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Randerson-Moor J, Davies J, Harland M, Nsengimana J, Bigirumurame T, Walker C, Laye J, Appleton ES, Ball G, Cook GP, Bishop DT, Salmond RJ, Newton-Bishop J. Systemic inflammation, the peripheral blood transcriptome and primary melanoma. J Invest Dermatol 2024:S0022-202X(24)00275-6. [PMID: 38583742 DOI: 10.1016/j.jid.2024.02.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 02/18/2024] [Accepted: 02/21/2024] [Indexed: 04/09/2024]
Abstract
Peripheral blood transcriptomes from 383 newly-diagnosed melanoma patients were subjected to differential gene expression analysis. The hypotheses were that impaired systemic immunity is associated with poorer prognosis (thicker tumors and fewer tumor infiltrating lymphocytes (TILs)) and evidence of systemic inflammation (high-sensitivity C-reactive protein (hsCRP) and fibrinogen levels). Higher fibrinogen levels were associated with thicker primaries. In single gene analysis hsCRP levels were significantly associated with higher blood CD274 expression, (coding for PD-L1), but each was independently prognostic, with hsCRP associated with increased mortality, and higher CD274 protective, independent of age. Pathway analysis identified downregulation of immune cell signalling pathways in the blood of people with thicker tumors and notable upregulation of STAT1 in people with brisk TILs. Transcriptomic data provided evidence for increased NFB signalling with higher inflammatory markers but with reduction in expression of HLA class II molecules and higher CD274 suggesting that aberrant systemic inflammation is a significant mediator of reduced immune function in melanoma. In summary, transcriptomic data revealed evidence of reduced immune function in patients with thicker tumors and fewer TILs, at diagnosis. Inflammatory markers were associated with thicker primaries and independently with death from melanoma suggesting that systemic inflammation contributes to that reduced immune function.
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Godson L, Alemi N, Nsengimana J, Cook GP, Clarke EL, Treanor D, Bishop DT, Newton-Bishop J, Gooya A, Magee D. Immune subtyping of melanoma whole slide images using multiple instance learning. Med Image Anal 2024; 93:103097. [PMID: 38325154 DOI: 10.1016/j.media.2024.103097] [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: 12/16/2022] [Revised: 01/15/2024] [Accepted: 01/25/2024] [Indexed: 02/09/2024]
Abstract
Determining early-stage prognostic markers and stratifying patients for effective treatment are two key challenges for improving outcomes for melanoma patients. Previous studies have used tumour transcriptome data to stratify patients into immune subgroups, which were associated with differential melanoma specific survival and potential predictive biomarkers. However, acquiring transcriptome data is a time-consuming and costly process. Moreover, it is not routinely used in the current clinical workflow. Here, we attempt to overcome this by developing deep learning models to classify gigapixel haematoxylin and eosin (H&E) stained pathology slides, which are well established in clinical workflows, into these immune subgroups. We systematically assess six different multiple instance learning (MIL) frameworks, using five different image resolutions and three different feature extraction methods. We show that pathology-specific self-supervised models using 10x resolution patches generate superior representations for the classification of immune subtypes. In addition, in a primary melanoma dataset, we achieve a mean area under the receiver operating characteristic curve (AUC) of 0.80 for classifying histopathology images into 'high' or 'low immune' subgroups and a mean AUC of 0.82 in an independent TCGA melanoma dataset. Furthermore, we show that these models are able to stratify patients into 'high' and 'low immune' subgroups with significantly different melanoma specific survival outcomes (log rank test, P< 0.005). We anticipate that MIL methods will allow us to find new biomarkers of high importance, act as a tool for clinicians to infer the immune landscape of tumours and stratify patients, without needing to carry out additional expensive genetic tests.
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Affiliation(s)
- Lucy Godson
- School of Computing, University of Leeds, Woodhouse, Leeds, LS2 9JT, United Kingdom.
| | - Navid Alemi
- School of Computing, University of Leeds, Woodhouse, Leeds, LS2 9JT, United Kingdom
| | - Jérémie Nsengimana
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Graham P Cook
- Leeds Institute of Medical Research, University of Leeds School of Medicine, St. James's University Hospital, Leeds, United Kingdom
| | - Emily L Clarke
- Department of Histopathology, Leeds Teaching Hospitals NHS Trust, Leeds, United Kingdom; Division of Pathology and Data Analytics, Leeds Institute of Cancer and Pathology, University of Leeds, Beckett Street, Leeds, LS9 7TF, United Kingdom
| | - Darren Treanor
- Department of Histopathology, Leeds Teaching Hospitals NHS Trust, Leeds, United Kingdom; Division of Pathology and Data Analytics, Leeds Institute of Cancer and Pathology, University of Leeds, Beckett Street, Leeds, LS9 7TF, United Kingdom; Department of Clinical Pathology and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden; Centre for Medical Image Science and Visualization (CMIV), Linköping University, Linköping, Sweden
| | - D Timothy Bishop
- Leeds Institute of Medical Research, University of Leeds School of Medicine, St. James's University Hospital, Leeds, United Kingdom
| | - Julia Newton-Bishop
- Division of Pathology and Data Analytics, Leeds Institute of Cancer and Pathology, University of Leeds, Beckett Street, Leeds, LS9 7TF, United Kingdom
| | - Ali Gooya
- School of Computing, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
| | - Derek Magee
- School of Computing, University of Leeds, Woodhouse, Leeds, LS2 9JT, United Kingdom
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Ye J, Liu F, Zhang L, Wu C, Jiang A, Xie T, Jiang H, Li Z, Luo P, Jiao J, Xiao J. MOCS, a novel classifier system integrated multimoics analysis refining molecular subtypes and prognosis for skin melanoma. J Biomol Struct Dyn 2024:1-17. [PMID: 38555737 DOI: 10.1080/07391102.2024.2329305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 02/08/2024] [Indexed: 04/02/2024]
Abstract
PURPOSE The present investigation focuses on Skin Cutaneous Melanoma (SKCM), a melanocytic carcinoma characterized by marked aggression, significant heterogeneity, and a complex etiological background, factors which collectively contribute to the challenge in prognostic determinations. We defined a novel classifier system specifically tailored for SKCM based on multiomics. METHODS We collected 423 SKCM samples with multi omics datasets to perform a consensus cluster analysis using 10 machine learning algorithms and verified in 2 independent cohorts. Clinical features, biological characteristics, immune infiltration pattern, therapeutic response and mutation landscape were compared between subtypes. RESULTS Based on consensus clustering algorithms, we identified two Multi-Omics-Based-Cancer-Subtypes (MOCS) in SKCM in TCGA project and validated in GSE19234 and GSE65904 cohorts. MOCS2 emerged as a subtype with poor prognosis, characterized by a complex immune microenvironment, dysfunctional anti-tumor immune state, high cancer stemness index, and genomic instability. MOCS2 exhibited resistance to chemotherapy agents like erlotinib and sunitinib while sensitive to rapamycin, NSC87877, MG132, and FH355. Additionally, ELSPBP1 was identified as the target involving in glycolysis and M2 macrophage infiltration in SKCM. CONCLUSIONS MOCS classification could stably predict prognosis of SKCM; patients with a high cancer stemness index combined with genomic instability may be predisposed to an immune exhaustion state.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Juelan Ye
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Fuchun Liu
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
| | - Luoshen Zhang
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
| | - Chunbiao Wu
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
- School of Health Science and Technology, University of Shanghai for Science and Technology, Shanghai, China
| | - Aimin Jiang
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Tianying Xie
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
- School of Health Science and Technology, University of Shanghai for Science and Technology, Shanghai, China
| | - Hao Jiang
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
- School of Health Science and Technology, University of Shanghai for Science and Technology, Shanghai, China
| | - Zhenxi Li
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
- School of Health Science and Technology, University of Shanghai for Science and Technology, Shanghai, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jian Jiao
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
| | - Jianru Xiao
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
- School of Health Science and Technology, University of Shanghai for Science and Technology, Shanghai, China
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Wang W, Zhang Z, Li W, Wei D, Xu J, Qian Y, Cao S, Lei D. Characterization of the immune cell function landscape in head and neck squamous carcinoma to assist in prognosis prediction and immunotherapy. Aging (Albany NY) 2023; 15:12588-12617. [PMID: 37955651 PMCID: PMC10683602 DOI: 10.18632/aging.205201] [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: 06/27/2023] [Accepted: 10/03/2023] [Indexed: 11/14/2023]
Abstract
BACKGROUND The malignant characteristics of cancer depend not only on intrinsic properties of cancer cells but also on the functions of infiltrating immune cells. In this study, we aimed to investigate the functional landscape of immune cells in head and neck squamous cell carcinoma (HNSCC). METHODS We employed single-sample gene set enrichment analysis to examine the immunophenotypes of HNSCC based on 29 immune cell functions (ICFs) in TCGA and GSE65858 datasets. We analyzed the clinical features, immune microenvironment, molecular profiles, and biological processes. Additionally, we developed and validated an ICF-based risk score for personalized prognosis prediction. We confirmed the value of the ICF score in our cohort using qRT-PCR and immunohistochemistry. Molecular docking was used to predict potential compounds for immunotherapy. RESULTS Three immunophenotypes (Immune-L, Immune-M, and Immune-H) were identified in 769 HNSCC samples. The characteristics of Immune-H were consistent with a "Hot" tumor, Immune-L was similar to a "Cold" tumor, and Immune-M exhibited intermediate features. The ICF risk score was associated with immune checkpoints, infiltrating immune cells, tumor mutation burden, and sensitivities to targeted/chemotherapeutic agents. Gene set variation analysis implicated the involvement of metabolic reprogramming pathways in the high-risk group. The combination of "Tumor Immune Dysfunction and Exclusion" and "Immunophenoscore" algorithms indicated that the low-risk group had a higher likelihood of benefiting from immunotherapy. Finally, we identified Eltrombopag and other compounds that may be beneficial for HNSCC immunotherapy. CONCLUSION Our study provides a novel perspective on the tumor microenvironment of HNSCC, aiding in the understanding of HNSCC heterogeneity and the development of personalized/precision medicine.
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Affiliation(s)
- Wenlun Wang
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, Jinan, Shandong, P.R. China
- NHC Key Laboratory of Otorhinolaryngology, Shandong University, Jinan, Shandong, P.R. China
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, P.R. China
| | - Zhouyi Zhang
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, Jinan, Shandong, P.R. China
- NHC Key Laboratory of Otorhinolaryngology, Shandong University, Jinan, Shandong, P.R. China
| | - Wenming Li
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, Jinan, Shandong, P.R. China
- NHC Key Laboratory of Otorhinolaryngology, Shandong University, Jinan, Shandong, P.R. China
| | - Dongmin Wei
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, Jinan, Shandong, P.R. China
- NHC Key Laboratory of Otorhinolaryngology, Shandong University, Jinan, Shandong, P.R. China
| | - Jianing Xu
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, Jinan, Shandong, P.R. China
- NHC Key Laboratory of Otorhinolaryngology, Shandong University, Jinan, Shandong, P.R. China
| | - Ye Qian
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, Jinan, Shandong, P.R. China
- NHC Key Laboratory of Otorhinolaryngology, Shandong University, Jinan, Shandong, P.R. China
| | - Shengda Cao
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, Jinan, Shandong, P.R. China
- NHC Key Laboratory of Otorhinolaryngology, Shandong University, Jinan, Shandong, P.R. China
| | - Dapeng Lei
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, Jinan, Shandong, P.R. China
- NHC Key Laboratory of Otorhinolaryngology, Shandong University, Jinan, Shandong, P.R. China
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Dall'Olmo L, Papa N, Surdo NC, Marigo I, Mocellin S. Alpha-melanocyte stimulating hormone (α-MSH): biology, clinical relevance and implication in melanoma. J Transl Med 2023; 21:562. [PMID: 37608347 PMCID: PMC10463388 DOI: 10.1186/s12967-023-04405-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 08/01/2023] [Indexed: 08/24/2023] Open
Abstract
Alpha-melanocyte stimulating hormone (α-MSH) and its receptor, melanocortin 1 receptor (MC1R), have been proposed as potential target for anti-cancer strategies in melanoma research, due to their tissue specific expression and involvement in melanocyte homeostasis. However, their role in prevention and treatment of melanoma is still debated and controversial. Although a large body of evidence supports α-MSH in preventing melanoma development, some preclinical findings suggest that the α-MSH downstream signalling may promote immune escape and cancer resistance to therapy. Additionally, in metastatic melanoma both MC1R and α-MSH have been reported to be overexpressed at levels much higher than normal cells. Furthermore, targeted therapy (e.g. BRAF inhibition in BRAFV600E mutant tumours) has been shown to enhance this phenomenon. Collectively, these data suggest that targeting MC1R could serve as an approach in the treatment of metastatic melanoma. In this review, we explore the molecular biology of α-MSH with particular emphasis into its tumor-related properties, whilst elaborating the experimental evidence currently available regarding the interplay between α-MSH/MC1R axis, melanoma and antitumor strategies.
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Affiliation(s)
- Luigi Dall'Olmo
- Department of Surgical Oncological and Gastroenterological Sciences, Padua University, Via Giustiniani 2, 35128, Padua, Italy.
- Istituto Oncologico Veneto IOV-IRCCS, 35128, Padua, Italy.
| | - Nicole Papa
- Istituto Oncologico Veneto IOV-IRCCS, 35128, Padua, Italy
| | - Nicoletta Concetta Surdo
- Neuroscience Institute, National Research Council of Italy (CNR), 35121, Padua, Italy
- Veneto Institute of Molecular Medicine VIMM, Foundation for Advanced Biomedical Research, 35129, Padua, Italy
| | - Ilaria Marigo
- Department of Surgical Oncological and Gastroenterological Sciences, Padua University, Via Giustiniani 2, 35128, Padua, Italy
- Istituto Oncologico Veneto IOV-IRCCS, 35128, Padua, Italy
| | - Simone Mocellin
- Department of Surgical Oncological and Gastroenterological Sciences, Padua University, Via Giustiniani 2, 35128, Padua, Italy
- Istituto Oncologico Veneto IOV-IRCCS, 35128, Padua, Italy
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6
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Alcalá Ramírez Del Puerto A, Hernández-Rodriguez JC, Sendín-Martín M, Ortiz-Alvarez J, Conejo-Mir Sánchez J, Pereyra-Rodriguez JJ. Skin cancer mortality in Spain: adjusted mortality rates by province and related risk factors. Int J Dermatol 2023; 62:776-782. [PMID: 36807202 DOI: 10.1111/ijd.16618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 01/05/2023] [Accepted: 01/30/2023] [Indexed: 02/22/2023]
Abstract
BACKGROUND Ultraviolet radiation is the main environmental risk factor responsible for the development of skin cancer. Other occupational, socioeconomic, and environmental factors appear to be related to the risk of skin cancer. Furthermore, the factors appear to differ for melanoma and non-melanoma skin cancer (NMSC). The purpose of this study is to analyze mortality rates of skin cancer in the different provinces of Spain and to determine the influence of socioeconomic conditions and other environmental and demographic factors in rates. METHODS Deaths from melanoma and NMSC in the period 2000-2019 were obtained as well as socioeconomic and environmental variables. Annual standardized mortality rates (SMR) were calculated for all Spanish provinces. The Pearson correlation coefficient was calculated. RESULTS The SMR of melanoma was 2.10/100,000 inhabitants, while that of NMSC was 1.28/100,000. At the provincial level, a great variability is confirmed. Gross domestic product showed a positive correlation with melanoma mortality but a negative correlation with NMSC. Other environmental and socioeconomic variables also showed correlation, as a positive correlation between tobacco sales and melanoma and between agricultural development and the NMSC. CONCLUSIONS There are still important differences between each province that must be taken into account when planning health care and resource distribution. This ecological and province-wise study helps to elucidate the relationship between social and ambient exposure determinants and skin cancer mortality in Spain.
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Affiliation(s)
| | | | | | - Juan Ortiz-Alvarez
- Dermatology Department, Hospital Universitario Virgen del Rocío, Sevilla, Spain
| | - Julián Conejo-Mir Sánchez
- Dermatology Department, Hospital Universitario Virgen del Rocío, Sevilla, Spain.,School of Medicine, Medicine Department, Sevilla University, Sevilla, Spain
| | - José Juan Pereyra-Rodriguez
- Dermatology Department, Hospital Universitario Virgen del Rocío, Sevilla, Spain.,School of Medicine, Medicine Department, Sevilla University, Sevilla, Spain
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7
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Ferrari L, Monti P, Favero C, Carugno M, Tarantini L, Maggioni C, Bonzini M, Pesatori AC, Bollati V. Association between night shift work and methylation of a subset of immune-related genes. Front Public Health 2023; 10:1083826. [PMID: 36711387 PMCID: PMC9877629 DOI: 10.3389/fpubh.2022.1083826] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 12/22/2022] [Indexed: 01/13/2023] Open
Abstract
Introduction Night shift (NS) work has been associated with an increased risk of different conditions characterized by altered inflammatory and immune responses, such as cardio-metabolic and infectious diseases, cancer, and obesity. Epigenetic modifications, such as DNA methylation, might mirror alterations in biological processes that are influenced by NS work. Methods The present study was conducted on 94 healthy female workers with different working schedules and aimed at identifying whether NS was associated with plasmatic concentrations of the inflammatory proteins NLRP3 and TNF-alpha, as well as with DNA methylation levels of ten human endogenous retroviral (HERV) sequences, and nine genes selected for their role in immune and inflammatory processes. We also explored the possible role of the body mass index (BMI) as an additional susceptibility factor that might influence the effects of NS work on the tested epigenetic modifications. Results and discussion We observed a positive association between NS and NLRP3 levels (p-value 0.0379). Moreover, NS workers retained different methylation levels for ERVFRD-1 (p-value = 0.0274), HERV-L (p-value = 0.0377), and HERV-P (p-value = 0.0140) elements, and for BIRC2 (p-value = 0.0460), FLRT3 (p-value = 0.0422), MIG6 (p-value = 0.0085), and SIRT1 (p-value = 0.0497) genes. We also observed that the BMI modified the relationship between NS and the methylation of ERVE, HERV-L, and ERVW-1 elements. Overall, our results suggest that HERV methylation could pose as a promising biomolecular sensor to monitor not only the effect of NS work but also the cumulative effect of multiple stressors.
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Affiliation(s)
- Luca Ferrari
- EPIGET Lab, Department of Clinical Sciences and Community Health, Università Degli Studi di Milano, Milan, Italy,Occupational Health Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy,*Correspondence: Luca Ferrari ✉
| | - Paola Monti
- EPIGET Lab, Department of Clinical Sciences and Community Health, Università Degli Studi di Milano, Milan, Italy
| | - Chiara Favero
- EPIGET Lab, Department of Clinical Sciences and Community Health, Università Degli Studi di Milano, Milan, Italy
| | - Michele Carugno
- EPIGET Lab, Department of Clinical Sciences and Community Health, Università Degli Studi di Milano, Milan, Italy,Occupational Health Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Letizia Tarantini
- EPIGET Lab, Department of Clinical Sciences and Community Health, Università Degli Studi di Milano, Milan, Italy
| | - Cristina Maggioni
- EPIGET Lab, Department of Clinical Sciences and Community Health, Università Degli Studi di Milano, Milan, Italy
| | - Matteo Bonzini
- EPIGET Lab, Department of Clinical Sciences and Community Health, Università Degli Studi di Milano, Milan, Italy,Occupational Health Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Angela Cecilia Pesatori
- EPIGET Lab, Department of Clinical Sciences and Community Health, Università Degli Studi di Milano, Milan, Italy,Occupational Health Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Valentina Bollati
- EPIGET Lab, Department of Clinical Sciences and Community Health, Università Degli Studi di Milano, Milan, Italy,Occupational Health Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
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8
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Chousakos E, Kose K, Kurtansky NR, Dusza SW, Halpern AC, Marghoob AA. Analyzing the Spatial Randomness in the Distribution of Acquired Melanocytic Neoplasms. J Invest Dermatol 2022; 142:3274-3281. [PMID: 35841946 PMCID: PMC10475172 DOI: 10.1016/j.jid.2022.06.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 06/11/2022] [Accepted: 06/20/2022] [Indexed: 01/05/2023]
Abstract
On the basis of the clinical impression and current knowledge, acquired melanocytic nevi and melanomas may not occur in random localizations. The goal of this study was to identify whether their distribution on the back is random and whether the location of melanoma correlates with its adjacent lesions. Therefore, patient-level and lesion-level spatial analyses were performed using the Clark‒Evans test for complete spatial randomness. A total of 311 patients with three-dimensional total body photography (average age of 40.08 [30‒49] years; male/female ratio: 128/183) with 5,108 eligible lesions in total were included in the study (mean sum of eligible lesions per patient of 16.42 [3‒199]). The patient-level analysis revealed that the distributions of acquired melanocytic neoplasms were more likely to deviate toward clustering than dispersion (average z-score of ‒0.55 [95% confidence interval = ‒0.69 to ‒0.41; P < 0.001]). The lesion-level analysis indicated a higher portion of melanomas (n = 57 of 72, 79.2% [95% confidence interval = 69.4‒88.9%]) appearing in proximity to neighboring melanocytic neoplasms than to nevi (n = 2,281 of 5,036, 45.3% [95% confidence interval = 43.9‒46.7%]). In conclusion, the nevi and melanomas' distribution on the back tends toward clustering as opposed to dispersion. Furthermore, melanomas are more likely to appear proximally to their neighboring neoplasms than to nevi. These findings may justify various oncogenic theories and improve diagnostic methodology.
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Affiliation(s)
- Emmanouil Chousakos
- Dermatology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA; 1(st) Department of Pathology, Medical School, National & Kapodistrian University of Athens, Athens, Greece.
| | - Kivanc Kose
- Dermatology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Nicholas R Kurtansky
- Dermatology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Stephen W Dusza
- Dermatology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Allan C Halpern
- Dermatology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ashfaq A Marghoob
- Dermatology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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9
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Conway K, Tsai YS, Edmiston SN, Parker JS, Parrish EA, Hao H, Kuan PF, Scott GA, Frank JS, Googe P, Ollila DW, Thomas NE. Characterization of the CpG Island Hypermethylated Phenotype Subclass in Primary Melanomas. J Invest Dermatol 2022; 142:1869-1881.e10. [PMID: 34843679 PMCID: PMC9135958 DOI: 10.1016/j.jid.2021.11.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/28/2021] [Accepted: 11/08/2021] [Indexed: 12/26/2022]
Abstract
Cutaneous melanoma can be lethal even if detected at an early stage. Epigenetic profiling may facilitate the identification of aggressive primary melanomas with unfavorable outcomes. We performed clustering of whole-genome methylation data to identify subclasses that were then assessed for survival, clinical features, methylation patterns, and biological pathways. Among 89 cutaneous primary invasive melanomas, we identified three methylation subclasses exhibiting low methylation, intermediate methylation, or hypermethylation of CpG islands, known as the CpG island methylator phenotype (CIMP). CIMP melanomas occurred as early as tumor stage 1b and, compared with low-methylation melanomas, were associated with age at diagnosis ≥65 years, lentigo maligna melanoma histologic subtype, presence of ulceration, higher American Joint Committee on Cancer stage and tumor stage, and lower tumor-infiltrating lymphocyte grade (all P < 0.05). Patients with CIMP melanomas had worse melanoma-specific survival (hazard ratio = 11.84; confidence interval = 4.65‒30.20) than those with low-methylation melanomas, adjusted for age, sex, American Joint Committee on Cancer stage, and tumor-infiltrating lymphocyte grade. Genes hypermethylated in CIMP compared with those in low-methylation melanomas included PTEN, VDR, PD-L1, TET2, and gene sets related to development/differentiation, the extracellular matrix, and immunity. CIMP melanomas exhibited hypermethylation of genes important in melanoma progression and tumor immunity, and although present in some early melanomas, CIMP was associated with worse survival independent of known prognostic factors.
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Affiliation(s)
- Kathleen Conway
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Dermatology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
| | - Yihsuan S Tsai
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sharon N Edmiston
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Genetics, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Eloise A Parrish
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Honglin Hao
- Department of Genetics, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Pei Fen Kuan
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, New York, USA
| | - Glynis A Scott
- Department of Dermatology, University of Rochester Medical Center, Rochester, New York, USA; Department of Pathology & Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Jill S Frank
- Department of Surgery, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Paul Googe
- Department of Dermatology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Pathology and Lab Medicine, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David W Ollila
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Surgery, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nancy E Thomas
- Department of Dermatology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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10
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Liu X, Wang X, Chai B, Wu Z, Gu Z, Zou H, Zhang H, Li Y, Sun Q, Fang W, Ma Z. miR-199a-3p/5p regulate tumorgenesis via targeting Rheb in non-small cell lung cancer. Int J Biol Sci 2022; 18:4187-4202. [PMID: 35844793 PMCID: PMC9274486 DOI: 10.7150/ijbs.70312] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 06/05/2022] [Indexed: 12/12/2022] Open
Abstract
Lung cancer is one of the deadliest cancers, in which non-small cell lung cancer (NSCLC) accounting for 85% and has a low survival rate of 5 years. Dysregulation of microRNAs (miRNAs) can participate in tumor regulation and many major diseases. In this study, we found that miR-199a-3p/5p were down-expressed in NSCLC tissue samples, cell lines, and the patient sample database. MiR-199a-3p/5p overexpression could significantly suppress cell proliferation, migration ability and promote apoptosis. Through software prediction, ras homolog enriched in brain (Rheb) was identified as a common target of miR-199a-3p and miR-199a-5p, which participated in regulating mTOR signaling pathway. The same effect of inhibiting NSCLC appeared after down-regulating the expression of Rheb. Furthermore, our findings revealed that miR-199a can significantly inhibit tumor growth and metastasis in vivo, which fully demonstrates that miR-199a plays a tumor suppressive role in NSCLC. In addition, miR-199a-3p/5p has been shown to enhance the sensitivity of gefitinib to EGFR-T790M in NSCLC. Collectively, these results prove that miR-199a-3p/5p can act as cancer suppressor genes to inhibit the mTOR signaling pathway by targeting Rheb, which in turn inhibits the regulatory process of NSCLC. Thus, to investigate the anti-cancer effect of pre-miR-199a/Rheb/mTOR axis in NSCLC, miR-199a-3p and miR-199a-5p have the potential to become an early diagnostic marker or therapeutic target for NSCLC.
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Affiliation(s)
- Xiaomin Liu
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Xianyi Wang
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Binshu Chai
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Zong Wu
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Zhitao Gu
- Department of Thoracic Surgery, Thoracic Cancer Institute, Shanghai Chest Hospital, Jiaotong University Medical School,Shanghai 200030, China
| | - Heng Zou
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Hui Zhang
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Yanli Li
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Qiangling Sun
- Department of Thoracic Surgery, Thoracic Cancer Institute, Shanghai Chest Hospital, Jiaotong University Medical School,Shanghai 200030, China
| | - Wentao Fang
- Department of Thoracic Surgery, Thoracic Cancer Institute, Shanghai Chest Hospital, Jiaotong University Medical School,Shanghai 200030, China
| | - Zhongliang Ma
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai 200444, China
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11
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Tímár J, Ladányi A. Molecular Pathology of Skin Melanoma: Epidemiology, Differential Diagnostics, Prognosis and Therapy Prediction. Int J Mol Sci 2022; 23:5384. [PMID: 35628196 PMCID: PMC9140388 DOI: 10.3390/ijms23105384] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 12/11/2022] Open
Abstract
Similar to other malignancies, TCGA network efforts identified the detailed genomic picture of skin melanoma, laying down the basis of molecular classification. On the other hand, genome-wide association studies discovered the genetic background of the hereditary melanomas and the susceptibility genes. These genetic studies helped to fine-tune the differential diagnostics of malignant melanocytic lesions, using either FISH tests or the myPath gene expression signature. Although the original genomic studies on skin melanoma were mostly based on primary tumors, data started to accumulate on the genetic diversity of the progressing disease. The prognostication of skin melanoma is still based on staging but can be completed with gene expression analysis (DecisionDx). Meanwhile, this genetic knowledge base of skin melanoma did not turn to the expected wide array of target therapies, except the BRAF inhibitors. The major breakthrough of melanoma therapy was the introduction of immune checkpoint inhibitors, which showed outstanding efficacy in skin melanoma, probably due to their high immunogenicity. Unfortunately, beyond BRAF, KIT mutations and tumor mutation burden, no clinically validated predictive markers exist in melanoma, although several promising biomarkers have been described, such as the expression of immune-related genes or mutations in the IFN-signaling pathway. After the initial success of either target or immunotherapies, sooner or later, relapses occur in the majority of patients, due to various induced genetic alterations, the diagnosis of which could be developed to novel predictive genetic markers.
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Affiliation(s)
- József Tímár
- 2nd Department of Pathology, Semmelweis University, 1191 Budapest, Hungary
| | - Andrea Ladányi
- Department of Surgical and Molecular Pathology and the National Tumor Biology Laboratory, National Institute of Oncology, 1122 Budapest, Hungary;
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12
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Liu Y, Sun J, Han D, Cui S, Yan X. Identification of Potential Biomarkers and Small Molecule Drugs for Cutaneous Melanoma Using Integrated Bioinformatic Analysis. Front Cell Dev Biol 2022; 10:858633. [PMID: 35433681 PMCID: PMC9006169 DOI: 10.3389/fcell.2022.858633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/16/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Cutaneous melanoma (CM) is a type of skin cancer with a high fatality rate, and its pathogenesis has not yet been fully elucidated. Methods: We obtained the gene expression datasets of CM through the Gene Expression Omnibus (GEO) database. Subsequently, robust rank aggregation (RRA) method was used to identify differentially expressed genes (DEGs) between CM cases and normal skin controls. Gene functional annotation was performed to explore the potential function of the DEGs. We built the protein–protein interaction (PPI) network by the Interactive Gene database retrieval tool (STRING) and selected hub modules by Molecular Complexity Detection (MCODE). We furthered and validated our results using the TCGA-GTEX dataset. Finally, potential small molecule drugs were predicted by CMap database and verified by molecular docking method. Results: A total of 135 DEGs were obtained by RRA synthesis analysis. GMPR, EMP3, SLC45A2, PDZD2, NPY1R, DLG5 and ADH1B were screened as potential targets for CM. Furazolidone was screened as a potential small molecule drug for the treatment of CM, and its mechanism may be related to the inhibition of CM cell proliferation by acting on GMPR. Conclusion: We identified seven prognostic therapeutic targets associated with CM and furazolidone could be used as a potential drug for CM treatment, providing new prognostic markers, potential therapeutic targets and small molecule drugs for the treatment and prevention of CM.
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Affiliation(s)
- Yong Liu
- School of Life Science, Beijing University of Chinese Medicine, Beijing, China
- Department of Dermatology, Shaanxi Provincial Hospital of Traditional Chinese Medicine, Xi’an, China
| | - Jiayi Sun
- School of Life Science, Beijing University of Chinese Medicine, Beijing, China
| | - Dongran Han
- School of Life Science, Beijing University of Chinese Medicine, Beijing, China
| | - Shengnan Cui
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Graduate School, China Academy of Chinese Medical Sciences, Beijing, China
- *Correspondence: Shengnan Cui, ; Xiaoning Yan,
| | - Xiaoning Yan
- Department of Dermatology, Shaanxi Provincial Hospital of Traditional Chinese Medicine, Xi’an, China
- *Correspondence: Shengnan Cui, ; Xiaoning Yan,
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13
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Zhang W, Kong Y, Li Y, Shi F, Lyu J, Sheng C, Wang S, Wang Q. Novel Molecular Determinants of Response or Resistance to Immune Checkpoint Inhibitor Therapies in Melanoma. Front Immunol 2022; 12:798474. [PMID: 35087523 PMCID: PMC8787219 DOI: 10.3389/fimmu.2021.798474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/16/2021] [Indexed: 12/13/2022] Open
Abstract
Background Immune checkpoint inhibitor (ICI) therapy dramatically prolongs melanoma survival. Currently, the identified ICI markers are sometimes ineffective. The objective of this study was to identify novel determinants of ICI efficacy. Methods We comprehensively curated pretreatment somatic mutational profiles and clinical information from 631 melanoma patients who received blockade therapy of immune checkpoints (i.e., CTLA-4, PD-1/PD-L1, or a combination). Significantly mutated genes (SMGs), mutational signatures, and potential molecular subtypes were determined. Their association with ICI responses was assessed simultaneously. Results We identified 27 SMGs, including four novel SMGs (COL3A1, NRAS, NARS2, and DCC) that are associated with ICI efficacy and well-known driver genes. COL3A1 mutations were associated with improved ICI overall survival (hazard ratio (HR): 0.64, 95% CI: 0.45-0.91, p = 0.012), whereas immune resistance was observed in patients with NRAS mutations (HR: 1.42, 95% CI: 1.10-1.82, p = 0.006). The presence of the tobacco smoking-related signature was significantly correlated with inferior prognoses (HR: 1.42, 95% CI: 1.11-1.82, p = 0.005). In addition, the signature resembling that of alkylating agents and a newly discovered signature both exhibited extended prognoses (both HR < 1, p < 0.05). Based on the activities of the extracted 6 mutational signatures, we identified one immune subtype that was significantly associated with better ICI outcomes (HR: 0.44, 95% CI: 0.23-0.87, p = 0.017). Conclusion We uncovered several novel SMGs and re-annotated mutational signatures that are linked to immunotherapy response or resistance. In addition, an immune subtype was found to exhibit favorable prognoses. Further studies are required to validate these findings.
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Affiliation(s)
- Wenjing Zhang
- Department of Health Statistics, Key Laboratory of Medicine and Health in Shandong Province, School of Public Health, Weifang Medical University, Weifang, China
| | - Yujia Kong
- Department of Health Statistics, Key Laboratory of Medicine and Health in Shandong Province, School of Public Health, Weifang Medical University, Weifang, China
| | - Yuting Li
- Tianjin Cancer Institute, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Fuyan Shi
- Department of Health Statistics, Key Laboratory of Medicine and Health in Shandong Province, School of Public Health, Weifang Medical University, Weifang, China
| | - Juncheng Lyu
- Department of Health Statistics, Key Laboratory of Medicine and Health in Shandong Province, School of Public Health, Weifang Medical University, Weifang, China
| | - Chao Sheng
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Suzhen Wang
- Department of Health Statistics, Key Laboratory of Medicine and Health in Shandong Province, School of Public Health, Weifang Medical University, Weifang, China
| | - Qinghua Wang
- Department of Health Statistics, Key Laboratory of Medicine and Health in Shandong Province, School of Public Health, Weifang Medical University, Weifang, China
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14
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Ladányi A, Rásó E, Barbai T, Vízkeleti L, Puskás LG, Kovács SA, Győrffy B, Tímár J. Identification of a Tumor Cell Associated Type I IFN Resistance Gene Expression Signature of Human Melanoma, the Components of Which Have a Predictive Potential for Immunotherapy. Int J Mol Sci 2022; 23:2704. [PMID: 35269844 PMCID: PMC8911010 DOI: 10.3390/ijms23052704] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 02/04/2023] Open
Abstract
We developed a human melanoma model using the HT168-M1 cell line to induce IFN-α2 resistance in vitro (HT168-M1res), which was proven to be maintained in vivo in SCID mice. Comparing the mRNA profile of in vitro cultured HT168-M1res cells to its sensitive counterpart, we found 79 differentially expressed genes (DEGs). We found that only a 13-gene core of the DEGs was stable in vitro and only a 4-gene core was stable in vivo. Using an in silico cohort of IFN-treated melanoma tissues, we validated a differentially expressed 9-gene core of the DEGs. Furthermore, using an in silico cohort of immune checkpoint inhibitor (ICI)-treated melanoma tissues, we tested the predictive power of the DEGs for the response rate. Analysis of the top four upregulated and top four downregulated genes of the DEGs identified WFDC1, EFNA3, DDX10, and PTBP1 as predictive genes, and analysis of the "stable" genes of DEGs for predictive potential of ICI response revealed another 13 genes, out of which CDCA4, SOX4, DEK, and HSPA1B were identified as IFN-regulated genes. Interestingly, the IFN treatment associated genes and the ICI-therapy predictive genes overlapped by three genes: WFDC1, BCAN, and MT2A, suggesting a connection between the two biological processes.
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Affiliation(s)
- Andrea Ladányi
- Department of Surgical and Molecular Pathology, National Institute of Oncology, 1122 Budapest, Hungary;
| | - Erzsébet Rásó
- 2nd Department of Pathology, Semmelweis University, 1091 Budapest, Hungary; (E.R.); (T.B.); (L.V.)
| | - Tamás Barbai
- 2nd Department of Pathology, Semmelweis University, 1091 Budapest, Hungary; (E.R.); (T.B.); (L.V.)
| | - Laura Vízkeleti
- 2nd Department of Pathology, Semmelweis University, 1091 Budapest, Hungary; (E.R.); (T.B.); (L.V.)
| | | | - Szonja A. Kovács
- Department of Bioinformatics, Semmelweis University, 1094 Budapest, Hungary; (S.A.K.); (B.G.)
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, 1094 Budapest, Hungary; (S.A.K.); (B.G.)
- Research Centre for Natural Sciences, Oncology Biomarkers Research Group, Institute of Enzymology, Eötvös Loránd Research Network, 1117 Budapest, Hungary
| | - József Tímár
- 2nd Department of Pathology, Semmelweis University, 1091 Budapest, Hungary; (E.R.); (T.B.); (L.V.)
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15
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Characterization and clinical relevance of PDGFRA pathway copy number variation gains across human cancers. Mol Genet Genomics 2022; 297:561-571. [PMID: 35212838 PMCID: PMC8960564 DOI: 10.1007/s00438-022-01860-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/22/2022] [Indexed: 12/04/2022]
Abstract
We investigated the copy number variation (CNV) of PDGFRA pathway across all common cancer types as well as its clinical relevance. This study included a total of 10,678 patients with pan-cancerous species involving 33 types of cancers and patient information was obtained from The Cancer Genome Atlas. According to the PDGFRA pathway CNV, all samples were divided into copy number gain (CN gain) group and No CN gain group. The analysis of loss of heterozygosity (LOH) fraction, CNV burden, tumor mutation burden (TMB), and the number of immunogenic mutations were performed, as well as the correlation analysis of PDGFRA pathway CN gain with tumor-related signaling pathways and tumor-infiltrating immune cell subpopulations. The results showed that CN gain of PDGFRA pathway in the cancer patients was associated with significantly shorter overall survival. The CN gain of PDGFRA pathway was identified as a prognostic risk factor for some tumors. CN gain was accompanied by an altered percentage of LOH, CNV burden, TMB, the number of immunogenic mutations were increased and tumor-infiltrating immune cell subpopulations were less. While certain tumor-related signaling pathways, such as hypoxia, cell cycle, DNA repair, and epithelial-mesenchymal transition were more enriched in the CN gain group, quiescence, and inflammation pathways were more enriched in the No CN gain group. In conclusion, PDGFRA pathway CNV gain may be a poor prognostic factor in cancer patients.
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16
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Fidanzi C, Manzo Margiotta F, Spinelli C, Janowska A, Dini V, Oranges T, Romanelli M, Morganti R, Viacava P, D'Erme AM, Bagnoni G. Risk factors in pediatric melanoma: a retrospective study of 39 cases. Melanoma Res 2021; 31:555-560. [PMID: 34570022 DOI: 10.1097/cmr.0000000000000778] [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: 10/20/2022]
Abstract
Pediatric melanoma is a rare form of the tumor whose epidemiology is widely increasing thanks to the improvement of dermoscopic and anatomopathologic diagnostic techniques. Although it is a tumor of considerable interest in adults, little has been described about the pediatric field. The objective of our study was then to identify the possible risk factors for the development of melanoma in the pediatric population. We performed a retrospective study conducted in the Melanoma and Skin Cancer Unit and Unit of Dermatology (Livorno, Italy). We analyzed a population of 38 children under 21 years with a diagnosis of melanoma. This population was compared with a control population of 114 children followed up in our dermatologic clinic. From our combined univariate-multivariate statistics analysis, the number of nevi [regression coefficient (RC) of 1.04 and odds ratio (OR) of 2.8 confidence interval (Cl, 1.2-6.6)], and family history of melanoma [RC of 1.99 and OR of 7.3 (Cl, 2.3-22.7)] emerged as possible risk factors for the development of melanoma. The identification of these elements would allow the physician to carry out a more targeted preliminary assessment of the patient, potentially decisive in cases of diagnostic doubt of the lesion. Our study also lays the foundations for identifying those children who, despite not having received a diagnosis of melanoma on histologic examination, should be considered as patients susceptible to a focused follow-up, because of the presence of the risk factors that emerged from our research.
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Affiliation(s)
- Cristian Fidanzi
- Unit of Dermatology, Department of Medical and Oncological Area, University of Pisa
| | - Flavia Manzo Margiotta
- Unit of Dermatology, Department of Medical and Oncological Area, University of Pisa
- Institute of Life Sciences, Scuola Superiore Sant'Anna
| | - Claudio Spinelli
- Pediatric, Adolescent and Young Adults Surgery Division, Department of Surgical, Medical, Pathological, Molecular and Critical Area, University of Pisa, Pisa
| | - Agata Janowska
- Unit of Dermatology, Department of Medical and Oncological Area, University of Pisa
| | - Valentina Dini
- Unit of Dermatology, Department of Medical and Oncological Area, University of Pisa
| | - Teresa Oranges
- Unit of Dermatology, Department of Medical and Oncological Area, University of Pisa
- Department of Health Sciences, Anna Meyer Children's University Hospital, University of Florence, Florence
| | - Marco Romanelli
- Unit of Dermatology, Department of Medical and Oncological Area, University of Pisa
| | - Riccardo Morganti
- Statistical Support to Clinical Trials Department, University of Pisa, Pisa
| | - Paolo Viacava
- Clinical Pathology Departmental Area, Services Department, Operative Union Of Pathological Anatomy, Livorno Hospital
| | - Angelo M D'Erme
- Melanoma and Skin Cancer Unit AVNO (Area Vasta Nord Ovest) and Unit of Dermatology, Specialist Surgery Area, Department Of General Surgery, Livorno Hospital, Livorno, Italy
| | - Giovanni Bagnoni
- Melanoma and Skin Cancer Unit AVNO (Area Vasta Nord Ovest) and Unit of Dermatology, Specialist Surgery Area, Department Of General Surgery, Livorno Hospital, Livorno, Italy
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17
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Vendramin R, Katopodi V, Cinque S, Konnova A, Knezevic Z, Adnane S, Verheyden Y, Karras P, Demesmaeker E, Bosisio FM, Kucera L, Rozman J, Gladwyn-Ng I, Rizzotto L, Dassi E, Millevoi S, Bechter O, Marine JC, Leucci E. Activation of the integrated stress response confers vulnerability to mitoribosome-targeting antibiotics in melanoma. J Exp Med 2021; 218:e20210571. [PMID: 34287642 PMCID: PMC8424468 DOI: 10.1084/jem.20210571] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/10/2021] [Accepted: 06/16/2021] [Indexed: 12/15/2022] Open
Abstract
The ability to adapt to environmental stress, including therapeutic insult, contributes to tumor evolution and drug resistance. In suboptimal conditions, the integrated stress response (ISR) promotes survival by dampening cytosolic translation. We show that ISR-dependent survival also relies on a concomitant up-regulation of mitochondrial protein synthesis, a vulnerability that can be exploited using mitoribosome-targeting antibiotics. Accordingly, such agents sensitized to MAPK inhibition, thus preventing the development of resistance in BRAFV600E melanoma models. Additionally, this treatment compromised the growth of melanomas that exhibited elevated ISR activity and resistance to both immunotherapy and targeted therapy. In keeping with this, pharmacological inactivation of ISR, or silencing of ATF4, rescued the antitumoral response to the tetracyclines. Moreover, a melanoma patient exposed to doxycycline experienced complete and long-lasting response of a treatment-resistant lesion. Our study indicates that the repurposing of mitoribosome-targeting antibiotics offers a rational salvage strategy for targeted therapy in BRAF mutant melanoma and a therapeutic option for NRAS-driven and immunotherapy-resistant tumors.
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Affiliation(s)
- Roberto Vendramin
- Laboratory for RNA Cancer Biology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Vicky Katopodi
- Laboratory for RNA Cancer Biology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Sonia Cinque
- Laboratory for RNA Cancer Biology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Angelina Konnova
- Laboratory for RNA Cancer Biology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Zorica Knezevic
- Laboratory for RNA Cancer Biology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Sara Adnane
- Laboratory for RNA Cancer Biology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Yvessa Verheyden
- Laboratory for RNA Cancer Biology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Panagiotis Karras
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
- Department of Oncology, Laboratory for Molecular Cancer Biology, Katholieke Universiteit Leuven, Belgium
| | - Ewout Demesmaeker
- Laboratory for RNA Cancer Biology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | - Lukas Kucera
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Jan Rozman
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | | | - Lara Rizzotto
- Trace, Leuven Cancer Institute, Katholieke Universiteit Leuven, Belgium
| | - Erik Dassi
- Laboratory of RNA Regulatory Networks, Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Stefania Millevoi
- Cancer Research Centre of Toulouse, Institut national de la santé et de la recherche médicale Joint Research Unit 1037, Toulouse, France
- Université Toulouse III Paul Sabatier, Toulouse, France
- Laboratoire d’Excellence “TOUCAN,” Toulouse, France
| | - Oliver Bechter
- Department of General Medical Oncology, Leuven Cancer Institute, Universitair Ziekenhuis Leuven, Leuven, Belgium
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
- Department of Oncology, Laboratory for Molecular Cancer Biology, Katholieke Universiteit Leuven, Belgium
| | - Eleonora Leucci
- Laboratory for RNA Cancer Biology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
- Trace, Leuven Cancer Institute, Katholieke Universiteit Leuven, Belgium
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18
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Liu G, Wu D, Wen Y, Cang S. Immune-associated molecular occurrence and prognosis predictor of hepatocellular carcinoma: an integrated analysis of GEO datasets. Bioengineered 2021; 12:5253-5265. [PMID: 34424809 PMCID: PMC8806587 DOI: 10.1080/21655979.2021.1962147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the fifth most common cancer and the second most common cause of cancer-related deaths worldwide. As immune response failure is the main factor in the occurrence and poor prognosis of HCC, our study aimed to develop an immune-associated molecular occurrence and prognosis predictor (IMOPP) of HCC. To that end, we discovered a 4-gene immune-associated gene signature: C-C motif chemokine ligand 14 (CCL14), kallikrein B1 (KLKB1), vasoactive intestinal peptide receptor 1 (VIPR1), and cluster of differentiation 4 (CD4). When tested on three cohorts as an immune-associated molecular occurrence predictor (IMOP), it had high sensitivity, specificity, and area under the receiver operating characteristics curve. When tested as an immune-associated molecular prognosis predictor (IMPP), it stratified the HCC prognosis for overall survival (Kaplan-Meier analysis, log rank P = 0.0016; Cox regression, HR = 1.832, 95% CI = 1.173-2.859, P = 0.008) and disease-free survival (Kaplan-Meier analysis, log rank P = 0.0227). IMPP also significantly correlated with the clinicopathological characteristics of HCC; integrating it with clinicopathological characteristics improved the accuracy of a nomogram for overall survival prediction (C-index: 0.7097 vs. 0.6631). In HCC tumor microenviroments, the proportion of CD8+ T cells significantly differed between IMOP-stratified groups. We conclude that IMOPP can potentially predict the occurrence of HCC in high-risk populations and improve prognostic accuracy by providing new biomarkers for risk stratification. In addition, we believe that the IMOP mechanism may be related to its effect on the proportion of CD8+ T cells in tumor-infiltrating lymphocytes.
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Affiliation(s)
- Guanjun Liu
- Department of Oncology, Henan Provincial People's Hospital, Zhengzhou, Henan, P.R. China.,Department of Oncology, People's Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China.,Department of Oncology, People's Hospital of Henan University, Zhengzhou, Henan, P.R. China
| | - Dongmei Wu
- Department of Radiotherapy, Xinxiang Center Hospital, Xinxiang, Henan, P.R. China
| | - Yiyang Wen
- Department of Oncology, Henan Provincial People's Hospital, Zhengzhou, Henan, P.R. China.,Department of Oncology, People's Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China.,Department of Oncology, People's Hospital of Henan University, Zhengzhou, Henan, P.R. China
| | - Shundong Cang
- Department of Oncology, Henan Provincial People's Hospital, Zhengzhou, Henan, P.R. China.,Department of Oncology, People's Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China.,Department of Oncology, People's Hospital of Henan University, Zhengzhou, Henan, P.R. China
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Liu D, Yang X, Wu X. Tumor Immune Microenvironment Characterization Identifies Prognosis and Immunotherapy-Related Gene Signatures in Melanoma. Front Immunol 2021; 12:663495. [PMID: 34025664 PMCID: PMC8134682 DOI: 10.3389/fimmu.2021.663495] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/21/2021] [Indexed: 01/16/2023] Open
Abstract
Background The tumor microenvironment (TME) involves infiltration of multiple immune cell subsets, which could influence the prognosis and clinical characteristics. The increasing evidence on the role of tumor-infiltrating lymphocytes (TILs) in primary and metastatic melanomas supports that the immune system is involved in the progression and outcomes of melanoma. However, the immune infiltration landscape in melanoma has not been systematically elucidated. Methods In this study, we used CIBERSORT and ESTIMATE algorithms to analyze immune infiltration pattern of 993 melanoma samples. Then we screened differential expression genes (DEGs) related to immune subtypes and survival. The immune cell infiltration (ICI) score was constructed by using principal-component analysis (PCA) based on immune signature genes from DGEs. Gene set enrichment analysis (GSEA) was applied to explore high and low ICI score related pathways. Finally, the predictive ability of ICI score was evaluated in survival prognosis and immunotherapy benefit. Result We identified three ICI clusters and three gene clusters associated with different immune subtypes and survival outcomes. Then the ICI score was constructed, and we found that high ICI score exhibited activated immune characteristics and better prognosis. High ICI score was significantly enriched in immune pathways and highly expressed immune signature genes. More importantly, we confirmed that melanoma patients with high ICI score had longer overall survival and rate of response to immunotherapy. Conclusion We presented a comprehensive immune infiltration landscape in melanoma. Our results will facilitate understanding of the melanoma tumor microenvironment and provide a new immune therapy strategy.
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Affiliation(s)
- Dan Liu
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, National Human Genetic Resources Sharing Service Platform, Tianjin, China
| | - Xue Yang
- Department of Medical Oncology, Tianjin Medical University General Hospital, Tianjin, China
| | - Xiongzhi Wu
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, National Human Genetic Resources Sharing Service Platform, Tianjin, China
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20
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Tian Y, Zeng J, Yang Z. MicroRNA-27b inhibits the development of melanoma by targeting MYC. Oncol Lett 2021; 21:370. [PMID: 33747226 PMCID: PMC7967934 DOI: 10.3892/ol.2021.12631] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 02/02/2021] [Indexed: 11/30/2022] Open
Abstract
Cutaneous malignant melanoma is a malignancy with one of the fastest increasing incidence rates worldwide; however, the mechanism underlying the occurrence and development of melanoma remains unclear. The aim of the present study was to identify novel biomarkers for the occurrence and development of melanoma. The results of the present study demonstrated that the expression levels of microRNA (miR)-27b were decreased in melanoma tissue samples compared with those in adjacent noncancerous tissue samples and cells according to online and experimental data. By contrast, MYC expression levels were upregulated in melanoma compared with those in adjacent noncancerous tissue samples. miR-27b overexpression significantly inhibited A375 and A2085 melanoma cell DNA synthesis, viability and invasive ability. Dual-luciferase reporter assay results demonstrated that miR-27b inhibited MYC expression through binding to the 3′-untranslated region of MYC mRNA. MYC knockdown in melanoma cells exerted similar effects to those of miR-27b overexpression on DNA synthesis, cell viability and invasive ability; the effects of miR-27b inhibition were significantly reversed by MYC knockdown. In conclusion, the miR-27b/MYC axis may modulate malignant melanoma cell biological behaviors and may be a potential target for melanoma treatment.
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Affiliation(s)
- Yi Tian
- Department of Dermatology, The Second Affiliated Hospital, Hunan University of Chinese Medicine, Changsha, Hunan 410005, P.R. China
| | - Juanni Zeng
- Department of Anorectal Disease, The Second Affiliated Hospital, Hunan University of Chinese Medicine, Changsha, Hunan 410005, P.R. China
| | - Zongliang Yang
- Department of Anorectal Disease, The Second Affiliated Hospital, Hunan University of Chinese Medicine, Changsha, Hunan 410005, P.R. China
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21
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Wong HSC, Chang WC. Single-cell melanoma transcriptomes depicting functional versatility and clinical implications of STIM1 in the tumor microenvironment. Am J Cancer Res 2021; 11:5092-5106. [PMID: 33859736 PMCID: PMC8039943 DOI: 10.7150/thno.54134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/06/2020] [Indexed: 12/31/2022] Open
Abstract
Rationale: Previous studies have implicated the functions of stromal interaction molecule 1 (STIM1) in immunity and malignancy, however, the specificity and effects of STIM1 expression in malignant and non-malignant cells in the tumor microenvironment are unclear. Methods: In the current study, we posed two central questions: (1) does STIM1 expression elicit different cellular programs in cell types within the melanoma tumor microenvironment (2) whether the expression of STIM1 and STIM1-coexpressed genes (SCGs) serve as prognostic indicators of patient's outcomes? To answer these questions, we dissected cell-specific STIM1-associated cellular programs in diverse cell types within the melanoma tumor microenvironment by measuring cell-type specificity of STIM1 expression and SCGs. Results: A distinct set of SCGs was highly affected in malignant melanoma cells, but not in the other cell types, suggesting the existence of malignant-cell-specific cellular programs reflected by STIM1 expression. In contrast to malignant cells, STIM1 expression appeared to trigger universal and non-specific biological functions in non-malignant cell types, as exemplified by the transcriptomes of macrophages and CD4+ T regulatory cells. Results from bioinformatic analyses indicated that SCGs in malignant cells may alter cell-cell interactions through cytokine/chemokine signaling and/or orchestrate immune infiltration into the tumor. Moreover, a prognostic association between SCGs in CD4+ T regulatory cells and patient's outcomes was identified. However, we didn't find any correlation between SCGs and responsiveness of immunotherapy. Conclusions: Overall, our results provide an integrated biological framework for understanding the functional and clinical consequences of cell-specific STIM1 expression in melanoma.
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22
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Digital Immunophenotyping Predicts Disease Free and Overall Survival in Early Stage Melanoma Patients. Cells 2021; 10:cells10020422. [PMID: 33671367 PMCID: PMC7922113 DOI: 10.3390/cells10020422] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/02/2021] [Accepted: 02/10/2021] [Indexed: 12/14/2022] Open
Abstract
Background: the prognostic significance of tumor infiltrating lymphocytes (TILs) in intermediate/thick primary cutaneous melanoma (PCM) remains controversial, partially because conventional evaluation is not reliable, due to inter-observer variability and diverse scoring methods. We aimed to assess the prognostic impact of the density and spatial distribution of immune cells in early stage intermediate/thick PCM. Materials and Methods: digital image acquisition and quantitative analysis of tissue immune biomarkers (CD3, CD4, CD8, CD68, PD-L1, CD163, FOX-P3, and PD-1) was carried out in a training cohort, which included patients with primary PCM ≥ 2 mm diagnosed, treated, and followed-up prospectively in three Italian centers. Results were validated in an independent Italian cohort. Results: in the training cohort, 100 Stage II–III melanoma patients were valuable. At multivariable analysis, a longer disease free survival (DFS) was statistically associated with higher levels of CD4+ intratumoral T-cells (aHR [100 cell/mm2 increase] 0.98, 95%CI 0.95–1.00, p = 0.041) and CD163+ inner peritumoral (aHR [high vs. low] 0.56, 95%CI 0.32–0.99, p = 0.047). A statistically significant longer DFS (aHR [high-high vs. low-low] 0.52, 95%CI 0.28–0.99, p = 0.047) and overall survival (OS) (aHR [high-high vs. low-low] 0.39, 95%CI 0.18–0.85, p = 0.018) was found in patients with a high density of both intratumoral CD8+ T-cells and CD68+ macrophages as compared to those with low density of both intratumoral CD8+ T-cells and CD68+ macrophages. Consistently, in the validation cohort, patients with high density of both intratumoral CD8+ and CD3+ T-cells were associated to a statistically better DFS (aHR[high-high vs. low-low] 0.24, 95%CI 0.10–0.56, p < 0.001) and those with high density of both intratumoral CD8+ and CD68+ were associated to a statistically longer OS (aHR[high-high vs. low-low] 0.28, 95%CI 0.09–0.86, p = 0.025). Conclusion: our findings suggest that a specific preexisting profile of T cells and macrophages distribution in melanomas may predict the risk of recurrence and death with potential implications for the stratification of stage II–III melanoma patients.
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23
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IRGM promotes melanoma cell survival through autophagy and is a promising prognostic biomarker for clinical application. MOLECULAR THERAPY-ONCOLYTICS 2020; 20:187-198. [PMID: 33665357 PMCID: PMC7889451 DOI: 10.1016/j.omto.2020.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/11/2020] [Indexed: 01/12/2023]
Abstract
Previously, we showed that mouse immunity-related guanosine triphosphatase (GTPase) family M protein 1 (Irgm1) promotes malignant melanoma progression by inducing cellular autophagy flux and metastasis. Human IRGM, a truncated protein functionally distinct from its mouse counterpart, has several splice isoforms. In this study, we analyzed the association of IRGM and human melanoma clinical prognosis and investigated the function of IRGM in human melanoma cells. Data from the training cohort (n = 144) showed that overexpression of IRGM is proportional to melanoma genesis and clinical stages in human tissue chips. A validation cohort (n = 78) further confirmed that IRGM is an independent risk factor promoting melanoma progression and is associated with poor survival of patients. Among IRGM isoforms, we found that IRGMb is responsible for such correlation. In addition, IRGM promoted melanoma cell survival through autophagy, both in vitro and in vivo. We further showed that the blockade of translocation of high-mobility group box 1 (HMGB1) from the nucleus to cytoplasm inhibits IRGM1-mediated cellular autophagy and reduces cell survival. IRGM functions as a positive regulator of melanoma progression through autophagy and may serve as a promising prognostic marker and therapeutic target.
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24
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Yu J, Xie M, Ge S, Chai P, Zhou Y, Ruan J. Hierarchical Clustering of Cutaneous Melanoma Based on Immunogenomic Profiling. Front Oncol 2020; 10:580029. [PMID: 33330057 PMCID: PMC7735560 DOI: 10.3389/fonc.2020.580029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 10/26/2020] [Indexed: 12/23/2022] Open
Abstract
Cutaneous melanoma is an aggressive malignancy with high heterogeneity. Several studies have been performed to identify cutaneous melanoma subtypes based on genomic profiling. However, few classifications based on assessments of immune-associated genes have limited clinical implications for cutaneous melanoma. Using 470 cutaneous melanoma samples from The Cancer Genome Atlas (TCGA), we calculated the enrichment levels of 29 immune-associated gene sets in each sample and hierarchically clustered them into Immunity High (Immunity_H, n=323, 68.7%), Immunity Medium (Immunity_M, n=135, 28.7%), and Immunity Low (Immunity_L, n=12, 2.6%) based on the ssGSEA score. The ESTIMATE algorithm was used to calculate stromal scores (range: -1,800.51-1,901.99), immune scores (range: -1,476.28-3,780.33), estimate scores (range: -2,618.28-5,098.14) and tumor purity (range: 0.216-0.976) and they were significantly correlated with immune subtypes (Kruskal-Wallis test, P < 0.001). The Immunity_H group tended to have higher expression levels of HLA and immune checkpoint genes (Kruskal-Wallis test, P < 0.05). The Immunity_H group had the highest level of naïve B cells, resting dendritic cells, M1 macrophages, resting NK cells, plasma cells, CD4 memory activated T cells, CD8 T cells, follicular helper T cells and regulatory T cells, and the Immunity_L group had better overall survival. The GO terms identified in the Immunity_H group were mainly immune related. In conclusion, immune signature-associated cutaneous melanoma subtypes play a role in cutaneous melanoma prognosis stratification. The construction of immune signature-associated cutaneous melanoma subtypes predicted possible patient outcomes and provided possible immunotherapy candidates.
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Affiliation(s)
| | | | | | - Peiwei Chai
- Department of Ophthalmology, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Yixiong Zhou
- Department of Ophthalmology, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Jing Ruan
- Department of Ophthalmology, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
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25
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Hargadon KM, Győrffy B, McGee TJ. Genomic and transcriptional changes in IFNγ pathway genes are putative biomarkers of response to ipilimumab immunotherapy in melanoma patients. Expert Rev Clin Immunol 2020; 16:1099-1103. [DOI: 10.1080/1744666x.2021.1847644] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Kristian M. Hargadon
- Hargadon Laboratory, Department of Biology, Hampden-Sydney College, Hampden-Sydney, VA, USA
| | - Balázs Győrffy
- TTK Cancer Biomarker Research Group, Budapest, Hungary
- Department of Bioinformatics and 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Taylor J. McGee
- Hargadon Laboratory, Department of Biology, Hampden-Sydney College, Hampden-Sydney, VA, USA
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26
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Solar UV Exposure and Mortality from Skin Tumors: An Update. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020. [PMID: 32918217 DOI: 10.1007/978-3-030-46227-7_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Solar UV exposure is critical and complex in the etiology and prognosis of skin cancer, particularly cutaneous malignant melanoma. Sun exposure and one of its "derivatives," vitamin D, have been implicated in protection against mortality from melanoma. However, the relationships are inconsistent. At this time, it is not possible to make clear recommendations for or against sun exposure in relationship to melanoma prognosis. However, this relationship deserves continued exploration.
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27
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Liu N, Liu Z, Liu X, Duan X, Huang Y, Jin Z, Niu Y, Zhang L, Chen H. Identification of an Immune-Related Prognostic Signature Associated With Immune Infiltration in Melanoma. Front Genet 2020; 11:1002. [PMID: 33005180 PMCID: PMC7484056 DOI: 10.3389/fgene.2020.01002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 08/06/2020] [Indexed: 12/29/2022] Open
Abstract
Melanoma is the leading cause of cancer-related death among skin tumors, with an increasing incidence worldwide. Few studies have effectively investigated the significance of an immune-related gene (IRG) signature for melanoma prognosis. Here, we constructed an IRGs prognostic signature using bioinformatics methods and evaluated and validated its predictive capability. Then, immune cell infiltration and tumor mutation burden (TMB) landscapes associated with this signature in melanoma were analyzed comprehensively. With the 10-IRG prognostic signature, melanoma patients in the low-risk group showed better survival with distinct features of high immune cell infiltration and TMB. Importantly, melanoma patients in this subgroup were significantly responsive to MAGE-A3 in the validation cohort. This immune-related prognostic signature is thus a reliable tool to predict melanoma prognosis; as the underlying mechanism of this signature is associated with immune infiltration and mutation burden, it might reflect the benefit of immunotherapy to patients.
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Affiliation(s)
- Nian Liu
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zijian Liu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xinxin Liu
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoru Duan
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuqiong Huang
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zilin Jin
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Niu
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liling Zhang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hongxiang Chen
- Department of Dermatology, The 6th Affifiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
- Department of Dermatology, Union Shenzhen Hospital, Huazhong University of Science and Technology, Shenzhen, China
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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28
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Emran AA, Nsengimana J, Punnia-Moorthy G, Schmitz U, Gallagher SJ, Newton-Bishop J, Tiffen JC, Hersey P. Study of the Female Sex Survival Advantage in Melanoma-A Focus on X-Linked Epigenetic Regulators and Immune Responses in Two Cohorts. Cancers (Basel) 2020; 12:E2082. [PMID: 32731355 PMCID: PMC7464825 DOI: 10.3390/cancers12082082] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/15/2020] [Accepted: 07/23/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Survival from melanoma is strongly related to patient sex, with females having a survival rate almost twice that of males. Many explanations have been proposed but have not withstood critical scrutiny. Prior analysis of different cancers with a sex bias has identified six X-linked genes that escape X chromosome inactivation in females and are, therefore, potentially involved in sex differences in survival. Four of the genes are well-known epigenetic regulators that are known to influence the expression of hundreds of other genes and signaling pathways in cancer. METHODS Survival and interaction analysis were performed on the skin cutaneous melanoma (SKCM) cohort in The Cancer Genome Atlas (TCGA), comparing high vs. low expression of KDM6A, ATRX, KDM5C, and DDX3X. The Leeds melanoma cohort (LMC) on 678 patients with primary melanoma was used as a validation cohort. RESULTS Analysis of TCGA data revealed that two of these genes-KDM6A and ATRX-were associated with improved survival from melanoma. Tumoral KDM6A was expressed at higher levels in females and was associated with inferred lymphoid infiltration into melanoma. Gene set analysis of high KDM6A showed strong associations with immune responses and downregulation of genes associated with Myc and other oncogenic pathways. The LMC analysis confirmed the prognostic significance of KDM6A and its interaction with EZH2 but also revealed the expression of KDM5C and DDX3X to be prognostically significant. The analysis also confirmed a partial correlation of KDM6A with immune tumor infiltrates. CONCLUSION When considered together, the results from these two series are consistent with the involvement of X-linked epigenetic regulators in the improved survival of females from melanoma. The identification of gene signatures associated with their expression presents insights into the development of new treatment initiatives but provides a basis for exploration in future studies.
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Affiliation(s)
- Abdullah Al Emran
- Melanoma Oncology and Immunology Program, The Centenary Institute, The University of Sydney, Royal Prince Alfred Hospital, Missenden Road, Camperdown NSW 2050, Australia; (A.A.E.); (G.P.-M.); (S.J.G.); (J.C.T.)
- Melanoma Institute Australia, The University of Sydney, Sydney NSW 2006, Australia
| | - Jérémie Nsengimana
- Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds LS2 9JT, UK; (J.N.); (J.N.-B.)
- Biostatistics Research Group, Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Gaya Punnia-Moorthy
- Melanoma Oncology and Immunology Program, The Centenary Institute, The University of Sydney, Royal Prince Alfred Hospital, Missenden Road, Camperdown NSW 2050, Australia; (A.A.E.); (G.P.-M.); (S.J.G.); (J.C.T.)
- Melanoma Institute Australia, The University of Sydney, Sydney NSW 2006, Australia
| | - Ulf Schmitz
- Computational Biomedicine Lab Centenary Institute, The University of Sydney, Camperdown NSW 2050, Australia;
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown NSW 2050, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown NSW 2050, Australia
| | - Stuart J. Gallagher
- Melanoma Oncology and Immunology Program, The Centenary Institute, The University of Sydney, Royal Prince Alfred Hospital, Missenden Road, Camperdown NSW 2050, Australia; (A.A.E.); (G.P.-M.); (S.J.G.); (J.C.T.)
- Melanoma Institute Australia, The University of Sydney, Sydney NSW 2006, Australia
| | - Julia Newton-Bishop
- Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds LS2 9JT, UK; (J.N.); (J.N.-B.)
| | - Jessamy C. Tiffen
- Melanoma Oncology and Immunology Program, The Centenary Institute, The University of Sydney, Royal Prince Alfred Hospital, Missenden Road, Camperdown NSW 2050, Australia; (A.A.E.); (G.P.-M.); (S.J.G.); (J.C.T.)
- Melanoma Institute Australia, The University of Sydney, Sydney NSW 2006, Australia
| | - Peter Hersey
- Melanoma Oncology and Immunology Program, The Centenary Institute, The University of Sydney, Royal Prince Alfred Hospital, Missenden Road, Camperdown NSW 2050, Australia; (A.A.E.); (G.P.-M.); (S.J.G.); (J.C.T.)
- Melanoma Institute Australia, The University of Sydney, Sydney NSW 2006, Australia
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Biological Factors behind Melanoma Response to Immune Checkpoint Inhibitors. Int J Mol Sci 2020; 21:ijms21114071. [PMID: 32517213 PMCID: PMC7313051 DOI: 10.3390/ijms21114071] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/01/2020] [Accepted: 06/02/2020] [Indexed: 12/14/2022] Open
Abstract
Modern immunotherapy together with targeted therapy has revolutionized the treatment of advanced melanoma. Inhibition of immune checkpoints significantly improved the median overall survival and gave hope to many melanoma patients. However, this treatment has three serious drawbacks: high cost, serious side effects, and an effectiveness limited only to approximately 50% of patients. Some patients do not derive any or short-term benefit from this treatment due to primary or secondary resistance. The response to immunotherapy depends on many factors that fall into three main categories: those associated with melanoma cells, those linked to a tumor and its microenvironment, and those classified as individual ontogenic and physiological features of the patient. The first category comprises expression of PD-L1 and HLA proteins on melanoma cells as well as genetic/genomic metrics such as mutational load, (de)activation of specific signaling pathways and epigenetic factors. The second category is the inflammatory status of the tumor: “hot” versus “cold” (i.e., high versus low infiltration of immune cells). The third category comprises metabolome and single nucleotide polymorphisms of specific genes. Here we present up-to-date data on those biological factors influencing melanoma response to immunotherapy with a special focus on signaling pathways regulating the complex process of anti-tumor immune response. We also discuss their potential predictive capacity.
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30
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Ou JY, Hanson HA, Ramsay JM, Kaddas HK, Pope CA, Leiser CL, VanDerslice J, Kirchhoff AC. Fine Particulate Matter Air Pollution and Mortality among Pediatric, Adolescent, and Young Adult Cancer Patients. Cancer Epidemiol Biomarkers Prev 2020; 29:1929-1939. [PMID: 32404444 DOI: 10.1158/1055-9965.epi-19-1363] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/28/2020] [Accepted: 03/03/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Air pollution is a carcinogen and causes pulmonary and cardiac complications. We examined the association of fine particulate matter pollution (PM2.5) and mortality from cancer and all causes among pediatric, adolescent, and young adult (AYA) patients with cancer in Utah, a state with considerable variation in PM2.5. METHODS We followed 2,444 pediatric (diagnosed ages 0-14) and 13,459 AYA (diagnosed ages 15-39) patients diagnosed in 1986-2015 from diagnosis to 5 and 10 years postdiagnosis, death, or emigration. We measured average monthly PM2.5 by ZIP code during follow-up. Separate pediatric and AYA multivariable Cox models estimated the association of PM2.5 and mortality. Among AYAs, we examined effect modification of PM2.5 and mortality by stage while controlling for cancer type. RESULTS Increases in PM2.5 per 5 μg/m3 were associated with cancer mortality in pediatric lymphomas and central nervous system (CNS) tumors at both time points, and all cause mortality in lymphoid leukemias [HR5-year = 1.32 (1.02-1.71)]. Among AYAs, PM2.5 per 5 μg/m3 was associated with cancer mortality in CNS tumors and carcinomas at both time points, and all cause mortality for all AYA cancer types [HR5-year = 1.06 (1.01-1.13)]. PM2.5 ≥12 μg/m3 was associated with cancer mortality among breast [HR5-year = 1.50 (1.29-1.74); HR10-year = 1.30 (1.13-1.50)] and colorectal cancers [HR5-year = 1.74 (1.29-2.35); HR10-year = 1.67 (1.20-2.31)] at both time points. Effect modification by stage was significant, with local tumors at highest risk. CONCLUSIONS PM2.5 was associated with mortality in pediatric and AYA patients with specific cancers. IMPACT Limiting PM2.5 exposure may be important for young cancer patients with certain cancers.See all articles in this CEBP Focus section, "Environmental Carcinogenesis: Pathways to Prevention."
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Affiliation(s)
- Judy Y Ou
- Huntsman Cancer Institute, Cancer Control and Population Sciences, University of Utah, Salt Lake City, Utah.
| | - Heidi A Hanson
- Huntsman Cancer Institute, Cancer Control and Population Sciences, University of Utah, Salt Lake City, Utah
- Department of Surgery, University of Utah School of Medicine, Salt Lake City, Utah
| | - Joemy M Ramsay
- Huntsman Cancer Institute, Cancer Control and Population Sciences, University of Utah, Salt Lake City, Utah
| | - Heydon K Kaddas
- Huntsman Cancer Institute, Cancer Control and Population Sciences, University of Utah, Salt Lake City, Utah
| | | | - Claire L Leiser
- Huntsman Cancer Institute, Cancer Control and Population Sciences, University of Utah, Salt Lake City, Utah
- Department of Population Health Sciences, University of Utah School of Medicine, Salt Lake City, Utah
| | - James VanDerslice
- Department of Family and Preventive Medicine, University of Utah School of Medicine, Salt Lake City, Utah
| | - Anne C Kirchhoff
- Huntsman Cancer Institute, Cancer Control and Population Sciences, University of Utah, Salt Lake City, Utah
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah
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31
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Juraleviciute M, Pozniak J, Nsengimana J, Harland M, Randerson-Moor J, Wernhoff P, Bassarova A, Øy GF, Trøen G, Flørenes VA, Bishop DT, Herlyn M, Newton-Bishop J, Slipicevic A. MX 2 is a novel regulator of cell cycle in melanoma cells. Pigment Cell Melanoma Res 2020; 33:446-457. [PMID: 31660681 PMCID: PMC7180100 DOI: 10.1111/pcmr.12837] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/07/2019] [Accepted: 10/18/2019] [Indexed: 12/14/2022]
Abstract
MX2 protein is a dynamin-like GTPase2 that has recently been identified as an interferon-induced restriction factor of HIV-1 and other primate lentiviruses. A single nucleotide polymorphism (SNP), rs45430, in an intron of the MX2 gene, was previously reported as a novel melanoma susceptibility locus in genome-wide association studies. Functionally, however, it is still unclear whether and how MX2 contributes to melanoma susceptibility and tumorigenesis. Here, we show that MX2 is differentially expressed in melanoma tumors and cell lines, with most metastatic cell lines showing lower MX2 expression than primary melanoma cell lines and melanocytes. Furthermore, high expression of MX2 RNA in primary melanoma tumors is associated with better patient survival. Overexpression of MX2 reduces in vivo proliferation partially through inhibition of AKT activation, suggesting that it can act as a tumor suppressor in melanoma. However, we have also identified a subset of melanoma cell lines with high endogenous MX2 expression where downregulation of MX2 leads to reduced proliferation. In these cells, MX2 downregulation interfered with DNA replication and cell cycle processes. Collectively, our data for the first time show that MX2 is functionally involved in the regulation of melanoma proliferation but that its function is context-dependent.
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Affiliation(s)
| | - Joanna Pozniak
- Division of Haematology and Immunology, Institute of Medical Research at St James's, University of Leeds, Leeds, UK
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Jérémie Nsengimana
- Division of Haematology and Immunology, Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Mark Harland
- Division of Haematology and Immunology, Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Juliette Randerson-Moor
- Division of Haematology and Immunology, Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Patrik Wernhoff
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Assia Bassarova
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Geir Frode Øy
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Gunhild Trøen
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | | | - David Timothy Bishop
- Division of Haematology and Immunology, Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | | | - Julia Newton-Bishop
- Division of Haematology and Immunology, Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Ana Slipicevic
- Department of Pathology, Oslo University Hospital, Oslo, Norway
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Wang P, Zhang X, Sun N, Zhao Z, He J. Comprehensive Analysis of the Tumor Microenvironment in Cutaneous Melanoma associated with Immune Infiltration. J Cancer 2020; 11:3858-3870. [PMID: 32328190 PMCID: PMC7171484 DOI: 10.7150/jca.44413] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 03/27/2020] [Indexed: 12/25/2022] Open
Abstract
Accumulating evidence suggests that the malignant phenotypes of cancers are determined not only by the intrinsic properties of cancer cells but also by components in the tumor microenvironment (TME). In this study, we comprehensively characterized the TME of cutaneous melanoma (CM). As a result, tumor stage, tissue site, ulceration, thickness as well as patient age, sex were associated with immune infiltration. Patients of higher immune infiltration exhibited better survival outcomes, and antitumor effector cells, such as CD8 T cells and M1 macrophages, were found in significantly higher numbers in those tissues. Differential expression of mRNAs and long non-coding RNAs (lncRNAs) was analyzed and utilized to construct an immune-related competing endogenous RNA network, in which a lncRNA-associated subnetwork that could positively regulate the expression of IFN-γ was highlighted. Functional analysis confirmed that this network was remarkably enriched in functional terms related to both immune response and tumor-intrinsic pathways. Finally, a total of 109 high-confidence prognostic genes were identified, and a gene module that contained several key immune checkpoint molecules or modulators (PD-1, PD-L1, PD-L2, and LCK) was screened, which confers survival benefit for CM patients as supported by both overall and relapse-free survival rates from different datasets.
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Affiliation(s)
- Pan Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Xinyu Zhang
- Department of body contouring and liposuction center, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100144, China
| | - Nan Sun
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Zhihong Zhao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
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Scortegagna M, Hockemeyer K, Dolgalev I, Poźniak J, Rambow F, Li Y, Feng Y, Tinoco R, Otero DC, Zhang T, Brown K, Bosenberg M, Bradley LM, Marine JC, Aifantis I, Ronai ZA. Siah2 control of T-regulatory cells limits anti-tumor immunity. Nat Commun 2020; 11:99. [PMID: 31911617 PMCID: PMC6946684 DOI: 10.1038/s41467-019-13826-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 11/28/2019] [Indexed: 12/23/2022] Open
Abstract
Understanding the mechanisms underlying anti-tumor immunity is pivotal for improving immune-based cancer therapies. Here, we report that growth of BRAF-mutant melanoma cells is inhibited, up to complete rejection, in Siah2-/- mice. Growth-inhibited tumors exhibit increased numbers of intra-tumoral activated T cells and decreased expression of Ccl17, Ccl22, and Foxp3. Marked reduction in Treg proliferation and tumor infiltration coincide with G1 arrest in tumor infiltrated Siah2-/- Tregs in vivo or following T cell stimulation in culture, attributed to elevated expression of the cyclin-dependent kinase inhibitor p27, a Siah2 substrate. Growth of anti-PD-1 therapy resistant melanoma is effectively inhibited in Siah2-/- mice subjected to PD-1 blockade, indicating synergy between PD-1 blockade and Siah2 loss. Low SIAH2 and FOXP3 expression is identified in immune responsive human melanoma tumors. Overall, Siah2 regulation of Treg recruitment and cell cycle progression effectively controls melanoma development and Siah2 loss in the host sensitizes melanoma to anti-PD-1 therapy.
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Affiliation(s)
- Marzia Scortegagna
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA.
| | - Kathryn Hockemeyer
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, 10016, USA
| | - Igor Dolgalev
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, 10016, USA
| | - Joanna Poźniak
- VIB Center for Cancer Biology Laboratory for Molecular Cancer Biology, KU Leuven Oncology Department, Leuven, Belgium
| | - Florian Rambow
- VIB Center for Cancer Biology Laboratory for Molecular Cancer Biology, KU Leuven Oncology Department, Leuven, Belgium
| | | | - Yongmei Feng
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Roberto Tinoco
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA.,Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, 92697, USA
| | - Dennis C Otero
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Kevin Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Marcus Bosenberg
- Departments of Dermatology, Pathology, Yale University, School of Medicine, New Haven, CT, 06520, USA
| | - Linda M Bradley
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Jean-Christophe Marine
- VIB Center for Cancer Biology Laboratory for Molecular Cancer Biology, KU Leuven Oncology Department, Leuven, Belgium
| | - Ioannis Aifantis
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, 10016, USA.
| | - Ze'ev A Ronai
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA.
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Muralidhar S, Filia A, Nsengimana J, Poźniak J, O'Shea SJ, Diaz JM, Harland M, Randerson-Moor JA, Reichrath J, Laye JP, van der Weyden L, Adams DJ, Bishop DT, Newton-Bishop J. Vitamin D-VDR Signaling Inhibits Wnt/β-Catenin-Mediated Melanoma Progression and Promotes Antitumor Immunity. Cancer Res 2019; 79:5986-5998. [PMID: 31690667 DOI: 10.1158/0008-5472.can-18-3927] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/12/2019] [Accepted: 10/01/2019] [Indexed: 11/16/2022]
Abstract
1α,25-Dihydroxyvitamin D3 signals via the vitamin D receptor (VDR). Higher serum vitamin D is associated with thinner primary melanoma and better outcome, although a causal mechanism has not been established. As patients with melanoma commonly avoid sun exposure, and consequent vitamin D deficiency might worsen outcomes, we interrogated 703 primary melanoma transcriptomes to understand the role of vitamin D-VDR signaling and replicated the findings in The Cancer Genome Atlas metastases. VDR expression was independently protective for melanoma-related death in both primary and metastatic disease. High tumor VDR expression was associated with upregulation of pathways mediating antitumor immunity and corresponding with higher imputed immune cell scores and histologically detected tumor-infiltrating lymphocytes. High VDR-expressing tumors had downregulation of proliferative pathways, notably Wnt/β-catenin signaling. Deleterious low VDR levels resulted from promoter methylation and gene deletion in metastases. Vitamin D deficiency (<25 nmol/L ∼ 10 ng/mL) shortened survival in primary melanoma in a VDR-dependent manner. In vitro functional validation studies showed that elevated vitamin D-VDR signaling inhibited Wnt/β-catenin signaling genes. Murine melanoma cells overexpressing VDR produced fewer pulmonary metastases than controls in tail-vein metastasis assays. In summary, vitamin D-VDR signaling contributes to controlling pro-proliferative/immunosuppressive Wnt/β-catenin signaling in melanoma and this is associated with less metastatic disease and stronger host immune responses. This is evidence of a causal relationship between vitamin D-VDR signaling and melanoma survival, which should be explored as a therapeutic target in primary resistance to checkpoint blockade. SIGNIFICANCE: VDR expression could potentially be used as a biomarker to stratify patients with melanoma that may respond better to immunotherapy.
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Affiliation(s)
- Sathya Muralidhar
- University of Leeds School of Medicine, Leeds, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Anastasia Filia
- Centre for Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | | | - Joanna Poźniak
- University of Leeds School of Medicine, Leeds, United Kingdom
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Sally J O'Shea
- University of Leeds School of Medicine, Leeds, United Kingdom
- Faculty of Medicine and Health, University College Cork, Cork, Ireland
- Mater Private Hospital Cork, Citygate, Mahon, Cork, Ireland
| | - Joey M Diaz
- University of Leeds School of Medicine, Leeds, United Kingdom
| | - Mark Harland
- University of Leeds School of Medicine, Leeds, United Kingdom
| | | | - Jörg Reichrath
- Center for Clinical and Experimental Photodermatology, The Saarland University Hospital, Homburg, Germany
| | - Jonathan P Laye
- University of Leeds School of Medicine, Leeds, United Kingdom
| | - Louise van der Weyden
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - David J Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - D T Bishop
- University of Leeds School of Medicine, Leeds, United Kingdom
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35
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Stadler R. The effect of smoking in melanoma outcome still remains an enigma. J Eur Acad Dermatol Venereol 2019; 33:2219-2220. [PMID: 31779040 DOI: 10.1111/jdv.16020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rudolf Stadler
- Johannes Wesling Medical Centre, UKRUB, University Clinic for Dermatology, University of Bochum, Minden, Germany
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36
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Nuclear Factor κB Signaling and Its Related Non-coding RNAs in Cancer Therapy. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 19:208-217. [PMID: 31841993 PMCID: PMC6920321 DOI: 10.1016/j.omtn.2019.11.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 11/04/2019] [Accepted: 11/07/2019] [Indexed: 12/19/2022]
Abstract
Nuclear factor κB (NF-κB) acts as a nuclear factor that is composed of five main subunits. It is a pluripotent and crucial dimer transcription factor that has a close relationship with many serious illnesses, especially its influences on cell proliferation, inflammation, and cancer initiation and progression. NF-κB acts as part of the signaling pathway and determines its effect on the expression of several other genes, such as epidermal growth factor receptor (EGFR), p53, signal transducer and activator of transcription 3 (STAT3), and non-coding RNA (ncRNA). Continuous activation of the NF-κB signaling pathway has been seen in many cancer types. While the NF-κB signaling pathway is tightly regulated in physiological settings, quite frequently it is constitutively activated in cancer, and the molecular biology mechanism underlying the deregulated activation of NF-κB signaling remains unclear. In this review, we discuss the regulatory role and possible clinical significance of ncRNA (microRNA [miRNA] and long non-coding RNA [lncRNA]) in NF-κB signaling in cancer, including in the conversion of inflammation to carcinogenesis. Non-coding RNA plays an essential and complex role in the NF-κB signaling pathway. NF-κB activation can also induce the ncRNA status. Targeting NF-κB signaling by ncRNA is becoming a promising strategy of drug development and cancer treatment.
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Zhu P, Zheng Z, Fu X, Li J, Yin C, Chou J, Wang Y, Liu Y, Chen Y, Bai J, Wu J, Chen S, Yu ZL. Arnicolide D exerts anti-melanoma effects and inhibits the NF-κB pathway. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2019; 64:153065. [PMID: 31408803 DOI: 10.1016/j.phymed.2019.153065] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 07/18/2019] [Accepted: 08/02/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Melanoma is a lethal cancer. NF-κB has been validated as a molecular target for melanoma treatment. Current therapies for melanoma have limitations. Novel targeted therapeutics are needed. Arnicolide D (Ar-D), a sesquiterpene lactone isolated from the dried whole plant of Centipeda minima (L.) A. Br. et Aschers., has been reported to inhibit NF-κB activity in colorectal cancer cells. PURPOSE To investigate the anti-melanoma effects of Ar-D in vitro and in vivo; and to determine whether Ar-D inhibits the NF-κB pathway in melanoma cells. METHODS A B16F10 allograft mouse model and two melanoma cell lines (A375 and B16F10) were used to investigate the anti-melanoma effects of Ar-D in vivo and in vitro. Dacarbazine was used as a positive control. Cell viability was assessed by MTT and crystal violet staining assays. Cell cycle arrest and apoptosis were analyzed by flow cytometry. Protein levels were determined by Immunoblotting. RESULTS In vivo assays showed that the average tumor weight in Ar-D-treated group (4 mg/kg, i.p, 15 days) was reduced by 53.7%, when compared with the control group. In vitro studies demonstrated that Ar-D reduced cell viability, induced G2/M cell cycle arrest and apoptosis, elevated levels of cell cycle regulatory proteins p53 and p21, and lowered levels of G2/M checkpoint proteins Cdc2 and Cyclin B1 in melanoma cells. Mechanistically, Ar-D inhibited the activity of IKKα/β, the degradation of IκBα, and the phosphorylation and expression of NF-κB p65 in melanoma cells. CONCLUSION Ar-D has anti-melanoma effects, and inhibition of the IKK/IκBα/NF-κB p65 pathway is involved in the effects.
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Affiliation(s)
- Peili Zhu
- Consun Chinese Medicines Research Centre for Renal Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China; Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China; Research and Development Centre for Natural Health Products, HKBU Shenzhen Research Institute and Continuing Education, Shenzhen, China
| | - Zhongyu Zheng
- Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Xiuqiong Fu
- Consun Chinese Medicines Research Centre for Renal Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China; Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China; Research and Development Centre for Natural Health Products, HKBU Shenzhen Research Institute and Continuing Education, Shenzhen, China
| | - Junkui Li
- Consun Chinese Medicines Research Centre for Renal Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China; Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China; Research and Development Centre for Natural Health Products, HKBU Shenzhen Research Institute and Continuing Education, Shenzhen, China
| | - Chengle Yin
- Consun Chinese Medicines Research Centre for Renal Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China; Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China; Research and Development Centre for Natural Health Products, HKBU Shenzhen Research Institute and Continuing Education, Shenzhen, China
| | - Jiyao Chou
- Consun Chinese Medicines Research Centre for Renal Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China; Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China; Research and Development Centre for Natural Health Products, HKBU Shenzhen Research Institute and Continuing Education, Shenzhen, China
| | - Yaping Wang
- Consun Chinese Medicines Research Centre for Renal Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China; Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China; Research and Development Centre for Natural Health Products, HKBU Shenzhen Research Institute and Continuing Education, Shenzhen, China
| | - Yuxi Liu
- Consun Chinese Medicines Research Centre for Renal Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China; Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China; Research and Development Centre for Natural Health Products, HKBU Shenzhen Research Institute and Continuing Education, Shenzhen, China
| | - Yingjie Chen
- Consun Chinese Medicines Research Centre for Renal Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China; Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China; Research and Development Centre for Natural Health Products, HKBU Shenzhen Research Institute and Continuing Education, Shenzhen, China
| | - Jingxuan Bai
- Consun Chinese Medicines Research Centre for Renal Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China; Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China; Research and Development Centre for Natural Health Products, HKBU Shenzhen Research Institute and Continuing Education, Shenzhen, China
| | - Jiaying Wu
- Consun Chinese Medicines Research Centre for Renal Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China; Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China; Research and Development Centre for Natural Health Products, HKBU Shenzhen Research Institute and Continuing Education, Shenzhen, China
| | - Sibao Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China.
| | - Zhi-Ling Yu
- Consun Chinese Medicines Research Centre for Renal Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China; Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China; Research and Development Centre for Natural Health Products, HKBU Shenzhen Research Institute and Continuing Education, Shenzhen, China.
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Ladányi A, Tímár J. Immunologic and immunogenomic aspects of tumor progression. Semin Cancer Biol 2019; 60:249-261. [PMID: 31419526 DOI: 10.1016/j.semcancer.2019.08.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/12/2019] [Accepted: 08/12/2019] [Indexed: 12/11/2022]
Abstract
Tumor progression to metastatic disease is characterized by continuous genetic alterations due to instability of the genome. Immune sensitivity was found to be linked to tumor mutational burden (TMB) and the resulting amount of neoantigens. However, APOBEC activity resulting in increase in TMB causes immune evasion. On the other hand, clonal or acquired genetic loss of HLA class I also hampers immune sensitivity of tumors. Rare amplification of the PD-L1 gene in cancers may render them sensitive to immune checkpoint inhibitors but involvement of broader regions of chromosome 9p may ultimately lead again to immune evasion due to inactivation of the IFN-γ signaling pathway. Such genetic changes may occur not only in the primary tumor but at any phase of progression: in lymphatic as well as in visceral metastases. Accordingly, it is rational to monitor these changes continuously during disease progression similar to target therapies. Moreover, beside temporal variability, genomic features of tumors such as mutation profiles, as well as the tumor immune microenvironment also show considerable inter- and intratumoral spatial heterogeneity, suggesting the necessity of multiple sampling in biomarker studies.
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Affiliation(s)
| | - József Tímár
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary.
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39
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Anichini A. Progress in Understanding Complexity and Determinants of Immune-Related Prognostic Subsets in Primary Melanoma. Cancer Res 2019; 79:2457-2459. [PMID: 31092407 DOI: 10.1158/0008-5472.can-19-0786] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 03/07/2019] [Accepted: 03/11/2019] [Indexed: 11/16/2022]
Abstract
Gene signatures are increasingly being used to infer the immune composition of the tumor microenvironment. This strategy holds the promise for earlier detection, identification of patients at higher risk of progression, and for understanding therapeutic response and resistance to immunotherapy. This gene signature approach is now being integrated with information from genomic changes, gene networks, and master immunoregulatory genes, and this development can lead to identify the main determinants shaping the tumor immune landscape. A study in this issue of Cancer Research indicates a way forward to discover prognostic immune-related subsets in primary melanoma and to understand major determinants impairing protective immunity in early stage of disease.See related article by Poźniak et al., p. 2684.
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Affiliation(s)
- Andrea Anichini
- Human Tumors Immunobiology Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.
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40
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Immunomodulatory and immunotherapeutic implications of tobacco smoking in squamous cell carcinomas and normal airway epithelium. Oncotarget 2019; 10:3835-3839. [PMID: 31231463 PMCID: PMC6570474 DOI: 10.18632/oncotarget.26982] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 05/13/2019] [Indexed: 01/10/2023] Open
Abstract
The mutagenic effects of tobacco smoking increase the risk of the development of cancers of the lung, head and neck, and other anatomic sites. In a comparison of squamous cell carcinomas of the lung and the head and neck, we find that the immunomodulatory effects of smoking differ based on anatomic site. In both sites, the mutational signature of smoking is strongly associated with somatic mutational load. In head and neck squamous cell carcinoma, the mutational signature of tobacco exposure is associated with a strongly immunosuppressive tumor microenvironment. In contrast, in lung squamous cell carcinoma, the opposite effect is seen, with the tumor immune microenvironment significantly more inflamed. These effects are mirrored in rates of response to immune checkpoint inhibitor immunotherapy, which tend to be higher in smokers with lung cancer, but lower in smokers with head and neck cancer. We find a similarly strong immunosuppressive effect of smoking in non-cancerous lung epithelium. Taken together, our findings show that the effects of mutational signatures on the immune microenvironment and response to immunotherapy can be affected by context such as cancer type, anatomic site, and histology.
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