1
|
Manjunath HS, James N, Mathew R, Al Hashmi M, Silcock L, Biunno I, De Blasio P, Manickam C, Tomei S. Human sample authentication in biomedical research: comparison of two platforms. Sci Rep 2021; 11:13982. [PMID: 34234171 PMCID: PMC8263568 DOI: 10.1038/s41598-021-92978-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 06/07/2021] [Indexed: 11/08/2022] Open
Abstract
Samples used in biomedical research are often collected over years, in some cases from subjects that may have died and thus cannot be retrieved in any way. The value of these samples is priceless. Sample misidentification or mix-up are unfortunately common problems in biomedical research and can eventually result in the publication of incorrect data. Here we have compared the Fluidigm SNPtrace and the Agena iPLEX Sample ID panels for the authentication of human genomic DNA samples. We have tested 14 pure samples and simulated their cross-contamination at different percentages (2%, 5%, 10%, 25% and 50%). For both panels, we report call rate, allele intensity/probability score, performance in distinguishing pure samples and contaminated samples at different percentages, and sex typing. We show that both panels are reliable and efficient methods for sample authentication and we highlight their advantages and disadvantages. We believe that the data provided here is useful for sample authentication especially in biorepositories and core facility settings.
Collapse
Affiliation(s)
| | | | - Rebecca Mathew
- Omics Core, Integrated Genomic Services, Research Branch, Sidra Medicine, PO 26999, Doha, Qatar
| | - Muna Al Hashmi
- Omics Core, Integrated Genomic Services, Research Branch, Sidra Medicine, PO 26999, Doha, Qatar
| | | | - Ida Biunno
- Integrated Systems Engineering, Milan, Italy
| | | | - Chidambaram Manickam
- Omics Core, Integrated Genomic Services, Research Branch, Sidra Medicine, PO 26999, Doha, Qatar
| | - Sara Tomei
- Omics Core, Integrated Genomic Services, Research Branch, Sidra Medicine, PO 26999, Doha, Qatar.
| |
Collapse
|
2
|
Mall R, Saad M, Roelands J, Rinchai D, Kunji K, Almeer H, Hendrickx W, M Marincola F, Ceccarelli M, Bedognetti D. Network-based identification of key master regulators associated with an immune-silent cancer phenotype. Brief Bioinform 2021; 22:6274817. [PMID: 33979427 PMCID: PMC8574720 DOI: 10.1093/bib/bbab168] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 03/24/2021] [Accepted: 04/09/2021] [Indexed: 12/15/2022] Open
Abstract
A cancer immune phenotype characterized by an active T-helper 1 (Th1)/cytotoxic response is associated with responsiveness to immunotherapy and favorable prognosis across different tumors. However, in some cancers, such an intratumoral immune activation does not confer protection from progression or relapse. Defining mechanisms associated with immune evasion is imperative to refine stratification algorithms, to guide treatment decisions and to identify candidates for immune-targeted therapy. Molecular alterations governing mechanisms for immune exclusion are still largely unknown. The availability of large genomic datasets offers an opportunity to ascertain key determinants of differential intratumoral immune response. We follow a network-based protocol to identify transcription regulators (TRs) associated with poor immunologic antitumor activity. We use a consensus of four different pipelines consisting of two state-of-the-art gene regulatory network inference techniques, regularized gradient boosting machines and ARACNE to determine TR regulons, and three separate enrichment techniques, including fast gene set enrichment analysis, gene set variation analysis and virtual inference of protein activity by enriched regulon analysis to identify the most important TRs affecting immunologic antitumor activity. These TRs, referred to as master regulators (MRs), are unique to immune-silent and immune-active tumors, respectively. We validated the MRs coherently associated with the immune-silent phenotype across cancers in The Cancer Genome Atlas and a series of additional datasets in the Prediction of Clinical Outcomes from Genomic Profiles repository. A downstream analysis of MRs specific to the immune-silent phenotype resulted in the identification of several enriched candidate pathways, including NOTCH1, TGF-$\beta $, Interleukin-1 and TNF-$\alpha $ signaling pathways. TGFB1I1 emerged as one of the main negative immune modulators preventing the favorable effects of a Th1/cytotoxic response.
Collapse
Affiliation(s)
- Raghvendra Mall
- Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Mohamad Saad
- Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Jessica Roelands
- Cancer Research Department, Research Branch, Sidra Medicince, Doha, Qatar
| | - Darawan Rinchai
- Cancer Research Department, Research Branch, Sidra Medicince, Doha, Qatar
| | - Khalid Kunji
- Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Hossam Almeer
- Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Wouter Hendrickx
- Cancer Research Department, Research Branch, Sidra Medicince, Doha, Qatar
| | | | - Michele Ceccarelli
- Department of Electrical Engineering and Information Technology (DIETI), University of Naples "Federico II", Via Claudio 21, 80215 Naples, Italy.,Biogem, Istituto di Biologia e Genetica Molecolare, Via Camporeale, Ariano Irpino (AV)
| | - Davide Bedognetti
- Cancer Research Department, Research Branch, Sidra Medicince, Doha, Qatar.,Department of Internal Medicine and Medical Specialities, University of Genova, Genova, Italy.,College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| |
Collapse
|
3
|
Al Hashmi M, Sastry KS, Silcock L, Chouchane L, Mattei V, James N, Mathew R, Bedognetti D, De Giorgi V, Murtas D, Liu W, Chouchane A, Temanni R, Seliger B, Wang E, Marincola FM, Tomei S. Differential responsiveness to BRAF inhibitors of melanoma cell lines BRAF V600E-mutated. J Transl Med 2020; 18:192. [PMID: 32393282 PMCID: PMC7216681 DOI: 10.1186/s12967-020-02350-8] [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: 03/08/2020] [Accepted: 04/24/2020] [Indexed: 12/14/2022] Open
Abstract
Background Most mutations in melanoma affect one critical amino acid on BRAF gene, resulting in the V600E substitution. Patient management is often based on the use of specific inhibitors targeting this mutation. Methods DNA and RNA mutation status was assessed in 15 melanoma cell lines by Sanger sequencing and RNA-seq. We tested the cell lines responsiveness to BRAF inhibitors (vemurafenib and PLX4720, BRAF-specific and sorafenib, BRAF non-specific). Cell proliferation was assessed by MTT colorimetric assay. BRAF V600E RNA expression was assessed by qPCR. Expression level of phosphorylated-ERK protein was assessed by Western Blotting as marker of BRAF activation. Results Three cell lines were discordant in the mutation detection (BRAF V600E at DNA level/Sanger sequencing and BRAF WT on RNA-seq). We initially postulated that those cell lines may express only the WT allele at the RNA level although mutated at the DNA level. A more careful analysis showed that they express low level of BRAF RNA and the expression may be in favor of the WT allele. We tested whether the discordant cell lines responded differently to BRAF-specific inhibitors. Their proliferation rate decreased after treatment with vemurafenib and PLX4720 but was not affected by sorafenib, suggesting a BRAF V600E biological behavior. Yet, responsiveness to the BRAF specific inhibitors was lower as compared to the control. Western Blot analysis revealed a decreased expression of p-ERK protein in the BRAF V600E control cell line and in the discordant cell lines upon treatment with BRAF-specific inhibitors. The discordant cell lines showed a lower responsiveness to BRAF inhibitors when compared to the BRAF V600E control cell line. The results obtained from the inhibition experiment and molecular analyses were also confirmed in three additional cell lines. Conclusion Cell lines carrying V600E mutation at the DNA level may respond differently to BRAF targeted treatment potentially due to a lower V600E RNA expression.
Collapse
Affiliation(s)
- Muna Al Hashmi
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Konduru S Sastry
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Lee Silcock
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Lotfi Chouchane
- Department of Genetic Medicine, Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Valentina Mattei
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Nicola James
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Rebecca Mathew
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Davide Bedognetti
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Valeria De Giorgi
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center, National Institutes of Health (NIH), Bethesda, USA
| | - Daniela Murtas
- Department of Biomedical Sciences, Section of Cytomorphology, University of Cagliari, Cagliari, Italy
| | - Wei Liu
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Aouatef Chouchane
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Ramzi Temanni
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Ena Wang
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar
| | - Francesco M Marincola
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar.,Refuge Biotechnologies, Menlo Park, CA, USA
| | - Sara Tomei
- Research Branch, Sidra Medical and Research Center, 26999, Doha, Qatar.
| |
Collapse
|
4
|
Abstract
BACKGROUND Monoallelic expression (MAE) is a frequent genomic phenomenon in normal tissues, however its role in cancer is yet to be fully understood. MAE is defined as the expression of a gene that is restricted to one allele in the presence of a diploid heterozygous genome. Constitutive MAE occurs for imprinted genes, odorant receptors and random X inactivation. Several studies in normal tissues have showed MAE in approximately 5-20% of the cases. However, little information exists on the MAE rate in cancer. In this study we assessed the presence and rate of MAE in melanoma. The genetic basis of melanoma has been studied in depth over the past decades, leading to the identification of mutations/genetic alterations responsible for melanoma development. METHODS To examine the role of MAE in melanoma we used 15 melanoma cell lines and compared their RNA-seq data with genotyping data obtained by the parental TIL (tumor infiltrating lymphocytes). Genotyping was performed using the Illumina HumanOmni1 beadchip. The RNA-seq library preparation and sequencing was performed using the Illumina TruSeq Stranded Total RNA Human Kit and subsequently sequenced using a HiSeq 2500 according to manufacturer's guidelines. By comparing genotyping data with RNA-seq data, we identified SNPs in which DNA genotypes were heterozygous and corresponding RNA genotypes were homozygous. All homozygous DNA genotypes were removed prior to the analysis. To confirm the validity to detect MAE, we examined heterozygous DNA genotypes from X chromosome of female samples as well as for imprinted and olfactory receptor genes and confirmed MAE. RESULTS MAE was detected in all 15 cell lines although to a different rate. When looking at the B-allele frequencies we found a preferential pattern of complete monoallelic expression rather then differential monoallelic expression across the 15 melanoma cell lines. As some samples showed high differences in the homozygous and heterozygous call rate, we looked at the single chromosomes and showed that MAE may be explained by underlying large copy number imbalances in some instances. Interestingly these regions included genes known to play a role in melanoma initiation and progression. Nevertheless, some chromosome regions showed MAE without CN imbalances suggesting that additional mechanisms (including epigenetic silencing) may explain MAE in melanoma. CONCLUSION The biological implications of MAE are yet to be realized. Nevertheless, our findings suggest that MAE is a common phenomenon in melanoma cell lines. Further analyses are currently being undertaken to evaluate whether MAE is gene/pathway specific and to understand whether MAE can be employed by cancers to achieve a more aggressive phenotype.
Collapse
|
5
|
Chen C, Gao FH. Th17 Cells Paradoxical Roles in Melanoma and Potential Application in Immunotherapy. Front Immunol 2019; 10:187. [PMID: 30800130 PMCID: PMC6375889 DOI: 10.3389/fimmu.2019.00187] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/22/2019] [Indexed: 12/24/2022] Open
Abstract
The progressive infiltration of immune cells is associated with the progression of melanoma. Specifically, Th17 cells in melanoma microenvironment have both antitumor and protumor effects. It is now necessary to understand the contradictory data associated with how Th17 cells play a role in melanoma. This review will summarize the current knowledge regarding the potential mechanisms that may be involved in the effects of Th17 cells in melanoma progression. Currently, since adoptive transferring Th17 cells has been successful in eradicating melanoma in mice, it offers promise for next-generation adoptive cell transfer, as ex vivo expanded stemness-like memory Th17 cells which are induced by distinct cytokines or pharmacologic reagents may be infused into melanoma patients to potentiate treatment outcome.
Collapse
Affiliation(s)
- Chen Chen
- Department of Oncology, Shanghai 9th People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Feng-Hou Gao
- Department of Oncology, Shanghai 9th People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
6
|
The immunologic constant of rejection classification refines the prognostic value of conventional prognostic signatures in breast cancer. Br J Cancer 2018; 119:1383-1391. [PMID: 30353048 PMCID: PMC6265245 DOI: 10.1038/s41416-018-0309-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 09/03/2018] [Accepted: 09/27/2018] [Indexed: 12/21/2022] Open
Abstract
Background The immunologic constant of rejection (ICR) is a broad phenomenon of Th-1 immunity-mediated, tissue-specific destruction. Methods We tested the prognostic value of a 20-gene ICR expression signature in 8766 early breast cancers. Results Thirty-three percent of tumours were ICR1, 29% ICR2, 23% ICR3, and 15% ICR4. In univariate analysis, ICR4 was associated with a 36% reduction in risk of metastatic relapse when compared with ICR1-3 (p = 2.30E–03). In multivariate analysis including notably the three major prognostic signatures (Recurrence score, 70-gene signature, ROR-P), ICR was the strongest predictive variable (p = 9.80E–04). ICR showed no prognostic value in the HR+/HER2− subtype, but prognostic value in the HER2+ and TN subtypes. Furthermore, in each molecular subtype and among the tumours defined as high risk by the three prognostic signatures, ICR4 patients had a 41–75% reduction in risk of relapse as compared with ICR1-3 patients. ICR added significant prognostic information to that provided by the clinico-genomic models in the overall population and in each molecular subtype. ICR4 was independently associated with achievement of pathological complete response to neoadjuvant chemotherapy (p = 2.97E–04). Conclusion ICR signature adds prognostic information to that of current proliferation-based signatures, with which it could be integrated to improve patients’ stratification and guide adjuvant treatment.
Collapse
|
7
|
Immune oncology, immune responsiveness and the theory of everything. J Immunother Cancer 2018; 6:50. [PMID: 29871670 PMCID: PMC5989400 DOI: 10.1186/s40425-018-0355-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 05/11/2018] [Indexed: 12/12/2022] Open
Abstract
Anti-cancer immunotherapy is encountering its own checkpoint. Responses are dramatic and long lasting but occur in a subset of tumors and are largely dependent upon the pre-existing immune contexture of individual cancers. Available data suggest that three landscapes best define the cancer microenvironment: immune-active, immune-deserted and immune-excluded. This trichotomy is observable across most solid tumors (although the frequency of each landscape varies depending on tumor tissue of origin) and is associated with cancer prognosis and response to checkpoint inhibitor therapy (CIT). Various gene signatures (e.g. Immunological Constant of Rejection - ICR and Tumor Inflammation Signature - TIS) that delineate these landscapes have been described by different groups. In an effort to explain the mechanisms of cancer immune responsiveness or resistance to CIT, several models have been proposed that are loosely associated with the three landscapes. Here, we propose a strategy to integrate compelling data from various paradigms into a “Theory of Everything”. Founded upon this unified theory, we also propose the creation of a task force led by the Society for Immunotherapy of Cancer (SITC) aimed at systematically addressing salient questions relevant to cancer immune responsiveness and immune evasion. This multidisciplinary effort will encompass aspects of genetics, tumor cell biology, and immunology that are pertinent to the understanding of this multifaceted problem.
Collapse
|
8
|
Hendrickx W, Simeone I, Anjum S, Mokrab Y, Bertucci F, Finetti P, Curigliano G, Seliger B, Cerulo L, Tomei S, Delogu LG, Maccalli C, Wang E, Miller LD, Marincola FM, Ceccarelli M, Bedognetti D. Identification of genetic determinants of breast cancer immune phenotypes by integrative genome-scale analysis. Oncoimmunology 2017; 6:e1253654. [PMID: 28344865 PMCID: PMC5353940 DOI: 10.1080/2162402x.2016.1253654] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 10/20/2016] [Accepted: 10/22/2016] [Indexed: 12/20/2022] Open
Abstract
Cancer immunotherapy is revolutionizing the clinical management of several tumors, but has demonstrated limited activity in breast cancer. The development of more effective treatments is hindered by incomplete knowledge of the genetic determinant of immune responsiveness. To fill this gap, we mined copy number alteration, somatic mutation, and expression data from The Cancer Genome Atlas (TCGA). By using RNA-sequencing data from 1,004 breast cancers, we defined distinct immune phenotypes characterized by progressive expression of transcripts previously associated with immune-mediated rejection. The T helper 1 (Th-1) phenotype (ICR4), which also displays upregulation of immune-regulatory transcripts such as PDL1, PD1, FOXP3, IDO1, and CTLA4, was associated with prolonged patients' survival. We validated these findings in an independent meta-cohort of 1,954 breast cancer gene expression data. Chromosome segment 4q21, which includes genes encoding for the Th-1 chemokines CXCL9-11, was significantly amplified only in the immune favorable phenotype (ICR4). The mutation and neoantigen load progressively decreased from ICR4 to ICR1 but could not fully explain immune phenotypic differences. Mutations of TP53 were enriched in the immune favorable phenotype (ICR4). Conversely, the presence of MAP3K1 and MAP2K4 mutations were tightly associated with an immune-unfavorable phenotype (ICR1). Using both the TCGA and the validation dataset, the degree of MAPK deregulation segregates breast tumors according to their immune disposition. These findings suggest that mutation-driven perturbations of MAPK pathways are linked to the negative regulation of intratumoral immune response in breast cancer. Modulations of MAPK pathways could be experimentally tested to enhance breast cancer immune sensitivity.
Collapse
Affiliation(s)
- Wouter Hendrickx
- Tumor Biology, Immunology, and Therapy Section, Division of Translational Medicine, Research Branch, Sidra Medical and Research Center , Doha, Qatar
| | - Ines Simeone
- Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar; Department of Science and Technology, University of Sannio, Benevento, Italy
| | - Samreen Anjum
- Qatar Computing Research Institute, Hamad Bin Khalifa University , Doha, Qatar
| | - Younes Mokrab
- Division of Biomedical Informatics, Research Branch, Sidra Medical and Research Center , Doha, Qatar
| | - François Bertucci
- Département d'Oncologie Moléculaire, Center de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Marseille, France; Département d'Oncologie Médicale, CRCM, Institut Paoli-Calmettes, Marseille, France; Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - Pascal Finetti
- Département d'Oncologie Moléculaire, Center de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes , INSERM UMR1068, CNRS UMR725 , Marseille, France
| | - Giuseppe Curigliano
- Division of Experimental Therapeutics, Division of Medical Oncology, European Institute of Oncology , Milan, Italy
| | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg , Halle, Germany
| | - Luigi Cerulo
- Department of Science and Technology, University of Sannio, Benevento, Italy; BIOGEM Research Center, Ariano Irpino, Italy
| | - Sara Tomei
- Division of Translational Medicine, Research Branch, Sidra Medical and Research Center , Doha, Qatar
| | - Lucia Gemma Delogu
- Department of Chemistry and Pharmacy, University of Sassari , Sassari, Italy
| | - Cristina Maccalli
- Tumor Biology, Immunology, and Therapy Section, Division of Translational Medicine, Research Branch, Sidra Medical and Research Center , Doha, Qatar
| | - Ena Wang
- Division of Translational Medicine, Research Branch, Sidra Medical and Research Center , Doha, Qatar
| | - Lance D Miller
- Department of Cancer Biology, Wake Forest School of Medicine , Winston-Salem, NC, USA
| | - Francesco M Marincola
- Office of the Chief Research Officer (CRO), Research Branch, Sidra Medical and Research Center , Doha, Qatar
| | - Michele Ceccarelli
- Qatar Computing Research Institute, Hamad Bin Khalifa University , Doha, Qatar
| | - Davide Bedognetti
- Tumor Biology, Immunology, and Therapy Section, Division of Translational Medicine, Research Branch, Sidra Medical and Research Center , Doha, Qatar
| |
Collapse
|
9
|
Salerno EP, Bedognetti D, Mauldin IS, Deacon DH, Shea SM, Pinczewski J, Obeid JM, Coukos G, Wang E, Gajewski TF, Marincola FM, Slingluff CL. Human melanomas and ovarian cancers overexpressing mechanical barrier molecule genes lack immune signatures and have increased patient mortality risk. Oncoimmunology 2016; 5:e1240857. [PMID: 28123876 PMCID: PMC5215363 DOI: 10.1080/2162402x.2016.1240857] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 09/19/2016] [Accepted: 09/20/2016] [Indexed: 01/05/2023] Open
Abstract
We have identified eight genes whose expression in human melanoma metastases and ovarian cancers is associated with a lack of Th1 immune signatures. They encode molecules with mechanical barrier function in the skin and other normal tissues and include filaggrin (FLG), tumor-associated calcium signal transducer 2 (TACSTD2), and six desmosomal proteins (DST, DSC3, DSP, PPL, PKP3, and JUP). This association has been validated in an independent series of 114 melanoma metastases. In these, DST expression alone is sufficient to identify melanomas without immune signatures, while FLG and the other six putative barrier molecules are overexpressed in a different subset of melanomas lacking immune signatures. Similar associations have been identified in a set of 186 ovarian cancers. RNA-seq data from 471 melanomas and 307 ovarian cancers in the TCGA database further support these findings and also reveal that overexpression of barrier molecules is strongly associated with early patient mortality for melanoma (p = 0.0002) and for ovarian cancer (p < 0.01). Interestingly, this association persists for FLG for melanoma (p = 0.012) and ovarian cancer (p = 0.006), whereas DST overexpression is negatively associated with CD8+ gene expression, but not with patient survival. Thus, overexpression of FLG or DST identifies two distinct patient populations with low immune cell infiltration in these cancers, but with different prognostic implications for each. These data raise the possibility that molecules with mechanical barrier function in skin and other tissues may be used by cancer cells to protect them from immune cell infiltration and immune-mediated destruction.
Collapse
Affiliation(s)
- Elise P Salerno
- Division of Surgical Oncology, Department of Surgery, University of Virginia , Charlottesville, VA, USA
| | - Davide Bedognetti
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD, USA; Sidra Medical and Research Center, Doha, Qatar
| | - Ileana S Mauldin
- Division of Surgical Oncology, Department of Surgery, University of Virginia , Charlottesville, VA, USA
| | - Donna H Deacon
- Division of Surgical Oncology, Department of Surgery, University of Virginia , Charlottesville, VA, USA
| | - Sofia M Shea
- Division of Surgical Oncology, Department of Surgery, University of Virginia, Charlottesville, VA, USA; Department of Pathology, University of Virginia Health System, Charlottesville, VA, USA
| | - Joel Pinczewski
- Division of Surgical Oncology, Department of Surgery, University of Virginia , Charlottesville, VA, USA
| | - Joseph M Obeid
- Division of Surgical Oncology, Department of Surgery, University of Virginia , Charlottesville, VA, USA
| | - George Coukos
- Ludwig Institute for Cancer Research, University of Lausanne , Lausanne, Switzerland
| | - Ena Wang
- Sidra Medical and Research Center , Doha, Qatar
| | | | | | - Craig L Slingluff
- Division of Surgical Oncology, Department of Surgery, University of Virginia , Charlottesville, VA, USA
| |
Collapse
|
10
|
Abstract
PURPOSE OF REVIEW Here, we focus on molecular biomarkers derived from transcriptomic studies to summarize the recent advances in our understanding of the mechanisms associated with differential prognosis and treatment outcome in breast cancer. RECENT FINDINGS Breast cancer is certainly immunogenic; yet it has been historically resistant to immunotherapy. In the past few years, refined immunotherapeutic manipulations have been shown to be effective in a significant proportion of cancer patients. For example, drugs targeting the PD-1 immune checkpoint have been proven to be an effective therapeutic approach in several solid tumors including melanoma and lung cancer. Very recently, the activity of such therapeutics has also been demonstrated in breast cancer patients. Pari passu with the development of novel immune modulators, the transcriptomic analysis of human tumors unveiled unexpected and paradoxical relationships between cancer cells and immune cells. SUMMARY This review examines our understanding of the molecular pathways associated with intratumoral immune response, which represents a critical step for the implementation of stratification strategies toward the development of personalized immunotherapy of breast cancer.
Collapse
|
11
|
Guennoun A, Sidahmed H, Maccalli C, Seliger B, Marincola FM, Bedognetti D. Harnessing the immune system for the treatment of melanoma: current status and future prospects. Expert Rev Clin Immunol 2016; 12:879-93. [PMID: 27070898 DOI: 10.1080/1744666x.2016.1176529] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
When malignant melanoma is diagnosed early, surgical resection is the intervention of choice and is often curative, but many patients present with unresectable disease at later stages. Due to its complex etiology paired with well-documented chemoresistance and high metastatic potential, patients with advanced melanoma had a poor prognosis, and the treatment of this disease remained unsatisfactory for many years. Recently, targeted therapy, immune checkpoint inhibition, or combinatory approaches have revolutionized the therapeutic options of melanoma allowing considerable improvement in disease control and survival. In this review we will summarize these novel therapeutic strategies with particular focus on combinatory immunotherapies and further discuss recent data derived from immunogenomic studies and potential options to improve the therapeutic efficacy of immune modulatory approaches.
Collapse
Affiliation(s)
- Andrea Guennoun
- a Division of Translational Medicine , Research Branch, Sidra Medical and Research Center , Doha , Qatar
| | - Heba Sidahmed
- a Division of Translational Medicine , Research Branch, Sidra Medical and Research Center , Doha , Qatar
| | - Cristina Maccalli
- b Tumor Biology, Immunology and Therapy Section, Division of Translational Medicine , Research Branch, Sidra Medical and Research Center , Doha , Qatar
| | - Barbara Seliger
- c Institute of Medical Immunology , Martin Luther University Halle-Wittenberg , Halle , Germany
| | - Francesco M Marincola
- d Office of the Chief Research Officer (CRO) , Research Branch, Sidra Medical and Research Center , Doha , Qatar
| | - Davide Bedognetti
- b Tumor Biology, Immunology and Therapy Section, Division of Translational Medicine , Research Branch, Sidra Medical and Research Center , Doha , Qatar
| |
Collapse
|
12
|
Miller LD, Chou JA, Black MA, Print C, Chifman J, Alistar A, Putti T, Zhou X, Bedognetti D, Hendrickx W, Pullikuth A, Rennhack J, Andrechek ER, Demaria S, Wang E, Marincola FM. Immunogenic Subtypes of Breast Cancer Delineated by Gene Classifiers of Immune Responsiveness. Cancer Immunol Res 2016; 4:600-10. [PMID: 27197066 DOI: 10.1158/2326-6066.cir-15-0149] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 02/16/2016] [Indexed: 12/24/2022]
Abstract
The abundance and functional orientation of tumor-infiltrating lymphocytes in breast cancer is associated with distant metastasis-free survival, yet how this association is influenced by tumor phenotypic heterogeneity is poorly understood. Here, a bioinformatics approach defined tumor biologic attributes that influence this association and delineated tumor subtypes that may differ in their ability to sustain durable antitumor immune responses. A large database of breast tumor expression profiles and associated clinical data was compiled, from which the ability of phenotypic markers to significantly influence the prognostic performance of a classification model that incorporates immune cell-specific gene signatures was ascertained. Markers of cell proliferation and intrinsic molecular subtype reproducibly distinguished two breast cancer subtypes that we refer to as immune benefit-enabled (IBE) and immune benefit-disabled (IBD). The IBE tumors, comprised mostly of highly proliferative tumors of the basal-like, HER2-enriched, and luminal B subtypes, could be stratified by the immune classifier into significantly different prognostic groups, while IBD tumors could not, indicating the potential for productive engagement of metastasis-protective immunity in IBE tumors, but not in IBD tumors. The prognostic stratification in IBE was independent of conventional variables. Gene network analysis predicted the activation of TNFα/IFNγ signaling pathways in IBE tumors and the activation of the transforming growth factor-β pathway in IBD tumors. This prediction supports a model in which breast tumors can be distinguished on the basis of their potential for metastasis-protective immune responsiveness. Whether IBE and IBD represent clinically relevant contexts for evaluating sensitivity to immunotherapeutic agents warrants further investigation. Cancer Immunol Res; 4(7); 600-10. ©2016 AACR.
Collapse
Affiliation(s)
- Lance D Miller
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina. The Comprehensive Cancer Center of Wake Forest University, Winston Salem, North Carolina.
| | - Jeff A Chou
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Michael A Black
- Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand
| | - Cristin Print
- Department of Molecular Medicine and Pathology and Maurice Wilkins Institute, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Julia Chifman
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Angela Alistar
- The Comprehensive Cancer Center of Wake Forest University, Winston Salem, North Carolina. Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Thomas Putti
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, National University Hospital, Singapore
| | - Xiaobo Zhou
- Department of Radiology, Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Davide Bedognetti
- Division of Translational Medicine, Sidra Medical and Research Center, Doha, Qatar
| | - Wouter Hendrickx
- Division of Translational Medicine, Sidra Medical and Research Center, Doha, Qatar
| | - Ashok Pullikuth
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Jonathan Rennhack
- Department of Physiology, Michigan State University, East Lansing, Michigan
| | - Eran R Andrechek
- Department of Physiology, Michigan State University, East Lansing, Michigan
| | - Sandra Demaria
- Department of Radiation Oncology and Pathology, Weill Cornell Medical College, New York, New York
| | - Ena Wang
- Division of Translational Medicine, Sidra Medical and Research Center, Doha, Qatar
| | - Francesco M Marincola
- Office of the Chief Research Officer, Research Branch, Sidra Medical and Research Center, Doha, Qatar
| |
Collapse
|
13
|
Bedognetti D, Maccalli C, Bader SBA, Marincola FM, Seliger B. Checkpoint Inhibitors and Their Application in Breast Cancer. Breast Care (Basel) 2016; 11:108-15. [PMID: 27239172 PMCID: PMC4881248 DOI: 10.1159/000445335] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Immune checkpoints are crucial for the maintenance of self-tolerance and for the modulation of immune responses in order to minimize tissue damage. Tumor cells take advantage of these mechanisms to evade immune recognition. A significant proportion of tumors, including breast cancers, can express co-inhibitory molecules that are important formediating the escape from T cell-mediated immune surveillance. The interaction of inhibitory receptors with their ligands can be blocked by specific molecules. Monoclonal antibodies (mAbs) directed against the cytotoxic T lymphocyte-associated antigen-4 (CTLA4) and, more recently, against the programmed cell death protein 1 (PD1), have been approved for the therapy of melanoma (anti-CTLA4 and anti-PD1 mAbs) and non-small cell lung cancer (anti-PD1 mAbs). Moreover, inhibition of PD1 signaling has shown extremely promising signs of activity in breast cancer. An increasing number of molecules directed against other immune checkpoints are currently under clinical development. In this review, we summarize the evidence supporting the implementation of checkpoint inhibition in breast cancer by reviewing in detail data on PD-L1 expression and its regulation. In addition, opportunities to boost anti-tumor immunity in breast cancer with checkpoint inhibitor-based immunotherapies alone and in combination with other treatment options will be discussed.
Collapse
Affiliation(s)
- Davide Bedognetti
- Tumor Biology, Immunology, and Therapy Section, Division of Translational Medicine, Sidra Medical and Research Center, Doha, Qatar
| | - Cristina Maccalli
- Tumor Biology, Immunology, and Therapy Section, Division of Translational Medicine, Sidra Medical and Research Center, Doha, Qatar
| | - Salha B.J. Al Bader
- National Center for Cancer Care and Research (NCCCR), and Hamad General Hospital, Doha, Qatar
| | - Francesco M. Marincola
- Office of the Chief Research Officer (CRO), Sidra Medical and Research Center, Doha, Qatar
| | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| |
Collapse
|
14
|
Bedognetti D, Hendrickx W, Ceccarelli M, Miller LD, Seliger B. Disentangling the relationship between tumor genetic programs and immune responsiveness. Curr Opin Immunol 2016; 39:150-8. [PMID: 26967649 DOI: 10.1016/j.coi.2016.02.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 02/03/2016] [Accepted: 02/04/2016] [Indexed: 12/13/2022]
Abstract
Correlative studies in humans have demonstrated that an active immune microenvironment characterized by the presence of a T-helper 1 immune response typifies a tumor phenotype associated with better outcome and increased responsiveness to immune manipulation. This phenotype also signifies the counter activation of immune-regulatory mechanisms. Variables modulating the development of an effective anti-tumor immune response are increasingly scrutinized as potential therapeutic targets. Genetic alterations of cancer cells that functionally influence intratumoral immune response include mutational load, specific mutations of genes involved in oncogenic pathways and copy number aberrations involving chemokine and cytokine genes. Inhibiting oncogenic pathways that prevent the development of the immune-favorable cancer phenotype may complement modern immunotherapeutic approaches.
Collapse
Affiliation(s)
- Davide Bedognetti
- Tumor Biology, Immunology and Therapy Section, Division of Translational Medicine, Research Branch, Sidra Medical and Research Center, Doha, Qatar.
| | - Wouter Hendrickx
- Tumor Biology, Immunology and Therapy Section, Division of Translational Medicine, Research Branch, Sidra Medical and Research Center, Doha, Qatar
| | - Michele Ceccarelli
- Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Lance D Miller
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle, Germany
| |
Collapse
|
15
|
Dugo M, Nicolini G, Tragni G, Bersani I, Tomassetti A, Colonna V, Del Vecchio M, De Braud F, Canevari S, Anichini A, Sensi M. A melanoma subtype with intrinsic resistance to BRAF inhibition identified by receptor tyrosine kinases gene-driven classification. Oncotarget 2016; 6:5118-33. [PMID: 25742786 PMCID: PMC4467137 DOI: 10.18632/oncotarget.3007] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 12/21/2014] [Indexed: 02/07/2023] Open
Abstract
Dysregulation of receptor tyrosine kinases (RTKs) contributes to several aspects of oncogenesis including drug resistance. In melanoma, distinct RTKs have been involved in BRAF inhibitors (BRAFi) resistance, yet the utility of RTKs expression pattern to identify intrinsically resistant tumors has not been assessed. Transcriptional profiling of RTKs and integration with a previous classification, reveals three robust subtypes in two independent datasets of melanoma cell lines and one cohort of melanoma samples. This classification was validated by Western blot in a panel of patient-derived melanoma cell lines. One of the subtypes identified here for the first time displayed the highest and lowest expression of EGFR and ERBB3, respectively, and included BRAF-mutant tumors all intrinsically resistant to BRAFi PLX4720, as assessed by analysis of the Cancer Cell Line Encyclopedia pharmacogenomic study and by in vitro growth inhibition assays. High levels of EGFR were detected, even before therapy, in tumor cells of one of three melanoma patients unresponsive to BRAFi. Use of different pharmacological inhibitors highlighted the relevance of PI3K/mTOR signaling for growth of this PLX4720-resistant subtype. Our results identify a specific molecular profile of melanomas intrinsically resistant to BRAFi and suggest the PI3K/mTOR pathway as a potential therapeutic target for these tumors.
Collapse
Affiliation(s)
- Matteo Dugo
- Functional Genomics and Bioinformatics, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Gabriella Nicolini
- Unit of Immunobiology of Human Tumors, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Gabrina Tragni
- Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Ilaria Bersani
- Unit of Immunobiology of Human Tumors, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Antonella Tomassetti
- Unit of Molecular Therapies, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Valentina Colonna
- Department of Clinical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Michele Del Vecchio
- Department of Clinical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Filippo De Braud
- Department of Clinical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Silvana Canevari
- Functional Genomics and Bioinformatics, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Andrea Anichini
- Unit of Immunobiology of Human Tumors, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Marialuisa Sensi
- Functional Genomics and Bioinformatics, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.,Unit of Immunobiology of Human Tumors, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| |
Collapse
|
16
|
Ascierto PA, Atkins M, Bifulco C, Botti G, Cochran A, Davies M, Demaria S, Dummer R, Ferrone S, Formenti S, Gajewski TF, Garbe C, Khleif S, Kiessling R, Lo R, Lorigan P, Arthur GM, Masucci G, Melero I, Mihm M, Palmieri G, Parmiani G, Puzanov I, Romero P, Schilling B, Seliger B, Stroncek D, Taube J, Tomei S, Zarour HM, Testori A, Wang E, Galon J, Ciliberto G, Mozzillo N, Marincola FM, Thurin M. Future perspectives in melanoma research: meeting report from the "Melanoma Bridge": Napoli, December 3rd-6th 2014. J Transl Med 2015; 13:374. [PMID: 26619946 PMCID: PMC4665874 DOI: 10.1186/s12967-015-0736-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 11/19/2015] [Indexed: 12/27/2022] Open
Abstract
The fourth "Melanoma Bridge Meeting" took place in Naples, December 3-6th, 2014. The four topics discussed at this meeting were: Molecular and Immunological Advances, Combination Therapies, News in Immunotherapy, and Tumor Microenvironment and Biomarkers. Until recently systemic therapy for metastatic melanoma patients was ineffective, but recent advances in tumor biology and immunology have led to the development of new targeted and immunotherapeutic agents that prolong progression-free survival (PFS) and overall survival (OS). New therapies, such as mitogen-activated protein kinase (MAPK) pathway inhibitors as well as other signaling pathway inhibitors, are being tested in patients with metastatic melanoma either as monotherapy or in combination, and all have yielded promising results. These include inhibitors of receptor tyrosine kinases (BRAF, MEK, and VEGFR), the phosphatidylinositol 3 kinase (PI3K) pathway [PI3K, AKT, mammalian target of rapamycin (mTOR)], activators of apoptotic pathway, and the cell cycle inhibitors (CDK4/6). Various locoregional interventions including radiotherapy and surgery are still valid approaches in treatment of advanced melanoma that can be integrated with novel therapies. Intrinsic, adaptive and acquired resistance occur with targeted therapy such as BRAF inhibitors, where most responses are short-lived. Given that the reactivation of the MAPK pathway through several distinct mechanisms is responsible for the majority of acquired resistance, it is logical to combine BRAF inhibitors with inhibitors of targets downstream in the MAPK pathway. For example, combination of BRAF/MEK inhibitors (e.g., dabrafenib/trametinib) have been demonstrated to improve survival compared to monotherapy. Application of novel technologies such sequencing have proven useful as a tool for identification of MAPK pathway-alternative resistance mechanism and designing other combinatorial therapies such as those between BRAF and AKT inhibitors. Improved survival rates have also been observed with immune-targeted therapy for patients with metastatic melanoma. Immune-modulating antibodies came to the forefront with anti-CTLA-4, programmed cell death-1 (PD-1) and PD-1 ligand 1 (PD-L1) pathway blocking antibodies that result in durable responses in a subset of melanoma patients. Agents targeting other immune inhibitory (e.g., Tim-3) or immune stimulating (e.g., CD137) receptors and other approaches such as adoptive cell transfer demonstrate clinical benefit in patients with melanoma as well. These agents are being studied in combination with targeted therapies in attempt to produce longer-term responses than those more typically seen with targeted therapy. Other combinations with cytotoxic chemotherapy and inhibitors of angiogenesis are changing the evolving landscape of therapeutic options and are being evaluated to prevent or delay resistance and to further improve survival rates for this patient population. This meeting's specific focus was on advances in combination of targeted therapy and immunotherapy. Both combination targeted therapy approaches and different immunotherapies were discussed. Similarly to the previous meetings, the importance of biomarkers for clinical application as markers for diagnosis, prognosis and prediction of treatment response was an integral part of the meeting. The overall emphasis on biomarkers supports novel concepts toward integrating biomarkers into contemporary clinical management of patients with melanoma across the entire spectrum of disease stage. Translation of the knowledge gained from the biology of tumor microenvironment across different tumors represents a bridge to impact on prognosis and response to therapy in melanoma.
Collapse
Affiliation(s)
- Paolo A Ascierto
- Istituto Nazionale Tumori, Fondazione "G. Pascale", Naples, Italy.
| | - Michael Atkins
- Georgetown-Lombardi Comprehensive Cancer Center, Washington, DC, USA.
| | - Carlo Bifulco
- Translational Molecular Pathology, Earle A. Chiles Research Institute, Providence Cancer Center, Portland, OR, USA.
| | - Gerardo Botti
- Istituto Nazionale Tumori, Fondazione "G. Pascale", Naples, Italy.
| | - Alistair Cochran
- Departments of Pathology and Laboratory Medicine and Surgery, David Geffen School of Medicine at University of California Los Angeles (UCLA), John Wayne Cancer Institute, Santa Monica, CA, USA.
| | - Michael Davies
- Department of Melanoma Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Sandra Demaria
- Departments of Radiation Oncology and Pathology, Weill Cornell Medical College, New York, NY, USA.
| | - Reinhard Dummer
- Skin Cancer Unit, Department of Dermatology, University Hospital Zürich, 8091, Zurich, Switzerland.
| | - Soldano Ferrone
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Silvia Formenti
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA.
| | - Thomas F Gajewski
- Departments of Medicine and of Pathology, Immunology and Cancer Program, The University of Chicago Medicine, Chicago, IL, USA.
| | - Claus Garbe
- Department of Dermatology, Center for Dermato Oncology, University of Tübingen, Tübingen, Germany.
| | - Samir Khleif
- Georgia Regents University Cancer Center, Georgia Regents University, Augusta, GA, USA.
| | - Rolf Kiessling
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden.
| | - Roger Lo
- Departments of Medicine and Molecular and Medical Pharmacology, David Geffen School of Medicine and Jonsson Comprehensive Cancer Center at the University of California Los Angeles (UCLA), Los Angeles, CA, USA.
| | - Paul Lorigan
- University of Manchester/Christie NHS Foundation Trust, Manchester, UK.
| | - Grant Mc Arthur
- Peter MacCallum Cancer Centre and University of Melbourne, Victoria, Australia.
| | - Giuseppe Masucci
- Department of Oncology-Pathology, The Karolinska Hospital, Stockholm, Sweden.
| | - Ignacio Melero
- Centro de Investigación Médica Aplicada, and Clinica Universidad de Navarra, Pamplona, Navarra, Spain.
| | - Martin Mihm
- Department of Dermatology, Harvard Medical School, Boston, MA, USA.
| | - Giuseppe Palmieri
- Unit of Cancer Genetics, Institute of Biomolecular Chemistry, National Research Council, Sassari, Italy.
| | - Giorgio Parmiani
- Division of Molecular Oncology, Unit of Bio-Immunotherapy of Solid Tumors, San Raffaele Institute, Milan, Italy.
| | - Igor Puzanov
- Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Pedro Romero
- Ludwig Cancer Research Center, University of Lausanne, Lausanne, Switzerland.
| | - Bastian Schilling
- Department of Dermatology, University Hospital, West German Cancer Center, University Duisburg-Essen, Essen, Germany. .,German Cancer Consortium (DKTK), Essen, Germany.
| | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle, Germany.
| | - David Stroncek
- Cell Processing Section, Department of Transfusion Medicine, Clinical Center, NIH, Bethesda, MD, USA.
| | - Janis Taube
- Department of Dermatology, Johns Hopkins University SOM, Baltimore, MD, USA.
| | - Sara Tomei
- Division of Translational Medicine, Sidra Medical and Research Center, Doha, Qatar.
| | - Hassane M Zarour
- Departments of Medicine, Immunology and Dermatology, University of Pittsburgh, Pittsburgh, PA, USA.
| | | | - Ena Wang
- Division of Translational Medicine, Sidra Medical and Research Centre, Doha, Qatar.
| | - Jérôme Galon
- INSERM, UMRS1138, Laboratory of Integrative Cancer Immunology, Université Paris Descartes, Sorbonne Paris Cité, Centre de Recherche des Cordeliers, Paris, France.
| | | | - Nicola Mozzillo
- Istituto Nazionale Tumori, Fondazione "G. Pascale", Naples, Italy.
| | | | - Magdalena Thurin
- Cancer Diagnosis Program, National Cancer Institute, NIH, Bethesda, MD, USA.
| |
Collapse
|
17
|
Thomas LE, Winston J, Rad E, Mort M, Dodd KM, Tee AR, McDyer F, Moore S, Cooper DN, Upadhyaya M. Evaluation of copy number variation and gene expression in neurofibromatosis type-1-associated malignant peripheral nerve sheath tumours. Hum Genomics 2015; 9:3. [PMID: 25884485 PMCID: PMC4367978 DOI: 10.1186/s40246-015-0025-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 01/18/2015] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Neurofibromatosis type-1 (NF1) is a complex neurogenetic disorder characterised by the development of benign and malignant tumours of the peripheral nerve sheath (MPNSTs). Whilst biallelic NF1 gene inactivation contributes to benign tumour formation, additional cellular changes in gene structure and/or expression are required to induce malignant transformation. Although few molecular profiling studies have been performed on the process of progression of pre-existing plexiform neurofibromas to MPNSTs, the integrated analysis of copy number alterations (CNAs) and gene expression is likely to be key to understanding the molecular mechanisms underlying NF1-MPNST tumorigenesis. In a pilot study, we employed this approach to identify genes differentially expressed between benign and malignant NF1 tumours. RESULTS SPP1 (osteopontin) was the most differentially expressed gene (85-fold increase in expression), compared to benign plexiform neurofibromas. Short hairpin RNA (shRNA) knockdown of SPP1 in NF1-MPNST cells reduced tumour spheroid size, wound healing and invasion in four different MPNST cell lines. Seventy-six genes were found to exhibit concordance between CNA and gene expression level. CONCLUSIONS Pathway analysis of these genes suggested that glutathione metabolism and Wnt signalling may be specifically involved in NF1-MPNST development. SPP1 is associated with malignant transformation in NF1-associated MPNSTs and could prove to be an important target for therapeutic intervention.
Collapse
Affiliation(s)
- Laura E Thomas
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK.
| | - Jincy Winston
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK.
| | - Ellie Rad
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK.
| | - Matthew Mort
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK.
| | - Kayleigh M Dodd
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK.
| | - Andrew R Tee
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK.
| | - Fionnuala McDyer
- Almac Diagnostics, 19 Seagoe Industrial Estate, Craigavon, Northern Ireland, BT63 5QD, UK.
| | - Stephen Moore
- Almac Diagnostics, 19 Seagoe Industrial Estate, Craigavon, Northern Ireland, BT63 5QD, UK.
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK.
| | - Meena Upadhyaya
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK.
| |
Collapse
|
18
|
Tomei S, Bedognetti D, De Giorgi V, Sommariva M, Civini S, Reinboth J, Al Hashmi M, Ascierto ML, Liu Q, Ayotte BD, Worschech A, Uccellini L, Ascierto PA, Stroncek D, Palmieri G, Chouchane L, Wang E, Marincola FM. The immune-related role of BRAF in melanoma. Mol Oncol 2014; 9:93-104. [PMID: 25174651 PMCID: PMC4500792 DOI: 10.1016/j.molonc.2014.07.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Revised: 07/08/2014] [Accepted: 07/17/2014] [Indexed: 11/17/2022] Open
Abstract
Background The existence of a dichotomy between immunologically active and quiescent tumor phenotypes has been recently recognized in several types of cancer. The activation of a Th1 type of immune signature has been shown to confer better prognosis and likelihood to respond to immunotherapy. However, whether such dichotomy depends on the genetic make‐up of individual cancers is not known yet. BRAF and NRAS mutations are commonly acquired during melanoma progression. Here we explored the role of BRAF and NRAS mutations in influencing the immune phenotype based on a classification previously identified by our group. Methods One‐hundred‐thirteen melanoma metastases underwent microarray analysis and BRAF and NRAS genotyping. Allele‐specific PCR was also performed in order to exclude low‐frequency mutations. Results Comparison between BRAF and NRAS mutant versus wild type samples identified mostly constituents or regulators of MAPK and related pathways. When testing gene lists discriminative of BRAF, NRAS and MAPK alterations, we found that 112 BRAF‐specific transcripts were able to distinguish the two immune‐related phenotypes already described in melanoma, with the poor phenotype associated mostly with BRAF mutation. Noteworthy, such association was stronger in samples displaying low BRAF mRNA expression. However, when testing NRAS mutations, we were not able to find the same association. Conclusion This study suggests that BRAF mutation‐related specific transcripts associate with a poor phenotype in melanoma and provide a nest for further investigation. BRAF and NRAS status was assessed in 113 melanoma metastases by Sanger sequencing and high sensitive allele‐specific PCR. The expression of BRAF‐specific genes categorized the metastases in two divergent groups. The mutant group associated with a poor phenotype. The association between BRAF mutation and the poor phenotype was stronger in samples displaying low BRAF mRNA expression. Functional interpretation of BRAF expression‐discriminative genes revealed pathways related to an unfavorable phenotype.
Collapse
Affiliation(s)
- Sara Tomei
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD 20892, USA; Department of Genetic Medicine, Weill Cornell Medical College in Qatar, PO Box 24144, Doha, Qatar; Sidra Medical and Research Center, P.O. Box 26999, Doha, Qatar.
| | - Davide Bedognetti
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD 20892, USA; Sidra Medical and Research Center, P.O. Box 26999, Doha, Qatar
| | - Valeria De Giorgi
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD 20892, USA
| | - Michele Sommariva
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD 20892, USA; Department of Biomedical Sciences for Health, Università degli Studi di Milano, Milan, Italy
| | - Sara Civini
- Cell Processing Section, Department of Transfusion Medicine, Clinical Center and Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD 20892, USA
| | - Jennifer Reinboth
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg 97074, Germany; Genelux Corporation, San Diego Science Center, San Diego 92109, USA
| | - Muna Al Hashmi
- Sidra Medical and Research Center, P.O. Box 26999, Doha, Qatar
| | - Maria Libera Ascierto
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD 20892, USA; Center of Excellence for Biomedical Research (CEBR), University of Genoa, Italy
| | - Qiuzhen Liu
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD 20892, USA
| | - Ben D Ayotte
- Department of Biology, Northern Michigan University, Marquette, MI, USA
| | - Andrea Worschech
- Department of Genetic Medicine, Weill Cornell Medical College in Qatar, PO Box 24144, Doha, Qatar
| | - Lorenzo Uccellini
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD 20892, USA; Institute of Infectious and Tropical Diseases, University of Milan, L. Sacco Hospital, Milan, Italy
| | - Paolo A Ascierto
- Istituto Nazionale Tumori Fondazione "G. Pascale", Via G. Semmola, Naples, Italy
| | - David Stroncek
- Cell Processing Section, Department of Transfusion Medicine, Clinical Center and Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD 20892, USA
| | - Giuseppe Palmieri
- Institute of Biomolecular Chemistry, National Research Council, Sassari, Italy
| | - Lotfi Chouchane
- Department of Genetic Medicine, Weill Cornell Medical College in Qatar, PO Box 24144, Doha, Qatar
| | - Ena Wang
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD 20892, USA; Sidra Medical and Research Center, P.O. Box 26999, Doha, Qatar
| | - Francesco M Marincola
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD 20892, USA; Sidra Medical and Research Center, P.O. Box 26999, Doha, Qatar
| |
Collapse
|
19
|
Direct T cell-tumour interaction triggers TH1 phenotype activation through the modification of the mesenchymal stromal cells transcriptional programme. Br J Cancer 2014; 110:2955-64. [PMID: 24809778 PMCID: PMC4056054 DOI: 10.1038/bjc.2014.235] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/18/2014] [Accepted: 04/09/2014] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Mesenchymal stromal cells (MSCs) are heterogeneous cells with immunoregulatory and wound-healing properties. In cancer, they are known to be an essential part of the tumour microenvironment. However, their role in tumour growth and rejection remains unclear. To investigate this, we co-cultured human MSCs, tumour infiltrating lymphocytes (TIL), and melanoma cells to investigate the role of MSCs in the tumour environment. METHODS Mesenchymal stromal cells were co-cultured with melanoma antigen-specific TIL that were stimulated either with HLA-A*0201(+) melanoma cells or with a corresponding clone that had lost HLA-A*0201 expression. RESULTS Activated TIL induced profound pro-inflammatory gene expression signature in MSCs. Analysis of culture supernatant found that MSCs secreted pro-inflammatory cytokines, including TH1 cytokines that have been previously associated with immune-mediated antitumor responses. In addition, immunohistochemical analysis on selected markers revealed that the same activated MSCs secreted both the TH1 cytokine (interleukin-12) and indoleamine 2,3 dioxygenase (IDO), a classical immunosuppressive factor. CONCLUSIONS This study reflected that the plasticity of MSCs is highly dependent upon microenvironment conditions. Tumour-activated TIL induced TH1 phenotype change in MSCs that is qualitatively similar to the previously described immunologic constant of rejection signature observed during immune-mediated, tissue-specific destruction. This response may be responsible for the in loco amplification of antigen-specific anti-cancer immune response.
Collapse
|
20
|
Liu Q, Tomei S, Ascierto ML, De Giorgi V, Bedognetti D, Dai C, Uccellini L, Spivey T, Pos Z, Thomas J, Reinboth J, Murtas D, Zhang Q, Chouchane L, Weiss GR, Slingluff CL, Lee PP, Rosenberg SA, Alter H, Yao K, Wang E, Marincola FM. Melanoma NOS1 expression promotes dysfunctional IFN signaling. J Clin Invest 2014; 124:2147-59. [PMID: 24691438 DOI: 10.1172/jci69611] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 01/22/2014] [Indexed: 12/28/2022] Open
Abstract
In multiple forms of cancer, constitutive activation of type I IFN signaling is a critical consequence of immune surveillance against cancer; however, PBMCs isolated from cancer patients exhibit depressed STAT1 phosphorylation in response to IFN-α, suggesting IFN signaling dysfunction. Here, we demonstrated in a coculture system that melanoma cells differentially impairs the IFN-α response in PBMCs and that the inhibitory potential of a particular melanoma cell correlates with NOS1 expression. Comparison of gene transcription and array comparative genomic hybridization (aCGH) between melanoma cells from different patients indicated that suppression of IFN-α signaling correlates with an amplification of the NOS1 locus within segment 12q22-24. Evaluation of NOS1 levels in melanomas and IFN responsiveness of purified PBMCs from patients indicated a negative correlation between NOS1 expression in melanomas and the responsiveness of PBMCs to IFN-α. Furthermore, in an explorative study, NOS1 expression in melanoma metastases was negatively associated with patient response to adoptive T cell therapy. This study provides a link between cancer cell phenotype and IFN signal dysfunction in circulating immune cells.
Collapse
|
21
|
Tomei S, Wang E, Delogu LG, Marincola FM, Bedognetti D. Non-BRAF-targeted therapy, immunotherapy, and combination therapy for melanoma. Expert Opin Biol Ther 2014; 14:663-86. [DOI: 10.1517/14712598.2014.890586] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
22
|
Pos Z, Spivey TL, Liu H, Sommariva M, Chen J, Wunderlich JR, Parisi G, Tomei S, Ayotte BD, Stroncek DF, Malek JA, Robbins PF, Rivoltini L, Maio M, Chouchane L, Wang E, Marincola FM. Longitudinal study of recurrent metastatic melanoma cell lines underscores the individuality of cancer biology. J Invest Dermatol 2013; 134:1389-1396. [PMID: 24270663 PMCID: PMC3989423 DOI: 10.1038/jid.2013.495] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 09/22/2013] [Accepted: 10/21/2013] [Indexed: 01/15/2023]
Abstract
Recurrent metastatic melanoma provides a unique opportunity to analyze disease evolution in metastatic cancer. Here, we followed up eight patients with an unusually prolonged history of metastatic melanoma, who developed a total of 26 recurrences over several years. Cell lines derived from each metastasis were analyzed by comparative genomic hybridization and global transcript analysis. We observed that conserved, patient-specific characteristics remain stable in recurrent metastatic melanoma even after years and several recurrences. Differences among individual patients exceeded within-patient lesion variability, both at the DNA copy number (P<0.001) and RNA gene expression level (P<0.001). Conserved patient-specific traits included expression of several cancer/testis antigens and the c-kit proto-oncogene throughout multiple recurrences. Interestingly, subsequent recurrences of different patients did not display consistent or convergent changes toward a more aggressive disease phenotype. Finally, sequential recurrences of the same patient did not descend progressively from each other, as irreversible mutations such as homozygous deletions were frequently not inherited from previous metastases. This study suggests that the late evolution of metastatic melanoma, which markedly turns an indolent disease into a lethal phase, is prone to preserve case-specific traits over multiple recurrences and occurs through a series of random events that do not follow a consistent stepwise process.
Collapse
Affiliation(s)
- Zoltan Pos
- Infectious Disease and Immunogenetics Section, Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA; Hungarian Academy of Sciences-Semmelweis University "Lendület" Experimental and Translational Immunomics Research Group, Budapest, Hungary; Department of Genetics, Cell, and Immunobiology, Semmelweis University, Budapest, Hungary
| | - Tara L Spivey
- Infectious Disease and Immunogenetics Section, Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA; Clinical Research Training Program (CRTP), National Institutes of Health, Bethesda, Maryland, USA; Department of General Surgery, Rush University Medical Center, Chicago, Illinois, USA
| | - Hui Liu
- Infectious Disease and Immunogenetics Section, Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Michele Sommariva
- Infectious Disease and Immunogenetics Section, Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA; Department of Biomedical Sciences for Health, Universita' degli Studi di Milano, Milan, Italy
| | - Jinguo Chen
- Infectious Disease and Immunogenetics Section, Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - John R Wunderlich
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Giulia Parisi
- Cancer Bioimmunotherapy Unit, Centro di Riferimento Oncologico, Aviano, Italy
| | - Sara Tomei
- Department of Genetic Medicine, Weill Cornell Medical College in Qatar, Education City, Doha, Qatar
| | - Ben D Ayotte
- Department of Biology, Northern Michigan University, Marquette, Michigan, USA
| | - David F Stroncek
- Cell Processing Section, Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Joel A Malek
- Department of Genetic Medicine, Weill Cornell Medical College in Qatar, Education City, Doha, Qatar
| | - Paul F Robbins
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Licia Rivoltini
- Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Michele Maio
- Cancer Bioimmunotherapy Unit, Centro di Riferimento Oncologico, Aviano, Italy
| | - Lotfi Chouchane
- Weill Cornell Medical College in Qatar, Education City, Doha, Qatar
| | - Ena Wang
- Infectious Disease and Immunogenetics Section, Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Francesco M Marincola
- Infectious Disease and Immunogenetics Section, Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA; Research Branch, Sidra Medical and Research Centre, Doha, Qatar.
| |
Collapse
|
23
|
CXCR3/CCR5 pathways in metastatic melanoma patients treated with adoptive therapy and interleukin-2. Br J Cancer 2013; 109:2412-23. [PMID: 24129241 PMCID: PMC3817317 DOI: 10.1038/bjc.2013.557] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 08/19/2013] [Accepted: 08/20/2013] [Indexed: 01/10/2023] Open
Abstract
Background: Adoptive therapy with tumour-infiltrating lymphocytes (TILs) induces durable complete responses (CR) in ∼20% of patients with metastatic melanoma. The recruitment of T cells through CXCR3/CCR5 chemokine ligands is critical for immune-mediated rejection. We postulated that polymorphisms and/or expression of CXCR3/CCR5 in TILs and the expression of their ligands in tumour influence the migration of TILs to tumours and tumour regression. Methods: Tumour-infiltrating lymphocytes from 142 metastatic melanoma patients enrolled in adoptive therapy trials were genotyped for CXCR3 rs2280964 and CCR5-Δ32 deletion, which encodes a protein not expressed on the cell surface. Expression of CXCR3/CCR5 in TILs and CXCR3/CCR5 and ligand genes in 113 available parental tumours was also assessed. Tumour-infiltrating lymphocyte data were validated by flow cytometry (N=50). Results: The full gene expression/polymorphism model, which includes CXCR3 and CCR5 expression data, CCR5-Δ32 polymorphism data and their interaction, was significantly associated with both CR and overall response (OR; P=0.0009, and P=0.007, respectively). More in detail, the predicted underexpression of both CXCR3 and CCR5 according to gene expression and polymorphism data (protein prediction model, PPM) was associated with response to therapy (odds ratio=6.16 and 2.32, for CR and OR, respectively). Flow cytometric analysis confirmed the PPM. Coordinate upregulation of CXCL9, CXCL10, CXCL11, and CCL5 in pretreatment tumour biopsies was associated with OR. Conclusion: Coordinate overexpression of CXCL9, CXCL10, CXCL11, and CCL5 in pretreatment tumours was associated with responsiveness to treatment. Conversely, CCR5-Δ32 polymorphism and CXCR3/CCR5 underexpression influence downregulation of the corresponding receptors in TILs and were associated with likelihood and degree of response.
Collapse
|
24
|
The Continuum of Cancer Immunosurveillance: Prognostic, Predictive, and Mechanistic Signatures. Immunity 2013; 39:11-26. [DOI: 10.1016/j.immuni.2013.07.008] [Citation(s) in RCA: 600] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 07/09/2013] [Indexed: 11/21/2022]
|
25
|
Murtas D, Maric D, De Giorgi V, Reinboth J, Worschech A, Fetsch P, Filie A, Ascierto ML, Bedognetti D, Liu Q, Uccellini L, Chouchane L, Wang E, Marincola FM, Tomei S. IRF-1 responsiveness to IFN-γ predicts different cancer immune phenotypes. Br J Cancer 2013; 109:76-82. [PMID: 23807161 PMCID: PMC3708578 DOI: 10.1038/bjc.2013.335] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 05/12/2013] [Accepted: 05/23/2013] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Several lines of evidence suggest a dichotomy between immune active and quiescent cancers, with the former associated with a good prognostic phenotype and better responsiveness to immunotherapy. Central to such dichotomy is the master regulator of the acute inflammatory process interferon regulatory factor (IRF)-1. However, it remains unknown whether the responsiveness of IRF-1 to cytokines is able to differentiate cancer immune phenotypes. METHODS IRF-1 activation was measured in 15 melanoma cell lines at basal level and after treatment with IFN-γ, TNF-α and a combination of both. Microarray analysis was used to compare transcriptional patterns between cell lines characterised by high or low IRF-1 activation. RESULTS We observed a strong positive correlation between IRF-1 activation at basal level and after IFN-γ and TNF-α treatment. Microarray demonstrated that three cell lines with low and three with high IRF-1 inducible translocation scores differed in the expression of 597 transcripts. Functional interpretation analysis showed mTOR and Wnt/β-cathenin as the top downregulated pathways in the cell lines with low inducible IRF-1 activation, suggesting that a low IRF-1 inducibility recapitulates a cancer phenotype already described in literature characterised by poor prognosis. CONCLUSION Our findings support the central role of IRF-1 in influencing different tumour phenotypes.
Collapse
Affiliation(s)
- D Murtas
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Tomei S, Adams S, Uccellini L, Bedognetti D, De Giorgi V, Erdenebileg N, Ascierto ML, Reinboth J, Liu Q, Bevilacqua G, Wang E, Mazzanti C, Marincola FM. Association between HRAS rs12628 and rs112587690 polymorphisms with the risk of melanoma in the North American population. Med Oncol 2012; 29:3456-61. [PMID: 22618666 PMCID: PMC3505523 DOI: 10.1007/s12032-012-0255-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 05/05/2012] [Indexed: 01/19/2023]
Abstract
HRAS belongs to the RAS genes superfamily. RAS genes are important players in several human tumors and the single-nucleotide polymorphism rs12628 has been shown to contribute to the risk of bladder, colon, gastrointestinal, oral, and thyroid carcinoma. We hypothesized that this SNP may affect the risk of cutaneous melanoma as well. HRAS gene contains a polymorphic region (rs112587690), a repeated hexanucleotide -GGGCCT- located in intron 1. Three alleles of this region, P1, P2, and P3, have been identified that contain two, three, and four repeats of the hexanucleotide, respectively. We investigated the clinical impact of these polymorphisms in a case-control study. A total of 141 melanoma patients and 118 healthy donors from the North America Caucasian population were screened for rs12628 and rs112587690 polymorphisms. Genotypes were assessed by capillary sequencing or fragment analysis, respectively, and rs12628 CC and rs112587690 P1P1 genotypes significantly associated with increased melanoma risk (OR = 3.83, p = 0.003; OR = 11.3, p = 0.033, respectively), while rs112587690 P1P3 frequency resulted significantly higher in the control group (OR = 0.5, p = 0.017). These results suggest that rs12628 C homozygosis may be considered a potential risk factor for melanoma development in the North American population possibly through the linkage to rs112587690.
Collapse
Affiliation(s)
- Sara Tomei
- Division of Surgical, Molecular, and Ultrastructural Pathology, Section of Molecular Pathology, University of Pisa and Pisa University Hospital, 56100, Pisa, Italy.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Uccellini L, De Giorgi V, Zhao Y, Tumaini B, Erdenebileg N, Dudley ME, Tomei S, Bedognetti D, Ascierto ML, Liu Q, Simon R, Kottyan L, Kaufman KM, Harley JB, Wang E, Rosenberg SA, Marincola FM. IRF5 gene polymorphisms in melanoma. J Transl Med 2012; 10:170. [PMID: 22909381 PMCID: PMC3492128 DOI: 10.1186/1479-5876-10-170] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 08/01/2012] [Indexed: 02/08/2023] Open
Abstract
Background Interferon regulatory factor (IRF)-5 is a transcription factor involved in type I interferon signaling whose germ line variants have been associated with autoimmune pathogenesis. Since relationships have been observed between development of autoimmunity and responsiveness of melanoma to several types of immunotherapy, we tested whether polymorphisms of IRF5 are associated with responsiveness of melanoma to adoptive therapy with tumor infiltrating lymphocytes (TILs). Methods 140 TILs were genotyped for four single nucleotide polymorphisms (rs10954213, rs11770589, rs6953165, rs2004640) and one insertion-deletion in the IRF5 gene by sequencing. Gene-expression profile of the TILs, 112 parental melanoma metastases (MM) and 9 cell lines derived from some metastases were assessed by Affymetrix Human Gene ST 1.0 array. Results Lack of A allele in rs10954213 (G > A) was associated with non-response (p < 0.005). Other polymorphisms in strong linkage disequilibrium with rs10954213 demonstrated similar trends. Genes differentially expressed in vitro between cell lines carrying or not the A allele could be applied to the transcriptional profile of 112 melanoma metastases to predict their responsiveness to therapy, suggesting that IRF5 genotype may influence immune responsiveness by affecting the intrinsic biology of melanoma. Conclusions This study is the first to analyze associations between melanoma immune responsiveness and IRF5 polymorphism. The results support a common genetic basis which may underline the development of autoimmunity and melanoma immune responsiveness.
Collapse
Affiliation(s)
- Lorenzo Uccellini
- Infectious Disease and Immunogenetics Section, Department of Transfusion Medicine, Clinical Center and trans-NIH Center for Human Immunology, National Institutes of Health, Bethesda, MD 20892, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|