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Zhang S, Xiao X, Yi Y, Wang X, Zhu L, Shen Y, Lin D, Wu C. Tumor initiation and early tumorigenesis: molecular mechanisms and interventional targets. Signal Transduct Target Ther 2024; 9:149. [PMID: 38890350 PMCID: PMC11189549 DOI: 10.1038/s41392-024-01848-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 04/23/2024] [Accepted: 04/27/2024] [Indexed: 06/20/2024] Open
Abstract
Tumorigenesis is a multistep process, with oncogenic mutations in a normal cell conferring clonal advantage as the initial event. However, despite pervasive somatic mutations and clonal expansion in normal tissues, their transformation into cancer remains a rare event, indicating the presence of additional driver events for progression to an irreversible, highly heterogeneous, and invasive lesion. Recently, researchers are emphasizing the mechanisms of environmental tumor risk factors and epigenetic alterations that are profoundly influencing early clonal expansion and malignant evolution, independently of inducing mutations. Additionally, clonal evolution in tumorigenesis reflects a multifaceted interplay between cell-intrinsic identities and various cell-extrinsic factors that exert selective pressures to either restrain uncontrolled proliferation or allow specific clones to progress into tumors. However, the mechanisms by which driver events induce both intrinsic cellular competency and remodel environmental stress to facilitate malignant transformation are not fully understood. In this review, we summarize the genetic, epigenetic, and external driver events, and their effects on the co-evolution of the transformed cells and their ecosystem during tumor initiation and early malignant evolution. A deeper understanding of the earliest molecular events holds promise for translational applications, predicting individuals at high-risk of tumor and developing strategies to intercept malignant transformation.
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Affiliation(s)
- Shaosen Zhang
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Xinyi Xiao
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Yonglin Yi
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Xinyu Wang
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Lingxuan Zhu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Changping Laboratory, 100021, Beijing, China
| | - Yanrong Shen
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Dongxin Lin
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Changping Laboratory, 100021, Beijing, China.
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China.
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou, 510060, China.
| | - Chen Wu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Changping Laboratory, 100021, Beijing, China.
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China.
- CAMS Oxford Institute, Chinese Academy of Medical Sciences, 100006, Beijing, China.
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Qin Q, Zhou Y, Guo J, Chen Q, Tang W, Li Y, You J, Li Q. Conserved methylation signatures associate with the tumor immune microenvironment and immunotherapy response. Genome Med 2024; 16:47. [PMID: 38566132 PMCID: PMC10985907 DOI: 10.1186/s13073-024-01318-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Aberrant DNA methylation is a major characteristic of cancer genomes. It remains unclear which biological processes determine epigenetic reprogramming and how these processes influence the variants in the cancer methylome, which can further impact cancer phenotypes. METHODS We performed pairwise permutations of 381,900 loci in 569 paired DNA methylation profiles of cancer tissue and matched normal tissue from The Cancer Genome Atlas (TCGA) and defined conserved differentially methylated positions (DMPs) based on the resulting null distribution. Then, we derived independent methylation signatures from 2,465 cancer-only methylation profiles from the TCGA and 241 cell line-based methylation profiles from the Genomics of Drug Sensitivity in Cancer (GDSC) cohort using nonnegative matrix factorization (NMF). We correlated DNA methylation signatures with various clinical and biological features, including age, survival, cancer stage, tumor immune microenvironment factors, and immunotherapy response. We inferred the determinant genes of these methylation signatures by integrating genomic and transcriptomic data and evaluated the impact of these signatures on cancer phenotypes in independent bulk and single-cell RNA/methylome cohorts. RESULTS We identified 7,364 differentially methylated positions (2,969 Hyper-DMPs and 4,395 Hypo-DMPs) in nine cancer types from the TCGA. We subsequently retrieved three highly conserved, independent methylation signatures (Hyper-MS1, Hypo-MS1, and Hypo-MS4) from cancer tissues and cell lines based on these Hyper and Hypo-DMPs. Our data suggested that Hypo-MS4 activity predicts poor survival and is associated with immunotherapy response and distant tumor metastasis, and Hypo-MS4 activity is related to TP53 mutation and FOXA1 binding specificity. In addition, we demonstrated a correlation between the activities of Hypo-MS4 in cancer cells and the fractions of regulatory CD4 + T cells with the expression levels of immunological genes in the tumor immune microenvironment. CONCLUSIONS Our findings demonstrated that the methylation signatures of distinct biological processes are associated with immune activity in the cancer microenvironment and predict immunotherapy response.
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Affiliation(s)
- Qingqing Qin
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361003, China
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, China
- Department of Pediatrics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, 361003, China
| | - Ying Zhou
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361003, China
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, China
- Department of Pediatrics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, 361003, China
| | - Jintao Guo
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361003, China
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, China
- Department of Pediatrics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, 361003, China
| | - Qinwei Chen
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361003, China
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, China
| | - Weiwei Tang
- Department of Medical Oncology, School of Medicine, The First Affiliated Hospital of Xiamen University and Institute of Hematology, Xiamen University, Xiamen, 361003, China
- Xiamen Key Laboratory of Antitumor Drug Transformation Research, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, The School of Clinical Medicine of Fujian, Medical University, Xiamen, 361003, China
| | - Yuchen Li
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361003, China
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, China
- Department of Pediatrics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, 361003, China
| | - Jun You
- Department of Gastrointestinal Oncology Surgery, The First Affiliated Hospital of Xiamen University, Cancer Center, Xiamen, 361003, China
| | - Qiyuan Li
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361003, China.
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, China.
- Department of Pediatrics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, 361003, China.
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Stark L, Kasajima A, Stögbauer F, Schmidl B, Rinecker J, Holzmann K, Färber S, Pfarr N, Steiger K, Wollenberg B, Ruland J, Winter C, Wirth M. Head and neck cancer of unknown primary: unveiling primary tumor sites through machine learning on DNA methylation profiles. Clin Epigenetics 2024; 16:47. [PMID: 38528631 PMCID: PMC10964705 DOI: 10.1186/s13148-024-01657-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 03/13/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND The unknown tissue of origin in head and neck cancer of unknown primary (hnCUP) leads to invasive diagnostic procedures and unspecific and potentially inefficient treatment options for patients. The most common histologic subtype, squamous cell carcinoma, can stem from various tumor primary sites, including the oral cavity, oropharynx, larynx, head and neck skin, lungs, and esophagus. DNA methylation profiles are highly tissue-specific and have been successfully used to classify tissue origin. We therefore developed a support vector machine (SVM) classifier trained with publicly available DNA methylation profiles of commonly cervically metastasizing squamous cell carcinomas (n = 1103) in order to identify the primary tissue of origin of our own cohort of squamous cell hnCUP patient's samples (n = 28). Methylation analysis was performed with Infinium MethylationEPIC v1.0 BeadChip by Illumina. RESULTS The SVM algorithm achieved the highest overall accuracy of tested classifiers, with 87%. Squamous cell hnCUP samples on DNA methylation level resembled squamous cell carcinomas commonly metastasizing into cervical lymph nodes. The most frequently predicted cancer localization was the oral cavity in 11 cases (39%), followed by the oropharynx and larynx (both 7, 25%), skin (2, 7%), and esophagus (1, 4%). These frequencies concord with the expected distribution of lymph node metastases in epidemiological studies. CONCLUSIONS On DNA methylation level, hnCUP is comparable to primary tumor tissue cancer types that commonly metastasize to cervical lymph nodes. Our SVM-based classifier can accurately predict these cancers' tissues of origin and could significantly reduce the invasiveness of hnCUP diagnostics and enable a more precise therapy after clinical validation.
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Affiliation(s)
- Leonhard Stark
- Department of Otolaryngology, Head and Neck Surgery, School of Medicine and Health, Technical University of Munich, Munich, Germany.
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine and Health, Technical University of Munich, Munich, Germany.
| | - Atsuko Kasajima
- Institute of Pathology, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Fabian Stögbauer
- Institute of Pathology, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Benedikt Schmidl
- Department of Otolaryngology, Head and Neck Surgery, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Jakob Rinecker
- Department of Otolaryngology, Head and Neck Surgery, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Katharina Holzmann
- Department of Otolaryngology, Head and Neck Surgery, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Sarah Färber
- Department of Otolaryngology, Head and Neck Surgery, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Nicole Pfarr
- Institute of Pathology, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Katja Steiger
- Institute of Pathology, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Barbara Wollenberg
- Department of Otolaryngology, Head and Neck Surgery, School of Medicine and Health, Technical University of Munich, Munich, Germany
- Partner Site Munich and German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Jürgen Ruland
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine and Health, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research, TranslaTUM, Technical University of Munich, Munich, Germany
- Partner Site Munich and German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Christof Winter
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine and Health, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research, TranslaTUM, Technical University of Munich, Munich, Germany
- Partner Site Munich and German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Markus Wirth
- Department of Otolaryngology, Head and Neck Surgery, School of Medicine and Health, Technical University of Munich, Munich, Germany
- Partner Site Munich and German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
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Wang Z, Wang X, Shi Y, Wu S, Ding Y, Yao G, Chen J. Advancements in elucidating the pathogenesis of actinic keratosis: present state and future prospects. Front Med (Lausanne) 2024; 11:1330491. [PMID: 38566927 PMCID: PMC10985158 DOI: 10.3389/fmed.2024.1330491] [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: 10/30/2023] [Accepted: 02/19/2024] [Indexed: 04/04/2024] Open
Abstract
Solar keratosis, also known as actinic keratosis (AK), is becoming increasingly prevalent. It is a benign tumor that develops in the epidermis. Individuals with AK typically exhibit irregular, red, scaly bumps or patches as a result of prolonged exposure to UV rays. These growths primarily appear on sun-exposed areas of the skin such as the face, scalp, and hands. Presently, dermatologists are actively studying AK due to its rising incidence rate in the United States. However, the underlying causes of AK remain poorly understood. Previous research has indicated that the onset of AK involves various mechanisms including UV ray-induced inflammation, oxidative stress, complex mutagenesis, resulting immunosuppression, inhibited apoptosis, dysregulated cell cycle, altered cell proliferation, tissue remodeling, and human papillomavirus (HPV) infection. AK can develop in three ways: spontaneous regression, persistence, or progression into invasive cutaneous squamous cell carcinoma (cSCC). Multiple risk factors and diverse signaling pathways collectively contribute to its complex pathogenesis. To mitigate the risk of cancerous changes associated with long-term UV radiation exposure, prompt identification, management, and prevention of AK are crucial. The objective of this review is to elucidate the primary mechanisms underlying AK malignancy and identify potential treatment targets for dermatologists in clinical settings.
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Affiliation(s)
- Zhongzhi Wang
- Department of Dermatology, Shanghai Fourth People’s Hospital, Tongji University, Shanghai, China
| | - Xiaolie Wang
- Department of Dermatology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yuanyang Shi
- Department of Dermatology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Siyu Wu
- Department of Dermatology, Shanghai Fourth People’s Hospital, Tongji University, Shanghai, China
| | - Yu Ding
- Department of Dermatology, Shanghai Fourth People’s Hospital, Tongji University, Shanghai, China
| | - Guotai Yao
- Department of Dermatology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Jianghan Chen
- Department of Dermatology, Shanghai Fourth People’s Hospital, Tongji University, Shanghai, China
- Department of Dermatology, Naval Medical Center, Naval Medical University, Shanghai, China
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Lee YB, Kim JI. Genetic Studies of Actinic Keratosis Development: Where Are We Now? Ann Dermatol 2023; 35:389-399. [PMID: 38086352 PMCID: PMC10733082 DOI: 10.5021/ad.23.072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/24/2023] [Accepted: 09/07/2023] [Indexed: 12/22/2023] Open
Abstract
Actinic keratosis (AK) is a common precancerous skin lesion that can develop into cutaneous squamous cell carcinoma (CSCC). AK is characterized by atypical keratinocytes in the skin's outer layer and is commonly found in sun-exposed areas. Like many precancerous lesions, the development of AK is closely associated with genetic mutations. The molecular biology and transcriptional mechanisms underlying AK development are not well understood. Ultraviolet (UV) light exposure, especially UVA and UVB radiation, is a significant risk factor for AK, causing DNA damage and mutagenic effects. Besides UV exposure, comorbidities like diabetes, rheumatoid arthritis, and psoriasis may also influence AK development. AK patients have shown associations with various internal malignancies, indicating potential vulnerability in cancer-associated genes. Treatment for AK includes cryosurgery, electrodesiccation and curettage, chemotherapeutic creams, photodynamic therapy, or topical immune-modulators. Genomic studies have identified genetic aberrations in AK, with common mutations found in genes like TP53, NOTCH1, and NOTCH2. The progression from AK to CSCC involves chromosomal aberrations and alterations in oncogenes and tumor-suppressor genes. The functional relationships among these genes are not fully understood, but network analysis provides insights into their potential mechanisms. Further research is needed to enhance our understanding of AK's pathogenesis and develop novel therapeutic approaches.
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Affiliation(s)
- Young Bok Lee
- Department of Biomedicine & Health Science, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Department of Dermatology, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Genomic Medicine Institute (GMI), Medical Research Center, Seoul National University, Seoul, Korea
| | - Jong-Il Kim
- Genomic Medicine Institute (GMI), Medical Research Center, Seoul National University, Seoul, Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea.
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Iglesia MD, Jayasinghe RG, Chen S, Terekhanova NV, Herndon JM, Storrs E, Karpova A, Zhou DC, Al Deen NN, Shinkle AT, Lu RJH, Caravan W, Houston A, Zhao Y, Sato K, Lal P, Street C, Rodrigues FM, Southard-Smith AN, Targino da Costa ALN, Zhu H, Mo CK, Crowson L, Fulton RS, Wyczalkowski MA, Fronick CC, Fulton LA, Sun H, Davies SR, Appelbaum EL, Chasnoff SE, Carmody M, Brooks C, Liu R, Wendl MC, Oh C, Bender D, Cruchaga C, Harari O, Bredemeyer A, Lavine K, Bose R, Margenthaler J, Held JM, Achilefu S, Ademuyiwa F, Aft R, Ma C, Colditz GA, Ju T, Oh ST, Fitzpatrick J, Hwang ES, Shoghi KI, Chheda MG, Veis DJ, Chen F, Fields RC, Gillanders WE, Ding L. Differential chromatin accessibility and transcriptional dynamics define breast cancer subtypes and their lineages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.31.565031. [PMID: 37961519 PMCID: PMC10634973 DOI: 10.1101/2023.10.31.565031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Breast cancer is a heterogeneous disease, and treatment is guided by biomarker profiles representing distinct molecular subtypes. Breast cancer arises from the breast ductal epithelium, and experimental data suggests breast cancer subtypes have different cells of origin within that lineage. The precise cells of origin for each subtype and the transcriptional networks that characterize these tumor-normal lineages are not established. In this work, we applied bulk, single-cell (sc), and single-nucleus (sn) multi-omic techniques as well as spatial transcriptomics and multiplex imaging on 61 samples from 37 breast cancer patients to show characteristic links in gene expression and chromatin accessibility between breast cancer subtypes and their putative cells of origin. We applied the PAM50 subtyping algorithm in tandem with bulk RNA-seq and snRNA-seq to reliably subtype even low-purity tumor samples and confirm promoter accessibility using snATAC. Trajectory analysis of chromatin accessibility and differentially accessible motifs clearly connected progenitor populations with breast cancer subtypes supporting the cell of origin for basal-like and luminal A and B tumors. Regulatory network analysis of transcription factors underscored the importance of BHLHE40 in luminal breast cancer and luminal mature cells, and KLF5 in basal-like tumors and luminal progenitor cells. Furthermore, we identify key genes defining the basal-like ( PRKCA , SOX6 , RGS6 , KCNQ3 ) and luminal A/B ( FAM155A , LRP1B ) lineages, with expression in both precursor and cancer cells and further upregulation in tumors. Exhausted CTLA4-expressing CD8+ T cells were enriched in basal-like breast cancer, suggesting altered means of immune dysfunction among breast cancer subtypes. We used spatial transcriptomics and multiplex imaging to provide spatial detail for key markers of benign and malignant cell types and immune cell colocation. These findings demonstrate analysis of paired transcription and chromatin accessibility at the single cell level is a powerful tool for investigating breast cancer lineage development and highlight transcriptional networks that define basal and luminal breast cancer lineages.
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Azimi A, Fernandez-Peñas P. Molecular Classifiers in Skin Cancers: Challenges and Promises. Cancers (Basel) 2023; 15:4463. [PMID: 37760432 PMCID: PMC10526380 DOI: 10.3390/cancers15184463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 08/29/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Skin cancers are common and heterogenous malignancies affecting up to two in three Australians before age 70. Despite recent developments in diagnosis and therapeutic strategies, the mortality rate and costs associated with managing patients with skin cancers remain high. The lack of well-defined clinical and histopathological features makes their diagnosis and classification difficult in some cases and the prognostication difficult in most skin cancers. Recent advancements in large-scale "omics" studies, including genomics, transcriptomics, proteomics, metabolomics and imaging-omics, have provided invaluable information about the molecular and visual landscape of skin cancers. On many occasions, it has refined tumor classification and has improved prognostication and therapeutic stratification, leading to improved patient outcomes. Therefore, this paper reviews the recent advancements in omics approaches and appraises their limitations and potential for better classification and stratification of skin cancers.
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Affiliation(s)
- Ali Azimi
- Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
- Department of Dermatology, Westmead Hospital, Westmead, NSW 2145, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia
| | - Pablo Fernandez-Peñas
- Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
- Department of Dermatology, Westmead Hospital, Westmead, NSW 2145, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia
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Schütz S, Solé-Boldo L, Lucena-Porcel C, Hoffmann J, Brobeil A, Lonsdorf AS, Rodríguez-Paredes M, Lyko F. Functionally distinct cancer-associated fibroblast subpopulations establish a tumor promoting environment in squamous cell carcinoma. Nat Commun 2023; 14:5413. [PMID: 37669956 PMCID: PMC10480447 DOI: 10.1038/s41467-023-41141-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 08/24/2023] [Indexed: 09/07/2023] Open
Abstract
Cutaneous squamous cell carcinoma (cSCC) is a serious public health problem due to its high incidence and metastatic potential. It may progress from actinic keratosis (AK), a precancerous lesion, or the in situ carcinoma, Bowen's disease (BD). During this progression, malignant keratinocytes activate dermal fibroblasts into tumor promoting cancer-associated fibroblasts (CAFs), whose origin and emergence remain largely unknown. Here, we generate and analyze >115,000 single-cell transcriptomes from healthy skin, BD and cSCC of male donors. Our results reveal immunoregulatory and matrix-remodeling CAF subtypes that may derive from pro-inflammatory and mesenchymal fibroblasts, respectively. These CAF subtypes are largely absent in AK and interact with different cell types to establish a pro-tumorigenic microenvironment. These findings are cSCC-specific and could not be recapitulated in basal cell carcinomas. Our study provides important insights into the potential origin and functionalities of dermal CAFs that will be highly beneficial for the specific targeting of the cSCC microenvironment.
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Affiliation(s)
- Sabrina Schütz
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120, Heidelberg, Germany
| | - Llorenç Solé-Boldo
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120, Heidelberg, Germany
| | - Carlota Lucena-Porcel
- Institute of Pathology, Ruprecht-Karls University of Heidelberg, 69120, Heidelberg, Germany
- Tissue Bank of the National Center for Tumor Diseases (NCT), 69120, Heidelberg, Germany
| | - Jochen Hoffmann
- Department of Dermatology, University Hospital, Ruprecht-Karls University of Heidelberg, 69120, Heidelberg, Germany
| | - Alexander Brobeil
- Institute of Pathology, Ruprecht-Karls University of Heidelberg, 69120, Heidelberg, Germany
- Tissue Bank of the National Center for Tumor Diseases (NCT), 69120, Heidelberg, Germany
| | - Anke S Lonsdorf
- Department of Dermatology, University Hospital, Ruprecht-Karls University of Heidelberg, 69120, Heidelberg, Germany
| | - Manuel Rodríguez-Paredes
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120, Heidelberg, Germany.
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120, Heidelberg, Germany.
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9
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Shahraki K, Shahraki K, Ghasemi Boroumand P, Sheervalilou R. Promotor methylation in ocular surface squamous neoplasia development: epigenetics implications in molecular diagnosis. Expert Rev Mol Diagn 2023; 23:753-769. [PMID: 37493058 DOI: 10.1080/14737159.2023.2240238] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 07/20/2023] [Indexed: 07/27/2023]
Abstract
INTRODUCTION Cancer is heavily influenced by epigenetic mechanisms that include DNA methylation, histone modifications, and non-coding RNA. A considerable proportion of human malignancies are believed to be associated with global DNA hypomethylation, with localized hypermethylation at promoters of certain genes. AREA COVERED The present review aims to emphasize on recent investigations on the epigenetic landscape of ocular surface squamous neoplasia, that could be targeted/explored using novel approaches such as personalized medicine. EXPERT OPINION While the former is thought to contribute to genomic instability, promoter-specific hypermethylation might facilitate tumorigenesis by silencing tumor suppressor genes. Ocular surface squamous neoplasia, the most prevalent type of ocular surface malignancy, is suggested to be affected by epigenetic mechanisms, as well. Although the exact role of epigenetics in ocular surface squamous neoplasia has mostly been unexplored, recent findings have greatly contributed to our understanding regarding this pathology of the eye.
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Affiliation(s)
- Kourosh Shahraki
- Ocular Tissue Engineering Research Center, Ophthalmic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Ophthalmology, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Kianoush Shahraki
- Department of Ophthalmology, Zahedan University of Medical Sciences, Zahedan, Iran
- Cornea Department, Farabi Eye Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Paria Ghasemi Boroumand
- ENT, Head and Neck Research Center and Department, Iran University of Medical Science, Tehran, Iran
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10
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Winge MCG, Kellman LN, Guo K, Tang JY, Swetter SM, Aasi SZ, Sarin KY, Chang ALS, Khavari PA. Advances in cutaneous squamous cell carcinoma. Nat Rev Cancer 2023:10.1038/s41568-023-00583-5. [PMID: 37286893 DOI: 10.1038/s41568-023-00583-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/06/2023] [Indexed: 06/09/2023]
Abstract
Human malignancies arise predominantly in tissues of epithelial origin, where the stepwise transformation from healthy epithelium to premalignant dysplasia to invasive neoplasia involves sequential dysregulation of biological networks that govern essential functions of epithelial homeostasis. Cutaneous squamous cell carcinoma (cSCC) is a prototype epithelial malignancy, often with a high tumour mutational burden. A plethora of risk genes, dominated by UV-induced sun damage, drive disease progression in conjunction with stromal interactions and local immunomodulation, enabling continuous tumour growth. Recent studies have identified subpopulations of SCC cells that specifically interact with the tumour microenvironment. These advances, along with increased knowledge of the impact of germline genetics and somatic mutations on cSCC development, have led to a greater appreciation of the complexity of skin cancer pathogenesis and have enabled progress in neoadjuvant immunotherapy, which has improved pathological complete response rates. Although measures for the prevention and therapeutic management of cSCC are associated with clinical benefit, the prognosis remains poor for advanced disease. Elucidating how the genetic mechanisms that drive cSCC interact with the tumour microenvironment is a current focus in efforts to understand, prevent and treat cSCC.
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Affiliation(s)
- Mårten C G Winge
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA
- Department of Dermatology, Stanford University, Redwood City, CA, USA
| | - Laura N Kellman
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Stanford Program in Cancer Biology, Stanford University, Stanford, CA, USA
| | - Konnie Guo
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA
| | - Jean Y Tang
- Department of Dermatology, Stanford University, Redwood City, CA, USA
| | - Susan M Swetter
- Department of Dermatology, Stanford University, Redwood City, CA, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA
| | - Sumaira Z Aasi
- Department of Dermatology, Stanford University, Redwood City, CA, USA
| | - Kavita Y Sarin
- Department of Dermatology, Stanford University, Redwood City, CA, USA
| | - Anne Lynn S Chang
- Department of Dermatology, Stanford University, Redwood City, CA, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA.
- Department of Dermatology, Stanford University, Redwood City, CA, USA.
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
- Stanford Program in Cancer Biology, Stanford University, Stanford, CA, USA.
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA.
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11
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Schäfer M, Schneider M, Müller T, Franz N, Braspenning-Wesch I, Stephan S, Schmidt G, Krijgsveld J, Helm D, Rösl F, Hasche D. Spatial tissue proteomics reveals distinct landscapes of heterogeneity in cutaneous papillomavirus-induced keratinocyte carcinomas. J Med Virol 2023; 95:e28850. [PMID: 37322807 DOI: 10.1002/jmv.28850] [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: 03/20/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/17/2023]
Abstract
Infection with certain cutaneous human papillomaviruses (HPV), in conjunction with chronic ultraviolet (UV) exposure, are the major cofactors of non-melanoma skin cancer (NMSC), the most frequent cancer type worldwide. Cutaneous squamous cell carcinomas (SCCs) as well as tumors in general represent three-dimensional entities determined by both temporal and spatial constraints. Whole tissue proteomics is a straightforward approach to understand tumorigenesis in better detail, but studies focusing on different progression states toward a dedifferentiated SCC phenotype on a spatial level are rare. Here, we applied an innovative proteomic workflow on formalin-fixed, paraffin-embedded (FFPE) epithelial tumors derived from the preclinical animal model Mastomys coucha. This rodent is naturally infected with its genuine cutaneous papillomavirus and closely mimics skin carcinogenesis in the context of cutaneous HPV infections in humans. We deciphered cellular networks by comparing diverse epithelial tissues with respect to their differentiation level and infection status. Our study reveals novel regulatory proteins and pathways associated with virus-induced tumor initiation and progression of SCCs. This approach provides the basis to better comprehend the multistep process of skin carcinogenesis.
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Affiliation(s)
- Miriam Schäfer
- Division of Viral Transformation Mechanisms, Research Program "Infection, Inflammation and Cancer", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Schneider
- Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Torsten Müller
- Division Proteomics of Stem Cells and Cancer, Research Program "Functional and Structural Genomics", German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Natascha Franz
- Division of Viral Transformation Mechanisms, Research Program "Infection, Inflammation and Cancer", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ilona Braspenning-Wesch
- Division of Viral Transformation Mechanisms, Research Program "Infection, Inflammation and Cancer", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sonja Stephan
- Division of Viral Transformation Mechanisms, Research Program "Infection, Inflammation and Cancer", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Gabriele Schmidt
- Core Facility Unit Light Microscopy, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jeroen Krijgsveld
- Division Proteomics of Stem Cells and Cancer, Research Program "Functional and Structural Genomics", German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Dominic Helm
- Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frank Rösl
- Division of Viral Transformation Mechanisms, Research Program "Infection, Inflammation and Cancer", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Hasche
- Division of Viral Transformation Mechanisms, Research Program "Infection, Inflammation and Cancer", German Cancer Research Center (DKFZ), Heidelberg, Germany
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12
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Grunt TW, Heller G. A critical appraisal of the relative contribution of tissue architecture, genetics, epigenetics and cell metabolism to carcinogenesis. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023:S0079-6107(23)00056-1. [PMID: 37268024 DOI: 10.1016/j.pbiomolbio.2023.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 05/22/2023] [Indexed: 06/04/2023]
Abstract
Here we contrast several carcinogenesis models. The somatic-mutation-theory posits mutations as main causes of malignancy. However, inconsistencies led to alternative explanations. For example, the tissue-organization-field-theory considers disrupted tissue-architecture as main cause. Both models can be reconciled using systems-biology-approaches, according to which tumors hover in states of self-organized criticality between order and chaos, are emergent results of multiple deviations and are subject to general laws of nature: inevitable variation(mutation) explainable by increased entropy(second-law-of-thermodynamics) or indeterminate decoherence upon measurement of superposed quantum systems(quantum mechanics), followed by Darwinian-selection. Genomic expression is regulated by epigenetics. Both systems cooperate. So cancer is neither just a mutational nor an epigenetic problem. Rather, epigenetics links environmental cues to endogenous genetics engendering a regulatory machinery that encompasses specific cancer-metabolic-networks. Interestingly, mutations occur at all levels of this machinery (oncogenes/tumor-suppressors, epigenetic-modifiers, structure-genes, metabolic-genes). Therefore, in most cases, DNA mutations may be the initial and crucial cancer-promoting triggers.
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Affiliation(s)
- Thomas W Grunt
- Cell Signaling and Metabolism Networks Program, Division of Oncology, Department of Medicine I, Medical University of Vienna, 1090, Vienna, Austria; Comprehensive Cancer Center, 1090, Vienna, Austria; Ludwig Boltzmann Institute for Hematology and Oncology, 1090, Vienna, Austria.
| | - Gerwin Heller
- Comprehensive Cancer Center, 1090, Vienna, Austria; Division of Oncology, Department of Medicine I, Medical University of Vienna, 1090, Vienna, Austria
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13
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Solé-Boldo L, Raddatz G, Gutekunst J, Gilliam O, Bormann F, Liberio MS, Hasche D, Antonopoulos W, Mallm JP, Lonsdorf AS, Rodríguez-Paredes M, Lyko F. Differentiation-related epigenomic changes define clinically distinct keratinocyte cancer subclasses. Mol Syst Biol 2022; 18:e11073. [PMID: 36121124 PMCID: PMC9484266 DOI: 10.15252/msb.202211073] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/17/2022] [Accepted: 08/30/2022] [Indexed: 11/09/2022] Open
Abstract
Keratinocyte cancers (KC) are the most prevalent malignancies in fair-skinned populations, posing a significant medical and economic burden to health systems. KC originate in the epidermis and mainly comprise basal cell carcinoma (BCC) and cutaneous squamous cell carcinoma (cSCC). Here, we combined single-cell multi-omics, transcriptomics, and methylomics to investigate the epigenomic dynamics during epidermal differentiation. We identified ~3,800 differentially accessible regions between undifferentiated and differentiated keratinocytes, corresponding to regulatory regions associated with key transcription factors. DNA methylation at these regions defined AK/cSCC subtypes with epidermal stem cell- or keratinocyte-like features. Using cell-type deconvolution tools and integration of bulk and single-cell methylomes, we demonstrate that these subclasses are consistent with distinct cells-of-origin. Further characterization of the phenotypic traits of the subclasses and the study of additional unstratified KC entities uncovered distinct clinical features for the subclasses, linking invasive and metastatic KC cases with undifferentiated cells-of-origin. Our study provides a thorough characterization of the epigenomic dynamics underlying human keratinocyte differentiation and uncovers novel links between KC cells-of-origin and their prognosis.
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Affiliation(s)
- Llorenç Solé-Boldo
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Günter Raddatz
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Julian Gutekunst
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Oliver Gilliam
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Felix Bormann
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Michelle S Liberio
- Single-cell Open Lab, German Cancer Research Center and Bioquant, Heidelberg, Germany
| | - Daniel Hasche
- Division of Viral Transformation Mechanisms, German Cancer Research Center, Heidelberg, Germany
| | - Wiebke Antonopoulos
- Tissue Bank of the National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jan-Philipp Mallm
- Single-cell Open Lab, German Cancer Research Center and Bioquant, Heidelberg, Germany.,Division of Chromatin Networks, German Cancer Research Center and Bioquant, Heidelberg, Germany
| | - Anke S Lonsdorf
- Department of Dermatology, University Hospital, Ruprecht-Karls University of Heidelberg, Heidelberg, Germany
| | - Manuel Rodríguez-Paredes
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany.,Institute of Toxicology, University Medical Center Mainz, Johannes Gutenberg University, Mainz, Germany
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
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14
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Svoboda LK, Perera BPU, Morgan RK, Polemi KM, Pan J, Dolinoy DC. Toxicoepigenetics and Environmental Health: Challenges and Opportunities. Chem Res Toxicol 2022; 35:1293-1311. [PMID: 35876266 PMCID: PMC9812000 DOI: 10.1021/acs.chemrestox.1c00445] [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] [Indexed: 01/07/2023]
Abstract
The rapidly growing field of toxicoepigenetics seeks to understand how toxicant exposures interact with the epigenome to influence disease risk. Toxicoepigenetics is a promising field of environmental health research, as integrating epigenetics into the field of toxicology will enable a more thorough evaluation of toxicant-induced disease mechanisms as well as the elucidation of the role of the epigenome as a biomarker of exposure and disease and possible mediator of exposure effects. Likewise, toxicoepigenetics will enhance our knowledge of how environmental exposures, lifestyle factors, and diet interact to influence health. Ultimately, an understanding of how the environment impacts the epigenome to cause disease may inform risk assessment, permit noninvasive biomonitoring, and provide potential opportunities for therapeutic intervention. However, the translation of research from this exciting field into benefits for human and animal health presents several challenges and opportunities. Here, we describe four significant areas in which we see opportunity to transform the field and improve human health by reducing the disease burden caused by environmental exposures. These include (1) research into the mechanistic role for epigenetic change in environment-induced disease, (2) understanding key factors influencing vulnerability to the adverse effects of environmental exposures, (3) identifying appropriate biomarkers of environmental exposures and their associated diseases, and (4) determining whether the adverse effects of environment on the epigenome and human health are reversible through pharmacologic, dietary, or behavioral interventions. We then highlight several initiatives currently underway to address these challenges.
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Affiliation(s)
- Laurie K Svoboda
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bambarendage P U Perera
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Rachel K Morgan
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Katelyn M Polemi
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Junru Pan
- Department Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
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15
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Capell BC. Loss of TET2 Tips the Scales Toward Tumorigenesis. J Invest Dermatol 2022; 142:1253-1255. [PMID: 35109986 PMCID: PMC9128576 DOI: 10.1016/j.jid.2021.11.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 12/25/2022]
Abstract
DNA methylation and demethylation function in the balance between cellular differentiation and cancer. Although the roles of DNA methyltransferases have been extensively explored in epidermal biology, ten-eleven translocation (TET) demethylase enzymes are poorly understood. In their new article in the Journal of Investigative Dermatology, Boudra et al. present evidence for a tumor-suppressive role of TET2 and its regulation of 5-hydroxymethylcytosine in the prevention of squamous cell carcinomas.
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Affiliation(s)
- Brian C Capell
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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16
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Koelsche C, von Deimling A. Methylation classifiers: brain tumors, sarcomas and what's next. Genes Chromosomes Cancer 2022; 61:346-355. [PMID: 35388566 DOI: 10.1002/gcc.23041] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/16/2022] [Accepted: 03/18/2022] [Indexed: 11/09/2022] Open
Abstract
Tumor classification has evolved over the last decades with technical progress contributing much to our current concepts. Among diagnostic hallmark novelties were immunostaining, Fluorescence in situ hybridization, Sanger sequencing followed by massive parallel DNA sequencing and recently, epigenetic analyses have entered the stage. Although each of these techniques was revolutionary and, in some way, also disruptive in certain diagnostic fields, it took years to decades for broad implementation into standard pathological-diagnostic algorithms. In contrast, DNA methylation profiling has been accepted in short time as a game changer with lasting impact on brain tumor classification and with potential for classification of other tumor types. This review provides a brief introduction in DNA methylation-based tumor classification. We present why DNA methylation signatures are attractive diagnostic biomarkers, discuss present achievements and future aims and explain the integration of methylation-based classifiers in diagnostic procedure. Finally, we provide an outlook on the challenges and opportunities associated with DNA methylation-based tumor profiling. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Christian Koelsche
- Department of General Pathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
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17
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Harms PW, Verhaegen ME, Vo JN, Tien JC, Pratt D, Su F, Dhanasekaran SM, Cao X, Mangelberger D, VanGoor J, Choi JE, Ma VT, Dlugosz AA, Chinnaiyan AM. Viral Status Predicts the Patterns of Genome Methylation and Decitabine Response in Merkel Cell Carcinoma. J Invest Dermatol 2022; 142:641-652. [PMID: 34474081 PMCID: PMC8860850 DOI: 10.1016/j.jid.2021.07.173] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 06/22/2021] [Accepted: 07/12/2021] [Indexed: 12/13/2022]
Abstract
Merkel cell carcinoma (MCC) is an aggressive cutaneous neuroendocrine carcinoma that is classified as Merkel cell polyomavirus-positive (virus positive [VP]) or Merkel cell polyomavirus-negative (virus negative [VN]). Epigenetic changes, such as DNA methylation, can alter gene expression and influence cancer progression. However, patterns of DNA methylation and the therapeutic efficacy of hypomethylating agents have not been fully explored in MCC. We characterized genome-wide DNA methylation in 16 MCC cell lines from both molecular subclasses in comparison with other cancer types and found that the overall profile of MCC is similar to that of small-cell lung carcinoma. Comparison of VP MCC with VN MCC revealed 2,260 differentially methylated positions. The hypomethylating agent decitabine upregulated the expression of antigen-presenting machinery in MCC cell lines and stimulated membrane expression of HLA-A in VP and VN MCC xenograft tumors. Decitabine also induced prominent caspase- and large T antigen‒independent cell death in VP MCC, whereas VN MCC cell lines displayed decreased proliferation without increased cell death. In mouse xenografts, decitabine significantly decreased the size of VP tumors but not that of VN tumors. Our findings indicate that viral status predicts genomic methylation patterns in MCC and that decitabine may be therapeutically effective against MCC through antiproliferative effects, cell death, and increased immune recognition.
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Affiliation(s)
- Paul W. Harms
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA,Department of Dermatology, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | - Josh N. Vo
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jean C. Tien
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Drew Pratt
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Fengyun Su
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Saravana M. Dhanasekaran
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Xuhong Cao
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Doris Mangelberger
- Department of Dermatology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Julia VanGoor
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jae Eun Choi
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Vincent T. Ma
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Andrzej A. Dlugosz
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA,Department of Dermatology, University of Michigan, Ann Arbor, MI, 48109, USA,Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Arul M. Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, 48109, USA,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, 48109, USA,Department of Urology, University of Michigan, Ann Arbor, MI, 48109, USA,Corresponding Author: Arul M. Chinnaiyan, M.D., Ph.D., Investigator, Howard Hughes Medical Institute, American Cancer Society Professor, S. P. Hicks Endowed Professor of Pathology, Rogel Cancer Center, University of Michigan Medical School, 1400 E. Medical Center Dr. 5316 CCGC, Ann Arbor, MI 48109-0602,
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18
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Wang Q, Zhang Y, Zhang B, Fu Y, Zhao X, Zhang J, Zuo K, Xing Y, Jiang S, Qin Z, Li E, Guo H, Liu Z, Yang J. Single-cell chromatin accessibility landscape in kidney identifies additional cell-of-origin in heterogenous papillary renal cell carcinoma. Nat Commun 2022; 13:31. [PMID: 35013217 PMCID: PMC8748507 DOI: 10.1038/s41467-021-27660-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 12/02/2021] [Indexed: 01/14/2023] Open
Abstract
Papillary renal cell carcinoma (pRCC) is the most heterogenous renal cell carcinoma. Patient survival varies and no effective therapies for advanced pRCC exist. Histological and molecular characterization studies have highlighted the heterogeneity of pRCC tumours. Recent studies identified the proximal tubule (PT) cell as a cell-of-origin for pRCC. However, it remains elusive whether other pRCC subtypes have different cell-of-origin. Here, by obtaining genome-wide chromatin accessibility profiles of normal human kidney cells using single-cell transposase-accessible chromatin-sequencing and comparing the profiles with pRCC samples, we discover that besides PT cells, pRCC can also originate from kidney collecting duct principal cells. We show pRCCs with different cell-of-origin exhibit different molecular characteristics and clinical behaviors. Further, metabolic reprogramming appears to mediate the progression of pRCC to the advanced state. Here, our results suggest that determining cell-of-origin and monitoring origin-dependent metabolism could potentially be useful for early diagnosis and treatment of pRCC.
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Affiliation(s)
- Qi Wang
- Medical School of Nanjing University, Nanjing, Jiangsu, 210093, China
| | - Yang Zhang
- Medical School of Nanjing University, Nanjing, Jiangsu, 210093, China
- National Clinical Research Center for Kidney Disease, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, 210002, China
| | - Bolei Zhang
- School of Computer Science, Nanjing University of Posts and Telecommunications, Nanjing, Jiangsu, 210023, China
| | - Yao Fu
- Department of Pathology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, 210008, China
| | - Xiaozhi Zhao
- Department of Urology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, 210008, China
| | - Jing Zhang
- Medical School of Nanjing University, Nanjing, Jiangsu, 210093, China
| | - Ke Zuo
- National Clinical Research Center for Kidney Disease, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, 210002, China
| | - Yuexian Xing
- National Clinical Research Center for Kidney Disease, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, 210002, China
| | - Song Jiang
- National Clinical Research Center for Kidney Disease, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, 210002, China
| | - Zhaohui Qin
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | - Erguang Li
- Medical School of Nanjing University, Nanjing, Jiangsu, 210093, China
| | - Hongqian Guo
- Department of Urology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, 210008, China.
| | - Zhihong Liu
- Medical School of Nanjing University, Nanjing, Jiangsu, 210093, China.
- National Clinical Research Center for Kidney Disease, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, 210002, China.
| | - Jingping Yang
- Medical School of Nanjing University, Nanjing, Jiangsu, 210093, China.
- National Clinical Research Center for Kidney Disease, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, 210002, China.
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, 210093, China.
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19
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Gravemeyer J, Spassova I, Verhaegen ME, Dlugosz AA, Hoffmann D, Lange A, Becker JC. DNA-methylation patterns imply a common cellular origin of virus- and UV-associated Merkel cell carcinoma. Oncogene 2022; 41:37-45. [PMID: 34667274 PMCID: PMC8724008 DOI: 10.1038/s41388-021-02064-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/22/2021] [Accepted: 10/04/2021] [Indexed: 02/07/2023]
Abstract
Merkel cell carcinoma (MCC) is a neuroendocrine tumor either induced by integration of the Merkel cell polyomavirus into the cell genome or by accumulation of UV-light-associated mutations (VP-MCC and UV-MCC). Whether VP- and UV-MCC have the same or different cellular origins is unclear; with mesenchymal or epidermal origins discussed. DNA-methylation patterns have a proven utility in determining cellular origins of cancers. Therefore, we used this approach to uncover evidence regarding the cell of origin of classical VP- and UV-MCC cell lines, i.e., cell lines with a neuroendocrine growth pattern (n = 9 and n = 4, respectively). Surprisingly, we observed high global similarities in the DNA-methylation of UV- and VP-MCC cell lines. CpGs of lower methylation in VP-MCC cell lines were associated with neuroendocrine marker genes such as SOX2 and INSM1, or linked to binding sites of EZH2 and SUZ12 of the polycomb repressive complex 2, i.e., genes with an impact on carcinogenesis and differentiation of neuroendocrine cancers. Thus, the observed differences appear to be rooted in viral compared to mutation-driven carcinogenesis rather than distinct cells of origin. To test this hypothesis, we used principal component analysis, to compare DNA-methylation data from different epithelial and non-epithelial neuroendocrine cancers and established a scoring model for epithelial and neuroendocrine characteristics. Subsequently, we applied this scoring model to the DNA-methylation data of the VP- and UV-MCC cell lines, revealing that both clearly scored as epithelial cancers. In summary, our comprehensive analysis of DNA-methylation suggests a common epithelial origin of UV- and VP-MCC cell lines.
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Affiliation(s)
- Jan Gravemeyer
- Translational Skin Cancer Research (TSCR), University Duisburg-Essen, Essen, Germany
- German Cancer Consortium (DKTK) & German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ivelina Spassova
- Translational Skin Cancer Research (TSCR), University Duisburg-Essen, Essen, Germany
- Department of Dermatology, University Hospital Essen, Essen, Germany
| | | | - Andrzej A Dlugosz
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Daniel Hoffmann
- Bioinformatics & Computational Biophysics, University Duisburg-Essen, Essen, Germany
| | - Anja Lange
- Bioinformatics & Computational Biophysics, University Duisburg-Essen, Essen, Germany
| | - Jürgen C Becker
- Translational Skin Cancer Research (TSCR), University Duisburg-Essen, Essen, Germany.
- German Cancer Consortium (DKTK) & German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Department of Dermatology, University Hospital Essen, Essen, Germany.
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20
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Varney SD, Wu L, Longmate WM, DiPersio CM, Van De Water L. Loss of integrin α9β1 on tumor keratinocytes enhances the stromal vasculature and growth of cutaneous tumors. J Invest Dermatol 2021; 142:1966-1975.e8. [PMID: 34843681 DOI: 10.1016/j.jid.2021.11.020] [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: 07/08/2021] [Revised: 11/02/2021] [Accepted: 11/12/2021] [Indexed: 10/19/2022]
Abstract
Angiogenesis is critical to tumor progression and the function of integrins in tumor angiogenesis is complex. Here we report that loss of integrin α9β1 expression from epidermal tumor cells is critical to maintain persistent stromal vessel density. Forced expression of α9 in transformed mouse keratinocytes dramatically reduces vessel density in allograft tumors, in vivo, compared to the same cells lacking α9β1. Moreover, α9 mRNA expression is dramatically reduced in mouse and human epidermal tumors as is α9β1-dependent gene regulation. Loss of tumor cell α9β1 occurs through at least two mechanisms: (1) ITGA9 gene copy number loss in human tumors, and (2) epigenetic silencing in mouse and human tumors. Importantly, we show that reversal of epigenetic silencing of Itga9 restores α9 expression in mouse keratinocytes, and that human tumors without ITGA9 copy number loss have increased promoter methylation. Our data suggest that for epidermal tumorigenesis to occur, tumor cells must avoid the tumor and angiogenic suppressive effects of α9β1 by repressing its expression through deletion and/or epigenetic silencing, thereby promoting stromal development and tumor growth.
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Affiliation(s)
| | | | | | | | - Livingston Van De Water
- Department of Surgery; Department of Regenerative & Cancer Cell Biology, Albany Medical College, Albany, NY 12208, USA
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21
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Tschirley AM, Stockwell PA, Rodger EJ, Eltherington O, Morison IM, Christensen N, Chatterjee A, Hibma M. The Mouse Papillomavirus Epigenetic Signature Is Characterised by DNA Hypermethylation after Lesion Regression. Viruses 2021; 13:v13102045. [PMID: 34696474 PMCID: PMC8539022 DOI: 10.3390/v13102045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/07/2021] [Indexed: 12/17/2022] Open
Abstract
Papillomaviruses (PVs) are double-stranded DNA tumour viruses that can infect cutaneous and mucosal epidermis. Human papillomavirus (HPV) types have been linked to the causality of cutaneous squamous cell carcinoma (cSCC); however, HPV DNA is not always detected in the resultant tumour. DNA methylation is an epigenetic change that can contribute to carcinogenesis. We hypothesise that the DNA methylation pattern in cells is altered following PV infection. We tested if DNA methylation was altered by PV infection in the mouse papillomavirus (MmuPV1) model. Immunosuppressed mice were infected with MmuPV1 on cutaneous tail skin. Immunosuppression was withdrawn for some mice, causing lesions to spontaneously regress. Reduced representation bisulphite sequencing was carried out on DNA from the actively infected lesions, visibly regressed lesions, and mock-infected control mice. DNA methylation libraries were generated and analysed for differentially methylated regions throughout the genome. The presence of MmuPV1 sequences was also assessed. We identified 834 predominantly differentially hypermethylated fragments in regressed lesions, and no methylation differences in actively infected lesions. The promoter regions of genes associated with tumorigenicity, including the tumour suppressor protein DAPK1 and mismatch repair proteins MSH6 and PAPD7, were hypermethylated. Viral DNA was detected in active lesions and in some lesions that had regressed. This is the first description of the genome-wide DNA methylation landscape for active and regressed MmuPV1 lesions. We propose that the DNA hypermethylation in the regressed lesions that we report here may increase the susceptibility of cells to ultraviolet-induced cSCC.
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Affiliation(s)
- Allison M. Tschirley
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand; (A.M.T.); (P.A.S.); (E.J.R.); (O.E.); (I.M.M.); (A.C.)
| | - Peter A. Stockwell
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand; (A.M.T.); (P.A.S.); (E.J.R.); (O.E.); (I.M.M.); (A.C.)
| | - Euan J. Rodger
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand; (A.M.T.); (P.A.S.); (E.J.R.); (O.E.); (I.M.M.); (A.C.)
| | - Oliver Eltherington
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand; (A.M.T.); (P.A.S.); (E.J.R.); (O.E.); (I.M.M.); (A.C.)
| | - Ian M. Morison
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand; (A.M.T.); (P.A.S.); (E.J.R.); (O.E.); (I.M.M.); (A.C.)
| | - Neil Christensen
- Department of Pathology, Pennsylvania State University, State College, PA 16802, USA;
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand; (A.M.T.); (P.A.S.); (E.J.R.); (O.E.); (I.M.M.); (A.C.)
| | - Merilyn Hibma
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand; (A.M.T.); (P.A.S.); (E.J.R.); (O.E.); (I.M.M.); (A.C.)
- Correspondence: ; Tel.: +64-3479-7726
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22
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Droll S, Bao X. Oh, the Mutations You'll Acquire! A Systematic Overview of Cutaneous Squamous Cell Carcinoma. Cell Physiol Biochem 2021; 55:89-119. [PMID: 34553848 PMCID: PMC8579759 DOI: 10.33594/000000433] [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] [Accepted: 09/05/2021] [Indexed: 12/15/2022] Open
Abstract
Nearly two million cases of cutaneous squamous cell carcinoma (cSCC) are diagnosed every year in the United States alone. cSCC is notable for both its prevalence and its propensity for invasion and metastasis. For many patients, surgery is curative. However, patients experiencing immunosuppression or recurrent, advanced, and metastatic disease still face limited therapeutic options and significant mortality. cSCC forms after decades of sun exposure and possesses the highest known mutation rate of all cancers. This mutational burden complicates efforts to identify the primary factors driving cSCC initiation and progression, which in turn hinders the development of targeted therapeutics. In this review, we summarize the mutations and alterations that have been observed in patients’ cSCC tumors, affecting signaling pathways, transcriptional regulators, and the microenvironment. We also highlight novel therapeutic opportunities in development and clinical trials.
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Affiliation(s)
- Stephenie Droll
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Xiaomin Bao
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA, .,Department of Dermatology, Northwestern University, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
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23
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Piipponen M, Riihilä P, Nissinen L, Kähäri VM. The Role of p53 in Progression of Cutaneous Squamous Cell Carcinoma. Cancers (Basel) 2021; 13:cancers13184507. [PMID: 34572732 PMCID: PMC8466956 DOI: 10.3390/cancers13184507] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 08/30/2021] [Accepted: 09/02/2021] [Indexed: 12/12/2022] Open
Abstract
Skin cancers are the most common types of cancer worldwide, and their incidence is increasing. Melanoma, basal cell carcinoma (BCC), and cutaneous squamous cell carcinoma (cSCC) are the three major types of skin cancer. Melanoma originates from melanocytes, whereas BCC and cSCC originate from epidermal keratinocytes and are therefore called keratinocyte carcinomas. Chronic exposure to ultraviolet radiation (UVR) is a common risk factor for skin cancers, but they differ with respect to oncogenic mutational profiles and alterations in cellular signaling pathways. cSCC is the most common metastatic skin cancer, and it is associated with poor prognosis in the advanced stage. An important early event in cSCC development is mutation of the TP53 gene and inactivation of the tumor suppressor function of the tumor protein 53 gene (TP53) in epidermal keratinocytes, which then leads to accumulation of additional oncogenic mutations. Additional genomic and proteomic alterations are required for the progression of premalignant lesion, actinic keratosis, to invasive and metastatic cSCC. Recently, the role of p53 in the invasion of cSCC has also been elucidated. In this review, the role of p53 in the progression of cSCC and as potential new therapeutic target for cSCC will be discussed.
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Affiliation(s)
- Minna Piipponen
- Department of Dermatology, University of Turku and Turku University Hospital, Hämeentie 11 TE6, FI-20520 Turku, Finland; (M.P.); (P.R.); (L.N.)
- FICAN West Cancer Centre Research Laboratory, University of Turku and Turku University Hospital, Kiinamyllynkatu 10, FI-20520 Turku, Finland
- Center for Molecular Medicine, Department of Medicine Solna, Dermatology and Venereology Division, Karolinska Institute, 17176 Stockholm, Sweden
| | - Pilvi Riihilä
- Department of Dermatology, University of Turku and Turku University Hospital, Hämeentie 11 TE6, FI-20520 Turku, Finland; (M.P.); (P.R.); (L.N.)
- FICAN West Cancer Centre Research Laboratory, University of Turku and Turku University Hospital, Kiinamyllynkatu 10, FI-20520 Turku, Finland
| | - Liisa Nissinen
- Department of Dermatology, University of Turku and Turku University Hospital, Hämeentie 11 TE6, FI-20520 Turku, Finland; (M.P.); (P.R.); (L.N.)
- FICAN West Cancer Centre Research Laboratory, University of Turku and Turku University Hospital, Kiinamyllynkatu 10, FI-20520 Turku, Finland
| | - Veli-Matti Kähäri
- Department of Dermatology, University of Turku and Turku University Hospital, Hämeentie 11 TE6, FI-20520 Turku, Finland; (M.P.); (P.R.); (L.N.)
- FICAN West Cancer Centre Research Laboratory, University of Turku and Turku University Hospital, Kiinamyllynkatu 10, FI-20520 Turku, Finland
- Correspondence: ; Tel.: +358-2-3131600
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24
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Meyer T, Sand M, Schmitz L, Stockfleth E. The Role of Circular RNAs in Keratinocyte Carcinomas. Cancers (Basel) 2021; 13:cancers13164240. [PMID: 34439394 PMCID: PMC8392367 DOI: 10.3390/cancers13164240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/18/2021] [Accepted: 08/18/2021] [Indexed: 12/19/2022] Open
Abstract
Keratinocyte carcinomas (KC) include basal cell carcinomas (BCC) and cutaneous squamous cell carcinomas (cSCC) and represents the most common cancer in Europe and North America. Both entities are characterized by a very high mutational burden, mainly UV signature mutations. Predominately mutated genes in BCC belong to the sonic hedgehog pathway, whereas, in cSCC, TP53, CDKN2A, NOTCH1/2 and others are most frequently mutated. In addition, the dysregulation of factors associated with epithelial to mesenchymal transition (EMT) was shown in invasive cSCC. The expression of factors associated with tumorigenesis can be controlled in several ways and include non-coding RNA molecules, such as micro RNAs (miRNA) long noncoding RNAs (lncRNA) and circular RNAs (circRNA). To update findings on circRNA in KC, we reviewed 13 papers published since 2016, identified in a PubMed search. In both BCC and cSCC, numerous circRNAs were identified that were differently expressed compared to healthy skin. Some of them were shown to target miRNAs that are also dysregulated in KC. Moreover, some studies confirmed the biological functions of individual circRNAs involved in cancer development. Thus, circRNAs may be used as biomarkers of disease and disease progression and represent potential targets of new therapeutic approaches for KC.
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Affiliation(s)
- Thomas Meyer
- Department of Dermatology St. Josef Hospital, Ruhr-University Bochum, Gudrunstr. 56, 44791 Bochum, Germany;
- Correspondence: ; Tel.: +49-234-5096014
| | - Michael Sand
- Department of Plastic and Reconstructive Surgery, St. Josef-Hospital, Heidbergweg 22–24, 45257 Essen, Germany;
| | - Lutz Schmitz
- Institute of Dermatopathology, MVZ Corius DermPath Bonn, GmbH, Trierer Strasse 70–72, 53115 Bonn, Germany;
| | - Eggert Stockfleth
- Department of Dermatology St. Josef Hospital, Ruhr-University Bochum, Gudrunstr. 56, 44791 Bochum, Germany;
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25
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Pacella G, Capell BC. Epigenetic and metabolic interplay in cutaneous squamous cell carcinoma. Exp Dermatol 2021; 30:1115-1125. [PMID: 33844325 PMCID: PMC8324523 DOI: 10.1111/exd.14354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/16/2021] [Accepted: 04/06/2021] [Indexed: 12/14/2022]
Abstract
With the ageing of the population and increased levels of recreational sun exposure and immunosuppression, cutaneous squamous cell carcinoma (cSCC), is both an enormous and expanding clinical and economic issue. Despite advances in therapy, up to 5000-8000 people are estimated to die every year from cSCC in the U.S., highlighting the need for both better prevention and treatments. Two emerging areas of scientific discovery that may offer new therapeutic approaches for cSCC are epigenetics and metabolism. Importantly, these disciplines display extensive crosstalk, with metabolic inputs contributing to the chromatin landscape, while the dynamic epigenome shapes transcriptional and cellular responses that feedback into cellular metabolism. Recent evidence suggests that indeed, epigenetic and metabolic dysregulation may be critical contributors to cSCC pathogenesis. Here, we synthesize the latest findings from these fast-moving fields, including how they may drive cSCC, yet also be harnessed for therapy.
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Affiliation(s)
- Gina Pacella
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Brian C. Capell
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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26
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Ko EK, Capell BC. Methyltransferases in the Pathogenesis of Keratinocyte Cancers. Cancers (Basel) 2021; 13:cancers13143402. [PMID: 34298617 PMCID: PMC8304454 DOI: 10.3390/cancers13143402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/02/2021] [Accepted: 07/04/2021] [Indexed: 12/13/2022] Open
Abstract
Recent evidence suggests that the disruption of gene expression by alterations in DNA, RNA, and histone methylation may be critical contributors to the pathogenesis of keratinocyte cancers (KCs), made up of basal cell carcinoma (BCC) and cutaneous squamous cell carcinoma (cSCC), which collectively outnumber all other human cancers combined. While it is clear that methylation modifiers are frequently dysregulated in KCs, the underlying molecular and mechanistic changes are only beginning to be understood. Intriguingly, it has recently emerged that there is extensive cross-talk amongst these distinct methylation processes. Here, we summarize and synthesize the latest findings in this space and highlight how these discoveries may uncover novel therapeutic approaches for these ubiquitous cancers.
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Affiliation(s)
- Eun Kyung Ko
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Brian C. Capell
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA;
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Correspondence:
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27
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Thomson J, Bewicke-Copley F, Anene CA, Gulati A, Nagano A, Purdie K, Inman GJ, Proby CM, Leigh IM, Harwood CA, Wang J. The Genomic Landscape of Actinic Keratosis. J Invest Dermatol 2021; 141:1664-1674.e7. [PMID: 33482222 PMCID: PMC8221374 DOI: 10.1016/j.jid.2020.12.024] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 12/10/2020] [Accepted: 12/15/2020] [Indexed: 01/12/2023]
Abstract
Actinic keratoses (AKs) are lesions of epidermal keratinocyte dysplasia and are precursors for invasive cutaneous squamous cell carcinoma (cSCC). Identifying the specific genomic alterations driving the progression from normal skin to skin with AK to skin with invasive cSCC is challenging because of the massive UVR-induced mutational burden characteristic at all stages of this progression. In this study, we report the largest AK whole-exome sequencing study to date and perform a mutational signature and candidate driver gene analysis on these lesions. We demonstrate in 37 AKs from both immunosuppressed and immunocompetent patients that there are significant similarities between AKs and cSCC in terms of mutational burden, copy number alterations, mutational signatures, and patterns of driver gene mutations. We identify 44 significantly mutated AK driver genes and confirm that these genes are similarly altered in cSCC. We identify azathioprine mutational signature in all AKs from patients exposed to the drug, providing further evidence for its role in keratinocyte carcinogenesis. cSCCs differ from AKs in having higher levels of intrasample heterogeneity. Alterations in signaling pathways also differ, with immune-related signaling and TGFβ signaling significantly more mutated in cSCC. Integrating our findings with independent gene expression datasets confirms that dysregulated TGFβ signaling may represent an important event in AK‒cSCC progression.
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Affiliation(s)
- Jason Thomson
- Centre for Cell Biology and Cutaneous Research, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom; Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom; Department of Dermatology, The Royal London Hospital, Barts Health NHS Trust, London, United Kingdom
| | - Findlay Bewicke-Copley
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Chinedu Anthony Anene
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Abha Gulati
- Centre for Cell Biology and Cutaneous Research, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom; Department of Dermatology, The Royal London Hospital, Barts Health NHS Trust, London, United Kingdom
| | - Ai Nagano
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Karin Purdie
- Centre for Cell Biology and Cutaneous Research, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Gareth J Inman
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom; Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Charlotte M Proby
- Division of Molecular and Clinical Medicine, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Irene M Leigh
- Centre for Cell Biology and Cutaneous Research, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Catherine A Harwood
- Centre for Cell Biology and Cutaneous Research, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom; Department of Dermatology, The Royal London Hospital, Barts Health NHS Trust, London, United Kingdom
| | - Jun Wang
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom.
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28
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Roth K, Coussement L, Knatko EV, Higgins M, Steyaert S, Proby CM, de Meyer T, Dinkova-Kostova AT. Clinically relevant aberrant Filip1l DNA methylation detected in a murine model of cutaneous squamous cell carcinoma. EBioMedicine 2021; 67:103383. [PMID: 34000624 PMCID: PMC8138604 DOI: 10.1016/j.ebiom.2021.103383] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Cutaneous squamous cell carcinomas (cSCC) are among the most common and highly mutated human malignancies. Understanding the impact of DNA methylation in cSCC may provide avenues for new therapeutic strategies. METHODS We used reduced-representation bisulfite sequencing for DNA methylation analysis of murine cSCC. Differential methylation was assessed at the CpG level using limma. Next, we compared with human cSCC Infinium HumanMethylation BeadArray data. Genes were considered to be of major relevance when they featured at least one significantly differentially methylated CpGs (RRBS) / probes (Infinium) with at least a 30% difference between tumour vs. control in both a murine gene and its human orthologue. The human EPIC Infinium data were used to distinguish two cSCC subtypes, stem-cell-like and keratinocyte-like tumours. FINDINGS We found increased average methylation in mouse cSCC (by 12.8%, p = 0.0011) as well as in stem-cell like (by 3.1%, p=0.002), but not keratinocyte-like (0.2%, p = 0.98), human cSCC. Comparison of differentially methylated genes revealed striking similarities between human and mouse cSCC. Locus specific methylation changes in mouse cSCC often occurred in regions of potential regulatory function, including enhancers and promoters. A key differentially methylated region was located in a potential enhancer of the tumour suppressor gene Filip1l and its expression was reduced in mouse tumours. Moreover, the FILIP1L locus showed hypermethylation in human cSCC and lower expression in human cSCC cell lines. INTERPRETATION Deregulation of DNA methylation is an important feature of murine and human cSCC that likely contributes to silencing of tumour suppressor genes, as shown for Filip1l. FUNDING British Skin Foundation, Cancer Research UK.
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Affiliation(s)
- Kevin Roth
- Jacqui Wood Cancer Centre, Division of Cellular Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, United Kingdom
| | - Louis Coussement
- Biobix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium; CRIG, Cancer Research Institute Ghent, Sint-Pietersnieuwstraat 25, 9000, Ghent, Belgium
| | - Elena V Knatko
- Jacqui Wood Cancer Centre, Division of Cellular Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, United Kingdom
| | - Maureen Higgins
- Jacqui Wood Cancer Centre, Division of Cellular Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, United Kingdom
| | - Sandra Steyaert
- Biobix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Charlotte M Proby
- Jacqui Wood Cancer Centre, Division of Cellular Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, United Kingdom
| | - Tim de Meyer
- Biobix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium; CRIG, Cancer Research Institute Ghent, Sint-Pietersnieuwstraat 25, 9000, Ghent, Belgium
| | - Albena T Dinkova-Kostova
- Jacqui Wood Cancer Centre, Division of Cellular Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, United Kingdom; Department of Pharmacology and Molecular Sciences and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA.
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Dnmt3a deficiency in the skin causes focal, canonical DNA hypomethylation and a cellular proliferation phenotype. Proc Natl Acad Sci U S A 2021; 118:2022760118. [PMID: 33846253 PMCID: PMC8072215 DOI: 10.1073/pnas.2022760118] [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: 12/30/2022] Open
Abstract
DNA hypomethylation is a feature of epidermal cells from aged and sun-exposed skin, but the mechanisms responsible for this methylation loss are not known. Dnmt3a is the dominant de novo DNA methyltransferase in the skin; while epidermal Dnmt3a deficiency creates a premalignant state in which keratinocytes are more easily transformed by topical mutagens, the conditions responsible for this increased susceptibility to transformation are not well understood. Using whole genome bisulfite sequencing, we identified a focal, canonical DNA hypomethylation phenotype in the epidermal cells of Dnmt3a-deficient mice. Single-cell transcriptomic analysis revealed an increased proportion of cells with a proliferative gene expression signature, while other populations in the skin were relatively unchanged. Although total DNMT3A deficiency has not been described in human disease states, rare patients with an overgrowth syndrome associated with behavioral abnormalities and an increased risk of cancer often have heterozygous, germline mutations in DNMT3A that reduce its function (Tatton-Brown Rahman syndrome [TBRS]). We evaluated the DNA methylation phenotype of the skin from a TBRS patient with a germline DNMT3A R882H mutation, which encodes a dominant-negative protein that reduces its methyltransferase function by ∼80%. We detected a focal, canonical hypomethylation phenotype that revealed considerable overlap with hypomethylated regions found in Dnmt3a-deficient mouse skin. Together, these data suggest that DNMT3A loss creates a premalignant epigenetic state associated with a hyperproliferative phenotype in the skin and further suggest that DNMT3A acts as a tumor suppressor in the skin.
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30
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Gravemeyer J, Lange A, Ritter C, Spassova I, Song L, Picard D, Remke M, Horny K, Sriram A, Gambichler T, Schadendorf D, Hoffmann D, Becker JC. Classical and Variant Merkel Cell Carcinoma Cell Lines Display Different Degrees of Neuroendocrine Differentiation and Epithelial-Mesenchymal Transition. J Invest Dermatol 2021; 141:1675-1686.e4. [PMID: 33600825 DOI: 10.1016/j.jid.2021.01.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 01/13/2021] [Accepted: 01/28/2021] [Indexed: 02/06/2023]
Abstract
Merkel cell carcinoma (MCC) is an aggressive neuroendocrine skin cancer characterized by high invasiveness, early metastases, and high mortality. Because of the lack of suitable animal models, most functional studies are performed using cell lines, some of which lack classical neuroendocrine growth characteristics. Here, we scrutinized the molecular characteristics of classical MCC and variant MCC cell lines by differential gene expression and the respective epigenetic regulation by microRNAs and DNA methylation. Cutaneous squamous cell carcinoma cell lines were used for comparison. The most striking observation was a lower expression of epithelial-mesenchymal transition-related genes in classical MCCs, which was accompanied by higher expression of the epithelial-mesenchymal transition-regulating microRNA clusters miR-200c-141 and miR-183-96-182 and hypomethylation of the respective microRNA loci. Experimental expression of the MCC lineage factor ATOH1 in variant MCCs resulted in an increased expression of miR-200c-141 paralleled by a reduction of genes associated with epithelial-mesenchymal transition, thus demonstrating a connection between neuroendocrine characteristics and the lack of epithelial-mesenchymal transition. Together, our observations not only reinforce concerns about the use of variant MCCs as proper MCC representatives, but also suggest variant MCCs as cells locked in an intermediate state between neuroendocrine and epithelial differentiation.
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Affiliation(s)
- Jan Gravemeyer
- Group of Translational Skin Cancer Research (TSCR), University Duisburg-Essen, Essen, Germany; German Cancer Consortium (DKTK) & German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anja Lange
- Bioinformatics and Computational Biophysics, University Duisburg-Essen, Essen, Germany
| | - Cathrin Ritter
- Group of Translational Skin Cancer Research (TSCR), University Duisburg-Essen, Essen, Germany; German Cancer Consortium (DKTK) & German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ivelina Spassova
- Group of Translational Skin Cancer Research (TSCR), University Duisburg-Essen, Essen, Germany
| | - Lina Song
- Group of Translational Skin Cancer Research (TSCR), University Duisburg-Essen, Essen, Germany
| | - Daniel Picard
- German Cancer Consortium (DKTK) & German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Clinical Immunology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Marc Remke
- German Cancer Consortium (DKTK) & German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Clinical Immunology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Kai Horny
- Group of Translational Skin Cancer Research (TSCR), University Duisburg-Essen, Essen, Germany; German Cancer Consortium (DKTK) & German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ashwin Sriram
- Group of Translational Skin Cancer Research (TSCR), University Duisburg-Essen, Essen, Germany; German Cancer Consortium (DKTK) & German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thilo Gambichler
- Skin Cancer Center, Department for Dermatology, Ruhr-University Bochum, Bochum, Germany
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen, Essen, Germany
| | - Daniel Hoffmann
- Bioinformatics and Computational Biophysics, University Duisburg-Essen, Essen, Germany
| | - Jürgen C Becker
- Group of Translational Skin Cancer Research (TSCR), University Duisburg-Essen, Essen, Germany; German Cancer Consortium (DKTK) & German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Dermatology, University Hospital Essen, Essen, Germany.
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31
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Traversi D, Pulliero A, Izzotti A, Franchitti E, Iacoviello L, Gianfagna F, Gialluisi A, Izzi B, Agodi A, Barchitta M, Calabrò GE, Hoxhaj I, Sassano M, Sbrogiò LG, Del Sole A, Marchiori F, Pitini E, Migliara G, Marzuillo C, De Vito C, Tamburro M, Sammarco ML, Ripabelli G, Villari P, Boccia S. Precision Medicine and Public Health: New Challenges for Effective and Sustainable Health. J Pers Med 2021; 11:135. [PMID: 33669364 PMCID: PMC7920275 DOI: 10.3390/jpm11020135] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/11/2021] [Accepted: 02/14/2021] [Indexed: 02/06/2023] Open
Abstract
The development of high-throughput omics technologies represents an unmissable opportunity for evidence-based prevention of adverse effects on human health. However, the applicability and access to multi-omics tests are limited. In Italy, this is due to the rapid increase of knowledge and the high levels of skill and economic investment initially necessary. The fields of human genetics and public health have highlighted the relevance of an implementation strategy at a national level in Italy, including integration in sanitary regulations and governance instruments. In this review, the emerging field of public health genomics is discussed, including the polygenic scores approach, epigenetic modulation, nutrigenomics, and microbiomes implications. Moreover, the Italian state of implementation is presented. The omics sciences have important implications for the prevention of both communicable and noncommunicable diseases, especially because they can be used to assess the health status during the whole course of life. An effective population health gain is possible if omics tools are implemented for each person after a preliminary assessment of effectiveness in the medium to long term.
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Affiliation(s)
- Deborah Traversi
- Department of Public Health and Pediatrics, University of Torino, Piazza Polonia 94, 10126 Torino, Italy;
| | - Alessandra Pulliero
- Department of Health Sciences School of Medicine, University of Genoa, 16132 Genova, Italy;
| | - Alberto Izzotti
- Department of Experimental Medicine, University of Genoa, 16132 Genova, Italy;
- IRCCS Ospedale Policlinico San Martino, 161632 Genova, Italy
| | - Elena Franchitti
- Department of Public Health and Pediatrics, University of Torino, Piazza Polonia 94, 10126 Torino, Italy;
| | - Licia Iacoviello
- Research Center in Epidemiology and Preventive Medicine (EPIMED), Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy; (L.I.); (F.G.)
- Department of Epidemiology and Prevention, IRCCS NEUROMED, 86077 Pozzilli, Italy; (A.G.); (B.I.)
| | - Francesco Gianfagna
- Research Center in Epidemiology and Preventive Medicine (EPIMED), Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy; (L.I.); (F.G.)
- Mediterranea Cardiocentro, 80122 Napoli, Italy
| | - Alessandro Gialluisi
- Department of Epidemiology and Prevention, IRCCS NEUROMED, 86077 Pozzilli, Italy; (A.G.); (B.I.)
| | - Benedetta Izzi
- Department of Epidemiology and Prevention, IRCCS NEUROMED, 86077 Pozzilli, Italy; (A.G.); (B.I.)
| | - Antonella Agodi
- Department of Medical and Surgical Sciences and Advanced Technologies “GF Ingrassia”, University of Catania, 95123 Catania, Italy; (A.A.); (M.B.)
| | - Martina Barchitta
- Department of Medical and Surgical Sciences and Advanced Technologies “GF Ingrassia”, University of Catania, 95123 Catania, Italy; (A.A.); (M.B.)
| | - Giovanna Elisa Calabrò
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (G.E.C.); (I.H.); (M.S.); (S.B.)
| | - Ilda Hoxhaj
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (G.E.C.); (I.H.); (M.S.); (S.B.)
| | - Michele Sassano
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (G.E.C.); (I.H.); (M.S.); (S.B.)
| | - Luca Gino Sbrogiò
- Dipartimento di Prevenzione, Az. ULSS3 Serenissima, 30174 Venezia, Italy;
| | | | | | - Erica Pitini
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Roma, Italy; (E.P.); (G.M.); (C.M.); (C.D.V.); (P.V.)
| | - Giuseppe Migliara
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Roma, Italy; (E.P.); (G.M.); (C.M.); (C.D.V.); (P.V.)
| | - Carolina Marzuillo
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Roma, Italy; (E.P.); (G.M.); (C.M.); (C.D.V.); (P.V.)
| | - Corrado De Vito
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Roma, Italy; (E.P.); (G.M.); (C.M.); (C.D.V.); (P.V.)
| | - Manuela Tamburro
- Department of Medicine and Health Sciences “Vincenzo Tiberio”, University of Molise, 86100 Campobasso, Italy; (M.T.); (M.L.S.); (G.R.)
| | - Michela Lucia Sammarco
- Department of Medicine and Health Sciences “Vincenzo Tiberio”, University of Molise, 86100 Campobasso, Italy; (M.T.); (M.L.S.); (G.R.)
| | - Giancarlo Ripabelli
- Department of Medicine and Health Sciences “Vincenzo Tiberio”, University of Molise, 86100 Campobasso, Italy; (M.T.); (M.L.S.); (G.R.)
| | - Paolo Villari
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Roma, Italy; (E.P.); (G.M.); (C.M.); (C.D.V.); (P.V.)
| | - Stefania Boccia
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (G.E.C.); (I.H.); (M.S.); (S.B.)
- Department of Woman and Child Health and Public Health-Public Health Area, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Roma, Italy
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Fania L, Didona D, Di Pietro FR, Verkhovskaia S, Morese R, Paolino G, Donati M, Ricci F, Coco V, Ricci F, Candi E, Abeni D, Dellambra E. Cutaneous Squamous Cell Carcinoma: From Pathophysiology to Novel Therapeutic Approaches. Biomedicines 2021; 9:171. [PMID: 33572373 PMCID: PMC7916193 DOI: 10.3390/biomedicines9020171] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 01/31/2021] [Accepted: 02/01/2021] [Indexed: 12/21/2022] Open
Abstract
Cutaneous squamous cell carcinoma (cSCC), a non-melanoma skin cancer, is a keratinocyte carcinoma representing one of the most common cancers with an increasing incidence. cSCC could be in situ (e.g., Bowen's disease) or an invasive form. A significant cSCC risk factor is advanced age, together with cumulative sun exposure, fair skin, prolonged immunosuppression, and previous skin cancer diagnoses. Although most cSCCs can be treated by surgery, a fraction of them recur and metastasize, leading to death. cSCC could arise de novo or be the result of a progression of the actinic keratosis, an in situ carcinoma. The multistage process of cSCC development and progression is characterized by mutations in the genes involved in epidermal homeostasis and by several alterations, such as epigenetic modifications, viral infections, or microenvironmental changes. Thus, cSCC development is a gradual process with several histological- and pathological-defined stages. Dermoscopy and reflectance confocal microscopy enhanced the diagnostic accuracy of cSCC. Surgical excision is the first-line treatment for invasive cSCC. Moreover, radiotherapy may be considered as a primary treatment in patients not candidates for surgery. Extensive studies of cSCC pathogenic mechanisms identified several pharmaceutical targets and allowed the development of new systemic therapies, including immunotherapy with immune checkpoint inhibitors, such as Cemiplimab, and epidermal growth factor receptor inhibitors for metastatic and locally advanced cSCC. Furthermore, the implementation of prevention measures has been useful in patient management.
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Affiliation(s)
- Luca Fania
- IDI-IRCCS, Dermatological Research Hospital, via di Monti di Creta 104, 00167 Rome, Italy; (F.R.D.P.); (S.V.); (R.M.); (F.R.); (F.R.); (E.C.); (D.A.); (E.D.)
| | - Dario Didona
- Department of Dermatology and Allergology, Philipps University, 35043 Marburg, Germany;
| | - Francesca Romana Di Pietro
- IDI-IRCCS, Dermatological Research Hospital, via di Monti di Creta 104, 00167 Rome, Italy; (F.R.D.P.); (S.V.); (R.M.); (F.R.); (F.R.); (E.C.); (D.A.); (E.D.)
| | - Sofia Verkhovskaia
- IDI-IRCCS, Dermatological Research Hospital, via di Monti di Creta 104, 00167 Rome, Italy; (F.R.D.P.); (S.V.); (R.M.); (F.R.); (F.R.); (E.C.); (D.A.); (E.D.)
| | - Roberto Morese
- IDI-IRCCS, Dermatological Research Hospital, via di Monti di Creta 104, 00167 Rome, Italy; (F.R.D.P.); (S.V.); (R.M.); (F.R.); (F.R.); (E.C.); (D.A.); (E.D.)
| | - Giovanni Paolino
- Unit of Dermatology, IRCCS Ospedale San Raffaele, 20132 Milano, Italy;
| | - Michele Donati
- Department of Pathology, University Hospital Campus Bio-Medico, 00128 Rome, Italy;
- Sikl’s Department of Pathology, Medical Faculty in Pilsen, Charles University in Prague, 30166 Pilsen, Czech Republic
| | - Francesca Ricci
- IDI-IRCCS, Dermatological Research Hospital, via di Monti di Creta 104, 00167 Rome, Italy; (F.R.D.P.); (S.V.); (R.M.); (F.R.); (F.R.); (E.C.); (D.A.); (E.D.)
| | - Valeria Coco
- Institute of Dermatology, A. Gemelli University Polyclinic, IRCCS and Foundation, Sacred Heart Catholic University, 00168 Rome, Italy;
| | - Francesco Ricci
- IDI-IRCCS, Dermatological Research Hospital, via di Monti di Creta 104, 00167 Rome, Italy; (F.R.D.P.); (S.V.); (R.M.); (F.R.); (F.R.); (E.C.); (D.A.); (E.D.)
| | - Eleonora Candi
- IDI-IRCCS, Dermatological Research Hospital, via di Monti di Creta 104, 00167 Rome, Italy; (F.R.D.P.); (S.V.); (R.M.); (F.R.); (F.R.); (E.C.); (D.A.); (E.D.)
- Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Damiano Abeni
- IDI-IRCCS, Dermatological Research Hospital, via di Monti di Creta 104, 00167 Rome, Italy; (F.R.D.P.); (S.V.); (R.M.); (F.R.); (F.R.); (E.C.); (D.A.); (E.D.)
| | - Elena Dellambra
- IDI-IRCCS, Dermatological Research Hospital, via di Monti di Creta 104, 00167 Rome, Italy; (F.R.D.P.); (S.V.); (R.M.); (F.R.); (F.R.); (E.C.); (D.A.); (E.D.)
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33
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Karoutas A, Akhtar A. Functional mechanisms and abnormalities of the nuclear lamina. Nat Cell Biol 2021; 23:116-126. [PMID: 33558730 DOI: 10.1038/s41556-020-00630-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 12/22/2020] [Indexed: 01/30/2023]
Abstract
Alterations in nuclear shape are present in human diseases and ageing. A compromised nuclear lamina is molecularly interlinked to altered chromatin functions and genomic instability. Whether these alterations are a cause or a consequence of the pathological state are important questions in biology. Here, we summarize the roles of nuclear envelope components in chromatin organization, phase separation and transcriptional and epigenetic regulation. Examining these functions in healthy backgrounds will guide us towards a better understanding of pathological alterations.
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Affiliation(s)
- Adam Karoutas
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.,Francis Crick Institute, London, UK
| | - Asifa Akhtar
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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34
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The proliferative history shapes the DNA methylome of B-cell tumors and predicts clinical outcome. ACTA ACUST UNITED AC 2020; 1:1066-1081. [PMID: 34079956 DOI: 10.1038/s43018-020-00131-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We report a systematic analysis of the DNA methylation variability in 1,595 samples of normal cell subpopulations and 14 tumor subtypes spanning the entire human B-cell lineage. Differential methylation among tumor entities relates to differences in cellular origin and to de novo epigenetic alterations, which allowed us to build an accurate machine learning-based diagnostic algorithm. We identify extensive patient-specific methylation variability in silenced chromatin associated with the proliferative history of normal and neoplastic B cells. Mitotic activity generally leaves both hyper- and hypomethylation imprints, but some B-cell neoplasms preferentially gain or lose DNA methylation. Subsequently, we construct a DNA methylation-based mitotic clock called epiCMIT, whose lapse magnitude represents a strong independent prognostic variable in B-cell tumors and is associated with particular driver genetic alterations. Our findings reveal DNA methylation as a holistic tracer of B-cell tumor developmental history, with implications in the differential diagnosis and prediction of clinical outcome.
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35
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Invasive squamous cell carcinomas and precursor lesions on UV-exposed epithelia demonstrate concordant genomic complexity in driver genes. Mod Pathol 2020; 33:2280-2294. [PMID: 32461624 PMCID: PMC7934000 DOI: 10.1038/s41379-020-0571-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/30/2020] [Accepted: 04/30/2020] [Indexed: 12/19/2022]
Abstract
Although squamous cell carcinomas (SCC) are the most frequent human solid tumor at many anatomic sites, the driving molecular alterations underlying their progression from precursor lesions are poorly understood, especially in the context of photodamage. Therefore, we used high-depth, targeted next-generation sequencing (NGS) of RNA and DNA from routine tissue samples to characterize the progression of both well- (cutaneous) and poorly (ocular) studied SCCs. We assessed 56 formalin-fixed paraffin-embedded (FFPE) cutaneous lesions (n = 8 actinic keratosis, n = 30 carcinoma in situ [CIS], n = 18 invasive) and 43 FFPE ocular surface lesions (n = 2 conjunctival/corneal intraepithelial neoplasia, n = 20 CIS, n = 21 invasive), from institutions in the US and Brazil. An additional seven cases of advanced cutaneous SCC were profiled by hybrid capture-based NGS of >1500 genes. The cutaneous and ocular squamous neoplasms displayed a predominance of UV-signature mutations. Precursor lesions had highly similar somatic genomic landscapes to SCCs, including chromosomal gains of 3q involving SOX2, and highly recurrent mutations and/or loss of heterozygosity events affecting tumor suppressors TP53 and CDKN2A. Additionally, we identify a novel molecular subclass of CIS with RB1 mutations. Among TP53 wild-type tumors, human papillomavirus transcript was detected in one matched pair of cutaneous CIS and SCC. Amplicon-based whole-transcriptome sequencing of select 20 cutaneous lesions demonstrated significant upregulation of pro-invasion genes in cutaneous SCCs relative to precursors, including MMP1, MMP3, MMP9, LAMC2, LGALS1, and TNFRSF12A. Together, ocular and cutaneous squamous neoplasms demonstrate similar alterations, supporting a common model for neoplasia in UV-exposed epithelia. Treatment modalities useful for cutaneous SCC may also be effective in ocular SCC given the genetic similarity between these tumor types. Importantly, in both systems, precursor lesions possess the full complement of major genetic changes seen in SCC, supporting non-genetic drivers of invasiveness.
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36
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Piipponen M, Nissinen L, Kähäri VM. Long non-coding RNAs in cutaneous biology and keratinocyte carcinomas. Cell Mol Life Sci 2020; 77:4601-4614. [PMID: 32462404 PMCID: PMC7599158 DOI: 10.1007/s00018-020-03554-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 04/29/2020] [Accepted: 05/15/2020] [Indexed: 12/12/2022]
Abstract
Long non-coding RNAs (lncRNAs) are a largely uncharacterized group of non-coding RNAs with diverse regulatory roles in various biological processes. Recent observations have elucidated the functional roles of lncRNAs in cutaneous biology, e.g. in proliferation and differentiation of epidermal keratinocytes and in cutaneous wound repair. Furthermore, the role of lncRNAs in keratinocyte-derived skin cancers is emerging, especially in cutaneous squamous cell carcinoma (cSCC), which presents a significant burden to health care services worldwide and causes high mortality as metastatic disease. Elucidation of the functions of keratinocyte-specific lncRNAs will improve understanding of the molecular pathogenesis of epidermal disorders and skin cancers and can be exploited in development of new diagnostic and therapeutic applications for keratinocyte carcinomas. In this review, we summarize the current evidence of functionally important lncRNAs in cutaneous biology and in keratinocyte carcinomas.
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Affiliation(s)
- Minna Piipponen
- Department of Dermatology, University of Turku and Turku University Hospital, Hämeentie 11 TE6, 20520, Turku, Finland
- Cancer Research Laboratory, Western Cancer Centre of the Cancer Center Finland (FICAN West), University of Turku and Turku University Hospital, Turku, Finland
| | - Liisa Nissinen
- Department of Dermatology, University of Turku and Turku University Hospital, Hämeentie 11 TE6, 20520, Turku, Finland
- Cancer Research Laboratory, Western Cancer Centre of the Cancer Center Finland (FICAN West), University of Turku and Turku University Hospital, Turku, Finland
| | - Veli-Matti Kähäri
- Department of Dermatology, University of Turku and Turku University Hospital, Hämeentie 11 TE6, 20520, Turku, Finland.
- Cancer Research Laboratory, Western Cancer Centre of the Cancer Center Finland (FICAN West), University of Turku and Turku University Hospital, Turku, Finland.
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37
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Espinet E, Gu Z, Imbusch CD, Giese NA, Büscher M, Safavi M, Weisenburger S, Klein C, Vogel V, Falcone M, Insua-Rodríguez J, Reitberger M, Thiel V, Kossi SO, Muckenhuber A, Sarai K, Lee AYL, Backx E, Zarei S, Gaida MM, Rodríguez-Paredes M, Donato E, Yen HY, Eils R, Schlesner M, Pfarr N, Hackert T, Plass C, Brors B, Steiger K, Weichenhan D, Arda HE, Rooman I, Kopp JL, Strobel O, Weichert W, Sprick MR, Trumpp A. Aggressive PDACs Show Hypomethylation of Repetitive Elements and the Execution of an Intrinsic IFN Program Linked to a Ductal Cell of Origin. Cancer Discov 2020; 11:638-659. [PMID: 33060108 DOI: 10.1158/2159-8290.cd-20-1202] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 11/16/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is characterized by extensive desmoplasia, which challenges the molecular analyses of bulk tumor samples. Here we FACS-purified epithelial cells from human PDAC and normal pancreas and derived their genome-wide transcriptome and DNA methylome landscapes. Clustering based on DNA methylation revealed two distinct PDAC groups displaying different methylation patterns at regions encoding repeat elements. Methylationlow tumors are characterized by higher expression of endogenous retroviral transcripts and double-stranded RNA sensors, which lead to a cell-intrinsic activation of an interferon signature (IFNsign). This results in a protumorigenic microenvironment and poor patient outcome. Methylationlow/IFNsignhigh and Methylationhigh/IFNsignlow PDAC cells preserve lineage traits, respective of normal ductal or acinar pancreatic cells. Moreover, ductal-derived Kras G12D/Trp53 -/- mouse PDACs show higher expression of IFNsign compared with acinar-derived counterparts. Collectively, our data point to two different origins and etiologies of human PDACs, with the aggressive Methylationlow/IFNsignhigh subtype potentially targetable by agents blocking intrinsic IFN signaling. SIGNIFICANCE: The mutational landscapes of PDAC alone cannot explain the observed interpatient heterogeneity. We identified two PDAC subtypes characterized by differential DNA methylation, preserving traits from normal ductal/acinar cells associated with IFN signaling. Our work suggests that epigenetic traits and the cell of origin contribute to PDAC heterogeneity.This article is highlighted in the In This Issue feature, p. 521.
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Affiliation(s)
- Elisa Espinet
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany. .,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Zuguang Gu
- Bioinformatics and Omics Data Analytics, DKFZ, Heidelberg, Germany.,Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Heidelberg, Germany
| | - Charles D Imbusch
- Division of Applied Bioinformatics, DKFZ and NCT, Heidelberg, Germany
| | - Nathalia A Giese
- Department of General and Visceral Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Magdalena Büscher
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Mariam Safavi
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Silke Weisenburger
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Corinna Klein
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany
| | - Vanessa Vogel
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany
| | - Mattia Falcone
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Jacob Insua-Rodríguez
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Manuel Reitberger
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Vera Thiel
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Steffi O Kossi
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany
| | | | - Karnjit Sarai
- Department of Cellular and Physiological Sciences, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alex Y L Lee
- Department of Cellular and Physiological Sciences, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Elyne Backx
- Laboratory of Molecular and Medical Oncology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Soheila Zarei
- Department of Cellular and Physiological Sciences, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthias M Gaida
- Institute of Pathology, University Hospital of Heidelberg, Heidelberg, Germany.,Institute of Pathology, University Medical Center JGU Mainz, Mainz, Germany
| | | | - Elisa Donato
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Hsi-Yu Yen
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Roland Eils
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Heidelberg, Germany.,Digital Health Centre, Berlin Institute of Health and Charité Universitätsmedizin Berlin, Berlin, Germany.,Health Data Science Unit, University Hospital and University of Heidelberg, Heidelberg, Germany
| | | | - Nicole Pfarr
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Thilo Hackert
- Department of General and Visceral Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Benedikt Brors
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Applied Bioinformatics, DKFZ and NCT, Heidelberg, Germany
| | - Katja Steiger
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Dieter Weichenhan
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Heidelberg, Germany
| | - H Efsun Arda
- Laboratory of Receptor Biology and Gene Expression, Center of Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Ilse Rooman
- Laboratory of Molecular and Medical Oncology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Janel L Kopp
- Department of Cellular and Physiological Sciences, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Oliver Strobel
- Department of General and Visceral Surgery, University Hospital Heidelberg, Heidelberg, Germany.,National Center of Tumor Diseases, NCT, Heidelberg, Germany
| | - Wilko Weichert
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Martin R Sprick
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Andreas Trumpp
- HI-STEM-Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, Heidelberg, Germany. .,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
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38
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de Oliveira NFP, de Souza BF, de Castro Coêlho M. UV Radiation and Its Relation to DNA Methylation in Epidermal Cells: A Review. EPIGENOMES 2020; 4:23. [PMID: 34968303 PMCID: PMC8594722 DOI: 10.3390/epigenomes4040023] [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: 09/09/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 12/22/2022] Open
Abstract
DNA methylation is the most studied epigenetic mark, and it can be altered by environmental factors. Among these factors, ultraviolet radiation (UV) is little explored within this context. While the relationship between UV radiation and DNA mutations is clear, little is known about the relationship between UV radiation and epimutations. The present study aimed to perform a literature review to determine the influence of artificial or natural (solar) UV radiation on the global and site-specific methylation profile of epidermal cells. A systematic review of the literature was carried out using the databases PubMed, Scopus, Cochrane, and Web of Science. Observational and intervention studies in cultured cells and animal or human models were included. Most studies showed a relationship between UV radiation and changes in the methylation profile, both global and site-specific. Hypermethylation and hypomethylation changes were detected, which varied according to the studied CpG site. In conclusion, UV radiation can alter the DNA methylation profile in epidermal cells derived from the skin. These data can be used as potential biomarkers for environmental exposure and skin diseases, in addition to being targets for treatments. On the other hand, UV radiation (phototherapy) can also be used as a tool to treat skin diseases. Thus, the data suggest that epigenetic homeostasis can be disrupted or restored by exposure to UV radiation according to the applied wavelength.
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Affiliation(s)
- Naila Francis Paulo de Oliveira
- Departamento de Biologia Molecular, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba—UFPB, João Pessoa 58051-900, Brazil;
- Programa de Pós Graduação em Odontologia, Centro de Ciências da Saúde, Universidade Federal da Paraíba—UFPB, João Pessoa 58051-900, Brazil;
| | - Beatriz Fernandes de Souza
- Departamento de Biologia Molecular, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba—UFPB, João Pessoa 58051-900, Brazil;
| | - Marina de Castro Coêlho
- Programa de Pós Graduação em Odontologia, Centro de Ciências da Saúde, Universidade Federal da Paraíba—UFPB, João Pessoa 58051-900, Brazil;
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39
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Nikolouzakis TK, Falzone L, Lasithiotakis K, Krüger-Krasagakis S, Kalogeraki A, Sifaki M, Spandidos DA, Chrysos E, Tsatsakis A, Tsiaoussis J. Current and Future Trends in Molecular Biomarkers for Diagnostic, Prognostic, and Predictive Purposes in Non-Melanoma Skin Cancer. J Clin Med 2020; 9:E2868. [PMID: 32899768 PMCID: PMC7564050 DOI: 10.3390/jcm9092868] [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: 08/03/2020] [Revised: 08/26/2020] [Accepted: 09/01/2020] [Indexed: 12/11/2022] Open
Abstract
Skin cancer represents the most common type of cancer among Caucasians and presents in two main forms: melanoma and non-melanoma skin cancer (NMSC). NMSC is an umbrella term, under which basal cell carcinoma (BCC), squamous cell carcinoma (SCC), and Merkel cell carcinoma (MCC) are found along with the pre-neoplastic lesions, Bowen disease (BD) and actinic keratosis (AK). Due to the mild nature of the majority of NMSC cases, research regarding their biology has attracted much less attention. Nonetheless, NMSC can bear unfavorable characteristics for the patient, such as invasiveness, local recurrence and distant metastases. In addition, late diagnosis is relatively common for a number of cases of NMSC due to the inability to recognize such cases. Recognizing the need for clinically and economically efficient modes of diagnosis, staging, and prognosis, the present review discusses the main etiological and pathological features of NMSC as well as the new and promising molecular biomarkers available including telomere length (TL), telomerase activity (TA), CpG island methylation (CIM), histone methylation and acetylation, microRNAs (miRNAs), and micronuclei frequency (MNf). The evaluation of all these aspects is important for the correct management of NMSC; therefore, the current review aims to assist future studies interested in exploring the diagnostic and prognostic potential of molecular biomarkers for these entities.
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Affiliation(s)
- Taxiarchis Konstantinos Nikolouzakis
- Laboratory of Anatomy-Histology-Embryology, Medical School, University of Crete, 71110 Heraklion, Crete, Greece;
- Department of General Surgery, University General Hospital of Heraklion, 71110 Heraklion, Crete, Greece; (K.L.); (E.C.)
| | - Luca Falzone
- Epidemiology Unit, IRCCS Istituto Nazionale Tumori ‘Fondazione G. Pascale’, I-80131 Naples, Italy;
| | - Konstantinos Lasithiotakis
- Department of General Surgery, University General Hospital of Heraklion, 71110 Heraklion, Crete, Greece; (K.L.); (E.C.)
| | | | - Alexandra Kalogeraki
- Department of Pathology-Cytopathology, Medical School, University of Crete, 70013 Heraklion, Crete, Greece;
| | - Maria Sifaki
- Centre of Toxicology Science and Research, Faculty of Medicine, University of Crete, 71003 Heraklion, Crete, Greece;
| | - Demetrios A. Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, 71003 Heraklion, Crete, Greece;
| | - Emmanuel Chrysos
- Department of General Surgery, University General Hospital of Heraklion, 71110 Heraklion, Crete, Greece; (K.L.); (E.C.)
| | - Aristidis Tsatsakis
- Centre of Toxicology Science and Research, Faculty of Medicine, University of Crete, 71003 Heraklion, Crete, Greece;
| | - John Tsiaoussis
- Laboratory of Anatomy-Histology-Embryology, Medical School, University of Crete, 71110 Heraklion, Crete, Greece;
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40
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Concomitant DNA methylation and transcriptome signatures define epidermal responses to acute solar UV radiation. Sci Rep 2020; 10:12918. [PMID: 32737342 PMCID: PMC7395768 DOI: 10.1038/s41598-020-69683-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/16/2020] [Indexed: 12/30/2022] Open
Abstract
The simultaneous analysis of different regulatory levels of biological phenomena by means of multi-omics data integration has proven an invaluable tool in modern precision medicine, yet many processes ultimately paving the way towards disease manifestation remain elusive and have not been studied in this regard. Here we investigated the early molecular events following repetitive UV irradiation of in vivo healthy human skin in depth on transcriptomic and epigenetic level. Our results provide first hints towards an immediate acquisition of epigenetic memories related to aging and cancer and demonstrate significantly correlated epigenetic and transcriptomic responses to irradiation stress. The data allowed the precise prediction of inter-individual UV sensitivity, and molecular subtyping on the integrated post-irradiation multi-omics data established the existence of three latent molecular phototypes. Importantly, further analysis suggested a form of melanin-independent DNA damage protection in subjects with higher innate UV resilience. This work establishes a high-resolution molecular landscape of the acute epidermal UV response and demonstrates the potential of integrative analyses to untangle complex and heterogeneous biological responses.
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41
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Boroni M, Zonari A, Reis de Oliveira C, Alkatib K, Ochoa Cruz EA, Brace LE, Lott de Carvalho J. Highly accurate skin-specific methylome analysis algorithm as a platform to screen and validate therapeutics for healthy aging. Clin Epigenetics 2020; 12:105. [PMID: 32660606 PMCID: PMC7359467 DOI: 10.1186/s13148-020-00899-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/03/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND DNA methylation (DNAm) age constitutes a powerful tool to assess the molecular age and overall health status of biological samples. Recently, it has been shown that tissue-specific DNAm age predictors may present superior performance compared to the pan- or multi-tissue counterparts. The skin is the largest organ in the body and bears important roles, such as body temperature control, barrier function, and protection from external insults. As a consequence of the constant and intimate interaction between the skin and the environment, current DNAm estimators, routinely trained using internal tissues which are influenced by other stimuli, are mostly inadequate to accurately predict skin DNAm age. RESULTS In the present study, we developed a highly accurate skin-specific DNAm age predictor, using DNAm data obtained from 508 human skin samples. Based on the analysis of 2,266 CpG sites, we accurately calculated the DNAm age of cultured skin cells and human skin biopsies. Age estimation was sensitive to the biological age of the donor, cell passage, skin disease status, as well as treatment with senotherapeutic drugs. CONCLUSIONS This highly accurate skin-specific DNAm age predictor constitutes a holistic tool that will be of great use in the analysis of human skin health status/molecular aging, as well as in the analysis of the potential of established and novel compounds to alter DNAm age.
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Affiliation(s)
- Mariana Boroni
- Bioinformatics and Computational Biology Lab, Division of Experimental and Translational Research, Brazilian National Cancer Institute, Rio de Janeiro, RJ, 20231-050, Brazil.
- OneSkin Technologies, San Francisco, USA.
| | | | | | | | | | | | - Juliana Lott de Carvalho
- OneSkin Technologies, San Francisco, USA
- Genomic Sciences and Biotechnology Program, Catholic University of Brasilia, Brasilia, Brazil
- Faculty of Medicine, University of Brasilia, Brasilia, Brazil
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42
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Yang D, Holsten T, Börnigen D, Frank S, Mawrin C, Glatzel M, Schüller U. Ependymoma relapse goes along with a relatively stable epigenome, but a severely altered tumor morphology. Brain Pathol 2020; 31:33-44. [PMID: 32633004 PMCID: PMC8018105 DOI: 10.1111/bpa.12875] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 06/08/2020] [Accepted: 06/18/2020] [Indexed: 11/30/2022] Open
Abstract
The molecular biology of ependymomas is not well understood and this is particularly true for ependymoma relapses. We aimed at finding out if and to which extent, relapses differ from their corresponding primary tumors on the morphological, chromosomal and epigenetic level. We investigated 24 matched ependymoma primary and relapsed tumor samples and, as a first step, compared cell density, necrosis, vessel proliferation, Ki67 proliferative index, trimethylation at H3K27 and expression of CXorf67. For the investigation of global methylation profiles, we used public data in order to analyze copy number variation profiles, differential methylation, methylation status and fractions of hypo‐ and hypermethylated CpGs in different epigenomic substructures. Morphologically, we found a significant increase with relapse in cell density and proliferation. H3K27 trimethylation and CXorf67 expression remained stable between primary and relapse tumor samples, and the analysis of DNA methylation profiles neither revealed significant differences in copy number variations nor differentially methylated regions. Significant differences in the methylation status were found for CpG islands, but also in N Shelves or S Shelves, depending on the molecular subgroup. The fraction of probes changing their methylation in the epigenomic substructures appeared subgroup‐specific. Most changes occur in CpG islands, for which relapsed tumors demonstrate higher methylation values than primary tumors. The morphological differences reflect increased aggressiveness upon ependymoma relapse, but, despite slight changes, this observation does not appear to be sufficiently explained by epigenetic changes.
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Affiliation(s)
- Denise Yang
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Till Holsten
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Daniela Börnigen
- Bioinformatics Core Unit, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stephan Frank
- Division for Neuropathology, University Hospital Basel, Basel, Switzerland
| | - Christian Mawrin
- Institute for Neuropathology, University of Magdeburg, Magdeburg, Germany
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, Hamburg, Germany.,Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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43
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Khan AQ, Ahmad F, Raza SS, Zarif L, Siveen KS, Sher G, Agha MV, Rashid K, Kulinski M, Buddenkotte J, Uddin S, Steinhoff M. Role of non-coding RNAs in the progression and resistance of cutaneous malignancies and autoimmune diseases. Semin Cancer Biol 2020; 83:208-226. [PMID: 32717336 DOI: 10.1016/j.semcancer.2020.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/28/2020] [Accepted: 07/06/2020] [Indexed: 02/06/2023]
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44
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Dejonckheere G, Suppa M, Del Marmol V, Meyer T, Stockfleth E. The actinic dysplasia syndrome - diagnostic approaches defining a new concept in field carcinogenesis with multiple cSCC. J Eur Acad Dermatol Venereol 2020; 33 Suppl 8:16-20. [PMID: 31833608 DOI: 10.1111/jdv.15949] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 08/23/2019] [Indexed: 12/19/2022]
Abstract
Usually, SCC lesions are surrounded by a number of clinically visible and non-visible (subclinical) areas of actinically damaged skin containing cells with dysplasia, and thus may be designated actinic dysplasia syndrome. The epithelial damage is caused mainly by UV radiation, inducing mutations in keratinocytes that may confer growth advantages resulting in preneoplastic fields. The development of visible dysplastic lesions (actinic keratosis - AK) and subsequent progression to invasive SCC requires further mutations in cancer-associated genes, like tumour suppressor genes and cell cycle regulators. Reflectance confocal microscopy (RCM) and optical coherence tomography (OCT) represent a considerable advantage for the investigation of field cancerization. In addition, imaging allows the non-invasive monitoring of topical treatments for AKs. RCM provides in vivo horizontal skin sections with a high, 1-μm lateral resolution (similar to histopathology) but with a limited penetration (about 200 μm), which can hamper the visualization of important areas such as the dermal-epidermal junction. Conventional OCT has better penetration (1-2 mm) at the expense of a more limited resolution (much lower than histopathology). Line-field confocal OCT (LC-OCT) combines the high precision of RCM and the good penetration of OCT in a single device and therefore appears to be very useful in diagnosing/managing AKs.
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Affiliation(s)
- G Dejonckheere
- Department of Dermatology and Venerology, Erasme Hospital, Free University of Brussels, Brussels, Belgium
| | - M Suppa
- Department of Dermatology and Venerology, Erasme Hospital, Free University of Brussels, Brussels, Belgium
| | - V Del Marmol
- Department of Dermatology and Venerology, Erasme Hospital, Free University of Brussels, Brussels, Belgium
| | - T Meyer
- Department of Dermatology, Venerology and Allergology, St. Josef Hospital, Ruhr-University, Bochum, Germany
| | - E Stockfleth
- Department of Dermatology, Venerology and Allergology, St. Josef Hospital, Ruhr-University, Bochum, Germany
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45
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Chang H, Sasson A, Srinivasan S, Golhar R, Greenawalt DM, Geese WJ, Green G, Zerba K, Kirov S, Szustakowski J. Bioinformatic Methods and Bridging of Assay Results for Reliable Tumor Mutational Burden Assessment in Non-Small-Cell Lung Cancer. Mol Diagn Ther 2020; 23:507-520. [PMID: 31250328 PMCID: PMC6675777 DOI: 10.1007/s40291-019-00408-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Introduction Tumor mutational burden (TMB) has emerged as a clinically relevant biomarker that may be associated with immune checkpoint inhibitor efficacy. Standardization of TMB measurement is essential for implementing diagnostic tools to guide treatment. Objective Here we describe the in-depth evaluation of bioinformatic TMB analysis by whole exome sequencing (WES) in formalin-fixed, paraffin-embedded samples from a phase III clinical trial. Methods In the CheckMate 026 clinical trial, TMB was retrospectively assessed in 312 patients with non-small-cell lung cancer (58% of the intent-to-treat population) who received first-line nivolumab treatment or standard-of-care chemotherapy. We examined the sensitivity of TMB assessment to bioinformatic filtering methods and assessed concordance between TMB data derived by WES and the FoundationOne® CDx assay. Results TMB scores comprising synonymous, indel, frameshift, and nonsense mutations (all mutations) were 3.1-fold higher than data including missense mutations only, but values were highly correlated (Spearman’s r = 0.99). Scores from CheckMate 026 samples including missense mutations only were similar to those generated from data in The Cancer Genome Atlas, but those including all mutations were generally higher. Using databases for germline subtraction (instead of matched controls) showed a trend for race-dependent increases in TMB scores. WES and FoundationOne CDx outputs were highly correlated (Spearman’s r = 0.90). Conclusions Parameter variation can impact TMB calculations, highlighting the need for standardization. Encouragingly, differences between assays could be accounted for by empirical calibration, suggesting that reliable TMB assessment across assays, platforms, and centers is achievable.
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Affiliation(s)
- Han Chang
- Translational Medicine, Bristol-Myers Squibb, Princeton, NJ, 08648, USA
| | - Ariella Sasson
- Translational Medicine, Bristol-Myers Squibb, Princeton, NJ, 08648, USA
| | - Sujaya Srinivasan
- Translational Medicine, Bristol-Myers Squibb, Princeton, NJ, 08648, USA
| | - Ryan Golhar
- Translational Medicine, Bristol-Myers Squibb, Princeton, NJ, 08648, USA
| | | | - William J Geese
- Translational Medicine, Bristol-Myers Squibb, Princeton, NJ, 08648, USA
| | - George Green
- Translational Medicine, Bristol-Myers Squibb, Princeton, NJ, 08648, USA
| | - Kim Zerba
- Global Biometric Sciences, Bristol-Myers Squibb, Princeton, NJ, USA
| | - Stefan Kirov
- Translational Medicine, Bristol-Myers Squibb, Princeton, NJ, 08648, USA
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Corchado-Cobos R, García-Sancha N, González-Sarmiento R, Pérez-Losada J, Cañueto J. Cutaneous Squamous Cell Carcinoma: From Biology to Therapy. Int J Mol Sci 2020; 21:ijms21082956. [PMID: 32331425 PMCID: PMC7216042 DOI: 10.3390/ijms21082956] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/18/2020] [Accepted: 04/20/2020] [Indexed: 12/13/2022] Open
Abstract
Cutaneous squamous cell carcinoma (CSCC) is the second most frequent cancer in humans and its incidence continues to rise. Although CSCC usually display a benign clinical behavior, it can be both locally invasive and metastatic. The signaling pathways involved in CSCC development have given rise to targetable molecules in recent decades. In addition, the high mutational burden and increased risk of CSCC in patients under immunosuppression were part of the rationale for developing the immunotherapy for CSCC that has changed the therapeutic landscape. This review focuses on the molecular basis of CSCC and the current biology-based approaches of targeted therapies and immune checkpoint inhibitors. Another purpose of this review is to explore the landscape of drugs that may induce or contribute to the development of CSCC. Beginning with the pathogenetic basis of these drug-induced CSCCs, we move on to consider potential therapeutic opportunities for overcoming this adverse effect.
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Affiliation(s)
- Roberto Corchado-Cobos
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC)-Centro de Investigación del cáncer (CIC)-CSIC, Laboratory 7, 37007 Salamanca, Spain; (R.C.-C.); (N.G.-S.); (J.P.-L.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Hospital Virgen de la Vega, 37007 Salamanca, Spain;
| | - Natalia García-Sancha
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC)-Centro de Investigación del cáncer (CIC)-CSIC, Laboratory 7, 37007 Salamanca, Spain; (R.C.-C.); (N.G.-S.); (J.P.-L.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Hospital Virgen de la Vega, 37007 Salamanca, Spain;
| | - Rogelio González-Sarmiento
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Hospital Virgen de la Vega, 37007 Salamanca, Spain;
- Molecular Medicine Unit, Department of Medicine, University of Salamanca, 37007 Salamanca, Spain
| | - Jesús Pérez-Losada
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC)-Centro de Investigación del cáncer (CIC)-CSIC, Laboratory 7, 37007 Salamanca, Spain; (R.C.-C.); (N.G.-S.); (J.P.-L.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Hospital Virgen de la Vega, 37007 Salamanca, Spain;
| | - Javier Cañueto
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC)-Centro de Investigación del cáncer (CIC)-CSIC, Laboratory 7, 37007 Salamanca, Spain; (R.C.-C.); (N.G.-S.); (J.P.-L.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Hospital Virgen de la Vega, 37007 Salamanca, Spain;
- Department of Dermatology, Complejo Asistencial Universitario de Salamanca, 37007 Salamanca, Spain
- Correspondence: ; Tel.: +34-923-291-100 (ext. 55574)
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Hervás-Marín D, Higgins F, Sanmartín O, López-Guerrero JA, Bañó MC, Igual JC, Quilis I, Sandoval J. Genome wide DNA methylation profiling identifies specific epigenetic features in high-risk cutaneous squamous cell carcinoma. PLoS One 2019; 14:e0223341. [PMID: 31860637 PMCID: PMC6924689 DOI: 10.1371/journal.pone.0223341] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 12/06/2019] [Indexed: 01/23/2023] Open
Abstract
Cutaneous squamous cell carcinoma (cSCC) is the second most common skin cancer. Although most cSCCs have good prognosis, a subgroup of high-risk cSCC has a higher frequency of recurrence and mortality. Therefore, the identification of molecular risk factors associated with this aggressive subtype is of major interest. In this work we carried out a global-scale approach to investigate the DNA-methylation profile in patients at different stages, from premalignant actinic keratosis to low-risk invasive and high-risk non-metastatic and metastatic cSCC. The results showed massive non-sequential changes in DNA-methylome and identified a minimal methylation signature that discriminates between stages. Importantly, a direct comparison of low-risk and high-risk stages revealed epigenetic traits characteristic of high-risk tumours. Finally, a prognostic prediction model in cSCC patients identified a methylation signature able to predict the overall survival of patients. Thus, the analysis of DNA-methylation in cSCC revealed changes during the evolution of the disease through the different stages that can be of great value not only in the diagnosis but also in the prognosis of the disease.
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Affiliation(s)
- David Hervás-Marín
- Department of Biostatistics, Instituto de Investigación Sanitaria La Fe, Valencia, Spain
| | - Faatiemah Higgins
- Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED) Universitat de València, Burjassot, Valencia, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat de València, Burjassot, Valencia, Spain
| | - Onofre Sanmartín
- Dermatology Department, Instituto Valenciano de Oncología, Valencia, Spain
- Facultad de Medicina, Universidad Católica de Valencia, Valencia, Spain
| | | | - M. Carmen Bañó
- Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED) Universitat de València, Burjassot, Valencia, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat de València, Burjassot, Valencia, Spain
| | - J. Carlos Igual
- Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED) Universitat de València, Burjassot, Valencia, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat de València, Burjassot, Valencia, Spain
| | - Inma Quilis
- Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED) Universitat de València, Burjassot, Valencia, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat de València, Burjassot, Valencia, Spain
| | - Juan Sandoval
- Biomarkers and Precision Medicine Unit (UByMP), Instituto de Investigación Sanitaria La Fe, Valencia, Spain
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Cytokine/chemokine profiles in squamous cell carcinoma correlate with precancerous and cancerous disease stage. Sci Rep 2019; 9:17754. [PMID: 31780824 PMCID: PMC6882799 DOI: 10.1038/s41598-019-54435-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 11/14/2019] [Indexed: 11/20/2022] Open
Abstract
Actinic Keratosis (AK), Intraepidermal Carcinoma (IEC), and Squamous Cell Carcinoma (SCC) are generally considered to be advancing stages of the same disease spectrum. However, while AK often regress spontaneously, and IEC often regress in response to immune-activating treatments, SCC typically do not regress. Therefore, it is vital to define whether fundamental immunological changes occur during progression to SCC. Here we show that proinflammatory cytokine expression, chemokine expression, and immune cell infiltration density change during progression to SCC. Our findings suggest a switch from predominantly proinflammatory cytokine production to chemokine production is a key feature of progression from precancer to cancer. Together, these observations propose a model that can underpin current research and open new avenues of exploration into the clinical significance of these profiles with respect to immunotherapeutic or other treatment outcomes.
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Köhler F, Rodríguez-Paredes M. DNA Methylation in Epidermal Differentiation, Aging, and Cancer. J Invest Dermatol 2019; 140:38-47. [PMID: 31427190 DOI: 10.1016/j.jid.2019.05.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/24/2019] [Accepted: 05/17/2019] [Indexed: 12/22/2022]
Abstract
The formation and maintenance of the epidermis depend on epidermal stem cell differentiation and must be tightly regulated. Epigenetic mechanisms such as DNA methylation allow the precise gene expression cascade needed during cellular differentiation. However, these mechanisms become deregulated during aging and tumorigenesis, where cellular function and identity become compromised. Here we provide a review of this rapidly developing field. We discuss recent discoveries related to epidermal homeostasis, aging, and cancer, including the functional role of DNA methyltransferases, the methylation clock, and the determination of tumor cells-of-origin. Finally, we focus on future advances, greatly influenced by single-cell sequencing technologies.
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Affiliation(s)
- Florian Köhler
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Manuel Rodríguez-Paredes
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany.
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50
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Abstract
Biomarker discovery and validation are necessary for improving the prediction of clinical outcomes and patient monitoring. Despite considerable interest in biomarker discovery and development, improvements in the range and quality of biomarkers are still needed. The main challenge is how to integrate preclinical data to obtain a reliable biomarker that can be measured with acceptable costs in routine clinical practice. Epigenetic alterations are already being incorporated as valuable candidates in the biomarker field. Furthermore, their reversible nature offers a promising opportunity to ameliorate disease symptoms by using epigenetic-based therapy. Thus, beyond helping to understand disease biology, clinical epigenetics is being incorporated into patient management in oncology, as well as being explored for clinical applicability for other human pathologies such as neurological and infectious diseases and immune system disorders.
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