1
|
Lin Z, Yang L. Identification of a CpG-based signature coupled with gene expression as prognostic indicators for melanoma: a preliminary study. Sci Rep 2024; 14:5302. [PMID: 38438381 PMCID: PMC10912562 DOI: 10.1038/s41598-023-50614-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 12/22/2023] [Indexed: 03/06/2024] Open
Abstract
DNA methylation is an important part of the genomic biology, which recently allowed the identification of key biomarkers for a variety of cancers, including cutaneous melanoma. Despite the current knowledge in cutaneous melanoma, there is a clear need for new efficient biomarkers in clinical application of detection. We use The Cancer Genome Atlas data as a training set and a multi-stage screening strategy to identify prognostic characteristics of melanoma based on DNA methylation. Three DNA methylation CpG sites were identified to be related to the overall survival in the skin cutaneous melanoma cohort. This signature was validated in two independent datasets from Gene Expression Omnibus. The stratified analysis by clinical stage, age, gender, and grade retained the statistical significance. The methylation signature was significantly correlated with immune cells and anti-tumor immune response. Moreover, gene expression corresponding to the candidate CpG locus was also significantly correlated with the survival rate of the patient. About 49% of the prognostic effects of methylation are mediated by affecting the expression of the corresponding genes. The prognostic characteristics of DNA methylation combined with clinical information provide a better prediction value tool for melanoma patients than the clinical information alone. However, more experiments are required to validate these findings. Overall, this signature presents a prospect of novel and wide-ranging applications for appropriate clinical adjuvant trails.
Collapse
Affiliation(s)
- Zhen Lin
- Cancer Center, Department of Medical Oncology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Liu Yang
- Cancer Center, Department of Medical Oncology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China.
| |
Collapse
|
2
|
Puentes C, Estrada A, Bohórquez M, Vélez A, Giraldo C, Echeverry M. Melanoma: clinical-pathological and molecular analysis in patients of Ibague city, Colombia. DUAZARY 2020. [DOI: 10.21676/2389783x.3217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
This study aimed to establish the clinicopathological characteristics of patients with melanoma and its association with BRAF gene mutations. The pathology reports and paraffin-embedded tumor samples from 47 women and 30 men with melanoma, with an average age of diagnosis of 60 years, were reviewed at the Hospital Federico Lleras Acosta of Ibague, between 2010 and 2016. The presence of V600E mutation at the exon 15 of BRAF gene, was analyzed in these tumoral samples by Sanger sequencing and visual inspection of the electropherograms. We also studied the clinicopathological variables with X2, t-Student and the Kaplan Meier index. Most of the lesions were located in the lower limbs (46.6%). The most frequent subtype was Acral Lentiginous Melanoma (41.8%). Most lesions were of poor prognosis: Breslow depth greater than 4.1 mm (52.7%), ulceration (61.4%) and medium or high mitotic rate (> 30 %). The V600E mutation was identified in five patients with large, deep and ulcerated tumors, four of them had less than four years of survival. In conclusion, there was a higher frequency of melanoma in women, V600E BRAF mutation was present in patients with advanced disease (high Breslow index) and, the probability of five-year survival was less than 40%.
Collapse
|
3
|
Guo W, Zhu L, Zhu R, Chen Q, Wang Q, Chen JQ. A four-DNA methylation biomarker is a superior predictor of survival of patients with cutaneous melanoma. eLife 2019; 8:e44310. [PMID: 31169496 PMCID: PMC6553943 DOI: 10.7554/elife.44310] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 04/29/2019] [Indexed: 01/01/2023] Open
Abstract
Cutaneous melanoma (CM) is a life-threatening form of skin cancer. Prognostic biomarkers can reliably stratify patients at initial melanoma diagnosis according to risk, and may inform clinical decisions. Here, we performed a retrospective, cohort-based study analyzing genome-wide DNA methylation of 461 patients with CM from the TCGA database. Cox regression analyses were conducted to establish a four-DNA methylation signature that was significantly associated with the overall survival (OS) of patients with CM, and that was validated in an independent cohort. Corresponding Kaplan-Meier analysis displayed a distinct separation in OS. The ROC analysis confirmed that the predictive signature performed well. Notably, this signature exhibited much higher predictive accuracy in comparison with known biomarkers. This signature was significantly correlated with immune checkpoint blockade (ICB) immunotherapy-related signatures, and may have potential as a guide for measures of responsiveness to ICB immunotherapy.
Collapse
Affiliation(s)
- Wenna Guo
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life SciencesNanjing UniversityNanjingChina
| | - Liucun Zhu
- School of Life SciencesShanghai UniversityShanghaiChina
| | - Rui Zhu
- School of Life SciencesShanghai UniversityShanghaiChina
| | - Qihan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life SciencesNanjing UniversityNanjingChina
| | - Qiang Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life SciencesNanjing UniversityNanjingChina
| | - Jian-Qun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life SciencesNanjing UniversityNanjingChina
| |
Collapse
|
4
|
Xu S, Sui J, Yang S, Liu Y, Wang Y, Liang G. Integrative analysis of competing endogenous RNA network focusing on long noncoding RNA associated with progression of cutaneous melanoma. Cancer Med 2018; 7:1019-1029. [PMID: 29522273 PMCID: PMC5911588 DOI: 10.1002/cam4.1315] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 12/04/2017] [Accepted: 12/04/2017] [Indexed: 12/12/2022] Open
Abstract
Cutaneous melanoma (CM) is the most malignant tumor of skin cancers because of its rapid development and high mortality rate. Long noncoding RNAs (lncRNAs), which play essential roles in the tumorigenesis and metastasis of CM and interplay with microRNAs (miRNAs) and mRNAs, are hopefully considered to be efficient biomarkers to detect deterioration during the progression of CM to improve the prognosis. Bioinformatics analysis was fully applied to predict the vital lncRNAs and the associated miRNAs and mRNAs, which eventually constructed the competing endogenous RNA (ceRNA) network to explain the RNA expression patterns in the progression of CM. Further statistical analysis emphasized the importance of these key genes, which were statistically significantly related to one or few clinical features from the ceRNA network. The results showed the lncRNAs MGC12926 and LINC00937 were verified to be strongly connected with the prognosis of CM patients.
Collapse
Affiliation(s)
- Siyi Xu
- Key Laboratory of Environmental Medicine EngineeringMinistry of EducationSchool of Public HealthSoutheast UniversityNanjingJiangsuChina
| | - Jing Sui
- Key Laboratory of Environmental Medicine EngineeringMinistry of EducationSchool of Public HealthSoutheast UniversityNanjingJiangsuChina
| | - Sheng Yang
- Key Laboratory of Environmental Medicine EngineeringMinistry of EducationSchool of Public HealthSoutheast UniversityNanjingJiangsuChina
| | - Yufeng Liu
- TCM of Jiangsu Provincial HospitalNanjingJiangsuChina
| | - Yan Wang
- Institute of DermatologyChinese Academy of Medical Sciences and Peking Union Medical CollegeJiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIsNanjingJiangsuChina
| | - Geyu Liang
- Key Laboratory of Environmental Medicine EngineeringMinistry of EducationSchool of Public HealthSoutheast UniversityNanjingJiangsuChina
| |
Collapse
|
5
|
Chen X, Guo W, Xu XJ, Su F, Wang Y, Zhang Y, Wang Q, Zhu L. Melanoma long non-coding RNA signature predicts prognostic survival and directs clinical risk-specific treatments. J Dermatol Sci 2017; 85:226-234. [PMID: 27955882 DOI: 10.1016/j.jdermsci.2016.12.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 10/11/2016] [Accepted: 12/05/2016] [Indexed: 12/19/2022]
Abstract
BACKGROUND Various studies have demonstrated that the Breslow thickness, tumor ulceration and mitotic index could serve as prognostic markers in patients with cutaneous melanoma. Recently, however, as these clinicopathological biomarkers lack efficient interpretation of endogenous mechanism of melanoma, the emphasis on the prognosis of melanoma has transformed to molecular tumor markers. OBJECTIVE This study was designed to identify survival-related long non-coding RNAs (lncRNAs), and based on the different expressions of these lncRNAs, clinical risk-specific diagnosis and adjuvant therapy could be employed on melanoma patients, especially patients in the early course of disease or patients with a Breslow thickness no more than 2mm. METHODS The clinical information and corresponding RNA expression data were obtained from The Cancer Genome Atlas dataset and Gene Expression Omnibus dataset (GSE65904). All samples were categorized into one training dataset and two validation datasets. Cox proportional hazard regression analysis was then used to identify survival-related lncRNAs and risk assessment signature was constructed in training dataset. Kaplan-Meier method was used to estimate the utility of this signature in predicting the duration of survival of patients both in the training dataset and two validation datasets. Meanwhile receiver operating characteristic analyses were used to evaluate the predictive effectiveness of this signature in two validation datasets. RESULTS It was found that the signature was effective while used for risk stratification, and Kaplan-Meier analyses indicated that the duration of survival of patients in high-risk groups were significantly shorter than that of low-risk groups. Moreover, areas under the receiver operating characteristic curve were 0.711 (95% confidence interval: 0.618-0.804) and 0.698 (95% confidence interval: 0.614-0.782) when this signature was used to predict the patients' duration of survival in two validation datasets respectively, indicating the superior specificity and sensitivity of this signature. CONCLUSION We identified a four-lncRNA prognostic signature with the ability of risk stratification for melanoma patients. Risk score acquired from this signature, combining with differential diagnosis and differential adjuvant therapy, could potentially improve the prognosis quality of life for patients, especially patients in the early course of disease or patients with a Breslow thickness no more than 2mm.
Collapse
Affiliation(s)
- Xijia Chen
- School of Life Sciences, Shanghai University, Shanghai, 200444, PR China
| | - Wenna Guo
- School of Life Sciences, Shanghai University, Shanghai, 200444, PR China; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, PR China
| | - Xin-Jian Xu
- Department of Mathematics, Shanghai University, Shanghai, 200444, PR China
| | - Fangchu Su
- School of Life Sciences, Shanghai University, Shanghai, 200444, PR China
| | - Yi Wang
- School of Life Sciences, Shanghai University, Shanghai, 200444, PR China
| | - Yingzheng Zhang
- School of Life Sciences, Shanghai University, Shanghai, 200444, PR China
| | - Qiang Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, PR China.
| | - Liucun Zhu
- School of Life Sciences, Shanghai University, Shanghai, 200444, PR China.
| |
Collapse
|
6
|
Roland CL, Ross MI, Hall CS, Laubacher B, Upshaw J, Anderson AE, Lucci A. Detection of circulating melanoma cells in the blood of melanoma patients: a preliminary study. Melanoma Res 2015; 25:335-41. [PMID: 26011119 PMCID: PMC5642955 DOI: 10.1097/cmr.0000000000000168] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Significant prognostic heterogeneity exists within the substages of melanoma; therefore, novel prognostic biomarkers are needed to provide information on the risk of recurrence. Limited available data suggest prognostic significance for circulating melanoma cells (CMCs); there is a need for a sensitive, reproducible, and standardized identification technique. Using a semiautomated technology, we sought to determine whether CMCs could be identified reliably in stage I-IV melanoma patients and whether the presence of CMC correlated with known prognostic factors. CMCs were detected in the peripheral blood (7.5 ml) of patients with stage I-IV melanoma (n=89) using the CellSearch system. CD146 cells were immunomagnetically enriched; nucleated HMW-MAA/CD45/CD34 cells were considered CMCs. One or more CMCs was detected in 45% of all patients, varying with stage of disease (stages I/II, III, and IV: 35, 44, and 86%, respectively; P=0.03, for stage I/II vs. stage IV); 55% had one CMC, 32% had two CMCs, and 13% had three or more CMCs identified. The presence of CMCs in the blood was associated with histologic subtype, particularly in patients with stage I/II disease (superficial spreading 18% vs. acral lentiginous 75%). Using a semiautomated technique, CMCs can be identified in a significant number of melanoma patients. These data support further study with longer follow-up and longitudinal/serial time points to better determine the identification rates and prognostic significance of CMCs in stage I-IV melanoma patients.
Collapse
Affiliation(s)
- Christina L Roland
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | | | | | | | | | | |
Collapse
|
7
|
Etzkorn JR, Sobanko JF, Elenitsas R, Newman JG, Goldbach H, Shin TM, Miller CJ. Low recurrence rates for in situ and invasive melanomas using Mohs micrographic surgery with melanoma antigen recognized by T cells 1 (MART-1) immunostaining: tissue processing methodology to optimize pathologic staging and margin assessment. J Am Acad Dermatol 2015; 72:840-50. [PMID: 25774012 DOI: 10.1016/j.jaad.2015.01.007] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 12/20/2014] [Accepted: 01/07/2015] [Indexed: 11/18/2022]
Abstract
BACKGROUND Various methods of tissue processing have been used to treat melanoma with Mohs micrographic surgery (MMS). OBJECTIVE We describe a method of treating melanoma with MMS that combines breadloaf frozen sectioning of the central debulking excision with complete peripheral and deep microscopic margin evaluation, allowing detection of upstaging and comprehensive pathologic margin assessment before reconstruction. METHODS We conducted a retrospective cohort study evaluating for local recurrence and upstaging in 614 invasive or in situ melanomas in 577 patients treated with this MMS tissue processing methodology using frozen sections with melanoma antigen recognized by T cells 1 (MART-1) immunostaining. Follow-up was available in 597 melanomas in 563 patients. RESULTS Local recurrence was identified in 0.34% (2/597) lesions with a mean follow-up time of 1026 days (2.8 years). Upstaging occurred in 34 of 614 lesions (5.5%), of which 97% (33/34) were detected by the Mohs surgeon before reconstruction. LIMITATIONS Limitations include retrospective study, intermediate follow-up time, and that the recurrence status of 39.6% of patients was self-reported. CONCLUSION Treating melanoma with MMS that combines breadloaf sectioning of the central debulking excision with complete peripheral and deep microscopic margin evaluation permits identification of upstaging and consideration of sentinel lymph node biopsy before definitive reconstruction and achieves low local recurrence rates compared with conventional excision.
Collapse
Affiliation(s)
| | - Joseph F Sobanko
- University of Pennsylvania Health System, Philadelphia, Pennsylvania
| | - Rosalie Elenitsas
- University of Pennsylvania Health System, Philadelphia, Pennsylvania
| | - Jason G Newman
- University of Pennsylvania Health System, Philadelphia, Pennsylvania
| | | | - Thuzar M Shin
- University of Pennsylvania Health System, Philadelphia, Pennsylvania
| | | |
Collapse
|
8
|
Scanlon P, Tian J, Zhong J, Silva I, Shapiro R, Pavlick A, Berman R, Osman I, Darvishian F. Enhanced immunohistochemical detection of neural infiltration in primary melanoma: is there a clinical value? Hum Pathol 2014; 45:1656-63. [PMID: 24890944 DOI: 10.1016/j.humpath.2014.04.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 03/27/2014] [Accepted: 04/02/2014] [Indexed: 11/17/2022]
Abstract
Neural infiltration in primary melanoma is a histopathologic feature that has been associated with desmoplastic histopathologic subtype and local recurrence in the literature. We tested the hypothesis that improved detection and characterization of neural infiltration into peritumoral or intratumoral location and perineural or intraneural involvement could have a prognostic relevance. We studied 128 primary melanoma cases prospectively accrued and followed at New York University using immunohistochemical detection with antihuman neurofilament protein and routine histology with hematoxylin and eosin. Neural infiltration, defined as the presence of tumor cells involving or immediately surrounding nerve foci, was identified and characterized using both detection methods. Neural infiltration rate of detection was enhanced by immunohistochemistry for neurofilament in matched-pair design (47% by immunohistochemistry versus 25% by routine histology). Immunohistochemical detection of neural infiltration was significantly associated with ulceration (P = .021), desmoplastic and acral lentiginous histologic subtype (P = .008), and head/neck/hands/feet tumor location (P = .037). Routinely detected neural infiltration was significantly associated with local recurrence (P = .010). Immunohistochemistry detected more intratumoral neural infiltration cases compared with routine histology (30% versus 3%, respectively). Peritumoral and intratumoral nerve location had no impact on clinical outcomes. Using a multivariate model controlling for stage, neither routinely detected neural infiltration nor enhanced immunohistochemical characterization of neural infiltration was significantly associated with disease-free or overall survival. Our data demonstrate that routinely detected neural infiltration is associated with local recurrence in all histologic subtypes but that improved detection and characterization of neural infiltration with immunohistochemistry in primary melanoma does not add to prognostic relevance.
Collapse
Affiliation(s)
- Patrick Scanlon
- Department of Dermatology, New York University School of Medicine, 10016, New York, NY; The New York University Interdisciplinary Melanoma Cooperative Group, 10016, New York, NY
| | - Jaiying Tian
- Department of Dermatology, New York University School of Medicine, 10016, New York, NY; The New York University Interdisciplinary Melanoma Cooperative Group, 10016, New York, NY
| | - Judy Zhong
- The New York University Interdisciplinary Melanoma Cooperative Group, 10016, New York, NY
| | - Ines Silva
- The New York University Interdisciplinary Melanoma Cooperative Group, 10016, New York, NY
| | - Richard Shapiro
- The New York University Interdisciplinary Melanoma Cooperative Group, 10016, New York, NY; Department of Surgery, New York University School of Medicine, 10016, New York, NY
| | - Anna Pavlick
- The New York University Interdisciplinary Melanoma Cooperative Group, 10016, New York, NY
| | - Russell Berman
- The New York University Interdisciplinary Melanoma Cooperative Group, 10016, New York, NY; Department of Surgery, New York University School of Medicine, 10016, New York, NY
| | - Iman Osman
- Department of Dermatology, New York University School of Medicine, 10016, New York, NY; The New York University Interdisciplinary Melanoma Cooperative Group, 10016, New York, NY
| | - Farbod Darvishian
- The New York University Interdisciplinary Melanoma Cooperative Group, 10016, New York, NY; Department of Pathology, New York University School of Medicine, 10016, New York, NY.
| |
Collapse
|