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Menéndez V, Solórzano JL, García-Cosío M, Alonso-Alonso R, Rodríguez M, Cereceda L, Fernández S, Díaz E, Montalbán C, Estévez M, Piris MA, García JF. Immune and stromal transcriptional patterns that influence the outcome of classic Hodgkin lymphoma. Sci Rep 2024; 14:710. [PMID: 38184757 PMCID: PMC10771441 DOI: 10.1038/s41598-024-51376-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/04/2024] [Indexed: 01/08/2024] Open
Abstract
Classic Hodgkin lymphoma (cHL) is characterized by a rich immune microenvironment as the main tumor component. It involves a broad range of cell populations, which are largely unexplored, even though they are known to be essential for growth and survival of Hodgkin and Reed-Sternberg cells. We profiled the gene expression of 25 FFPE cHL samples using NanoString technology and resolved their microenvironment compositions using cell-deconvolution tools, thereby generating patient-specific signatures. The results confirm individual immune fingerprints and recognize multiple clusters enriched in refractory patients, highlighting the relevance of: (1) the composition of immune cells and their functional status, including myeloid cell populations (M1-like, M2-like, plasmacytoid dendritic cells, myeloid-derived suppressor cells, etc.), CD4-positive T cells (exhausted, regulatory, Th17, etc.), cytotoxic CD8 T and natural killer cells; (2) the balance between inflammatory signatures (such as IL6, TNF, IFN-γ/TGF-β) and MHC-I/MHC-II molecules; and (3) several cells, pathways and genes related to the stroma and extracellular matrix remodeling. A validation model combining relevant immune and stromal signatures identifies patients with unfavorable outcomes, producing the same results in an independent cHL series. Our results reveal the heterogeneity of immune responses among patients, confirm previous findings, and identify new functional phenotypes of prognostic and predictive utility.
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Affiliation(s)
- Victoria Menéndez
- Translational Research, Fundación MD Anderson International España. Madrid, 28033, Madrid, Spain
| | - José L Solórzano
- Translational Research, Fundación MD Anderson International España. Madrid, 28033, Madrid, Spain
- Pathology Department, MD Anderson Cancer Center Madrid, C/Arturo Soria, 270, 28033, Madrid, Spain
| | - Mónica García-Cosío
- Pathology Department, Hospital Universitario Ramón y Cajal, 28034, Madrid, Spain
| | - Ruth Alonso-Alonso
- Pathology Department, IIS Hospital Universitario Fundación Jiménez Díaz, 28040, Madrid, Spain
- Center for Biomedical Network Research on Cancer (CIBERONC), ISCIII, 28029, Madrid, Spain
| | - Marta Rodríguez
- Pathology Department, IIS Hospital Universitario Fundación Jiménez Díaz, 28040, Madrid, Spain
- Center for Biomedical Network Research on Cancer (CIBERONC), ISCIII, 28029, Madrid, Spain
| | - Laura Cereceda
- Translational Research, Fundación MD Anderson International España. Madrid, 28033, Madrid, Spain
- Pathology Department, MD Anderson Cancer Center Madrid, C/Arturo Soria, 270, 28033, Madrid, Spain
| | - Sara Fernández
- Translational Research, Fundación MD Anderson International España. Madrid, 28033, Madrid, Spain
- Pathology Department, MD Anderson Cancer Center Madrid, C/Arturo Soria, 270, 28033, Madrid, Spain
| | - Eva Díaz
- Translational Research, Fundación MD Anderson International España. Madrid, 28033, Madrid, Spain
| | - Carlos Montalbán
- Hematology Department, MD Anderson Cancer Center Madrid, 28033, Madrid, Spain
| | - Mónica Estévez
- Hematology Department, MD Anderson Cancer Center Madrid, 28033, Madrid, Spain
| | - Miguel A Piris
- Pathology Department, IIS Hospital Universitario Fundación Jiménez Díaz, 28040, Madrid, Spain
- Center for Biomedical Network Research on Cancer (CIBERONC), ISCIII, 28029, Madrid, Spain
| | - Juan F García
- Translational Research, Fundación MD Anderson International España. Madrid, 28033, Madrid, Spain.
- Pathology Department, MD Anderson Cancer Center Madrid, C/Arturo Soria, 270, 28033, Madrid, Spain.
- Center for Biomedical Network Research on Cancer (CIBERONC), ISCIII, 28029, Madrid, Spain.
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2
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Patrício A, Costa RS, Henriques R. On the challenges of predicting treatment response in Hodgkin's Lymphoma using transcriptomic data. BMC Med Genomics 2023; 16:170. [PMID: 37474945 PMCID: PMC10360230 DOI: 10.1186/s12920-023-01508-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 04/03/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUND Despite the advancements in multiagent chemotherapy in the past years, up to 10% of Hodgkin's Lymphoma (HL) cases are refractory to treatment and, after remission, patients experience an elevated risk of death from all causes. These complications are dependent on the treatment and therefore an increase in the prognostic accuracy of HL can help improve these outcomes and control treatment-related toxicity. Due to the low incidence of this cancer, there is a lack of works comprehensively assessing the predictability of treatment response, especially by resorting to machine learning (ML) advances and high-throughput technologies. METHODS We present a methodology for predicting treatment response after two courses of Adriamycin, Bleomycin, Vinblastine and Dacarbazine (ABVD) chemotherapy, through the analysis of gene expression profiles using state-of-the-art ML algorithms. We work with expression levels of tumor samples of Classical Hodgkin's Lymphoma patients, obtained through the NanoString's nCounter platform. The presented approach combines dimensionality reduction procedures and hyperparameter optimization of various elected classifiers to retrieve reference predictability levels of refractory response to ABVD treatment using the regulatory profile of diagnostic tumor samples. In addition, we propose a data transformation procedure to map the original data space into a more discriminative one using biclustering, where features correspond to discriminative putative regulatory modules. RESULTS Through an ensemble of feature selection procedures, we identify a set of 14 genes highly representative of the result of an fuorodeoxyglucose Positron Emission Tomography (FDG-PET) after two courses of ABVD chemotherapy. The proposed methodology further presents an increased performance against reference levels, with the proposed space transformation yielding improvements in the majority of the tested predictive models (e.g. Decision Trees show an improvement of 20pp in both precision and recall). CONCLUSIONS Taken together, the results reveal improvements for predicting treatment response in HL disease by resorting to sophisticated statistical and ML principles. This work further consolidates the current hypothesis on the structural difficulty of this prognostic task, showing that there is still a considerable gap to be bridged for these technologies to reach the necessary maturity for clinical practice.
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Affiliation(s)
- André Patrício
- INESC-ID and Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
- IDMEC, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Rafael S. Costa
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- IDMEC, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Rui Henriques
- INESC-ID and Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
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3
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Torricelli F, Donati B, Reggiani F, Manicardi V, Piana S, Valli R, Lococo F, Ciarrocchi A. Spatially resolved, high-dimensional transcriptomics sorts out the evolution of biphasic malignant pleural mesothelioma: new paradigms for immunotherapy. Mol Cancer 2023; 22:114. [PMID: 37460925 PMCID: PMC10351128 DOI: 10.1186/s12943-023-01816-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/27/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Malignant Pleural Mesothelioma (MPM) is a dreadful disease escaping the classical genetic model of cancer evolution and characterized by wide heterogeneity and transcriptional plasticity. Clinical evolution of MPM is marked by a progressive transdifferentiation that converts well differentiated epithelioid (E) cells into undifferentiated and pleomorphic sarcomatoid (S) phenotypes. Catching the way this transition takes place is necessary to understand how MPM develops and progresses and it is mandatory to improve patients' management and life expectancy. Bulk transcriptomic approaches, while providing a significant overview, failed to resolve the timing of this evolution and to identify the hierarchy of molecular events through which this transition takes place. METHODS We applied a spatially resolved, high-dimensional transcriptomic approach to study MPM morphological evolution. 139 regions across 8 biphasic MPMs (B-MPMs) were profiled using the GeoMx™Digital Spatial Profiler to reconstruct the positional context of transcriptional activities and the spatial topology of MPM cells interactions. Validation was conducted on an independent large cohort of 84 MPMs by targeted digital barcoding analysis. RESULTS Our results demonstrated the existence of a complex circular ecosystem in which, within a strong asbestos-driven inflammatory environment, MPM and immune cells affect each other to support S-transdifferentiation. We also showed that TGFB1 polarized M2-Tumor Associated Macrophages foster immune evasion and that TGFB1 expression correlates with reduced survival probability. CONCLUSIONS Besides providing crucial insights into the multidimensional interactions governing MPM clinical evolution, these results open new perspectives to improve the use of immunotherapy in this disease.
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Affiliation(s)
- F Torricelli
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, 42123, Italy
| | - B Donati
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, 42123, Italy
| | - F Reggiani
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, 42123, Italy
| | - V Manicardi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, 42123, Italy
| | - S Piana
- Pathology Unit, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, 42123, Italy
| | - R Valli
- Pathology Unit, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, 42123, Italy
| | - F Lococo
- Thoracic Surgery Unit, IRCCS-Fondazione Policlinico Gemelli, Roma, Italia
- Catholic University of the Sacred Heart, Roma, Italia
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, 42123, Italy.
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4
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Godfrey J, Chen X, Sunseri N, Cooper A, Yu J, Varlamova A, Zarubin D, Popov Y, Jacobson C, Postovalova E, Xiang Z, Nomie K, Bagaev A, Venkataraman G, Zha Y, Tumuluru S, Smith SM, Kline JP. TIGIT is a key inhibitory checkpoint receptor in lymphoma. J Immunother Cancer 2023; 11:e006582. [PMID: 37364933 PMCID: PMC10410806 DOI: 10.1136/jitc-2022-006582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND PD-1 checkpoint blockade therapy (CBT) has greatly benefited patients with select solid tumors and lymphomas but has limited efficacy against diffuse large B-cell lymphoma (DLBCL). Because numerous inhibitory checkpoint receptors have been implicated in driving tumor-specific T cell dysfunction, we hypothesized that combinatorial CBT would enhance the activity of anti-PD-1-based therapy in DLBCL. T cell immunoglobulin and immunoreceptor tyrosine-based inhibitory motif domain (TIGIT) is a coinhibitory receptor expressed on dysfunctional tumor-infiltrating T cells, and TIGIT blockade has demonstrated encouraging activity in combination with PD-1 blockade in murine tumor models and in clinical studies. However, the degree to which TIGIT mediates T cell dysfunction in DLBCL has not been fully explored. RESULTS Here, we demonstrate that TIGIT is broadly expressed on lymphoma-infiltrating T cells (LITs) across a variety of human lymphomas and is frequently coexpressed with PD-1. TIGIT expression is particularly common on LITs in DLBCL, where TIGIT+ LITs often form distinct cellular communities and exhibit significant contact with malignant B cells. TIGIT+/PD-1+ LITs from human DLBCL and murine lymphomas exhibit hypofunctional cytokine production on ex vivo restimulation. In mice with established, syngeneic A20 B-cell lymphomas, TIGIT or PD-1 mono-blockade leads to modest delays in tumor outgrowth, whereas PD-1 and TIGIT co-blockade results in complete rejection of A20 lymphomas in most mice and significantly prolongs survival compared with mice treated with monoblockade therapy. CONCLUSIONS These results provide rationale for clinical investigation of TIGIT and PD-1 blockade in lymphomas, including DLBCL.
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Affiliation(s)
- James Godfrey
- Hematology, City of Hope Comprehensive Cancer Center, Duarte, California, USA
| | - Xiufen Chen
- Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, USA
| | - Nicole Sunseri
- Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, USA
| | - Alan Cooper
- Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, USA
| | - Jovian Yu
- Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, USA
| | | | | | | | | | | | | | | | | | | | - Yuanyuan Zha
- Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, USA
| | - Sravya Tumuluru
- Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, USA
| | - Sonali M Smith
- Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, USA
| | - Justin P Kline
- Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, USA
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5
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D’Angelo A, Kilili H, Chapman R, Generali D, Tinhofer I, Luminari S, Donati B, Ciarrocchi A, Giannini R, Moretto R, Cremolini C, Pietrantonio F, Sobhani N, Bonazza D, Prins R, Song SG, Jeon YK, Pisignano G, Cinelli M, Bagby S, Urrutia AO. Immune-related pan-cancer gene expression signatures of patient survival revealed by NanoString-based analyses. PLoS One 2023; 18:e0280364. [PMID: 36649303 PMCID: PMC9844904 DOI: 10.1371/journal.pone.0280364] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/28/2022] [Indexed: 01/18/2023] Open
Abstract
The immune system plays a central role in the onset and progression of cancer. A better understanding of transcriptional changes in immune cell-related genes associated with cancer progression, and their significance in disease prognosis, is therefore needed. NanoString-based targeted gene expression profiling has advantages for deployment in a clinical setting over RNA-seq technologies. We analysed NanoString PanCancer Immune Profiling panel gene expression data encompassing 770 genes, and overall survival data, from multiple previous studies covering 10 different cancer types, including solid and blood malignancies, across 515 patients. This analysis revealed an immune gene signature comprising 39 genes that were upregulated in those patients with shorter overall survival; of these 39 genes, three (MAGEC2, SSX1 and ULBP2) were common to both solid and blood malignancies. Most of the genes identified have previously been reported as relevant in one or more cancer types. Using Cibersort, we investigated immune cell levels within individual cancer types and across groups of cancers, as well as in shorter and longer overall survival groups. Patients with shorter survival had a higher proportion of M2 macrophages and γδ T cells. Patients with longer overall survival had a higher proportion of CD8+ T cells, CD4+ T memory cells, NK cells and, unexpectedly, T regulatory cells. Using a transcriptomics platform with certain advantages for deployment in a clinical setting, our multi-cancer meta-analysis of immune gene expression and overall survival data has identified a specific transcriptional profile associated with poor overall survival.
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Affiliation(s)
- Alberto D’Angelo
- Department of Life Sciences, University of Bath, Bath, United Kingdom
- Oncology Department, Royal United Hospital, Bath, United Kingdom
- * E-mail:
| | - Huseyin Kilili
- Milner Centre, Department of Life Sciences, University of Bath, Bath, United Kingdom
| | - Robert Chapman
- Department of Medicine, The Princess Alexandra Hospital, Harlow, United Kingdom
| | - Daniele Generali
- Multidisciplinary Unit of Breast Pathology and Translational Research, Cremona Hospital, Cremona, Italy
| | - Ingeborg Tinhofer
- Department of Radiooncology and Radiotherapy, Charite´ University Hospital, Berlin, Germany
| | - Stefano Luminari
- Hematology Unit, Azienda USL-IRCCS, Reggio Emilia, Italy
- Surgical, Medical and Dental Department of Morphological Sciences Related to Transplant, Oncology and Regenerative Medicine, University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Benedetta Donati
- Translational Research Laboratory, Azienda USL-IRCCS, Reggio Emilia, Italy
| | - Alessia Ciarrocchi
- Translational Research Laboratory, Azienda USL-IRCCS, Reggio Emilia, Italy
| | - Riccardo Giannini
- Department of Surgery, Clinical, Molecular and Critical Care Pathology, University of Pisa, Pisa, Italy
| | - Roberto Moretto
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Chiara Cremolini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | | | - Navid Sobhani
- Section of Epidemiology and Population Science, Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Debora Bonazza
- Department of Medical, Surgical and Health Sciences, Cattinara Hospital, University of Trieste, Trieste, Italy
| | - Robert Prins
- Department of Neurosurgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Seung Geun Song
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yoon Kyung Jeon
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | | | - Mattia Cinelli
- Department of Life Sciences, University of Bath, Bath, United Kingdom
| | - Stefan Bagby
- Department of Life Sciences, University of Bath, Bath, United Kingdom
| | - Araxi O. Urrutia
- Milner Centre, Department of Life Sciences, University of Bath, Bath, United Kingdom
- Instituto de Ecologia, UNAM, Ciudad de Mexico, Mexico
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6
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Durmo R, Donati B, Rebaud L, Cottereau AS, Ruffini A, Nizzoli ME, Ciavarella S, Vegliante MC, Nioche C, Meignan M, Merli F, Versari A, Ciarrocchi A, Buvat I, Luminari S. Prognostic value of lesion dissemination in doxorubicin, bleomycin, vinblastine, and dacarbazine-treated, interimPET-negative classical Hodgkin Lymphoma patients: A radio-genomic study. Hematol Oncol 2022; 40:645-657. [PMID: 35606338 PMCID: PMC9796042 DOI: 10.1002/hon.3025] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/16/2022] [Indexed: 12/30/2022]
Abstract
We evaluated the prognostic role of the largest distance between two lesions (Dmax), defined by positron emission tomography (PET) in a retrospective cohort of newly diagnosed classical Hodgkin Lymphoma (cHL) patients. We also explored the molecular bases underlying Dmax through a gene expression analysis of diagnostic biopsies. We included patients diagnosed with cHL from 2007 to 2020, initially treated with ABVD, with available baseline PET for review, and with at least two FDG avid lesions. Patients with available RNA from diagnostic biopsy were eligible for gene expression analysis. Dmax was deduced from the three-dimensional coordinates of the baseline metabolic tumor volume (MTV) and its effect on progression free survival (PFS) was evaluated. Gene expression profiles were correlated with Dmax and analyzed using CIBERSORTx algorithm to perform deconvolution. The study was conducted on 155 eligible cHL patients. Using its median value of 20 cm, Dmax was the only variable independently associated with PFS (HR = 2.70, 95% CI 1.1-6.63, pValue = 0.03) in multivariate analysis of PFS for all patients and for those with early complete metabolic response (iPET-). Among patients with iPET-low Dmax was associated with a 4-year PFS of 90% (95% CI 82.0-98.9) significantly better compared to high Dmax (4-year PFS 72.4%, 95% CI 61.9-84.6). From the analysis of gene expression profiles differences in Dmax were mostly associated with variations in the expression of microenvironmental components. In conclusion our results support tumor dissemination measured through Dmax as novel prognostic factor for cHL patients treated with ABVD.
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Affiliation(s)
- Rexhep Durmo
- Nuclear Medicine UnitAzienda USL‐IRCCSReggio EmiliaItaly,PhD Program in Clinical and Experimental Medicine (CEM)University of Modena and Reggio EmiliaModenaItaly
| | - Benedetta Donati
- Translational Research LaboratoryAzienda USL‐IRCCSReggio EmiliaItaly
| | - Louis Rebaud
- Laboratoire d’Imagerie Translationnelle en OncologieInstitut Curie, U1288 Inserm, PSLOrsayFrance,Siemens HealthineersSaint‐DenisFrance
| | | | | | | | - Sabino Ciavarella
- Hematology and Cell Therapy UnitIRCCS‐Istituto Tumori 'Giovanni Paolo II'BariItaly
| | | | - Christophe Nioche
- Laboratoire d’Imagerie Translationnelle en OncologieInstitut Curie, U1288 Inserm, PSLOrsayFrance
| | - Michel Meignan
- Lysa ImagingHenri Mondor University Hospital, AP‐HP, University Paris EastCreteilFrance
| | | | | | | | - Irene Buvat
- Laboratoire d’Imagerie Translationnelle en OncologieInstitut Curie, U1288 Inserm, PSLOrsayFrance
| | - Stefano Luminari
- Hematology UnitAzienda USL‐IRCCSReggio EmiliaItaly,Surgical, Medical and Dental Department of Morphological Sciences Related to Transplant, Oncology and Regenerative MedicineUniversity of Modena and Reggio EmiliaReggio EmiliaItaly
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7
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Lorenzini E, Torricelli F, Zamponi R, Donati B, Manicardi V, Sauta E, Faria do Valle I, Reggiani F, Gugnoni M, Manzotti G, Fragliasso V, Vitale E, Piana S, Sancisi V, Ciarrocchi A. KAP1 is a new non-genetic vulnerability of malignant pleural mesothelioma (MPM). NAR Cancer 2022; 4:zcac024. [PMID: 35910692 PMCID: PMC9336180 DOI: 10.1093/narcan/zcac024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/29/2022] [Accepted: 07/16/2022] [Indexed: 11/16/2022] Open
Abstract
Malignant pleural mesothelioma (MPM) is a rare and incurable cancer, which incidence is increasing in many countries. MPM escapes the classical genetic model of cancer evolution, lacking a distinctive genetic fingerprint. Omics profiling revealed extensive heterogeneity failing to identify major vulnerabilities and restraining development of MPM-oriented therapies. Here, we performed a multilayered analysis based on a functional genome-wide CRISPR/Cas9 screening integrated with patients molecular and clinical data, to identify new non-genetic vulnerabilities of MPM. We identified a core of 18 functionally-related genes as essential for MPM cells. The chromatin reader KAP1 emerged as a dependency of MPM. We showed that KAP1 supports cell growth by orchestrating the expression of a G2/M-specific program, ensuring mitosis correct execution. Targeting KAP1 transcriptional function, by using CDK9 inhibitors resulted in a dramatic loss of MPM cells viability and shutdown of the KAP1-mediated program. Validation analysis on two independent MPM-patients sets, including a consecutive, retrospective cohort of 97 MPM, confirmed KAP1 as new non-genetic dependency of MPM and proved the association of its dependent gene program with reduced patients’ survival probability. Overall these data: provided new insights into the biology of MPM delineating KAP1 and its target genes as building blocks of its clinical aggressiveness.
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Affiliation(s)
- Eugenia Lorenzini
- Laboratory of Translational Research , Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
- Cellular and Molecular Biology PhD Program, University of Bologna, 40126 Bologna , Italy
| | - Federica Torricelli
- Laboratory of Translational Research , Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Raffaella Zamponi
- Laboratory of Translational Research , Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Benedetta Donati
- Laboratory of Translational Research , Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Veronica Manicardi
- Laboratory of Translational Research , Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
- Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia , 41121 Modena , Italy
| | - Elisabetta Sauta
- Laboratory of Translational Research , Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
- Department of Electrical, Computer and Biomedical Engineering, University of Pavi, , 27100 Pavia , Italy
| | - Italo Faria do Valle
- Department of Physics, Center for Complex Network Research, Northeastern University , Boston , MA 02115 , USA
| | - Francesca Reggiani
- Laboratory of Translational Research , Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Mila Gugnoni
- Laboratory of Translational Research , Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Gloria Manzotti
- Laboratory of Translational Research , Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Valentina Fragliasso
- Laboratory of Translational Research , Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Emanuele Vitale
- Laboratory of Translational Research , Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
- Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia , 41121 Modena , Italy
| | - Simonetta Piana
- Pathology Unit , Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Valentina Sancisi
- Laboratory of Translational Research , Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research , Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
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8
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Casagrande N, Borghese C, Aldinucci D. Current and Emerging Approaches to Study Microenvironmental Interactions and Drug Activity in Classical Hodgkin Lymphoma. Cancers (Basel) 2022; 14:cancers14102427. [PMID: 35626032 PMCID: PMC9139207 DOI: 10.3390/cancers14102427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/06/2022] [Accepted: 05/11/2022] [Indexed: 11/24/2022] Open
Abstract
Simple Summary In classical Hodgkin Lymphoma (cHL), the tumor microenvironment (TME) plays an important role in tumor progression and treatment response, making its evaluation critical for determining prognosis, treatment strategies and predicting an increase in drug toxicity. Therefore, there is a need to utilize more complex systems to study the cHL-TME and its interplay with tumor cells. To evaluate new anticancer drugs and to find the mechanisms of drug resistance, this review summarizes emerging approaches for the analysis of the TME composition and to identify the state of the disease; the in vitro techniques used to determine the mechanisms involved in the building of an immunosuppressive and protective TME; new 3-dimensional (3D) models, the heterospheroids (HS), developed to mimic TME interactions. Here, we describe the present and likely future clinical applications indicated by the results of these studies and propose a classification for the in vitro culture methods used to study TME interactions in cHL. Abstract Classic Hodgkin lymphoma is characterized by a few tumor cells surrounded by a protective and immunosuppressive tumor microenvironment (TME) composed by a wide variety of noncancerous cells that are an active part of the disease. Therefore, new techniques to study the cHL-TME and new therapeutic strategies targeting specifically tumor cells, reactivating the antitumor immunity, counteracting the protective effects of the TME, were developed. Here, we describe new methods used to study the cell composition, the phenotype, and the spatial distribution of Hodgkin and Reed–Sternberg (HRS) cells and of noncancerous cells in tumor tissues. Moreover, we propose a classification, with increasing complexity, of the in vitro functional studies used to clarify the interactions leading not only to HRS cell survival, growth and drug resistance, but also to the immunosuppressive tumor education of monocytes, T lymphocytes and fibroblasts. This classification also includes new 3-dimensional (3D) models, obtained by cultivating HRS cells in extracellular matrix scaffolds or in sponge scaffolds, under non-adherent conditions with noncancerous cells to form heterospheroids (HS), implanted in developing chick eggs (ovo model). We report results obtained with these approaches and their applications in clinical setting.
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Hodgkin Lymphoma: A Special Microenvironment. J Clin Med 2021; 10:jcm10204665. [PMID: 34682791 PMCID: PMC8541076 DOI: 10.3390/jcm10204665] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/18/2021] [Accepted: 09/28/2021] [Indexed: 12/11/2022] Open
Abstract
Classical Hodgkin’s lymphoma (cHL) is one of the most particular lymphomas for the few tumor cells surrounded by an inflammatory microenvironment. Reed-Sternberg (RS) and Hodgkin (H) cells reprogram and evade antitumor mechanisms of the normal cells present in the microenvironment. The cells of microenvironment are essential for growth and survival of the RS/H cells and are recruited through the effect of cytokines/chemokines. We summarize recent advances in gene expression profiling (GEP) analysis applied to study microenvironment component in cHL. We also describe the main therapies that target not only the neoplastic cells but also the cellular components of the background.
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Donati B, Ferrari A, Ruffini A, Manzotti G, Fragliasso V, Merli F, Zanelli M, Valli R, Luminari S, Ciarrocchi A. Gene expression profile unveils diverse biological effect of serum vitamin D in Hodgkin's and diffuse large B-cell lymphoma. Hematol Oncol 2020; 39:205-214. [PMID: 33215701 DOI: 10.1002/hon.2827] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/05/2020] [Accepted: 11/14/2020] [Indexed: 12/21/2022]
Abstract
The primary function of 25(OH)Vitamin D (VitD) is to control calcium; however, recent evidence associated serum VitD deficiency to high aggressiveness and worse outcome in different type of malignancies including lymphomas, and the reasons of such effect are to be defined. In this study, we investigated the association of VitD blood levels with gene expression in a retrospective cohort of 181 lymphomas (104 diffuse large B-cell lymphomas [DLBCLs] and 77 classical Hodgkin's lymphomas [cHLs]) of whom 116 with available gene expression profiles (52 DLBCLs and 64 cHLs, respectively). In DLBCL, VitD deficiency did not cause significant alteration in gene expression suggesting different mechanisms of action including a possible systemic effect or an effect on pharmacokinetics. By contrast, in cHLs, VitD deficiency induced profound changes in the transcriptional program leading to the NF-κB-mediated activation of stress-protective and pro-survival pathways. Coherently, VitD signaling defined by vitamin D Receptor (VDR) expression analysis, resulted highly activated in cHLs but not in DLBCLs. Even if preliminary, these data represent the first evidence of a direct role of VitD in the biology of cHL and suggest a multimodality and disease-specific activity of this vitamin in lymphomas.
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Affiliation(s)
- Benedetta Donati
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Angela Ferrari
- Hematology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Alessia Ruffini
- Gruppo Amici Dell'Ematologia Foundation_GrADE, Reggio Emilia, Italy
| | - Gloria Manzotti
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Valentina Fragliasso
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Francesco Merli
- Hematology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Magda Zanelli
- Pathology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Riccardo Valli
- Pathology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Stefano Luminari
- Hematology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
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