; Krebsforschungszentrums (DKFZ); Heidelberg Deutschland
- Klinik für Dermatologie, Venerologie und Allergologie, Universitätsmedizin Mannheim, Ruprecht-Karls-Universität Heidelberg; Mannheim Deutschland
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29
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Gaiser MR, von Bubnoff N, Gebhardt C, Utikal JS. Liquid biopsy to monitor melanoma patients. J Dtsch Dermatol Ges 2018. [PMID: 29512873 DOI: 10.1111/ddg.13461] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
During the last six years, several innovative, systemic therapies for the treatment of metastatic malignant melanoma (MM) have emerged. Conventional chemotherapy has been superseded by novel first-line therapies, including systemic immunotherapies (anti-CTLA4 and anti-PD1; authorization of anti-PDL1 is anticipated) and therapies targeting specific mutations (BRAF, NRAS, and c-KIT). Thus, treating physicians are confronted with new challenges, such as stratifying patients for appropriate treatments and monitoring long-term responders for progression. Consequently, reliable methods for monitoring disease progression or treatment resistance are necessary. Localized and advanced cancers may generate circulating tumor cells and circulating tumor DNA (ctDNA) that can be detected and quantified from peripheral blood samples (liquid biopsy). For melanoma patients, liquid biopsy results may be useful as novel predictive biomarkers to guide therapeutic decisions, particularly in the context of mutation-based targeted therapies. The challenges of using liquid biopsy include strict criteria for the phenotypic nature of circulating MM cells or their fragments and the instability of ctDNA in blood. The limitations of liquid biopsy in routine diagnostic testing are discussed in this review.
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Affiliation(s)
- Maria Rita Gaiser
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, Germany
| | - Nikolas von Bubnoff
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center University of Freiburg, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoffer Gebhardt
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, Germany
| | - Jochen Sven Utikal
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, Germany
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30
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Lan YT, Chen MH, Fang WL, Hsieh CC, Lin CH, Jhang FY, Yang SH, Lin JK, Chen WS, Jiang JK, Lin PC, Chang SC. Clinical relevance of cell-free DNA in gastrointestinal tract malignancy. Oncotarget 2018; 8:3009-3017. [PMID: 27936467 PMCID: PMC5356859 DOI: 10.18632/oncotarget.13821] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/30/2016] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Cell-free DNA (cfDNA) extracted from blood has become a clinically feasible biomarker in various types of cancer. However, the clinical significance of cfDNA in gastrointestinal (GI) tract cancer among Asian populations requires further investigation. RESULTS The median cfDNA copy number was highest in esophageal cancer, followed by colorectal cancer and gastric cancer, which were all significantly higher than those of healthy individuals. The cfDNA levels were higher in GI tract cancer, followed by those in carcinoma in situ and then healthy individuals (P = 0.019). During the postoperative surveillance, the cfDNA level tended to be more sensitive than the carcinoembryonic antigen level in predicting recurrence. For recurrent gastric cancer, a persistently high cfDNA level and an increasing trend was observed after surgery. For stage IV colorectal cancer, dynamic changes in the cfDNA level were correlated with the responses to chemotherapy and surgery. MATERIALS AND METHODS Blood samples were collected from 95 healthy individuals and from 855 patients diagnosed with GI tract malignancy, including 98 with esophageal cancer, 428 with stomach cancer, 329 with colorectal cancer and 30 with carcinoma in situ. The copy numbers of extracted cfDNA were analyzed and compared among the different types of GI cancers. CONCLUSIONS The cfDNA level can serve as a feasible biomarker for detecting tumors in GI tract cancer. The cfDNA level may play a role in predicting tumor responses to chemotherapy and surgery in colorectal cancer; tumor recurrence should be considered in gastric cancer with a persistently high cfDNA level after surgery.
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Affiliation(s)
- Yuan-Tzu Lan
- Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of Surgery, National Yang-Ming University, Taipei, Taiwan
| | - Ming-Huang Chen
- Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Wen-Liang Fang
- Department of Surgery, National Yang-Ming University, Taipei, Taiwan.,Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chih-Cheng Hsieh
- Division of Thoracic Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Chien-Hsing Lin
- Genome Research Center, National Yang-Ming University, Taipei City, Taiwan
| | - Fang-Yu Jhang
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Shung-Haur Yang
- Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of Surgery, National Yang-Ming University, Taipei, Taiwan
| | - Jen-Kou Lin
- Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of Surgery, National Yang-Ming University, Taipei, Taiwan
| | - Wei-Shone Chen
- Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of Surgery, National Yang-Ming University, Taipei, Taiwan
| | - Jeng-Kai Jiang
- Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of Surgery, National Yang-Ming University, Taipei, Taiwan
| | - Pei-Ching Lin
- School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Department of Clinical Pathology, Yang-Ming Branch, Taipei City Hospital, Taipei, Taiwan
| | - Shih-Ching Chang
- Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of Surgery, National Yang-Ming University, Taipei, Taiwan
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31
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Qi F, Yin Z, Wang G, Zeng S. Clinical and Prognostic Significance of O 6-Methylguanine-DNA Methyltransferase Promoter Methylation in Patients with Melanoma: A Systematic Meta-Analysis. Ann Dermatol 2018; 30:129-135. [PMID: 29606808 PMCID: PMC5839882 DOI: 10.5021/ad.2018.30.2.129] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/15/2017] [Accepted: 09/19/2017] [Indexed: 12/12/2022] Open
Abstract
Tumor suppressor gene O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation has been reported in melanoma. However, the clinical and prognostic significance of MGMT promoter methylation in patients with melanoma remained to be determined. A systematic search was performed to identify eligible papers published. The overall odds ratios (ORs) or hazard ratios and their 95% confidence intervals were calculated. Final 12 eligible publications involving Caucasian population were performed in this study, including 1,071 metastatic melanoma patients, 154 primary melanoma patients, and 211 normal controls. MGMT promoter methylation was significantly higher in primary or metastatic melanoma than in normal controls (p<0.05). No difference of MGMT promoter methylation was found in primary and metastatic melanoma (p=0.432). When metastatic melanoma was compared to normal controls, subgroup analysis showed the correlation between MGMT promoter methylation and different sample materials (tissue: OR=7.01, p<0.001 and blood: OR=12.04, p=0.005). MGMT promoter methylation was not associated with response to drug therapy and the prognosis in overall survival and progression-free survival for multivariate analysis. Our results show that MGMT promoter methylation may be correlated with the increased risk of primary or metastatic melanoma. Based on blood samples, MGMT promoter methylation may become a noninvasive biomarker for the detection of metastatic melanoma. Further additional clinical studies are necessary.
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Affiliation(s)
- Fang Qi
- Department of Dermatology, Tianjin First Center Hospital, Tianjin, China
| | - Zhiqi Yin
- Department of Pathology, Tianjin First Center Hospital, Tianjin, China
| | - Guangping Wang
- Department of Dermatology, Tianjin First Center Hospital, Tianjin, China
| | - Sanwu Zeng
- Department of Dermatology, Tianjin First Center Hospital, Tianjin, China
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32
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Kumari S, Husain N, Agarwal A, Neyaz A, Gupta S, Chaturvedi A, Lohani M, Sonkar AA. Diagnostic Value of Circulating Free DNA Integrity and Global Methylation Status in Gall Bladder Carcinoma. Pathol Oncol Res 2018; 25:925-936. [PMID: 29376201 DOI: 10.1007/s12253-017-0380-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 12/20/2017] [Indexed: 12/18/2022]
Abstract
The current study investigates the role of circulating free DNA (cfDNA) as a liquid biopsy in diagnosis gall bladder carcinoma (GBC) utilizing levels of long DNA fragments (ALU247) derived from tumor necrosis, short apoptotic fragments (ALU115) denoting total cfDNA and cfDNA integrity denoting ratio of ALU247 and ALU115. The global methylation status of cfDNA was also estimated with the hypothesis that these parameters provide a diagnostic distinction between cancer and non-cancer subjects, with higher or altered values favoring presence of malignancy. Study group included 60 cases of GBC and 36 controls including diseased controls (cholecystitis) and healthy subjects. Median levels of ALU115, ALU247 and cfDNA integrity were significantly different in GBC at 1790.88, 673.75, 0.4718 vs. controls at 840.73, 165.03, 0.1989 ng/ml respectively. Global DNA methylation was not significantly different between GBC at 0.679% and controls at 0.695%. The sensitivity and specificity of ALU 247 in discriminating GBC from controls was highest with a sensitivity, specificity and diagnostic accuracy of 80.0%, 86.1% and 82.2% respectively. Global DNA methylation showed lowest sensitivity of 55.0% and specificity of 50.0%. Clinico-pathological parameters showing significant association with cfDNA integrity, on ROC curve analysis, showed significant diagnostic discrimination of the tumor stage, lymphovascular invasion, disease stage and grade histology. This is a first time analysis of ALU115, ALU247 and cfDNA integrity in the diagnosis of GBC and confirms that the combination of ALU247 and cfDNA integrity provides good sensitivity, specificity and diagnostic accuracy in discriminating GBC from controls as well correlates with aggressive disease parameters.
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Affiliation(s)
- Swati Kumari
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, U.P., 226010, India.,Department of Biosciences, Integral University, Lucknow, U.P., 226026, India
| | - Nuzhat Husain
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, U.P., 226010, India.
| | - Akash Agarwal
- Department of Surgical Oncology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, U.P., 226010, India
| | - Azfar Neyaz
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, U.P., 226010, India
| | - Sameer Gupta
- Department of Surgical Oncology, King George's Medical University, Lucknow, U.P., 226003, India
| | - Arun Chaturvedi
- Department of Surgical Oncology, King George's Medical University, Lucknow, U.P., 226003, India
| | - Mohtashim Lohani
- Department of Biosciences, Integral University, Lucknow, U.P., 226026, India
| | - Abhinav Arun Sonkar
- Department of Surgery, King George's Medical University, Lucknow, U.P., 226003, India
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33
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Nakano Y, Kitago M, Matsuda S, Nakamura Y, Fujita Y, Imai S, Shinoda M, Yagi H, Abe Y, Hibi T, Fujii-Nishimura Y, Takeuchi A, Endo Y, Itano O, Kitagawa Y. KRAS mutations in cell-free DNA from preoperative and postoperative sera as a pancreatic cancer marker: a retrospective study. Br J Cancer 2018; 118:662-669. [PMID: 29360815 PMCID: PMC5846073 DOI: 10.1038/bjc.2017.479] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 12/03/2017] [Accepted: 12/04/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) has very poor prognosis despite existing multimodal therapies. This study aimed to investigate whether KRAS mutations at codons 12/13 in cell-free DNA (cfDNA) from preoperative and postoperative sera from patients with PDAC can serve as a predictive biomarker for treatment response and outcomes after surgery. METHODS Preoperative and postoperative serum samples obtained from 45 patients with PDAC whom underwent curative pancreatectomy at our institution between January 2013 and July 2016 were retrospectively analysed. Peptide nucleic acid-directed PCR clamping was used to identify KRAS mutations in cfDNA. RESULTS Among the 45 patients enrolled, 11 (24.4%) and 20 (44.4%) had KRAS mutations in cfDNA from preoperative and postoperative sera, respectively. Multivariate analysis revealed that KRAS mutations in postoperative serum (hazard ratio (HR)=2.919; 95% confidence interval (CI)=1.109-5.621; P=0.027) are an independent prognostic factor for disease-free survival. Furthermore, the shift from wild-type KRAS in preoperative to mutant KRAS in postoperative cfDNA (HR=9.419; 95% Cl=2.015-44.036; P=0.004) was an independent prognostic factor for overall survival. CONCLUSIONS Changes in KRAS mutation status between preoperative and postoperative cfDNA may be a useful predictive biomarker for survival and treatment response.
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Affiliation(s)
- Yutaka Nakano
- Department of Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Minoru Kitago
- Department of Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Sachiko Matsuda
- Department of Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Yuki Nakamura
- Department of Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Yusuke Fujita
- Department of Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Shunichi Imai
- Department of Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Masahiro Shinoda
- Department of Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Hiroshi Yagi
- Department of Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Yuta Abe
- Department of Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Taizo Hibi
- Department of Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Yoko Fujii-Nishimura
- Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Ayano Takeuchi
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Yutaka Endo
- Department of Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Osamu Itano
- Hepato-Biliary-Pancreatic and Gastrointestinal Surgery, International University of Health and Welfare School of Medicine, 14-1-6 Kokufudai Ichikawa-shi, Chiba 272-0827, Japan
| | - Yuko Kitagawa
- Department of Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
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34
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Lim SY, Lee JH, Diefenbach RJ, Kefford RF, Rizos H. Liquid biomarkers in melanoma: detection and discovery. Mol Cancer 2018; 17:8. [PMID: 29343260 PMCID: PMC5772714 DOI: 10.1186/s12943-018-0757-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 01/02/2018] [Indexed: 12/18/2022] Open
Abstract
A vast array of tumor-derived genetic, proteomic and cellular components are constantly released into the circulation of cancer patients. These molecules including circulating tumor DNA and RNA, proteins, tumor and immune cells are emerging as convenient and accurate liquid biomarkers of cancer. Circulating cancer biomarkers provide invaluable information on cancer detection and diagnosis, prognosticate patient outcomes, and predict treatment response. In this era of effective molecular targeted treatments and immunotherapies, there is now an urgent need to implement use of these circulating biomarkers in the clinic to facilitate personalized therapy. In this review, we present recent findings in circulating melanoma biomarkers, examine the challenges and promise of evolving technologies used for liquid biomarker discovery, and discuss future directions and perspectives in melanoma biomarker research.
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Affiliation(s)
- Su Yin Lim
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia.,Melanoma Institute Australia, Sydney, NSW, Australia
| | - Jenny H Lee
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia.,Melanoma Institute Australia, Sydney, NSW, Australia
| | - Russell J Diefenbach
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia.,Melanoma Institute Australia, Sydney, NSW, Australia
| | - Richard F Kefford
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia.,Melanoma Institute Australia, Sydney, NSW, Australia.,Department of Medical Oncology, Crown Princess Mary Cancer Centre, Westmead and Blacktown Hospitals, Sydney, NSW, Australia
| | - Helen Rizos
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia. .,Melanoma Institute Australia, Sydney, NSW, Australia. .,Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, Sydney, NSW, 2109, Australia.
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35
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Macías M, Alegre E, Díaz-Lagares A, Patiño A, Pérez-Gracia JL, Sanmamed M, López-López R, Varo N, González A. Liquid Biopsy: From Basic Research to Clinical Practice. Adv Clin Chem 2017; 83:73-119. [PMID: 29304904 DOI: 10.1016/bs.acc.2017.10.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Liquid biopsy refers to the molecular analysis in biological fluids of nucleic acids, subcellular structures, especially exosomes, and, in the context of cancer, circulating tumor cells. In the last 10 years, there has been an intensive research in liquid biopsy to achieve a less invasive and more precise personalized medicine. Molecular assessment of these circulating biomarkers can complement or even surrogate tissue biopsy. Because of this research, liquid biopsy has been introduced in clinical practice, especially in oncology, prenatal screening, and transplantation. Here we review the biology, methodological approaches, and clinical applications of the main biomarkers involved in liquid biopsy.
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Affiliation(s)
| | - Estibaliz Alegre
- Clínica Universidad de Navarra, Pamplona, Spain; The Health Research Institute of Navarra (IDISNA), Pamplona, Spain
| | - Angel Díaz-Lagares
- Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS), CIBERONC, Santiago de Compostela, Spain; Roche-CHUS Joint Unit, University Clinical Hospital of Santiago (CHUS), Santiago de Compostela, Spain
| | - Ana Patiño
- Clínica Universidad de Navarra, Pamplona, Spain; The Health Research Institute of Navarra (IDISNA), Pamplona, Spain
| | - Jose L Pérez-Gracia
- Clínica Universidad de Navarra, Pamplona, Spain; The Health Research Institute of Navarra (IDISNA), Pamplona, Spain
| | - Miguel Sanmamed
- Yale University School of Medicine, New Haven, CT, United States
| | - Rafael López-López
- Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS), CIBERONC, Santiago de Compostela, Spain; Roche-CHUS Joint Unit, University Clinical Hospital of Santiago (CHUS), Santiago de Compostela, Spain
| | - Nerea Varo
- Clínica Universidad de Navarra, Pamplona, Spain; The Health Research Institute of Navarra (IDISNA), Pamplona, Spain
| | - Alvaro González
- Clínica Universidad de Navarra, Pamplona, Spain; The Health Research Institute of Navarra (IDISNA), Pamplona, Spain.
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36
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Abstract
The field of genomic biomarkers in melanoma has evolved dramatically in the past few decades. Whereas much of the prior focus was on molecular assessment of tumor tissue, circulating tumor cells (CTCs), and cell-free circulating tumor DNA (ctDNA) as sources of a "liquid biopsy" in cancer patients provide promising potential as a method to assess tumor progression, identify targets for therapy, and evaluate clinical response to treatment. Blood biomarker assays have the advantage of being noninvasive, allow for dynamic evaluation of disease over a serial time frame, and help to address the issue of tissue sampling bias and tumor heterogeneity. However, there remains an assortment of technologies and techniques to isolate and detect CTCs and ctDNA and a standardized method has yet to be established. Despite these challenges, multiple studies have already demonstrated the clinical prognostic utility of blood-based genomic biomarker assays. With the advent of next-generation sequencing and genome-wide ctDNA analysis, this will undoubtedly lead to an improved understanding of tumor progression, help to identify new targets for treatment, and improve monitoring of treatment response and development of resistance.
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Affiliation(s)
- Kelly Huynh
- Department of Surgical Oncology, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA 90404
| | - Dave S B Hoon
- Department of Molecular Oncology John Wayne Cancer Institute at Providence Saint John's Health Center Santa Monica, California
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37
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Lauschke VM, Barragan I, Ingelman-Sundberg M. Pharmacoepigenetics and Toxicoepigenetics: Novel Mechanistic Insights and Therapeutic Opportunities. Annu Rev Pharmacol Toxicol 2017; 58:161-185. [PMID: 29029592 DOI: 10.1146/annurev-pharmtox-010617-053021] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Pharmacological treatment and exposure to xenobiotics can cause substantial changes in epigenetic signatures. The majority of these epigenetic changes, caused by the compounds in question, occur downstream of transcriptional activation mechanisms, whereby the epigenetic alterations can create a transcriptional memory and stably modulate cell function. The increasing understanding of epigenetic mechanisms and their importance in disease has prompted the development of therapeutic interventions that target epigenetic modulatory mechanisms, particularly in oncology where inhibitors of epigenetic-modifying proteins (epidrugs) have been successfully used in treatment, mostly in combination with standard-of-care chemotherapy, either provoking direct cytotoxicity or inhibiting resistance to anticancer drugs. In addition, emerging methods for detecting epigenetically modified DNA in bodily fluids may provide information about tumor phenotype or drug treatment success. However, it is important to note that many technical pitfalls, such as the nondeconvolution of methylcytosine and hydroxymethylcytosine, compromise epigenetic analyses and the interpretation of results. In this review, we provide an update on the field, with an emphasis on the novel therapeutic opportunities made possible by epidrugs.
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Affiliation(s)
- Volker M Lauschke
- Pharmacogenetics Section, Department of Physiology and Pharmacology, Karolinska Institutet, SE-171 77 Stockholm, Sweden;
| | - Isabel Barragan
- Pharmacoepigenetics Group, Department of Physiology and Pharmacology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Magnus Ingelman-Sundberg
- Pharmacogenetics Section, Department of Physiology and Pharmacology, Karolinska Institutet, SE-171 77 Stockholm, Sweden;
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38
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Gong M, Shi W, Qi J, Shao G, Shi Z, Wang J, Chen J, Chu R. Alu hypomethylation and MGMT hypermethylation in serum as biomarkers of glioma. Oncotarget 2017; 8:76797-76806. [PMID: 29100349 PMCID: PMC5652743 DOI: 10.18632/oncotarget.20012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/12/2017] [Indexed: 02/05/2023] Open
Abstract
In order to improve prognosis of glioma patients, better tools are required for early diagnosis and treatment. Serum cell-free DNA methylation levels of Alu, MGMT, P16, RASSF1A from 124 glioma patients and 58 healthy controls were detected by the bisulfite sequencing. The median methylation level of Alu was 46.15% (IQR, 36.57%-54.00%) and 60.85% (IQR, 57.23%-65.68%) in glioma patients and healthy controls respectively. The median methylation level of MGMT in glioma samples was 64.65% (IQR, 54.87%-74.37%) compared to 38.30% (IQR, 34.13%-45.45%) in healthy controls, and all revealed significant differences including P16. However, the median methylation level of RASSF1A was not significantly altered in glioma patients. Furthermore, the methylation levels of Alu and MGMT in serum had a good diagnostic value, and was higher than P16. Interestingly, combination of Alu and MGMT identified additional patients, which were missed by either diagnosis alone. In the Alu group, the patients with high levels were associated with an increased survival rate compared to those who with low levels, with similar results observed in the MGMT group. In the present study, we demonstrated that the methylation level of Alu and MGMT in serum had a better diagnostic value than P16. Moreover, combined analysis of Alu and MGMT showed higher sensitivity for glioma diagnosis. Therefore, both serum Alu and MGMT methylation levels may represent a novel prognostic factor for glioma patients.
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Affiliation(s)
- Mingjie Gong
- Department of Neurosurgery, Changshu No. 2 People's Hospital (The 5th Clinical Medical College of Yangzhou University), Changshu, Jiangsu Province, China
| | - Wei Shi
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Jing Qi
- Comprehensive Surgical Laboratory, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Guoping Shao
- Department of Neurosurgery, Changshu No. 2 People's Hospital (The 5th Clinical Medical College of Yangzhou University), Changshu, Jiangsu Province, China
| | - Zhenghua Shi
- Department of Neurosurgery, Changshu No. 2 People's Hospital (The 5th Clinical Medical College of Yangzhou University), Changshu, Jiangsu Province, China
| | - Junxiang Wang
- Department of Neurosurgery, Changshu No. 2 People's Hospital (The 5th Clinical Medical College of Yangzhou University), Changshu, Jiangsu Province, China
| | - Jian Chen
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Rongtao Chu
- Department of Neurosurgery, Changshu No. 2 People's Hospital (The 5th Clinical Medical College of Yangzhou University), Changshu, Jiangsu Province, China
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39
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Calapre L, Warburton L, Millward M, Ziman M, Gray ES. Circulating tumour DNA (ctDNA) as a liquid biopsy for melanoma. Cancer Lett 2017; 404:62-69. [PMID: 28687355 DOI: 10.1016/j.canlet.2017.06.030] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 06/16/2017] [Accepted: 06/16/2017] [Indexed: 01/10/2023]
Abstract
Circulating tumour DNA (ctDNA) has emerged as a promising blood-based biomarker for monitoring disease status of patients with advanced cancers. In melanoma, ctDNA has been shown to have clinical value as an alternative tumour source for the detection clinically targetable mutations for the assessment of response to therapy. This review provides a critical summary of the evidence that gives credence to the utility of ctDNA as a biomarker for monitoring of disease status in advanced melanoma and the steps required for its implementation into clinical settings.
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Affiliation(s)
- Leslie Calapre
- School of Medical Science, Edith Cowan University, Joondalup, WA, Australia.
| | - Lydia Warburton
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
| | - Michael Millward
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, WA, Australia; School of Medicine and Pharmacology, The University of Western Australia, Crawley, Western Australia, Australia
| | - Mel Ziman
- School of Medical Science, Edith Cowan University, Joondalup, WA, Australia; School of Pathology and Laboratory Medicine, University of Western Australia, Crawley, WA, Australia
| | - Elin S Gray
- School of Medical Science, Edith Cowan University, Joondalup, WA, Australia
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40
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Plasma Circulating Tumor DNA Levels for the Monitoring of Melanoma Patients: Landscape of Available Technologies and Clinical Applications. BIOMED RESEARCH INTERNATIONAL 2017; 2017:5986129. [PMID: 28484715 PMCID: PMC5397613 DOI: 10.1155/2017/5986129] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 03/08/2017] [Accepted: 03/22/2017] [Indexed: 12/18/2022]
Abstract
Melanoma is a cutaneous cancer with an increasing worldwide prevalence and high mortality due to unresectable or metastatic stages. Mutations in BRAF, NRAS, or KIT are present in more than 60% of melanoma cases, but a useful blood-based biomarker for the clinical monitoring of melanoma patients is still lacking. Thus, the analysis of circulating tumor cells (CTCs) and/or cell-free circulating tumor DNA (ctDNA) analysis from blood (liquid biopsies) appears to be a promising noninvasive, repeatable, and systemic sampling tool for detecting and monitoring melanoma. Here, we review the molecular biology-based strategies used for ctDNA quantification in melanoma patients, as well as their main clinical applications. Droplet digital PCR (ddPCR) and next generation sequencing (NGS) technologies appear to be two versatile and complementary strategies to study rare variant mutations for the detection and monitoring of melanoma progression. Among the different clinical uses of ctDNA, we highlight the assessment of molecular heterogeneity and the identification of genetic determinants for targeted therapy as well as the analysis of acquired resistance. Importantly, ctDNA quantification might also be a novel biomarker with a prognostic value for melanoma patients.
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41
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Micevic G, Theodosakis N, Bosenberg M. Aberrant DNA methylation in melanoma: biomarker and therapeutic opportunities. Clin Epigenetics 2017; 9:34. [PMID: 28396701 PMCID: PMC5381063 DOI: 10.1186/s13148-017-0332-8] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/24/2017] [Indexed: 12/18/2022] Open
Abstract
Aberrant DNA methylation is an epigenetic hallmark of melanoma, known to play important roles in melanoma formation and progression. Recent advances in genome-wide methylation methods have provided the means to identify differentially methylated genes, methylation signatures, and potential biomarkers. However, despite considerable effort and advances in cataloging methylation changes in melanoma, many questions remain unanswered. The aim of this review is to summarize recent developments, emerging trends, and important unresolved questions in the field of aberrant DNA methylation in melanoma. In addition to reviewing recent developments, we carefully synthesize the findings in an effort to provide a framework for understanding the current state and direction of the field. To facilitate clarity, we divided the review into DNA methylation changes in melanoma, biomarker opportunities, and therapeutic developments. We hope this review contributes to accelerating the utilization of the diagnostic, prognostic, and therapeutic potential of DNA methylation for the benefit of melanoma patients.
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Affiliation(s)
- Goran Micevic
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520 USA.,Department of Pathology, Yale University School of Medicine, New Haven, CT 06520 USA
| | - Nicholas Theodosakis
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520 USA.,Department of Pathology, Yale University School of Medicine, New Haven, CT 06520 USA
| | - Marcus Bosenberg
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520 USA.,Department of Pathology, Yale University School of Medicine, New Haven, CT 06520 USA
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42
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Hao YX, Li YM, Ye M, Guo YY, Li QW, Peng XM, Wang Q, Zhang SF, Zhao HX, Zhang H, Li GH, Zhu JH, Xiao WH. KRAS and BRAF mutations in serum exosomes from patients with colorectal cancer in a Chinese population. Oncol Lett 2017; 13:3608-3616. [PMID: 28521461 PMCID: PMC5431267 DOI: 10.3892/ol.2017.5889] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 01/26/2017] [Indexed: 12/13/2022] Open
Abstract
The efficacy of epidermal growth factor receptor- targeted therapy is significantly associated with Kirsten rat sarcoma viral oncogene homolog (KRAS) and B-raf serine/threonine kinase proto-oncogene (BRAF) mutation in patients with colorectal cancer (CRC), for which the standard gene testing is currently performed using tumor tissue DNA. The aim of the present study was to compare the presence of KRAS and BRAF mutations in the serum exosome and primary tumor tissue from patients with CRC. Genomic DNA were extracted from the tumor tissues of 35 patients with histologically-confirmed CRC and exosomal mRNA were obtained from peripheral blood, which were collected from the corresponding patients prior to surgery. Three mutations in the KRAS gene (codons 12, 13 and 61) and a mutation in the BRAF gene (codon 600) were detected using a polymerase chain reaction-based sequencing method and their presence were compared between tumor tissues and the matched serum exosomes. The KRAS mutation rates in tumor tissues and the matched serum exosomes were 57.6 and 42.4%, respectively, which was not significantly different (P=0.063). The detection rate of the BRAF mutation was 24.2 and 18.2% in tumor tissues and the matched serum exosomes, respectively, and there was no significant difference (P=0.500). The patients with CRC that had a KRAS mutation of codon 12 in exon 2 in their tumor tissues and serum exosomes were significantly older compared with those without this mutation (tumor tissue, P=0.002; serum exosome, P=0.022). The sensitivity of KRAS and BRAF mutation detection using exosomal mRNA was 73.7 and 75%, respectively. The specificity of the detected mutations exhibited an efficiency of 100%, and the total consistency rate was 94.9 and 93.9% for KRAS and BRAF mutations, respectively. These results suggested that serum exosomal mRNA may be used as a novel source for the rapid and non-invasive genotyping of patients with CRC.
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Affiliation(s)
- Yi-Xin Hao
- Department of Oncology, The First Affiliated Hospital of The People's Liberation Army General Hospital, Beijing 100039, P.R. China
| | - Yong-Mei Li
- Department of Oncology, Changhai Hospital, Second Military Medical University, Shanghai 200433, P.R. China
| | - Ming Ye
- Department of Oncology, The First Affiliated Hospital of The People's Liberation Army General Hospital, Beijing 100039, P.R. China
| | - Yan-Yan Guo
- Department of Oncology, The First Affiliated Hospital of The People's Liberation Army General Hospital, Beijing 100039, P.R. China
| | - Qiu-Wen Li
- Department of Oncology, The First Affiliated Hospital of The People's Liberation Army General Hospital, Beijing 100039, P.R. China
| | - Xiu-Mei Peng
- Department of Oncology, The First Affiliated Hospital of The People's Liberation Army General Hospital, Beijing 100039, P.R. China
| | - Qi Wang
- Department of Oncology, The First Affiliated Hospital of The People's Liberation Army General Hospital, Beijing 100039, P.R. China
| | - Shu-Fang Zhang
- Department of Oncology, The First Affiliated Hospital of The People's Liberation Army General Hospital, Beijing 100039, P.R. China
| | - Hui-Xia Zhao
- Department of Oncology, The First Affiliated Hospital of The People's Liberation Army General Hospital, Beijing 100039, P.R. China
| | - He Zhang
- Department of Oncology, The First Affiliated Hospital of The People's Liberation Army General Hospital, Beijing 100039, P.R. China
| | - Guang-Hui Li
- Department of Oncology, The First Affiliated Hospital of The People's Liberation Army General Hospital, Beijing 100039, P.R. China
| | - Jian-Hua Zhu
- Department of Oncology, The First Affiliated Hospital of The People's Liberation Army General Hospital, Beijing 100039, P.R. China
| | - Wen-Hua Xiao
- Department of Oncology, The First Affiliated Hospital of The People's Liberation Army General Hospital, Beijing 100039, P.R. China
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The relationship between RASSF1A gene promoter methylation and the susceptibility and prognosis of melanoma: A meta-analysis and bioinformatics. PLoS One 2017; 12:e0171676. [PMID: 28207831 PMCID: PMC5312935 DOI: 10.1371/journal.pone.0171676] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Accepted: 01/24/2017] [Indexed: 01/23/2023] Open
Abstract
Background The function of the tumor suppressor gene RASSF1A in cancer cells has been detailed in many studies. However, due to the methylation of its promoter, the expression of RASSF1A is missing in most cancers. In the literature, we found that the conclusion regarding the relationship between RASSF1A gene promoter methylation and the susceptibility and prognosis of melanoma was not unified. This study adopts the use of a meta-analysis and bioinformatics to explore the relationship between RASSF1A gene promoter methylation and the susceptibility and prognosis of melanoma. Methods Data on melanoma susceptibility were downloaded from the PubMed, Cochrane Library, Web of Science and Google Scholar databases, which were analyzed via a meta-analysis. The effect sizes were estimated by measuring an odds ratio (OR) with a 95% confidence interval (CI). We also used a chi-squared-based Q test to examine the between-study heterogeneity, and used funnel plots to evaluate publication bias. The data on melanoma prognosis, which were analyzed by bioinformatics methods, were downloaded from The Cancer Genome Atlas (TCGA) project. The effect sizes were estimated by measuring the hazard ratios (HRs) with a 95% confidence interval (CI). Results Our meta-analysis included 10 articles. We found that RASSF1A gene promoter methylation was closely related to melanoma susceptibility (OR = 12.67, 95% CI: 6.16 ∼ 26.05, z = 6.90, P<0.0001 according to a fixed effects model and OR = 9.25, 95% CI: 4.37 ∼ 19.54, z = 5.82, P<0.0001 according to a random effects model). The results of the meta-analysis did not reveal any heterogeneity (tau2 = 0.00; H = 1 [1; 1.55]; I2 = 0% [0%; 58.6%], P = 0.5158) or publication bias (t = 0.87, P = 0.4073 by Egger’s test; Z = 0.45, P = 0.6547 by Begg’s test); therefore, we believe that the results of our meta-analysis were more reliable. To explore the relationship between RASSF1A gene methylation, the prognosis of melanoma and the clinical features of this cancer type, we used the melanoma DNA methylation data and clinical data from TCGA project. We found that RASSF1A gene promoter methylation and melanoma prognosis did not demonstrate any relationship (HR was 0.94 (95% CI = [0.69; 1.27], P = 0.694) with disease-free survival and 0.74 (95% CI = [0.53; 1.05], P = 0.106) for overall survival), and no significant difference was observed between RASSF1A gene promoter methylation and the clinical-pathological features of melanoma. Conclusions In conclusion, the meta-analysis of the data in these articles provides strong evidence that the methylation status of the RASSF1A gene promoter was strongly related to melanoma susceptibility. Our bioinformatics analysis revealed no significant difference between RASSF1A gene promoter methylation and the prognosis and clinical-pathological features of melanoma.
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Hao YX, Fu Q, Guo YY, Ye M, Zhao HX, Wang Q, Peng XM, Li QW, Wang RL, Xiao WH. Effectiveness of circulating tumor DNA for detection of KRAS gene mutations in colorectal cancer patients: a meta-analysis. Onco Targets Ther 2017; 10:945-953. [PMID: 28243130 PMCID: PMC5317324 DOI: 10.2147/ott.s123954] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Circulating tumor DNA (ctDNA) can be identified in the peripheral blood of patients and harbors the genomic alterations found in tumor tissues, which provides a noninvasive approach for detection of gene mutations. We conducted this meta-analysis to investigate whether ctDNA can be used for monitoring KRAS gene mutations in colorectal cancer (CRC) patients. Medline, Embase, Cochrane Library and Web of Science were searched for the included eligible studies in English, and data were extracted for statistical analysis according to the numbers of true-positive (TP), true-negative (TN), false-positive (FP) and false-negative (FN) cases. Sensitivity, specificity and diagnostic odds ratio (DOR) were calculated, and the area under the receiver operating characteristic curve (AUROC) was used to evaluate the diagnostic performance. After independent searching and reviewing, 21 studies involving 1,812 cancer patients were analyzed. The overall sensitivity, specificity and DOR were 0.67 (95% confidence interval [CI] =0.55-0.78), 0.96 (95% CI =0.93-0.98) and 53.95 (95% CI =26.24-110.92), respectively. The AUROC was 0.95 (95% CI =0.92-0.96), which indicated the high diagnostic accuracy of ctDNA. After stratified analysis, we found the higher diagnostic accuracy in subgroup of patients detected in blood sample of plasma. The ctDNA may be an ideal source for detection of KRAS gene mutations in CRC patients with high specificity and diagnostic value.
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Affiliation(s)
- Yi-Xin Hao
- Department of Oncology, First Affiliated Hospital
| | - Qiang Fu
- Department of Anesthesiology, People's Liberation Army General Hospital, Beijing, People's Republic of China
| | - Yan-Yan Guo
- Department of Oncology, First Affiliated Hospital
| | - Ming Ye
- Department of Oncology, First Affiliated Hospital
| | - Hui-Xia Zhao
- Department of Oncology, First Affiliated Hospital
| | - Qi Wang
- Department of Oncology, First Affiliated Hospital
| | - Xiu-Mei Peng
- Department of Oncology, First Affiliated Hospital
| | - Qiu-Wen Li
- Department of Oncology, First Affiliated Hospital
| | | | - Wen-Hua Xiao
- Department of Oncology, First Affiliated Hospital
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Wang J, Hua W, Huang SK, Fan K, Takeshima L, Mao Y, Hoon DSB. RASSF8 regulates progression of cutaneous melanoma through nuclear factor-κb. Oncotarget 2016; 6:30165-77. [PMID: 26334503 PMCID: PMC4745788 DOI: 10.18632/oncotarget.5030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 08/03/2015] [Indexed: 12/31/2022] Open
Abstract
Our group previously demonstrated that the RASSF1 gene has a significant tumor suppressor role in cutaneous melanoma. The RASSF8 gene is a member of the N-terminal RASSF gene family. Previously, we identified RASSF8 (HOJ1, NCBI Gene ID:11228) expression in cutaneous melanoma; however the functional role of RASSF8 in melanoma is not known. RASSF8 expression was assessed in melanoma cell lines and tumors of different AJCC stages. Results indicated that RASSF8 expression was low in metastatic melanoma lines and decreased with melanoma progression. We then explored the mechanism of RASSF8 downregulation in melanoma by assessing methylation of RASSF8 and demonstrated that methylation of RASSF8 gene promoter was higher in advanced than in early stages melanomas. Functional activity of RASSF8 in melanoma lines by knockdown and overexpression of RASSF8 demonstrated that RASSF8 expression significantly inhibited cell growth, cell migration and invasion, whereas knockdown of RASSF8 expression significantly increased cell growth, cell migration and invasion of melanoma cells by increasing expression of P65 and its downstream target IL-6. Moreover RASSF8 was found to induce apoptosis in melanoma cells by activating the P53-P21 pathway, and also in vivo studies demonstrated that inhibiting RASSF8 increases the tumorigenic properties of human melanoma xenografts. These results suggest that RASSF8 plays a significant role in suppressing the progression of cutaneous melanoma.
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Affiliation(s)
- Jinhua Wang
- Department of Molecular Oncology, John Wayne Cancer Institute (JWCI), Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Wei Hua
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Sharon K Huang
- Department of Molecular Oncology, John Wayne Cancer Institute (JWCI), Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Kun Fan
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Ling Takeshima
- Department of Molecular Oncology, John Wayne Cancer Institute (JWCI), Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Dave S B Hoon
- Department of Molecular Oncology, John Wayne Cancer Institute (JWCI), Providence Saint John's Health Center, Santa Monica, CA, USA
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Abstract
PURPOSE OF REVIEW Over the last years, our understanding in molecular biology of melanoma has grown significantly and many genetic alterations have been identified affecting melanoma pathogenesis. This growing evidence has led to the development of targeted therapies which are showing promising clinical results. In addition to genetic alterations, an increasing number of studies have recently demonstrated the role of epigenetics in melanoma development and progression. Here, we summarize the current data on epigenetic research in melanoma. RECENT FINDINGS MicroRNA (miRNA) expression profiling studies have identified several miRNAs implicated in melanoma cell cycle and proliferation, cell migration and invasion, as well as miRNAs involved in apoptosis and immune response. Abnormal methylation profiling has been associated with melanoma progression and to date aberrant hypermethylation in more than 70 genes has been described. Recent works have highlighted the increasing evidence of the role of histone modification as a central regulatory event in melanoma pathogenesis. SUMMARY Many of these epigenetic biomarkers may have potential diagnostic, prognostic and therapeutic implications. Future approach might be using a combination of genetic and epigenetic biomarkers.
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Warton K, Mahon KL, Samimi G. Methylated circulating tumor DNA in blood: power in cancer prognosis and response. Endocr Relat Cancer 2016; 23:R157-71. [PMID: 26764421 PMCID: PMC4737995 DOI: 10.1530/erc-15-0369] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/13/2016] [Indexed: 12/12/2022]
Abstract
Circulating tumor DNA (ctDNA) in the plasma or serum of cancer patients provides an opportunity for non-invasive sampling of tumor DNA. This 'liquid biopsy' allows for interrogations of DNA such as quantity, chromosomal alterations, sequence mutations and epigenetic changes, and can be used to guide and improve treatment throughout the course of the disease. This tremendous potential for real-time 'tracking' in a cancer patient has led to substantial research efforts in the ctDNA field. ctDNA can be distinguished from non-tumor DNA by the presence of tumor-specific mutations and copy number variations, and also by aberrant DNA methylation, with both DNA sequence and methylation changes corresponding to those found in the tumor. Aberrant methylation of specific promoter regions can be a very consistent feature of cancer, in contrast to mutations, which typically occur at a wide range of sites. This consistency makes ctDNA methylation amenable to the design of widely applicable clinical assays. In this review, we examine ctDNA methylation in the context of monitoring disease status, treatment response and determining the prognosis of cancer patients.
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Affiliation(s)
- Kristina Warton
- Garvan Institute of Medical ResearchThe Kinghorn Cancer Centre and St Vincent's Clinical School, 370 Victoria Street, Darlinghurst, Sydeny, New South Wales, AustraliaChris O'Brien LifehouseCamperdown, New South Wales, Australia
| | - Kate L Mahon
- Garvan Institute of Medical ResearchThe Kinghorn Cancer Centre and St Vincent's Clinical School, 370 Victoria Street, Darlinghurst, Sydeny, New South Wales, AustraliaChris O'Brien LifehouseCamperdown, New South Wales, Australia Garvan Institute of Medical ResearchThe Kinghorn Cancer Centre and St Vincent's Clinical School, 370 Victoria Street, Darlinghurst, Sydeny, New South Wales, AustraliaChris O'Brien LifehouseCamperdown, New South Wales, Australia
| | - Goli Samimi
- Garvan Institute of Medical ResearchThe Kinghorn Cancer Centre and St Vincent's Clinical School, 370 Victoria Street, Darlinghurst, Sydeny, New South Wales, AustraliaChris O'Brien LifehouseCamperdown, New South Wales, Australia
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Huang SK, Hoon DSB. Liquid biopsy utility for the surveillance of cutaneous malignant melanoma patients. Mol Oncol 2016; 10:450-63. [PMID: 26778792 PMCID: PMC5307330 DOI: 10.1016/j.molonc.2015.12.008] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 12/04/2015] [Accepted: 12/08/2015] [Indexed: 01/01/2023] Open
Abstract
Cutaneous melanoma is one of the highest incident-rate cancers with increasing prevalence in Western societies. Despite the advent of new approved therapeutics, the 5-year overall survival rate of stage IV melanoma patients remains below 15%. Current treatments for late stage disease have shown higher efficacy when treated at a lower disease burden. Thus, blood-based biomarkers capable of detecting melanoma prior to clinically evident distant metastasis, will improve the treatment and outcomes for melanoma patients. To that end, effective treatment of melanoma necessitates identification of patients at risk for developing distant metastases. Furthermore, employing blood biomarkers that monitor cancer progression over the course of treatment is a promising solution to post-treatment drug resistance often developed in melanoma patients. Non-invasive blood biomarker assays allow for regular dynamic monitoring of disease. "Liquid Biopsy" of blood, which exploits circulating tumor cells (CTCs), cell-free circulating tumor DNA (ctDNA) and cell-free circulating microRNA (cmiRNA), has been shown to detect prognostic factors for relapse in AJCC stage III and stage IV melanoma patients. Moreover, molecular characterization of CTC and analysis of various forms of ctDNA present promising potential in development of individualized therapy for melanoma patients. New approaches such as massive parallel sequencing (MPS) provide a comprehensive view of the disease progression, allowing for the selection of therapeutic options for individual patients. With advancements of improving molecular assays, liquid biopsy analysis as a powerful, routine clinical assay for melanoma patients, is highly promising prospective.
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Affiliation(s)
- Sharon K Huang
- Department of Molecular Oncology, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA 90404, United States
| | - Dave S B Hoon
- Department of Molecular Oncology, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA 90404, United States.
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Salvianti F, Orlando C, Massi D, De Giorgi V, Grazzini M, Pazzagli M, Pinzani P. Tumor-Related Methylated Cell-Free DNA and Circulating Tumor Cells in Melanoma. Front Mol Biosci 2016; 2:76. [PMID: 26779490 PMCID: PMC4705904 DOI: 10.3389/fmolb.2015.00076] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/14/2015] [Indexed: 12/18/2022] Open
Abstract
Solid tumor release into the circulation cell-free DNA (cfDNA) and circulating tumor cells (CTCs) which represent promising biomarkers for cancer diagnosis. Circulating tumor DNA may be studied in plasma from cancer patients by detecting tumor specific alterations, such as genetic or epigenetic modifications. Ras association domain family 1 isoform A (RASSF1A) is a tumor suppressor gene silenced by promoter hypermethylation in a variety of human cancers including melanoma. The aim of the present study was to assess the diagnostic performance of a tumor-related methylated cfDNA marker in melanoma patients and to compare this parameter with the presence of CTCs. RASSF1A promoter methylation was quantified in cfDNA by qPCR in a consecutive series of 84 melanoma patients and 68 healthy controls. In a subset of 68 cases, the presence of CTCs was assessed by a filtration method (Isolation by Size of Epithelial Tumor Cells, ISET) as well as by an indirect method based on the detection of tyrosinase mRNA by RT-qPCR. The distribution of RASSF1A methylated cfDNA was investigated in cases and controls and the predictive capability of this parameter was assessed by means of the area under the ROC curve (AUC). The percentage of cases with methylated RASSF1A promoter in cfDNA was significantly higher in each class of melanoma patients (in situ, invasive and metastatic) than in healthy subjects (Pearson chi-squared test, p < 0.001). The concentration of RASSF1A methylated cfDNA in the subjects with a detectable quantity of methylated alleles was significantly higher in melanoma patients than in controls. The biomarker showed a good predictive capability (in terms of AUC) in discriminating between melanoma patients and healthy controls. This epigenetic marker associated to cfDNA did not show a significant correlation with the presence of CTCs, but, when the two parameters are jointly considered, we obtain a higher sensitivity of the detection of positive cases in invasive and metastatic melanomas. Our data suggest that cell-free tumor DNA and CTCs represent two complementary aspects of the liquid biopsy which may improve the diagnosis and the clinical management of melanoma patients.
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Affiliation(s)
- Francesca Salvianti
- Department of Clinical, Experimental and Biomedical Sciences, University of Florence Florence, Italy
| | - Claudio Orlando
- Department of Clinical, Experimental and Biomedical Sciences, University of Florence Florence, Italy
| | - Daniela Massi
- Division of Pathology, Department of Surgery and Translational Medicine, University of Florence Florence, Italy
| | - Vincenzo De Giorgi
- Division of Dermatology, Department of Surgery and Traslational Medicine, University of Florence Florence, Italy
| | - Marta Grazzini
- Division of Dermatology, Department of Surgery and Traslational Medicine, University of Florence Florence, Italy
| | - Mario Pazzagli
- Department of Clinical, Experimental and Biomedical Sciences, University of Florence Florence, Italy
| | - Pamela Pinzani
- Department of Clinical, Experimental and Biomedical Sciences, University of Florence Florence, Italy
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Xin Y, Li Z, Chan MT, Wu WKK. Circulating epigenetic biomarkers in melanoma. Tumour Biol 2015; 37:1487-92. [DOI: 10.1007/s13277-015-4599-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 12/07/2015] [Indexed: 01/21/2023] Open
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