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Casolino R, Beer PA, Chakravarty D, Davis MB, Malapelle U, Mazzarella L, Normanno N, Pauli C, Subbiah V, Turnbull C, Westphalen CB, Biankin AV. Interpreting and integrating genomic tests results in clinical cancer care: Overview and practical guidance. CA Cancer J Clin 2024; 74:264-285. [PMID: 38174605 DOI: 10.3322/caac.21825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/07/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024] Open
Abstract
The last decade has seen rapid progress in the use of genomic tests, including gene panels, whole-exome sequencing, and whole-genome sequencing, in research and clinical cancer care. These advances have created expansive opportunities to characterize the molecular attributes of cancer, revealing a subset of cancer-associated aberrations called driver mutations. The identification of these driver mutations can unearth vulnerabilities of cancer cells to targeted therapeutics, which has led to the development and approval of novel diagnostics and personalized interventions in various malignancies. The applications of this modern approach, often referred to as precision oncology or precision cancer medicine, are already becoming a staple in cancer care and will expand exponentially over the coming years. Although genomic tests can lead to better outcomes by informing cancer risk, prognosis, and therapeutic selection, they remain underutilized in routine cancer care. A contributing factor is a lack of understanding of their clinical utility and the difficulty of results interpretation by the broad oncology community. Practical guidelines on how to interpret and integrate genomic information in the clinical setting, addressed to clinicians without expertise in cancer genomics, are currently limited. Building upon the genomic foundations of cancer and the concept of precision oncology, the authors have developed practical guidance to aid the interpretation of genomic test results that help inform clinical decision making for patients with cancer. They also discuss the challenges that prevent the wider implementation of precision oncology.
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Affiliation(s)
- Raffaella Casolino
- Wolfson Wohl Cancer Research Center, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Philip A Beer
- Wolfson Wohl Cancer Research Center, School of Cancer Sciences, University of Glasgow, Glasgow, UK
- Hull York Medical School, York, UK
| | | | - Melissa B Davis
- Department of Surgery, Weill Cornell Medicine, New York City, New York, USA
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Luca Mazzarella
- Laboratory of Translational Oncology and Division of Gastrointestinal Medical Oncology and Neuroendocrine Tumors IEO European Institute of Oncology, IRCCS, Milan, Italy
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori, IRCCS "Fondazione G. Pascale", Naples, Italy
| | - Chantal Pauli
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Vivek Subbiah
- Sarah Cannon Research Institute, Nashville, Tennessee, USA
| | - Clare Turnbull
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- National Cancer Registration and Analysis Service, National Health Service (NHS) England, London, UK
- Cancer Genetics Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - C Benedikt Westphalen
- Department of Medicine III, Ludwig Maximilians University (LMU) Hospital Munich, Munich, Germany
- Comprehensive Cancer Center, LMU Hospital Munich, Munich, Germany
- German Cancer Consortium, LMU Hospital Munich, Munich, Germany
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Center, School of Cancer Sciences, University of Glasgow, Glasgow, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK
- South Western Sydney Clinical School, Liverpool, New South Wales, Australia
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Colomer R, Miranda J, Romero-Laorden N, Hornedo J, González-Cortijo L, Mouron S, Bueno MJ, Mondéjar R, Quintela-Fandino M. Usefulness and real-world outcomes of next generation sequencing testing in patients with cancer: an observational study on the impact of selection based on clinical judgement. EClinicalMedicine 2023; 60:102029. [PMID: 37304496 PMCID: PMC10248077 DOI: 10.1016/j.eclinm.2023.102029] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 06/13/2023] Open
Abstract
Background Next Generation Sequencing (NGS) panels are increasingly used in advanced patients with cancer to guide therapy. There is, however, controversy about when should these panels be used, and about their impact on the clinical course. Methods In an observational study of 139 patients with cancer having an NGS test [from January 1st, 2017 to December 30th, 2020, in two hospitals (Hospital Universitario de La Princesa and Hospital Universitario Quironsalud Madrid) from Spain], we evaluated whether the clinical course (progression-free survival, PFS) was influenced by drug-based criteria [druggable alterations, receiving a recommended drug, having a favourable ESCAT category (ESMO Scale for Clinical Actionability of molecular Targets)] or clinical judgement criteria. Findings In 111 of 139 cases that were successfully profiled, PFS was not significantly influenced by either having druggable alterations [median PFS for patients with druggable alterations was 170 (95% C.I.: 139-200) days compared to 299 (95% C.I.: 114-483) for those without; p = 0.37], receiving a proposed matching agent [median PFS for patients receiving a genomics-informed drug was 195 days (95% C.I.: 144-245), compared with 156 days for those that did not (95% C.I.: 85-226); p = 0.50], or having favourable ESCAT categories [median PFS for patients with ESCAT I-III was 183 days (95% C.I.: 104-261), compared with 180 (95% C.I.:144-215) for patients with ESCAT IV-X; p = 0.87]. In contrast, NGS testing performed within clinical judgement showed a significantly improved PFS [median PFS for patients that were profiled under the recommended scenarios was 319 days (95% C.I.: 0-658), compared to 123 days (95% C.I.: 89-156) in the non-recommended categories; p = 0.0020]. Interpretation According to our data, real-world outcomes after NGS testing provide evidence of the benefit of clinical judgement in patients with either advanced cancers that routinely need multiple genetic markers, patients with advanced rare cancers, or patients that are screened for molecular clinical trials. By contrast, NGS does not seem to be valuable when performed in cases with a poor PS, rapidly progressing cancer, short expected lifetime, or cases with no standard therapeutic options. Funding RC, NR-L and MQF are recipients of the PMP22/00032 grant, funded by the ISCIII and co-funded by the European Regional Development Fund (ERDF). The study also received funds from the CRIS Contra el Cancer Foundation.
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Affiliation(s)
- Ramon Colomer
- Department of Medicine, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Chair of Personalised Precision Medicine, Universidad Autonoma de Madrid (UAM – Fundación Instituto Roche), Madrid, Spain
- Medical Oncology Division, Hospital Universitario La Princesa, Madrid, Spain
- Breast Cancer Clinical Research Unit, Centro Nacional de Investigaciones Oncologicas (CNIO), Madrid, Spain
| | - Jesús Miranda
- University Hospital Quironsalud Madrid, Madrid, Spain
| | | | | | | | - Silvana Mouron
- Breast Cancer Clinical Research Unit, Centro Nacional de Investigaciones Oncologicas (CNIO), Madrid, Spain
| | - Maria J. Bueno
- Breast Cancer Clinical Research Unit, Centro Nacional de Investigaciones Oncologicas (CNIO), Madrid, Spain
| | - Rebeca Mondéjar
- Department of Medicine, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Chair of Personalised Precision Medicine, Universidad Autonoma de Madrid (UAM – Fundación Instituto Roche), Madrid, Spain
- Medical Oncology Division, Hospital Universitario La Princesa, Madrid, Spain
| | - Miguel Quintela-Fandino
- Department of Medicine, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Chair of Personalised Precision Medicine, Universidad Autonoma de Madrid (UAM – Fundación Instituto Roche), Madrid, Spain
- Breast Cancer Clinical Research Unit, Centro Nacional de Investigaciones Oncologicas (CNIO), Madrid, Spain
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Barresi V, Lawlor RT, Mafficini A, Gilioli E, Scarpa A. Metastatic grade 1 meningioma lacking genetic abnormalities commonly associated with bad prognosis. Pathol Res Pract 2022; 238:154089. [PMID: 36067609 DOI: 10.1016/j.prp.2022.154089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 11/29/2022]
Abstract
AIMS Meningioma metastasis is a rare event, observed primarily in World Health Organization (WHO) grade 3 tumors, although it has also been reported in WHO grade 1 meningiomas. This study aims at clarifying whether the metastasis of a WHO grade 1 meningioma was associated with genetic abnormalities commonly found in cases that are more aggressive. METHODS Using next generation sequencing of a panel of 174 genes, we analyzed the genetic alterations of a WHO grade 1 skull-base meningioma and its paired lung metastases detected 22 years after craniotomy. RESULTS Similar to the primary tumor, lung metastases did not show mitoses or histological signs of malignancy. Consistent with their origin from intracranial tumor, they harbored the same genetic alterations as this one. These consisted of the pathogenic mutation p. E17K of AKT1 and variants of unknown significance in NOTCH1 (p. P2133T), SERPINB8 (p. H359Y) and SMARCA4 (p. P277S). CONCLUSIONS The E17K AKT1 mutation is frequently found in skull base meningiomas and without prognostic significance. Our findings suggest that metastasis of grade 1 meningiomas is independent of genetic alterations (CDKN2A homozygous deletion, pTERT mutation, or 1p, 9p, 14q and 18q loss of heterozygosity) commonly found in more aggressive tumors.
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Affiliation(s)
- Valeria Barresi
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy.
| | - Rita T Lawlor
- ARC-NET Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Andrea Mafficini
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy; ARC-NET Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Eliana Gilioli
- Department of Pathology and Diagnostics, Unit of Anatomic Pathology, Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy; ARC-NET Research Centre, University and Hospital Trust of Verona, Verona, Italy
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Fusion Gene Detection and Quantification by Asymmetric Capture Sequencing (aCAP-Seq). J Mol Diagn 2022; 24:1113-1127. [PMID: 35963522 DOI: 10.1016/j.jmoldx.2022.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/14/2022] [Accepted: 07/21/2022] [Indexed: 11/23/2022] Open
Abstract
Several fusion genes such as BCR::ABL1, FIP1L1::PDGFRA, and PML::RARA are now efficiently targeted by specific therapies in patients with leukemia. Although these therapies have significantly improved patient outcomes, leukemia relapse and progression remain clinical concerns. Most myeloid next-generation sequencing (NGS) panels do not detect or quantify these fusions. It therefore remains difficult to decipher the clonal architecture and dynamics of myeloid malignancy patients, although these factors can affect clinical decisions and provide pathophysiologic insights. An asymmetric capture sequencing strategy (aCAP-Seq) and a bioinformatics algorithm (HmnFusion) were developed to detect and quantify MBCR::ABL1, μBCR::ABL1, PML::RARA, and FIP1L1::PDGFRA fusion genes in an NGS panel targeting 41 genes. One-hundred nineteen DNA samples derived from 106 patients were analyzed by conventional methods at diagnosis or on follow-up and were sequenced with this NGS myeloid panel. The specificity and sensitivity of fusion detection by aCAP-Seq were 100% and 98.1%, respectively, with a limit of detection estimated at 0.1%. Fusion quantifications were linear from 0.1% to 50%. Breakpoint locations and sequences identified by NGS were concordant with results obtained by Sanger sequencing. Finally, this new sensitive and cost-efficient NGS method allowed integrated analysis of resistant chronic myeloid leukemia patients and thus will be of interest to elucidate the mutational landscape and clonal architecture of myeloid malignancies driven by these fusion genes at diagnosis, relapse, or progression.
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Role of Precision Oncology in Type II Endometrial and Prostate Cancers in the African Population: Global Cancer Genomics Disparities. Int J Mol Sci 2022; 23:ijms23020628. [PMID: 35054814 PMCID: PMC8776204 DOI: 10.3390/ijms23020628] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 02/05/2023] Open
Abstract
Precision oncology can be defined as molecular profiling of tumors to identify targetable alterations. Emerging research reports the high mortality rates associated with type II endometrial cancer in black women and with prostate cancer in men of African ancestry. The lack of adequate genetic reference information from the African genome is one of the major obstacles in exploring the benefits of precision oncology in the African context. Whilst external factors such as the geography, environment, health-care access and socio-economic status may contribute greatly towards the disparities observed in type II endometrial and prostate cancers in black populations compared to Caucasians, the contribution of African ancestry to the contribution of genetics to the etiology of these cancers cannot be ignored. Non-coding RNAs (ncRNAs) continue to emerge as important regulators of gene expression and the key molecular pathways involved in tumorigenesis. Particular attention is focused on activated/repressed genes and associated pathways, while the redundant pathways (pathways that have the same outcome or activate the same downstream effectors) are often ignored. However, comprehensive evidence to understand the relationship between type II endometrial cancer, prostate cancer and African ancestry remains poorly understood. The sub-Saharan African (SSA) region has both the highest incidence and mortality of both type II endometrial and prostate cancers. Understanding how the entire transcriptomic landscape of these two reproductive cancers is regulated by ncRNAs in an African cohort may help elucidate the relationship between race and pathological disparities of these two diseases. This review focuses on global disparities in medicine, PCa and ECa. The role of precision oncology in PCa and ECa in the African population will also be discussed.
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Integrative characterization of intraductal tubulopapillary neoplasm (ITPN) of the pancreas and associated invasive adenocarcinoma. Mod Pathol 2022; 35:1929-1943. [PMID: 36056133 PMCID: PMC9708572 DOI: 10.1038/s41379-022-01143-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/18/2022] [Accepted: 07/18/2022] [Indexed: 12/24/2022]
Abstract
Pancreatic intraductal tubulopapillary neoplasm (ITPN) is a recently recognized intraductal neoplasm. This study aimed to clarify the clinicopathologic and molecular features of this entity, based on a multi-institutional cohort of 16 pancreatic ITPNs and associated adenocarcinomas. The genomic profiles were analyzed using histology-driven multi-regional sequencing to provide insight on tumor heterogeneity and evolution. Furthermore, an exploratory transcriptomic characterization was performed on eight invasive adenocarcinomas. The clinicopathologic parameters and molecular alterations were further analyzed based on survival indices. The main findings were as follows: 1) the concomitant adenocarcinomas, present in 75% of cases, were always molecularly associated with the intraductal components. These data definitively establish ITPN as origin of invasive pancreatic adenocarcinoma; 2) alterations restricted to infiltrative components included mutations in chromatin remodeling genes ARID2, ASXL1, and PBRM1, and ERBB2-P3H4 fusion; 3) pancreatic ITPN can arise in the context of genetic syndromes, such as BRCA-germline and Peutz-Jeghers syndrome; 4) mutational profile: mutations in the classical PDAC drivers are present, but less frequently, in pancreatic ITPN; 5) novel genomic alterations were observed, including amplification of the Cyclin and NOTCH family genes and ERBB2, fusions involving RET and ERBB2, and RB1 disruptive variation; 6) chromosomal alterations: the most common was 1q gain (75% of cases); 7) by transcriptome analysis, ITPN-associated adenocarcinomas clustered into three subtypes that correlate with the activation of signaling mechanism pathways and tumor microenvironment, displaying squamous features in their majority; and 8) TP53 mutational status is a marker for adverse prognosis. ITPNs are precursor lesions of pancreatic cancer with a high malignant transformation risk. A personalized approach for patients with ITPN should recognize that such neoplasms could arise in the context of genetic syndromes. BRCA alterations, ERBB2 and RET fusions, and ERBB2 amplification are novel targets in precision oncology. The TP53 mutation status can be used as a prognostic biomarker.
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Barresi V, Simbolo M, Mafficini A, Martini M, Calicchia M, Piredda ML, Ciaparrone C, Bonizzato G, Ammendola S, Caffo M, Pinna G, Sala F, Lawlor RT, Ghimenton C, Scarpa A. IDH-wild type glioblastomas featuring at least 30% giant cells are characterized by frequent RB1 and NF1 alterations and hypermutation. Acta Neuropathol Commun 2021; 9:200. [PMID: 34952640 PMCID: PMC8709962 DOI: 10.1186/s40478-021-01304-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/08/2021] [Indexed: 01/07/2023] Open
Abstract
Giant cell glioblastoma (GC-GBM) is a rare variant of IDH-wt GBM histologically characterized by the presence of numerous multinucleated giant cells and molecularly considered a hybrid between IDH-wt and IDH-mutant GBM. The lack of an objective definition, specifying the percentage of giant cells required for this diagnosis, may account for the absence of a definite molecular profile of this variant. This study aimed to clarify the molecular landscape of GC-GBM, exploring the mutations and copy number variations of 458 cancer-related genes, tumor mutational burden (TMB), and microsatellite instability (MSI) in 39 GBMs dichotomized into having 30-49% (15 cases) or ≥ 50% (24 cases) GCs. The type and prevalence of the genetic alterations in this series was not associated with the GCs content (< 50% or ≥ 50%). Most cases (82% and 51.2%) had impairment in TP53/MDM2 and PTEN/PI3K pathways, but a high proportion also featured TERT promoter mutations (61.5%) and RB1 (25.6%) or NF1 (25.6%) alterations. EGFR amplification was detected in 18% cases in association with a shorter overall survival (P = 0.004). Sixteen (41%) cases had a TMB > 10 mut/Mb, including two (5%) that harbored MSI and one with a POLE mutation. The frequency of RB1 and NF1 alterations and TMB counts were significantly higher compared to 567 IDH wild type (P < 0.0001; P = 0.0003; P < 0.0001) and 26 IDH-mutant (P < 0.0001; P = 0.0227; P < 0.0001) GBMs in the TCGA PanCancer Atlas cohort. These findings demonstrate that the molecular landscape of GBMs with at least 30% giant cells is dominated by the impairment of TP53/MDM2 and PTEN/PI3K pathways, and additionally characterized by frequent RB1 alterations and hypermutation and by EGFR amplification in more aggressive cases. The high frequency of hypermutated cases suggests that GC-GBMs might be candidates for immune check-point inhibitors clinical trials.
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Affiliation(s)
- Valeria Barresi
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy
| | - Michele Simbolo
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy
| | - Andrea Mafficini
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy
| | - Maurizio Martini
- Unit of Anatomic Pathology, Catholic University of Sacred Hearth, Rome, Italy
| | - Martina Calicchia
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy
| | - Maria Liliana Piredda
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy
| | - Chiara Ciaparrone
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy
| | - Giada Bonizzato
- ARC-NET Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Serena Ammendola
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy
| | - Maria Caffo
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Section of Neurosurgery, University of Messina, Messina, Italy
| | - Giampietro Pinna
- Department of Neurosciences, Unit of Neurosurgery, Hospital Trust of Verona, Verona, Italy
| | - Francesco Sala
- Department of Neurosciences, Biomedicines and Movement Sciences, Institute of Neurosurgery, University of Verona, Verona, Italy
| | - Rita Teresa Lawlor
- ARC-NET Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Claudio Ghimenton
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy
- ARC-NET Research Centre, University and Hospital Trust of Verona, Verona, Italy
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Lawlor RT, Mafficini A, Sciammarella C, Cantù C, Rusev BC, Piredda ML, Antonello D, Grimaldi S, Bonizzato G, Sperandio N, Marchegiani G, Malleo G, Pea A, Salvia R, Mombello A, Mazzoleni G, Nottegar A, Hanspeter E, Riva G, Tomezzoli A, Bencivenga M, de Manzoni G, Pedron S, Paolino G, Mattiolo P, Brosens LA, Silvestris N, Fassan M, Cooke SL, Beer PA, Milella M, Adsay VN, Cheng L, Scarpa A, Luchini C. Genomic characterization of hepatoid tumors: context matters. Hum Pathol 2021; 118:30-41. [PMID: 34562502 DOI: 10.1016/j.humpath.2021.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 09/10/2021] [Indexed: 12/30/2022]
Abstract
Hepatoid tumors (HT) are rare neoplasms morphologically resembling hepatocellular carcinoma, which arise in several organs other than the liver. A comprehensive molecular profile of this group of neoplasms is still lacking. Genomic characterization of 19 HTs from different organs (three colon HTs, four esophagogastric HTs, four biliary HTs, six genitourinary HTs, two lung HTs) was performed using a multigene next-generation sequencing panel. NGS unraveled a composite molecular profile of HT. Their genetic alterations were clearly clustered by tumor site: (i) colorectal HT displayed microsatellite instability, high tumor mutational burden, mutations in ARID1A/B genes and NCOA4-RET gene fusion (2/3 cases); (ii) gastric HT had TP53 mutations (2/4); (iii) biliary HT displayed loss of CDKN2A (3/4) and loss of chromosome 18 (2/4); (iv) genital HT showed gain of chromosome 12 (3/6); (v) lung HT had STK11 somatic mutations (2/2). The only commonly mutated gene occurring in HT of different sites was TP53 (8/19 cases: colon 2, esophagogastric 2, biliary 2, genital 1, lungs 1). This study shows that most genetic alterations of HT were clustered by site, indicating that context matters. The novel potential targets for HT precision oncology are also clustered based on the anatomic origin. This study shed light on the biology of these rare cancers and may have important consequences for treatment decisions and clinical trial selection for HT patients.
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Affiliation(s)
- Rita T Lawlor
- ARC-Net Research Center for Applied Research on Cancer, University of Verona, 37134 Verona, Italy
| | - Andrea Mafficini
- ARC-Net Research Center for Applied Research on Cancer, University of Verona, 37134 Verona, Italy; Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Concetta Sciammarella
- ARC-Net Research Center for Applied Research on Cancer, University of Verona, 37134 Verona, Italy
| | - Cinzia Cantù
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Borislav C Rusev
- ARC-Net Research Center for Applied Research on Cancer, University of Verona, 37134 Verona, Italy
| | - Maria L Piredda
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Davide Antonello
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Sonia Grimaldi
- ARC-Net Research Center for Applied Research on Cancer, University of Verona, 37134 Verona, Italy
| | - Giada Bonizzato
- ARC-Net Research Center for Applied Research on Cancer, University of Verona, 37134 Verona, Italy
| | - Nicola Sperandio
- ARC-Net Research Center for Applied Research on Cancer, University of Verona, 37134 Verona, Italy
| | - Giovanni Marchegiani
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Giuseppe Malleo
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Antonio Pea
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Roberto Salvia
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Aldo Mombello
- ARC-Net Research Center for Applied Research on Cancer, University of Verona, 37134 Verona, Italy
| | - Guido Mazzoleni
- Department of Pathology, Central Hospital of Bolzano, 39100 Bolzano, Italy
| | - Alessia Nottegar
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Esther Hanspeter
- Department of Pathology, Central Hospital of Bolzano, 39100 Bolzano, Italy
| | - Giulio Riva
- Department of Diagnostics, Pathology Unit, San Bortolo Hospital, 36100 Vicenza, Italy
| | - Anna Tomezzoli
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Maria Bencivenga
- Unit of General and Upper GI Surgery, University of Verona, 37134 Verona, Italy
| | - Giovanni de Manzoni
- Unit of General and Upper GI Surgery, University of Verona, 37134 Verona, Italy
| | - Serena Pedron
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Gaetano Paolino
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Paola Mattiolo
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Lodewijk A Brosens
- Department of Pathology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands; Department of Pathology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Nicola Silvestris
- IRCCS Istituto Tumori "Giovanni Paolo II" of Bari, and Department of Biomedical Sciences and Human Oncology, University of Bari "Aldo Moro", 70121 Bari, Italy
| | - Matteo Fassan
- Department of Medicine (DIMED), University of Padua, 35121 Padua, Italy
| | - Susanna L Cooke
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Bearsden, G61 1QH Glasgow, UK
| | - Philip A Beer
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Bearsden, G61 1QH Glasgow, UK; Sanger Institute, Wellcome Trust Genome Campus, CB10 1SA Cambridge, UK
| | - Michele Milella
- Department of Medicine, Section of Oncology, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Volkan N Adsay
- Department of Pathology, Koç University Hospital and Koç University Research Center for Translational Medicine (KUTTAM), 34010 Istanbul, Turkey
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, 46202 Indianapolis, IN, USA
| | - Aldo Scarpa
- ARC-Net Research Center for Applied Research on Cancer, University of Verona, 37134 Verona, Italy; Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy.
| | - Claudio Luchini
- ARC-Net Research Center for Applied Research on Cancer, University of Verona, 37134 Verona, Italy; Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy.
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Casolino R, Paiella S, Azzolina D, Beer PA, Corbo V, Lorenzoni G, Gregori D, Golan T, Braconi C, Froeling FEM, Milella M, Scarpa A, Pea A, Malleo G, Salvia R, Bassi C, Chang DK, Biankin AV. Homologous Recombination Deficiency in Pancreatic Cancer: A Systematic Review and Prevalence Meta-Analysis. J Clin Oncol 2021; 39:2617-2631. [PMID: 34197182 PMCID: PMC8331063 DOI: 10.1200/jco.20.03238] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 04/13/2021] [Accepted: 05/26/2021] [Indexed: 12/20/2022] Open
Abstract
PURPOSE To analyze the prevalence of homologous recombination deficiency (HRD) in patients with pancreatic ductal adenocarcinoma (PDAC). MATERIALS AND METHODS We conducted a systematic review and meta-analysis of the prevalence of HRD in PDAC from PubMed, Scopus, and Cochrane Library databases, and online cancer genomic data sets. The main outcome was pooled prevalence of somatic and germline mutations in the better characterized HRD genes (BRCA1, BRCA2, PALB2, ATM, ATR, CHEK2, RAD51, and the FANC genes). The secondary outcomes were prevalence of germline mutations overall, and in sporadic and familial cases; prevalence of germline BRCA1/2 mutations in Ashkenazi Jewish (AJ); and prevalence of HRD based on other definitions (ie, alterations in other genes, genomic scars, and mutational signatures). Random-effects modeling with the Freeman-Tukey transformation was used for the analyses. PROSPERO registration number: (CRD42020190813). RESULTS Sixty studies with 21,842 participants were included in the systematic review and 57 in the meta-analysis. Prevalence of germline and somatic mutations was BRCA1: 0.9%, BRCA2: 3.5%, PALB2: 0.2%, ATM: 2.2%, CHEK2: 0.3%, FANC: 0.5%, RAD51: 0.0%, and ATR: 0.1%. Prevalence of germline mutations was BRCA1: 0.9% (2.4% in AJ), BRCA2: 3.8% (8.2% in AJ), PALB2: 0.2%, ATM: 2%, CHEK2: 0.3%, and FANC: 0.4%. No significant differences between sporadic and familial cases were identified. HRD prevalence ranged between 14.5%-16.5% through targeted next-generation sequencing and 24%-44% through whole-genome or whole-exome sequencing allowing complementary genomic analysis, including genomic scars and other signatures (surrogate markers of HRD). CONCLUSION Surrogate readouts of HRD identify a greater proportion of patients with HRD than analyses limited to gene-level approaches. There is a clear need to harmonize HRD definitions and to validate the optimal biomarker for treatment selection. Universal HRD screening including integrated somatic and germline analysis should be offered to all patients with PDAC.
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Affiliation(s)
- Raffaella Casolino
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
- Department of Medicine, University and Hospital Trust of Verona, Verona, Italy
| | - Salvatore Paiella
- General and Pancreatic Surgery Unit, Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Danila Azzolina
- Unit of Biostatistics, Epidemiology and Public Health, Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova, Padova, Italy
- Research Support Unit, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Philip A. Beer
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
- Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Vincenzo Corbo
- Section of Pathology, Department of Diagnostics and Public Health, University and Hospital Trust of Verona, Verona, Italy
- ARC-Net Research Centre, University of Verona, Verona, Italy
| | - Giulia Lorenzoni
- Unit of Biostatistics, Epidemiology and Public Health, Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova, Padova, Italy
| | - Dario Gregori
- Unit of Biostatistics, Epidemiology and Public Health, Department of Cardiac, Thoracic, Vascular Sciences, and Public Health, University of Padova, Padova, Italy
| | - Talia Golan
- The Oncology Institute, Sheba Medical Center at Tel-Hashomer, Tel Aviv University, Tel Aviv, Israel
| | - Chiara Braconi
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
- Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom
| | - Fieke E. M. Froeling
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Michele Milella
- Section of Oncology, Department of Medicine, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- Section of Pathology, Department of Diagnostics and Public Health, University and Hospital Trust of Verona, Verona, Italy
- ARC-Net Research Centre, University of Verona, Verona, Italy
| | - Antonio Pea
- General and Pancreatic Surgery Unit, Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Giuseppe Malleo
- General and Pancreatic Surgery Unit, Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Roberto Salvia
- General and Pancreatic Surgery Unit, Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Claudio Bassi
- General and Pancreatic Surgery Unit, Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - David K. Chang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Andrew V. Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom
- Faculty of Medicine, South Western Sydney Clinical School, University of NSW, Liverpool, Australia
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Normanno N, Apostolides K, de Lorenzo F, Beer PA, Henderson R, Sullivan R, Biankin AV, Horgan D, Lawler M. Cancer Biomarkers in the era of precision oncology: Addressing the needs of patients and health systems. Semin Cancer Biol 2021; 84:293-301. [PMID: 34389490 DOI: 10.1016/j.semcancer.2021.08.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 07/30/2021] [Accepted: 08/02/2021] [Indexed: 10/20/2022]
Abstract
Cancer Biomarkers are the key to unlocking the promise of precision oncology, selecting which patients will respond to a more personalised treatment while sparing non-responders the therapy-related toxicity. In this paper, we highlight the primacy of cancer biomarkers, but focus on their importance to patients and to health systems. We also highlight how cancer biomarkers represent value for money. We emphasise the need for cancer biomarkers infrastructure to be embedded into European health systems. We also highlight the need to deploy multiple biomarker testing to deliver the optimal benefit for patients and health systems and consider cancer biomarkers from the perspective of cost, value and regulation. Cancer biomarkers must also be situated in the context of the upcoming In Vitro Diagnostics Regulation, which may pose certain challenges (e.g. non-compliance of laboratory developed tests, leading to cancer biomarker shortages and increased costs) that need to be overcome. Cancer biomarkers must be embedded in the real world of oncology delivery and testing must be implemented across Europe, with the intended aim of narrowing, not widening the inequity gap for patients. Cancer patients must be placed firmly at the centre of a cancer biomarker informed precision oncology care agenda.
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Affiliation(s)
- Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori - IRCCS - "Fondazione G. Pascale", Napoli, Italy
| | - Kathi Apostolides
- European Cancer Patient Coalition, Rue Montoyer 40, 1000, Brussels, Belgium
| | | | - Philip A Beer
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland, G61 1QH, United Kingdom; Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, United Kingdom
| | - Raymond Henderson
- Diaceutics PLC, Belfast, United Kingdom; Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, United Kingdom
| | - Richard Sullivan
- King's College London, Institute of Cancer Policy, Guy's Hospital, Great Maze Pond, London, SE1 9RT, United Kingdom
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland, G61 1QH, United Kingdom; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, G31 2ER, United Kingdom; South Western Sydney Clinical School, Goulburn St, Liverpool, NSW, 2170, Australia
| | - Denis Horgan
- European Alliance for Personalised Medicine, Avenue de l'Armee Legerlaan 10, 1040, Brussels, Belgium
| | - Mark Lawler
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, United Kingdom.
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