Hepatocellular carcinomas (HCCs) are a heterogeneous group of tumors that differ in risk factors and genetic alterations. In Italy, particularly Southern Italy, chronic hepatitis C virus (HCV) infection represents the main cause of HCC. Using high-density oligoarrays, we identified consistent differences in gene-expression between HCC and normal liver tissue. Expression patterns in HCC were also readily distinguishable from those associated with liver metastases. To characterize molecular events relevant to hepatocarcinogenesis and identify biomarkers for early HCC detection, gene expression profiling of 71 liver biopsies from HCV-related primary HCC and corresponding HCV-positive non-HCC hepatic tissue, as well as gastrointestinal liver metastases paired with the apparently normal peri-tumoral liver tissue, were compared to 6 liver biopsies from healthy individuals. Characteristic gene signatures were identified when normal tissue was compared with HCV-related primary HCC, corresponding HCV-positive non-HCC as well as gastrointestinal liver metastases. Pathway analysis classified the cellular and biological functions of the genes differentially expressed as related to regulation of gene expression and post-translational modification in HCV-related primary HCC; cellular Growth and Proliferation, and Cell-To-Cell Signaling and Interaction in HCV-related non HCC samples; Cellular Growth and Proliferation and Cell Cycle in metastasis. Also characteristic gene signatures were identified of HCV-HCC progression for early HCC diagnosis.
Conclusions
A diagnostic molecular signature complementing conventional pathologic assessment was identified.
doi:10.1371/journal.pone.0056153
PMCID: PMC3575468
PMID: 23441164
Ascierto, Maria Libera | Kmieciak, Maciej | Idowu, Michael O. | Manjili, Rose | Zhao, Yingdong | Grimes, Margaret | Dumur, Catherine | Wang, Ena | Ramakrishnan, Viswanathan | Wang, Xiang-Yang | Bear, Harry D. | Marincola, Francesco M. | Manjili, Masoud H.
The clinical significance of tumor-infiltrating immune cells has been reported in a variety of human carcinomas including breast cancer. However, molecular signature of tumor-infiltrating immune cells and their prognostic value in breast cancer patients remain elusive. We hypothesized that a distinct network of immune function genes at the tumor site can predict a low risk versus high risk of distant relapse in breast cancer patients regardless of the status of ER, PR, or HER-2/neu in their tumors. We conducted retrospective studies in a diverse cohort of breast cancer patients with a 1–5 year tumor relapse versus those with up to 7 years relapse-free survival. The RNAs were extracted from the frozen tumor specimens at the time of diagnosis and subjected to microarray analysis and real-time RT-PCR. Paraffin-embedded tissues were also subjected to immunohistochemistry staining. We determined that a network of immune function genes involved in B cell development, interferon signaling associated with allograft rejection and autoimmune reaction, antigen presentation pathway, and cross talk between adaptive and innate immune responses were exclusively upregulated in patients with relapse-free survival. Among the 299 genes, five genes which included B cell response genes were found to predict with >85% accuracy relapse-free survival. Real-time RT-PCR confirmed the 5-gene prognostic signature that was distinct from an FDA-cleared 70-gene signature of MammaPrint panel and from the Oncotype DX recurrence score assay panel. These data suggest that neoadjuvant immunotherapy in patients with high risk of relapse may reduce tumor recurrence by inducing the immune function genes.
doi:10.1007/s10549-011-1470-x
PMCID: PMC3431022
PMID: 21479927
Breast cancer prognosis; Tumor relapse; Tumor microenvironment; Immune response; Neoadjuvant immunotherapy
Seliger, Barbara | Dressler, Sven P. | Massa, Chiara | Recktenwald, Christian V. | Altenberend, Florian | Bukur, Juergen | Marincola, Francesco M. | Wang, Ena | Stevanovic, Stefan | Lichtenfels, Rudolf
The presentation of tumor antigen-derived peptides by human leukocyte antigen (HLA) class I surface antigens on tumor cells is a key prerequisite to trigger effective T-cell responses in cancer patients. Multiple complementary strategies like cDNA and serological expression cloning, reverse immunology and different ‘ome’-based methods have been employed to identify potential T-cell targets. This report focuses on a ligandomic profiling approach leading to the identification of 49 naturally processed HLA class I peptide ligands presented on the cell surface of renal cell carcinoma (RCC) cells. The source proteins of the defined HLA ligands are classified according to their biological function and subcellular localization. Previously established cDNA microarray data of paired tissue specimen of RCC and renal epithelium assessed the transcriptional regulation for 28 source proteins. In addition, HLA-A2-restricted, peptide-specific T cells directed against a HLA ligand derived from sulfiredoxin-1 (SRXN1) were generated, which were able to recognize and lyse ligand-presenting target cells in a HLA class I-restricted manner. Furthermore, tumor-infiltrating T cells isolated from a RCC patient were also able to kill SRXN1 expressing tumor cells. Thus, this experimental strategy might be suited to define potential candidate biomarkers and novel targets for T-cell-based immunotherapies of this disease.
doi:10.1002/pmic.201000486
PMCID: PMC3517181
PMID: 21595034
Biomarkers; Cell biology; HLA antigens; Peptide ligands; Renal cell carcinoma; T-cell response
Longo, Diane M. | Louie, Brent | Putta, Santosh | Evensen, Erik | Ptacek, Jason | Cordeiro, James | Wang, Ena | Pos, Zoltan | Hawtin, Rachael E. | Marincola, Francesco M. | Cesano, Alessandra
A greater understanding of the function of the human immune system at the single-cell level in healthy individuals is critical for discerning aberrant cellular behavior that occurs in settings such as autoimmunity, immunosenescence, and cancer. To achieve this goal, a systems-level approach capable of capturing the response of the interdependent immune cell types to external stimuli is required. In this study, an extensive characterization of signaling responses in multiple immune cell subpopulations within PBMCs from a cohort of 60 healthy donors was performed using single-cell network profiling (SCNP). SCNP is a multiparametric flow cytometry-based approach that enables the simultaneous measurement of basal and evoked signaling in multiple cell subsets within heterogeneous populations. In addition to establishing the interindividual degree of variation within a broad panel of immune signaling responses, the possible association of any observed variation with demographic variables including age and race was investigated. Using half of the donors as a training set, multiple age- and race-associated variations in signaling responses in discrete cell subsets were identified, and several were subsequently confirmed in the remaining samples (test set). Such associations may provide insight into age-related immune alterations associated with high infection rates and diminished protection following vaccination and into the basis for ethnic differences in autoimmune disease incidence and treatment response. SCNP allowed for the generation of a functional map of healthy immune cell signaling responses that can provide clinically relevant information regarding both the mechanisms underlying immune pathological conditions and the selection and effect of therapeutics.
doi:10.4049/jimmunol.1102514
PMCID: PMC3517183
PMID: 22246624
doi:10.2217/imt.11.125
PMCID: PMC3517186
PMID: 21995565
Purpose
We have previously shown that within tumors, recombinant interleukin-2 (rIL-2, Aldesleukin) consistently activates tumor-associated macrophages and up-regulates interferon stimulated genes (ISGs) while inducing minimal migration, activation or proliferation of T-cells. These effects are independent of tumor response to treatment. Here, we prospectively evaluated transcriptional alterations induced by rIL-2 in peripheral blood mononuclear cells (PBMCs) and within melanoma metastases.
Experimental Design
We evaluated gene expression changes by serially comparing pre- to post-treatment samples in 14 patients and also compared transcriptional differences among lesions displaying different responsiveness to therapy, focusing on 2 lesions decreasing in size and 2 remaining stable (responding lesions) compared to non-responding ones.
Results
As previously described, the effects of rIL-2 were dramatic within PBMC, while effects within the tumor microenvironment were lesion-specific and limited. However, distinct signatures specific to response could be observed in responding lesions pre-treatment that were amplified following rIL-2 administration. These signatures match the functional profile observed in other human or experimental models in which immune-mediated tissue-specific destruction (TSD) occurs underlying a common pathways leading to rejection. Moreover, the signatures observed in pre-treatment lesions were qualitatively similar to those associated with TSD underlining a determinism to immune responsiveness that depends upon the genetic background of the host or the intrinsic genetic makeup of individual tumors.
Conclusions
This is the first prospectively collected insight on global transcriptional events occurring during high-dose rIL-2 therapy in melanoma metastases responding to treatment.
doi:10.1158/1078-0432.CCR-11-1650
PMCID: PMC3229653
PMID: 21976537
Tomei, Sara | Adams, Sharon | Uccellini, Lorenzo | Bedognetti, Davide | De Giorgi, Valeria | Erdenebileg, Narnygerel | Ascierto, Maria Libera | Reinboth, Jennifer | Liu, Qiuzhen | Bevilacqua, Generoso | Wang, Ena | Mazzanti, Chiara | Marincola, Francesco M.
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.
doi:10.1007/s12032-012-0255-3
PMCID: PMC3505523
PMID: 22618666
HRAS; Polymorphism; Melanoma; rs12628; rs112587690
Despite recent advances in the understanding of the biology of renal cell carcinoma (RCC) and the implementation of novel targeted therapies, the overall 5 years’ survival rate for RCC patients remains disappointing. Late presentation, tumor heterogeneity and in particular the lack of molecular biomarkers for early detection and classification represent major obstacles. Global, untargeted comparative analysis of RCC vs tumor adjacent renal epithelium (NN) samples by high throughput analyses both at the transcriptome and proteome level have identified signatures, which might further clarify the molecular differences of RCC subtypes and might allow the identification of suitable therapeutic targets and diagnostic/prognostic biomarkers, but none thereof has yet been implemented in routine clinical use. The increasing knowledge regarding the functional role of noncoding microRNA (miR) in physiological, developmental, and pathophysiological processes by shaping the protein expression profile might provide an important link to improve the definition of disease-relevant regulatory networks. Taking into account that miR profiling of RCC and NN provides robust signatures discriminating between malignant and normal tissues, the concept of evaluating and scoring miR/protein pairs might represent a strategy for the selection and prioritization of potential biomarkers and their translation into practical use.
doi:10.1021/pr1011137
PMCID: PMC3506708
PMID: 21142213
RCC; miR; proteomics; biomarker
Carretero, Rafael | Wang, Ena | Rodriguez, Ana I. | Reinboth, Jennifer | Ascierto, Maria L. | Engle, Alyson M. | Liu, Hui | Camacho, Francisco M. | Marincola, Francesco M. | Garrido, Federico | Cabrera, Teresa
We present the results of a comparative gene expression analysis of 15 metastases (10 regressing and 5 progressing) obtained from 2 melanoma patients with mixed response following different forms of immunotherapy. Whole genome transcriptional analysis clearly indicate that regression of melanoma metastases is due to an acute immune rejection mediated by the upregulation of genes involved in antigen presentation and interferon mediated response (STAT-1/IRF-1) in all the regressing metastases from both patients. In contrast, progressing metastases showed low transcription levels of genes involved in these pathways. Histological analysis showed T cells and HLA-DR positive infiltrating cells in the regressing but not in the progressing metastases. Quantitative expression analysis of HLA-A, B and C genes on microdisected tumoral regions indicate higher HLA expression in regressing than in progressing metastases. The molecular signature obtained in melanoma rejection appeared to be similar to that observed in other forms of immune-mediated tissue-specific rejection such as allograft, pathogen clearance, graft versus host or autoimmune disease, supporting the immunological constant of rejection. We favor the idea that the major factor determining the success or failure of immunotherapy is the nature of HLA Class I alterations in tumor cells and not the type of immunotherapy used. If the molecular alteration is reversible by the immunotherapy, the HLA expression will be upregulated and the lesion will be recognized and rejected. In contrast, if the defect is structural the MHC Class I expression will remain unchanged and the lesion will progress.
doi:10.1002/ijc.26471
PMCID: PMC3504975
PMID: 21964766
melanoma; metastasis; immunotherapy; rejection; HLA; IRF-1
Bot, Adrian | Ahn, Mark | Bosch, Marnix | Brockstedt, Dirk | Butterfield, Lisa H | Cornforth, Andrew | Harrop, Richard | Kast, W Martin | Koya, Richard | Marincola, Francesco | Margolin, Kim | McCoy, Candice | Pawelec, Graham | Rothman, John | Ramirez-Montagut, Teresa | Schlom, Jeffrey | Srivastava, Pramod | Wallis, Sarah | Walter, Steffen | Wang, Ena | Waslif, John
While there has been significant progress in advancing novel immune therapies to the bedside, much more needs to be done to fully tap into the potential of the immune system. It has become increasingly clear that besides practical and operational challenges, the heterogeneity of cancer and the limited efficacy profile of current immunotherapy platforms are the two main hurdles. Nevertheless, the promising clinical data of several approaches point to a roadmap that carries the promise to significantly advance cancer immunotherapy. A new annual series sponsored by Arrowhead Publishers and Conferences aims at bringing together scientific and business leadership from academia and industry, to identify, share and discuss most current priorities in research and translation of novel immune interventions. This Editorial provides highlights of the first event held earlier this year and outlines the focus of the second meeting to be held in 2013 that will be dedicated to stem cells and immunotherapy.
doi:10.1186/1479-5876-10-218
PMCID: PMC3551774
PMID: 23127127
Qian, Mengjia | Wu, Duojiao | Wang, Ena | Marincola, Francesco M | Wang, Wei | Rhodes, William | Liebman, Michael | Bai, Chunxue | Lam, Ching-Wan | Marko-Varga, Gyorgy | Fehniger, Thomas E | Andersson, Roland | Wang, Xiangdong
Background
Clinical translational medicine (CTM) is an emerging area comprising multidisciplinary research from basic science to medical applications and entails a close collaboration among hospital, academia and industry.
Findings
This Session focused discussing on new models for project development and promotion in translational medicine. The conference stimulated the scientific and commercial communication of project development between academies and companies, shared the advanced knowledge and expertise of clinical applications, and created the environment for collaborations.
Conclusions
Although strategic collaborations between corporate and academic institutions have resulted in a state of resurgence in the market, new cooperation models still need time to tell whether they will improve the translational medicine process.
doi:10.1186/2001-1326-1-25
PMCID: PMC3561049
PMID: 23369198
Bedognetti, Davide | Sertoli, Mario Roberto | Pronzato, Paolo | Del Mastro, Lucia | Venturini, Marco | Taveggia, Paola | Zanardi, Elisa | Siffredi, Guido | Pastorino, Simona | Queirolo, Paola | Gardin, Giovanni | Wang, Ena | Monzeglio, Clara | Boccardo, Francesco | Bruzzi, Paolo
Background
The most appropriate timing of chemotherapy and hormone therapy administration is a critical issue in early breast cancer patients. The purpose of our study was to compare the efficacy of concurrent vs sequential administration of adjuvant chemotherapy and tamoxifen.
Methods
Women with node-positive primary breast cancer were randomly assigned to receive tamoxifen (20 mg/d for 5 years) during (concurrent arm) or after (sequential arm) adjuvant chemotherapy. Chemotherapy consisted of alternating regimens of cyclophosphamide, epidoxorubicin, and 5-fluorouracil and cyclophosphamide, methotrexate, and 5-fluorouracil every 21 days for a total of 12 cycles. The primary endpoint was overall survival (OS), and secondary endpoints were toxic effects and disease-free survival (DFS). No provision for interim analyses was made in the original study protocol. Survival curves were estimated by the Kaplan–Meier method. Multivariable Cox regression models, adjusted for age, menopausal status, tumor stage, and lymph node and hormone receptor status, were used to estimate hazard ratios (HRs) and 95% confidence intervals (CIs). All statistical tests were two-sided.
Results
From 1985 to 1992, 431 patients were randomly assigned and studied according to the intention-to-treat principle. After a maximum of 15.4 years of follow-up (median 12.3 years), the estimated actuarial 10-year OS was equivalent for the two study arms (concurrent arm: 111 patients, 66%, 95% CI = 59% to 72%; sequential arm: 114 patients, 65%, 95% CI = 59% to 72%, P = .86). No differences in DFS and toxic effects were evident. Four interim analyses were performed, but no alpha error adjustment was necessary because of the largely negative results of this final analysis (sequential vs concurrent arm: HR of death = 1.06, 95% CI = 0.78 to 1.44, P = .76; HR of relapse = 1.16, 95% CI = 0.88 to 1.52, P = .36).
Conclusions
No statistically significant differences in OS, DFS, and toxic effects between concurrent and sequential adjuvant chemo- and hormone therapies were observed. Our study does not support the superiority of one schedule of chemo- and hormone-therapy administration over the other. However, because of the limited statistical power of the study, these results must be considered with caution.
doi:10.1093/jnci/djr351
PMCID: PMC3202939
PMID: 21921285
doi:10.1186/1479-5876-10-S2-A44
PMCID: PMC3479845
doi:10.1186/1479-5876-10-S2-A46
PMCID: PMC3480007
Galon, Jérôme | Pagès, Franck | Marincola, Francesco M | Angell, Helen K | Thurin, Magdalena | Lugli, Alessandro | Zlobec, Inti | Berger, Anne | Bifulco, Carlo | Botti, Gerardo | Tatangelo, Fabiana | Britten, Cedrik M | Kreiter, Sebastian | Chouchane, Lotfi | Delrio, Paolo | Arndt, Hartmann | Asslaber, Martin | Maio, Michele | Masucci, Giuseppe V | Mihm, Martin | Vidal-Vanaclocha, Fernando | Allison, James P | Gnjatic, Sacha | Hakansson, Leif | Huber, Christoph | Singh-Jasuja, Harpreet | Ottensmeier, Christian | Zwierzina, Heinz | Laghi, Luigi | Grizzi, Fabio | Ohashi, Pamela S | Shaw, Patricia A | Clarke, Blaise A | Wouters, Bradly G | Kawakami, Yutaka | Hazama, Shoichi | Okuno, Kiyotaka | Wang, Ena | O'Donnell-Tormey, Jill | Lagorce, Christine | Pawelec, Graham | Nishimura, Michael I | Hawkins, Robert | Lapointe, Réjean | Lundqvist, Andreas | Khleif, Samir N | Ogino, Shuji | Gibbs, Peter | Waring, Paul | Sato, Noriyuki | Torigoe, Toshihiko | Itoh, Kyogo | Patel, Prabhu S | Shukla, Shilin N | Palmqvist, Richard | Nagtegaal, Iris D | Wang, Yili | D'Arrigo, Corrado | Kopetz, Scott | Sinicrope, Frank A | Trinchieri, Giorgio | Gajewski, Thomas F | Ascierto, Paolo A | Fox, Bernard A
Prediction of clinical outcome in cancer is usually achieved by histopathological evaluation of tissue samples obtained during surgical resection of the primary tumor. Traditional tumor staging (AJCC/UICC-TNM classification) summarizes data on tumor burden (T), presence of cancer cells in draining and regional lymph nodes (N) and evidence for metastases (M). However, it is now recognized that clinical outcome can significantly vary among patients within the same stage. The current classification provides limited prognostic information, and does not predict response to therapy. Recent literature has alluded to the importance of the host immune system in controlling tumor progression. Thus, evidence supports the notion to include immunological biomarkers, implemented as a tool for the prediction of prognosis and response to therapy. Accumulating data, collected from large cohorts of human cancers, has demonstrated the impact of immune-classification, which has a prognostic value that may add to the significance of the AJCC/UICC TNM-classification. It is therefore imperative to begin to incorporate the ‘Immunoscore’ into traditional classification, thus providing an essential prognostic and potentially predictive tool. Introduction of this parameter as a biomarker to classify cancers, as part of routine diagnostic and prognostic assessment of tumors, will facilitate clinical decision-making including rational stratification of patient treatment. Equally, the inherent complexity of quantitative immunohistochemistry, in conjunction with protocol variation across laboratories, analysis of different immune cell types, inconsistent region selection criteria, and variable ways to quantify immune infiltration, all underline the urgent requirement to reach assay harmonization. In an effort to promote the Immunoscore in routine clinical settings, an international task force was initiated. This review represents a follow-up of the announcement of this initiative, and of the J Transl Med. editorial from January 2012. Immunophenotyping of tumors may provide crucial novel prognostic information. The results of this international validation may result in the implementation of the Immunoscore as a new component for the classification of cancer, designated TNM-I (TNM-Immune).
doi:10.1186/1479-5876-10-205
PMCID: PMC3554496
PMID: 23034130
Petrizzo, Annacarmen | Tornesello, Maria Lina | Napolitano, Maria | D'Alessio, Giovanna | Salomone Megna, Angelo | Dolcetti, Riccardo | De Re, Valli | Wang, Ena | Marincola, Franco M. | Buonaguro, Franco M. | Buonaguro, Luigi | Ray, Ranjit
Hepatitis C virus (HCV) has been identified as one of the major risk factors for type II mixed cryoglobulinemia (MC), during the clinical evolution of chronic hepatitis, which may lead to development of B cell non-Hodgkin's lymphoma (NHL). We have previously shown that the candidate idiotype vaccine, based on the IGKV3-20 light chain protein, is able to induce activation and maturation of circulating antigen presenting cells (APCs) in both HCV-positive and HCV-negative healthy control subjects, with production of Th2-type cytokines. Here, the effect of the recombinant IGKV3-20 protein on human peripheral blood mononuclear cells (PBMCs) from HCV-positive subjects, with known blood levels of cryoglobulins, is shown via gene expression profiling analysis combined to multiparameter flow cytometry and multiplex analyses of cytokines.
doi:10.1371/journal.pone.0044870
PMCID: PMC3445594
PMID: 23028651
Purpose
Abnormalities in the constitutive and IFN-γ–inducible HLA class I surface antigen expression of tumor cells is often associated with an impaired expression of components of the antigen processing machinery (APM). Hence, we analyzed whether there exists a link between the IFN-γ signaling pathway, constitutive HLA class I APM component expression, and IFN-γ resistance.
Experimental Design
The basal and IFN-γ–inducible expression profiles of HLA class I APM and IFN-γ signal transduction cascade components were assessed in melanoma cells by real-time PCR (RT-PCR), Western blot analysis and/or flow cytometry, the integrity of the Janus activated kinase (JAK) 2 locus by comparative genomic hybridization. JAK2 was transiently overexpressed in JAK2− cells. The effect of IFN-γ on the cell growth was assessed by XTT [2,3-bis(2-methoxy-4-nitro-S-sulfophenynl)-H-tetrazolium-5-carboxanilide inner salt] assay.
Results
The analysis of 8 melanoma cell lines linked the IFN-γ unresponsiveness of Colo 857 cells determined by lack of inducibility of HLA class I surface expression on IFN-γ treatment to a deletion of JAK2 on chromosome 9, whereas other IFN-γ signaling pathway components were not affected. In addition, the constitutive HLA class I APM component expression levels were significantly reduced in JAK2− cells. Furthermore, JAK2-deficient cells were also resistant to the antiproliferative effect of IFN-γ. Transfection of wild-type JAK2 into JAK2− Colo 857 not only increased the basal APM expression but also restored their IFN-γ sensitivity.
Conclusions
Impaired JAK2 expression in melanoma cells leads to reduced basal expression of MHC class I APM components and impairs their IFN-γ inducibility, suggesting that malfunctional IFN-γ signaling might cause HLA class I abnormalities.
doi:10.1158/1078-0432.CCR-10-2114
PMCID: PMC3426200
PMID: 21248298
Uccellini, Lorenzo | De Giorgi, Valeria | Zhao, Yingdong | Tumaini, Barbara | Erdenebileg, Narnygerel | Dudley, Mark E | Tomei, Sara | Bedognetti, Davide | Ascierto, Maria Libera | Liu, Qiuzhen | Simon, Richard | Kottyan, Leah | Kaufman, Kenneth M | Harley, John B | Wang, Ena | Rosenberg, Steven A | Marincola, Francesco M
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.
doi:10.1186/1479-5876-10-170
PMCID: PMC3492128
PMID: 22909381
Monacoa, Alessandro | Marincola, Francesco M. | Sabatino, Marianna | Pos, Zoltan | Tornesello, Maria Lina | Stroncek, David F. | Wang, Ena | Lewis, George K. | Buonaguro, Franco M. | Buonaguroc, Luigi
The global transcriptional profile of peripheral blood mononuclear cells (PBMCs) stimulated with HIV candidate vaccine (virus-like particles, VLPs) has been evaluated in HIV-infected patients with low/high viral load compared to healthy volunteers. Baseline activation of chemokine production was observed in PBMC from HIV-infected patients and innate immune stimulation with HIV-VLPs was not blunted. The immune profile among HIV-infected patients was found to be qualitatively similar but quantitatively extremely variable. This diversity was independent of viral load and it might be dependent on individual immunogenetic traits or concurrent immunological status.
This ex vivo screening strategy represents an efficient tool for guiding modifications/optimizations of vaccination strategies and understanding failures in individuals enrolled in clinical trials.
doi:10.1016/j.febslet.2009.07.060
PMCID: PMC3418664
PMID: 19665024
Immunogenomics; Vaccine; HIV-1; Peripheral blood mononuclear cell
Chen, Xiaoming | Andersson, Roland | Cho, William CS | Christiani, David | Coico, Richard | Drazen, Jeffery | Ege, Markus | Fehniger, Thomas | Gao, Hongwei | Jin, Kunlin | Liebman, Michael N | Lopez, Elena | Marraro, Giuseppe | Marko-Varga, Gyorgy | Marincola, Francesco M | Popescu, Laurentiu M | Spada, Claudio | Shahzad, Aamir | Wang, Ena | Wang, Wei | Wang, Xiangdong | Wang, Yong-Xiao | Xia, Jinglin | Qu, Jia
Background
Supported by the International Society for Translational Medicine (ISTM), Wenzhou Medical College and the First Affiliated Hospital of Wenzhou Medical College, the International Conference on Translational Medicine (ICTM) was held on October 22–23, 2011 in Wenzhou, China. Nearly 800 registrants attended the meeting, primarily representing institutes and hospitals in Europe, The United States of America, And Asia, and China. The meeting was chaired and organized by Dr. Xiangdong Wang, Xiaoming Chen, Richard Coico, Jeffrey M. Drazen, Richard Horton, Francesco M. Marincola, Laurentiu M. Popescu, Jia Qu and Aamir Shahzad.
Findings
The meeting focused on the communication of the need to foster translational medicine (TM) by building and broadening bridges between basic research and clinical studies at the international level. The meeting included distinguished TM experts from academia, the pharmaceutical and diagnostics industries, government agencies, regulators, and clinicians and provided the opportunity to identify shared interests and efforts for collaborative approaches utilizing cutting edge technologies, innovative approaches and novel therapeutic interventions. The meeting defined the concept of TM in its two-way operational scheme and emphasized the need for bed to bench efforts based directly on clinical observation.
Conclusions
It was the meeting participants’ realization that the shared main goals of TM include breaking the separation between clinic practice and basic research, establishing positive feedback by understanding the basis of expected and unexpected clinical outcomes and accelerating basic research relevant to human suffering. The primary objectives of the meeting were two-fold: to accelerate the two-way translation by informing the participants representing the different disciplines about the state of art activities around TM approaches; and to identify areas that need to be supported by redirecting limited resources as well as identifying new sources of funding. This report summarizes key concepts presented during the meeting representing the state-of-art translational research and salient aspects of the ensuing discussions.
doi:10.1186/2001-1326-1-15
PMCID: PMC3561055
PMID: 23369397
Translational Medicine (TM); International Society for Translational Medicine (ISTM); the International Conference on Translational Medicine (ICTM); Biomarkers; Biobank globalization and networking
In this issue of Immunity, Chaussabel et al. (2008) apply an inductive approach to pathway discovery identifying modular units that govern human immune biology.
doi:10.1016/j.immuni.2008.07.002
PMCID: PMC3417224
PMID: 18631452
The identification of tumor antigens (TA) recognized by T cells led to the design of therapeutic strategies aimed at eliciting adaptive-immune responses. The last decade experience has shown that, although active immunization can induce enhancement of anti-cancer T cell precursors (easily detectable in standard assays), most often they are unable to induce tumor regression and, consequently, have scarce impact on overall survival. Moreover, in the few occasions when tumor rejection occurs, the mechanisms determining this phenomenon remain poorly understood, and data derived from in vivo human observations are rare. The advent of high-throughput gene expression analysis (microarrays) has cast new lights on unrecognized mechanisms that are now deemed as central for the development of an efficient immune-mediated tumor rejection. The aim of this article is to review the data about the molecular signature associated with this process. We believe that the description of how the mechanism of immune-mediated tissue destruction occurs would contribute to understand why it happens, thereby allowing to develop more effective immune-therapeutic strategies.
doi:10.1586/erv.10.55
PMCID: PMC3411321
PMID: 20518712
Microarray; microarrays; gene expression; cancer immunotherapy; vaccine therapy; tumor rejection; melanoma; immunologic constant
Seliger, Barbara | Dressler, Sven P. | Wang, Ena | Kellner, Roland | Recktenwald, Christian V. | Lottspeich, Friedrich | Marincola, Francesco M. | Baumgärtner, Maja | Atkins, Derek | Lichtenfels, Rudolf
Results obtained from expression profilings of renal cell carcinoma using different “ome”-based approaches and comprehensive data analysis demonstrated that proteome-based technologies and cDNA microarray analyses complement each other during the discovery phase for disease-related candidate biomarkers. The integration of the respective data revealed the uniqueness and complementarities of the different technologies. While comparative cDNA microarray analyses though restricted to upregulated targets largely revealed genes involved in controlling gene/protein expression (19%) and signal transduction processes (13%), proteomics/PROTEOMEX-defined candidate biomarkers include enzymes of the cellular metabolism (36%), transport proteins (12%) and cell motility/structural molecules (10%). Candidate biomarkers defined by proteomics and PROTEOMEX are frequently shared, whereas the sharing rate between cDNA microarray and proteome-based profilings is limited. Putative candidate biomarkers provide insights into their cellular (dys)function and their diagnostic/prognostic value but still warrant further validation in larger patient numbers. Based on the fact that merely 3 candidate biomarkers were shared by all applied technologies, namely annexin A4, tubulin alpha-1A chain and ubiquitin carboxyl-terminal hydrolase L1 the analysis at a single hierarchical level of biological regulation seems to provide only limited results thus emphasizing the importance and benefit of performing rather combinatorial screenings which can complement the standard clinical predictors.
doi:10.1002/pmic.200700288
PMCID: PMC3410642
PMID: 19235166
RCC; transcriptomics; proteome-based technologies; biomarkers
Wang, Ena | Monaco, Alessandro | Monsurró, Vladia | Sabatino, Marianna | Pos, Zoltan | Uccellini, Lorenzo | Wang, Jeanne | Worschech, Andrea | Stroncek, David F | Marincola, Francesco M
Anti-cancer vaccines have not matched the clinical expectations projected from their ability to induce consistently systemic anti-cancer T-cell responses. Thus, a dichotomy is observed between the immunological and clinical endpoints of anti-cancer immunization. Anti-cancer vaccines have clearly demonstrated that highly specific T-cell responses can be induced that can recognize autologous cancer antigens in patients with cancer. This ability is an outstanding achievement of modern biotechnology, yielding one of the most specific types of potential anti-cancer reagents. However, systemic, vaccine-induced anti-cancer responses exemplify a broader immunological paradox: cytotoxic T-cells can coexist within the same organism with their target cells not only in the context of cancer, but also in the context of chronic infections, well-controlled allo-transplant reactions and autoimmunity. According to this view, anti-cancer immune responses are a facet of a tissue-specific autoimmune phenomenon specific for cancer tissue that may or may not result in the successful immune-destruction of target cells, depending on an assortment of genetic factors related to the background of the host or evolving phenotypes of a heterogeneous cancer environment. This feature article summarizes the current understanding of the mechanisms leading to tumor rejection in humans as well as in experimental models, in the context of the broader immunological phenomenon leading to tissue-specific destruction. Anti-cancer vaccines that may not induce clinically significant anti-cancer responses independently could function as a unique tool to enhance the specificity of the response of the host against cancer, provided that strategies are implemented to amplify the immune reaction initiated by vaccine-induced antibodies and/or T-cells.
PMCID: PMC3410731
PMID: 19431094
Cancer vaccines; melanoma; rejection; tumor immunology
Summary
It is becoming increasingly recognized that experimental animal models, while useful to address monothematic biological questions, bear unpredictable relevance to human disease. Several reasons have been proposed. However, the uncontrollable nature of human genetics and the heterogeneity of disease that with difficulty can be replicated experimentally play a leading role. Comparative immunology is a term that generally refers to the analysis of shared or diverging facets of immunology among species; these comparisons are carried according to the principle that evolutionarily conserved themes outline biologic functions universally relevant for survival. We propose that a similar strategy could be applied searching for themes shared by distinct immune pathologies within our own species. Identification of common patterns may outline pathways necessary for a particular determinism to occur such as tissue-specific rejection or tolerance. This approach is founded on the unproven but sensible presumption that Nature does not require an infinite plethora of redundant mechanisms to reach its purposes. Thus, immune pathologies must follow, at least in part, common means that determine their onset and maintenance. Commonalities among diseases can, in turn, be segregated from disease-specific patterns uncovering essential mechanisms that may represent universal targets for immunotherapy.
doi:10.2217/imt.09.10
PMCID: PMC3407973
PMID: 20635956
Comparative immunology; tumor immunology: vaccines; chronic infection