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Myers MA, Arnold BJ, Bansal V, Balaban M, Mullen KM, Zaccaria S, Raphael BJ. HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data. Genome Biol 2024; 25:130. [PMID: 38773520 PMCID: PMC11110434 DOI: 10.1186/s13059-024-03267-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 05/03/2024] [Indexed: 05/24/2024] Open
Abstract
Bulk DNA sequencing of multiple samples from the same tumor is becoming common, yet most methods to infer copy-number aberrations (CNAs) from this data analyze individual samples independently. We introduce HATCHet2, an algorithm to identify haplotype- and clone-specific CNAs simultaneously from multiple bulk samples. HATCHet2 extends the earlier HATCHet method by improving identification of focal CNAs and introducing a novel statistic, the minor haplotype B-allele frequency (mhBAF), that enables identification of mirrored-subclonal CNAs. We demonstrate HATCHet2's improved accuracy using simulations and a single-cell sequencing dataset. HATCHet2 analysis of 10 prostate cancer patients reveals previously unreported mirrored-subclonal CNAs affecting cancer genes.
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Affiliation(s)
- Matthew A Myers
- Department of Computer Science, Princeton University, Princeton, USA
| | - Brian J Arnold
- Center for Statistics and Machine Learning, Princeton University, Princeton, USA
| | - Vineet Bansal
- Princeton Research Computing, Princeton University, Princeton, NJ, USA
| | - Metin Balaban
- Department of Computer Science, Princeton University, Princeton, USA
| | - Katelyn M Mullen
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simone Zaccaria
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK.
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Hocking AJ, Mortimer LA, Farrall AL, Russell PA, Klebe S. Establishing mesothelioma patient-derived organoid models from malignant pleural effusions. Lung Cancer 2024; 191:107542. [PMID: 38555809 DOI: 10.1016/j.lungcan.2024.107542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/19/2024] [Accepted: 03/25/2024] [Indexed: 04/02/2024]
Abstract
OBJECTIVES Pleural mesothelioma is a cancer arising in the cells that line the lungs and chest wall with poor survival and poor response to first-line therapy. Organoid models of cancer can faithfully recapitulate the genetic and histopathological characteristics of individualized tumors and have potential to be used for precision medicine, however methods of establishing patient-derived mesothelioma organoids have not been well established in the published literature. MATERIALS AND METHODS Long-term mesothelioma patient-derived organoids were established from ten malignant pleural effusion fluids. Mesothelioma patient-derived organoids were compared to the corresponding biopsy tissue specimens using immunohistochemistry labelling for select diagnostic markers and the TruSight Oncology-500 sequencing assay. Cell viability in response to the chemotherapeutic drug cisplatin was assessed. RESULTS We established five mesothelioma patient-derived organoid cultures from ten malignant pleural effusion fluids collected from nine individuals with pleural mesothelioma. Mesothelioma patient-derived organoids typically reflected the histopathological and genomic features of patients' matched biopsy specimens and displayed cytotoxic sensitivity to cisplatin in vitro. CONCLUSION This is the first study of its kind to establish long-term mesothelioma organoid cultures from malignant pleural effusions and report on their utility to test individuals' chemotherapeutic sensitivities ex vivo.
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Affiliation(s)
- Ashleigh J Hocking
- College of Medicine and Public Health, Flinders University, Adelaide, Australia.
| | - Lauren A Mortimer
- College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Alexandra L Farrall
- College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Prudence A Russell
- LifeStrands Genomics and TissuPath Pathology, Mount Waverley, Victoria, Australia
| | - Sonja Klebe
- College of Medicine and Public Health, Flinders University, Adelaide, Australia; Anatomical Pathology, SA Pathology, Flinders Medical Centre, Bedford Park, Australia
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Hung YP, Chirieac LR. Molecular and Immunohistochemical Testing in Mesothelioma and Other Mesothelial Lesions. Arch Pathol Lab Med 2024; 148:e77-e89. [PMID: 38190277 DOI: 10.5858/arpa.2023-0213-ra] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2023] [Indexed: 01/10/2024]
Abstract
CONTEXT.— Molecular testing has increasingly been utilized in the evaluation of mesothelioma. Diffuse mesothelioma comprises multiple distinct genetic subgroups. While most diffuse mesotheliomas lack oncogenic kinase mutations and instead harbor alterations involving tumor suppressors and chromatin regulators, a minor subset of tumors is characterized by uncommon alterations such as germline mutations, genomic near-haploidization, ALK rearrangement, ATF1 rearrangement, or EWSR1::YY1 fusion. OBJECTIVE.— To provide updates on the salient molecular features of diffuse mesothelioma, mesothelioma in situ, and other mesothelial lesions: well-differentiated papillary mesothelial tumor, adenomatoid tumor, peritoneal inclusion cyst, and others. We consider the diagnostic, prognostic, and predictive utility of molecular testing in mesothelial lesions. DATA SOURCES.— We performed a literature review of recently described genetic features, molecular approaches, and immunohistochemical tools, including BAP1, MTAP, and merlin in mesothelioma and other mesothelial lesions. CONCLUSIONS.— Our evolving understanding of the molecular diversity of diffuse mesothelioma and other mesothelial lesions has led to considerable changes in pathology diagnostic practice, including the application of immunohistochemical markers such as BAP1, MTAP, and merlin (NF2), which are surrogates of mutation status. In young patients and/or those without significant asbestos exposure, unusual mesothelioma genetics such as germline mutations, ALK rearrangement, and ATF1 rearrangement should be considered.
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MESH Headings
- Humans
- Mesothelioma/diagnosis
- Mesothelioma/genetics
- Mesothelioma/metabolism
- Mesothelioma/pathology
- Immunohistochemistry
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Biomarkers, Tumor/analysis
- Neoplasms, Mesothelial/diagnosis
- Neoplasms, Mesothelial/genetics
- Neoplasms, Mesothelial/metabolism
- Neoplasms, Mesothelial/pathology
- Mesothelioma, Malignant/diagnosis
- Mesothelioma, Malignant/genetics
- Mesothelioma, Malignant/pathology
- Mesothelioma, Malignant/metabolism
- Mutation
- Tumor Suppressor Proteins
- Ubiquitin Thiolesterase
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Affiliation(s)
- Yin P Hung
- From the Department of Pathology, Massachusetts General Hospital. Boston (Hung)
- the Department of Pathology, Harvard Medical School, Boston, Massachusetts (Hung, Chirieac)
| | - Lucian R Chirieac
- the Department of Pathology, Harvard Medical School, Boston, Massachusetts (Hung, Chirieac)
- the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Chirieac)
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Congedo MT, West EC, Evangelista J, Mattingly AA, Calabrese G, Sassorossi C, Nocera A, Chiappetta M, Flamini S, Abenavoli L, Margaritora S, Boccuto L, Lococo F. The genetic susceptibility in the development of malignant pleural mesothelioma: somatic and germline variants, clinicopathological features and implication in practical medical/surgical care: a narrative review. J Thorac Dis 2024; 16:671-687. [PMID: 38410609 PMCID: PMC10894363 DOI: 10.21037/jtd-23-611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/18/2023] [Indexed: 02/28/2024]
Abstract
Background and Objective Malignant pleural mesothelioma (MPM) is a very aggressive primary tumor of the pleura whose main risk factor is exposure to asbestos. However, only a minority of exposed people develops MPM and the incidence of MPM cases without an apparent association with asbestos exposure has been increasing in recent years, suggesting that genetic predisposing factors may play a crucial role. In addition, several studies reported familial cases of MPM, suggesting that heredity may be an important and underestimated feature in MPM development. Several candidate genes have been associated with a predisposition to MPM and most of them play a role in DNA repair mechanisms: overall, approximately 20% of MPM cases may be related to genetic predisposition. A particular category of patients with high susceptibility to MPM is represented by carriers of pathogenic variants in the BAP1 gene. Germline variants in BAP1 predispose to the development of MPM following an autosomal dominant pattern of inheritance in the familial cases. MPMs in these patients are significantly less aggressive, and patients require a multidisciplinary approach that involves genetic counseling, medical genetics, pathology, surgical, medical, and radiation oncology expertise. In the present narrative review, we presented a comprehensive overview of genetic susceptibility in the development of MPM. Methods The narrative review is based on a selective literature carried out in PubMed in 2023. Inclusion criteria were original articles in English language, and clinical trials (randomized, prospective, or retrospective). Key Content and Findings We summarized the somatic and germline variants and the differences in terms of clinicopathological features and prognosis between gene-related MPM (GR-MPM) and asbestos-related MPM (AR-MPM). We also discussed the indications for screening, genetic testing, and surveillance of patients with BAP1 germline variants. Conclusions In this narrative review, we have emphasized that the BAP1 gene's harmful germline variations are inherited in an autosomal dominant manner in familial cases. MPMs in individuals with these variations are less severe, and their medical care necessitates a collaborative effort. Additionally, we have outlined the current therapeutic prospects for MPM, including the possibility of gene-specific therapy, which is currently promising but still requires clinical validation.
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Affiliation(s)
| | - Elizabeth Casey West
- Healthcare Genetics and Genomics, School of Nursing, Clemson University, Clemson, SC, USA
| | - Jessica Evangelista
- Thoracic Surgery, A. Gemelli University Hospital Foundation IRCCS, Rome, Italy
- Catholic University of Sacred Heart, Rome, Italy
| | - Aubrey Anne Mattingly
- Healthcare Genetics and Genomics, School of Nursing, Clemson University, Clemson, SC, USA
| | - Giuseppe Calabrese
- Thoracic Surgery, A. Gemelli University Hospital Foundation IRCCS, Rome, Italy
| | - Carolina Sassorossi
- Thoracic Surgery, A. Gemelli University Hospital Foundation IRCCS, Rome, Italy
| | - Adriana Nocera
- Thoracic Surgery, A. Gemelli University Hospital Foundation IRCCS, Rome, Italy
| | - Marco Chiappetta
- Thoracic Surgery, A. Gemelli University Hospital Foundation IRCCS, Rome, Italy
| | - Sara Flamini
- Thoracic Surgery, A. Gemelli University Hospital Foundation IRCCS, Rome, Italy
| | - Ludovico Abenavoli
- Department of Health Sciences, “Magna Græcia” University, Catanzaro, Italy
| | - Stefano Margaritora
- Thoracic Surgery, A. Gemelli University Hospital Foundation IRCCS, Rome, Italy
- Catholic University of Sacred Heart, Rome, Italy
| | - Luigi Boccuto
- Healthcare Genetics and Genomics, School of Nursing, Clemson University, Clemson, SC, USA
| | - Filippo Lococo
- Thoracic Surgery, A. Gemelli University Hospital Foundation IRCCS, Rome, Italy
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Febres-Aldana CA, Fanaroff R, Offin M, Zauderer MG, Sauter JL, Yang SR, Ladanyi M. Diffuse Pleural Mesothelioma: Advances in Molecular Pathogenesis, Diagnosis, and Treatment. ANNUAL REVIEW OF PATHOLOGY 2024; 19:11-42. [PMID: 37722697 DOI: 10.1146/annurev-pathol-042420-092719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
Diffuse pleural mesothelioma (DPM) is a highly aggressive malignant neoplasm arising from the mesothelial cells lining the pleural surfaces. While DPM is a well-recognized disease linked to asbestos exposure, recent advances have expanded our understanding of molecular pathogenesis and transformed our clinical practice. This comprehensive review explores the current concepts and emerging trends in DPM, including risk factors, pathobiology, histologic subtyping, and therapeutic management, with an emphasis on a multidisciplinary approach to this complex disease.
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Affiliation(s)
- Christopher A Febres-Aldana
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA; ,
| | - Rachel Fanaroff
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA; ,
| | - Michael Offin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Marjorie G Zauderer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jennifer L Sauter
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA; ,
| | - Soo-Ryum Yang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA; ,
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA; ,
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Ventura L, Lee M, Baranowski R, Hargrave J, Sheaff M, Waller D. Perioperative discordance in mesothelioma cell type after pleurectomy/decortication-a possible detrimental effect of neoadjuvant chemotherapy due to epithelial to mesenchymal transition? INTERDISCIPLINARY CARDIOVASCULAR AND THORACIC SURGERY 2023; 37:ivad145. [PMID: 37851340 PMCID: PMC10653780 DOI: 10.1093/icvts/ivad145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/17/2023] [Indexed: 10/19/2023]
Abstract
OBJECTIVES The goal was to evaluate the accuracy of preoperative histological assessment and the factors affecting the accuracy and the subsequent effect on postoperative survival after surgical treatment for malignant pleural mesothelioma (MPM). METHODS We analysed the perioperative course of patients who underwent surgery for MPM in a single institution over a 5-year period. The primary end point was to evaluate the proportion of histological discordance between preoperative assessment and postoperative histological diagnosis. The secondary end point was to evaluate its prognostic effect on postoperative survival after surgical treatment. RESULTS One-hundred and twenty-nine patients were included in this study. Histological discordance between preoperative assessment and postoperative histological diagnosis was found in 27 of 129 patients (20.9%): epithelial to biphasic/sarcomatoid (negative discordance) in 24 and biphasic to epithelial (positive discordance) in 3 (P-value < 0.001). All 24 patients who exhibited epithelial-to-mesenchymal transition (EMT) had received neoadjuvant chemotherapy (P-value: 0.006). In the 34 patients who underwent upfront surgery, only 1 case (2.9%) of EMT was identified (P-value: 0.127). EMT was not associated with a less invasive method of biopsy (P-value: 0.058) or with the volume or maximum diameter of the biopsy (P-value: 0.358 and 0.518, respectively), but it was significantly associated with the receipt of neoadjuvant chemotherapy (P-value: 0.006). At a median follow-up of 17 months (IQR: 11.0-28.0), 50 (39%) patients are still alive. Overall survival was significantly reduced in those patients who received neoadjuvant chemotherapy and who exhibited discordance (EMT) compared to those who did not: 11 (95% CI: 6.2-15.8) months versus 19 (95% CI: 14.2-23.8) months (P-value < 0.001). In addition, there was no difference in overall survival between those who received neoadjuvant chemotherapy and those who had upfront surgery: 16 (95% CI: 2.5-19.5) months versus 30 (95% CI: 11.6-48.4) months (P-value: 0.203). CONCLUSIONS The association of neoadjuvant chemotherapy with perioperative histological discordance can be explained by EMT, which leads to worse survival. Therefore, there is an argument for the preferential use of upfront surgery in the treatment of otherwise resectable MPM.
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Affiliation(s)
- Luigi Ventura
- Barts Thorax Centre, St Bartholomew's Hospital, London, UK
| | - Michelle Lee
- Barts Thorax Centre, St Bartholomew's Hospital, London, UK
| | | | | | - Michael Sheaff
- Barts Thorax Centre, St Bartholomew's Hospital, London, UK
| | - David Waller
- Barts Thorax Centre, St Bartholomew's Hospital, London, UK
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7
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Kwok DW, Stevers NO, Nejo T, Chen LH, Etxeberria I, Jung J, Okada K, Cove MC, Lakshmanachetty S, Gallus M, Barpanda A, Hong C, Chan GKL, Wu SH, Ramos E, Yamamichi A, Liu J, Watchmaker P, Ogino H, Saijo A, Du A, Grishanina N, Woo J, Diaz A, Chang SM, Phillips JJ, Wiita AP, Klebanoff CA, Costello JF, Okada H. Tumor-wide RNA splicing aberrations generate immunogenic public neoantigens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.19.563178. [PMID: 37904942 PMCID: PMC10614978 DOI: 10.1101/2023.10.19.563178] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
T-cell-mediated immunotherapies are limited by the extent to which cancer-specific antigens are homogenously expressed throughout a tumor. We reasoned that recurrent splicing aberrations in cancer represent a potential source of tumor-wide and public neoantigens, and to test this possibility, we developed a novel pipeline for identifying neojunctions expressed uniformly within a tumor across diverse cancer types. Our analyses revealed multiple neojunctions that recur across patients and either exhibited intratumor heterogeneity or, in some cases, were tumor-wide. We identified CD8+ T-cell clones specific for neoantigens derived from tumor-wide and conserved neojunctions in GNAS and RPL22 , respectively. TCR-engineered CD8 + T-cells targeting these mutations conferred neoantigen-specific tumor cell eradication. Furthermore, we revealed that cancer-specific dysregulation in splicing factor expression leads to recurrent neojunction expression. Together, these data reveal that a subset of neojunctions are both intratumorally conserved and public, providing the molecular basis for novel T-cell-based immunotherapies that address intratumoral heterogeneity.
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8
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Dong B, Lu Y, He S, Li B, Li Y, Lai Q, Li W, Ji S, Chen Y, Dai L, Chen L. Multisite and multitimepoint proteomics reveal that patent foramen ovale closure improves migraine and epilepsy by reducing right-to-left shunt-induced hypoxia. MedComm (Beijing) 2023; 4:e334. [PMID: 37576864 PMCID: PMC10422075 DOI: 10.1002/mco2.334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/02/2023] [Accepted: 03/12/2023] [Indexed: 08/15/2023] Open
Abstract
Patent foramen ovale (PFO) is a congenital defect in the partition between two atria, which may cause right-to-left shunt (RLS), leading to neurological chronic diseases with episodic manifestations (NCDEMs), such as migraine and epilepsy. However, whether PFO closure was effective in improving NCDEMs and the mechanism were unclear. Twenty-eight patients with migraine or epilepsy who underwent PFO closure were recruited. Notably, approximately half of patients received 50% or more reduction in seizure or headache attacks. Meanwhile, the postoperative blood oxygen partial pressure and oxygen saturation were elevated after PFO closure. Multisite (peripheral, right, and left atrial) and multitimepoint (before and after surgery) plasma proteomics from patients showed that the levels of free hemoglobin and cell adhesion molecules (CAMs) were significantly increased after PFO closure, which may be related to the relief of the hypoxic state. Furtherly, the omics data from multiple brain regions of mice revealed that a large number of proteins were differentially expressed in the occipital region in response to PFO, including redox molecules and CAMs, suggesting PFO-caused hypoxia may have great impacts on occipital region. Collectively, PFO may cause NCDEMs due to RLS-induced hypoxia, and PFO closure could prevent RLS to improve migraine and epilepsy.
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Affiliation(s)
- Bosi Dong
- Department of NeurologyWest China HospitalSichuan UniversityChengduSichuanChina
| | - Ying Lu
- State Key Laboratory of BiotherapyNational Clinical Research Center for Geriatrics and Department of General PracticeWest China HospitalSichuan Universityand Collaborative Innovation Center of BiotherapyChengduSichuanChina
| | - Siyu He
- State Key Laboratory of BiotherapyNational Clinical Research Center for Geriatrics and Department of General PracticeWest China HospitalSichuan Universityand Collaborative Innovation Center of BiotherapyChengduSichuanChina
| | - Baichuan Li
- Department of NeurologyWest China HospitalSichuan UniversityChengduSichuanChina
| | - Yajiao Li
- Department of CardiologyWest China HospitalSichuan UniversityChengduSichuanChina
| | - Qi Lai
- Department of NeurologyWest China HospitalSichuan UniversityChengduSichuanChina
| | - Wanling Li
- Department of NeurologyWest China HospitalSichuan UniversityChengduSichuanChina
| | - Shuming Ji
- Department of Clinical Research ManagementWest China HospitalSichuan UniversityChengduSichuanChina
| | - Yucheng Chen
- Department of CardiologyWest China HospitalSichuan UniversityChengduSichuanChina
| | - Lunzhi Dai
- State Key Laboratory of BiotherapyNational Clinical Research Center for Geriatrics and Department of General PracticeWest China HospitalSichuan Universityand Collaborative Innovation Center of BiotherapyChengduSichuanChina
| | - Lei Chen
- Department of NeurologyWest China HospitalSichuan UniversityChengduSichuanChina
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Cedres S, Serna G, Gonzalez-Medina A, Valdivia A, Assaf-Pastrana JD, Iranzo P, Callejo A, Pardo N, Navarro A, Martinez-Marti A, Priano I, Fasani R, Guardia X, Gonzalo J, Carbonell C, Frigola J, Amat R, Navarro V, Dienstmann R, Vivancos A, Nuciforo P, Felip E. Expression of TILs and Patterns of Gene Expression from Paired Samples of Malignant Pleural Mesothelioma (MPM) Patients. Cancers (Basel) 2023; 15:3611. [PMID: 37509274 PMCID: PMC10377125 DOI: 10.3390/cancers15143611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/31/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
MPM is an aggressive disease with an immunosuppressive tumor microenvironment, and interest in exploring immunotherapy in this disease has been increasing. In the first line of treatment, the combination of nivolumab and ipilimumab demonstrated an improvement in survival over chemotherapy. The presence of TILs has been recognized as a marker of antitumor immune response to chemotherapy in solid tumors. The aim of our study is to identify the effect of treatment on immune cells and the immune gene profile in MPM. We investigated the changes in expression of TILs in 10 human MPM paired tumor tissues using immunohistochemistry and gene expression analysis from paired untreated and treated samples. In this small series, we demonstrated that during the evolution of disease without any treatment there was an increase in the inflammatory component in tumor samples. After systemic treatment there was a decrease in the number of TILs. We observed that after systemic treatment or disease progression immune gene signatures were suppressed. Our integrated analysis of paired samples with immune profile and genomic changes on MPM suggested that during the evolution of the disease the immune system tends to switch, turning off with treatment.
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Affiliation(s)
- Susana Cedres
- Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, 08035 Barcelona, Spain
| | - Garazi Serna
- Molecular Oncology Group, Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | | | - Augusto Valdivia
- Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, 08035 Barcelona, Spain
| | - Juan David Assaf-Pastrana
- Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, 08035 Barcelona, Spain
| | - Patricia Iranzo
- Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, 08035 Barcelona, Spain
| | - Ana Callejo
- Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, 08035 Barcelona, Spain
| | - Nuria Pardo
- Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, 08035 Barcelona, Spain
| | - Alejandro Navarro
- Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, 08035 Barcelona, Spain
| | - Alex Martinez-Marti
- Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, 08035 Barcelona, Spain
| | - Ilaria Priano
- Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, 08035 Barcelona, Spain
| | - Roberta Fasani
- Molecular Oncology Group, Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Xavier Guardia
- Molecular Oncology Group, Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Javier Gonzalo
- Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Caterina Carbonell
- Clinical Research Department, Vall d'Hebron Institute of Oncology (VHIO), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Joan Frigola
- Clinical Research Department, Vall d'Hebron Institute of Oncology (VHIO), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Ramon Amat
- Clinical Research Department, Vall d'Hebron Institute of Oncology (VHIO), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Victor Navarro
- Oncology Data Science Group, Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Rodrigo Dienstmann
- Oncology Data Science Group, Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Ana Vivancos
- Cancer Genomics Lab, Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Paolo Nuciforo
- Molecular Oncology Group, Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Enriqueta Felip
- Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, 08035 Barcelona, Spain
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Chen Y, Dai X, Wang J, Tao C, Wang Y, Zhu Q, Wang Z, Zhang T, Lan Q, Zhao J. Heterogenous profiles between primary lung cancers and paired brain metastases reveal tumor evolution. Front Oncol 2023; 13:1026099. [PMID: 37384291 PMCID: PMC10293929 DOI: 10.3389/fonc.2023.1026099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 05/30/2023] [Indexed: 06/30/2023] Open
Abstract
Background Brain metastases (BMs) are the most common central nervous system (CNS) malignant tumors, with rapid disease progression and extremely poor prognosis. The heterogeneity between primary lung cancers and BMs leads to the divergent efficacy of the adjuvant therapy response to primary tumors and BMs. However, the extent of heterogeneity between primary lung cancers and BMs, and the evolutionary process remains little known. Methods To deeply insight into the extent of inter-tumor heterogeneity at a single-patient level and the process of these evolutions, we retrospectively analyzed a total of 26 tumor samples from 10 patients with matched primary lung cancers and BMs. One patient underwent four times brain metastatic lesion surgery with diverse locations and one operation for the primary lesion. The genomic and immune heterogeneity between primary lung cancers and BMs were evaluated by utilizing whole-exome sequencing (WESeq) and immunohistochemical analysis. Results In addition to inheriting genomic phenotype and molecular phenotype from the primary lung cancers, massive unique genomic phenotype and molecular phenotype were also observed in BMs, which revealed unimaginable complexity of tumor evolution and extensive heterogeneity among lesions at a single-patient level. By analysis of a multi-metastases case (Case 3) of cancer cells' subclonal composition, we found similar multiple subclonal clusters in the four spatial and temporal isolated brain metastatic focus, with the characteristics of polyclonal dissemination. Our study also verified that the expression level of immune checkpoints-related molecule Programmed Death-Ligand 1 (PD-L1) (P = 0.0002) and the density of tumor-infiltrating lymphocytes (TILs) (P = 0.0248) in BMs were significantly lower than that in paired primary lung cancers. Additionally, tumor microvascular density (MVD) also differed between primary tumors and paired BMs, indicating that temporal and spatial diversity profoundly contributes to the evolution of BMs heterogeneity. Conclusion Our study revealed the significance of temporal and spatial factors to the evolution of tumor heterogeneity by multi-dimensional analysis of matched primary lung cancers and BMs, which also provided novel insight for formulating individualized treatment strategies for BMs.
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Affiliation(s)
- Yanming Chen
- Department of Neurosurgery, Second Affiliated Hospital of Soochow University, Suzhou, China
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Xiaoxiao Dai
- Department of Pathology, Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Ji Wang
- Department of Neurosurgery, Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Chuming Tao
- Department of Neurosurgery, Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Ye Wang
- Health Management Center, Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Qing Zhu
- Department of Neurosurgery, Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhongyong Wang
- Department of Neurosurgery, Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Tan Zhang
- Department of Neurosurgery, Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Qing Lan
- Department of Neurosurgery, Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Jizong Zhao
- Department of Neurosurgery, Second Affiliated Hospital of Soochow University, Suzhou, China
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
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11
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Laure A, Rigutto A, Kirschner MB, Opitz L, Grob L, Opitz I, Felley-Bosco E, Hiltbrunner S, Curioni-Fontecedro A. Genomic and Transcriptomic Analyses of Malignant Pleural Mesothelioma (MPM) Samples Reveal Crucial Insights for Preclinical Testing. Cancers (Basel) 2023; 15:2813. [PMID: 37345150 DOI: 10.3390/cancers15102813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/15/2023] [Accepted: 05/15/2023] [Indexed: 06/23/2023] Open
Abstract
Cell lines are extensively used to study cancer biology. However, the use of highly passaged commercial cell lines has to be questioned, as they do not closely resemble the originating tumor. To understand the reliability of preclinical models for Malignant pleural mesothelioma (MPM) studies, we have performed whole transcriptome and whole exome analyses of fresh frozen MPM tumors and compared them to cell lines generated from these tumors, as well as commercial cell lines and a preclinical MPM mouse model. Patient-derived cell lines were generated from digested fresh tumors and whole exome sequencing was performed on DNA isolated from formalin-fixed, paraffin-embedded (FFPE) tumor samples, corresponding patient-derived cell lines, and normal tissue. RNA sequencing libraries were prepared from 10 fresh frozen tumor samples, the 10 corresponding patient-derived cell lines, and 7 commercial cell lines. Our results identified alterations in tumor suppressor genes such as FBXW7, CDKN2A, CDKN2B, and MTAP, all known to drive MPM tumorigenesis. Patient-derived cell lines correlate to a high degree with their originating tumor. Gene expressions involved in multiple pathways such as EMT, apoptosis, myogenesis, and angiogenesis are upregulated in tumor samples when compared to patient-derived cell lines; however, they are downregulated in commercial cell lines compared to patient-derived cell lines, indicating significant differences between the two model systems. Our results show that the genome and transcriptome of tumors correlate to a higher degree with patient-derived cell lines rather than commercial cell lines. These results are of major relevance for the scientific community in regard to using cell lines as an appropriate model, resembling the pathway of interest to avoid misleading results for clinical applications.
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Affiliation(s)
- Alexander Laure
- Faculty of Science and Medicine, University of Fribourg, CH-1700 Fribourg, Switzerland
- Faculty of Science, University of Zurich, CH-8006 Zurich, Switzerland
| | - Angelica Rigutto
- Faculty of Science and Medicine, University of Fribourg, CH-1700 Fribourg, Switzerland
- Faculty of Science, University of Zurich, CH-8006 Zurich, Switzerland
| | - Michaela B Kirschner
- Department of Thoracic Surgery, University Hospital Zurich, CH-8091 Zurich, Switzerland
| | - Lennart Opitz
- Functional Genomics Center Zurich, Swiss Federal Institute of Technology, University of Zurich, CH-8057 Zurich, Switzerland
| | - Linda Grob
- NEXUS Personalized Health Technologies, ETH Zurich, CH-8092 Zurich, Switzerland
- Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Isabelle Opitz
- Faculty of Science, University of Zurich, CH-8006 Zurich, Switzerland
- Department of Thoracic Surgery, University Hospital Zurich, CH-8091 Zurich, Switzerland
| | - Emanuela Felley-Bosco
- Faculty of Science, University of Zurich, CH-8006 Zurich, Switzerland
- Laboratory of Molecular Oncology, Department of Thoracic Surgery, University Hospital Zurich, CH-8091 Zurich, Switzerland
| | - Stefanie Hiltbrunner
- Faculty of Science and Medicine, University of Fribourg, CH-1700 Fribourg, Switzerland
- Department of Medical Oncology and Haematology, University Hospital Zurich, CH-8091 Zurich, Switzerland
| | - Alessandra Curioni-Fontecedro
- Faculty of Science and Medicine, University of Fribourg, CH-1700 Fribourg, Switzerland
- Department of Medical Oncology and Haematology, University Hospital Zurich, CH-8091 Zurich, Switzerland
- Department of Oncology, HFR Fribourg-Hôpital Cantonal, CH-1708 Fribourg, Switzerland
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12
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George JT, Levine H. Optimal cancer evasion in a dynamic immune microenvironment generates diverse post-escape tumor antigenicity profiles. eLife 2023; 12:82786. [PMID: 37096883 PMCID: PMC10129331 DOI: 10.7554/elife.82786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 03/24/2023] [Indexed: 04/26/2023] Open
Abstract
The failure of cancer treatments, including immunotherapy, continues to be a major obstacle in preventing durable remission. This failure often results from tumor evolution, both genotypic and phenotypic, away from sensitive cell states. Here, we propose a mathematical framework for studying the dynamics of adaptive immune evasion that tracks the number of tumor-associated antigens available for immune targeting. We solve for the unique optimal cancer evasion strategy using stochastic dynamic programming and demonstrate that this policy results in increased cancer evasion rates compared to a passive, fixed strategy. Our foundational model relates the likelihood and temporal dynamics of cancer evasion to features of the immune microenvironment, where tumor immunogenicity reflects a balance between cancer adaptation and host recognition. In contrast with a passive strategy, optimally adaptive evaders navigating varying selective environments result in substantially heterogeneous post-escape tumor antigenicity, giving rise to immunogenically hot and cold tumors.
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Affiliation(s)
- Jason T George
- Department of Biomedical Engineering, Texas A&M University, Houston, United States
- Engineering Medicine Program, Texas A&M University, Houston, United States
- Center for Theoretical Biological Physics, Rice University, Houston, United States
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, United States
- Department of Physics, Northeastern University, Boston, United States
- Department of Bioengineering, Northeastern University, Boston, United States
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13
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Sekido Y, Sato T. NF2 alteration in mesothelioma. FRONTIERS IN TOXICOLOGY 2023; 5:1161995. [PMID: 37180489 PMCID: PMC10168293 DOI: 10.3389/ftox.2023.1161995] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/06/2023] [Indexed: 05/16/2023] Open
Abstract
The NF2 tumor suppressor gene is a frequent somatically mutated gene in mesothelioma, with 30%-40% mesotheliomas showing NF2 inactivation. NF2 encodes merlin, a member of the ezrin, radixin, and moesin (ERM) family of proteins that regulate cytoskeleton and cell signaling. Recent genome analysis revealed that NF2 alteration may be a late event in mesothelioma development, suggesting that NF2 mutation confers a more aggressive phenotype to mesothelioma cells and may not be directly caused by asbestos exposure. The Hippo tumor-suppressive and mTOR prooncogenic signaling pathways are crucial cell-signaling cascades regulated by merlin. Although the exact role and timing of NF2 inactivation in mesothelioma cells remain to be elucidated, targeting the NF2/merlin-Hippo pathway may be a new therapeutic strategy for patients with mesothelioma.
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Affiliation(s)
- Yoshitaka Sekido
- Division of Cancer Biology, Aichi Cancer Center Research Institute, Nagoya, Japan
- Division of Molecular and Cellular Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tatsuhiro Sato
- Division of Cancer Biology, Aichi Cancer Center Research Institute, Nagoya, Japan
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14
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Benefits and Challenges of Inhibiting EZH2 in Malignant Pleural Mesothelioma. Cancers (Basel) 2023; 15:cancers15051537. [PMID: 36900330 PMCID: PMC10000483 DOI: 10.3390/cancers15051537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/25/2023] [Accepted: 02/26/2023] [Indexed: 03/04/2023] Open
Abstract
Malignant pleural mesothelioma (MPM) is an aggressive thoracic cancer that is mainly associated with prior exposure to asbestos fibers. Despite being a rare cancer, its global rate is increasing and the prognosis remains extremely poor. Over the last two decades, despite the constant research of new therapeutic options, the combination chemotherapy with cisplatin and pemetrexed has remained the only first-line therapy for MPM. The recent approval of immune checkpoint blockade (ICB)-based immunotherapy has opened new promising avenues of research. However, MPM is still a fatal cancer with no effective treatments. Enhancer of zeste homolog 2 (EZH2) is a histone methyl transferase that exerts pro-oncogenic and immunomodulatory activities in a variety of tumors. Accordingly, a growing number of studies indicate that EZH2 is also an oncogenic driver in MPM, but its effects on tumor microenvironments are still largely unexplored. This review describes the state-of-the-art of EZH2 in MPM biology and discusses its potential use both as a diagnostic and therapeutic target. We highlight current gaps of knowledge, the filling of which will likely favor the entry of EZH2 inhibitors within the treatment options for MPM patients.
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15
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The Pattern of RNA Editing Changes in Pleural Mesothelioma upon Epithelial-Mesenchymal Transition. Int J Mol Sci 2023; 24:ijms24032874. [PMID: 36769192 PMCID: PMC9917482 DOI: 10.3390/ijms24032874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/20/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Pleural mesothelioma (PM) is a cancer where epithelioid, biphasic and sarcomatoid histotypes are observed. Sarcomatoid PM is characterized by mesenchymal features. Multi-omics have been used to characterize the epithelial-to-mesenchymal (EMT) phenotype at the molecular level. We contribute to this effort by including the analysis of RNA editing. We extracted samples with the highest vs. lowest Epithelial score from two PM cohorts and observed increased RNA editing in introns and decreased RNA editing in 3'UTR upon EMT. The same was observed in primary PM primary cultures stratified by transcriptomics analysis into two groups, one of them enriched with mesenchymal features. Our data demonstrate that, as has been observed in other cancer types, RNA editing associates to EMT phenotype in PM.
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16
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Stern E, Caruso S, Meiller C, Mishalian I, Hirsch TZ, Bayard Q, Tadmor CT, Wald H, Jean D, Wald O. Deep dive into the immune response against murine mesothelioma permits design of novel anti-mesothelioma therapeutics. Front Immunol 2023; 13:1026185. [PMID: 36685577 PMCID: PMC9846605 DOI: 10.3389/fimmu.2022.1026185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/31/2022] [Indexed: 01/06/2023] Open
Abstract
Given the need to improve the efficacy of standard-of-care immunotherapy (anti-CTLA-4 + anti-PD-1) in human malignant pleural mesothelioma (hMPM), we thoroughly characterized the immunobiology of the AB12 murine mesothelioma (MM) model, aiming to increase its accuracy in predicting the response of hMPM to immunotherapy and in designing novel anti-hMPM treatments. Specifically, we used immunologic, transcriptomic and survival analyses, to synchronize the MM tumor growth phases and immune evolution with the histo-molecular and immunological characteristics of hMPM while also determining the anti-MM efficacy of standard-of-care anti-hMPM immunotherapy as a benchmark that novel therapeutics should meet. We report that early-, intermediate- and advanced- AB12 tumors are characterized by a bell-shaped anti-tumor response that peaks in intermediate tumors and decays in advanced tumors. We further show that intermediate- and advanced- tumors match with immune active ("hot") and immune inactive ("cold") hMPM respectively, and that they respond to immunotherapy in a manner that corresponds well with its performance in real-life settings. Finally, we show that in advanced tumors, addition of cisplatin to anti CTLA-4 + anti PD-1 can extend mice survival and invigorate the decaying anti-tumor response. Therefore, we highlight this triple combination as a worthy candidate to improve clinical outcomes in hMPM.
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Affiliation(s)
- Esther Stern
- Gene Therapy Institute, Hadassah Hebrew University Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Stefano Caruso
- Centre de Recherche des Cordeliers, Inserm, Sorbonne Université, Université Paris Cité, team Functional Genomics of Solid Tumors, Paris, France
| | - Clément Meiller
- Centre de Recherche des Cordeliers, Inserm, Sorbonne Université, Université Paris Cité, team Functional Genomics of Solid Tumors, Paris, France
| | - Inbal Mishalian
- Gene Therapy Institute, Hadassah Hebrew University Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Theo Z. Hirsch
- Centre de Recherche des Cordeliers, Inserm, Sorbonne Université, Université Paris Cité, team Functional Genomics of Solid Tumors, Paris, France
| | - Quentin Bayard
- Centre de Recherche des Cordeliers, Inserm, Sorbonne Université, Université Paris Cité, team Functional Genomics of Solid Tumors, Paris, France
| | - Carmit T. Tadmor
- Gene Therapy Institute, Hadassah Hebrew University Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Tel Aviv University, Tel Aviv, Israel
| | - Hanna Wald
- Gene Therapy Institute, Hadassah Hebrew University Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Didier Jean
- Centre de Recherche des Cordeliers, Inserm, Sorbonne Université, Université Paris Cité, team Functional Genomics of Solid Tumors, Paris, France
| | - Ori Wald
- Gene Therapy Institute, Hadassah Hebrew University Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Cardiothoracic Surgery, Hadassah Hebrew University Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
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17
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Hariharan A, Qi W, Rehrauer H, Wu L, Ronner M, Wipplinger M, Kresoja‐Rakic J, Sun S, Oton‐Gonzalez L, Sculco M, Serre‐Beinier V, Meiller C, Blanquart C, Fonteneau J, Vrugt B, Rüschoff JH, Opitz I, Jean D, de Perrot M, Felley‐Bosco E. Heterogeneous RNA editing and influence of ADAR2 on mesothelioma chemoresistance and the tumor microenvironment. Mol Oncol 2022; 16:3949-3974. [PMID: 36221913 PMCID: PMC9718120 DOI: 10.1002/1878-0261.13322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 09/13/2022] [Accepted: 10/11/2022] [Indexed: 12/24/2022] Open
Abstract
We previously observed increased levels of adenosine-deaminase-acting-on-dsRNA (Adar)-dependent RNA editing during mesothelioma development in mice exposed to asbestos. The aim of this study was to characterize and assess the role of ADAR-dependent RNA editing in mesothelioma. We found that tumors and mesothelioma primary cultures have higher ADAR-mediated RNA editing compared to mesothelial cells. Unsupervised clustering of editing in different genomic regions revealed heterogeneity between tumor samples as well as mesothelioma primary cultures. ADAR2 expression levels are higher in BRCA1-associated protein 1 wild-type tumors, with corresponding changes in RNA editing in transcripts and 3'UTR. ADAR2 knockdown and rescue models indicated a role in cell proliferation, altered cell cycle, increased sensitivity to antifolate treatment, and type-1 interferon signaling upregulation, leading to changes in the microenvironment in vivo. Our data indicate that RNA editing contributes to mesothelioma heterogeneity and highlights an important role of ADAR2 not only in growth regulation in mesothelioma but also in chemotherapy response, in addition to regulating inflammatory response downstream of sensing nucleic acid structures.
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Affiliation(s)
- Ananya Hariharan
- Laboratory of Molecular Oncology, Department of Thoracic SurgeryUniversity Hospital ZurichSwitzerland
| | - Weihong Qi
- Functional Genomics Center, ETH ZurichUniversity of ZurichSwitzerland
| | - Hubert Rehrauer
- Functional Genomics Center, ETH ZurichUniversity of ZurichSwitzerland
| | - Licun Wu
- Latner Thoracic Surgery Laboratories, Division of Thoracic SurgeryUniversity Health NetworkTorontoCanada
| | - Manuel Ronner
- Laboratory of Molecular Oncology, Department of Thoracic SurgeryUniversity Hospital ZurichSwitzerland
| | - Martin Wipplinger
- Laboratory of Molecular Oncology, Department of Thoracic SurgeryUniversity Hospital ZurichSwitzerland
| | - Jelena Kresoja‐Rakic
- Laboratory of Molecular Oncology, Department of Thoracic SurgeryUniversity Hospital ZurichSwitzerland
| | - Suna Sun
- Laboratory of Molecular Oncology, Department of Thoracic SurgeryUniversity Hospital ZurichSwitzerland
| | - Lucia Oton‐Gonzalez
- Laboratory of Molecular Oncology, Department of Thoracic SurgeryUniversity Hospital ZurichSwitzerland
| | - Marika Sculco
- Laboratory of Molecular Oncology, Department of Thoracic SurgeryUniversity Hospital ZurichSwitzerland
| | | | - Clément Meiller
- Centre de Recherche des Cordeliers, InsermSorbonne Université, Université Paris Cité, Functional Genomics of Solid TumorsFrance
| | - Christophe Blanquart
- Nantes Université, Inserm UMR 1307, CNRS UMR 6075, Université d'Angers, CRCI2NAFrance
| | | | - Bart Vrugt
- Institute of Pathology and Molecular PathologyUniversity Hospital ZurichSwitzerland
| | - Jan Hendrik Rüschoff
- Institute of Pathology and Molecular PathologyUniversity Hospital ZurichSwitzerland
| | - Isabelle Opitz
- Department of Thoracic SurgeryUniversity Hospital ZurichSwitzerland
| | - Didier Jean
- Centre de Recherche des Cordeliers, InsermSorbonne Université, Université Paris Cité, Functional Genomics of Solid TumorsFrance
| | - Marc de Perrot
- Latner Thoracic Surgery Laboratories, Division of Thoracic SurgeryUniversity Health NetworkTorontoCanada
| | - Emanuela Felley‐Bosco
- Laboratory of Molecular Oncology, Department of Thoracic SurgeryUniversity Hospital ZurichSwitzerland
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18
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Hiltbrunner S, Fleischmann Z, Sokol ES, Zoche M, Felley-Bosco E, Curioni-Fontecedro A. Genomic landscape of pleural and peritoneal mesothelioma tumours. Br J Cancer 2022; 127:1997-2005. [PMID: 36138075 PMCID: PMC9681755 DOI: 10.1038/s41416-022-01979-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/25/2022] [Accepted: 08/31/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Malignant pleural and peritoneal mesotheliomas are rare malignancies with unacceptable poor prognoses and limited treatment options. The genomic landscape is mainly characterised by the loss of tumour suppressor genes and mutations in DNA repair genes. Currently, data from next-generation sequencing (NGS) of mesothelioma tumours is restricted to a limited number of cases; moreover, data comparing molecular features of mesothelioma from the pleural and peritoneal origin with NGS are lacking. METHODS We analysed 1113 pleural mesothelioma and 355 peritoneal mesothelioma samples. All tumours were sequenced with the FoundationOne® or FoundationOne®CDx assay for detection of substitutions, insertion-deletions, copy-number alterations and selected rearrangements in at least 324 cancer genes. RESULTS This analysis revealed alterations in 19 genes with an overall prevalence of at least 2%. Alterations in BAP1, CDKN2A, CDKN2B, NF2, MTAP, TP53 and SETD2 occurred with a prevalence of at least 10%. Peritoneal, compared to pleural mesothelioma, was characterised by a lower prevalence of alterations in CDKN2A, CDKN2B and MTAP. Moreover, we could define four distinct subgroups according to alterations in BAP1 and CDKN2A/B. Alterations in Hedgehog pathway-related genes (PTCH1/2 and SUFU) and Hippo pathway-related gene (NF2) as well as KRAS, EGFR, PDGFRA/B, ERBB2 and FGFR3 were detected in both cohorts. CONCLUSION Here, we report the molecular aberrations from the largest cohort of patients with mesothelioma. This analysis identified a proportion of patients with targetable alterations and suggests that molecular profiling can identify new treatment options for patients with mesothelioma.
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Affiliation(s)
- Stefanie Hiltbrunner
- grid.412004.30000 0004 0478 9977Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland ,grid.7400.30000 0004 1937 0650University of Zurich, Zurich, Switzerland
| | - Zoe Fleischmann
- grid.418158.10000 0004 0534 4718Foundation Medicine, Cambridge, MA USA
| | - Ethan S. Sokol
- grid.418158.10000 0004 0534 4718Foundation Medicine, Cambridge, MA USA
| | - Martin Zoche
- grid.412004.30000 0004 0478 9977Pathology Department, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Emanuela Felley-Bosco
- grid.7400.30000 0004 1937 0650University of Zurich, Zurich, Switzerland ,grid.412004.30000 0004 0478 9977Laboratory of Molecular Oncology, Department of Thoracic Surgery, University Hospital Zurich, Zurich, Switzerland
| | - Alessandra Curioni-Fontecedro
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland. .,University of Zurich, Zurich, Switzerland.
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19
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Chapel DB, Hornick JL, Barlow J, Bueno R, Sholl LM. Clinical and molecular validation of BAP1, MTAP, P53, and Merlin immunohistochemistry in diagnosis of pleural mesothelioma. Mod Pathol 2022; 35:1383-1397. [PMID: 35459788 PMCID: PMC9529776 DOI: 10.1038/s41379-022-01081-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/16/2022] [Accepted: 03/28/2022] [Indexed: 12/28/2022]
Abstract
BAP1 and MTAP immunostains play an important role in diagnosis of mesothelioma, but additional markers are needed to increase sensitivity. We analyzed 84 pleural mesotheliomas (51 epithelioid, 27 biphasic, 6 sarcomatoid) by a hybrid-capture next-generation sequencing (NGS) panel including complete coverage of coding and splicing regions for BAP1, CDKN2A/MTAP, NF2, and TP53 and correlated molecular findings with diagnostic immunostains for BAP1, MTAP, Merlin, and p53, respectively. Fifty-seven reactive mesothelial proliferations served as benign comparators. Loss of BAP1, MTAP, and Merlin protein expression were, respectively, 54%, 46%, and 52% sensitive and 100% specific for mesothelioma. Two-marker immunopanels of BAP1 + MTAP, BAP1 + Merlin, and MTAP + Merlin were 79%, 85%, and 71% sensitive for mesothelioma, while a three-marker immunopanel of BAP1 + MTAP + Merlin was 90% sensitive. Diffuse (mutant-pattern) p53 immunostaining was seen in only 6 (7%) tumors but represented the only immunohistochemical abnormality in 2 cases. Null-pattern p53 was not specific for malignancy. An immunopanel of BAP1 + MTAP + Merlin + p53 was 93% sensitive for mesothelioma, and panel NGS detected a pathogenic alteration in BAP1, MTAP, NF2, and/or TP53 in 95%. Together, 83 (99%) of 84 tumors showed a diagnostic alteration by either immunohistochemistry or panel NGS. Adding Merlin to the standard BAP1 + MTAP immunopanel increases sensitivity for mesothelioma without sacrificing specificity. p53 immunohistochemistry and panel NGS with complete coverage of BAP1, CDKN2A/MTAP, TP53, and NF2 may be useful in diagnostically challenging cases.
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Affiliation(s)
- David B Chapel
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA.
- Department of Pathology, University of Michigan - Michigan Medicine, Ann Arbor, MI, 48109, USA.
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Julianne Barlow
- Department of Thoracic Surgery, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Raphael Bueno
- Department of Thoracic Surgery, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Center for Advanced Molecular Diagnostics, Brigham and Women's Hospital, Boston, MA, 02115, USA
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20
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Lam SK, Mutsaers SE. Editorial: Novel agents and combinations for treatment of malignant pleural mesothelioma in pre-clinical models. Front Pharmacol 2022; 13:1015959. [PMID: 36147341 PMCID: PMC9486835 DOI: 10.3389/fphar.2022.1015959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Sze-Kwan Lam
- Division of Respiratory Medicine, Department of Medicine, Queen Mary Hospital, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- *Correspondence: Sze-Kwan Lam,
| | - Steven Eugene Mutsaers
- Institute for Respiratory Health, University of Western Australia, Nedlands, WA, Australia
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21
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Gao Y, Kruithof-de Julio M, Peng RW, Dorn P. Organoids as a Model for Precision Medicine in Malignant Pleural Mesothelioma: Where Are We Today? Cancers (Basel) 2022; 14:cancers14153758. [PMID: 35954422 PMCID: PMC9367391 DOI: 10.3390/cancers14153758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/26/2022] [Accepted: 07/29/2022] [Indexed: 12/10/2022] Open
Abstract
Simple Summary Malignant pleural mesothelioma (MPM) is an extremely lethal cancer, notoriously known for its limited treatment options, lack of targeted therapies, and catastrophic survival rates. MPM tumors are highly heterogeneous and exhibit substantial variance in the genome landscape among individual patients, characterized by widespread loss-of-function mutations of tumor suppressor genes (TSGs) that are difficult to target. Therefore, there is an urgent and unmet need for novel therapeutic targets and strategies for personalized treatment. Patient-derived organoids (PDOs), the next generation tumor models that have significantly influenced the discovery of anticancer drugs and biomarkers of response to therapies in many other cancers, are emerging and promise to play a critical role in understanding the biology of MPM and, importantly, in identifying and developing precision oncology approaches tailored to specific subsets of MPM patients. Abstract MPM is an aggressive tumor originating from pleural mesothelial cells. A characteristic feature of the disease is the dominant prevalence of therapeutically intractable inactivating alterations in TSGs, making MPM one of the most difficult cancers to treat and the epitome of a cancer characterized by a significant lack of therapy options and an extremely poor prognosis (5-year survival rate of only 5% to 10%). Extensive interpatient heterogeneity poses another major challenge for targeted therapy of MPM, warranting stratified therapy for specific subgroups of MPM patients. Accurate preclinical models are critical for the discovery of new therapies and the development of personalized medicine. Organoids, an in vitro ‘organ-like’ 3D structure derived from patient tumor tissue that faithfully mimics the biology and complex architecture of cancer and largely overcomes the limitations of other existing models, are the next-generation tumor model. Although organoids have been successfully produced and used in many cancers, the development of MPM organoids is still in its infancy. Here, we provide an overview of recent advances in cancer organoids, focusing on the progress and challenges in MPM organoid development. We also elaborate the potential of MPM organoids for understanding MPM pathobiology, discovering new therapeutic targets, and developing personalized treatments for MPM patients.
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Affiliation(s)
- Yanyun Gao
- Department of General Thoracic Surgery, Inselspital, Bern University Hospital, University of Bern, 3008 Bern, Switzerland;
- Department of BioMedical Research (DBMR), Oncology-Thoracic Malignancies (OTM), University of Bern, 3008 Bern, Switzerland
| | - Marianna Kruithof-de Julio
- Urology Research Laboratory, Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland;
- Department for BioMedical Research (DBMR), Translation Organoid Research, University of Bern, 3008 Bern, Switzerland
- Department of Urology, Inselspital, Bern University Hospital, 3008 Bern, Switzerland
| | - Ren-Wang Peng
- Department of General Thoracic Surgery, Inselspital, Bern University Hospital, University of Bern, 3008 Bern, Switzerland;
- Department of BioMedical Research (DBMR), Oncology-Thoracic Malignancies (OTM), University of Bern, 3008 Bern, Switzerland
- Correspondence: (R.-W.P.); (P.D.); Tel.: +41-31-684-0462 (R.-W.P.); +41-31-632-3745 (P.D.)
| | - Patrick Dorn
- Department of General Thoracic Surgery, Inselspital, Bern University Hospital, University of Bern, 3008 Bern, Switzerland;
- Department of BioMedical Research (DBMR), Oncology-Thoracic Malignancies (OTM), University of Bern, 3008 Bern, Switzerland
- Correspondence: (R.-W.P.); (P.D.); Tel.: +41-31-684-0462 (R.-W.P.); +41-31-632-3745 (P.D.)
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22
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Towards Personalized Sampling in Clear Cell Renal Cell Carcinomas. Cancers (Basel) 2022; 14:cancers14143381. [PMID: 35884442 PMCID: PMC9322795 DOI: 10.3390/cancers14143381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 12/29/2022] Open
Abstract
Simple Summary Intratumor heterogeneity (ITH) is a constant event in malignant tumors and the cause of most therapeutic failures in modern oncology. Since clear cell renal cell carcinoma (CCRCC) is a paradigm of ITH, an appropriate tumor sampling is mandatory to unveil its histological and genomic complexity. Several strategies have been developed for such a purpose, trading-off cost and benefit. Here, we propose an evolution of the previous multisite tumor sampling (MSTS) strategy based on the last findings in the spatial distribution of metastasizing clones. This new personalized MSTS pays special attention to sample by sectors peripheral zones of the tumor, where ITH is high. Abstract Intratumor heterogeneity (ITH) is a constant evolutionary event in all malignant tumors, and clear cell renal cell carcinoma (CCRCC) is a paradigmatic example. ITH is responsible for most therapeutic failures in the era of precision oncology, so its precise detection remains a must in modern medicine. Unfortunately, classic sampling protocols do not resolve the problem as expected and several strategies have been being implemented in recent years to improve such detection. Basically, multisite tumor sampling (MSTS) and the homogenization of the residual tumor tissue are on display. A next step of the MSTS strategy considering the recently discovered patterns of ITH regionalization is presented here, the so-called personalized MSTS (pMSTS). This modification consists of paying more attention to sample the tumor periphery since it is this area with maximum levels of ITH.
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23
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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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24
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Dai Z, Peng X, Guo Y, Shen X, Ding W, Fu J, Liang Z, Song J. Metabolic pathway-based molecular subtyping of colon cancer reveals clinical immunotherapy potential and prognosis. J Cancer Res Clin Oncol 2022; 149:2393-2416. [PMID: 35731273 DOI: 10.1007/s00432-022-04070-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 05/11/2022] [Indexed: 11/28/2022]
Abstract
PURPOSE Colon cancer presents challenges to clinical diagnosis and management due to its high heterogeneity. For more efficient and convenient diagnosis and treatment of colon cancer, we are committed to characterizing the molecular features of colon cancer by pioneering a classification system based on metabolic pathways. METHODS Based on the 113 metabolic pathways and genes collected in the previous stage, we scored and filtered the metabolic pathways of each sample in the training set by ssGSEA, and obtained 16 metabolic pathways related to colon cancer recurrence. In consistent clustering of training set samples with recurrence-related metabolic pathway scores, we identified two robust molecular subtypes of colon cancer (MC1 and MC2). Furthermore, we performed multi-angle analysis on the survival differences of subtypes, metabolic characteristics, clinical characteristics, functional enrichment, immune infiltration, differences with other subtypes, stemness indices, TIDE prediction, and drug sensitivity, and finally constructed colon cancer prognostic model. RESULTS The results showed that the MC1 subtype had a poor prognosis based on higher immune activity and immune checkpoint gene expression. The MC2 subtype is associated with high metabolic activity and low expression of immune checkpoint genes and a better prognosis. The MC2 subtype was more responsive to PD-L1 immunotherapy than the MC1 subclass. However, we did not observe significant differences in tumor mutational burden between the two. CONCLUSION Two molecular subtypes of colon cancer based on metabolic pathways have distinct immune signatures. Constructing prognostic models based on subtype differential genes provides valuable reference for personalized therapy targeting unique tumor metabolic signatures.
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Affiliation(s)
- Zhujiang Dai
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China.,Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Xiang Peng
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China.,Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Yuegui Guo
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China.,Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Xia Shen
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China.,Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Wenjun Ding
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China.,Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Jihong Fu
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China.,Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China
| | - Zhonglin Liang
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China. .,Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China.
| | - Jinglue Song
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China. .,Shanghai Colorectal Cancer Research Center, Shanghai, 200092, China.
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25
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Martens M, Kreidl F, Ehrhart F, Jean D, Mei M, Mortensen HM, Nash A, Nymark P, Evelo CT, Cerciello F. A Community-Driven, Openly Accessible Molecular Pathway Integrating Knowledge on Malignant Pleural Mesothelioma. Front Oncol 2022; 12:849640. [PMID: 35558518 PMCID: PMC9088009 DOI: 10.3389/fonc.2022.849640] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/29/2022] [Indexed: 12/28/2022] Open
Abstract
Malignant pleural mesothelioma (MPM) is a highly aggressive malignancy mainly triggered by exposure to asbestos and characterized by complex biology. A significant body of knowledge has been generated over the decades by the research community which has improved our understanding of the disease toward prevention, diagnostic opportunities and new treatments. Omics technologies are opening for additional levels of information and hypotheses. Given the growing complexity and technological spread of biological knowledge in MPM, there is an increasing need for an integrating tool that may allow scientists to access the information and analyze data in a simple and interactive way. We envisioned that a platform to capture this widespread and fast-growing body of knowledge in a machine-readable and simple visual format together with tools for automated large-scale data analysis could be an important support for the work of the general scientist in MPM and for the community to share, critically discuss, distribute and eventually advance scientific results. Toward this goal, with the support of experts in the field and informed by existing literature, we have developed the first version of a molecular pathway model of MPM in the biological pathway database WikiPathways. This provides a visual and interactive overview of interactions and connections between the most central genes, proteins and molecular pathways known to be involved or altered in MPM. Currently, 455 unique genes and 247 interactions are included, derived after stringent manual curation of an initial 39 literature references. The pathway model provides a directly employable research tool with links to common databases and repositories for the exploration and the analysis of omics data. The resource is publicly available in the WikiPathways database (Wikipathways : WP5087) and continues to be under development and curation by the community, enabling the scientists in MPM to actively participate in the prioritization of shared biological knowledge.
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Affiliation(s)
- Marvin Martens
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
| | - Franziska Kreidl
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
| | - Friederike Ehrhart
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands.,Department of Bioinformatics - BiGCaT, MHeNs, Maastricht University, Maastricht, Netherlands
| | - Didier Jean
- Centre de Recherche des Cordeliers, Inserm, Sorbonne Université, Université de Paris, Functional Genomics of Solid Tumors, Paris, France
| | - Merlin Mei
- Oak Ridge Associated Universities, Research Triangle Park, Durham, NC, United States.,Center for Public Health and Environmental Assessment, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, United States
| | - Holly M Mortensen
- Center for Public Health and Environmental Assessment, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, United States
| | - Alistair Nash
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, WA, Australia
| | - Penny Nymark
- Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden
| | - Chris T Evelo
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands.,Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands
| | - Ferdinando Cerciello
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
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26
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Cantini L, Laniado I, Murthy V, Sterman D, Aerts JGJV. Immunotherapy for mesothelioma: Moving beyond single immune check point inhibition. Lung Cancer 2022; 165:91-101. [PMID: 35114509 DOI: 10.1016/j.lungcan.2022.01.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 01/20/2022] [Indexed: 12/29/2022]
Abstract
Malignant pleural mesothelioma (MPM) is an aggressive neoplasm with low survival rates. Platinum-based chemotherapy has represented the cornerstone of treatment for over a decade, prompting the investigation of new therapeutic strategies both in the early stage of the disease and in the advanced setting. The advent of immune check-point inhibitors (ICIs) has recently revamped the enthusiasm for using immunotherapy also in MPM. However, results from first clinical trials using single immune check-point inhibition have been conflicting, and this may be mainly attributed to the lack of specific biomarkers as well as to intra- and inter- patient heterogeneity. The phase III Checkmate743 firstly demonstrated the superiority of an ICI combination (nivolumab plus ipilimumab) over chemotherapy in the first-line treatment of unresectable MPM, leading to FDA approval of this regimen and showing that moving beyond single immune check point inhibition might be a successful strategy to overcome resistance in the majority of MPM patients. In this review, we describe the emerging immunotherapy strategies for the treatment of MPM. We also discuss how refining the approach in pre-clinical studies towards a more holistic perspective (which takes into account not only genetic but also pathophysiological vulnerabilities) and strengthening multi-institutional collaboration in clinical trials is finally helping the clinical development of immunotherapy in MPM.
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Affiliation(s)
- Luca Cantini
- Department of Pulmonary Medicine, Erasmus MC Cancer Institute, Rotterdam, the Netherlands; Clinical Oncology, Università Politecnica Delle Marche, AOU Ospedali Riuniti Ancona, Italy
| | - Isaac Laniado
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University (NYU), School of Medicine/NYU Langone Medical Center, New York, NY, United States
| | - Vivek Murthy
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University (NYU), School of Medicine/NYU Langone Medical Center, New York, NY, United States
| | - Daniel Sterman
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University (NYU), School of Medicine/NYU Langone Medical Center, New York, NY, United States
| | - Joachim G J V Aerts
- Department of Pulmonary Medicine, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
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27
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Current Management and Future Perspective in Pleural Mesothelioma. Cancers (Basel) 2022; 14:cancers14041044. [PMID: 35205798 PMCID: PMC8869935 DOI: 10.3390/cancers14041044] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/11/2022] [Accepted: 02/12/2022] [Indexed: 11/16/2022] Open
Abstract
Pleural mesothelioma is an aggressive malignancy arising from pleural mesothelial cell lining, predominantly associated with prior exposure to asbestos. The ban on asbestos use has led to its lower incidence in many countries, but globally the disease burden is expected to rise. Therefore, well-planned research is needed to develop more effective, tolerable and affordable drugs. The development of novel treatment has been too slow, with only two regimens of systemic therapy with robust phase 3 data approved formally to date. The treatment scenario for resectable disease remains controversial. However, recent developments in the understanding of disease and clinical trials have been encouraging, and may add better treatment options in the coming years. In this review, we discuss the current treatment options for pleural mesothelioma and shed light on some recent studies and ongoing trials.
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28
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Sauter JL, Dacic S, Galateau-Salle F, Attanoos RL, Butnor KJ, Churg A, Husain AN, Kadota K, Khoor A, Nicholson AG, Roggli V, Schmitt F, Tsao MS, Travis WD. The 2021 World Health Organization Classification of Tumors of the Pleura: Advances since the 2015 Classification. J Thorac Oncol 2022; 17:608-622. [PMID: 35026477 DOI: 10.1016/j.jtho.2021.12.014] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/14/2021] [Accepted: 12/31/2021] [Indexed: 12/01/2022]
Abstract
Significant changes in the 2021 World Health Organization (WHO) Classification of Tumors of the Pleura and Pericardium since the 2015 WHO Classification include: 1) Pleural and pericardial tumors have been combined in one chapter whereas in the 2015 WHO, pericardial tumors were classified with cardiac tumors; 2) Well-differentiated papillary mesothelioma (WDPM) has been renamed well-differentiated papillary mesothelial tumor (WDPMT) given growing evidence that these tumors exhibit relatively indolent behavior; 3) Localized and diffuse mesothelioma no longer include the term "malignant" as a prefix; 4) Mesothelioma in situ (MIS) has been added to the 2021 classification since these lesions can now be recognized by loss of BAP1 and/or MTAP by immunohistochemistry and/or CDKN2A homozygous deletion by FISH; 5) The three main histologic subtypes (i.e. epithelioid, biphasic and sarcomatoid) remain the same but architectural patterns, cytologic and stromal features are more formally incorporated into the 2021 classification based on their prognostic significance; 6) Nuclear grading for epithelioid diffuse mesothelioma is introduced and it is recommended to record this and other histologically prognostic features in pathology reports; 7) BAP1, EZH2 and MTAP immunohistochemistry have been shown to be useful in separating benign mesothelial proliferations from mesothelioma; 8) Biphasic mesothelioma can be diagnosed in small biopsies showing both epithelioid and sarcomatoid components even if the amount of one component is less than 10%; and 9) The most frequently altered genes in diffuse pleural mesothelioma include BAP 1, CDKN2A, NF2, TP53, SETD2 and SETB1.
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Affiliation(s)
- Jennifer L Sauter
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States.
| | - Sanja Dacic
- Department of Pathology University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States
| | - Francoise Galateau-Salle
- MESOPATH Centre Leon Berard, Lyon, France, Unit of Cancer Research Center INSERM U1052-CNRS5286R, Lyon France
| | - Richard L Attanoos
- Department of Cellular Pathology, University Hospital of Wales and School of Medicine, Cardiff University, Wales, United Kingdom
| | - Kelly J Butnor
- Department of Pathology & Laboratory Medicine, The University of Vermont Medical Center, Burlington, Vermont, United States
| | - Andrew Churg
- Dept of Pathology, Vancouver General Hospital and University of British Columbia, Vancouver, British Columbia, Canada
| | - Aliya N Husain
- Department of Pathology, University of Chicago, Chicago, Illinois, United States
| | - Kyuichi Kadota
- Department of Pathology, Faculty of Medicine, Shimane University
| | - Andras Khoor
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Jacksonville, Florida, United States
| | - Andrew G Nicholson
- Royal Brompton and Harefield Hospitals, and National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Victor Roggli
- Department of Pathology, Duke University Medical Center, Durham, North Carolina, United States
| | - Fernando Schmitt
- RISE@Cintesis, Medical Faculty of Porto University, Porto, Portugal; Unit of Molecular Pathology of IPATIMUP, Porto, Portugal
| | - Ming-Sound Tsao
- Department of Pathology, University Health Network, Princess Margaret Cancer Centre, Toronto, Canada
| | - William D Travis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States
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