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Khunger A, Piazza E, Warren S, Smith TH, Ren X, White A, Elliott N, Cesano A, Beechem JM, Kirkwood JM, Tarhini AA. CTLA-4 blockade and interferon-α induce proinflammatory transcriptional changes in the tumor immune landscape that correlate with pathologic response in melanoma. PLoS One 2021; 16:e0245287. [PMID: 33428680 PMCID: PMC7799833 DOI: 10.1371/journal.pone.0245287] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/24/2020] [Indexed: 12/18/2022] Open
Abstract
Patients with locally/regionally advanced melanoma were treated with neoadjuvant combination immunotherapy with high-dose interferon α-2b (HDI) and ipilimumab in a phase I clinical trial. Tumor specimens were obtained prior to the initiation of neoadjuvant therapy, at the time of surgery and progression if available. In this study, gene expression profiles of tumor specimens (N = 27) were investigated using the NanoString nCounter® platform to evaluate associations with clinical outcomes (pathologic response, radiologic response, relapse-free survival (RFS), and overall survival (OS)) and define biomarkers associated with tumor response. The Tumor Inflammation Signature (TIS), an 18-gene signature that enriches for response to Programmed cell death protein 1 (PD-1) checkpoint blockade, was also evaluated for association with clinical response and survival. It was observed that neoadjuvant ipilimumab-HDI therapy demonstrated an upregulation of immune-related genes, chemokines, and transcription regulator genes involved in immune cell activation, function, or cell proliferation. Importantly, increased expression of baseline pro-inflammatory genes CCL19, CD3D, CD8A, CD22, LY9, IL12RB1, C1S, C7, AMICA1, TIAM1, TIGIT, THY1 was associated with longer OS (p < 0.05). In addition, multiple genes that encode a component or a regulator of the extracellular matrix such as MMP2 and COL1A2 were identified post-treatment as being associated with longer RFS and OS. In all baseline tissues, high TIS scores were associated with longer OS (p = 0.0166). Also, downregulated expression of cell proliferation-related genes such as CUL1, CCND1 and AAMP at baseline was associated with pathological and radiological response (unadjusted p < 0.01). In conclusion, we identified numerous genes that play roles in multiple biological pathways involved in immune activation, immune suppression and cell proliferation correlating with pathological/radiological responses following neoadjuvant immunotherapy highlighting the complexity of immune responses modulated by immunotherapy. Our observations suggest that TIS may be a useful biomarker for predicting survival outcomes with combination immunotherapy.
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Affiliation(s)
- Arjun Khunger
- Department of Internal Medicine, Memorial Hospital West, Pembroke Pines, Florida, United States of America
| | - Erin Piazza
- NanoString® Technologies, Inc., Seattle, Washington, United States of America
| | - Sarah Warren
- NanoString® Technologies, Inc., Seattle, Washington, United States of America
| | - Thomas H. Smith
- NanoString® Technologies, Inc., Seattle, Washington, United States of America
| | - Xing Ren
- NanoString® Technologies, Inc., Seattle, Washington, United States of America
| | - Andrew White
- NanoString® Technologies, Inc., Seattle, Washington, United States of America
| | - Nathan Elliott
- NanoString® Technologies, Inc., Seattle, Washington, United States of America
| | - Alessandra Cesano
- ESSA Pharma, South San Francisco, California, United States of America
| | - Joseph M. Beechem
- NanoString® Technologies, Inc., Seattle, Washington, United States of America
| | - John M. Kirkwood
- UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, United States of America
| | - Ahmad A. Tarhini
- Department of Cutaneous Oncology and Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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Monosomy 3 Influences Epithelial-Mesenchymal Transition Gene Expression in Uveal Melanoma Patients; Consequences for Liquid Biopsy. Int J Mol Sci 2020; 21:ijms21249651. [PMID: 33348918 PMCID: PMC7767066 DOI: 10.3390/ijms21249651] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022] Open
Abstract
Despite outstanding advances in diagnosis and the treatment of primary uveal melanoma (UM), nearly 50% of UM patients develop metastases via hematogenous dissemination, driven by the epithelial-mesenchymal transition (EMT). Despite the failure in UM to date, a liquid biopsy may offer a feasible non-invasive approach for monitoring metastatic disease progression and addressing protracted dormancy. To detect circulating tumor cells (CTCs) in UM patients, we evaluated the mRNA expression of EMT-associated transcription factors in CD45-depleted blood fraction, using qRT-PCR. ddPCR was employed to assess UM-specific GNA11, GNAQ, PLCβ4, and CYSLTR2 mutations in plasma DNA. Moreover, microarray analysis was performed on total RNA isolated from tumor tissues to estimate the prognostic value of EMT-associated gene expression. In total, 42 primary UM and 11 metastatic patients were enrolled. All CD45-depleted samples were negative for CTC when compared to the peripheral blood fraction of 60 healthy controls. Tumor-specific mutations were detected in the plasma of 21.4% patients, merely, in 9.4% of primary UM, while 54.5% in metastatic patients. Unsupervised hierarchical clustering of differentially expressed EMT genes showed significant differences between monosomy 3 and disomy 3 tumors. Newly identified genes can serve as non-invasive prognostic biomarkers that can support therapeutic decisions.
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Kaštelan S, Antunica AG, Oresković LB, Pelčić G, Kasun E, Hat K. Immunotherapy for Uveal Melanoma - Current Knowledge and Perspectives. Curr Med Chem 2020; 27:1350-1366. [DOI: 10.2174/0929867326666190704141444] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 06/09/2019] [Accepted: 06/14/2019] [Indexed: 12/17/2022]
Abstract
Uveal melanoma is the most prevalent primary intraocular tumour in adults with
the incidence between five and six cases per million people in the United States and Europe.
The prognosis of patients with uveal melanoma is unfavourable with a 5-year survival rate of
50-70% despite significant advances in local tumour treatment using radiotherapy or surgical
resection. Approximately 50% of the patients develop metastases within 15 years from initial
diagnosis, mostly in the liver. The median survival rate after the onset of metastases is 6
months. Potential treatment options for metastatic uveal melanoma are chemotherapy, targeted
therapy, and immunotherapy but no method showed satisfactory results. Immunotherapy
with checkpoint inhibition showed promising results in the treatment of cutaneous melanoma;
however, it did not appear to be equally effective with uveal melanoma. This may be
due to differences in mutational burden, expression of neoantigens between these two types of
tumour, immunosuppressive tumour microenvironment, and low immunogenicity and immune
privilege of uveal melanoma. Considering the disappointing results of treatment with
anti-CTLA-4 and PD-1/PD-L1 blockade in patients with advanced uveal melanoma several
new forms of therapies are being developed. This may include immunotherapy with
IMCgp100, glembatumumab vedotin and the infusion of autologous TILs, targeted therapy
with selective MEK inhibitors, epigenetic therapy, and nanotherapy. Better insight into the
molecular and genetic profile of uveal melanoma will facilitate detection of new prognostic
biomarkers and thus enable a better modification of the existing immunotherapy methods and
development of new forms of treatment specifically designed for uveal melanoma patients.
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Affiliation(s)
- Snježana Kaštelan
- Department of Ophthalmology, University Hospital Dubrava, Zagreb, Croatia
| | | | | | - Goran Pelčić
- Department of Ophthalmology, Faculty of Medicine, University of Rijeka and Clinical Hospital Center Rijeka, Rijeka, Croatia
| | - Ema Kasun
- School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Koraljka Hat
- Department of Maxillofacial Surgery, University Hospital Dubrava, Zagreb, Croatia
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Pan H, Lu L, Cui J, Yang Y, Wang Z, Fan X. Immunological analyses reveal an immune subtype of uveal melanoma with a poor prognosis. Aging (Albany NY) 2020; 12:1446-1464. [PMID: 31954372 PMCID: PMC7053626 DOI: 10.18632/aging.102693] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 12/25/2019] [Indexed: 12/11/2022]
Abstract
Uveal melanoma is an aggressive intraocular malignancy that often exhibits low immunogenicity. Metastatic uveal melanoma samples frequently exhibit monosomy 3 or BAP1 deficiency. In this study, we used bioinformatic methods to investigate the immune infiltration of uveal melanoma samples in public datasets. We first performed Gene Set Enrichment/Variation Analyses to detect immunological pathways that are altered in tumors with monosomy 3 or BAP1 deficiency. We then conducted an unsupervised clustering analysis to identify distinct immunologic molecular subtypes of uveal melanoma. We used CIBERSORT and ESTIMATE with RNA-seq data from The Cancer Genome Atlas and the GSE22138 microarray dataset to determine the sample-level immune subpopulations and immune scores of uveal melanoma samples. The Kaplan-Meier method and log-rank test were used to assess the prognostic value of particular immune cells and genes in uveal melanoma samples. Through these approaches, we discovered uveal melanoma-specific immunologic features, which may provide new insights into the tumor microenvironment and enhance the development of immunotherapies in the future.
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Affiliation(s)
- Hui Pan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Linna Lu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Junqi Cui
- Department of Pathology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Yuan Yang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Zhaoyang Wang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Xianqun Fan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
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