1
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Wee Y, Wang J, Wilson EC, Rich CP, Rogers A, Tong Z, DeGroot E, Gopal YNV, Davies MA, Ekiz HA, Tay JKH, Stubben C, Boucher KM, Oviedo JM, Fairfax KC, Williams MA, Holmen SL, Wolff RK, Grossmann AH. Tumour-intrinsic endomembrane trafficking by ARF6 shapes an immunosuppressive microenvironment that drives melanomagenesis and response to checkpoint blockade therapy. Nat Commun 2024; 15:6613. [PMID: 39098861 PMCID: PMC11298541 DOI: 10.1038/s41467-024-50881-1] [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: 01/04/2024] [Accepted: 07/24/2024] [Indexed: 08/06/2024] Open
Abstract
Tumour-host immune interactions lead to complex changes in the tumour microenvironment (TME), impacting progression, metastasis and response to therapy. While it is clear that cancer cells can have the capacity to alter immune landscapes, our understanding of this process is incomplete. Herein we show that endocytic trafficking at the plasma membrane, mediated by the small GTPase ARF6, enables melanoma cells to impose an immunosuppressive TME that accelerates tumour development. This ARF6-dependent TME is vulnerable to immune checkpoint blockade therapy (ICB) but in murine melanoma, loss of Arf6 causes resistance to ICB. Likewise, downregulation of ARF6 in patient tumours correlates with inferior overall survival after ICB. Mechanistically, these phenotypes are at least partially explained by ARF6-dependent recycling, which controls plasma membrane density of the interferon-gamma receptor. Collectively, our findings reveal the importance of endomembrane trafficking in outfitting tumour cells with the ability to shape their immune microenvironment and respond to immunotherapy.
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Affiliation(s)
- Yinshen Wee
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
- School of Dentistry, Taipei Medical University, Taipei, Taiwan
| | - Junhua Wang
- Huntsman Cancer Institute, Salt Lake City, UT, USA
- Department of Oncologic Sciences, University of Utah, Salt Lake City, UT, USA
| | - Emily C Wilson
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Coulson P Rich
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Aaron Rogers
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Zongzhong Tong
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Evelyn DeGroot
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Y N Vashisht Gopal
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael A Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - H Atakan Ekiz
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Gulbahce, Urla, Izmir, Turkey
| | - Joshua K H Tay
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Chris Stubben
- Bioinformatics Shared Resource, Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Kenneth M Boucher
- Cancer Biostatistics Shared Resource, Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Juan M Oviedo
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Keke C Fairfax
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Matthew A Williams
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Sheri L Holmen
- Huntsman Cancer Institute, Salt Lake City, UT, USA
- Department of Oncologic Sciences, University of Utah, Salt Lake City, UT, USA
- Department of Surgery, University of Utah, Salt Lake City, UT, USA
| | - Roger K Wolff
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Allie H Grossmann
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.
- Huntsman Cancer Institute, Salt Lake City, UT, USA.
- Department of Oncologic Sciences, University of Utah, Salt Lake City, UT, USA.
- Providence Cancer Institute of Oregon, Earle A. Chiles Research Institute, Portland, OR, USA.
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2
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Noma IHY, Carvalho LADC, Camarena DEM, Silva RO, Moraes Junior MOD, de Souza ST, Newton-Bishop J, Nsengimana J, Maria-Engler SS. Peroxiredoxin-2 represses NRAS-mutated melanoma cells invasion by modulating EMT markers. Biomed Pharmacother 2024; 177:116953. [PMID: 38955087 DOI: 10.1016/j.biopha.2024.116953] [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: 03/12/2024] [Revised: 06/05/2024] [Accepted: 06/15/2024] [Indexed: 07/04/2024] Open
Abstract
The second most common mutation in melanoma occurs in NRAS oncogene, being a more aggressive disease that has no effective approved treatment. Besides, cellular plasticity limits better outcomes of the advanced and therapy-resistant patients. Peroxiredoxins (PRDXs) control cellular processes through direct hydrogen peroxide oxidation or by redox-relaying processes. Here, we demonstrated that PRDX2 could act as a modulator of multiple EMT markers in NRAS-mutated melanomas. PRDX2 knockdown lead to phenotypic changes towards invasion in human reconstructed skin and the treatment with a PRDX mimetic (gliotoxin), decreased migration in PRDX2-deficient cells. We also confirmed the favorable clinical outcome of patients expressing PRDX2 in a large primary melanoma cohort. This study contributes to our knowledge about genes involved in phenotype switching and opens a new perspective for PRDX2 as a biomarker and target in NRAS-mutated melanomas.
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Affiliation(s)
- Isabella Harumi Yonehara Noma
- Department of Clinical and Toxicological Analysis, School of Pharmaceutical Sciences, University of São Paulo, Avenida Professor Lineu Prestes, 580, São Paulo, SP 05508-00, Brazil
| | - Larissa Anastacio da Costa Carvalho
- Department of Clinical and Toxicological Analysis, School of Pharmaceutical Sciences, University of São Paulo, Avenida Professor Lineu Prestes, 580, São Paulo, SP 05508-00, Brazil
| | - Denisse Esther Mallaupoma Camarena
- Department of Clinical and Toxicological Analysis, School of Pharmaceutical Sciences, University of São Paulo, Avenida Professor Lineu Prestes, 580, São Paulo, SP 05508-00, Brazil
| | - Renaira Oliveira Silva
- Department of Clinical and Toxicological Analysis, School of Pharmaceutical Sciences, University of São Paulo, Avenida Professor Lineu Prestes, 580, São Paulo, SP 05508-00, Brazil
| | - Manoel Oliveira de Moraes Junior
- Department of Clinical and Toxicological Analysis, School of Pharmaceutical Sciences, University of São Paulo, Avenida Professor Lineu Prestes, 580, São Paulo, SP 05508-00, Brazil
| | - Sophia Tavares de Souza
- Department of Clinical and Toxicological Analysis, School of Pharmaceutical Sciences, University of São Paulo, Avenida Professor Lineu Prestes, 580, São Paulo, SP 05508-00, Brazil
| | - Julia Newton-Bishop
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds LS9 7TF, UK
| | - Jérémie Nsengimana
- Biostatistics Research Group, Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4BN, UK
| | - Silvya Stuchi Maria-Engler
- Department of Clinical and Toxicological Analysis, School of Pharmaceutical Sciences, University of São Paulo, Avenida Professor Lineu Prestes, 580, São Paulo, SP 05508-00, Brazil.
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3
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Chen MY, Zhang F, Goedegebuure SP, Gillanders WE. Dendritic cell subsets and implications for cancer immunotherapy. Front Immunol 2024; 15:1393451. [PMID: 38903502 PMCID: PMC11188312 DOI: 10.3389/fimmu.2024.1393451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/22/2024] [Indexed: 06/22/2024] Open
Abstract
Dendritic cells (DCs) play a central role in the orchestration of effective T cell responses against tumors. However, their functional behavior is context-dependent. DC type, transcriptional program, location, intratumoral factors, and inflammatory milieu all impact DCs with regard to promoting or inhibiting tumor immunity. The following review introduces important facets of DC function, and how subset and phenotype can affect the interplay of DCs with other factors in the tumor microenvironment. It will also discuss how current cancer treatment relies on DC function, and survey the myriad ways with which immune therapy can more directly harness DCs to enact antitumor cytotoxicity.
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Affiliation(s)
- Michael Y. Chen
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, United States
| | - Felicia Zhang
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, United States
| | - Simon Peter Goedegebuure
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, United States
- Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital, Washington University School of Medicine, St. Louis, MO, United States
| | - William E. Gillanders
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, United States
- Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital, Washington University School of Medicine, St. Louis, MO, United States
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4
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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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5
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Wise DR, Pachynski RK, Denmeade SR, Aggarwal RR, Deng J, Febles VA, Balar AV, Economides MP, Loomis C, Selvaraj S, Haas M, Kagey MH, Newman W, Baum J, Troxel AB, Griglun S, Leis D, Yang N, Aranchiy V, Machado S, Waalkes E, Gargano G, Soamchand N, Puranik A, Chattopadhyay P, Fedal E, Deng FM, Ren Q, Chiriboga L, Melamed J, Sirard CA, Wong KK. A Phase 1/2 multicenter trial of DKN-01 as monotherapy or in combination with docetaxel for the treatment of metastatic castration-resistant prostate cancer (mCRPC). Prostate Cancer Prostatic Dis 2024:10.1038/s41391-024-00798-z. [PMID: 38341461 DOI: 10.1038/s41391-024-00798-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024]
Abstract
BACKGROUND Dickkopf-related protein 1 (DKK1) is a Wingless-related integrate site (Wnt) signaling modulator that is upregulated in prostate cancers (PCa) with low androgen receptor expression. DKN-01, an IgG4 that neutralizes DKK1, delays PCa growth in pre-clinical DKK1-expressing models. These data provided the rationale for a clinical trial testing DKN-01 in patients with metastatic castration-resistant PCa (mCRPC). METHODS This was an investigator-initiated parallel-arm phase 1/2 clinical trial testing DKN-01 alone (monotherapy) or in combination with docetaxel 75 mg/m2 (combination) for men with mCRPC who progressed on ≥1 AR signaling inhibitors. DKK1 status was determined by RNA in-situ expression. The primary endpoint of the phase 1 dose escalation cohorts was the determination of the recommended phase 2 dose (RP2D). The primary endpoint of the phase 2 expansion cohorts was objective response rate by iRECIST criteria in patients treated with the combination. RESULTS 18 pts were enrolled into the study-10 patients in the monotherapy cohorts and 8 patients in the combination cohorts. No DLTs were observed and DKN-01 600 mg was determined as the RP2D. A best overall response of stable disease occurred in two out of seven (29%) evaluable patients in the monotherapy cohort. In the combination cohort, five out of seven (71%) evaluable patients had a partial response (PR). A median rPFS of 5.7 months was observed in the combination cohort. In the combination cohort, the median tumoral DKK1 expression H-score was 0.75 and the rPFS observed was similar between patients with DKK1 H-score ≥1 versus H-score = 0. CONCLUSION DKN-01 600 mg was well tolerated. DKK1 blockade has modest anti-tumor activity as a monotherapy for mCRPC. Anti-tumor activity was observed in the combination cohorts, but the response duration was limited. DKK1 expression in the majority of mCRPC is low and did not clearly correlate with anti-tumor activity of DKN-01 plus docetaxel.
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Affiliation(s)
- David R Wise
- Department of Medicine, Laura & Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
| | - Russell K Pachynski
- Division of Oncology, Department of Medicine, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Samuel R Denmeade
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, MD, USA
| | - Rahul R Aggarwal
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Jiehui Deng
- Department of Medicine, Laura & Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Victor Adorno Febles
- Department of Medicine, Laura & Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
- New York Harbor Veterans Healthcare System, New York, NY, USA
| | - Arjun V Balar
- Department of Medicine, Laura & Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Minas P Economides
- Department of Medicine, Laura & Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Cynthia Loomis
- Department of Pathology and DART Experimental Pathology Research Laboratory, NYU Langone Health, New York, NY, USA
| | - Shanmugapriya Selvaraj
- Department of Pathology and DART Experimental Pathology Research Laboratory, NYU Langone Health, New York, NY, USA
| | | | | | | | - Jason Baum
- Leap Therapeutics, Inc, Cambridge, MA, USA
| | - Andrea B Troxel
- Division of Biostatistics, Department of Population Health at NYU Grossman School of Medicine, New York, NY, USA
| | - Sarah Griglun
- Department of Medicine, Laura & Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Dayna Leis
- Department of Medicine, Laura & Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Nina Yang
- Department of Medicine, Laura & Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Viktoriya Aranchiy
- Department of Medicine, Laura & Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Sabrina Machado
- Department of Medicine, Laura & Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Erika Waalkes
- Department of Medicine, Laura & Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Gabrielle Gargano
- Department of Medicine, Laura & Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Nadia Soamchand
- Department of Medicine, Laura & Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Amrutesh Puranik
- Department of Medicine, Laura & Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
- Precision Immunology Laboratory, Perlmutter Cancer Center, NYU Langone Health, New York, NY, 10016, USA
| | - Pratip Chattopadhyay
- Precision Immunology Laboratory, Perlmutter Cancer Center, NYU Langone Health, New York, NY, 10016, USA
| | - Ezeddin Fedal
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Fang-Ming Deng
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Qinghu Ren
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Luis Chiriboga
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Jonathan Melamed
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | | | - Kwok-Kin Wong
- Department of Medicine, Laura & Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
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6
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Sajeev A, BharathwajChetty B, Vishwa R, Alqahtani MS, Abbas M, Sethi G, Kunnumakkara AB. Crosstalk between Non-Coding RNAs and Wnt/β-Catenin Signaling in Head and Neck Cancer: Identification of Novel Biomarkers and Therapeutic Agents. Noncoding RNA 2023; 9:63. [PMID: 37888209 PMCID: PMC10610319 DOI: 10.3390/ncrna9050063] [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: 08/21/2023] [Revised: 09/25/2023] [Accepted: 10/08/2023] [Indexed: 10/28/2023] Open
Abstract
Head and neck cancers (HNC) encompass a broad spectrum of neoplastic disorders characterized by significant morbidity and mortality. While contemporary therapeutic interventions offer promise, challenges persist due to tumor recurrence and metastasis. Central to HNC pathogenesis is the aberration in numerous signaling cascades. Prominently, the Wnt signaling pathway has been critically implicated in the etiology of HNC, as supported by a plethora of research. Equally important, variations in the expression of non-coding RNAs (ncRNAs) have been identified to modulate key cancer phenotypes such as cellular proliferation, epithelial-mesenchymal transition, metastatic potential, recurrence, and treatment resistance. This review aims to provide an exhaustive insight into the multifaceted influence of ncRNAs on HNC, with specific emphasis on their interactions with the Wnt/β-catenin (WBC) signaling axis. We further delineate the effect of ncRNAs in either exacerbating or attenuating HNC progression via interference with WBC signaling. An overview of the mechanisms underlying the interplay between ncRNAs and WBC signaling is also presented. In addition, we described the potential of various ncRNAs in enhancing the efficacy of chemotherapeutic and radiotherapeutic modalities. In summary, this assessment posits the potential of ncRNAs as therapeutic agents targeting the WBC signaling pathway in HNC management.
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Affiliation(s)
- Anjana Sajeev
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Guwahati, Guwahati 781039, Assam, India; (A.S.); (B.B.); (R.V.)
| | - Bandari BharathwajChetty
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Guwahati, Guwahati 781039, Assam, India; (A.S.); (B.B.); (R.V.)
| | - Ravichandran Vishwa
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Guwahati, Guwahati 781039, Assam, India; (A.S.); (B.B.); (R.V.)
| | - Mohammed S. Alqahtani
- Radiological Sciences Department, College of Applied Medical Sciences, King Khalid University, Abha 61421, Saudi Arabia;
- BioImaging Unit, Space Research Centre, Michael Atiyah Building, University of Leicester, Leicester LE1 7RH, UK
| | - Mohamed Abbas
- Electrical Engineering Department, College of Engineering, King Khalid University, Abha 61421, Saudi Arabia;
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
| | - Ajaikumar B. Kunnumakkara
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Guwahati, Guwahati 781039, Assam, India; (A.S.); (B.B.); (R.V.)
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7
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Wee Y, Wang J, Wilson EC, Rich CP, Rogers A, Tong Z, DeGroot E, Gopal YV, Davies MA, Ekiz HA, Tay JK, Stubben C, Boucher KM, Oviedo JM, Fairfax KC, Williams MA, Holmen SL, Wolff RK, Grossmann AH. ARF6-dependent endocytic trafficking of the Interferon-γ receptor drives adaptive immune resistance in cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.29.560199. [PMID: 37873189 PMCID: PMC10592860 DOI: 10.1101/2023.09.29.560199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Adaptive immune resistance (AIR) is a protective process used by cancer to escape elimination by CD8+ T cells. Inhibition of immune checkpoints PD-1 and CTLA-4 specifically target Interferon-gamma (IFNγ)-driven AIR. AIR begins at the plasma membrane where tumor cell-intrinsic cytokine signaling is initiated. Thus, plasma membrane remodeling by endomembrane trafficking could regulate AIR. Herein we report that the trafficking protein ADP-Ribosylation Factor 6 (ARF6) is critical for IFNγ-driven AIR. ARF6 prevents transport of the receptor to the lysosome, augmenting IFNγR expression, tumor intrinsic IFNγ signaling and downstream expression of immunosuppressive genes. In murine melanoma, loss of ARF6 causes resistance to immune checkpoint blockade (ICB). Likewise, low expression of ARF6 in patient tumors correlates with inferior outcomes with ICB. Our data provide new mechanistic insights into tumor immune escape, defined by ARF6-dependent AIR, and support that ARF6-dependent endomembrane trafficking of the IFNγ receptor influences outcomes of ICB.
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Affiliation(s)
- Yinshen Wee
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
- These authors contributed equally
- current contact information: School of Dentistry, Taipei Medical University, Taiwan
| | - Junhua Wang
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
- These authors contributed equally
| | - Emily C. Wilson
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
| | - Coulson P. Rich
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
| | - Aaron Rogers
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
| | - Zongzhong Tong
- Department of Pathology, University of Utah, Salt Lake City, Utah
| | - Evelyn DeGroot
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Y.N. Vashisht Gopal
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael A. Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - H. Atakan Ekiz
- Department of Molecular Biology and Genetics, Izmir institute of Technology, Gulbahce, Urla, 35430, Izmir, Turkey
| | - Joshua K.H. Tay
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
| | - Chris Stubben
- Bioinformatics Shared Resource, Huntsman Cancer Institute, Salt Lake City, Utah
| | - Kenneth M. Boucher
- Cancer Biostatistics Shared Resource, Huntsman Cancer Institute, Salt Lake City, Utah
| | - Juan M. Oviedo
- Department of Pathology, University of Utah, Salt Lake City, Utah
| | - Keke C. Fairfax
- Department of Pathology, University of Utah, Salt Lake City, Utah
| | - Matthew A. Williams
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
| | - Sheri L. Holmen
- Huntsman Cancer Institute, Salt Lake City, Utah
- Department of Surgery, University of Utah, Salt Lake City, Utah
| | - Roger K. Wolff
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
| | - Allie H. Grossmann
- Department of Pathology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, Salt Lake City, Utah
- Lead contact
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8
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Kaya NA, Tai D, Lim X, Lim JQ, Lau MC, Goh D, Phua CZJ, Wee FYT, Joseph CR, Lim JCT, Neo ZW, Ye J, Cheung L, Lee J, Loke KSH, Gogna A, Yao F, Lee MY, Shuen TWH, Toh HC, Hilmer A, Chan YS, Lim TKH, Tam WL, Choo SP, Yeong J, Zhai W. Multimodal molecular landscape of response to Y90-resin microsphere radioembolization followed by nivolumab for advanced hepatocellular carcinoma. J Immunother Cancer 2023; 11:e007106. [PMID: 37586766 PMCID: PMC10432632 DOI: 10.1136/jitc-2023-007106] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2023] [Indexed: 08/18/2023] Open
Abstract
BACKGROUND Combination therapy with radioembolization (yttrium-90)-resin microspheres) followed by nivolumab has shown a promising response rate of 30.6% in a Phase II trial (CA209-678) for advanced hepatocellular carcinoma (HCC); however, the response mechanisms and relevant biomarkers remain unknown. METHODS By collecting both pretreatment and on-treatment samples, we performed multimodal profiling of tissue and blood samples and investigated molecular changes associated with favorable responses in 33 patients from the trial. RESULTS We found that higher tumor mutation burden, NCOR1 mutations and higher expression of interferon gamma pathways occurred more frequently in responders. Meanwhile, non-responders tended to be enriched for a novel Asian-specific transcriptomic subtype (Kaya_P2) with a high frequency of chromosome 16 deletions and upregulated cell cycle pathways. Strikingly, unlike other cancer types, we did not observe any association between T-cell populations and treatment response, but tumors from responders had a higher proportion of CXCL9+/CXCR3+ macrophages. Moreover, biomarkers discovered in previous immunotherapy trials were not predictive in the current cohort, suggesting a distinctive molecular landscape associated with differential responses to the combination therapy. CONCLUSIONS This study unraveled extensive molecular changes underlying distinctive responses to the novel treatment and pinpointed new directions for harnessing combination therapy in patients with advanced HCC.
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Affiliation(s)
- Neslihan Arife Kaya
- Genome Institute of Singapore (GIS), Agency for Science(A*STAR), Technology and Research, Singapore
| | - David Tai
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore
- Duke NUS Medical School, Singapore
| | - Xinru Lim
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Jia Qi Lim
- Genome Institute of Singapore (GIS), Agency for Science(A*STAR), Technology and Research, Singapore
| | - Mai Chan Lau
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore
- Bioinformatics Institute (BII), Agency of Science Technology and Research, Singapore
| | - Denise Goh
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Cheryl Zi Jin Phua
- Genome Institute of Singapore (GIS), Agency for Science(A*STAR), Technology and Research, Singapore
| | - Felicia Yu Ting Wee
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Craig Ryan Joseph
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Jeffrey Chun Tatt Lim
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Zhen Wei Neo
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Jiangfeng Ye
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Lawrence Cheung
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Joycelyn Lee
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore
- Duke NUS Medical School, Singapore
| | - Kelvin S H Loke
- Duke NUS Medical School, Singapore
- Department of Nuclear Medicine and Molecular Imaging, Singapore General Hospital, Singapore
| | - Apoorva Gogna
- Department of Vascular and Interventional Radiology, Singapore General Hospital, Singapore
| | - Fei Yao
- Genome Institute of Singapore (GIS), Agency for Science(A*STAR), Technology and Research, Singapore
| | - May Yin Lee
- Genome Institute of Singapore (GIS), Agency for Science(A*STAR), Technology and Research, Singapore
| | | | - Han Chong Toh
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Axel Hilmer
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Koln, Cologne, Germany
| | - Yun Shen Chan
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, Guangdong Province, China
| | - Tony Kiat-Hon Lim
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - Wai Leong Tam
- Genome Institute of Singapore (GIS), Agency for Science(A*STAR), Technology and Research, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Su Pin Choo
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Joe Yeong
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - Weiwei Zhai
- Genome Institute of Singapore (GIS), Agency for Science(A*STAR), Technology and Research, Singapore
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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9
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Pelizzaro F, Farinati F, Trevisani F. Immune Checkpoint Inhibitors in Hepatocellular Carcinoma: Current Strategies and Biomarkers Predicting Response and/or Resistance. Biomedicines 2023; 11:1020. [PMID: 37189643 PMCID: PMC10135644 DOI: 10.3390/biomedicines11041020] [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: 01/27/2023] [Revised: 02/28/2023] [Accepted: 03/06/2023] [Indexed: 03/29/2023] Open
Abstract
In recent years, immune checkpoint inhibitors (ICIs) have revolutionized the treatment of patients with hepatocellular carcinoma (HCC). Following the positive results of the IMbrave150 trial, the combination of atezolizumab (an anti-PD-L1 antibody) and bevacizumab (an anti-VEGF antibody) became the standard of care frontline treatment for patients with advanced stage HCC. Several other trials evaluated immunotherapy in HCC, demonstrating that ICIs-based regimens are currently the most effective treatment strategies and expanding the therapeutic possibilities. Despite the unprecedent rates of objective tumor response, not all patients benefit from treatment with ICIs. Therefore, in order to select the appropriate therapy as well as to correctly allocate medical resources and avoid unnecessary treatment-related toxicities, there is great interest in identifying the predictive biomarkers of response or resistance to immunotherapy-based regimens. Immune classes of HCC, genomic signatures, anti-drug antibodies, and patient-related factors (e.g., etiology of liver disease, gut microbiota diversity) have been associated to the response to ICIs, but none of the proposed biomarkers have been translated into clinical practice so far. Considering the crucial importance of this topic, in this review we aim to summarize the available data on tumor and clinical features associated with the response or resistance of HCC to immunotherapies.
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Affiliation(s)
- Filippo Pelizzaro
- Department of Surgery, Oncology and Gastroenterology, University of Padova, 35128 Padova, Italy
- Gastroenterology Unit, Azienda Ospedale-Università di Padova, 35128 Padova, Italy
| | - Fabio Farinati
- Department of Surgery, Oncology and Gastroenterology, University of Padova, 35128 Padova, Italy
- Gastroenterology Unit, Azienda Ospedale-Università di Padova, 35128 Padova, Italy
| | - Franco Trevisani
- Department of Medical and Surgical Sciences, University of Bologna, 40126 Bologna, Italy
- Unit of Semeiotics, Liver and Alcohol-Related Diseases, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
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10
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TGF-β2 antisense oligonucleotide enhances T-cell mediated anti-tumor activities by IL-2 via attenuation of fibrotic reaction in a humanized mouse model of pancreatic ductal adenocarcinoma. Biomed Pharmacother 2023; 159:114212. [PMID: 36610224 DOI: 10.1016/j.biopha.2022.114212] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/20/2022] [Accepted: 12/31/2022] [Indexed: 01/07/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive cancers, with high mortality and recurrence rate. In this study, we generated a human immune system mouse model by transplanting human peripheral blood mononuclear cells into NSG-B2m mice followed by xenografting AsPC-1 cells, after which we assessed the role of transforming growth factor-β2 (TGF-β2) in T-cell-mediated anti-tumor immunity. We observed that inhibiting the TGF-β2 production by TGF-β2 antisense oligonucleotide (TASO) combined with IL-2 delays pancreatic cancer growth. Co-treatment of TASO and IL-2 had little effect on the SMAD-dependent pathway, but significantly inhibited the Akt phosphorylation and sequentially activated GSK-3β. Activation of GSK-3β by TASO subsequently suppressed β-catenin and α-SMA expression and resulted in attenuated fibrotic reactions, facilitating the infiltration of CD8 + cytotoxic T lymphocytes (CTLs) into the tumor. TGF-β2 inhibition suppressed the Foxp3 + regulatory T-cells in peripheral blood and tumors, thereby enhancing the tumoricidal effects of CTLs associated with increased granzyme B and cleaved caspase-3. Moreover, changes in the T-cell composition in peripheral blood and at the tumor site by TASO and IL-2 induced the increase of pro-inflammatory cytokines such as IFN-γ and TNF-α and the decrease of anti-inflammatory cytokines such as TGF-βs. These results indicate that the TGF-β2 inhibition by TASO combined with IL-2 enhances the T-cell mediated anti-tumor immunity against SMAD4-mutated PDAC by modulating the tumor-associated fibrosis, suggesting that TASO in combination with IL-2 may be a promising immunotherapeutic intervention for PDAC.
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11
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Castro MV, Barbero GA, Máscolo P, Villanueva MB, Nsengimana J, Newton-Bishop J, Illescas E, Quezada MJ, Lopez-Bergami P. ROR2 promotes epithelial-mesenchymal transition by hyperactivating ERK in melanoma. J Cell Commun Signal 2023; 17:75-88. [PMID: 35723796 PMCID: PMC10030744 DOI: 10.1007/s12079-022-00683-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 05/23/2022] [Indexed: 12/19/2022] Open
Abstract
Receptor tyrosine kinase-like orphan receptor 2 (ROR2) is a protein with important functions during embryogenesis that is dysregulated in human cancer. An intriguing feature of this receptor is that it plays opposite roles in different tumor types either promoting or inhibiting tumor progression. Understanding the complex role of this receptor requires a more profound exploration of both the altered biological and molecular mechanisms. Here, we describe that ROR2 promotes Epithelial-Mesenchymal Transition (EMT) by inducing cadherin switch and the upregulation of the transcription factors ZEB1, Twist, Slug, Snail, and HIF1A, together with a mesenchymal phenotype and increased migration. We show that ROR2 activates both p38 and ERK mitogen-activated protein kinase pathways independently of Wnt5a. Further, we demonstrated that the upregulation of EMT-related proteins depends on the hyperactivation of the ERK pathway far above the typical high constitutive activity observed in melanoma. In addition, ROR2 also promoted ERK phosphorylation, EMT, invasion, and necrosis in xenotransplanted mice. ROR2 also associates with EMT in tumor samples from melanoma patients where analysis of large cohorts revealed that increased ROR2 levels are linked to EMT signatures. This important role of ROR2 translates into melanoma patient' s prognosis since elevated ROR2 levels reduced overall survival and distant metastasis-free survival of patients with lymph node metastasis. In sum, these results demonstrate that ROR2 contributes to melanoma progression by inducing EMT and necrosis and can be an attractive therapeutic target for melanoma.
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Affiliation(s)
- María Victoria Castro
- Centro de Estudios Biomédicos, Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, Hidalgo 775, 6th Floor, Lab 602., 1405, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1425, Buenos Aires, Argentina
| | - Gastón Alexis Barbero
- Centro de Estudios Biomédicos, Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, Hidalgo 775, 6th Floor, Lab 602., 1405, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1425, Buenos Aires, Argentina
| | - Paula Máscolo
- Centro de Estudios Biomédicos, Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, Hidalgo 775, 6th Floor, Lab 602., 1405, Buenos Aires, Argentina
| | - María Belén Villanueva
- Centro de Estudios Biomédicos, Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, Hidalgo 775, 6th Floor, Lab 602., 1405, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1425, Buenos Aires, Argentina
| | - Jérémie Nsengimana
- Biostatistics Research Group, Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | | | - Edith Illescas
- Centro de Estudios Biomédicos, Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, Hidalgo 775, 6th Floor, Lab 602., 1405, Buenos Aires, Argentina
| | - María Josefina Quezada
- Centro de Estudios Biomédicos, Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, Hidalgo 775, 6th Floor, Lab 602., 1405, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1425, Buenos Aires, Argentina
| | - Pablo Lopez-Bergami
- Centro de Estudios Biomédicos, Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, Hidalgo 775, 6th Floor, Lab 602., 1405, Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1425, Buenos Aires, Argentina.
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12
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Sorting Transcriptomics Immune Information from Tumor Molecular Features Allows Prediction of Response to Anti-PD1 Therapy in Patients with Advanced Melanoma. Int J Mol Sci 2023; 24:ijms24010801. [PMID: 36614248 PMCID: PMC9821399 DOI: 10.3390/ijms24010801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/21/2022] [Accepted: 12/27/2022] [Indexed: 01/05/2023] Open
Abstract
Immunotherapy based on anti-PD1 antibodies has improved the outcome of advanced melanoma. However, prediction of response to immunotherapy remains an unmet need in the field. Tumor PD-L1 expression, mutational burden, gene profiles and microbiome profiles have been proposed as potential markers but are not used in clinical practice. Probabilistic graphical models and classificatory algorithms were used to classify melanoma tumor samples from a TCGA cohort. A cohort of patients with advanced melanoma treated with PD-1 inhibitors was also analyzed. We established that gene expression data can be grouped in two different layers of information: immune and molecular. In the TCGA, the molecular classification provided information on processes such as epidermis development and keratinization, melanogenesis, and extracellular space and membrane. The immune layer classification was able to distinguish between responders and non-responders to immunotherapy in an independent series of patients with advanced melanoma treated with PD-1 inhibitors. We established that the immune information is independent than molecular features of the tumors in melanoma TCGA cohort, and an immune classification of these tumors was established. This immune classification was capable to determine what patients are going to respond to immunotherapy in a new cohort of patients with advanced melanoma treated with PD-1 inhibitors Therefore, this immune signature could be useful to the clinicians to identify those patients who will respond to immunotherapy.
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13
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Birkeälv S, Harland M, Matsuyama LSAS, Rashid M, Mehta I, Laye JP, Haase K, Mell T, Iyer V, Robles‐Espinoza CD, McDermott U, van Loo P, Kuijjer ML, Possik PA, Maria Engler SS, Bishop DT, Newton‐Bishop J, Adams DJ. Mutually exclusive genetic interactions and gene essentiality shape the genomic landscape of primary melanoma. J Pathol 2023; 259:56-68. [PMID: 36219477 PMCID: PMC10098817 DOI: 10.1002/path.6019] [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: 07/02/2022] [Revised: 09/02/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022]
Abstract
Melanoma is a heterogenous malignancy with an unpredictable clinical course. Most patients who present in the clinic are diagnosed with primary melanoma, yet large-scale sequencing efforts have focused primarily on metastatic disease. In this study we sequence-profiled 524 American Joint Committee on Cancer Stage I-III primary tumours. Our analysis of these data reveals recurrent driver mutations, mutually exclusive genetic interactions, where two genes were never or rarely co-mutated, and an absence of co-occurring genetic events. Further, we intersected copy number calls from our primary melanoma data with whole-genome CRISPR screening data to identify the transcription factor interferon regulatory factor 4 (IRF4) as a melanoma-associated dependency. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Sofia Birkeälv
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
| | - Mark Harland
- Division of Haematology and ImmunologyUniversity of Leeds School of MedicineLeedsUK
| | - Larissa Satiko Alcantara Sekimoto Matsuyama
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical SciencesUniversity of Sao PauloSao PauloBrazil
| | - Mamun Rashid
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
| | - Ishan Mehta
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
| | - Jonathan P Laye
- Division of Haematology and ImmunologyUniversity of Leeds School of MedicineLeedsUK
| | | | - Tracey Mell
- Division of Haematology and ImmunologyUniversity of Leeds School of MedicineLeedsUK
| | - Vivek Iyer
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
| | - Carla Daniela Robles‐Espinoza
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
- Laboratorio Internacional de Investigación sobre el Genoma HumanoUniversidad Nacional Autónoma de México, Campus JuriquillaSantiago de QuerétaroMexico
| | - Ultan McDermott
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
| | | | - Marieke L Kuijjer
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, Faculty of MedicineUniversity of OsloOsloNorway
- Department of Pathology and Leiden Center for Computational OncologyLeiden University Medical CenterLeidenthe Netherlands
| | - Patricia A Possik
- Division of Experimental and Translational ResearchBrazilian National Cancer InstituteRio de JaneiroBrazil
| | - Silvya Stuchi Maria Engler
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical SciencesUniversity of Sao PauloSao PauloBrazil
| | - D Timothy Bishop
- Division of Haematology and ImmunologyUniversity of Leeds School of MedicineLeedsUK
| | - Julia Newton‐Bishop
- Division of Haematology and ImmunologyUniversity of Leeds School of MedicineLeedsUK
| | - David J Adams
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
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14
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Umar SA, Dong B, Nihal M, Chang H. Frizzled receptors in melanomagenesis: From molecular interactions to target identification. Front Oncol 2022; 12:1096134. [PMID: 36620565 PMCID: PMC9816865 DOI: 10.3389/fonc.2022.1096134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Frizzled (FZD) proteins are receptors for the WNT family ligands. Inherited human diseases and genetic experiments using knockout mice have revealed a central role of FZDs in multiple aspects of embryonic development and tissue homeostasis. Misregulated FZD signaling has also been found in many cancers. Recent studies on three out of the ten mammalian FZDs in melanoma have shown that they promote tumor cell proliferation and invasion, via the activation of the canonical WNT/β-catenin or non-canonical PCP signaling pathway. In this concise review, we summarize our current knowledge of individual FZDs in melanoma, discuss the involvement of both the canonical and non-canonical pathways, and describe ongoing efforts to target the FZD receptors for melanoma treatment.
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Affiliation(s)
- Sheikh A. Umar
- Department of Dermatology, University of Wisconsin-Madison, Madison, WI, United States
| | - Bo Dong
- Department of Dermatology, University of Wisconsin-Madison, Madison, WI, United States
| | - Minakshi Nihal
- William S. Middleton Memorial Veterans Hospital, Madison, WI, United States
| | - Hao Chang
- Department of Dermatology, University of Wisconsin-Madison, Madison, WI, United States,William S. Middleton Memorial Veterans Hospital, Madison, WI, United States,*Correspondence: Hao Chang,
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15
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Ji W, Niu X, Yu Y, Li Z, Gu L, Lu S. SMO mutation predicts the effect of immune checkpoint inhibitor: From NSCLC to multiple cancers. Front Immunol 2022; 13:955800. [DOI: 10.3389/fimmu.2022.955800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
BackgroundThe emergence of immune checkpoint inhibitors (ICIs) is one of the most promising breakthroughs for the treatment of multiple cancer types, but responses vary. Growing evidence points to a link between developmental signaling pathway-related genes and antitumor immunity, but the association between the genomic alterations in these genes and the response to ICIs still needs to be elucidated.MethodsClinical data and sequencing data from published studies and our cohort were collected to analyze the association of the mutation status of SMO with the efficacy of ICI therapy in the non-small cell lung cancer (NSCLC) cohort and the pan-cancer cohort. Furthermore, the correlation between SMO mutation and immunotherapeutic biomarkers such as immune cell infiltration, immune-related genes, and underlying signaling pathways was analyzed. Three SMO mutant plasmids were transfected into cells to explore the SMO mutation status in the context of its expression and cell growth.ResultIn the NSCLC discovery cohort, the median progression-free survival in the SMO mutant (SMO_MUT) was longer than that in the wild type (SMO_WT) (23.0 vs. 3.8 months, adjusted p = 0.041). This finding was further confirmed in the NSCLC validation cohort (8.7 vs. 5.1 months, adjusted p = 0.013). In the pan-cancer cohort (n = 1,347), a significant overall survival advantage was observed in patients with SMO mutations [not reached (NR) vs. 18 months, adjusted p = 0.024]. In the subgroup analysis, the survival advantage of SMO_MUT against SMO_WT was prominent and consistent across genders, ages, treatment types, cancer types, and the tumor mutation burden (TMB) status (all pinteraction > 0.05). In an in vitro experiment, we found that both the mutant and wild-type plasmids can promote the expression of SMO, but the mutant plasmid had lower SMO mRNA and protein levels than the wild type. In CCK-8 experiments, we found that SMO_MUT plasmids can improve the growth of Calu-1 and PC-9 cells, but this capability varied between different mutations and cells. Upon further exploration, the SMO mutation status was found to be related to a higher TMB, more neoantigen load, more DNA damage repair (DDR) mutations, higher microsatellite instability (MSI) score, and higher CD8+ T-cell infiltration.ConclusionsThe SMO mutation status is an independent prognostic factor that can be used to predict better clinical outcomes of ICI treatment across multiple cancer types.
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Genetic and Methylation Analysis of CTNNB1 in Benign and Malignant Melanocytic Lesions. Cancers (Basel) 2022; 14:cancers14174066. [PMID: 36077603 PMCID: PMC9454999 DOI: 10.3390/cancers14174066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/19/2022] [Accepted: 07/26/2022] [Indexed: 11/21/2022] Open
Abstract
Simple Summary Recurrent CTNNB1 exon 3 mutations have been recognized in the distinct group of melanocytic tumors showing deep penetrating nevus-like morphology and in 1–2% of advanced melanoma. We performed a detailed genetic analysis of difficult-to-classify nevi and melanomas with CTNNB1 mutations and found that benign tumors (nevi) show characteristic morphological, genetic and epigenetic traits, which distinguish them from other nevi and melanoma. Malignant CTNNB1-mutant tumors (melanoma) demonstrated a different genetic profile, grouping clearly with other non-CTNNB1 melanomas in methylation assays. To further evaluate the role of CTNNB1 mutations in melanoma, we assessed a large cohort of clinically sequenced melanomas, identifying 38 tumors with CTNNB1 exon 3 mutations, including recurrent S45 (n = 13, 34%), G34 (n = 5, 13%), and S27 (n = 5, 13%) mutations. Locations and histological subtype of CTNNB1-mutated melanoma varied; none were reported as showing deep penetrating nevus-like morphology. The most frequent concurrent activating mutations were BRAF V600 (55%) and NRAS Q61 (34%). Abstract Melanocytic neoplasms have been genetically characterized in detail during the last decade. Recurrent CTNNB1 exon 3 mutations have been recognized in the distinct group of melanocytic tumors showing deep penetrating nevus-like morphology. In addition, they have been identified in 1–2% of advanced melanoma. Performing a detailed genetic analysis of difficult-to-classify nevi and melanomas with CTNNB1 mutations, we found that benign tumors (nevi) show characteristic morphological, genetic and epigenetic traits, which distinguish them from other nevi and melanoma. Malignant CTNNB1-mutant tumors (melanomas) demonstrated a different genetic profile, instead grouping clearly with other non-CTNNB1 melanomas in methylation assays. To further evaluate the role of CTNNB1 mutations in melanoma, we assessed a large cohort of clinically sequenced melanomas, identifying 38 tumors with CTNNB1 exon 3 mutations, including recurrent S45 (n = 13, 34%), G34 (n = 5, 13%), and S27 (n = 5, 13%) mutations. Locations and histological subtype of CTNNB1-mutated melanoma varied; none were reported as showing deep penetrating nevus-like morphology. The most frequent concurrent activating mutations were BRAF V600 (n = 21, 55%) and NRAS Q61 (n = 13, 34%). In our cohort, four of seven (58%) and one of nine (11%) patients treated with targeted therapy (BRAF and MEK Inhibitors) or immune-checkpoint therapy, respectively, showed disease control (partial response or stable disease). In summary, CTNNB1 mutations are associated with a unique melanocytic tumor type in benign tumors (nevi), which can be applied in a diagnostic setting. In advanced disease, no clear characteristics distinguishing CTNNB1-mutant from other melanomas were observed; however, studies of larger, optimally prospective, cohorts are warranted.
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17
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Attrill GH, Lee H, Tasker AT, Adegoke NA, Ferguson AL, da Silva IP, Saw RPM, Thompson JF, Palendira U, Long GV, Ferguson PM, Scolyer RA, Wilmott JS. Detailed spatial immunophenotyping of primary melanomas reveals immune cell subpopulations associated with patient outcome. Front Immunol 2022; 13:979993. [PMID: 36003398 PMCID: PMC9393646 DOI: 10.3389/fimmu.2022.979993] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
While the tumor immune microenvironment (TIME) of metastatic melanoma has been well characterized, the primary melanoma TIME is comparatively poorly understood. Additionally, although the association of tumor-infiltrating lymphocytes with primary melanoma patient outcome has been known for decades, it is not considered in the current AJCC melanoma staging system. Detailed immune phenotyping of advanced melanoma has revealed multiple immune biomarkers, including the presence of CD8+ T-cells, for predicting response to immunotherapies. However, in primary melanomas, immune biomarkers are lacking and CD8+ T-cells have yet to be extensively characterized. As recent studies combining immune features and clinicopathologic characteristics have created more accurate predictive models, this study sought to characterize the TIME of primary melanomas and identify predictors of patient outcome. We first phenotyped CD8+ T cells in fresh stage II primary melanomas using flow cytometry (n = 6), identifying a CD39+ tumor-resident CD8+ T-cell subset enriched for PD-1 expression. We then performed Opal multiplex immunohistochemistry and quantitative pathology-based immune profiling of CD8+ T-cell subsets, along with B cells, NK cells, Langerhans cells and Class I MHC expression in stage II primary melanoma specimens from patients with long-term follow-up (n = 66), comparing patients based on their recurrence status at 5 years after primary diagnosis. A CD39+CD103+PD-1- CD8+ T-cell population (P2) comprised a significantly higher proportion of intratumoral and stromal CD8+ T-cells in patients with recurrence-free survival (RFS) ≥5 years vs those with RFS <5 years (p = 0.013). Similarly, intratumoral B cells (p = 0.044) and a significantly higher B cell density at the tumor/stromal interface were associated with RFS. Both P2 and B cells localized in significantly closer proximity to melanoma cells in patients who remained recurrence-free (P2 p = 0.0139, B cell p = 0.0049). Our results highlight how characterizing the TIME in primary melanomas may provide new insights into how the complex interplay of the immune system and tumor can modify the disease outcomes. Furthermore, in the context of current clinical trials of adjuvant anti-PD-1 therapies in high-risk stage II primary melanoma, assessment of B cells and P2 could identify patients at risk of recurrence and aid in long-term treatment decisions at the point of primary melanoma diagnosis.
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Affiliation(s)
- Grace H. Attrill
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Hansol Lee
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Annie T. Tasker
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Nurudeen A. Adegoke
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Angela L. Ferguson
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- Centenary Institute, The University of Sydney, Sydney, NSW, Australia
| | - Ines Pires da Silva
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- Westmead and Blacktown Hospitals, Sydney, NSW, Australia
| | - Robyn P. M. Saw
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Royal Prince Alfred Hospital, Sydney, NSW, Australia
- Mater Hospital, North Sydney, NSW, Australia
| | - John F. Thompson
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Royal Prince Alfred Hospital, Sydney, NSW, Australia
- Mater Hospital, North Sydney, NSW, Australia
| | - Umaimainthan Palendira
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- Centenary Institute, The University of Sydney, Sydney, NSW, Australia
| | - Georgina V. Long
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- Mater Hospital, North Sydney, NSW, Australia
- Royal North Shore Hospital, St Leonards, NSW, Australia
| | - Peter M. Ferguson
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Royal Prince Alfred Hospital, Sydney, NSW, Australia
- NSW Health Pathology, Sydney, NSW, Australia
| | - Richard A. Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- Royal Prince Alfred Hospital, Sydney, NSW, Australia
- NSW Health Pathology, Sydney, NSW, Australia
| | - James S. Wilmott
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- *Correspondence: James S. Wilmott,
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18
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Shui IM, Liu XQ, Zhao Q, Kim ST, Sun Y, Yearley JH, Choudhury T, Webber AL, Krepler C, Cristescu R, Lee J. Baseline and post-treatment biomarkers of resistance to anti-PD-1 therapy in acral and mucosal melanoma: an observational study. J Immunother Cancer 2022; 10:jitc-2022-004879. [PMID: 35793874 PMCID: PMC9260847 DOI: 10.1136/jitc-2022-004879] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2022] [Indexed: 12/14/2022] Open
Abstract
Background Immunotherapies targeting programmed cell death-1 (PD-1) and its ligands have improved clinical outcomes for advanced melanoma. However, many tumors exhibit primary resistance or acquire secondary resistance after an initial positive response. The mechanisms of resistance are not well understood, and no validated predictive biomarkers are available. This exploratory study aimed to characterize baseline differences and molecular changes arising during treatment in acral and mucosal melanomas that exhibited primary or secondary resistance to anti-PD-1 monotherapy. Methods This was an observational retrospective study of 124 patients who had been treated for metastatic acral or mucosal melanoma with anti-PD-1 monotherapy. Tumor samples were collected at baseline (all patients) and post-treatment (resistant tumors only) and were assayed by immunohistochemistry, whole-exome sequencing, and RNA sequencing. Results At baseline, more non-progressor than resistant tumors exhibited expression of PD-L1, immune cell infiltration, and high tumor mutational burden (TMB); baseline PD-L1 expression was also more common in secondary-resistant than in primary-resistant tumors as well as in late versus early secondary-resistant tumors. Non-progressor tumors also had higher median baseline expression of an 18-gene T cell-inflamed gene expression profile (TcellinfGEP). Among resistant tumors, the proportion of PD-L1-positive melanomas and the expression of the TcellinfGEP mRNA signature increased during treatment, while the expression of mRNA signatures related to WNT and INFA1 signaling decreased. There was evidence for greater changes from baseline in secondary-resistant versus primary-resistant tumors for some markers, including expression of RAS-related and WNT-related mRNA signatures and density of CD11c+ and FOXP3+ T cells. Greater changes in CD11c+ cell density were observed in early compared with late secondary-resistant tumors. Conclusions Our findings suggest that TcellinfGEP and PD-L1 expression, TMB, immune cell infiltration, and RAS and WNT signaling warrant further investigation as potential mechanisms and/or biomarkers of anti-PD-1 therapy resistance in acral and mucosal melanomas. Confirmation of these findings in larger populations is needed.
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Affiliation(s)
| | | | - Qing Zhao
- Merck & Co., Inc, Rahway, New Jersey, USA
| | - Seung Tae Kim
- Hematology and Oncology, Samsung Medical Center, Gangnam-gu, South Korea
| | - Yuan Sun
- Merck & Co., Inc, Rahway, New Jersey, USA
| | | | | | | | | | | | - Jeeyun Lee
- Hematology and Oncology, Samsung Medical Center, Gangnam-gu, South Korea
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19
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Conway K, Tsai YS, Edmiston SN, Parker JS, Parrish EA, Hao H, Kuan PF, Scott GA, Frank JS, Googe P, Ollila DW, Thomas NE. Characterization of the CpG Island Hypermethylated Phenotype Subclass in Primary Melanomas. J Invest Dermatol 2022; 142:1869-1881.e10. [PMID: 34843679 PMCID: PMC9135958 DOI: 10.1016/j.jid.2021.11.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/28/2021] [Accepted: 11/08/2021] [Indexed: 12/26/2022]
Abstract
Cutaneous melanoma can be lethal even if detected at an early stage. Epigenetic profiling may facilitate the identification of aggressive primary melanomas with unfavorable outcomes. We performed clustering of whole-genome methylation data to identify subclasses that were then assessed for survival, clinical features, methylation patterns, and biological pathways. Among 89 cutaneous primary invasive melanomas, we identified three methylation subclasses exhibiting low methylation, intermediate methylation, or hypermethylation of CpG islands, known as the CpG island methylator phenotype (CIMP). CIMP melanomas occurred as early as tumor stage 1b and, compared with low-methylation melanomas, were associated with age at diagnosis ≥65 years, lentigo maligna melanoma histologic subtype, presence of ulceration, higher American Joint Committee on Cancer stage and tumor stage, and lower tumor-infiltrating lymphocyte grade (all P < 0.05). Patients with CIMP melanomas had worse melanoma-specific survival (hazard ratio = 11.84; confidence interval = 4.65‒30.20) than those with low-methylation melanomas, adjusted for age, sex, American Joint Committee on Cancer stage, and tumor-infiltrating lymphocyte grade. Genes hypermethylated in CIMP compared with those in low-methylation melanomas included PTEN, VDR, PD-L1, TET2, and gene sets related to development/differentiation, the extracellular matrix, and immunity. CIMP melanomas exhibited hypermethylation of genes important in melanoma progression and tumor immunity, and although present in some early melanomas, CIMP was associated with worse survival independent of known prognostic factors.
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Affiliation(s)
- Kathleen Conway
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Dermatology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
| | - Yihsuan S Tsai
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sharon N Edmiston
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Genetics, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Eloise A Parrish
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Honglin Hao
- Department of Genetics, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Pei Fen Kuan
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, New York, USA
| | - Glynis A Scott
- Department of Dermatology, University of Rochester Medical Center, Rochester, New York, USA; Department of Pathology & Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Jill S Frank
- Department of Surgery, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Paul Googe
- Department of Dermatology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Pathology and Lab Medicine, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David W Ollila
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Surgery, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nancy E Thomas
- Department of Dermatology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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20
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Chauhan JS, Hölzel M, Lambert JP, Buffa FM, Goding CR. The MITF regulatory network in melanoma. Pigment Cell Melanoma Res 2022; 35:517-533. [PMID: 35771179 PMCID: PMC9545041 DOI: 10.1111/pcmr.13053] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/09/2022] [Accepted: 06/28/2022] [Indexed: 12/02/2022]
Abstract
Bidirectional interactions between plastic tumor cells and the microenvironment critically impact tumor evolution and metastatic dissemination by enabling cancer cells to adapt to microenvironmental stresses by switching phenotype. In melanoma, a key determinant of phenotypic identity is the microphthalmia‐associated transcription factor MITF that promotes proliferation, suppresses senescence, and anticorrelates with immune infiltration and therapy resistance. What determines whether MITF can activate or repress genes associated with specific phenotypes, or how signaling regulating MITF might impact immune infiltration is poorly understood. Here, we find that MITF binding to genes associated with high MITF is via classical E/M‐box motifs, but genes downregulated when MITF is high contain FOS/JUN/AP1/ATF3 sites. Significantly, the repertoire of MITF‐interacting factors identified here includes JUN and ATF3 as well as many previously unidentified interactors. As high AP1 activity is a hallmark of MITFLow, invasive, slow‐cycling, therapy resistant cells, the ability of MITF to repress AP1‐regulated genes provides an insight into how MITF establishes and maintains a pro‐proliferative phenotype. Moreover, although β‐catenin has been linked to immune exclusion, many Hallmark β‐catenin signaling genes are associated with immune infiltration. Instead, low MITF together with Notch signaling is linked to immune infiltration in both mouse and human melanoma tumors.
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Affiliation(s)
- Jagat S Chauhan
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Michael Hölzel
- Institute of Experimental Oncology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Jean-Philippe Lambert
- Department of Molecular Medicine and Cancer Research Centre, Université Laval, Quebec, Canada.,Endocrinology - Nephrology Axis, CHU de Québec - Université Laval Research Center, QC, Canada.,CHU de Québec Research Center, CHUL, 2705 Boulevard Laurier, Quebec, Canada
| | - Francesca M Buffa
- Department of Oncology, University of Oxford, Headington, Oxford, UK
| | - Colin R Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
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21
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Bakr MN, Takahashi H, Kikuchi Y. Analysis of Melanoma Gene Expression Signatures at the Single-Cell Level Uncovers 45-Gene Signature Related to Prognosis. Biomedicines 2022; 10:biomedicines10071478. [PMID: 35884783 PMCID: PMC9313451 DOI: 10.3390/biomedicines10071478] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/12/2022] [Accepted: 06/19/2022] [Indexed: 11/16/2022] Open
Abstract
Since the current melanoma clinicopathological staging system remains restricted to predicting survival outcomes, establishing precise prognostic targets is needed. Here, we used gene expression signature (GES) classification and Cox regression analyses to biologically characterize melanoma cells at the single-cell level and construct a prognosis-related gene signature for melanoma. By analyzing publicly available scRNA-seq data, we identified six distinct GESs (named: “Anti-apoptosis”, “Immune cell interactions”, “Melanogenesis”, “Ribosomal biogenesis”, “Extracellular structure organization”, and “Epithelial-Mesenchymal Transition (EMT)”). We verified these GESs in the bulk RNA-seq data of patients with skin cutaneous melanoma (SKCM) from The Cancer Genome Atlas (TCGA). Four GESs (“Immune cell interactions”, “Melanogenesis”, “Ribosomal biogenesis”, and “Extracellular structure organization”) were significantly correlated with prognosis (p = 1.08 × 10−5, p = 0.042, p = 0.001, and p = 0.031, respectively). We identified a prognostic signature of melanoma composed of 45 genes (MPS_45). MPS_45 was validated in TCGA-SKCM (HR = 1.82, p = 9.08 × 10−6) and three other melanoma datasets (GSE65904: HR = 1.73, p = 0.006; GSE19234: HR = 3.83, p = 0.002; and GSE53118: HR = 1.85, p = 0.037). MPS_45 was independently associated with survival (p = 0.002) and was proved to have a high potential for predicting prognosis in melanoma patients.
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Affiliation(s)
- Mohamed Nabil Bakr
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima 739-8526, Japan;
- National Institute of Oceanography and Fisheries (NIOF), Cairo 11516, Egypt
| | - Haruko Takahashi
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima 739-8526, Japan;
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima 739-8526, Japan
- Correspondence: (H.T.); (Y.K.); Tel.: +81-82-424-7440 (Y.K.)
| | - Yutaka Kikuchi
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima 739-8526, Japan;
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima 739-8526, Japan
- Correspondence: (H.T.); (Y.K.); Tel.: +81-82-424-7440 (Y.K.)
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22
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Papaiz DD, Rius FE, Ayub ALP, Origassa CS, Gujar H, Pessoa DDO, Reis EM, Nsengimana J, Newton‐Bishop J, Mason CE, Weisenberger DJ, Liang G, Jasiulionis MG. Genes regulated by DNA methylation are involved in distinct phenotypes during melanoma progression and are prognostic factors for patients. Mol Oncol 2022; 16:1913-1930. [PMID: 35075772 PMCID: PMC9067153 DOI: 10.1002/1878-0261.13185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 01/03/2022] [Accepted: 01/21/2022] [Indexed: 11/09/2022] Open
Abstract
In addition to mutations, epigenetic alterations are important contributors to malignant transformation and tumor progression. The aim of this work was to identify epigenetic events in which promoter or gene body DNA methylation induces gene expression changes that drive melanocyte malignant transformation and metastasis. We previously developed a linear mouse model of melanoma progression consisting of spontaneously immortalized melanocytes, premalignant melanocytes, a nonmetastatic tumorigenic, and a metastatic cell line. Here, through the integrative analysis of methylome and transcriptome data, we identified the relationship between promoter and/or gene body DNA methylation alterations and gene expression in early, intermediate, and late stages of melanoma progression. We identified adenylate cyclase type 3 (Adcy3) and inositol polyphosphate 4-phosphatase type II (Inpp4b), which affect tumor growth and metastatic potential, respectively. Importantly, the gene expression and DNA methylation profiles found in this murine model of melanoma progression were correlated with available clinical data from large population-based primary melanoma cohorts, revealing potential prognostic markers.
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Affiliation(s)
- Debora D’Angelo Papaiz
- Pharmacology DepartmentEscola Paulista de MedicinaUniversidade Federal de São PauloBrazil
| | | | - Ana Luísa Pedroso Ayub
- Pharmacology DepartmentEscola Paulista de MedicinaUniversidade Federal de São PauloBrazil
| | - Clarice S. Origassa
- Pharmacology DepartmentEscola Paulista de MedicinaUniversidade Federal de São PauloBrazil
| | - Hemant Gujar
- Department of UrologyUniversity of Southern CaliforniaLos AngelesCAUSA
| | | | | | - Jérémie Nsengimana
- Biostatistics Research GroupFaculty of Medical SciencesPopulation Health Sciences InstituteNewcastle UniversityUK
- University of Leeds School of MedicineUK
| | | | | | - Daniel J. Weisenberger
- Department of Biochemistry and Molecular MedicineUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Gangning Liang
- Department of UrologyUniversity of Southern CaliforniaLos AngelesCAUSA
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23
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Wang M, Zadeh S, Pizzolla A, Thia K, Gyorki DE, McArthur GA, Scolyer RA, Long G, Wilmott JS, Andrews MC, Au-Yeung G, Weppler A, Sandhu S, Trapani JA, Davis MJ, Neeson PJ. Characterization of the treatment-naive immune microenvironment in melanoma with BRAF mutation. J Immunother Cancer 2022; 10:e004095. [PMID: 35383113 PMCID: PMC8984014 DOI: 10.1136/jitc-2021-004095] [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] [Accepted: 03/14/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Patients with BRAF-mutant and wild-type melanoma have different response rates to immune checkpoint blockade therapy. However, the reasons for this remain unknown. To address this issue, we investigated the precise immune composition resulting from BRAF mutation in treatment-naive melanoma to determine whether this may be a driver for different response to immunotherapy. METHODS In this study, we characterized the treatment-naive immune context in patients with BRAF-mutant and BRAF wild-type (BRAF-wt) melanoma using data from single-cell RNA sequencing, bulk RNA sequencing, flow cytometry and immunohistochemistry (IHC). RESULTS In single-cell data, BRAF-mutant melanoma displayed a significantly reduced infiltration of CD8+ T cells and macrophages but also increased B cells, natural killer (NK) cells and NKT cells. We then validated this finding using bulk RNA-seq data from the skin cutaneous melanoma cohort in The Cancer Genome Atlas and deconvoluted the data using seven different algorithms. Interestingly, BRAF-mutant tumors had more CD4+ T cells than BRAF-wt samples in both primary and metastatic cohorts. In the metastatic cohort, BRAF-mutant melanoma demonstrated more B cells but less CD8+ T cell infiltration when compared with BRAF-wt samples. In addition, we further investigated the immune cell infiltrate using flow cytometry and multiplex IHC techniques. We confirmed that BRAF-mutant melanoma metastases were enriched for CD4+ T cells and B cells and had a co-existing decrease in CD8+ T cells. Furthermore, we then identified B cells were associated with a trend for improved survival (p=0.078) in the BRAF-mutant samples and Th2 cells were associated with prolonged survival in the BRAF-wt samples. CONCLUSIONS In conclusion, treatment-naive BRAF-mutant melanoma has a distinct immune context compared with BRAF-wt melanoma, with significantly decreased CD8+ T cells and increased B cells and CD4+ T cells in the tumor microenvironment. These findings indicate that further mechanistic studies are warranted to reveal how this difference in immune context leads to improved outcome to combination immune checkpoint blockade in BRAF-mutant melanoma.
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Affiliation(s)
- Minyu Wang
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Soroor Zadeh
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Computing and Information Systems, University of Melbourne VCCC, Parkville, Victoria, Australia
| | - Angela Pizzolla
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Kevin Thia
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Centre for Cancer Immunotherapy, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - David E Gyorki
- Division of Cancer Surgery, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Grant A McArthur
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Richard A Scolyer
- The University of Sydney, Melanoma Institute Australia, Sydney, New South Wales, Australia
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Georgina Long
- Melanoma Institute Australia, North Sydney, New South Wales, Australia
- Department of Medical Oncology, Royal North Shore Hospital, Sydney, New South Wales, Australia
| | - James S Wilmott
- Melanoma Institute Australia, North Sydney, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Miles C Andrews
- Department of Medicine, Central Clinical School, Monash University, Clayton, Victoria, Australia
| | - George Au-Yeung
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Ali Weppler
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Shahneen Sandhu
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Joseph A Trapani
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Melissa J Davis
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Computing and Information Systems, University of Melbourne VCCC, Parkville, Victoria, Australia
| | - Paul Joseph Neeson
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
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24
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Liu J, Xu J, Luo B, Tang J, Hou Z, Zhu Z, Zhu L, Yao G, Li C. Immune Landscape and an RBM38-Associated Immune Prognostic Model with Laboratory Verification in Malignant Melanoma. Cancers (Basel) 2022; 14:cancers14061590. [PMID: 35326741 PMCID: PMC8946480 DOI: 10.3390/cancers14061590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary The primary treatment of malignant melanoma is a classical regimen of surgery combined with chemotherapy, targeted drugs, and immunotherapy. The purpose of this study was to explore the immune response mechanism of RNA binding protein RBM38 in the development of melanoma with the screening of effective immunodiagnostic models and targeted therapy. We found that RBM38, as an oncogene, promotes the proliferation, invasion, and migration of melanoma cells and is associated with immune infiltration and pathways. Our investigation presented the prognostic significance of RBM38-associated immune signature. In addition, this model may provide a potential strategy for improving the survival and immunotherapy of melanoma patients. Abstract Background: Current studies have revealed that RNA-binding protein RBM38 is closely related to tumor development, while its role in malignant melanoma remains unclear. Therefore, this research aimed to investigate the function of RBM38 in melanoma and the prognosis of the disease. Methods: Functional experiments (CCK-8 assay, cell colony formation, transwell cell migration/invasion experiment, wound healing assay, nude mouse tumor formation, and immunohistochemical analysis) were applied to evaluate the role of RBM38 in malignant melanoma. Immune-associated differentially expressed genes (DEGs) on RBM38 related immune pathways were comprehensively analyzed based on RNA sequencing results. Results: We found that high expression of RBM38 promoted melanoma cell proliferation, invasion, and migration, and RBM38 was associated with immune infiltration. Then, a five-gene (A2M, NAMPT, LIF, EBI3, and ERAP1) model of RBM38-associated immune DEGs was constructed and validated. Our signature showed superior prognosis capacity compared with other melanoma prognostic signatures. Moreover, the risk score of our signature was connected with the infiltration of immune cells, immune-regulatory proteins, and immunophenoscore in melanoma. Conclusions: We constructed an immune prognosis model using RBM38-related immune DEGs that may help evaluate melanoma patient prognosis and immunotherapy modalities.
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Affiliation(s)
- Jinfang Liu
- Department of Plastic and Burns Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 GuangZhou Rd, Nanjing 210029, China; (J.L.); (B.L.); (J.T.); (Z.H.); (Z.Z.)
| | - Jun Xu
- Department of Oncology, The Third Affiliated Hospital of Soochow University, Soochow 213000, China;
| | - Binlin Luo
- Department of Plastic and Burns Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 GuangZhou Rd, Nanjing 210029, China; (J.L.); (B.L.); (J.T.); (Z.H.); (Z.Z.)
| | - Jian Tang
- Department of Plastic and Burns Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 GuangZhou Rd, Nanjing 210029, China; (J.L.); (B.L.); (J.T.); (Z.H.); (Z.Z.)
| | - Zuoqiong Hou
- Department of Plastic and Burns Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 GuangZhou Rd, Nanjing 210029, China; (J.L.); (B.L.); (J.T.); (Z.H.); (Z.Z.)
| | - Zhechen Zhu
- Department of Plastic and Burns Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 GuangZhou Rd, Nanjing 210029, China; (J.L.); (B.L.); (J.T.); (Z.H.); (Z.Z.)
| | - Lingjun Zhu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China;
| | - Gang Yao
- Department of Plastic and Burns Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 GuangZhou Rd, Nanjing 210029, China; (J.L.); (B.L.); (J.T.); (Z.H.); (Z.Z.)
- Correspondence: (G.Y.); (C.L.)
| | - Chujun Li
- Department of Plastic and Burns Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 GuangZhou Rd, Nanjing 210029, China; (J.L.); (B.L.); (J.T.); (Z.H.); (Z.Z.)
- Correspondence: (G.Y.); (C.L.)
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Davies J, Muralidhar S, Randerson-Moor J, Harland M, O'Shea S, Diaz J, Walker C, Nsengimana J, Laye J, Mell T, Chan M, Appleton L, Birkeälv S, Adams DJ, Cook GP, Ball G, Bishop DT, Newton-Bishop JA. Ulcerated melanoma: Systems biology evidence of inflammatory imbalance towards pro-tumourigenicity. Pigment Cell Melanoma Res 2022; 35:252-267. [PMID: 34826184 DOI: 10.1111/pcmr.13023] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/03/2021] [Accepted: 11/23/2021] [Indexed: 01/05/2023]
Abstract
Microscopic ulceration is an independent predictor of melanoma death. Here, we used systems biology to query the role of host and tumour-specific processes in defining the phenotype. Albumin level as a measure of systemic inflammation was predictive of fewer tumour-infiltrating lymphocytes and poorer survival in the Leeds Melanoma Cohort. Ulcerated melanomas were thicker and more mitotically active (with corresponding transcriptomic upregulated cell cycle pathways). Sequencing identified tumoural p53 and APC mutations, and TUBB2B amplification as associated with the phenotype. Ulcerated tumours had perturbed expression of cytokine genes, consistent with protumourigenic inflammation and histological and transcriptomic evidence for reduced adaptive immune cell infiltration. Pathway/network analysis of multiomic data using neural networks highlighted a role for the β-catenin pathway in the ulceration, linking genomic changes in the tumour to immunosuppression and cell proliferation. In summary, the data suggest that ulceration is in part associated with genomic changes but that host factors also predict melanoma death with evidence of reduced immune responses to the tumour.
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Affiliation(s)
- John Davies
- Leeds Institute of Data Analytics, University of Leeds, Leeds, UK
| | - Sathya Muralidhar
- Division of Molecular Pathology, The Institute of Cancer Research, Sutton, UK
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | | | - Mark Harland
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Sally O'Shea
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
- Dermatology Department, South Infirmary-Victoria University Hospital Cork and University College Cork, Cork, Ireland
| | - Joey Diaz
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Christy Walker
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Jérémie Nsengimana
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
- Population Health Sciences Institute, University of Newcastle, Newcastle upon Tyne, UK
| | - Jon Laye
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Tracey Mell
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - May Chan
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Lizzie Appleton
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
- Division of Radiotherapy and Imaging, Institute of Cancer Research, London, UK
| | - Sofia Birkeälv
- Experimental Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - David J Adams
- Experimental Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Graham P Cook
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Graham Ball
- School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - David T Bishop
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
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Abstract
Liver cancer, more specifically hepatocellular carcinoma (HCC), is the second leading cause of cancer-related death and its incidence is increasing globally. Around 50% of patients with HCC receive systemic therapies, traditionally sorafenib or lenvatinib in the first line and regorafenib, cabozantinib or ramucirumab in the second line. In the past 5 years, immune-checkpoint inhibitors have revolutionized the management of HCC. The combination of atezolizumab and bevacizumab has been shown to improve overall survival relative to sorafenib, resulting in FDA approval of this regimen. More recently, durvalumab plus tremelimumab yielded superior overall survival versus sorafenib and atezolizumab plus cabozantinib yielded superior progression-free survival. In addition, pembrolizumab monotherapy and the combination of nivolumab plus ipilimumab have received FDA Accelerated Approval in the second-line setting based on early efficacy data. Despite these major advances, the molecular underpinnings governing immune responses and evasion remain unclear. The immune microenvironment has crucial roles in the development and progression of HCC and distinct aetiology-dependent immune features have been defined. Inflamed and non-inflamed classes of HCC and genomic signatures have been associated with response to immune-checkpoint inhibitors, yet no validated biomarker is available to guide clinical decision-making. This Review provides information on the immune microenvironments underlying the response or resistance of HCC to immunotherapies. In addition, current evidence from phase III trials on the efficacy, immune-related adverse events and aetiology-dependent mechanisms of response are described. Finally, we discuss emerging trials assessing immunotherapies across all stages of HCC that might change the management of this disease in the near future.
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Liu C, Liu Y, Yu Y, Zhao Y, Yu A. Comprehensive analysis of ferroptosis-related genes and prognosis of cutaneous melanoma. BMC Med Genomics 2022; 15:39. [PMID: 35232428 PMCID: PMC8886785 DOI: 10.1186/s12920-022-01194-z] [Citation(s) in RCA: 12] [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: 07/22/2021] [Accepted: 02/24/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Cutaneous Melanoma (CM) is a malignant disease with increasing incidence and high mortality. Ferroptosis is a new kind of cell death and related to tumor blood and lymphatic metastasis. This study aims at using bioinformatics technology to construct a prognostic signature and identify ferroptosis-related biomarkers to improve the prognosis and treatment of cutaneous melanoma. METHODS We used bioinformatics tools to analyze RNA sequencing expression data with clinical information from multiple databases, utilized varieties of statistical methods to construct a ferroptosis-related prognostic signature of cutaneous melanoma and screened out specific genes with independent prognostic ability. RESULTS We obtained 22 ferroptosis-related (P < 0.05) prognostic DEGs in the uniCox regression analysis, among which 10 high-expressed genes (ATG5, CHAC1, FANCD2, FBXL5, HMOX2, HSPB1, NQO1, PEBP1, PRNP, SLC3A2) were screened out by LASSO regression analysis to establish a predictive model. Meanwhile, the ferroptosis-related signature and the nomogram we drew performed an excellent performance based on Kaplan-Meier (K-M), Receiver operating characteristic (ROC) and calibration curves. Univariate and multivariable cox analyses displayed that our model was greater than other prognostic features. GO and KEGG analyses revealed that 10-biomarker signature was mainly related to epidermis differentiation and immunity. ssGSEA analysis indicated that the immune status between the two risk groups was highly different. Besides, we found that two genes (CP, ZEB1) had independent prognostic ability and can be applied for drug research. Both genes were highly related to immunity. GSEA illustrated that ZEB1 may be involved in cellular functions such as proliferation, apoptosis, and migration, while CP was closely connected to immune cell related functions. CONCLUSION The present study suggested a 10-biomarker signature can be clinically used to predict the prognosis of cutaneous melanoma, which was better than conventional factors. CP and ZEB1 were independent prognostic genes and can be applied to guide treatment. In addition, ZEB1 mutation was highly related to overall survival in cutaneous melanoma, while CP may be associated with tumor progression. Our study comprehensively analyzed the relationship between iron metabolism, ferroptosis-related genes, and the prognosis of cutaneous melanoma, provided new insight for molecular mechanisms and treatment of ferroptosis and cutaneous melanoma.
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Affiliation(s)
- Changjiang Liu
- Department of Orthopedics, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, People's Republic of China
| | - Yuhang Liu
- Department of Orthopedics, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, People's Republic of China
| | - Yifeng Yu
- Department of Orthopedics, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, People's Republic of China
| | - Yong Zhao
- Department of Orthopedics, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, People's Republic of China
| | - Aixi Yu
- Department of Orthopedics, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, People's Republic of China.
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Targeting GPCRs and Their Signaling as a Therapeutic Option in Melanoma. Cancers (Basel) 2022; 14:cancers14030706. [PMID: 35158973 PMCID: PMC8833576 DOI: 10.3390/cancers14030706] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 01/27/2022] [Accepted: 01/27/2022] [Indexed: 12/10/2022] Open
Abstract
Simple Summary Sixteen G-protein-coupled receptors (GPCRs) have been involved in melanogenesis or melanomagenesis. Here, we review these GPCRs, their associated signaling, and therapies. Abstract G-protein-coupled receptors (GPCRs) serve prominent roles in melanocyte lineage physiology, with an impact at all stages of development, as well as on mature melanocyte functions. GPCR ligands are present in the skin and regulate melanocyte homeostasis, including pigmentation. The role of GPCRs in the regulation of pigmentation and, consequently, protection against external aggression, such as ultraviolet radiation, has long been established. However, evidence of new functions of GPCRs directly in melanomagenesis has been highlighted in recent years. GPCRs are coupled, through their intracellular domains, to heterotrimeric G-proteins, which induce cellular signaling through various pathways. Such signaling modulates numerous essential cellular processes that occur during melanomagenesis, including proliferation and migration. GPCR-associated signaling in melanoma can be activated by the binding of paracrine factors to their receptors or directly by activating mutations. In this review, we present melanoma-associated alterations of GPCRs and their downstream signaling and discuss the various preclinical models used to evaluate new therapeutic approaches against GPCR activity in melanoma. Recent striking advances in our understanding of the structure, function, and regulation of GPCRs will undoubtedly broaden melanoma treatment options in the future.
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29
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Castro MV, Barbero GA, Villanueva MB, Grumolato L, Nsengimana J, Newton-Bishop J, Illescas E, Quezada MJ, Lopez-Bergami P. ROR2 has a protective role in melanoma by inhibiting Akt activity, cell-cycle progression, and proliferation. J Biomed Sci 2021; 28:76. [PMID: 34774050 PMCID: PMC8590781 DOI: 10.1186/s12929-021-00776-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/07/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Receptor tyrosine kinase-like orphan receptor 2 (ROR2) is a Wnt5a receptor aberrantly expressed in cancer that was shown to either suppress or promote carcinogenesis in different tumor types. Our goal was to study the role of ROR2 in melanoma. METHODS Gain and loss-of-function strategies were applied to study the biological function of ROR2 in melanoma. Proliferation assays, flow cytometry, and western blotting were used to evaluate cell proliferation and changes in expression levels of cell-cycle and proliferation markers. The role of ROR2 in tumor growth was assessed in xenotransplantation experiments followed by immunohistochemistry analysis of the tumors. The role of ROR2 in melanoma patients was assessed by analysis of clinical data from the Leeds Melanoma Cohort. RESULTS Unlike previous findings describing ROR2 as an oncogene in melanoma, we describe that ROR2 prevents tumor growth by inhibiting cell-cycle progression and the proliferation of melanoma cells. The effect of ROR2 is mediated by inhibition of Akt phosphorylation and activity which, in turn, regulates the expression, phosphorylation, and localization of major cell-cycle regulators including cyclins (A, B, D, and E), CDK1, CDK4, RB, p21, and p27. Xenotransplantation experiments demonstrated that ROR2 also reduces proliferation in vivo, resulting in inhibition of tumor growth. In agreement with these findings, a higher ROR2 level favors thin and non-ulcerated primary melanomas with reduced mitotic rate and better prognosis. CONCLUSION We conclude that the expression of ROR2 slows down the growth of primary tumors and contributes to prolonging melanoma survival. Our results demonstrate that ROR2 has a far more complex role than originally described.
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Affiliation(s)
- María Victoria Castro
- grid.440480.c0000 0000 9361 4204Centro de Estudios Biomédicos, Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, 1405 Buenos Aires, Argentina ,grid.423606.50000 0001 1945 2152Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1425 Buenos Aires, Argentina
| | - Gastón Alexis Barbero
- grid.440480.c0000 0000 9361 4204Centro de Estudios Biomédicos, Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, 1405 Buenos Aires, Argentina ,grid.423606.50000 0001 1945 2152Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1425 Buenos Aires, Argentina
| | - María Belén Villanueva
- grid.440480.c0000 0000 9361 4204Centro de Estudios Biomédicos, Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, 1405 Buenos Aires, Argentina ,grid.423606.50000 0001 1945 2152Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1425 Buenos Aires, Argentina
| | - Luca Grumolato
- grid.10400.350000 0001 2108 3034INSERM U982, Institute for Research and Innovation in Biomedicine, University of Rouen, 76183 Rouen, France
| | - Jérémie Nsengimana
- grid.1006.70000 0001 0462 7212Biostatistics Research Group, Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH UK
| | | | - Edith Illescas
- grid.440480.c0000 0000 9361 4204Centro de Estudios Biomédicos, Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, 1405 Buenos Aires, Argentina
| | - María Josefina Quezada
- grid.440480.c0000 0000 9361 4204Centro de Estudios Biomédicos, Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, 1405 Buenos Aires, Argentina ,grid.423606.50000 0001 1945 2152Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1425 Buenos Aires, Argentina
| | - Pablo Lopez-Bergami
- Centro de Estudios Biomédicos, Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, 1405, Buenos Aires, Argentina. .,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1425, Buenos Aires, Argentina. .,Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico, Universidad Maimonides, Hidalgo 775, 6th Floor, Lab 602., 1405, Buenos Aires, Argentina.
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30
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Campbell NR, Rao A, Hunter MV, Sznurkowska MK, Briker L, Zhang M, Baron M, Heilmann S, Deforet M, Kenny C, Ferretti LP, Huang TH, Perlee S, Garg M, Nsengimana J, Saini M, Montal E, Tagore M, Newton-Bishop J, Middleton MR, Corrie P, Adams DJ, Rabbie R, Aceto N, Levesque MP, Cornell RA, Yanai I, Xavier JB, White RM. Cooperation between melanoma cell states promotes metastasis through heterotypic cluster formation. Dev Cell 2021; 56:2808-2825.e10. [PMID: 34529939 DOI: 10.1016/j.devcel.2021.08.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 07/07/2021] [Accepted: 08/20/2021] [Indexed: 02/08/2023]
Abstract
Melanomas can have multiple coexisting cell states, including proliferative (PRO) versus invasive (INV) subpopulations that represent a "go or grow" trade-off; however, how these populations interact is poorly understood. Using a combination of zebrafish modeling and analysis of patient samples, we show that INV and PRO cells form spatially structured heterotypic clusters and cooperate in the seeding of metastasis, maintaining cell state heterogeneity. INV cells adhere tightly to each other and form clusters with a rim of PRO cells. Intravital imaging demonstrated cooperation in which INV cells facilitate dissemination of less metastatic PRO cells. We identified the TFAP2 neural crest transcription factor as a master regulator of clustering and PRO/INV states. Isolation of clusters from patients with metastatic melanoma revealed a subset with heterotypic PRO-INV clusters. Our data suggest a framework for the co-existence of these two divergent cell populations, in which heterotypic clusters promote metastasis via cell-cell cooperation.
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Affiliation(s)
- Nathaniel R Campbell
- Weill Cornell/Rockefeller Memorial Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA; Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anjali Rao
- Institute for Computational Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Miranda V Hunter
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Magdalena K Sznurkowska
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology (ETH) Zurich, 8093 Zurich, Switzerland
| | - Luzia Briker
- Department of Dermatology, University of Zürich Hospital, University of Zürich, Zurich, Switzerland
| | - Maomao Zhang
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Maayan Baron
- Institute for Computational Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Silja Heilmann
- Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Maxime Deforet
- Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Colin Kenny
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Lorenza P Ferretti
- Department of Dermatology, University of Zürich Hospital, University of Zürich, Zurich, Switzerland; Department of Molecular Mechanisms of Disease, University of Zürich, Zurich, Switzerland
| | - Ting-Hsiang Huang
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sarah Perlee
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Manik Garg
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, UK
| | - Jérémie Nsengimana
- Leeds Institute of Medical Research at St. James's, University of Leeds School of Medicine, Leeds, UK
| | - Massimo Saini
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology (ETH) Zurich, 8093 Zurich, Switzerland
| | - Emily Montal
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mohita Tagore
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Julia Newton-Bishop
- Leeds Institute of Medical Research at St. James's, University of Leeds School of Medicine, Leeds, UK
| | - Mark R Middleton
- Oxford NIHR Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, UK
| | - Pippa Corrie
- Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - David J Adams
- Experimental Cancer Genetics, the Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Roy Rabbie
- Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Experimental Cancer Genetics, the Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Nicola Aceto
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology (ETH) Zurich, 8093 Zurich, Switzerland
| | - Mitchell P Levesque
- Department of Dermatology, University of Zürich Hospital, University of Zürich, Zurich, Switzerland
| | - Robert A Cornell
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Itai Yanai
- Institute for Computational Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Joao B Xavier
- Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Richard M White
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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31
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Bi O, Anene CA, Nsengimana J, Shelton M, Roberts W, Newton-Bishop J, Boyne JR. SFPQ promotes an oncogenic transcriptomic state in melanoma. Oncogene 2021; 40:5192-5203. [PMID: 34218270 PMCID: PMC8376646 DOI: 10.1038/s41388-021-01912-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 06/17/2021] [Indexed: 02/06/2023]
Abstract
The multifunctional protein, splicing factor, proline- and glutamine-rich (SFPQ) has been implicated in numerous cancers often due to interaction with coding and non-coding RNAs, however, its role in melanoma remains unclear. We report that knockdown of SFPQ expression in melanoma cells decelerates several cancer-associated cell phenotypes, including cell growth, migration, epithelial to mesenchymal transition, apoptosis, and glycolysis. RIP-seq analysis revealed that the SFPQ-RNA interactome is reprogrammed in melanoma cells and specifically enriched with key melanoma-associated coding and long non-coding transcripts, including SOX10, AMIGO2 and LINC00511 and in most cases SFPQ is required for the efficient expression of these genes. Functional analysis of two SFPQ-enriched lncRNA, LINC00511 and LINC01234, demonstrated that these genes independently contribute to the melanoma phenotype and a more detailed analysis of LINC00511 indicated that this occurs in part via modulation of the miR-625-5p/PKM2 axis. Importantly, analysis of a large clinical cohort revealed that elevated expression of SFPQ in primary melanoma tumours may have utility as a prognostic biomarker. Together, these data suggest that SFPQ is an important driver of melanoma, likely due to SFPQ-RNA interactions promoting the expression of numerous oncogenic transcripts.
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Affiliation(s)
- O Bi
- School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - C A Anene
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - J Nsengimana
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - M Shelton
- School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - W Roberts
- School of Clinical and Applied Science, Leeds Beckett University, Leeds, UK
| | | | - J R Boyne
- School of Applied Sciences, University of Huddersfield, Huddersfield, UK.
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32
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Patton EE, Mueller KL, Adams DJ, Anandasabapathy N, Aplin AE, Bertolotto C, Bosenberg M, Ceol CJ, Burd CE, Chi P, Herlyn M, Holmen SL, Karreth FA, Kaufman CK, Khan S, Kobold S, Leucci E, Levy C, Lombard DB, Lund AW, Marie KL, Marine JC, Marais R, McMahon M, Robles-Espinoza CD, Ronai ZA, Samuels Y, Soengas MS, Villanueva J, Weeraratna AT, White RM, Yeh I, Zhu J, Zon LI, Hurlbert MS, Merlino G. Melanoma models for the next generation of therapies. Cancer Cell 2021; 39:610-631. [PMID: 33545064 PMCID: PMC8378471 DOI: 10.1016/j.ccell.2021.01.011] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 12/12/2022]
Abstract
There is a lack of appropriate melanoma models that can be used to evaluate the efficacy of novel therapeutic modalities. Here, we discuss the current state of the art of melanoma models including genetically engineered mouse, patient-derived xenograft, zebrafish, and ex vivo and in vitro models. We also identify five major challenges that can be addressed using such models, including metastasis and tumor dormancy, drug resistance, the melanoma immune response, and the impact of aging and environmental exposures on melanoma progression and drug resistance. Additionally, we discuss the opportunity for building models for rare subtypes of melanomas, which represent an unmet critical need. Finally, we identify key recommendations for melanoma models that may improve accuracy of preclinical testing and predict efficacy in clinical trials, to help usher in the next generation of melanoma therapies.
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Affiliation(s)
- E Elizabeth Patton
- MRC Human Genetics Unit and Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK.
| | - Kristen L Mueller
- Melanoma Research Alliance, 730 15th Street NW, Washington, DC 20005, USA.
| | - David J Adams
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Niroshana Anandasabapathy
- Department of Dermatology, Meyer Cancer Center, Program in Immunology and Microbial Pathogenesis, Weill Cornell Medicine, New York, NY 10026, USA
| | - Andrew E Aplin
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Corine Bertolotto
- Université Côte d'Azur, Nice, France; INSERM, Biology and Pathologies of Melanocytes, Team 1, Equipe Labellisée Ligue 2020, Centre Méditerranéen de Médecine Moléculaire, Nice, France
| | - Marcus Bosenberg
- Departments of Dermatology, Pathology, and Immunobiology, Yale University, New Haven, CT, USA
| | - Craig J Ceol
- Program in Molecular Medicine and Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Christin E Burd
- Departments of Molecular Genetics, Cancer Biology, and Genetics, The Ohio State University, Biomedical Research Tower, Room 918, 460 W. 12th Avenue, Columbus, OH 43210, USA
| | - Ping Chi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | | | - Sheri L Holmen
- Department of Surgery, University of Utah Health Sciences Center, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Florian A Karreth
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Charles K Kaufman
- Washington University School of Medicine, Department of Medicine, Division of Oncology, Department of Developmental Biology, McDonnell Science Building, 4518 McKinley Avenue, St. Louis, MO 63110, USA
| | - Shaheen Khan
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Sebastian Kobold
- Center of Integrated Protein Science Munich (CIPS-M) and Division of Clinical Pharmacology, Department of Medicine IV, Klinikum der Universität München, LMU, Munich, Germany; Member of the German Center for Lung Research (DZL), German Center for Translational Cancer Research (DKTK), partner site Munich, Munich, Germany
| | - Eleonora Leucci
- Laboratory for RNA Cancer Biology, Department of Oncology, LKI, KU Leuven, 3000 Leuven, Belgium; Trace, Department of Oncology, LKI, KU Leuven, 3000 Leuven, Belgium
| | - Carmit Levy
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - David B Lombard
- Department of Pathology, Institute of Gerontology, and Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Amanda W Lund
- Ronald O. Perelman Department of Dermatology and Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Kerrie L Marie
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Richard Marais
- CRUK Manchester Institute, The University of Manchester, Alderley Park, Macclesfield SK10 4TG, UK
| | - Martin McMahon
- Department of Dermatology & Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Carla Daniela Robles-Espinoza
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Boulevard Juriquilla 3001, Santiago de Querétaro 76230, Mexico; Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Ze'ev A Ronai
- Cancer Center, Sanford Burnham Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Yardena Samuels
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Maria S Soengas
- Spanish National Cancer Research Centre, 28029 Madrid, Spain
| | - Jessie Villanueva
- The Wistar Institute, Molecular and Cellular Oncogenesis Program, Philadelphia, PA, USA
| | - Ashani T Weeraratna
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, and Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Richard M White
- Department of Cancer Biology & Genetics and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Iwei Yeh
- Departments of Dermatology and Pathology, University of California, San Francisco, CA, USA
| | - Jiyue Zhu
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA, USA
| | - Leonard I Zon
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, MA, USA
| | - Marc S Hurlbert
- Melanoma Research Alliance, 730 15th Street NW, Washington, DC 20005, USA
| | - Glenn Merlino
- Center for Cancer Research, NCI, NIH, 37 Convent Drive, Bethesda, MD 20892, USA.
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Transcriptional signatures underlying dynamic phenotypic switching and novel disease biomarkers in a linear cellular model of melanoma progression. Neoplasia 2021; 23:439-455. [PMID: 33845354 PMCID: PMC8042650 DOI: 10.1016/j.neo.2021.03.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/21/2021] [Accepted: 03/12/2021] [Indexed: 11/23/2022] Open
Abstract
Despite advances in therapeutics, the progression of melanoma to metastasis still confers a poor outcome to patients. Nevertheless, there is a scarcity of biological models to understand cellular and molecular changes taking place along disease progression. Here, we characterized the transcriptome profiles of a multi-stage murine model of melanoma progression comprising a nontumorigenic melanocyte lineage (melan-a), premalignant melanocytes (4C), nonmetastatic (4C11-) and metastasis-prone (4C11+) melanoma cells. Clustering analyses have grouped the 4 cell lines according to their differentiated (melan-a and 4C11+) or undifferentiated/"mesenchymal-like" (4C and 4C11-) morphologies, suggesting dynamic gene expression patterns associated with the transition between these phenotypes. The cell plasticity observed in the murine melanoma progression model was corroborated by molecular markers described during stepwise human melanoma differentiation, as the differentiated cell lines in our model exhibit upregulation of transitory and melanocytic markers, whereas "mesenchymal-like" cells show increased expression of undifferentiated and neural crest-like markers. Sets of differentially expressed genes (DEGs) were detected at each transition step of tumor progression, and transcriptional signatures related to malignancy, metastasis and epithelial-to-mesenchymal transition were identified. Finally, DEGs were mapped to their human orthologs and evaluated in uni- and multivariate survival analyses using gene expression and clinical data of 703 drug-naïve primary melanoma patients, revealing several independent candidate prognostic markers. Altogether, these results provide novel insights into the molecular mechanisms underlying the phenotypic switch taking place during melanoma progression, reveal potential drug targets and prognostic biomarkers, and corroborate the translational relevance of this unique sequential model of melanoma progression.
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Juraleviciute M, Nsengimana J, Newton-Bishop J, Hendriks GJ, Slipicevic A. MX2 mediates establishment of interferon response profile, regulates XAF1, and can sensitize melanoma cells to targeted therapy. Cancer Med 2021; 10:2840-2854. [PMID: 33734579 PMCID: PMC8026919 DOI: 10.1002/cam4.3846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 02/02/2021] [Accepted: 02/23/2021] [Indexed: 01/05/2023] Open
Abstract
MX2 is an interferon inducible gene that is mostly known for its antiviral activity. We have previously demonstrated that MX2 is also associated with the tumorigenesis process in melanoma. However, it remains unknown which molecular mechanisms are regulated by MX2 in response to interferon signaling in this disease. Here, we report that MX2 is necessary for the establishment of an interferon‐induced transcriptional profile partially through regulation of STAT1 phosphorylation and other interferon‐related downstream factors, including proapoptotic tumor suppressor XAF1. MX2 and XAF1 expression tightly correlate in both cultured melanoma cell lines and in patient‐derived primary and metastatic tumors, where they also are significantly related with survival. MX2 mediates IFN growth‐inhibitory signals in both XAF1 dependent and independent ways and in a cell type and context‐dependent manner. Higher MX2 expression renders melanoma cells more sensitive to targeted therapy drugs such as vemurafenib and trametinib; however, this effect is XAF1 independent. In summary, we uncovered a new mechanism in the complex regulation of interferon signaling in melanoma that can influence both survival and response to therapy.
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Affiliation(s)
- Marina Juraleviciute
- Department of Pathology, Oslo University Hospital, Oslo, Norway.,Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Jérémie Nsengimana
- Faculty of Medical Sciences, Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Julia Newton-Bishop
- Division of Haematology and Immunology, Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Gert J Hendriks
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ana Slipicevic
- Department of Pathology, Oslo University Hospital, Oslo, Norway
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35
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Li Z, Liu Y, Fang X, Shu Z. Nanomaterials Enhance the Immunomodulatory Effect of Molecular Targeted Therapy. Int J Nanomedicine 2021; 16:1631-1661. [PMID: 33688183 PMCID: PMC7935456 DOI: 10.2147/ijn.s290346] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/23/2021] [Indexed: 01/22/2023] Open
Abstract
Molecular targeted therapy, a tumor therapy strategy that inhibits specific oncogenic targets, has been shown to modulate the immune response. In addition to directly inhibiting the proliferation and metastasis of tumor cells, molecular targeted drugs can activate the immune system through a variety of mechanisms, including by promoting tumor antigen processing and presentation, increasing intratumoral T cell infiltration, enhancing T cell activation and function, and attenuating the immunosuppressive effect of the tumor microenvironment. However, poor water solubility, insufficient accumulation at the tumor site, and nonspecific targeting of immune cells limit their application. To this end, a variety of nanomaterials have been developed to overcome these obstacles and amplify the immunomodulatory effects of molecular targeted drugs. In this review, we summarize the impact of molecular targeted drugs on the antitumor immune response according to their mechanisms, highlight the advantages of nanomaterials in enhancing the immunomodulatory effect of molecular targeted therapy, and discuss the current challenges and future prospects.
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Affiliation(s)
- Zhongmin Li
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, 130033, People's Republic of China
| | - Yilun Liu
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, 130033, People's Republic of China
| | - Xuedong Fang
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, 130033, People's Republic of China
| | - Zhenbo Shu
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, 130033, People's Republic of China
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36
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Relecom A, Merhi M, Inchakalody V, Uddin S, Rinchai D, Bedognetti D, Dermime S. Emerging dynamics pathways of response and resistance to PD-1 and CTLA-4 blockade: tackling uncertainty by confronting complexity. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:74. [PMID: 33602280 PMCID: PMC7893879 DOI: 10.1186/s13046-021-01872-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/08/2021] [Indexed: 02/08/2023]
Abstract
Immune checkpoint inhibitors provide considerable therapeutic benefit in a range of solid cancers as well as in a subgroup of hematological malignancies. Response rates are however suboptimal, and despite considerable efforts, predicting response to immune checkpoint inhibitors ahead of their administration in a given patient remains elusive. The study of the dynamics of the immune system and of the tumor under immune checkpoint blockade brought insight into the mechanisms of action of these therapeutic agents. Equally relevant are the mechanisms of adaptive resistance to immune checkpoint inhibitors that have been uncovered through this approach. In this review, we discuss the dynamics of the immune system and of the tumor under immune checkpoint blockade emanating from recent studies on animal models and humans. We will focus on mechanisms of action and of resistance conveying information predictive of therapeutic response.
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Affiliation(s)
- Allan Relecom
- Department of Medical Oncology, Translational Research Institute, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Maysaloun Merhi
- Department of Medical Oncology, Translational Research Institute, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Varghese Inchakalody
- Department of Medical Oncology, Translational Research Institute, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Shahab Uddin
- Translational Research Institute & Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Darawan Rinchai
- Cancer Research Program, Research Branch, Sidra Medicine, Doha, Qatar
| | - Davide Bedognetti
- Cancer Research Program, Research Branch, Sidra Medicine, Doha, Qatar. .,Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy. .,College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
| | - Said Dermime
- Department of Medical Oncology, Translational Research Institute, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar. .,College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
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37
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Garg M, Couturier DL, Nsengimana J, Fonseca NA, Wongchenko M, Yan Y, Lauss M, Jönsson GB, Newton-Bishop J, Parkinson C, Middleton MR, Bishop DT, McDonald S, Stefanos N, Tadross J, Vergara IA, Lo S, Newell F, Wilmott JS, Thompson JF, Long GV, Scolyer RA, Corrie P, Adams DJ, Brazma A, Rabbie R. Tumour gene expression signature in primary melanoma predicts long-term outcomes. Nat Commun 2021; 12:1137. [PMID: 33602918 PMCID: PMC7893180 DOI: 10.1038/s41467-021-21207-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 01/15/2021] [Indexed: 02/08/2023] Open
Abstract
Adjuvant systemic therapies are now routinely used following resection of stage III melanoma, however accurate prognostic information is needed to better stratify patients. We use differential expression analyses of primary tumours from 204 RNA-sequenced melanomas within a large adjuvant trial, identifying a 121 metastasis-associated gene signature. This signature strongly associated with progression-free (HR = 1.63, p = 5.24 × 10-5) and overall survival (HR = 1.61, p = 1.67 × 10-4), was validated in 175 regional lymph nodes metastasis as well as two externally ascertained datasets. The machine learning classification models trained using the signature genes performed significantly better in predicting metastases than models trained with clinical covariates (pAUROC = 7.03 × 10-4), or published prognostic signatures (pAUROC < 0.05). The signature score negatively correlated with measures of immune cell infiltration (ρ = -0.75, p < 2.2 × 10-16), with a higher score representing reduced lymphocyte infiltration and a higher 5-year risk of death in stage II melanoma. Our expression signature identifies melanoma patients at higher risk of metastases and warrants further evaluation in adjuvant clinical trials.
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Affiliation(s)
- Manik Garg
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, UK
| | - Dominique-Laurent Couturier
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, UK
| | - Jérémie Nsengimana
- University of Leeds School of Medicine, Leeds, United Kingdom
- Biostatistics Research Group, Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Nuno A Fonseca
- CIBIO/InBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Rua Padre Armando Quintas, 4485-601, Vairão, Portugal
| | - Matthew Wongchenko
- Oncology Biomarker Development, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Yibing Yan
- Oncology Biomarker Development, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Martin Lauss
- Lund University Cancer Center, Lund University, Lund, Sweden
| | - Göran B Jönsson
- Lund University Cancer Center, Lund University, Lund, Sweden
| | | | - Christine Parkinson
- Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Mark R Middleton
- Oxford NIHR Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, UK
| | | | - Sarah McDonald
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Nikki Stefanos
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - John Tadross
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Ismael A Vergara
- Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Serigne Lo
- Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Felicity Newell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - James S Wilmott
- Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - John F Thompson
- Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Discipline of Surgery, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Royal North Shore and Mater Hospitals, Sydney, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and New South Wales Health Pathology, Sydney, NSW, Australia
| | - Pippa Corrie
- Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - David J Adams
- Experimental Cancer Genetics, The Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, UK
| | - Roy Rabbie
- Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Experimental Cancer Genetics, The Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK.
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38
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Gerhard GM, Bill R, Messemaker M, Klein AM, Pittet MJ. Tumor-infiltrating dendritic cell states are conserved across solid human cancers. J Exp Med 2021; 218:e20200264. [PMID: 33601412 PMCID: PMC7754678 DOI: 10.1084/jem.20200264] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/23/2020] [Accepted: 10/12/2020] [Indexed: 12/11/2022] Open
Abstract
Dendritic cells (DCs) contribute a small fraction of the tumor microenvironment but are emerging as an essential antitumor component based on their ability to foster T cell immunity and immunotherapy responses. Here, we discuss our expanding view of DC heterogeneity in human tumors, as revealed with meta-analysis of single-cell transcriptome profiling studies. We further examine tumor-infiltrating DC states that are conserved across patients, cancer types, and species and consider the fundamental and clinical relevance of these findings. Finally, we provide an outlook on research opportunities to further explore mechanisms governing tumor-infiltrating DC behavior and functions.
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Affiliation(s)
- Genevieve M. Gerhard
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Ruben Bill
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Marius Messemaker
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Allon M. Klein
- Department of Systems Biology, Harvard Medical School, Boston, MA
| | - Mikael J. Pittet
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
- Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
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39
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Conway JR, Dietlein F, Taylor-Weiner A, AlDubayan S, Vokes N, Keenan T, Reardon B, He MX, Margolis CA, Weirather JL, Haq R, Schilling B, Stephen Hodi F, Schadendorf D, Liu D, Van Allen EM. Integrated molecular drivers coordinate biological and clinical states in melanoma. Nat Genet 2020; 52:1373-1383. [PMID: 33230298 PMCID: PMC8054830 DOI: 10.1038/s41588-020-00739-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/14/2020] [Indexed: 01/05/2023]
Abstract
We performed harmonized molecular and clinical analysis on 1,048 melanomas and discovered markedly different global genomic properties among subtypes (BRAF, (N)RAS, NF1, Triple Wild-Type), subtype-specific preferences for secondary driver genes, and active mutational processes previously unreported in melanoma. Secondary driver genes significantly enriched in specific subtypes reflected preferential dysregulation of additional pathways, such as induction of TGF-β signaling in BRAF melanomas and inactivation of the SWI/SNF complex in (N)RAS melanomas, and select co-mutation patterns coordinated selective response to immune checkpoint blockade. We also defined the mutational landscape of Triple Wild-Type melanomas and identified enrichment of DNA repair defect signatures in this subtype, which were associated with transcriptional downregulation of key DNA repair genes and may revive previously discarded or currently unconsidered therapeutic modalities for genomically stratified melanoma patient subsets. Broadly, harmonized meta-analysis of melanoma whole-exomes identified distinct molecular drivers that may point to multiple opportunities for biological and therapeutic investigation.
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Affiliation(s)
- Jake R Conway
- Division of Medical Sciences, Harvard University, Boston, MA, USA.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Felix Dietlein
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amaro Taylor-Weiner
- Division of Medical Sciences, Harvard University, Boston, MA, USA.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Saud AlDubayan
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, King Saud bin Abdul-Aziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Natalie Vokes
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Tanya Keenan
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Brendan Reardon
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Meng Xiao He
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Harvard Graduate Program in Biophysics, Boston, MA, USA
| | - Claire A Margolis
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jason L Weirather
- Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rizwan Haq
- Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bastian Schilling
- Department of Dermatology, University Hospital Würzburg, Würzburg, Germany.,Department of Dermatology, University Hospital, Essen, Germany.,German Cancer Consortium of Translational Cancer Research, German Cancer Research Center, Heidelberg, Germany
| | - F Stephen Hodi
- Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital, Essen, Germany.,German Cancer Consortium of Translational Cancer Research, German Cancer Research Center, Heidelberg, Germany
| | - David Liu
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Eliezer M Van Allen
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA, USA.
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40
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Bellei B, Migliano E, Picardo M. A Framework of Major Tumor-Promoting Signal Transduction Pathways Implicated in Melanoma-Fibroblast Dialogue. Cancers (Basel) 2020; 12:cancers12113400. [PMID: 33212834 PMCID: PMC7697272 DOI: 10.3390/cancers12113400] [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: 09/18/2020] [Revised: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Melanoma cells reside in a complex stromal microenvironment, which is a critical component of disease onset and progression. Mesenchymal or fibroblastic cell type are the most abundant cellular element of tumor stroma. Factors secreted by melanoma cells can activate non-malignant associated fibroblasts to become melanoma associate fibroblasts (MAFs). MAFs promote tumorigenic features by remodeling the extracellular matrix, supporting tumor cells proliferation, neo-angiogenesis and drug resistance. Additionally, environmental factors may contribute to the acquisition of pro-tumorigenic phenotype of fibroblasts. Overall, in melanoma, perturbed tissue homeostasis contributes to modulation of major oncogenic intracellular signaling pathways not only in tumor cells but also in neighboring cells. Thus, targeted molecular therapies need to be considered from the reciprocal point of view of melanoma and stromal cells. Abstract The development of a modified stromal microenvironment in response to neoplastic onset is a common feature of many tumors including cutaneous melanoma. At all stages, melanoma cells are embedded in a complex tissue composed by extracellular matrix components and several different cell populations. Thus, melanomagenesis is not only driven by malignant melanocytes, but also by the altered communication between melanocytes and non-malignant cell populations, including fibroblasts, endothelial and immune cells. In particular, cancer-associated fibroblasts (CAFs), also referred as melanoma-associated fibroblasts (MAFs) in the case of melanoma, are the most abundant stromal cells and play a significant contextual role in melanoma initiation, progression and metastasis. As a result of dynamic intercellular molecular dialogue between tumor and the stroma, non-neoplastic cells gain specific phenotypes and functions that are pro-tumorigenic. Targeting MAFs is thus considered a promising avenue to improve melanoma therapy. Growing evidence demonstrates that aberrant regulation of oncogenic signaling is not restricted to transformed cells but also occurs in MAFs. However, in some cases, signaling pathways present opposite regulation in melanoma and surrounding area, suggesting that therapeutic strategies need to carefully consider the tumor–stroma equilibrium. In this novel review, we analyze four major signaling pathways implicated in melanomagenesis, TGF-β, MAPK, Wnt/β-catenin and Hyppo signaling, from the complementary point of view of tumor cells and the microenvironment.
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Affiliation(s)
- Barbara Bellei
- Laboratory of Cutaneous Physiopathology and Integrated Center of Metabolomics Research, San Gallicano Dermatological Institute, IRCCS, 00144 Rome, Italy;
- Correspondence: ; Tel.: +39-0652666246
| | - Emilia Migliano
- Department of Plastic and Regenerative Surgery, San Gallicano Dermatological Institute, IRCCS, 00144 Rome, Italy;
| | - Mauro Picardo
- Laboratory of Cutaneous Physiopathology and Integrated Center of Metabolomics Research, San Gallicano Dermatological Institute, IRCCS, 00144 Rome, Italy;
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41
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Grasso CS, Tsoi J, Onyshchenko M, Abril-Rodriguez G, Ross-Macdonald P, Wind-Rotolo M, Champhekar A, Medina E, Torrejon DY, Shin DS, Tran P, Kim YJ, Puig-Saus C, Campbell K, Vega-Crespo A, Quist M, Martignier C, Luke JJ, Wolchok JD, Johnson DB, Chmielowski B, Hodi FS, Bhatia S, Sharfman W, Urba WJ, Slingluff CL, Diab A, Haanen JBAG, Algarra SM, Pardoll DM, Anagnostou V, Topalian SL, Velculescu VE, Speiser DE, Kalbasi A, Ribas A. Conserved Interferon-γ Signaling Drives Clinical Response to Immune Checkpoint Blockade Therapy in Melanoma. Cancer Cell 2020; 38:500-515.e3. [PMID: 32916126 PMCID: PMC7872287 DOI: 10.1016/j.ccell.2020.08.005] [Citation(s) in RCA: 178] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/17/2020] [Accepted: 08/10/2020] [Indexed: 12/21/2022]
Abstract
We analyze the transcriptome of baseline and on-therapy tumor biopsies from 101 patients with advanced melanoma treated with nivolumab (anti-PD-1) alone or combined with ipilimumab (anti-CTLA-4). We find that T cell infiltration and interferon-γ (IFN-γ) signaling signatures correspond most highly with clinical response to therapy, with a reciprocal decrease in cell-cycle and WNT signaling pathways in responding biopsies. We model the interaction in 58 human cell lines, where IFN-γ in vitro exposure leads to a conserved transcriptome response unless cells have IFN-γ receptor alterations. This conserved IFN-γ transcriptome response in melanoma cells serves to amplify the antitumor immune response. Therefore, the magnitude of the antitumor T cell response and the corresponding downstream IFN-γ signaling are the main drivers of clinical response or resistance to immune checkpoint blockade therapy.
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Affiliation(s)
- Catherine S Grasso
- Jonsson Comprehensive Cancer Center at the University of California, Los Angeles (UCLA), Los Angeles, CA, USA; Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| | - Jennifer Tsoi
- Jonsson Comprehensive Cancer Center at the University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Mykola Onyshchenko
- Jonsson Comprehensive Cancer Center at the University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Gabriel Abril-Rodriguez
- Jonsson Comprehensive Cancer Center at the University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | | | - Megan Wind-Rotolo
- Translational Bioinformatics, Bristol-Myers Squibb, Hopewell, NJ, USA
| | - Ameya Champhekar
- Jonsson Comprehensive Cancer Center at the University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Egmidio Medina
- Jonsson Comprehensive Cancer Center at the University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Davis Y Torrejon
- Jonsson Comprehensive Cancer Center at the University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Daniel Sanghoon Shin
- Jonsson Comprehensive Cancer Center at the University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Phuong Tran
- Jonsson Comprehensive Cancer Center at the University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Yeon Joo Kim
- Jonsson Comprehensive Cancer Center at the University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Cristina Puig-Saus
- Jonsson Comprehensive Cancer Center at the University of California, Los Angeles (UCLA), Los Angeles, CA, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Katie Campbell
- Jonsson Comprehensive Cancer Center at the University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Agustin Vega-Crespo
- Jonsson Comprehensive Cancer Center at the University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Michael Quist
- Jonsson Comprehensive Cancer Center at the University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | | | | | - Jedd D Wolchok
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Bartosz Chmielowski
- Jonsson Comprehensive Cancer Center at the University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - F Stephen Hodi
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Dana Farber Cancer Institute, Boston, MA, USA
| | | | - William Sharfman
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Walter J Urba
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, OR, USA
| | | | - Adi Diab
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - Drew M Pardoll
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valsamo Anagnostou
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Suzanne L Topalian
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Victor E Velculescu
- Bloomberg-Kimmel Institute for Cancer Immunotherapy and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Anusha Kalbasi
- Jonsson Comprehensive Cancer Center at the University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Antoni Ribas
- Jonsson Comprehensive Cancer Center at the University of California, Los Angeles (UCLA), Los Angeles, CA, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
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42
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Attrill GH, Ferguson PM, Palendira U, Long GV, Wilmott JS, Scolyer RA. The tumour immune landscape and its implications in cutaneous melanoma. Pigment Cell Melanoma Res 2020; 34:529-549. [PMID: 32939993 DOI: 10.1111/pcmr.12926] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 08/01/2020] [Accepted: 08/23/2020] [Indexed: 12/21/2022]
Abstract
The field of tumour immunology has rapidly advanced in the last decade, leading to the advent of effective immunotherapies for patients with advanced cancers. This highlights the critical role of the immune system in determining tumour development and outcome. The tumour immune microenvironment (TIME) is highly heterogeneous, and the interactions between tumours and the immune system are vastly complex. Studying immune cell function in the TIME will provide an improved understanding of the mechanisms underpinning these interactions. This review examines the role of immune cell populations in the TIME based on their phenotype, function and localisation, as well as contextualising their position in the dynamic relationship between tumours and the immune system. We discuss the function of immune cell populations, examine their impact on patient outcome and highlight gaps in current understanding of their roles in the TIME, both in cancers in general and specifically in melanoma. Studying the TIME by evaluating both pro-tumour and anti-tumour effects may elucidate the conditions which lead to tumour growth and metastasis or immune-mediated tumour regression. Moreover, an in-depth understanding of these conditions could contribute to improved prognostication, more effective use of current immunotherapies and guide the development of novel treatment strategies and therapies.
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Affiliation(s)
- Grace H Attrill
- Melanoma Institute Australia, The University of Sydney, Sydney, Australia.,Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Peter M Ferguson
- Melanoma Institute Australia, The University of Sydney, Sydney, Australia.,Sydney Medical School, The University of Sydney, Sydney, Australia.,Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and New South Wales Health Pathology, Sydney, Australia
| | - Umaimainthan Palendira
- Melanoma Institute Australia, The University of Sydney, Sydney, Australia.,Discipline of Infectious Diseases and Immunology, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, Sydney, Australia.,Sydney Medical School, The University of Sydney, Sydney, Australia.,Mater and North Shore Hospitals, Sydney, Australia
| | - James S Wilmott
- Melanoma Institute Australia, The University of Sydney, Sydney, Australia.,Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, Australia.,Sydney Medical School, The University of Sydney, Sydney, Australia.,Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and New South Wales Health Pathology, Sydney, Australia
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43
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Wang L, Gao Y, Zhang G, Li D, Wang Z, Zhang J, Hermida LC, He L, Wang Z, Si J, Geng S, Ai R, Ning F, Cheng C, Deng H, Dimitrov DS, Sun Y, Huang Y, Wang D, Hu X, Wei Z, Wang W, Liao X. Enhancing KDM5A and TLR activity improves the response to immune checkpoint blockade. Sci Transl Med 2020; 12. [DOI: 10.1126/scitranslmed.aax2282] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
The bifunctional compound D18 improves checkpoint blockade efficacy by increasing KDM5A and PD-L1 abundance and inducing TLR7/8 activation.
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Affiliation(s)
- Liangliang Wang
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Human Brain Protection, Tsinghua University, Beijing 100084, China
| | - Yan Gao
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Human Brain Protection, Tsinghua University, Beijing 100084, China
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing 100006, China
| | - Gao Zhang
- Department of Neurosurgery and The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC 27710, USA
| | - Dan Li
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Human Brain Protection, Tsinghua University, Beijing 100084, China
| | - Zhenda Wang
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Human Brain Protection, Tsinghua University, Beijing 100084, China
| | - Jie Zhang
- Department of Computer Science, College of Computing Sciences, New Jersey Institute of Technology, Neswark, NJ 07102, USA
| | - Leandro C. Hermida
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Center for Bioinformatics and Computational Biology, Department of Computer Science, University of Maryland, College Park, MD 20742, USA
| | - Lei He
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Human Brain Protection, Tsinghua University, Beijing 100084, China
| | - Zhisong Wang
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Human Brain Protection, Tsinghua University, Beijing 100084, China
| | - Jingwen Si
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Human Brain Protection, Tsinghua University, Beijing 100084, China
| | - Shuang Geng
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), College of Chemistry, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Rizi Ai
- Department of Chemistry and Biochemistry, 9500 Gilman Drive, UC San Diego, La Jolla, CA 92093, USA
| | - Fei Ning
- Institute of Immunology and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Chaoran Cheng
- Department of Computer Science, College of Computing Sciences, New Jersey Institute of Technology, Neswark, NJ 07102, USA
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | | | - Yan Sun
- Lanzhou Institute of Husbandry and Pharmaceutical Science of CAAS, Lanzhou 730050, China
| | - Yanyi Huang
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), College of Chemistry, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Dong Wang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xiaoyu Hu
- Institute of Immunology and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Zhi Wei
- Department of Computer Science, College of Computing Sciences, New Jersey Institute of Technology, Neswark, NJ 07102, USA
| | - Wei Wang
- Department of Chemistry and Biochemistry, 9500 Gilman Drive, UC San Diego, La Jolla, CA 92093, USA
| | - Xuebin Liao
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Human Brain Protection, Tsinghua University, Beijing 100084, China
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44
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Azevedo H, Pessoa GC, de Luna Vitorino FN, Nsengimana J, Newton-Bishop J, Reis EM, da Cunha JPC, Jasiulionis MG. Gene co-expression and histone modification signatures are associated with melanoma progression, epithelial-to-mesenchymal transition, and metastasis. Clin Epigenetics 2020; 12:127. [PMID: 32831131 PMCID: PMC7444266 DOI: 10.1186/s13148-020-00910-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 07/20/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND We have previously developed a murine cellular system that models the transformation from melanocytes to metastatic melanoma cells. This model was established by cycles of anchorage impediment of melanocytes and consists of four cell lines: differentiated melanocytes (melan-a), pre-malignant melanocytes (4C), malignant (4C11-), and metastasis-prone (4C11+) melanoma cells. Here, we searched for transcriptional and epigenetic signatures associated with melanoma progression and metastasis by performing a gene co-expression analysis of transcriptome data and a mass-spectrometry-based profiling of histone modifications in this model. RESULTS Eighteen modules of co-expressed genes were identified, and some of them were associated with melanoma progression, epithelial-to-mesenchymal transition (EMT), and metastasis. The genes in these modules participate in biological processes like focal adhesion, cell migration, extracellular matrix organization, endocytosis, cell cycle, DNA repair, protein ubiquitination, and autophagy. Modules and hub signatures related to EMT and metastasis (turquoise, green yellow, and yellow) were significantly enriched in genes associated to patient survival in two independent melanoma cohorts (TCGA and Leeds), suggesting they could be sources of novel prognostic biomarkers. Clusters of histone modifications were also linked to melanoma progression, EMT, and metastasis. Reduced levels of H4K5ac and H4K8ac marks were seen in the pre-malignant and tumorigenic cell lines, whereas the methylation patterns of H3K4, H3K56, and H4K20 were related to EMT. Moreover, the metastatic 4C11+ cell line showed higher H3K9me2 and H3K36me3 methylation, lower H3K18me1, H3K23me1, H3K79me2, and H3K36me2 marks and, in agreement, downregulation of the H3K36me2 methyltransferase Nsd1. CONCLUSIONS We uncovered transcriptional and histone modification signatures that may be molecular events driving melanoma progression and metastasis, which can aid in the identification of novel prognostic genes and drug targets for treating the disease.
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Affiliation(s)
- Hátylas Azevedo
- Division of Urology, Department of Surgery, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Guilherme Cavalcante Pessoa
- Department of Pharmacology, Universidade Federal de São Paulo (UNIFESP), Rua Pedro de Toledo 669 5 andar, Vila Clementino, São Paulo, SP, 04039032, Brazil
| | | | - Jérémie Nsengimana
- Institute of Medical Research at St James's, University of Leeds School of Medicine, Leeds, UK
- Biostatistics Research Group, Population Health Sciences Institute, Newcastle University, Newcastle, United Kingdom
| | - Julia Newton-Bishop
- Institute of Medical Research at St James's, University of Leeds School of Medicine, Leeds, UK
| | - Eduardo Moraes Reis
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Júlia Pinheiro Chagas da Cunha
- Laboratório de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo, Brazil
| | - Miriam Galvonas Jasiulionis
- Department of Pharmacology, Universidade Federal de São Paulo (UNIFESP), Rua Pedro de Toledo 669 5 andar, Vila Clementino, São Paulo, SP, 04039032, Brazil.
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45
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Wouters J, Kalender-Atak Z, Minnoye L, Spanier KI, De Waegeneer M, Bravo González-Blas C, Mauduit D, Davie K, Hulselmans G, Najem A, Dewaele M, Pedri D, Rambow F, Makhzami S, Christiaens V, Ceyssens F, Ghanem G, Marine JC, Poovathingal S, Aerts S. Robust gene expression programs underlie recurrent cell states and phenotype switching in melanoma. Nat Cell Biol 2020; 22:986-998. [PMID: 32753671 DOI: 10.1038/s41556-020-0547-3] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 06/23/2020] [Indexed: 02/07/2023]
Abstract
Melanoma cells can switch between a melanocytic and a mesenchymal-like state. Scattered evidence indicates that additional intermediate state(s) may exist. Here, to search for such states and decipher their underlying gene regulatory network (GRN), we studied 10 melanoma cultures using single-cell RNA sequencing (RNA-seq) as well as 26 additional cultures using bulk RNA-seq. Although each culture exhibited a unique transcriptome, we identified shared GRNs that underlie the extreme melanocytic and mesenchymal states and the intermediate state. This intermediate state is corroborated by a distinct chromatin landscape and is governed by the transcription factors SOX6, NFATC2, EGR3, ELF1 and ETV4. Single-cell migration assays confirmed the intermediate migratory phenotype of this state. Using time-series sampling of single cells after knockdown of SOX10, we unravelled the sequential and recurrent arrangement of GRNs during phenotype switching. Taken together, these analyses indicate that an intermediate state exists and is driven by a distinct and stable 'mixed' GRN rather than being a symbiotic heterogeneous mix of cells.
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Affiliation(s)
- Jasper Wouters
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Zeynep Kalender-Atak
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium.,Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Liesbeth Minnoye
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Katina I Spanier
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Maxime De Waegeneer
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Carmen Bravo González-Blas
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - David Mauduit
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Kristofer Davie
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Gert Hulselmans
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Ahmad Najem
- Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Michael Dewaele
- Center for Cancer Biology, VIB-KU Leuven, Leuven, Belgium.,Department of Oncology, KU Leuven, Leuven, Belgium
| | - Dennis Pedri
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium.,Center for Cancer Biology, VIB-KU Leuven, Leuven, Belgium.,Department of Oncology, KU Leuven, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Florian Rambow
- Center for Cancer Biology, VIB-KU Leuven, Leuven, Belgium.,Department of Oncology, KU Leuven, Leuven, Belgium
| | - Samira Makhzami
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Valerie Christiaens
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Ghanem Ghanem
- Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Jean-Christophe Marine
- Center for Cancer Biology, VIB-KU Leuven, Leuven, Belgium.,Department of Oncology, KU Leuven, Leuven, Belgium
| | | | - Stein Aerts
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium. .,Department of Human Genetics, KU Leuven, Leuven, Belgium.
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46
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Emran AA, Nsengimana J, Punnia-Moorthy G, Schmitz U, Gallagher SJ, Newton-Bishop J, Tiffen JC, Hersey P. Study of the Female Sex Survival Advantage in Melanoma-A Focus on X-Linked Epigenetic Regulators and Immune Responses in Two Cohorts. Cancers (Basel) 2020; 12:E2082. [PMID: 32731355 PMCID: PMC7464825 DOI: 10.3390/cancers12082082] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/15/2020] [Accepted: 07/23/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Survival from melanoma is strongly related to patient sex, with females having a survival rate almost twice that of males. Many explanations have been proposed but have not withstood critical scrutiny. Prior analysis of different cancers with a sex bias has identified six X-linked genes that escape X chromosome inactivation in females and are, therefore, potentially involved in sex differences in survival. Four of the genes are well-known epigenetic regulators that are known to influence the expression of hundreds of other genes and signaling pathways in cancer. METHODS Survival and interaction analysis were performed on the skin cutaneous melanoma (SKCM) cohort in The Cancer Genome Atlas (TCGA), comparing high vs. low expression of KDM6A, ATRX, KDM5C, and DDX3X. The Leeds melanoma cohort (LMC) on 678 patients with primary melanoma was used as a validation cohort. RESULTS Analysis of TCGA data revealed that two of these genes-KDM6A and ATRX-were associated with improved survival from melanoma. Tumoral KDM6A was expressed at higher levels in females and was associated with inferred lymphoid infiltration into melanoma. Gene set analysis of high KDM6A showed strong associations with immune responses and downregulation of genes associated with Myc and other oncogenic pathways. The LMC analysis confirmed the prognostic significance of KDM6A and its interaction with EZH2 but also revealed the expression of KDM5C and DDX3X to be prognostically significant. The analysis also confirmed a partial correlation of KDM6A with immune tumor infiltrates. CONCLUSION When considered together, the results from these two series are consistent with the involvement of X-linked epigenetic regulators in the improved survival of females from melanoma. The identification of gene signatures associated with their expression presents insights into the development of new treatment initiatives but provides a basis for exploration in future studies.
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Affiliation(s)
- Abdullah Al Emran
- Melanoma Oncology and Immunology Program, The Centenary Institute, The University of Sydney, Royal Prince Alfred Hospital, Missenden Road, Camperdown NSW 2050, Australia; (A.A.E.); (G.P.-M.); (S.J.G.); (J.C.T.)
- Melanoma Institute Australia, The University of Sydney, Sydney NSW 2006, Australia
| | - Jérémie Nsengimana
- Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds LS2 9JT, UK; (J.N.); (J.N.-B.)
- Biostatistics Research Group, Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Gaya Punnia-Moorthy
- Melanoma Oncology and Immunology Program, The Centenary Institute, The University of Sydney, Royal Prince Alfred Hospital, Missenden Road, Camperdown NSW 2050, Australia; (A.A.E.); (G.P.-M.); (S.J.G.); (J.C.T.)
- Melanoma Institute Australia, The University of Sydney, Sydney NSW 2006, Australia
| | - Ulf Schmitz
- Computational Biomedicine Lab Centenary Institute, The University of Sydney, Camperdown NSW 2050, Australia;
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown NSW 2050, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown NSW 2050, Australia
| | - Stuart J. Gallagher
- Melanoma Oncology and Immunology Program, The Centenary Institute, The University of Sydney, Royal Prince Alfred Hospital, Missenden Road, Camperdown NSW 2050, Australia; (A.A.E.); (G.P.-M.); (S.J.G.); (J.C.T.)
- Melanoma Institute Australia, The University of Sydney, Sydney NSW 2006, Australia
| | - Julia Newton-Bishop
- Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds LS2 9JT, UK; (J.N.); (J.N.-B.)
| | - Jessamy C. Tiffen
- Melanoma Oncology and Immunology Program, The Centenary Institute, The University of Sydney, Royal Prince Alfred Hospital, Missenden Road, Camperdown NSW 2050, Australia; (A.A.E.); (G.P.-M.); (S.J.G.); (J.C.T.)
- Melanoma Institute Australia, The University of Sydney, Sydney NSW 2006, Australia
| | - Peter Hersey
- Melanoma Oncology and Immunology Program, The Centenary Institute, The University of Sydney, Royal Prince Alfred Hospital, Missenden Road, Camperdown NSW 2050, Australia; (A.A.E.); (G.P.-M.); (S.J.G.); (J.C.T.)
- Melanoma Institute Australia, The University of Sydney, Sydney NSW 2006, Australia
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47
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Gajos-Michniewicz A, Czyz M. WNT Signaling in Melanoma. Int J Mol Sci 2020; 21:E4852. [PMID: 32659938 PMCID: PMC7402324 DOI: 10.3390/ijms21144852] [Citation(s) in RCA: 128] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022] Open
Abstract
WNT-signaling controls important cellular processes throughout embryonic development and adult life, so any deregulation of this signaling can result in a wide range of pathologies, including cancer. WNT-signaling is classified into two categories: β-catenin-dependent signaling (canonical pathway) and β-catenin-independent signaling (non-canonical pathway), the latter can be further divided into WNT/planar cell polarity (PCP) and calcium pathways. WNT ligands are considered as unique directional growth factors that contribute to both cell proliferation and polarity. Origin of cancer can be diverse and therefore tissue-specific differences can be found in WNT-signaling between cancers, including specific mutations contributing to cancer development. This review focuses on the role of the WNT-signaling pathway in melanoma. The current view on the role of WNT-signaling in cancer immunity as well as a short summary of WNT pathway-related drugs under investigation are also provided.
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Affiliation(s)
| | - Malgorzata Czyz
- Department of Molecular Biology of Cancer, Medical University of Lodz, 6/8 Mazowiecka Street, 92–215 Lodz, Poland;
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48
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Kato S, Weng QY, Insco ML, Chen KY, Muralidhar S, Pozniak J, Diaz JMS, Drier Y, Nguyen N, Lo JA, van Rooijen E, Kemeny LV, Zhan Y, Feng Y, Silkworth W, Powell CT, Liau BB, Xiong Y, Jin J, Newton-Bishop J, Zon LI, Bernstein BE, Fisher DE. Gain-of-Function Genetic Alterations of G9a Drive Oncogenesis. Cancer Discov 2020; 10:980-997. [PMID: 32269030 PMCID: PMC7334057 DOI: 10.1158/2159-8290.cd-19-0532] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 02/05/2020] [Accepted: 04/03/2020] [Indexed: 11/16/2022]
Abstract
Epigenetic regulators, when genomically altered, may become driver oncogenes that mediate otherwise unexplained pro-oncogenic changes lacking a clear genetic stimulus, such as activation of the WNT/β-catenin pathway in melanoma. This study identifies previously unrecognized recurrent activating mutations in the G9a histone methyltransferase gene, as well as G9a genomic copy gains in approximately 26% of human melanomas, which collectively drive tumor growth and an immunologically sterile microenvironment beyond melanoma. Furthermore, the WNT pathway is identified as a key tumorigenic target of G9a gain-of-function, via suppression of the WNT antagonist DKK1. Importantly, genetic or pharmacologic suppression of mutated or amplified G9a using multiple in vitro and in vivo models demonstrates that G9a is a druggable target for therapeutic intervention in melanoma and other cancers harboring G9a genomic aberrations. SIGNIFICANCE: Oncogenic G9a abnormalities drive tumorigenesis and the "cold" immune microenvironment by activating WNT signaling through DKK1 repression. These results reveal a key druggable mechanism for tumor development and identify strategies to restore "hot" tumor immune microenvironments.This article is highlighted in the In This Issue feature, p. 890.
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Affiliation(s)
- Shinichiro Kato
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Qing Yu Weng
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Megan L Insco
- Howard Hughes Medical Institute, Chevy Chase, Maryland
- Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, Massachusetts
| | - Kevin Y Chen
- Howard Hughes Medical Institute, Chevy Chase, Maryland
- Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, Massachusetts
| | - Sathya Muralidhar
- Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Joanna Pozniak
- Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Joey Mark S Diaz
- Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Yotam Drier
- Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Nhu Nguyen
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Jennifer A Lo
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Ellen van Rooijen
- Howard Hughes Medical Institute, Chevy Chase, Maryland
- Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Lajos V Kemeny
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Yao Zhan
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Yang Feng
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Whitney Silkworth
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - C Thomas Powell
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - Yan Xiong
- Mount Sinai Center for Therapeutics Discovery, Department of Pharmaceutical Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Department of Pharmaceutical Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Julia Newton-Bishop
- Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Leonard I Zon
- Howard Hughes Medical Institute, Chevy Chase, Maryland
- Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Bradley E Bernstein
- Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - David E Fisher
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts.
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49
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Juraleviciute M, Pozniak J, Nsengimana J, Harland M, Randerson-Moor J, Wernhoff P, Bassarova A, Øy GF, Trøen G, Flørenes VA, Bishop DT, Herlyn M, Newton-Bishop J, Slipicevic A. MX 2 is a novel regulator of cell cycle in melanoma cells. Pigment Cell Melanoma Res 2020; 33:446-457. [PMID: 31660681 PMCID: PMC7180100 DOI: 10.1111/pcmr.12837] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/07/2019] [Accepted: 10/18/2019] [Indexed: 12/14/2022]
Abstract
MX2 protein is a dynamin-like GTPase2 that has recently been identified as an interferon-induced restriction factor of HIV-1 and other primate lentiviruses. A single nucleotide polymorphism (SNP), rs45430, in an intron of the MX2 gene, was previously reported as a novel melanoma susceptibility locus in genome-wide association studies. Functionally, however, it is still unclear whether and how MX2 contributes to melanoma susceptibility and tumorigenesis. Here, we show that MX2 is differentially expressed in melanoma tumors and cell lines, with most metastatic cell lines showing lower MX2 expression than primary melanoma cell lines and melanocytes. Furthermore, high expression of MX2 RNA in primary melanoma tumors is associated with better patient survival. Overexpression of MX2 reduces in vivo proliferation partially through inhibition of AKT activation, suggesting that it can act as a tumor suppressor in melanoma. However, we have also identified a subset of melanoma cell lines with high endogenous MX2 expression where downregulation of MX2 leads to reduced proliferation. In these cells, MX2 downregulation interfered with DNA replication and cell cycle processes. Collectively, our data for the first time show that MX2 is functionally involved in the regulation of melanoma proliferation but that its function is context-dependent.
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Affiliation(s)
| | - Joanna Pozniak
- Division of Haematology and Immunology, Institute of Medical Research at St James's, University of Leeds, Leeds, UK
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Jérémie Nsengimana
- Division of Haematology and Immunology, Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Mark Harland
- Division of Haematology and Immunology, Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Juliette Randerson-Moor
- Division of Haematology and Immunology, Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Patrik Wernhoff
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Assia Bassarova
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Geir Frode Øy
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Gunhild Trøen
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | | | - David Timothy Bishop
- Division of Haematology and Immunology, Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | | | - Julia Newton-Bishop
- Division of Haematology and Immunology, Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Ana Slipicevic
- Department of Pathology, Oslo University Hospital, Oslo, Norway
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50
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Kim KH, Kim HK, Kim HD, Kim CG, Lee H, Han JW, Choi SJ, Jeong S, Jeon M, Kim H, Koh J, Ku BM, Park SH, Ahn MJ, Shin EC. PD-1 blockade-unresponsive human tumor-infiltrating CD8 + T cells are marked by loss of CD28 expression and rescued by IL-15. Cell Mol Immunol 2020; 18:385-397. [PMID: 32332901 DOI: 10.1038/s41423-020-0427-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 03/22/2020] [Indexed: 12/15/2022] Open
Abstract
Blockade of programmed death-1 (PD-1) reinvigorates exhausted CD8+ T cells, resulting in tumor regression in cancer patients. Recently, reinvigoration of exhausted CD8+ T cells following PD-1 blockade was shown to be CD28-dependent in mouse models. Herein, we examined the role of CD28 in anti-PD-1 antibody-induced human T cell reinvigoration using tumor-infiltrating CD8+ T cells (CD8+ TILs) obtained from non-small-cell lung cancer patients. Single-cell analysis demonstrated a distinct expression pattern of CD28 between mouse and human CD8+ TILs. Furthermore, we found that human CD28+CD8+ but not CD28-CD8+ TILs responded to PD-1 blockade irrespective of B7/CD28 blockade, indicating that CD28 costimulation in human CD8+ TILs is dispensable for PD-1 blockade-induced reinvigoration and that loss of CD28 expression serves as a marker of anti-PD-1 antibody-unresponsive CD8+ TILs. Transcriptionally and phenotypically, PD-1 blockade-unresponsive human CD28-PD-1+CD8+ TILs exhibited characteristics of terminally exhausted CD8+ T cells with low TCF1 expression. Notably, CD28-PD-1+CD8+ TILs had preserved machinery to respond to IL-15, and IL-15 treatment enhanced the proliferation of CD28-PD-1+CD8+ TILs as well as CD28+PD-1+CD8+ TILs. Taken together, these results show that loss of CD28 expression is a marker of PD-1 blockade-unresponsive human CD8+ TILs with a TCF1- signature and provide mechanistic insights into combining IL-15 with anti-PD-1 antibodies.
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Affiliation(s)
- Kyung Hwan Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.,Department of Radiation Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hong Kwan Kim
- Department of Thoracic and Cardiovascular Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hyung-Don Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Chang Gon Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Hoyoung Lee
- Biomedical Science and Engineering Interdisciplinary Program, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Ji Won Han
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Seong Jin Choi
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Seongju Jeong
- Biomedical Science and Engineering Interdisciplinary Program, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Minwoo Jeon
- Biomedical Science and Engineering Interdisciplinary Program, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Hyunglae Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Jiae Koh
- Research Institute for Future Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.,Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
| | - Bo Mi Ku
- Research Institute for Future Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Su-Hyung Park
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Myung-Ju Ahn
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea. .,Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
| | - Eui-Cheol Shin
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.
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