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Muijlwijk T, Nauta IH, van der Lee A, Grünewald KJT, Brink A, Ganzevles SH, Baatenburg de Jong RJ, Atanesyan L, Savola S, van de Wiel MA, Peferoen LAN, Bloemena E, van de Ven R, Leemans CR, Poell JB, Brakenhoff RH. Hallmarks of a genomically distinct subclass of head and neck cancer. Nat Commun 2024; 15:9060. [PMID: 39428388 PMCID: PMC11491468 DOI: 10.1038/s41467-024-53390-3] [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: 02/07/2024] [Accepted: 10/09/2024] [Indexed: 10/22/2024] Open
Abstract
Cancer is caused by an accumulation of somatic mutations and copy number alterations (CNAs). Besides mutations, these copy number changes are key characteristics of cancer development. Nonetheless, some tumors show hardly any CNAs, a remarkable phenomenon in oncogenesis. Head and neck squamous cell carcinomas (HNSCCs) arise by either exposure to carcinogens, or infection with the human papillomavirus (HPV). HPV-negative HNSCCs are generally characterized by many CNAs and frequent mutations in CDKN2A, TP53, FAT1, and NOTCH1. Here, we present the hallmarks of the distinct subgroup of HPV-negative HNSCC with no or few CNAs (CNA-quiet) by genetic profiling of 802 oral cavity squamous cell carcinomas (OCSCCs). In total, 73 OCSCC (9.1%) are classified as CNA-quiet and 729 as CNA-other. The CNA-quiet group is characterized by wild-type TP53, frequent CASP8 and HRAS mutations, and a less immunosuppressed tumor immune microenvironment with lower density of regulatory T cells. Patients with CNA-quiet OCSCC are older, more often women, less frequently current smokers, and have a better 5-year overall survival compared to CNA-other OCSCC. This study demonstrates that CNA-quiet OCSCC should be considered as a distinct, clinically relevant subclass. Given the clinical characteristics, the patient group with these tumors will rapidly increase in the aging population.
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Affiliation(s)
- Tara Muijlwijk
- Amsterdam UMC, location Vrije Universiteit Amsterdam, Otolaryngology / Head and Neck Surgery, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Cancer Immunology, Amsterdam, The Netherlands
| | - Irene H Nauta
- Amsterdam UMC, location Vrije Universiteit Amsterdam, Otolaryngology / Head and Neck Surgery, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Anabel van der Lee
- Amsterdam UMC, location Vrije Universiteit Amsterdam, Otolaryngology / Head and Neck Surgery, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Cancer Immunology, Amsterdam, The Netherlands
| | - Kari J T Grünewald
- Amsterdam UMC, location Vrije Universiteit Amsterdam, Otolaryngology / Head and Neck Surgery, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Arjen Brink
- Amsterdam UMC, location Vrije Universiteit Amsterdam, Otolaryngology / Head and Neck Surgery, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Sonja H Ganzevles
- Amsterdam UMC, location Vrije Universiteit Amsterdam, Otolaryngology / Head and Neck Surgery, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Cancer Immunology, Amsterdam, The Netherlands
| | | | | | - Suvi Savola
- MRC Holland, Oncogenetics, Amsterdam, The Netherlands
| | - Mark A van de Wiel
- Amsterdam UMC, Epidemiology & Data Science, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Laura A N Peferoen
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
- Amsterdam UMC, location Vrije Universiteit Amsterdam, Pathology, Amsterdam, The Netherlands
- Academic Center for Dentistry, Maxillofacial Surgery/ Oral Pathology, Amsterdam, The Netherlands
| | - Elisabeth Bloemena
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
- Amsterdam UMC, location Vrije Universiteit Amsterdam, Pathology, Amsterdam, The Netherlands
- Academic Center for Dentistry, Maxillofacial Surgery/ Oral Pathology, Amsterdam, The Netherlands
| | - Rieneke van de Ven
- Amsterdam UMC, location Vrije Universiteit Amsterdam, Otolaryngology / Head and Neck Surgery, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Cancer Immunology, Amsterdam, The Netherlands
| | - C René Leemans
- Amsterdam UMC, location Vrije Universiteit Amsterdam, Otolaryngology / Head and Neck Surgery, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Jos B Poell
- Amsterdam UMC, location Vrije Universiteit Amsterdam, Otolaryngology / Head and Neck Surgery, Amsterdam, The Netherlands.
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands.
| | - Ruud H Brakenhoff
- Amsterdam UMC, location Vrije Universiteit Amsterdam, Otolaryngology / Head and Neck Surgery, Amsterdam, The Netherlands.
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands.
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2
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Deng Z, Liu J, Yu YV, Jin YN. Machine learning-based identification of an immunotherapy-related signature to enhance outcomes and immunotherapy responses in melanoma. Front Immunol 2024; 15:1451103. [PMID: 39355255 PMCID: PMC11442245 DOI: 10.3389/fimmu.2024.1451103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 08/27/2024] [Indexed: 10/03/2024] Open
Abstract
Background Immunotherapy has revolutionized skin cutaneous melanoma treatment, but response variability due to tumor heterogeneity necessitates robust biomarkers for predicting immunotherapy response. Methods We used weighted gene co-expression network analysis (WGCNA), consensus clustering, and 10 machine learning algorithms to develop the immunotherapy-related gene model (ITRGM) signature. Multi-omics analyses included bulk and single-cell RNA sequencing of melanoma patients, mouse bulk RNA sequencing, and pathology sections of melanoma patients. Results We identified 66 consensus immunotherapy prognostic genes (CITPGs) using WGCNA and differentially expressed genes (DEGs) from two melanoma cohorts. The CITPG-high group showed better prognosis and enriched immune activities. DEGs between CITPG-high and CITPG-low groups in the TCGA-SKCM cohort were analyzed in three additional melanoma cohorts using univariate Cox regression, resulting in 44 consensus genes. Using 101 machine learning algorithm combinations, we constructed the ITRGM signature based on seven model genes. The ITRGM outperformed 37 published signatures in predicting immunotherapy prognosis across the training cohort, three testing cohorts, and a meta-cohort. It effectively stratified patients into high-risk or low-risk groups for immunotherapy response. The low-risk group, with high levels of model genes, correlated with increased immune characteristics such as tumor mutation burden and immune cell infiltration, indicating immune-hot tumors with a better prognosis. The ITRGM's relationship with the tumor immune microenvironment was further validated in our experiments using pathology sections with GBP5, an important model gene, and CD8 IHC analysis. The ITRGM also predicted better immunotherapy response in eight cohorts, including urothelial carcinoma and stomach adenocarcinoma, indicating broad applicability. Conclusions The ITRGM signature is a stable and robust predictor for stratifying melanoma patients into 'immune-hot' and 'immune-cold' tumors, enhancing prognosis and response to immunotherapy.
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Affiliation(s)
- Zaidong Deng
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan
University, Wuhan University, Wuhan, China
| | - Jie Liu
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan
University, Wuhan University, Wuhan, China
| | - Yanxun V. Yu
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan
University, Wuhan University, Wuhan, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University,
Wuhan, China
| | - Youngnam N. Jin
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan
University, Wuhan University, Wuhan, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University,
Wuhan, China
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3
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Trocchia M, Ventrici A, Modestino L, Cristinziano L, Ferrara AL, Palestra F, Loffredo S, Capone M, Madonna G, Romanelli M, Ascierto PA, Galdiero MR. Innate Immune Cells in Melanoma: Implications for Immunotherapy. Int J Mol Sci 2024; 25:8523. [PMID: 39126091 PMCID: PMC11313504 DOI: 10.3390/ijms25158523] [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: 07/12/2024] [Revised: 07/31/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024] Open
Abstract
The innate immune system, composed of neutrophils, basophils, eosinophils, myeloid-derived suppressor cells (MDSCs), macrophages, dendritic cells (DCs), mast cells (MCs), and innate lymphoid cells (ILCs), is the first line of defense. Growing evidence demonstrates the crucial role of innate immunity in tumor initiation and progression. Several studies support the idea that innate immunity, through the release of pro- and/or anti-inflammatory cytokines and tumor growth factors, plays a significant role in the pathogenesis, progression, and prognosis of cutaneous malignant melanoma (MM). Cutaneous melanoma is the most common skin cancer, with an incidence that rapidly increased in recent decades. Melanoma is a highly immunogenic tumor, due to its high mutational burden. The metastatic form retains a high mortality. The advent of immunotherapy revolutionized the therapeutic approach to this tumor and significantly ameliorated the patients' clinical outcome. In this review, we will recapitulate the multiple roles of innate immune cells in melanoma and the related implications for immunotherapy.
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Affiliation(s)
- Marialuisa Trocchia
- Department of Translational Medical Sciences (DiSMeT), University of Naples Federico II, 80138 Naples, Italy; (M.T.); (A.V.); (A.L.F.); (F.P.); (S.L.)
| | - Annagioia Ventrici
- Department of Translational Medical Sciences (DiSMeT), University of Naples Federico II, 80138 Naples, Italy; (M.T.); (A.V.); (A.L.F.); (F.P.); (S.L.)
| | - Luca Modestino
- Department of Internal Medicine and Clinical Immunology, University Hospital of Naples Federico II, 80138 Naples, Italy;
| | - Leonardo Cristinziano
- Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, 80138 Naples, Italy;
| | - Anne Lise Ferrara
- Department of Translational Medical Sciences (DiSMeT), University of Naples Federico II, 80138 Naples, Italy; (M.T.); (A.V.); (A.L.F.); (F.P.); (S.L.)
| | - Francesco Palestra
- Department of Translational Medical Sciences (DiSMeT), University of Naples Federico II, 80138 Naples, Italy; (M.T.); (A.V.); (A.L.F.); (F.P.); (S.L.)
| | - Stefania Loffredo
- Department of Translational Medical Sciences (DiSMeT), University of Naples Federico II, 80138 Naples, Italy; (M.T.); (A.V.); (A.L.F.); (F.P.); (S.L.)
- Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, 80138 Naples, Italy;
| | - Mariaelena Capone
- Melanoma, Cancer Immunotherapy, and Development Therapeutics Unit, Istituto Nazionale Tumori IRCCS Fondazione “G. Pascale”, 80138 Naples, Italy; (M.C.); (G.M.); (M.R.); (P.A.A.)
| | - Gabriele Madonna
- Melanoma, Cancer Immunotherapy, and Development Therapeutics Unit, Istituto Nazionale Tumori IRCCS Fondazione “G. Pascale”, 80138 Naples, Italy; (M.C.); (G.M.); (M.R.); (P.A.A.)
| | - Marilena Romanelli
- Melanoma, Cancer Immunotherapy, and Development Therapeutics Unit, Istituto Nazionale Tumori IRCCS Fondazione “G. Pascale”, 80138 Naples, Italy; (M.C.); (G.M.); (M.R.); (P.A.A.)
| | - Paolo Antonio Ascierto
- Melanoma, Cancer Immunotherapy, and Development Therapeutics Unit, Istituto Nazionale Tumori IRCCS Fondazione “G. Pascale”, 80138 Naples, Italy; (M.C.); (G.M.); (M.R.); (P.A.A.)
| | - Maria Rosaria Galdiero
- Department of Translational Medical Sciences (DiSMeT), University of Naples Federico II, 80138 Naples, Italy; (M.T.); (A.V.); (A.L.F.); (F.P.); (S.L.)
- Department of Internal Medicine and Clinical Immunology, University Hospital of Naples Federico II, 80138 Naples, Italy;
- Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, 80138 Naples, Italy;
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Ye J, Liu F, Zhang L, Wu C, Jiang A, Xie T, Jiang H, Li Z, Luo P, Jiao J, Xiao J. MOCS, a novel classifier system integrated multimoics analysis refining molecular subtypes and prognosis for skin melanoma. J Biomol Struct Dyn 2024:1-17. [PMID: 38555737 DOI: 10.1080/07391102.2024.2329305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 02/08/2024] [Indexed: 04/02/2024]
Abstract
PURPOSE The present investigation focuses on Skin Cutaneous Melanoma (SKCM), a melanocytic carcinoma characterized by marked aggression, significant heterogeneity, and a complex etiological background, factors which collectively contribute to the challenge in prognostic determinations. We defined a novel classifier system specifically tailored for SKCM based on multiomics. METHODS We collected 423 SKCM samples with multi omics datasets to perform a consensus cluster analysis using 10 machine learning algorithms and verified in 2 independent cohorts. Clinical features, biological characteristics, immune infiltration pattern, therapeutic response and mutation landscape were compared between subtypes. RESULTS Based on consensus clustering algorithms, we identified two Multi-Omics-Based-Cancer-Subtypes (MOCS) in SKCM in TCGA project and validated in GSE19234 and GSE65904 cohorts. MOCS2 emerged as a subtype with poor prognosis, characterized by a complex immune microenvironment, dysfunctional anti-tumor immune state, high cancer stemness index, and genomic instability. MOCS2 exhibited resistance to chemotherapy agents like erlotinib and sunitinib while sensitive to rapamycin, NSC87877, MG132, and FH355. Additionally, ELSPBP1 was identified as the target involving in glycolysis and M2 macrophage infiltration in SKCM. CONCLUSIONS MOCS classification could stably predict prognosis of SKCM; patients with a high cancer stemness index combined with genomic instability may be predisposed to an immune exhaustion state.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Juelan Ye
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Fuchun Liu
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
| | - Luoshen Zhang
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
| | - Chunbiao Wu
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
- School of Health Science and Technology, University of Shanghai for Science and Technology, Shanghai, China
| | - Aimin Jiang
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Tianying Xie
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
- School of Health Science and Technology, University of Shanghai for Science and Technology, Shanghai, China
| | - Hao Jiang
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
- School of Health Science and Technology, University of Shanghai for Science and Technology, Shanghai, China
| | - Zhenxi Li
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
- School of Health Science and Technology, University of Shanghai for Science and Technology, Shanghai, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jian Jiao
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
| | - Jianru Xiao
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
- School of Health Science and Technology, University of Shanghai for Science and Technology, Shanghai, China
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Dakilah I, Harb A, Abu-Gharbieh E, El-Huneidi W, Taneera J, Hamoudi R, Semreen MH, Bustanji Y. Potential of CDC25 phosphatases in cancer research and treatment: key to precision medicine. Front Pharmacol 2024; 15:1324001. [PMID: 38313315 PMCID: PMC10834672 DOI: 10.3389/fphar.2024.1324001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/04/2024] [Indexed: 02/06/2024] Open
Abstract
The global burden of cancer continues to rise, underscoring the urgency of developing more effective and precisely targeted therapies. This comprehensive review explores the confluence of precision medicine and CDC25 phosphatases in the context of cancer research. Precision medicine, alternatively referred to as customized medicine, aims to customize medical interventions by taking into account the genetic, genomic, and epigenetic characteristics of individual patients. The identification of particular genetic and molecular drivers driving cancer helps both diagnostic accuracy and treatment selection. Precision medicine utilizes sophisticated technology such as genome sequencing and bioinformatics to elucidate genetic differences that underlie the proliferation of cancer cells, hence facilitating the development of customized therapeutic interventions. CDC25 phosphatases, which play a crucial role in governing the progression of the cell cycle, have garnered significant attention as potential targets for cancer treatment. The dysregulation of CDC25 is a characteristic feature observed in various types of malignancies, hence classifying them as proto-oncogenes. The proteins in question, which operate as phosphatases, play a role in the activation of Cyclin-dependent kinases (CDKs), so promoting the advancement of the cell cycle. CDC25 inhibitors demonstrate potential as therapeutic drugs for cancer treatment by specifically blocking the activity of CDKs and modulating the cell cycle in malignant cells. In brief, precision medicine presents a potentially fruitful option for augmenting cancer research, diagnosis, and treatment, with an emphasis on individualized care predicated upon patients' genetic and molecular profiles. The review highlights the significance of CDC25 phosphatases in the advancement of cancer and identifies them as promising candidates for therapeutic intervention. This statement underscores the significance of doing thorough molecular profiling in order to uncover the complex molecular characteristics of cancer cells.
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Affiliation(s)
- Ibraheem Dakilah
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Amani Harb
- Department of Basic Sciences, Faculty of Arts and Sciences, Al-Ahliyya Amman University, Amman, Jordan
| | - Eman Abu-Gharbieh
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Waseem El-Huneidi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Jalal Taneera
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Rifat Hamoudi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Division of Surgery and Interventional Science, University College London, London, United Kingdom
| | - Mohammed H Semreen
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
| | - Yasser Bustanji
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- School of Pharmacy, The University of Jordan, Amman, Jordan
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