1
|
Yaacov A, Ben Cohen G, Landau J, Hope T, Simon I, Rosenberg S. Cancer mutational signatures identification in clinical assays using neural embedding-based representations. Cell Rep Med 2024; 5:101608. [PMID: 38866015 DOI: 10.1016/j.xcrm.2024.101608] [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: 09/27/2023] [Revised: 03/28/2024] [Accepted: 05/16/2024] [Indexed: 06/14/2024]
Abstract
While mutational signatures provide a plethora of prognostic and therapeutic insights, their application in clinical-setting, targeted gene panels is extremely limited. We develop a mutational representation model (which learns and embeds specific mutation signature connections) that enables prediction of dominant signatures with only a few mutations. We predict the dominant signatures across more than 60,000 tumors with gene panels, delineating their landscape across different cancers. Dominant signature predictions in gene panels are of clinical importance. These included UV, tobacco, and apolipoprotein B mRNA editing enzyme, catalytic polypeptide (APOBEC) signatures that are associated with better survival, independently from mutational burden. Further analyses reveal gene and mutation associations with signatures, such as SBS5 with TP53 and APOBEC with FGFR3S249C. In a clinical use case, APOBEC signature is a robust and specific predictor for resistance to epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs). Our model provides an easy-to-use way to detect signatures in clinical setting assays with many possible clinical implications for an unprecedented number of cancer patients.
Collapse
Affiliation(s)
- Adar Yaacov
- Gaffin Center for Neuro-Oncology, Sharett Institute for Oncology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel; The Wohl Institute for Translational Medicine, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel; Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Gil Ben Cohen
- Gaffin Center for Neuro-Oncology, Sharett Institute for Oncology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel; The Wohl Institute for Translational Medicine, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jakob Landau
- Gaffin Center for Neuro-Oncology, Sharett Institute for Oncology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel; The Wohl Institute for Translational Medicine, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tom Hope
- School of Computer Science and Engineering, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Itamar Simon
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shai Rosenberg
- Gaffin Center for Neuro-Oncology, Sharett Institute for Oncology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel; The Wohl Institute for Translational Medicine, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
| |
Collapse
|
2
|
Ostroverkhova D, Sheng Y, Panchenko A. Are Next-Generation Pathogenicity Predictors Applicable to Cancer? J Mol Biol 2024; 436:168644. [PMID: 38848867 DOI: 10.1016/j.jmb.2024.168644] [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: 05/06/2024] [Revised: 06/01/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024]
Abstract
Next-generation pathogenicity predictors are designed to identify pathogenic mutations in genetic disorders but are increasingly used to detect driver mutations in cancer. Despite this, their suitability for cancer is not fully established. Here we have assessed the effectiveness of next-generation pathogenicity predictors when applied to cancer by using a comprehensive experimental benchmark of cancer driver and neutral mutations. Our findings indicate that state-of-the-art methods AlphaMissense and VARITY demonstrate commendable performance despite generally underperforming compared to cancer-specific methods. This is notable considering that these methods do not explicitly incorporate cancer-related data in their training and have made concerted efforts to prevent data leakage from the human-curated training and test sets. Nevertheless, it should be mentioned that a significant limitation of using pathogenicity predictors for cancer arises from their inability to detect cancer potential driver mutations specific for a particular cancer type.
Collapse
Affiliation(s)
| | - Yiru Sheng
- Department of Biology and Molecular Sciences, Queen's University, Canada
| | - Anna Panchenko
- Department of Pathology and Molecular Medicine, Queen's University, Canada; Department of Biology and Molecular Sciences, Queen's University, Canada; School of Computing, Queen's University, Canada; Ontario Institute of Cancer Research, Canada.
| |
Collapse
|
3
|
Gorlov IP, Gorlova OY, Tsavachidis S, Amos CI. Strength of selection in lung tumors correlates with clinical features better than tumor mutation burden. Sci Rep 2024; 14:12732. [PMID: 38831004 PMCID: PMC11148192 DOI: 10.1038/s41598-024-63468-z] [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: 12/08/2023] [Accepted: 05/29/2024] [Indexed: 06/05/2024] Open
Abstract
Single nucleotide substitutions are the most common type of somatic mutations in cancer genome. The goal of this study was to use publicly available somatic mutation data to quantify negative and positive selection in individual lung tumors and test how strength of directional and absolute selection is associated with clinical features. The analysis found a significant variation in strength of selection (both negative and positive) among tumors, with median selection tending to be negative even though tumors with strong positive selection also exist. Strength of selection estimated as the density of missense mutations relative to the density of silent mutations showed only a weak correlation with tumor mutation burden. In the "all histology together" analysis we found that absolute strength of selection was strongly correlated with all clinically relevant features analyzed. In histology-stratified analysis selection was strongest in small cell lung cancer. Selection in adenocarcinoma was somewhat higher compared to squamous cell carcinoma. The study suggests that somatic mutation- based quantifying of directional and absolute selection in individual tumors can be a useful biomarker of tumor aggressiveness.
Collapse
Affiliation(s)
- Ivan P Gorlov
- Institute for Clinical and Translational Research, Baylor College of Medicine, One Baylor Plaza, Mailstop: BCM451, Houston, TX, 77030, USA.
| | - Olga Y Gorlova
- Institute for Clinical and Translational Research, Baylor College of Medicine, One Baylor Plaza, Mailstop: BCM451, Houston, TX, 77030, USA
| | - Spyridon Tsavachidis
- Institute for Clinical and Translational Research, Baylor College of Medicine, One Baylor Plaza, Mailstop: BCM451, Houston, TX, 77030, USA
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, One Baylor Plaza, Mailstop: BCM451, Houston, TX, 77030, USA
| |
Collapse
|
4
|
Gallon R, Brekelmans C, Martin M, Bours V, Schamschula E, Amberger A, Muleris M, Colas C, Dekervel J, De Hertogh G, Coupier J, Colleye O, Sepulchre E, Burn J, Brems H, Legius E, Wimmer K. Constitutional mismatch repair deficiency mimicking Lynch syndrome is associated with hypomorphic mismatch repair gene variants. NPJ Precis Oncol 2024; 8:119. [PMID: 38789506 PMCID: PMC11126593 DOI: 10.1038/s41698-024-00603-z] [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: 10/13/2023] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Lynch syndrome (LS) and constitutional mismatch repair deficiency (CMMRD) are distinct cancer syndromes caused, respectively, by mono- and bi-allelic germline mismatch repair (MMR) variants. LS predisposes to mainly gastrointestinal and genitourinary cancers in adulthood. CMMRD predisposes to brain, haematological, and LS-spectrum cancers from childhood. Two suspected LS patients with first cancer diagnosis aged 27 or 38 years were found to be homozygous for an MMR (likely) pathogenic variant, MSH6 c.3226C>T (p.(Arg1076Cys)), or variant of uncertain significance (VUS), MLH1 c.306G>A (p.(Glu102=)). MLH1 c.306G>A was shown to cause leaky exon 3 skipping. The apparent genotype-phenotype conflict was resolved by detection of constitutional microsatellite instability in both patients, a hallmark feature of CMMRD. A hypomorphic effect of these and other variants found in additional late onset CMMRD cases, identified by literature review, likely explains a LS-like phenotype. CMMRD testing in carriers of compound heterozygous or homozygous MMR VUS may find similar cases and novel hypomorphic variants. Individualised management of mono- and bi-allelic carriers of hypomorphic MMR variants is needed until we better characterise the associated phenotypes.
Collapse
Affiliation(s)
- Richard Gallon
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.
| | | | | | | | - Esther Schamschula
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Albert Amberger
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Martine Muleris
- Département de Génétique, AP-HP.Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France
- Inserm UMRS_938, Sorbonne Université, Centre de Recherche Saint Antoine, Paris, France
| | - Chrystelle Colas
- Département de Génétique, Institut Curie, Paris, France
- INSERM U830, Université de Paris, Paris, France
| | - Jeroen Dekervel
- Department of Digestive Oncology, University Hospital Leuven, Leuven, Belgium
| | - Gert De Hertogh
- Department of Pathology, University Hospital Leuven, Leuven, Belgium
| | | | | | | | - John Burn
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Hilde Brems
- Centre for Human Genetics, University Hospital Leuven, Leuven, Belgium
| | - Eric Legius
- Centre for Human Genetics, University Hospital Leuven, Leuven, Belgium
| | - Katharina Wimmer
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria.
| |
Collapse
|
5
|
Gustav M, Reitsam NG, Carrero ZI, Loeffler CML, van Treeck M, Yuan T, West NP, Quirke P, Brinker TJ, Brenner H, Favre L, Märkl B, Stenzinger A, Brobeil A, Hoffmeister M, Calderaro J, Pujals A, Kather JN. Deep learning for dual detection of microsatellite instability and POLE mutations in colorectal cancer histopathology. NPJ Precis Oncol 2024; 8:115. [PMID: 38783059 PMCID: PMC11116442 DOI: 10.1038/s41698-024-00592-z] [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: 11/07/2023] [Accepted: 04/14/2024] [Indexed: 05/25/2024] Open
Abstract
In the spectrum of colorectal tumors, microsatellite-stable (MSS) tumors with DNA polymerase ε (POLE) mutations exhibit a hypermutated profile, holding the potential to respond to immunotherapy similarly to their microsatellite-instable (MSI) counterparts. Yet, due to their rarity and the associated testing costs, systematic screening for these mutations is not commonly pursued. Notably, the histopathological phenotype resulting from POLE mutations is theorized to resemble that of MSI. This resemblance not only could facilitate their detection by a transformer-based Deep Learning (DL) system trained on MSI pathology slides, but also indicates the possibility for MSS patients with POLE mutations to access enhanced treatment options, which might otherwise be overlooked. To harness this potential, we trained a Deep Learning classifier on a large dataset with the ground truth for microsatellite status and subsequently validated its capabilities for MSI and POLE detection across three external cohorts. Our model accurately identified MSI status in both the internal and external resection cohorts using pathology images alone. Notably, with a classification threshold of 0.5, over 75% of POLE driver mutant patients in the external resection cohorts were flagged as "positive" by a DL system trained on MSI status. In a clinical setting, deploying this DL model as a preliminary screening tool could facilitate the efficient identification of clinically relevant MSI and POLE mutations in colorectal tumors, in one go.
Collapse
Affiliation(s)
- Marco Gustav
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | | | - Zunamys I Carrero
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Chiara M L Loeffler
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany
- Department of Medicine I, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Marko van Treeck
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Tanwei Yuan
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nicholas P West
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Philip Quirke
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Titus J Brinker
- Digital Biomarkers for Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Loëtitia Favre
- Université Paris Est Créteil, INSERM, IMRB, Créteil, France
- Assistance Publique-Hôpitaux de Paris, Henri Mondor-Albert Chenevier University Hospital, Department of Pathology, Créteil, France
- INSERM, U955, Team Oncogenèse des lymphomes et tumeurs de la Neurofibromatose 1, Créteil, France
| | - Bruno Märkl
- Pathology, Faculty of Medicine, University of Augsburg, Augsburg, Germany
| | | | - Alexander Brobeil
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Tissue Bank of the National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Julien Calderaro
- Université Paris Est Créteil, INSERM, IMRB, Créteil, France
- Assistance Publique-Hôpitaux de Paris, Henri Mondor-Albert Chenevier University Hospital, Department of Pathology, Créteil, France
- INSERM, U955, Team Oncogenèse des lymphomes et tumeurs de la Neurofibromatose 1, Créteil, France
| | - Anaïs Pujals
- Université Paris Est Créteil, INSERM, IMRB, Créteil, France
- Assistance Publique-Hôpitaux de Paris, Henri Mondor-Albert Chenevier University Hospital, Department of Pathology, Créteil, France
- INSERM, U955, Team Oncogenèse des lymphomes et tumeurs de la Neurofibromatose 1, Créteil, France
| | - Jakob Nikolas Kather
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany.
- Department of Medicine I, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom.
- Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, Heidelberg, Germany.
| |
Collapse
|
6
|
Palova H, Das A, Pokorna P, Bajciova V, Pavelka Z, Jezova M, Pal K, Dimayacyac JR, Negm L, Stengs L, Bianchi V, Vejmelkova K, Noskova K, Jarosova M, Mejstrikova S, Mudry P, Kyr M, Merta T, Tinka P, Drabova K, Aulicka S, Jugas R, Tabori U, Slaby O, Sterba J. Precision immuno-oncology approach for four malignant tumors in siblings with constitutional mismatch repair deficiency syndrome. NPJ Precis Oncol 2024; 8:110. [PMID: 38773265 PMCID: PMC11109258 DOI: 10.1038/s41698-024-00597-8] [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: 10/20/2023] [Accepted: 05/03/2024] [Indexed: 05/23/2024] Open
Abstract
Constitutional mismatch repair deficiency (CMMRD) is a rare syndrome characterized by an increased incidence of cancer. It is caused by biallelic germline mutations in one of the four mismatch repair genes (MMR) genes: MLH1, MSH2, MSH6, or PMS2. Accurate diagnosis accompanied by a proper molecular genetic examination plays a crucial role in cancer management and also has implications for other family members. In this report, we share the impact of the diagnosis and challenges during the clinical management of two brothers with CMMRD from a non-consanguineous family harbouring compound heterozygous variants in the PMS2 gene. Both brothers presented with different phenotypic manifestations and cancer spectrum. Treatment involving immune checkpoint inhibitors significantly contributed to prolonged survival in both patients affected by lethal gliomas. The uniform hypermutation also allowed immune-directed treatment using nivolumab for the B-cell lymphoma, thereby limiting the intensive chemotherapy exposure in this young patient who remains at risk for subsequent malignancies.
Collapse
Affiliation(s)
- Hana Palova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Anirban Das
- Division of Haematology Oncology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Petra Pokorna
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Viera Bajciova
- Department of Pediatric Oncology, University Hospital Brno, and Faculty of Medicine, ERN PaedCan Center, Masaryk University, Brno, Czech Republic
| | - Zdenek Pavelka
- Department of Pediatric Oncology, University Hospital Brno, and Faculty of Medicine, ERN PaedCan Center, Masaryk University, Brno, Czech Republic
| | - Marta Jezova
- Department of Pathology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Karol Pal
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jose R Dimayacyac
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Logine Negm
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Lucie Stengs
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Vanessa Bianchi
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Klara Vejmelkova
- Department of Pediatric Oncology, University Hospital Brno, and Faculty of Medicine, ERN PaedCan Center, Masaryk University, Brno, Czech Republic
| | - Kristyna Noskova
- Department of Pharmacology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Clinical Pharmacy Section of Hospital Pharmacy, University Hospital Brno, Brno, Czech Republic
| | - Marie Jarosova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Sona Mejstrikova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Peter Mudry
- Department of Pediatric Oncology, University Hospital Brno, and Faculty of Medicine, ERN PaedCan Center, Masaryk University, Brno, Czech Republic
| | - Michal Kyr
- Department of Pediatric Oncology, University Hospital Brno, and Faculty of Medicine, ERN PaedCan Center, Masaryk University, Brno, Czech Republic
| | - Tomas Merta
- Department of Pediatric Oncology, University Hospital Brno, and Faculty of Medicine, ERN PaedCan Center, Masaryk University, Brno, Czech Republic
| | - Pavel Tinka
- Department of Pediatric Oncology, University Hospital Brno, and Faculty of Medicine, ERN PaedCan Center, Masaryk University, Brno, Czech Republic
| | - Klara Drabova
- Institute of Medical Genetics and Genomics, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Stefania Aulicka
- Department of Pediatric Neurology, University Hospital Brno, and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Robin Jugas
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Uri Tabori
- Division of Haematology Oncology, The Hospital for Sick Children, Toronto, ON, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ondrej Slaby
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.
| | - Jaroslav Sterba
- Department of Pediatric Oncology, University Hospital Brno, and Faculty of Medicine, ERN PaedCan Center, Masaryk University, Brno, Czech Republic.
| |
Collapse
|
7
|
Tuffaha MZ, Castellano D, Colome CS, Gutenkunst RN, Wahl LM. Non-hypermutator cancers access driver mutations through reversals in germline mutational bias. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.30.591900. [PMID: 38746331 PMCID: PMC11092619 DOI: 10.1101/2024.04.30.591900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Cancer is an evolutionary disease driven by mutations in asexually-reproducing somatic cells. In asexual microbes, bias reversals in the mutation spectrum can speed adaptation by increasing access to previously undersampled beneficial mutations. By analyzing tumors from 20 tissues, along with normal tissue and the germline, we demonstrate this effect in cancer. Non-hypermutated tumors reverse the germline mutation bias and have consistent spectra across tissues. These spectra changes carry the signature of hypoxia, and they facilitate positive selection in cancer genes. Hypermutated and non-hypermutated tumors thus acquire driver mutations differently: hypermutated tumors by higher mutation rates and non-hypermutated tumors by changing the mutation spectrum to reverse the germline mutation bias.
Collapse
Affiliation(s)
- Marwa Z. Tuffaha
- Department of Mathematics, Western University, London, Ontario N6A 5B7, Canada
| | - David Castellano
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Claudia Serrano Colome
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Ryan N. Gutenkunst
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Lindi M. Wahl
- Department of Mathematics, Western University, London, Ontario N6A 5B7, Canada
| |
Collapse
|
8
|
Ambrosini M, Rousseau B, Manca P, Artz O, Marabelle A, André T, Maddalena G, Mazzoli G, Intini R, Cohen R, Cercek A, Segal NH, Saltz L, Varghese AM, Yaeger R, Nusrat M, Goldberg Z, Ku GY, El Dika I, Margalit O, Grinshpun A, Kasi P, Schilsky R, Lutfi A, Shacham-Shmueli E, Khan Afghan M, Weiss L, Westphalen CB, Conca V, Decker B, Randon G, Elez E, Fakih M, Schrock AB, Cremolini C, Jayachandran P, Overman MJ, Lonardi S, Pietrantonio F. Immune checkpoint inhibitors for POLE or POLD1 proofreading-deficient metastatic colorectal cancer. Ann Oncol 2024:S0923-7534(24)00104-2. [PMID: 38777726 DOI: 10.1016/j.annonc.2024.03.009] [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: 02/09/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND POLE and POLD1 proofreading deficiency (POLE/D1pd) define a rare subtype of ultramutated metastatic colorectal cancer (mCRC; over 100 mut/Mb). Disease-specific data about the activity and efficacy of immune checkpoint inhibitors (ICIs) in POLE/D1pd mCRC are lacking and it is unknown whether outcomes may be different from mismatch repair-deficient (dMMR)/microsatellite instability-high (MSI-H) mCRCs treated with ICIs. PATIENTS AND METHODS In this global study, we collected 27 patients with mCRC harboring POLE/D1 mutations leading to proofreading deficiency and treated with anti-programmed cell death-ligand 1 alone +/- anti-cytotoxic T-lymphocyte antigen-4 agents. We collected clinicopathological and genomic characteristics, response, and survival outcomes after ICIs of POLE/D1pd mCRC and compared them with a cohort of 610 dMMR/MSI-H mCRC patients treated with ICIs. Further genomic analyses were carried out in an independent cohort of 7241 CRCs to define POLE and POLD1pd molecular profiles and mutational signatures. RESULTS POLE/D1pd was associated with younger age, male sex, fewer RAS/BRAF driver mutations, and predominance of right-sided colon cancers. Patients with POLE/D1pd mCRC showed a significantly higher overall response rate (ORR) compared to dMMR/MSI-H mCRC (89% versus 54%; P = 0.01). After a median follow-up of 24.9 months (interquartile range: 11.3-43.0 months), patients with POLE/D1pd showed a significantly superior progression-free survival (PFS) compared to dMMR/MSI-H mCRC [hazard ratio (HR) = 0.24, 95% confidence interval (CI) 0.08-0.74, P = 0.01] and superior overall survival (OS) (HR = 0.38, 95% CI 0.12-1.18, P = 0.09). In multivariable analyses including the type of DNA repair defect, POLE/D1pd was associated with significantly improved PFS (HR = 0.17, 95% CI 0.04-0.69, P = 0.013) and OS (HR = 0.24, 95% CI 0.06-0.98, P = 0.047). Molecular profiling showed that POLE/D1pd tumors have higher tumor mutational burden (TMB). Responses were observed in both subtypes and were associated with the intensity of POLE/D1pd signature. CONCLUSIONS Patients with POLE/D1pd mCRC showed more favorable outcomes compared to dMMR/MSI-H mCRC to treatment with ICIs in terms of tumor response and survival.
Collapse
Affiliation(s)
- M Ambrosini
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - B Rousseau
- Memorial Sloan Kettering Cancer Center, New York, USA
| | - P Manca
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy; Memorial Sloan Kettering Cancer Center, New York, USA
| | - O Artz
- Memorial Sloan Kettering Cancer Center, New York, USA
| | - A Marabelle
- Department of Therapeutic Innovation and Phase 1 clinical trials, Inserm, Gustave Roussy, Université Paris Saclay, Villejuif
| | - T André
- Sorbonne Université and Department of Medical Oncology, Hôpital Saint Antoine, Paris, France
| | - G Maddalena
- Istituto Oncologico Veneto, IRCCS, Padua, Italy
| | - G Mazzoli
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - R Intini
- Istituto Oncologico Veneto, IRCCS, Padua, Italy
| | - R Cohen
- Sorbonne Université and Department of Medical Oncology, Hôpital Saint Antoine, Paris, France
| | - A Cercek
- Memorial Sloan Kettering Cancer Center, New York, USA
| | - N H Segal
- Memorial Sloan Kettering Cancer Center, New York, USA
| | - L Saltz
- Memorial Sloan Kettering Cancer Center, New York, USA
| | - A M Varghese
- Memorial Sloan Kettering Cancer Center, New York, USA
| | - R Yaeger
- Memorial Sloan Kettering Cancer Center, New York, USA
| | - M Nusrat
- Memorial Sloan Kettering Cancer Center, New York, USA
| | - Z Goldberg
- Memorial Sloan Kettering Cancer Center, New York, USA
| | - G Y Ku
- Memorial Sloan Kettering Cancer Center, New York, USA
| | - I El Dika
- Memorial Sloan Kettering Cancer Center, New York, USA
| | - O Margalit
- Oncology Department, Sheba Medical Center and Tel-Aviv University Medicine Faculty, Tel-Aviv
| | - A Grinshpun
- Sharett Institute of Oncology, Hadassah Medical Center, and Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - P Kasi
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City
| | | | - A Lutfi
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City
| | - E Shacham-Shmueli
- Oncology Department, Sheba Medical Center and Tel-Aviv University Medicine Faculty, Tel-Aviv
| | - M Khan Afghan
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City
| | - L Weiss
- Department of Internal Medicine III and Comprehensive Cancer Center, Klinikum Grosshadern, University Hospital, Ludwig Maximilian University of Munich, Munich; German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - C B Westphalen
- Department of Internal Medicine III and Comprehensive Cancer Center, Klinikum Grosshadern, University Hospital, Ludwig Maximilian University of Munich, Munich; German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - V Conca
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - B Decker
- Foundation Medicine, Cambridge, USA
| | - G Randon
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - E Elez
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - M Fakih
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte
| | | | - C Cremolini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - P Jayachandran
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles
| | - M J Overman
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S Lonardi
- Istituto Oncologico Veneto, IRCCS, Padua, Italy
| | - F Pietrantonio
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.
| |
Collapse
|
9
|
Park SJ, Ju S, Goh SH, Yoon BH, Park JL, Kim JH, Lee S, Lee SJ, Kwon Y, Lee W, Park KC, Lee GK, Park SY, Kim S, Kim SY, Han JY, Lee C. Proteogenomic Characterization Reveals Estrogen Signaling as a Target for Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations. Cancer Res 2024; 84:1491-1503. [PMID: 38607364 DOI: 10.1158/0008-5472.can-23-1551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 10/24/2023] [Accepted: 01/18/2024] [Indexed: 04/13/2024]
Abstract
Never-smoker lung adenocarcinoma (NSLA) is prevalent in Asian populations, particularly in women. EGFR mutations and anaplastic lymphoma kinase (ALK) fusions are major genetic alterations observed in NSLA, and NSLA with these alterations have been well studied and can be treated with targeted therapies. To provide insights into the molecular profile of NSLA without EGFR and ALK alterations (NENA), we selected 141 NSLA tissues and performed proteogenomic characterization, including whole genome sequencing (WGS), transcriptomic, methylation EPIC array, total proteomic, and phosphoproteomic analyses. Forty patients with NSLA harboring EGFR and ALK alterations and seven patients with NENA with microsatellite instability were excluded. Genome analysis revealed that TP53 (25%), KRAS (22%), and SETD2 (11%) mutations and ROS1 fusions (14%) were the most frequent genetic alterations in NENA patients. Proteogenomic impact analysis revealed that STK11 and ERBB2 somatic mutations had broad effects on cancer-associated genes in NENA. DNA copy number alteration analysis identified 22 prognostic proteins that influenced transcriptomic and proteomic changes. Gene set enrichment analysis revealed estrogen signaling as the key pathway activated in NENA. Increased estrogen signaling was associated with proteogenomic alterations, such as copy number deletions in chromosomes 14 and 21, STK11 mutation, and DNA hypomethylation of LLGL2 and ST14. Finally, saracatinib, an Src inhibitor, was identified as a potential drug for targeting activated estrogen signaling in NENA and was experimentally validated in vitro. Collectively, this study enhanced our understanding of NENA NSLA by elucidating the proteogenomic landscape and proposed saracatinib as a potential treatment for this patient population that lacks effective targeted therapies. SIGNIFICANCE The proteogenomic landscape in never-smoker lung cancer without known driver mutations reveals prognostic proteins and enhanced estrogen signaling that can be targeted as a potential therapeutic strategy to improve patient outcomes.
Collapse
Affiliation(s)
- Seung-Jin Park
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Shinyeong Ju
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Sung-Ho Goh
- National Cancer Center, Goyang, Republic of Korea
| | - Byoung-Ha Yoon
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Jong-Lyul Park
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Jeong-Hwan Kim
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Seonjeong Lee
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology, Seoul, Republic of Korea
| | - Sang-Jin Lee
- National Cancer Center, Goyang, Republic of Korea
| | - Yumi Kwon
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Wonyeop Lee
- National Cancer Center, Goyang, Republic of Korea
| | - Kyung Chan Park
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | | | | | - Sunshin Kim
- National Cancer Center, Goyang, Republic of Korea
| | - Seon-Young Kim
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Ji-Youn Han
- National Cancer Center, Goyang, Republic of Korea
| | - Cheolju Lee
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology, Seoul, Republic of Korea
| |
Collapse
|
10
|
Kroeze E, Weijers DD, Kleisman MM, Ilan U, Bladergroen RS, Hagelaar R, Meijerink JPP, Jongmans MCJ, Loeffen JLC, Kuiper RP. T-cell lymphoblastic lymphoma in constitutional mismatch repair deficiency (CMMRD): Exploring treatment opportunities. Hemasphere 2024; 8:e73. [PMID: 38741596 PMCID: PMC11089271 DOI: 10.1002/hem3.73] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/26/2024] [Accepted: 04/01/2024] [Indexed: 05/16/2024] Open
Affiliation(s)
- Emma Kroeze
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
| | - Dilys D. Weijers
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
| | | | - Uri Ilan
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
| | | | - Rico Hagelaar
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - Jules P. P. Meijerink
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
- Present address:
Acerta‐Pharma (AstraZeneca)OssThe Netherlands
| | - Marjolijn C. J. Jongmans
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
- Department of Genetics, Utrecht University Medical CenterUtrecht UniversityUtrechtThe Netherlands
| | | | - Roland P. Kuiper
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
- Department of Genetics, Utrecht University Medical CenterUtrecht UniversityUtrechtThe Netherlands
| |
Collapse
|
11
|
Débare H, Blanc F, Piton G, Leplat JJ, Vincent-Naulleau S, Rivière J, Vilotte M, Marthey S, Lecardonnel J, Coville JL, Estellé J, Rau A, Bourneuf E, Egidy G. Malignant features of minipig melanomas prior to spontaneous regression. Sci Rep 2024; 14:9240. [PMID: 38649394 PMCID: PMC11035550 DOI: 10.1038/s41598-024-59741-w] [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: 10/04/2023] [Accepted: 04/15/2024] [Indexed: 04/25/2024] Open
Abstract
In MeLiM minipigs, melanomas develop around birth, can metastasize, and have histopathologic characteristics similar to humans. Interestingly, MeLiM melanomas eventually regress. This favorable outcome raises the question of their malignancy, which we investigated. We clinically followed tens of tumors from onset to first signs of regression. Transcriptome analysis revealed an enrichment of all cancer hallmarks in melanomas, although no activating or suppressing somatic mutation were found in common driver genes. Analysis of tumor cell genomes revealed high mutation rates without UV signature. Canonical proliferative, survival and angiogenic pathways were detected in MeLiM tumor cells all along progression stages. Functionally, we show that MeLiM melanoma cells are capable to grow in immunocompromised mice, with serial passages and for a longer time than in MeLiM pigs. Pigs set in place an immune response during progression with dense infiltration by myeloid cells while melanoma cells are deficient in B2M expression. To conclude, our data on MeLiM melanomas reveal several malignancy characteristics. The combination of these features with the successful spontaneous regression of these tumors make it an outstanding model to study an efficient anti-tumor immune response.
Collapse
Affiliation(s)
- Héloïse Débare
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Fany Blanc
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Guillaume Piton
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
- Université Paris-Saclay, CEA, Stabilité Génétique Cellules Souches Et Radiations, 92260, Fontenay-Aux-Roses, France
- Université de Paris Cité, CEA, Stabilité Génétique Cellules Souches Et Radiations, 92260, Fontenay-Aux-Roses, France
| | - Jean-Jacques Leplat
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
- Université Paris-Saclay, CEA, Stabilité Génétique Cellules Souches Et Radiations, 92260, Fontenay-Aux-Roses, France
| | - Silvia Vincent-Naulleau
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
- Université Paris-Saclay, CEA, Stabilité Génétique Cellules Souches Et Radiations, 92260, Fontenay-Aux-Roses, France
- Université de Paris Cité, CEA, Stabilité Génétique Cellules Souches Et Radiations, 92260, Fontenay-Aux-Roses, France
| | - Julie Rivière
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Micalis, 78350, Jouy-en-Josas, France
| | - Marthe Vilotte
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Sylvain Marthey
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Jérôme Lecardonnel
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Jean-Luc Coville
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Jordi Estellé
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Andrea Rau
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Emmanuelle Bourneuf
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
- Université Paris-Saclay, CEA, Stabilité Génétique Cellules Souches Et Radiations, 92260, Fontenay-Aux-Roses, France
- Université de Paris Cité, CEA, Stabilité Génétique Cellules Souches Et Radiations, 92260, Fontenay-Aux-Roses, France
| | - Giorgia Egidy
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.
| |
Collapse
|
12
|
Weijers DD, Hirsch S, Bakhuizen JJ, van Engelen N, Kester LA, Kranendonk MEG, Hiemcke-Jiwa LS, de Vos-Kerkhof E, Loeffen JLC, Autry RJ, Pajtler KW, Jäger N, Jongmans MCJ, Kuiper RP. Molecular analysis of cancer genomes in children with Lynch syndrome: Exploring causal associations. Int J Cancer 2024; 154:1455-1463. [PMID: 38175816 DOI: 10.1002/ijc.34832] [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: 06/30/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 01/06/2024]
Abstract
Lynch syndrome (LS) predisposes to cancer in adulthood and is caused by heterozygous germline variants in a mismatch repair (MMR) gene. Recent studies show an increased prevalence of LS among children with cancer, suggesting a causal relationship. For LS-spectrum (LSS) cancers, including high-grade gliomas and colorectal cancer, causality has been supported by typical MMR-related tumor characteristics, but for non-LSS cancers, causality is unclear. We characterized 20 malignant tumors of 18 children with LS, including 16 non-LSS tumors. We investigated second hits, tumor mutational load, mutational signatures and MMR protein expression. In all LSS tumors and three non-LSS tumors, we detected MMR deficiency caused by second hit somatic alterations. Furthermore, these MMR-deficient tumors carried driver variants that likely originated as a consequence of MMR deficiency. However, in 13 non-LSS tumors (81%), a second hit and MMR deficiency were absent, thus a causal link between LS and cancer development in these children is lacking. These findings demonstrate that causality of LS in children with cancer, which can be determined by molecular tumor characterization, seems to be restricted to specific tumor types. Large molecular and epidemiological studies are needed to further refine the tumor spectrum in children with LS.
Collapse
Affiliation(s)
- Dilys D Weijers
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Steffen Hirsch
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jette J Bakhuizen
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Genetics, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | | | - Lennart A Kester
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Laura S Hiemcke-Jiwa
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Jan L C Loeffen
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Robert J Autry
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Kristian W Pajtler
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Natalie Jäger
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Marjolijn C J Jongmans
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Genetics, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Roland P Kuiper
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Genetics, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| |
Collapse
|
13
|
Nádorvári ML, Lotz G, Kulka J, Kiss A, Tímár J. Microsatellite instability and mismatch repair protein deficiency: equal predictive markers? Pathol Oncol Res 2024; 30:1611719. [PMID: 38655493 PMCID: PMC11036414 DOI: 10.3389/pore.2024.1611719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/27/2024] [Indexed: 04/26/2024]
Abstract
Current clinical guidelines recommend mismatch repair (MMR) protein immunohistochemistry (IHC) or molecular microsatellite instability (MSI) tests as predictive markers of immunotherapies. Most of the pathological guidelines consider MMR protein IHC as the gold standard test to identify cancers with MMR deficiency and recommend molecular MSI tests only in special circumstances or to screen for Lynch syndrome. However, there are data in the literature which suggest that the two test types may not be equal. For example, molecular epidemiology studies reported different rates of deficient MMR (dMMR) and MSI in various cancer types. Additionally, direct comparisons of the two tests revealed relatively frequent discrepancies between MMR IHC and MSI tests, especially in non-colorectal and non-endometrial cancers and in cases with unusual dMMR phenotypes. There are also scattered clinical data showing that the efficacy of immune checkpoint inhibitors is different if the patient selection was based on dMMR versus MSI status of the cancers. All these observations question the current dogma that dMMR phenotype and genetic MSI status are equal predictive markers of the immunotherapies.
Collapse
Affiliation(s)
| | | | | | | | - József Tímár
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary
| |
Collapse
|
14
|
Gikandi A, Chi SN, Yeo KK, O'Neill AF, Shulman DS, DuBois SG, Collins NB. Off-label prescribing of immune checkpoint inhibitor therapy at a single pediatric cancer center. Cancer Med 2024; 13:e7154. [PMID: 38629258 PMCID: PMC11022150 DOI: 10.1002/cam4.7154] [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: 10/25/2023] [Revised: 01/26/2024] [Accepted: 03/22/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Immune checkpoint inhibitors (ICI) have improved outcomes in a variety of adult cancers and are prescribed with increasing frequency across oncology. However, patterns of off-label use of ICI in pediatrics remain unclear. METHODS This is a single-institution, retrospective cohort study evaluating off-label ICI use in pediatric and young adult patients with cancer treated at our institution from 2014 to 2022. Response was based on clinician assessment derived from clinical records. Immune-related adverse events (iRAEs) were classified according to CTCAE v5.0. RESULTS We identified 50 unique patients treated with off-label ICI (28 with solid tumors, 20 with central nervous system (CNS) tumors, 2 with hematologic malignancies). At time of ICI initiation, only five patients (10%) had localized disease, and all but one patient was treated in the relapsed/refractory setting. All patients were treated with the FDA-approved weight-based dosing recommendations. Overall, there was disease control in 21 patients (42%), with best response including one complete response (melanoma), two partial responses (high-grade glioma, CNS nongerminomatous germ cell tumor), and 18 patients with stable disease. Forty-four patients (88%) eventually experienced disease progression. Among 22 patients (44%) experiencing iRAEs, 10 (20%) had a grade ≥3 irAE, 12 (24%) required corticosteroids, and 14 (28%) required ICI discontinuation. irAE occurrence was associated with significantly improved progression-free survival (HR 0.35; 95% CI: 0.18 to 0.68; p = 0.002) and overall survival (HR 0.33; 95% CI: 0.17 to 0.66; p = 0.002). CONCLUSIONS At our institution, ICI was most commonly prescribed in the relapsed/refractory setting to patients with metastatic disease. The treatment was generally well-tolerated in the pediatric population. The overall response rate was low, and the majority of patients eventually experienced disease progression. A few patients, however, had durable treatment responses. Further studies are needed to identify which pediatric patients are most likely to benefit from ICI.
Collapse
Affiliation(s)
| | - Susan N Chi
- Harvard Medical School, Boston, Massachusetts, USA
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Kee Kiat Yeo
- Harvard Medical School, Boston, Massachusetts, USA
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Allison F O'Neill
- Harvard Medical School, Boston, Massachusetts, USA
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts, USA
| | - David S Shulman
- Harvard Medical School, Boston, Massachusetts, USA
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Steven G DuBois
- Harvard Medical School, Boston, Massachusetts, USA
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Natalie B Collins
- Harvard Medical School, Boston, Massachusetts, USA
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
15
|
Edsjö A, Gisselsson D, Staaf J, Holmquist L, Fioretos T, Cavelier L, Rosenquist R. Current and emerging sequencing-based tools for precision cancer medicine. Mol Aspects Med 2024; 96:101250. [PMID: 38330674 DOI: 10.1016/j.mam.2024.101250] [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: 11/14/2023] [Accepted: 01/22/2024] [Indexed: 02/10/2024]
Abstract
Current precision cancer medicine is dependent on the analyses of a plethora of clinically relevant genomic aberrations. During the last decade, next-generation sequencing (NGS) has gradually replaced most other methods for precision cancer diagnostics, spanning from targeted tumor-informed assays and gene panel sequencing to global whole-genome and whole-transcriptome sequencing analyses. The shift has been impelled by a clinical need to assess an increasing number of genomic alterations with diagnostic, prognostic and predictive impact, including more complex biomarkers (e.g. microsatellite instability, MSI, and homologous recombination deficiency, HRD), driven by the parallel development of novel targeted therapies and enabled by the rapid reduction in sequencing costs. This review focuses on these sequencing-based methods, puts their emergence in a historic perspective, highlights their clinical utility in diagnostics and decision-making in pediatric and adult cancer, as well as raises challenges for their clinical implementation. Finally, the importance of applying sensitive tools for longitudinal monitoring of treatment response and detection of measurable residual disease, as well as future avenues in the rapidly evolving field of sequencing-based methods are discussed.
Collapse
Affiliation(s)
- Anders Edsjö
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden; Division of Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden.
| | - David Gisselsson
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden; Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Johan Staaf
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon Village, Lund, Sweden
| | - Louise Holmquist
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Thoas Fioretos
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden; Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden; Clinical Genomics Lund, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Lucia Cavelier
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden; Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|
16
|
Forster VJ, Aronson M, Zhang C, Chung J, Sudhaman S, Galati MA, Kelly J, Negm L, Ercan AB, Stengs L, Durno C, Edwards M, Komosa M, Oldfield LE, Nunes NM, Pedersen S, Wellum J, Siddiqui I, Bianchi V, Weil BR, Fox VL, Pugh TJ, Kamihara J, Tabori U. Biallelic EPCAM deletions induce tissue-specific DNA repair deficiency and cancer predisposition. NPJ Precis Oncol 2024; 8:69. [PMID: 38467830 PMCID: PMC10928233 DOI: 10.1038/s41698-024-00537-6] [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: 06/28/2023] [Accepted: 02/08/2024] [Indexed: 03/13/2024] Open
Abstract
We report a case of Mismatch Repair Deficiency (MMRD) caused by germline homozygous EPCAM deletion leading to tissue-specific loss of MSH2. Through the use of patient-derived cells and organoid technologies, we performed stepwise in vitro differentiation of colonic and brain organoids from reprogrammed EPCAMdel iPSC derived from patient fibroblasts. Differentiation of iPSC to epithelial-colonic organoids exhibited continuous increased EPCAM expression and hypermethylation of the MSH2 promoter. This was associated with loss of MSH2 expression, increased mutational burden, MMRD signatures and MS-indel accumulation, the hallmarks of MMRD. In contrast, maturation into brain organoids and examination of blood and fibroblasts failed to show similar processes, preserving MMR proficiency. The combined use of iPSC, organoid technologies and functional genomics analyses highlights the potential of cutting-edge cellular and molecular analysis techniques to define processes controlling tumorigenesis and uncovers a new paradigm of tissue-specific MMRD, which affects the clinical management of these patients.
Collapse
Affiliation(s)
- V J Forster
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - M Aronson
- Zane Cohen Centre, Sinai Health System and Faculty of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - C Zhang
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - J Chung
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - S Sudhaman
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - M A Galati
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - J Kelly
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - L Negm
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - A B Ercan
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - L Stengs
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - C Durno
- Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, ON, Canada
| | - M Edwards
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - M Komosa
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - N M Nunes
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - S Pedersen
- University Health Network, Toronto, ON, Canada
| | - J Wellum
- University Health Network, Toronto, ON, Canada
| | - I Siddiqui
- Department of Paediatric Laboratory Medicine and Pathobiology, Division of Pathology, The Hospital for Sick Children, Toronto, ON, Canada
| | - V Bianchi
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - B R Weil
- Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - V L Fox
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
| | - T J Pugh
- University Health Network, Toronto, ON, Canada
| | - J Kamihara
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - U Tabori
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada.
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
17
|
Rosendahl Huber A, Pleguezuelos-Manzano C, Puschhof J, Ubels J, Boot C, Saftien A, Verheul M, Trabut LT, Groenen N, van Roosmalen M, Ouyang KS, Wood H, Quirke P, Meijer G, Cuppen E, Clevers H, van Boxtel R. Improved detection of colibactin-induced mutations by genotoxic E. coli in organoids and colorectal cancer. Cancer Cell 2024; 42:487-496.e6. [PMID: 38471458 DOI: 10.1016/j.ccell.2024.02.009] [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: 09/21/2022] [Revised: 01/26/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024]
Abstract
Co-culture of intestinal organoids with a colibactin-producing pks+E. coli strain (EcC) revealed mutational signatures also found in colorectal cancer (CRC). E. coli Nissle 1917 (EcN) remains a commonly used probiotic, despite harboring the pks operon and inducing double strand DNA breaks. We determine the mutagenicity of EcN and three CRC-derived pks+E. coli strains with an analytical framework based on sequence characteristic of colibactin-induced mutations. All strains, including EcN, display varying levels of mutagenic activity. Furthermore, a machine learning approach attributing individual mutations to colibactin reveals that patients with colibactin-induced mutations are diagnosed at a younger age and that colibactin can induce a specific APC mutation. These approaches allow the sensitive detection of colibactin-induced mutations in ∼12% of CRC genomes and even in whole exome sequencing data, representing a crucial step toward pinpointing the mutagenic activity of distinct pks+E. coli strains.
Collapse
Affiliation(s)
- Axel Rosendahl Huber
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Cayetano Pleguezuelos-Manzano
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Jens Puschhof
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands; Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
| | - Joske Ubels
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Charelle Boot
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Aurelia Saftien
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands; Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Mark Verheul
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Laurianne T Trabut
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Niels Groenen
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Markus van Roosmalen
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Kyanna S Ouyang
- Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Henry Wood
- Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Phil Quirke
- Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Gerrit Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Edwin Cuppen
- University Medical Center Utrecht, Utrecht, the Netherlands; Hartwig Medical Foundation, Amsterdam, the Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands; Roche Pharmaceutical Research and Early Development, 4058 Basel, Switzerland.
| | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands.
| |
Collapse
|
18
|
Yao X, Feng M, Wang W. The Clinical and Pathological Characteristics of POLE-Mutated Endometrial Cancer: A Comprehensive Review. Cancer Manag Res 2024; 16:117-125. [PMID: 38463556 PMCID: PMC10921942 DOI: 10.2147/cmar.s445055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 02/08/2024] [Indexed: 03/12/2024] Open
Abstract
Endometrial cancer shows high histological and molecular heterogeneity. The POLE mutation is a significant molecular alteration in endometrial cancer, leading to the identification of a specific subtype known as POLE-mutated endometrial cancer. This subtype exhibits a high tumor mutation burden, abundant lymphocyte infiltration, and a favorable prognosis, making it a promising candidate for immune checkpoint inhibitor therapy. This paper presents a comprehensive review of the clinical and pathological characteristics, outcomes, treatment advancements, pathogenic POLE gene detection, and alternative testing methods for POLE-mutated endometrial cancer.
Collapse
Affiliation(s)
- Xiaohong Yao
- Department of Pathology, West China Second University Hospital, Sichuan University, Sichuan, Chengdu, People’s Republic of China
| | - Min Feng
- Department of Pathology, West China Second University Hospital, Sichuan University, Sichuan, Chengdu, People’s Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, People's Republic of China
| | - Wei Wang
- Department of Pathology, West China Second University Hospital, Sichuan University, Sichuan, Chengdu, People’s Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, People's Republic of China
| |
Collapse
|
19
|
Desai S, Ahmad S, Bawaskar B, Rashmi S, Mishra R, Lakhwani D, Dutt A. Singleton mutations in large-scale cancer genome studies: uncovering the tail of cancer genome. NAR Cancer 2024; 6:zcae010. [PMID: 38487301 PMCID: PMC10939354 DOI: 10.1093/narcan/zcae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 02/23/2024] [Indexed: 03/17/2024] Open
Abstract
Singleton or low-frequency driver mutations are challenging to identify. We present a domain driver mutation estimator (DOME) to identify rare candidate driver mutations. DOME analyzes positions analogous to known statistical hotspots and resistant mutations in combination with their functional and biochemical residue context as determined by protein structures and somatic mutation propensity within conserved PFAM domains, integrating the CADD scoring scheme. Benchmarked against seven other tools, DOME exhibited superior or comparable accuracy compared to all evaluated tools in the prediction of functional cancer drivers, with the exception of one tool. DOME identified a unique set of 32 917 high-confidence predicted driver mutations from the analysis of whole proteome missense variants within domain boundaries across 1331 genes, including 1192 noncancer gene census genes, emphasizing its unique place in cancer genome analysis. Additionally, analysis of 8799 TCGA (The Cancer Genome Atlas) and in-house tumor samples revealed 847 potential driver mutations, with mutations in tyrosine kinase members forming the dominant burden, underscoring its higher significance in cancer. Overall, DOME complements current approaches for identifying novel, low-frequency drivers and resistant mutations in personalized therapy.
Collapse
Affiliation(s)
- Sanket Desai
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, Maharashtra, India
| | - Suhail Ahmad
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, Maharashtra, India
| | - Bhargavi Bawaskar
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
| | - Sonal Rashmi
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
| | - Rohit Mishra
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
| | - Deepika Lakhwani
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
| | - Amit Dutt
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, Maharashtra, India
- Department of Genetics, University of Delhi, South Campus, New Delhi 110021, India
| |
Collapse
|
20
|
Rivera‐de‐Torre E, Lampadariou S, Møiniche M, Bohn MF, Kazemi SM, Laustsen AH. Discovery of broadly-neutralizing antibodies against brown recluse spider and Gadim scorpion sphingomyelinases using consensus toxins as antigens. Protein Sci 2024; 33:e4901. [PMID: 38358130 PMCID: PMC10868436 DOI: 10.1002/pro.4901] [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: 04/19/2023] [Revised: 01/01/2024] [Accepted: 01/03/2024] [Indexed: 02/16/2024]
Abstract
Broadly-neutralizing monoclonal antibodies are becoming increasingly important tools for treating infectious diseases and animal envenomings. However, designing and developing broadly-neutralizing antibodies can be cumbersome using traditional low-throughput iterative protein engineering methods. Here, we present a new high-throughput approach for the standardized discovery of broadly-neutralizing monoclonal antibodies relying on phage display technology and consensus antigens representing average sequences of related proteins. We showcase the utility of this approach by applying it to toxic sphingomyelinases from the venoms of species from very distant orders of the animal kingdom, the recluse spider and Gadim scorpion. First, we designed a consensus sphingomyelinase and performed three rounds of phage display selection, followed by DELFIA-based screening and ranking, and benchmarked this to a similar campaign involving cross-panning against recombinant versions of the native toxins. Second, we identified two scFvs that not only bind the consensus toxins, but which can also neutralize sphingomyelinase activity of native whole venom in vitro. Finally, we conclude that the phage display campaign involving the use of the consensus toxin was more successful in yielding cross-neutralizing scFvs than the phage display campaign involving cross-panning.
Collapse
Affiliation(s)
| | - Stefanos Lampadariou
- Department of Biotechnology and BiomedicineTechnical University of DenmarkKongens LyngbyDenmark
| | - Mark Møiniche
- Department of Biotechnology and BiomedicineTechnical University of DenmarkKongens LyngbyDenmark
| | - Markus F. Bohn
- Department of Biotechnology and BiomedicineTechnical University of DenmarkKongens LyngbyDenmark
| | | | - Andreas H. Laustsen
- Department of Biotechnology and BiomedicineTechnical University of DenmarkKongens LyngbyDenmark
| |
Collapse
|
21
|
Ahmad O, Ahmad T, Pfister SM. IDH mutation, glioma immunogenicity, and therapeutic challenge of primary mismatch repair deficient IDH-mutant astrocytoma PMMRDIA: a systematic review. Mol Oncol 2024. [PMID: 38339779 DOI: 10.1002/1878-0261.13598] [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: 09/27/2023] [Revised: 12/28/2023] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
In 2021, Suwala et al. described Primary Mismatch Repair Deficient IDH-mutant Astrocytoma (PMMRDIA) as a distinct group of gliomas. In unsupervised clustering, PMMRDIA forms distinct cluster, separate from other IDH-mutant gliomas, including IDH-mutant gliomas with secondary mismatch repair (MMR) deficiency. In the published cohort, three patients received treatment with an immune checkpoint blocker (ICB), yet none exhibited a response, which aligns with existing knowledge about the decreased immunogenicity of IDH-mutant gliomas in comparison to IDH-wildtype. In the case of PMMRDIA, the inherent resistance to the standard-of-care temozolomide caused by MMR deficiency is an additional challenge. It is known that a gain-of-function mutation of IDH1/2 genes produces the oncometabolite R-2-hydroxyglutarate (R-2-HG), which increases DNA and histone methylation contributing to the characteristic glioma-associated CpG island methylator phenotype (G-CIMP). While other factors could be involved in remodeling the tumor microenvironment (TME) of IDH-mutant gliomas, this systematic review emphasizes the role of R-2-HG and the subsequent G-CIMP in immune suppression. This highlights a potential actionable pathway to enhance the response of ICB, which might be relevant for addressing the unmet therapeutic challenge of PMMRDIA.
Collapse
Affiliation(s)
- Olfat Ahmad
- Division of Pediatric Neurooncology, Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
- University of Oxford, Oxford, UK
- King Hussein Cancer Center (KHCC), Amman, Jordan
| | - Tahani Ahmad
- Department of Pediatric Neuroradiology, IWK Health Center, Halifax, Canada
- Dalhousie University, Halifax, Canada
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| |
Collapse
|
22
|
Barzi A, Weipert CM, Espenschied CR, Raymond VM, Wang-Gillam A, Nezami MA, Gordon EJ, Mahadevan D, Mody K. ERBB2 (HER2) amplifications and co-occurring KRAS alterations in the circulating cell-free DNA of pancreatic ductal adenocarcinoma patients and response to HER2 inhibition. Front Oncol 2024; 14:1339302. [PMID: 38406801 PMCID: PMC10885695 DOI: 10.3389/fonc.2024.1339302] [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: 11/15/2023] [Accepted: 01/16/2024] [Indexed: 02/27/2024] Open
Abstract
Purpose Despite accumulating data regarding the genomic landscape of pancreatic ductal adenocarcinoma (PDAC), olaparib is the only biomarker-driven FDA-approved targeted therapy with a PDAC-specific approval. Treating ERBB2(HER2)-amplified PDAC with anti-HER2 therapy has been reported with mixed results. Most pancreatic adenocarcinomas have KRAS alterations, which have been shown to be a marker of resistance to HER2-targeted therapies in other malignancies, though the impact of these alterations in pancreatic cancer is unknown. We describe two cases of ERBB2-amplified pancreatic cancer patients treated with anti-HER2 therapy and provide data on the frequency of ERBB2 amplifications and KRAS alterations identified by clinical circulating cell-free DNA testing. Methods De-identified molecular test results for all patients with pancreatic cancer who received clinical cell-free circulating DNA analysis (Guardant360) between 06/2014 and 01/2018 were analyzed. Cell-free circulating DNA analysis included next-generation sequencing of up to 73 genes, including select small insertion/deletions, copy number amplifications, and fusions. Results Of 1,791 patients with pancreatic adenocarcinoma, 36 (2.0%) had an ERBB2 amplification, 26 (72.2%) of whom had a KRAS alteration. Treatment data were available for seven patients. Two were treated with anti-HER2 therapy after their cell-free circulating DNA result, with both benefiting from therapy, including one with a durable response to trastuzumab and no KRAS alteration detected until progression. Conclusion Our case series illustrates that certain patients with ERBB2-amplified pancreatic adenocarcinoma may respond to anti-HER2 therapy and gain several months of prolonged survival. Our data suggests KRAS mutations as a possible mechanism of primary and acquired resistance to anti-HER2 therapy in pancreatic cancer. Additional studies are needed to clarify the role of KRAS in resistance to anti-HER2 therapy.
Collapse
Affiliation(s)
- Afsaneh Barzi
- Department of Medical Oncology & Therapeutics Research, City of Hope National Medical Center, Duarte, CA, United States
| | | | | | | | - Andrea Wang-Gillam
- Division of Oncology, Siteman Cancer Center, St. Louis, MO, United States
| | | | - Eva J. Gordon
- Private Health Management, Inc., Los Angeles, CA, United States
| | - Daruka Mahadevan
- Division of Hematology and Oncology, Department of Medicine, University of Texas Health, San Antonio, San Antonio, TX, United States
| | - Kabir Mody
- Division of Hematology-Oncology, Department of Medicine, Mayo Clinic, Jacksonville, FL, United States
| |
Collapse
|
23
|
Das A, Fernandez NR, Levine A, Bianchi V, Stengs LK, Chung J, Negm L, Dimayacyac JR, Chang Y, Nobre L, Ercan AB, Sanchez-Ramirez S, Sudhaman S, Edwards M, Larouche V, Samuel D, Van Damme A, Gass D, Ziegler DS, Bielack SS, Koschmann C, Zelcer S, Yalon-Oren M, Campino GA, Sarosiek T, Nichols KE, Loret De Mola R, Bielamowicz K, Sabel M, Frojd CA, Wood MD, Glover JM, Lee YY, Vanan M, Adamski JK, Perreault S, Chamdine O, Hjort MA, Zapotocky M, Carceller F, Wright E, Fedorakova I, Lossos A, Tanaka R, Osborn M, Blumenthal DT, Aronson M, Bartels U, Huang A, Ramaswamy V, Malkin D, Shlien A, Villani A, Dirks PB, Pugh TJ, Getz G, Maruvka YE, Tsang DS, Ertl-Wagner B, Hawkins C, Bouffet E, Morgenstern DA, Tabori U. Combined Immunotherapy Improves Outcome for Replication-Repair-Deficient (RRD) High-Grade Glioma Failing Anti-PD-1 Monotherapy: A Report from the International RRD Consortium. Cancer Discov 2024; 14:258-273. [PMID: 37823831 PMCID: PMC10850948 DOI: 10.1158/2159-8290.cd-23-0559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/28/2023] [Accepted: 10/10/2023] [Indexed: 10/13/2023]
Abstract
Immune checkpoint inhibition (ICI) is effective for replication-repair-deficient, high-grade gliomas (RRD-HGG). The clinical/biological impact of immune-directed approaches after failing ICI monotherapy is unknown. We performed an international study on 75 patients treated with anti-PD-1; 20 are progression free (median follow-up, 3.7 years). After second progression/recurrence (n = 55), continuing ICI-based salvage prolonged survival to 11.6 months (n = 38; P < 0.001), particularly for those with extreme mutation burden (P = 0.03). Delayed, sustained responses were observed, associated with changes in mutational spectra and the immune microenvironment. Response to reirradiation was explained by an absence of deleterious postradiation indel signatures (ID8). CTLA4 expression increased over time, and subsequent CTLA4 inhibition resulted in response/stable disease in 75%. RAS-MAPK-pathway inhibition led to the reinvigoration of peripheral immune and radiologic responses. Local (flare) and systemic immune adverse events were frequent (biallelic mismatch-repair deficiency > Lynch syndrome). We provide a mechanistic rationale for the sustained benefit in RRD-HGG from immune-directed/synergistic salvage therapies. Future approaches need to be tailored to patient and tumor biology. SIGNIFICANCE Hypermutant RRD-HGG are susceptible to checkpoint inhibitors beyond initial progression, leading to improved survival when reirradiation and synergistic immune/targeted agents are added. This is driven by their unique biological and immune properties, which evolve over time. Future research should focus on combinatorial regimens that increase patient survival while limiting immune toxicity. This article is featured in Selected Articles from This Issue, p. 201.
Collapse
Affiliation(s)
- Anirban Das
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
- Department of Paediatric Haematology and Oncology, Tata Medical Center, Kolkata, India
- Department of Paediatrics, University of Toronto, Toronto, Canada
| | - Nicholas R. Fernandez
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Adrian Levine
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Vanessa Bianchi
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Lucie K. Stengs
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Jiil Chung
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Logine Negm
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Jose Rafael Dimayacyac
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Yuan Chang
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Liana Nobre
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Ayse B. Ercan
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Santiago Sanchez-Ramirez
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Sumedha Sudhaman
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Melissa Edwards
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Valerie Larouche
- Pediatric Haematology/Oncology Department, CHU de Québec-Université Laval, Quebec City, Canada
| | - David Samuel
- Department of Paediatric Oncology, Valley Children's Hospital, Madera, California
| | - An Van Damme
- Department of Paediatric Haematology and Oncology, Saint Luc University Hospital, Université Catholique de Louvain, Brussels, Belgium
| | - David Gass
- Atrium Health/Levine Children's Hospital, Charlotte, North Carolina
| | - David S. Ziegler
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, Australia
- School of Clinical Medicine, UNSW Sydney, Sydney, Australia
| | - Stefan S. Bielack
- Department of Pediatric Oncology, Hematology and Immunology, Center for Childhood, Adolescent, and Women's Medicine, Stuttgart Cancer Center, Klinikum Stuttgart, Stuttgart, Germany
| | - Carl Koschmann
- Pediatric Hematology/Oncology, C.S. Mott Children's Hospital, University of Michigan, Ann Arbor, Michigan
| | - Shayna Zelcer
- Department of Pediatrics, London Health Sciences Centre, London, Canada
| | - Michal Yalon-Oren
- Department of Paediatric Haematology-Oncology, Sheba Medical Centre, Ramat Gan, Israel
| | - Gadi Abede Campino
- Department of Paediatric Haematology-Oncology, Sheba Medical Centre, Ramat Gan, Israel
| | | | - Kim E. Nichols
- Department of Oncology, St Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Kevin Bielamowicz
- Department of Pediatrics, Section of Pediatric Hematology/Oncology, The University of Arkansas for Medical Sciences/Arkansas Children's Hospital, Little Rock, Arkansas
| | - Magnus Sabel
- Department of Paediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg & Queen Silvia Children's Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Charlotta A. Frojd
- Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Matthew D. Wood
- Neuropathology, Oregon Health & Science University Department of Pathology, Portland, Oregon
| | - Jason M. Glover
- Department of Pediatric Hematology/Oncology, Randall Children's Hospital, Portland, Oregon
| | - Yi-Yen Lee
- Department of Neurosurgery, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Magimairajan Vanan
- Pediatric Hematology-Oncology, CancerCare Manitoba, Winnipeg, Canada
- CancerCare Manitoba Research Institute, Pediatrics and Child Health, University of Manitoba, Winnipeg, Canada
| | - Jenny K. Adamski
- Neuro-oncology Division, Birmingham Children's Hospital, Birmingham, United Kingdom
| | - Sebastien Perreault
- Neurosciences Department, Child Neurology Division, CHU Sainte-Justine, Montreal, Canada
| | - Omar Chamdine
- Pediatric Hematology Oncology, King Fahad Specialist Hospital Dammam, Eastern Province, Saudi Arabia
| | - Magnus Aasved Hjort
- Department of Paediatric Haematology and Oncology, St. Olav's University Hospital, Trondheim, Norway
| | - Michal Zapotocky
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, University Hospital Motol, Charles University, Prague, Czech Republic
| | - Fernando Carceller
- Paediatric and Adolescent Neuro-Oncology and Drug Development, The Royal Marsden NHS Foundation Trust & Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Erin Wright
- Division of Neuro-Oncology, Akron Children's Hospital, Akron, Ohio
| | - Ivana Fedorakova
- Clinic of Pediatric Oncology and Hematology, University Children's Hospital, Banská Bystrica, Slovakia
| | - Alexander Lossos
- Department of Oncology, Leslie and Michael Gaffin Centre for Neuro-Oncology, Hadassah-Hebrew University Medical Centre, Jerusalem, Israel
| | - Ryuma Tanaka
- Division of Hematology/Oncology/Blood and Marrow Transplantation, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Michael Osborn
- Women's and Children's Hospital, North Adelaide, Australia
| | - Deborah T. Blumenthal
- Neuro-Oncology Service, Tel-Aviv Medical Center, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Melyssa Aronson
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Canada
| | - Ute Bartels
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Canada
- Department of Paediatrics, University of Toronto, Toronto, Canada
| | - Annie Huang
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Vijay Ramaswamy
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - David Malkin
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- Department of Paediatrics, University of Toronto, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Adam Shlien
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Anita Villani
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Canada
- Department of Paediatrics, University of Toronto, Toronto, Canada
| | - Peter B. Dirks
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
- Division of Neurosurgery, The Hospital for Sick Children, Toronto, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Trevor J. Pugh
- Ontario Institute for Cancer Research, Princess Margaret Cancer Centre, Toronto, Canada
| | - Gad Getz
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Derek S. Tsang
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Birgit Ertl-Wagner
- Department of Diagnostic Imaging, The Hospital for Sick Children, Toronto, Canada
| | - Cynthia Hawkins
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Eric Bouffet
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Canada
| | - Daniel A. Morgenstern
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Canada
- Department of Paediatrics, University of Toronto, Toronto, Canada
| | - Uri Tabori
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| |
Collapse
|
24
|
Tamura D, Abe M, Hiraki H, Sasaki N, Yashima‐Abo A, Ikarashi D, Kato R, Kato Y, Maekawa S, Kanehira M, Takata R, Maejima K, Sasagawa S, Fujita M, Suzuki Y, Nakagawa H, Iwaya T, Nishizuka SS, Obara W. Postoperative recurrence detection using individualized circulating tumor DNA in upper tract urothelial carcinoma. Cancer Sci 2024; 115:529-539. [PMID: 38083992 PMCID: PMC10859621 DOI: 10.1111/cas.16025] [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: 07/28/2023] [Revised: 10/13/2023] [Accepted: 11/06/2023] [Indexed: 02/13/2024] Open
Abstract
Biomarkers that could detect the postoperative recurrence of upper tract urothelial carcinoma (UTUC) have not been established. In this prospective study, we aim to evaluate the utility of individualized circulating tumor DNA (ctDNA) monitoring using digital PCR (dPCR) as a tumor recurrence biomarker for UTUC in the perioperative period. Twenty-three patients who underwent radical nephroureterectomy (RNU) were included. In each patient, whole exome sequencing by next-generation sequencing and TERT promoter sequencing of tumor DNA were carried out. Case-specific gene mutations were selected from sequencing analysis to examine ctDNA by dPCR analysis. We also prospectively collected plasma and urine ctDNA from each patient. The longitudinal variant allele frequencies of ctDNA during the perioperative period were plotted. Case-specific gene mutations were detected in 22 cases (96%) from ctDNA in the preoperative samples. Frequently detected genes were TERT (39%), FGFR3 (26%), TP53 (22%), and HRAS (13%). In all cases, we obtained plasma and urine samples for 241 time points and undertook individualized ctDNA monitoring for 2 years after RNU. Ten patients with intravesical recurrence had case-specific ctDNA detected in urine at the time of recurrence. The mean lead time of urinary ctDNA in intravesical recurrence was 60 days (range, 0-202 days). Two patients with distal metastasis had case-specific ctDNA in plasma at the time of metastasis. In UTUC, tumor-specific gene mutations can be monitored postoperatively as ctDNA in plasma and urine. Individualized ctDNA might be a minimally invasive biomarker for the early detection of postoperative recurrence.
Collapse
Affiliation(s)
- Daichi Tamura
- Department of UrologyIwate Medical University School of MedicineYahabaJapan
| | - Masakazu Abe
- Department of UrologyIwate Medical University School of MedicineYahabaJapan
- Division of Biomedical Research and DevelopmentIwate Medical University Institute for Biomedical SciencesYahabaJapan
| | - Hayato Hiraki
- Division of Biomedical Research and DevelopmentIwate Medical University Institute for Biomedical SciencesYahabaJapan
| | - Noriyuki Sasaki
- Division of Biomedical Research and DevelopmentIwate Medical University Institute for Biomedical SciencesYahabaJapan
| | - Akiko Yashima‐Abo
- Division of Biomedical Research and DevelopmentIwate Medical University Institute for Biomedical SciencesYahabaJapan
| | - Daiki Ikarashi
- Department of UrologyIwate Medical University School of MedicineYahabaJapan
| | - Renpei Kato
- Department of UrologyIwate Medical University School of MedicineYahabaJapan
| | - Yoichiro Kato
- Department of UrologyIwate Medical University School of MedicineYahabaJapan
| | - Shigekatsu Maekawa
- Department of UrologyIwate Medical University School of MedicineYahabaJapan
| | - Mitsugu Kanehira
- Department of UrologyIwate Medical University School of MedicineYahabaJapan
| | - Ryo Takata
- Department of UrologyIwate Medical University School of MedicineYahabaJapan
| | - Kazuhiro Maejima
- Laboratory for Cancer GenomicsRIKEN Center for Integrative Medical SciencesYokohamaJapan
| | - Shota Sasagawa
- Laboratory for Cancer GenomicsRIKEN Center for Integrative Medical SciencesYokohamaJapan
| | - Masashi Fujita
- Laboratory for Cancer GenomicsRIKEN Center for Integrative Medical SciencesYokohamaJapan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical SciencesThe University of TokyoKashiwaJapan
| | - Hidewaki Nakagawa
- Laboratory for Cancer GenomicsRIKEN Center for Integrative Medical SciencesYokohamaJapan
| | - Takeshi Iwaya
- Department of Clinical OncologyIwate Medical University School of MedicineYahabaJapan
| | - Satoshi S. Nishizuka
- Division of Biomedical Research and DevelopmentIwate Medical University Institute for Biomedical SciencesYahabaJapan
| | - Wataru Obara
- Department of UrologyIwate Medical University School of MedicineYahabaJapan
| |
Collapse
|
25
|
Sakakida T, Ishikawa T, Doi T, Morita R, Kataoka S, Miyake H, Yamaguchi K, Moriguchi M, Sogame Y, Yasuda H, Iwasaku M, Konishi H, Takayama K, Itoh Y. Genomic profile and clinical features of MSI-H and TMB-high pancreatic cancers: real-world data from C-CAT database. J Gastroenterol 2024; 59:145-156. [PMID: 38006445 DOI: 10.1007/s00535-023-02058-8] [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: 05/21/2023] [Accepted: 11/01/2023] [Indexed: 11/27/2023]
Abstract
BACKGROUND Microsatellite instability high (MSI-H) and tumor mutational burden high (TMB-high) pancreatic cancer are rare, and information is lacking. Based on the C-CAT database, we analyzed the clinical and genomic characteristics of patients with these subtypes. METHODS We retrospectively reviewed data on 2206 patients with unresectable pancreatic adenocarcinoma enrolled in C-CAT between July 2019 and January 2022. The clinical features, proportion of genomic variants classified as oncogenic/pathogenic in C-CAT, overall response rate (ORR), disease control rate (DCR), and time to treatment failure (TTF) of chemotherapy as first-line treatment were evaluated. RESULTS Numbers of patients with MSI-H and TMB-high were 7 (0.3%) and 39 (1.8%), respectively. All MSI-H patients were TMB-high. MSI-H and TMB-high patients harbored more mismatch repair genes, such as MSH2, homologous recombination-related genes, such as ATR and BRCA2, and other genes including BRAF, KMT2D, and SMARCA4. None of the 6 MSI-H patients who received chemotherapy achieved a clinical response, including 4 patients treated with gemcitabine plus nab-paclitaxel (GnP) therapy, whose DCR was significantly lower than that of microsatellite stable (MSS) patients (0 vs. 67.0%, respectively, p = 0.01). Among the TMB-high and TMB-low groups, no significant differences were shown in ORR, DCR (17.1 vs. 23.1% and 57.1 vs. 63.1%, respectively), or median TTF (25.9 vs. 28.0 weeks, respectively) of overall first-line chemotherapy. CONCLUSIONS MSI-H and TMB-high pancreatic cancers showed some distinct genomic and clinical features from our real-world data. These results suggest the importance of adapting optimal treatment strategies according to the genomic alterations.
Collapse
Affiliation(s)
- Tomoki Sakakida
- Department of Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho, Hirokoji agaru, Kawaramachi Street, Kamigyoku, Kyoto, Kyoto, 602-8566, Japan
- Department of Cancer Genome Medical Center, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takeshi Ishikawa
- Department of Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho, Hirokoji agaru, Kawaramachi Street, Kamigyoku, Kyoto, Kyoto, 602-8566, Japan.
- Department of Cancer Genome Medical Center, Kyoto Prefectural University of Medicine, Kyoto, Japan.
- Outpatient Oncology Unit, Kyoto Prefectural University of Medicine, Kyoto, Japan.
| | - Toshifumi Doi
- Department of Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho, Hirokoji agaru, Kawaramachi Street, Kamigyoku, Kyoto, Kyoto, 602-8566, Japan
- Department of Cancer Genome Medical Center, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Ryuichi Morita
- Department of Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho, Hirokoji agaru, Kawaramachi Street, Kamigyoku, Kyoto, Kyoto, 602-8566, Japan
- Department of Cancer Genome Medical Center, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Seita Kataoka
- Department of Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho, Hirokoji agaru, Kawaramachi Street, Kamigyoku, Kyoto, Kyoto, 602-8566, Japan
| | - Hayato Miyake
- Department of Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho, Hirokoji agaru, Kawaramachi Street, Kamigyoku, Kyoto, Kyoto, 602-8566, Japan
| | - Kanji Yamaguchi
- Department of Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho, Hirokoji agaru, Kawaramachi Street, Kamigyoku, Kyoto, Kyoto, 602-8566, Japan
| | - Michihisa Moriguchi
- Department of Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho, Hirokoji agaru, Kawaramachi Street, Kamigyoku, Kyoto, Kyoto, 602-8566, Japan
| | - Yoshio Sogame
- Department of Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho, Hirokoji agaru, Kawaramachi Street, Kamigyoku, Kyoto, Kyoto, 602-8566, Japan
| | - Hiroaki Yasuda
- Department of Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho, Hirokoji agaru, Kawaramachi Street, Kamigyoku, Kyoto, Kyoto, 602-8566, Japan
| | - Masahiro Iwasaku
- Department of Cancer Genome Medical Center, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hideyuki Konishi
- Department of Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho, Hirokoji agaru, Kawaramachi Street, Kamigyoku, Kyoto, Kyoto, 602-8566, Japan
| | - Koichi Takayama
- Department of Cancer Genome Medical Center, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Outpatient Oncology Unit, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoshito Itoh
- Department of Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho, Hirokoji agaru, Kawaramachi Street, Kamigyoku, Kyoto, Kyoto, 602-8566, Japan
| |
Collapse
|
26
|
Shah SM, Demidova EV, Ringenbach S, Faezov B, Andrake M, Gandhi A, Mur P, Viana-Errasti J, Xiu J, Swensen J, Valle L, Dunbrack RL, Hall MJ, Arora S. Exploring Co-occurring POLE Exonuclease and Non-exonuclease Domain Mutations and Their Impact on Tumor Mutagenicity. CANCER RESEARCH COMMUNICATIONS 2024; 4:213-225. [PMID: 38282550 PMCID: PMC10812383 DOI: 10.1158/2767-9764.crc-23-0312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/05/2023] [Accepted: 01/02/2024] [Indexed: 01/13/2024]
Abstract
POLE driver mutations in the exonuclease domain (ExoD driver) are prevalent in several cancers, including colorectal cancer and endometrial cancer, leading to dramatically ultra-high tumor mutation burden (TMB). To understand whether POLE mutations that are not classified as drivers (POLE Variant) contribute to mutagenesis, we assessed TMB in 447 POLE-mutated colorectal cancers, endometrial cancers, and ovarian cancers classified as TMB-high ≥10 mutations/Mb (mut/Mb) or TMB-low <10 mut/Mb. TMB was significantly highest in tumors with "POLE ExoD driver plus POLE Variant" (colorectal cancer and endometrial cancer, P < 0.001; ovarian cancer, P < 0.05). TMB increased with additional POLE variants (P < 0.001), but plateaued at 2, suggesting an association between the presence of these variants and TMB. Integrated analysis of AlphaFold2 POLE models and quantitative stability estimates predicted the impact of multiple POLE variants on POLE functionality. The prevalence of immunogenic neoepitopes was notably higher in the "POLE ExoD driver plus POLE Variant" tumors. Overall, this study reveals a novel correlation between POLE variants in POLE ExoD-driven tumors, and ultra-high TMB. Currently, only select pathogenic ExoD mutations with a reliable association with ultra-high TMB inform clinical practice. Thus, these findings are hypothesis-generating, require functional validation, and could potentially inform tumor classification, treatment responses, and clinical outcomes. SIGNIFICANCE Somatic POLE ExoD driver mutations cause proofreading deficiency that induces high TMB. This study suggests a novel modifier role for POLE variants in POLE ExoD-driven tumors, associated with ultra-high TMB. These data, in addition to future functional studies, may inform tumor classification, therapeutic response, and patient outcomes.
Collapse
Affiliation(s)
- Shreya M. Shah
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- Science Scholars Program, Temple University, Philadelphia, Pennsylvania
| | - Elena V. Demidova
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation
| | - Salena Ringenbach
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- Lewis Katz School of Medicine, Temple University, Bethlehem, Pennsylvania
| | - Bulat Faezov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation
- Program in Cancer Signaling and Microenvironment, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Mark Andrake
- Program in Cancer Signaling and Microenvironment, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Arjun Gandhi
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- University College Dublin School of Medicine and Medical Science, Dublin, Ireland
| | - Pilar Mur
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Julen Viana-Errasti
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | | | | | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Roland L. Dunbrack
- Program in Cancer Signaling and Microenvironment, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Michael J. Hall
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Sanjeevani Arora
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| |
Collapse
|
27
|
Ostroverkhova D, Tyryshkin K, Beach AK, Moore EA, Masoudi-Sobhanzadeh Y, Barbari SR, Rogozin IB, Shaitan KV, Panchenko AR, Shcherbakova PV. DNA polymerase ε and δ variants drive mutagenesis in polypurine tracts in human tumors. Cell Rep 2024; 43:113655. [PMID: 38219146 PMCID: PMC10830898 DOI: 10.1016/j.celrep.2023.113655] [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: 07/14/2023] [Revised: 11/07/2023] [Accepted: 12/19/2023] [Indexed: 01/16/2024] Open
Abstract
Alterations in the exonuclease domain of DNA polymerase ε cause ultramutated cancers. These cancers accumulate AGA>ATA transversions; however, their genomic features beyond the trinucleotide motifs are obscure. We analyze the extended DNA context of ultramutation using whole-exome sequencing data from 524 endometrial and 395 colorectal tumors. We find that G>T transversions in POLE-mutant tumors predominantly affect sequences containing at least six consecutive purines, with a striking preference for certain positions within polypurine tracts. Using this signature, we develop a machine-learning classifier to identify tumors with hitherto unknown POLE drivers and validate two drivers, POLE-E978G and POLE-S461L, by functional assays in yeast. Unlike other pathogenic variants, the E978G substitution affects the polymerase domain of Pol ε. We further show that tumors with POLD1 drivers share the extended signature of POLE ultramutation. These findings expand the understanding of ultramutation mechanisms and highlight peculiar mutagenic properties of polypurine tracts in the human genome.
Collapse
Affiliation(s)
- Daria Ostroverkhova
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, ON, Canada
| | - Kathrin Tyryshkin
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, ON, Canada
| | - Annette K Beach
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Elizabeth A Moore
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Yosef Masoudi-Sobhanzadeh
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, ON, Canada
| | - Stephanie R Barbari
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, ON, Canada.
| | - Polina V Shcherbakova
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA.
| |
Collapse
|
28
|
Guerrini-Rousseau L, Pasmant E, Muleris M, Abbou S, Adam-De-Beaumais T, Brugieres L, Cabaret O, Colas C, Cotteret S, Decq P, Dufour C, Guillerm E, Rouleau E, Varlet P, Zili S, Vidaud D, Grill J. Neurofibromatosis type 1 mosaicism in patients with constitutional mismatch repair deficiency. J Med Genet 2024; 61:158-162. [PMID: 37775264 PMCID: PMC10850717 DOI: 10.1136/jmg-2023-109235] [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: 02/23/2023] [Accepted: 08/21/2023] [Indexed: 10/01/2023]
Abstract
Differential diagnosis between constitutional mismatch repair deficiency (CMMRD) and neurofibromatosis type 1 (NF1) is crucial as treatment and surveillance differ. We report the case of a girl with a clinical diagnosis of sporadic NF1 who developed a glioblastoma. Immunohistochemistry for MMR proteins identified PMS2 loss in tumour and normal cells and WES showed the tumour had an ultra-hypermutated phenotype, supporting the diagnosis of CMMRD. Germline analyses identified two variants (one pathogenic variant and one classified as variant(s) of unknown significance) in the PMS2 gene and subsequent functional assays on blood lymphocytes confirmed the diagnosis of CMMRD. The large plexiform neurofibroma of the thigh and the freckling were however more compatible with NF1. Indeed, a NF1 PV (variant allele frequencies of 20%, 3% and 9% and in blood, skin and saliva samples, respectively) was identified confirming a mosaicism for NF1. Retrospective analysis of a French cohort identified NF1 mosaicism in blood DNA in 2 out of 22 patients with CMMRD, underlining the existence of early postzygotic PV of NF1 gene in patients with CMMRD whose tumours have been frequently reported to exhibit somatic NF1 mutations. It highlights the potential role of this pathway in the pathogenesis of CMMRD-associated gliomas and argues in favour of testing MEK inhibitors in this context.
Collapse
Affiliation(s)
- Léa Guerrini-Rousseau
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Molecular Predictors and New Targets in Oncology, Inserm U981 Team "Genomics and Oncogenesis of pediatric Brain Tumors", Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Eric Pasmant
- Department of Molecular Genetics, Hôpital Cochin, DMU BioPhyGen, AP-HP Centre-Université Paris Cité, Paris, France
- Inserm U1016-CNRS UMR8104, Institut Cochin, Université Paris Cité, CARPEM, Paris, France
| | - Martine Muleris
- Department of Genetics, Hôpital Pitié-Salpêtrière. AP-HP. Sorbonne Université, Paris, France
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, Equipe Instabilité des Microsatellites et Cancer, Equipe labellisée par la Ligue Nationale contre le Cancer, F-75012 Paris, France
| | - Samuel Abbou
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Molecular Predictors and New Targets in Oncology, Inserm U981 Team "Genomics and Oncogenesis of pediatric Brain Tumors", Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Tiphaine Adam-De-Beaumais
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Laurence Brugieres
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Molecular Predictors and New Targets in Oncology, Inserm U981 Team "Genomics and Oncogenesis of pediatric Brain Tumors", Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Odile Cabaret
- Department of Medical Biology and Pathology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Chrystelle Colas
- Department of Genetics, Institut Curie, PSL Research University, Paris, France
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par la Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris, France
| | - Sophie Cotteret
- Department of Medical Biology and Pathology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Philippe Decq
- Neurosurgery Department, Beaujon Hospital, Paris Cité University, Paris, France
| | - Christelle Dufour
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Molecular Predictors and New Targets in Oncology, Inserm U981 Team "Genomics and Oncogenesis of pediatric Brain Tumors", Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Erell Guillerm
- Department of Genetics, Hôpital Pitié-Salpêtrière. AP-HP. Sorbonne Université, Paris, France
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, Equipe Instabilité des Microsatellites et Cancer, Equipe labellisée par la Ligue Nationale contre le Cancer, F-75012 Paris, France
| | - Etienne Rouleau
- Department of Medical Biology and Pathology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Pascale Varlet
- Service de Neuropathologie, GHU Psychiatrie et Neurosciences, site Sainte-Anne, Paris, France
| | - Saïma Zili
- Molecular Predictors and New Targets in Oncology, Inserm U981 Team "Genomics and Oncogenesis of pediatric Brain Tumors", Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Dominique Vidaud
- Department of Molecular Genetics, Hôpital Cochin, DMU BioPhyGen, AP-HP Centre-Université Paris Cité, Paris, France
| | - Jacques Grill
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Molecular Predictors and New Targets in Oncology, Inserm U981 Team "Genomics and Oncogenesis of pediatric Brain Tumors", Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| |
Collapse
|
29
|
Selves J, de Castro E Gloria H, Brunac AC, Saffi J, Guimbaud R, Brousset P, Hoffmann JS. Exploring the basis of heterogeneity of cancer aggressiveness among the mutated POLE variants. Life Sci Alliance 2024; 7:e202302290. [PMID: 37891003 PMCID: PMC10610022 DOI: 10.26508/lsa.202302290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/04/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
Germline pathogenic variants in the exonuclease domain of the replicative DNA polymerase Pol ε encoded by the POLE gene, predispose essentially to colorectal and endometrial tumors by inducing an ultramutator phenotype. It is still unclear whether all the POLE alterations influence similar strength tumorigenesis, immune microenvironment, and treatment response. In this review, we summarize the current understanding of the mechanisms and consequences of POLE mutations in human malignancies; we highlight the heterogeneity of mutation rate and cancer aggressiveness among POLE variants, propose some mechanistic basis underlining such heterogeneity, and discuss novel considerations for the choice and efficacy of therapies of POLE tumors.
Collapse
Affiliation(s)
- Janick Selves
- Department of Pathology, Institut Universitaire du Cancer-Oncopole de Toulouse; Centre Hospitalier Universitaire (CHU), Toulouse, France
- Université Fédérale Toulouse Midi-Pyrénées, Université Toulouse III Paul Sabatier, INSERM, CRCT, Toulouse, France
| | - Helena de Castro E Gloria
- Laboratory of Genetic Toxicology, Federal University of Health Sciences of Porto Alegre, Porto Alegre, Brazil
| | - Anne-Cécile Brunac
- Department of Pathology, Institut Universitaire du Cancer-Oncopole de Toulouse; Centre Hospitalier Universitaire (CHU), Toulouse, France
| | - Jenifer Saffi
- Laboratory of Genetic Toxicology, Federal University of Health Sciences of Porto Alegre, Porto Alegre, Brazil
| | - Rosine Guimbaud
- Université Fédérale Toulouse Midi-Pyrénées, Université Toulouse III Paul Sabatier, INSERM, CRCT, Toulouse, France
- Department of Digestive Oncology, Centre Hospitalier Universitaire (CHU), Toulouse, France
- Department of Digestive Surgery, Centre Hospitalier Universitaire (CHU), Toulouse, France
| | - Pierre Brousset
- Department of Pathology, Institut Universitaire du Cancer-Oncopole de Toulouse; Centre Hospitalier Universitaire (CHU), Toulouse, France
- Université Fédérale Toulouse Midi-Pyrénées, Université Toulouse III Paul Sabatier, INSERM, CRCT, Toulouse, France
- Laboratoire d'Excellence Toulouse Cancer (TOUCAN), Toulouse, France
| | - Jean-Sébastien Hoffmann
- Department of Pathology, Institut Universitaire du Cancer-Oncopole de Toulouse; Centre Hospitalier Universitaire (CHU), Toulouse, France
- Laboratoire d'Excellence Toulouse Cancer (TOUCAN), Toulouse, France
| |
Collapse
|
30
|
Roy B, Knapke S, Pillay-Smiley N, Zhang X, Queen K, Sisson R. Current practice of cancer predisposition testing in pediatric patients with CNS tumors in the United States. Pediatr Blood Cancer 2024; 71:e30725. [PMID: 37859593 DOI: 10.1002/pbc.30725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/10/2023] [Accepted: 10/06/2023] [Indexed: 10/21/2023]
Abstract
An estimated 8.6% of all pediatric patients with central nervous system tumors (CNSTs) have underlying hereditary cancer predisposition (HCP). Identifying HCP affects risk assessment and medical management options for the patients and their family members. However, there is a lack of consensus on the optimal germline genetic testing (GT) approach for pediatric patients with CNSTs. As a first step in addressing the need for consensus, we surveyed oncology and genetics providers from 47 institutions in professional organizations across the United States. We investigated their current practice (e.g., GT decisions and ordering practices) when assessing pediatric patients with CNSTs for HCP. We received 60 responses from 21 pediatric oncologists, 10 neuro-oncologists, 28 genetics providers, and one neuro-oncologist/geneticist. Results demonstrate genetic counselors, followed by oncologists, most often facilitated consent, ordered testing, and selected which test to order. The most ordered test was a multi-gene panel (60%). Of 18 CNST diagnoses, choroid plexus carcinoma (CPC) was the diagnosis for which most providers (78%) reported they would offer GT. For medulloblastoma, 56% overall reported they would offer GT (64% of genetics providers, 62% of neuro-oncologists, 20% of pediatric oncologists; p = .050). Findings suggest that even for the CNSTs most commonly known to be associated with HCP regardless of family history, there was variability in providers' decisions to offer GT. The lack of consensus in GT decisions in our study indicates inconsistencies in the genetics care of pediatric patients with CNSTs, demonstrating a need for consensus guidelines to promote consistent genetics care.
Collapse
Affiliation(s)
- Baylee Roy
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
- Leadership Education in Neurodevelopmental and related Disabilities, University of Cincinnati and Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Sara Knapke
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Natasha Pillay-Smiley
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Xue Zhang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Kate Queen
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Rebecca Sisson
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| |
Collapse
|
31
|
Mundt D, Melguizo-Gavilanes I, Tumu AY, Dubner S, Walters MK, McFarlane L. Somatic POLE Mutation and Ultra-Hypermutated Genotype in a De Novo High-Grade, Isocitrate Dehydrogenase Wild-Type Glioma: Treatment Implications. JCO Precis Oncol 2024; 8:e2300324. [PMID: 38237101 DOI: 10.1200/po.23.00324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/29/2023] [Accepted: 10/26/2023] [Indexed: 01/23/2024] Open
Abstract
Pembrolizumab leads to a durable response in ultra-hypermutated, high-grade, glioma.
Collapse
|
32
|
Hadad S, Gupta R, Oberheim Bush NA, Taylor JW, Villanueva-Meyer JE, Young JS, Wu J, Ravindranathan A, Zhang Y, Warrier G, McCoy L, Shai A, Pekmezci M, Perry A, Bollen AW, Phillips JJ, Braunstein SE, Raleigh DR, Theodosopoulos P, Aghi MK, Chang EF, Hervey-Jumper SL, Costello JF, de Groot J, Butowski NA, Clarke JL, Chang SM, Berger MS, Molinaro AM, Solomon DA. "De novo replication repair deficient glioblastoma, IDH-wildtype" is a distinct glioblastoma subtype in adults that may benefit from immune checkpoint blockade. Acta Neuropathol 2023; 147:3. [PMID: 38079020 PMCID: PMC10713691 DOI: 10.1007/s00401-023-02654-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/24/2023] [Accepted: 10/24/2023] [Indexed: 12/18/2023]
Abstract
Glioblastoma is a clinically and molecularly heterogeneous disease, and new predictive biomarkers are needed to identify those patients most likely to respond to specific treatments. Through prospective genomic profiling of 459 consecutive primary treatment-naïve IDH-wildtype glioblastomas in adults, we identified a unique subgroup (2%, 9/459) defined by somatic hypermutation and DNA replication repair deficiency due to biallelic inactivation of a canonical mismatch repair gene. The deleterious mutations in mismatch repair genes were often present in the germline in the heterozygous state with somatic inactivation of the remaining allele, consistent with glioblastomas arising due to underlying Lynch syndrome. A subset of tumors had accompanying proofreading domain mutations in the DNA polymerase POLE and resultant "ultrahypermutation". The median age at diagnosis was 50 years (range 27-78), compared with 63 years for the other 450 patients with conventional glioblastoma (p < 0.01). All tumors had histologic features of the giant cell variant of glioblastoma. They lacked EGFR amplification, lacked combined trisomy of chromosome 7 plus monosomy of chromosome 10, and only rarely had TERT promoter mutation or CDKN2A homozygous deletion, which are hallmarks of conventional IDH-wildtype glioblastoma. Instead, they harbored frequent inactivating mutations in TP53, NF1, PTEN, ATRX, and SETD2 and recurrent activating mutations in PDGFRA. DNA methylation profiling revealed they did not align with known reference adult glioblastoma methylation classes, but instead had unique globally hypomethylated epigenomes and mostly classified as "Diffuse pediatric-type high grade glioma, RTK1 subtype, subclass A". Five patients were treated with immune checkpoint blockade, four of whom survived greater than 3 years. The median overall survival was 36.8 months, compared to 15.5 months for the other 450 patients (p < 0.001). We conclude that "De novo replication repair deficient glioblastoma, IDH-wildtype" represents a biologically distinct subtype in the adult population that may benefit from prospective identification and treatment with immune checkpoint blockade.
Collapse
Affiliation(s)
- Sara Hadad
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Rohit Gupta
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Nancy Ann Oberheim Bush
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Jennie W Taylor
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Javier E Villanueva-Meyer
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA, USA
| | - Jacob S Young
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Jasper Wu
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Ajay Ravindranathan
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Yalan Zhang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Gayathri Warrier
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Lucie McCoy
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Anny Shai
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Melike Pekmezci
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Arie Perry
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Andrew W Bollen
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Steve E Braunstein
- Department of Radiation Oncology, University of California, San Francisco, CA, USA
| | - David R Raleigh
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Radiation Oncology, University of California, San Francisco, CA, USA
| | - Philip Theodosopoulos
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Manish K Aghi
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Edward F Chang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Shawn L Hervey-Jumper
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - John de Groot
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Nicholas A Butowski
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Jennifer L Clarke
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Susan M Chang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Mitchel S Berger
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Annette M Molinaro
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA.
| | - David A Solomon
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA.
| |
Collapse
|
33
|
Baranov E, Nowak JA. Pathologic Evaluation of Therapeutic Biomarkers in Colorectal Adenocarcinoma. Surg Pathol Clin 2023; 16:635-650. [PMID: 37863556 DOI: 10.1016/j.path.2023.05.002] [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] [Indexed: 10/22/2023]
Abstract
Molecular testing is an essential component of the pathologic evaluation of colorectal carcinoma providing diagnostic, prognostic, and predictive therapeutic information. Mismatch repair status evaluation is required for all tumors. Advanced and metastatic tumors also require determination of tumor mutational burden, KRAS, NRAS, and BRAF mutation status, ERBB2 amplification status, and NTRK and RET gene rearrangement status to guide therapy. Multiple assays, including immunohistochemistry, microsatellite instability testing, MLH1 promoter methylation, and next-generation sequencing, are typically needed. Pathologists must be aware of these requirements to optimally triage tissue. Advances in colorectal cancer molecular diagnostics will continue to drive refinements in colorectal cancer personalized therapy.
Collapse
Affiliation(s)
- Esther Baranov
- Department of Pathology, Brigham & Women's Hospital, 75 Francis Street, Boston, MA 02115, USA
| | - Jonathan A Nowak
- Department of Pathology, Brigham & Women's Hospital, 75 Francis Street, Boston, MA 02115, USA.
| |
Collapse
|
34
|
Catalano M, Iannone LF, Nesi G, Nobili S, Mini E, Roviello G. Immunotherapy-related biomarkers: Confirmations and uncertainties. Crit Rev Oncol Hematol 2023; 192:104135. [PMID: 37717881 DOI: 10.1016/j.critrevonc.2023.104135] [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: 03/16/2023] [Revised: 08/18/2023] [Accepted: 09/12/2023] [Indexed: 09/19/2023] Open
Abstract
Immunotherapy profoundly changed oncology treatment, becoming one of the main therapeutical strategies. Remarkable improvement has been achieved in survival outcomes, but the percentage of patients who benefit from immunotherapy is still limited. Only one-third of patients receiving immune checkpoint inhibitors (ICIs) achieve long-term response. Several patients are not responsive to treatment or relapse after an initial response. To date, programmed death-ligand 1, microsatellite instability, and tumor mutational burden are the three biomarkers validated to predict the ICIs response, but a single variable seems still insufficient in the patient's selection. Considering the substantial and increasing use of these drugs, the identification of new predictive biomarkers of ICI response is of paramount importance. We summarize the state of the art and the clinical use of immune biomarkers in oncology, highlighting the strength and weaknesses of currently approved biomarkers, describing the emerging tissues and circulating biomarkers, and outlining future perspectives.
Collapse
Affiliation(s)
- Martina Catalano
- 1 Section of Clinical Pharmacology and Oncology, Department of Health Sciences, University of Florence, 50139 Florence, Italy
| | - Luigi Francesco Iannone
- 1 Section of Clinical Pharmacology and Oncology, Department of Health Sciences, University of Florence, 50139 Florence, Italy
| | - Gabriella Nesi
- Section of Pathological Anatomy, Department of Health Sciences, University of Florence, 50139 Florence, Italy
| | - Stefania Nobili
- Department of Neuroscience, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, 50139 Florence, Italy
| | - Enrico Mini
- 1 Section of Clinical Pharmacology and Oncology, Department of Health Sciences, University of Florence, 50139 Florence, Italy
| | - Giandomenico Roviello
- 1 Section of Clinical Pharmacology and Oncology, Department of Health Sciences, University of Florence, 50139 Florence, Italy.
| |
Collapse
|
35
|
Das A, Tabori U, Sambira Nahum LC, Collins NB, Deyell R, Dvir R, Faure-Conter C, Hassall TE, Minturn JE, Edwards M, Brookes E, Bianchi V, Levine A, Stone SC, Sudhaman S, Sanchez Ramirez S, Ercan AB, Stengs L, Chung J, Negm L, Getz G, Maruvka YE, Ertl-Wagner B, Ohashi PS, Pugh T, Hawkins C, Bouffet E, Morgenstern DA. Efficacy of Nivolumab in Pediatric Cancers with High Mutation Burden and Mismatch Repair Deficiency. Clin Cancer Res 2023; 29:4770-4783. [PMID: 37126021 PMCID: PMC10690097 DOI: 10.1158/1078-0432.ccr-23-0411] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/23/2023] [Accepted: 04/27/2023] [Indexed: 05/02/2023]
Abstract
PURPOSE Checkpoint inhibitors have limited efficacy for children with unselected solid and brain tumors. We report the first prospective pediatric trial (NCT02992964) using nivolumab exclusively for refractory nonhematologic cancers harboring tumor mutation burden (TMB) ≥5 mutations/megabase (mut/Mb) and/or mismatch repair deficiency (MMRD). PATIENTS AND METHODS Twenty patients were screened, and 10 were ultimately included in the response cohort of whom nine had TMB >10 mut/Mb (three initially eligible based on MMRD) and one patient had TMB between 5 and 10 mut/Mb. RESULTS Delayed immune responses contributed to best overall response of 50%, improving on initial objective responses (20%) and leading to 2-year overall survival (OS) of 50% [95% confidence interval (CI), 27-93]. Four children, including three with refractory malignant gliomas are in complete remission at a median follow-up of 37 months (range, 32.4-60), culminating in 2-year OS of 43% (95% CI, 18.2-100). Biomarker analyses confirmed benefit in children with germline MMRD, microsatellite instability, higher activated and lower regulatory circulating T cells. Stochastic mutation accumulation driven by underlying germline MMRD impacted the tumor microenvironment, contributing to delayed responses. No benefit was observed in the single patient with an MMR-proficient tumor and TMB 7.4 mut/Mb. CONCLUSIONS Nivolumab resulted in durable responses and prolonged survival for the first time in a pediatric trial of refractory hypermutated cancers including malignant gliomas. Novel biomarkers identified here need to be translated rapidly to clinical care to identify children who can benefit from checkpoint inhibitors, including upfront management of cancer. See related commentary by Mardis, p. 4701.
Collapse
Affiliation(s)
- Anirban Das
- Hospital for Sick Children and Department of Paediatrics, University of Toronto, Toronto, Ontario
| | - Uri Tabori
- Hospital for Sick Children and Department of Paediatrics, University of Toronto, Toronto, Ontario
| | - Lauren C. Sambira Nahum
- Hospital for Sick Children and Department of Paediatrics, University of Toronto, Toronto, Ontario
| | - Natalie B. Collins
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | | | - Rina Dvir
- Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | | | | | - Jane E. Minturn
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Melissa Edwards
- Hospital for Sick Children and Department of Paediatrics, University of Toronto, Toronto, Ontario
| | - Elissa Brookes
- Hospital for Sick Children and Department of Paediatrics, University of Toronto, Toronto, Ontario
| | - Vanessa Bianchi
- Hospital for Sick Children and Department of Paediatrics, University of Toronto, Toronto, Ontario
| | - Adrian Levine
- Hospital for Sick Children and Department of Paediatrics, University of Toronto, Toronto, Ontario
| | - Simone C. Stone
- Princess Margaret Cancer Centre and University of Toronto, Toronto, Ontario
| | - Sumedha Sudhaman
- Hospital for Sick Children and Department of Paediatrics, University of Toronto, Toronto, Ontario
| | - Santiago Sanchez Ramirez
- Hospital for Sick Children and Department of Paediatrics, University of Toronto, Toronto, Ontario
| | - Ayse B. Ercan
- Hospital for Sick Children and Department of Paediatrics, University of Toronto, Toronto, Ontario
| | - Lucie Stengs
- Hospital for Sick Children and Department of Paediatrics, University of Toronto, Toronto, Ontario
| | - Jill Chung
- Hospital for Sick Children and Department of Paediatrics, University of Toronto, Toronto, Ontario
| | - Logine Negm
- Hospital for Sick Children and Department of Paediatrics, University of Toronto, Toronto, Ontario
| | - Gad Getz
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Birgit Ertl-Wagner
- Hospital for Sick Children and Department of Paediatrics, University of Toronto, Toronto, Ontario
| | - Pamela S. Ohashi
- Princess Margaret Cancer Centre and University of Toronto, Toronto, Ontario
| | - Trevor Pugh
- Princess Margaret Cancer Centre and University of Toronto, Toronto, Ontario
| | - Cynthia Hawkins
- Hospital for Sick Children and Department of Paediatrics, University of Toronto, Toronto, Ontario
| | - Eric Bouffet
- Hospital for Sick Children and Department of Paediatrics, University of Toronto, Toronto, Ontario
| | - Daniel A. Morgenstern
- Hospital for Sick Children and Department of Paediatrics, University of Toronto, Toronto, Ontario
| |
Collapse
|
36
|
Stourac J, Borko S, Khan RT, Pokorna P, Dobias A, Planas-Iglesias J, Mazurenko S, Pinto G, Szotkowska V, Sterba J, Slaby O, Damborsky J, Bednar D. PredictONCO: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning. Brief Bioinform 2023; 25:bbad441. [PMID: 38066711 PMCID: PMC10709543 DOI: 10.1093/bib/bbad441] [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: 06/22/2023] [Revised: 10/25/2023] [Accepted: 11/10/2023] [Indexed: 12/18/2023] Open
Abstract
PredictONCO 1.0 is a unique web server that analyzes effects of mutations on proteins frequently altered in various cancer types. The server can assess the impact of mutations on the protein sequential and structural properties and apply a virtual screening to identify potential inhibitors that could be used as a highly individualized therapeutic approach, possibly based on the drug repurposing. PredictONCO integrates predictive algorithms and state-of-the-art computational tools combined with information from established databases. The user interface was carefully designed for the target specialists in precision oncology, molecular pathology, clinical genetics and clinical sciences. The tool summarizes the effect of the mutation on protein stability and function and currently covers 44 common oncological targets. The binding affinities of Food and Drug Administration/ European Medicines Agency -approved drugs with the wild-type and mutant proteins are calculated to facilitate treatment decisions. The reliability of predictions was confirmed against 108 clinically validated mutations. The server provides a fast and compact output, ideal for the often time-sensitive decision-making process in oncology. Three use cases of missense mutations, (i) K22A in cyclin-dependent kinase 4 identified in melanoma, (ii) E1197K mutation in anaplastic lymphoma kinase 4 identified in lung carcinoma and (iii) V765A mutation in epidermal growth factor receptor in a patient with congenital mismatch repair deficiency highlight how the tool can increase levels of confidence regarding the pathogenicity of the variants and identify the most effective inhibitors. The server is available at https://loschmidt.chemi.muni.cz/predictonco.
Collapse
Affiliation(s)
- Jan Stourac
- Loschmidt Laboratories, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Loschmidt Laboratories, RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Simeon Borko
- Loschmidt Laboratories, RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
- IT4Innovations Centre of Excellence, Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic
| | - Rayyan T Khan
- Loschmidt Laboratories, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Petra Pokorna
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Adam Dobias
- Loschmidt Laboratories, RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Joan Planas-Iglesias
- Loschmidt Laboratories, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Loschmidt Laboratories, RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Stanislav Mazurenko
- Loschmidt Laboratories, RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Gaspar Pinto
- Loschmidt Laboratories, RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Veronika Szotkowska
- Loschmidt Laboratories, RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jaroslav Sterba
- Department of Paediatric Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Ondrej Slaby
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Loschmidt Laboratories, RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Loschmidt Laboratories, RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
| |
Collapse
|
37
|
Weber CAM, Krönke N, Volk V, Auber B, Förster A, Trost D, Geffers R, Esmaeilzadeh M, Lalk M, Nabavi A, Samii A, Krauss JK, Feuerhake F, Hartmann C, Wiese B, Brand F, Weber RG. Rare germline variants in POLE and POLD1 encoding the catalytic subunits of DNA polymerases ε and δ in glioma families. Acta Neuropathol Commun 2023; 11:184. [PMID: 37990341 PMCID: PMC10664377 DOI: 10.1186/s40478-023-01689-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 11/11/2023] [Indexed: 11/23/2023] Open
Abstract
Pathogenic germline variants in the DNA polymerase genes POLE and POLD1 cause polymerase proofreading-associated polyposis, a dominantly inherited disorder with increased risk of colorectal carcinomas and other tumors. POLE/POLD1 variants may result in high somatic mutation and neoantigen loads that confer susceptibility to immune checkpoint inhibitors (ICIs). To explore the role of POLE/POLD1 germline variants in glioma predisposition, whole-exome sequencing was applied to leukocyte DNA of glioma patients from 61 tumor families with at least one glioma case each. Rare heterozygous POLE/POLD1 missense variants predicted to be deleterious were identified in glioma patients from 10 (16%) families, co-segregating with the tumor phenotype in families with available DNA from several tumor patients. Glioblastoma patients carrying rare POLE variants had a mean overall survival of 21 months. Additionally, germline variants in POLD1, located at 19q13.33, were detected in 2/34 (6%) patients with 1p/19q-codeleted oligodendrogliomas, while POLE variants were identified in 2/4 (50%) glioblastoma patients with a spinal metastasis. In 13/15 (87%) gliomas from patients carrying POLE/POLD1 variants, features of defective polymerase proofreading, e.g. hypermutation, POLE/POLD1-associated mutational signatures, multinucleated cells, and increased intratumoral T cell response, were observed. In a CRISPR/Cas9-derived POLE-deficient LN-229 glioblastoma cell clone, a mutator phenotype and delayed S phase progression were detected compared to wildtype POLE cells. Our data provide evidence that rare POLE/POLD1 germline variants predispose to gliomas that may be susceptible to ICIs. Data compiled here suggest that glioma patients carrying POLE/POLD1 variants may be recognized by cutaneous manifestations, e.g. café-au-lait macules, and benefit from surveillance colonoscopy.
Collapse
Affiliation(s)
- Christine A M Weber
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Nicole Krönke
- Department of Neuropathology, Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Valery Volk
- Department of Neuropathology, Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Bernd Auber
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Alisa Förster
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | | | - Robert Geffers
- Genome Analytics Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Michael Lalk
- Department of Neurosurgery, KRH Klinikum Nordstadt, Hannover, Germany
| | - Arya Nabavi
- Department of Neurosurgery, KRH Klinikum Nordstadt, Hannover, Germany
| | - Amir Samii
- Department of Neurosurgery, International Neuroscience Institute, Hannover, Germany
| | - Joachim K Krauss
- Department of Neurosurgery, Hannover Medical School, Hannover, Germany
| | - Friedrich Feuerhake
- Department of Neuropathology, Institute of Pathology, Hannover Medical School, Hannover, Germany
- Institute for Neuropathology, University Clinic Freiburg, Freiburg, Germany
| | - Christian Hartmann
- Department of Neuropathology, Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Bettina Wiese
- Department of Neurosurgery, Hannover Medical School, Hannover, Germany
- Department of Neurology, Henriettenstift, Diakovere Krankenhaus gGmbH, Hannover, Germany
| | - Frank Brand
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Ruthild G Weber
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
| |
Collapse
|
38
|
Gomez F, Fisk B, McMichael JF, Mosior M, Foltz JA, Skidmore ZL, Duncavage EJ, Miller CA, Abel H, Li YS, Russler-Germain DA, Krysiak K, Watkins MP, Ramirez CA, Schmidt A, Martins Rodrigues F, Trani L, Khanna A, Wagner JA, Fulton RS, Fronick CC, O'Laughlin MD, Schappe T, Cashen AF, Mehta-Shah N, Kahl BS, Walker J, Bartlett NL, Griffith M, Fehniger TA, Griffith OL. Ultra-Deep Sequencing Reveals the Mutational Landscape of Classical Hodgkin Lymphoma. CANCER RESEARCH COMMUNICATIONS 2023; 3:2312-2330. [PMID: 37910143 PMCID: PMC10648575 DOI: 10.1158/2767-9764.crc-23-0140] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/27/2023] [Accepted: 10/24/2023] [Indexed: 11/03/2023]
Abstract
The malignant Hodgkin and Reed Sternberg (HRS) cells of classical Hodgkin lymphoma (cHL) are scarce in affected lymph nodes, creating a challenge to detect driver somatic mutations. As an alternative to cell purification techniques, we hypothesized that ultra-deep exome sequencing would allow genomic study of HRS cells, thereby streamlining analysis and avoiding technical pitfalls. To test this, 31 cHL tumor/normal pairs were exome sequenced to approximately 1,000× median depth of coverage. An orthogonal error-corrected sequencing approach verified >95% of the discovered mutations. We identified mutations in genes novel to cHL including: CDH5 and PCDH7, novel stop gain mutations in IL4R, and a novel pattern of recurrent mutations in pathways regulating Hippo signaling. As a further application of our exome sequencing, we attempted to identify expressed somatic single-nucleotide variants (SNV) in single-nuclei RNA sequencing (snRNA-seq) data generated from a patient in our cohort. Our snRNA analysis identified a clear cluster of cells containing a somatic SNV identified in our deep exome data. This cluster has differentially expressed genes that are consistent with genes known to be dysregulated in HRS cells (e.g., PIM1 and PIM3). The cluster also contains cells with an expanded B-cell clonotype further supporting a malignant phenotype. This study provides proof-of-principle that ultra-deep exome sequencing can be utilized to identify recurrent mutations in HRS cells and demonstrates the feasibility of snRNA-seq in the context of cHL. These studies provide the foundation for the further analysis of genomic variants in large cohorts of patients with cHL. SIGNIFICANCE Our data demonstrate the utility of ultra-deep exome sequencing in uncovering somatic variants in Hodgkin lymphoma, creating new opportunities to define the genes that are recurrently mutated in this disease. We also show for the first time the successful application of snRNA-seq in Hodgkin lymphoma and describe the expression profile of a putative cluster of HRS cells in a single patient.
Collapse
Affiliation(s)
- Felicia Gomez
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
| | - Bryan Fisk
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Joshua F. McMichael
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Matthew Mosior
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Jennifer A. Foltz
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Zachary L. Skidmore
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Eric J. Duncavage
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri
| | - Christopher A. Miller
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Haley Abel
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Yi-Shan Li
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri
| | - David A. Russler-Germain
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Kilannin Krysiak
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri
| | - Marcus P. Watkins
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Cody A. Ramirez
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Alina Schmidt
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Fernanda Martins Rodrigues
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Lee Trani
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Ajay Khanna
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Julia A. Wagner
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Robert S. Fulton
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Catrina C. Fronick
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Michelle D. O'Laughlin
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Timothy Schappe
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Amanda F. Cashen
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Neha Mehta-Shah
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Brad S. Kahl
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Jason Walker
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Nancy L. Bartlett
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Malachi Griffith
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri
| | - Todd A. Fehniger
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
| | - Obi L. Griffith
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri
| |
Collapse
|
39
|
Lózsa R, Németh E, Gervai JZ, Márkus BG, Kollarics S, Gyüre Z, Tóth J, Simon F, Szüts D. DNA mismatch repair protects the genome from oxygen-induced replicative mutagenesis. Nucleic Acids Res 2023; 51:11040-11055. [PMID: 37791890 PMCID: PMC10639081 DOI: 10.1093/nar/gkad775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/23/2023] [Accepted: 09/12/2023] [Indexed: 10/05/2023] Open
Abstract
DNA mismatch repair (MMR) corrects mismatched DNA bases arising from multiple sources including polymerase errors and base damage. By detecting spontaneous mutagenesis using whole genome sequencing of cultured MMR deficient human cell lines, we show that a primary role of MMR is the repair of oxygen-induced mismatches. We found an approximately twofold higher mutation rate in MSH6 deficient DLD-1 cells or MHL1 deficient HCT116 cells exposed to atmospheric conditions as opposed to mild hypoxia, which correlated with oxidant levels measured using electron paramagnetic resonance spectroscopy. The oxygen-induced mutations were dominated by T to C base substitutions and single T deletions found primarily on the lagging strand. A broad sequence context preference, dependence on replication timing and a lack of transcriptional strand bias further suggested that oxygen-induced mutations arise from polymerase errors rather than oxidative base damage. We defined separate low and high oxygen-specific MMR deficiency mutation signatures common to the two cell lines and showed that the effect of oxygen is observable in MMR deficient cancer genomes, where it best correlates with the contribution of mutation signature SBS21. Our results imply that MMR corrects oxygen-induced genomic mismatches introduced by a replicative process in proliferating cells.
Collapse
Affiliation(s)
- Rita Lózsa
- Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
| | - Eszter Németh
- Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
| | - Judit Z Gervai
- Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
| | - Bence G Márkus
- Stavropoulos Center for Complex Quantum Matter, Department of Physics and Astronomy, University of Notre Dame, Notre Dame, IN 46556, USA
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, H-1525 Budapest, Hungary
- Department of Physics, Institute of Physics, Budapest University of Technology and Economics, H-1111 Budapest, Hungary
| | - Sándor Kollarics
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, H-1525 Budapest, Hungary
- Department of Physics, Institute of Physics, Budapest University of Technology and Economics, H-1111 Budapest, Hungary
| | - Zsolt Gyüre
- Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
- Doctoral School of Molecular Medicine, Semmelweis University, H-1085 Budapest, Hungary
- Turbine Simulated Cell Technologies, H-1027 Budapest, Hungary
| | - Judit Tóth
- Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, H-1111 Budapest, Hungary
| | - Ferenc Simon
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, H-1525 Budapest, Hungary
- Department of Physics, Institute of Physics, Budapest University of Technology and Economics, H-1111 Budapest, Hungary
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
- National Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| |
Collapse
|
40
|
Zappa E, Vitali A, Anders K, Molenaar JJ, Wienke J, Künkele A. Adoptive cell therapy in paediatric extracranial solid tumours: current approaches and future challenges. Eur J Cancer 2023; 194:113347. [PMID: 37832507 PMCID: PMC10695178 DOI: 10.1016/j.ejca.2023.113347] [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: 07/17/2023] [Revised: 09/03/2023] [Accepted: 09/09/2023] [Indexed: 10/15/2023]
Abstract
Immunotherapy has ignited hope to cure paediatric solid tumours that resist traditional therapies. Among the most promising methods is adoptive cell therapy (ACT). Particularly, ACT using T cells equipped with chimeric antigen receptors (CARs) has moved into the spotlight in clinical studies. However, the efficacy of ACT is challenged by ACT-intrinsic factors, like lack of activation or T cell exhaustion, as well as immune evasion strategies of paediatric solid tumours, such as their highly immunosuppressive microenvironment. Novel strategies, including ACT using innate-like lymphocytes, innovative cell engineering techniques, and ACT combination therapies, are being developed and will be crucial to overcome these challenges. Here, we discuss the main classes of ACT for the treatment of paediatric extracranial solid tumours, reflect on the available preclinical and clinical evidence supporting promising strategies, and address the challenges that ACT is still facing. Ultimately, we highlight state-of-the-art developments and opportunities for new therapeutic options, which hold great potential for improving outcomes in this challenging patient population.
Collapse
Affiliation(s)
- Elisa Zappa
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Alice Vitali
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany.
| | - Kathleen Anders
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jan J Molenaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Department of Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Judith Wienke
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Annette Künkele
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| |
Collapse
|
41
|
Karamitopoulou E. Emerging Prognostic and Predictive Factors in Pancreatic Cancer. Mod Pathol 2023; 36:100328. [PMID: 37714333 DOI: 10.1016/j.modpat.2023.100328] [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: 05/17/2023] [Revised: 08/23/2023] [Accepted: 08/29/2023] [Indexed: 09/17/2023]
Abstract
Pancreatic cancer is a lethal disease with increasing incidence and high recurrence rates and is currently resistant to conventional therapies. Moreover, it displays extensive morphologic and molecular intratumoral and intertumoral heterogeneity and a mostly low mutational burden, failing to induce significant antitumor immunity. Thus, immunotherapy has shown limited effect in pancreatic cancer, except in rare tumors with microsatellite instability, constituting <1% of the cases. Currently, new methods, including single-cell and single-nucleus RNA sequencing, have refined and expanded the 2-group molecular classification based on bulk RNA sequencing (classical and basal-like subtypes), identifying hybrid forms and providing us with a comprehensive map of the tumor cell subsets that drive gene expression during tumor evolution, simultaneously giving us insight into therapy resistance and metastasis. Additionally, deeper profiling of the tumor microenvironment of pancreatic cancer by using spatial analyses and multiplex imaging techniques has improved our understanding of the heterogeneous distribution of both adaptive and innate immune components with their protumor and antitumor properties. By integrating host immune response patterns, as defined by spatial transcriptomic and proteomic analysis and multiplex immunofluorescence, with molecular and morphologic features of the tumors, we can increasingly understand the genetic, immunologic, and morphologic background of pancreatic cancer and recognize the potential predictors for different treatment modalities.
Collapse
Affiliation(s)
- Eva Karamitopoulou
- Institute of Tissue Medicine and Pathology, University of Bern, Bern, Switzerland; Pathology Institute Enge, Zurich, Switzerland.
| |
Collapse
|
42
|
Mur P, Viana-Errasti J, García-Mulero S, Magraner-Pardo L, Muñoz IG, Pons T, Capellá G, Pineda M, Feliubadaló L, Valle L. Recommendations for the classification of germline variants in the exonuclease domain of POLE and POLD1. Genome Med 2023; 15:85. [PMID: 37848928 PMCID: PMC10580551 DOI: 10.1186/s13073-023-01234-y] [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: 04/14/2023] [Accepted: 09/13/2023] [Indexed: 10/19/2023] Open
Abstract
BACKGROUND Germline variants affecting the proofreading activity of polymerases epsilon and delta cause a hereditary cancer and adenomatous polyposis syndrome characterized by tumors with a high mutational burden and a specific mutational spectrum. In addition to the implementation of multiple pieces of evidence for the classification of gene variants, POLE and POLD1 variant classification is particularly challenging given that non-disruptive variants affecting the proofreading activity of the corresponding polymerase are the ones associated with cancer. In response to an evident need in the field, we have developed gene-specific variant classification recommendations, based on the ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology) criteria, for the assessment of non-disruptive variants located in the sequence coding for the exonuclease domain of the polymerases. METHODS A training set of 23 variants considered pathogenic or benign was used to define the usability and strength of the ACMG/AMP criteria. Population frequencies, computational predictions, co-segregation data, phenotypic and tumor data, and functional results, among other features, were considered. RESULTS Gene-specific variant classification recommendations for non-disruptive variants located in the exonuclease domain of POLE and POLD1 were defined. The resulting recommendations were applied to 128 exonuclease domain variants reported in the literature and/or public databases. A total of 17 variants were classified as pathogenic or likely pathogenic, and 17 as benign or likely benign. CONCLUSIONS Our recommendations, with room for improvement in the coming years as more information become available on carrier families, tumor molecular characteristics and functional assays, are intended to serve the clinical and scientific communities and help improve diagnostic performance, avoiding variant misclassifications.
Collapse
Affiliation(s)
- Pilar Mur
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
- Department of Health of Catalonia, Catalan Cancer Plan, Barcelona, Spain.
| | - Julen Viana-Errasti
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Sandra García-Mulero
- Department of Health of Catalonia, Catalan Cancer Plan, Barcelona, Spain
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology, Hospitalet de Llobregat, Barcelona, Spain
| | - Lorena Magraner-Pardo
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research (ICR), London, UK
| | - Inés G Muñoz
- Protein Crystallography Unit, Structural Biology Program, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Tirso Pons
- Department of Immunology and Oncology, National Center for Biotechnology (CNB-CSIC), Spanish National Research Council, Madrid, Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Lidia Feliubadaló
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
| |
Collapse
|
43
|
Broeker CD, Ortiz MMO, Murillo MS, Andrechek ER. Integrative multi-omic sequencing reveals the MMTV-Myc mouse model mimics human breast cancer heterogeneity. Breast Cancer Res 2023; 25:120. [PMID: 37805590 PMCID: PMC10559619 DOI: 10.1186/s13058-023-01723-3] [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: 04/25/2023] [Accepted: 09/30/2023] [Indexed: 10/09/2023] Open
Abstract
BACKGROUND Breast cancer is a complex and heterogeneous disease with distinct subtypes and molecular profiles corresponding to different clinical outcomes. Mouse models of breast cancer are widely used, but their relevance in capturing the heterogeneity of human disease is unclear. Previous studies have shown the heterogeneity at the gene expression level for the MMTV-Myc model, but have only speculated on the underlying genetics. METHODS Tumors from the microacinar, squamous, and EMT histological subtypes of the MMTV-Myc mouse model of breast cancer underwent whole genome sequencing. The genomic data obtained were then integrated with previously obtained matched sample gene expression data and extended to additional samples of each histological subtype, totaling 42 gene expression samples. High correlation was observed between genetic copy number events and resulting gene expression by both Spearman's rank correlation coefficient and the Kendall rank correlation coefficient. These same genetic events are conserved in humans and are indicative of poor overall survival by Kaplan-Meier analysis. A supervised machine learning algorithm trained on METABRIC gene expression data was used to predict the analogous human breast cancer intrinsic subtype from mouse gene expression data. RESULTS Herein, we examine three common histological subtypes of the MMTV-Myc model through whole genome sequencing and have integrated these results with gene expression data. Significantly, key genomic alterations driving cell signaling pathways were well conserved within histological subtypes. Genomic changes included frequent, co-occurring mutations in KIT and RARA in the microacinar histological subtype as well as SCRIB mutations in the EMT subtype. EMT tumors additionally displayed strong KRAS activation signatures downstream of genetic activating events primarily ascribed to KRAS activating mutations, but also FGFR2 amplification. Analogous genetic events in human breast cancer showed stark decreases in overall survival. In further analyzing transcriptional heterogeneity of the MMTV-Myc model, we report a supervised machine learning model that classifies MMTV-Myc histological subtypes and other mouse models as being representative of different human intrinsic breast cancer subtypes. CONCLUSIONS We conclude the well-established MMTV-Myc mouse model presents further opportunities for investigation of human breast cancer heterogeneity.
Collapse
Affiliation(s)
- Carson D Broeker
- Department of Biochemistry and Molecular Biology, Michigan State University, 567 Wilson Road, BPS Room 2120, East Lansing, MI, 48824, USA
| | - Mylena M O Ortiz
- Genetics and Genomics Science Program, Michigan State University, 567 Wilson Road, BPS Room 2120, East Lansing, MI, 48824, USA
| | - Michael S Murillo
- Department of Computational Mathematics, Science, and Engineering, Michigan State University, 428 South Shaw Lane, Engineering Building Room 1508C, East Lansing, MI, 48824, USA
- Department of Chemical Engineering and Materials Science, Michigan State University, 428 South Shaw Lane, Engineering Building Room 1508C, East Lansing, MI, 48824, USA
| | - Eran R Andrechek
- Department of Physiology, Michigan State University, 567 Wilson Road, BPS Room 2194, East Lansing, MI, 48824, USA.
| |
Collapse
|
44
|
Yan X, Qu F, Zhou Y. Progress of immune checkpoint inhibitors therapy for non-small cell lung cancer with brain metastases. Lung Cancer 2023; 184:107322. [PMID: 37611495 DOI: 10.1016/j.lungcan.2023.107322] [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: 07/10/2023] [Revised: 07/22/2023] [Accepted: 08/05/2023] [Indexed: 08/25/2023]
Abstract
About 40% of patients with non-small cell lung cancer (NSCLC) develop brain metastases (BMs) throughout the disease, and the occurrence of BMs is considered to have a fairly high mortality rate. Therefore, the management of brain metastases in NSCLC patients is a clinical challenge. Currently, multidisciplinary diagnosis and treatment methods are often used to achieve effective control of intracranial disease and prolong survival. Immunotherapy (IT) is one of the core therapies for NSCLC. Single or combined IT represented by immune checkpoint inhibitors(ICIs) of programmed death-1(PD-1)/ programmed cell death-ligand 1 (PD-L1) can significantly improve the prognosis of patients with advanced NSCLC.ICIs has been shown to be safe and effective in patients with BMs, although patients with BMs are mostly underrepresented in randomized clinical trials. In this review, we summarized the mechanism of ICIs in the treatment of BMs, and the clinical research and treatment progress of ICIs and their combination with other therapies in patients with BMs s from NSCLC.
Collapse
Affiliation(s)
- Xin Yan
- Department of Oncology, Affiliated Dalian Third People's Hospital of Dalian Medical University, 116033, China
| | - Fanjie Qu
- Department of Oncology, Affiliated Dalian Third People's Hospital of Dalian Medical University, 116033, China.
| | - Yi Zhou
- Department of Oncology, Affiliated Dalian Third People's Hospital of Dalian Medical University, 116033, China
| |
Collapse
|
45
|
Zhang Y, Wang X, Zhu Y, Liang C, Zhao L, Meng Q, Yin JC, Shi Y, Wang F, Qin F, Xuan J. Case Report: Cancer spectrum and genetic characteristics of a de novo germline POLD1 p.L606M variant-induced polyposis syndrome. Front Oncol 2023; 13:1222873. [PMID: 37746257 PMCID: PMC10516538 DOI: 10.3389/fonc.2023.1222873] [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: 05/15/2023] [Accepted: 07/20/2023] [Indexed: 09/26/2023] Open
Abstract
Germline variations in the DNA polymerase genes, POLE and POLD1, can lead to a hereditary cancer syndrome that is characterized by frequent gastrointestinal polyposis and multiple primary malignant tumors. However, because of its rare occurrence, this disorder has not been extensively studied. In this report, we present the case of a 22-year-old female patient who had been diagnosed with gastrointestinal polyposis, breast fibroadenoma, multiple primary colorectal cancers, and glioblastoma (grade IV) within a span of 4 years. Next-generation sequencing analysis revealed a germline variant in POLD1 (c.1816C>A; p.L606M). In silico analysis using protein functional predicting software, including SIFT, Polyphen, GERP++, and CADD, further confirmed the pathogenicity of POLD1 p.L606M (classified as ACMG grade Class 4). In line with polymerase deficiency, both rectal cancer and glioblastoma tissues exhibited a high tumor mutation burden, with 16.9 muts/Mb and 347.1 muts/Mb, respectively. Interestingly, the patient has no family history of cancer, and gene examination of both parents confirms that this is a de novo germline variant. Therefore, molecular screening for POLD1 may be necessary for patients with such a cancer spectrum, regardless of their family history.
Collapse
Affiliation(s)
- Ying Zhang
- Department of Pathology, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu, China
| | - Xiaolu Wang
- Department of Oncology, The Affiliated Hospital, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Yuning Zhu
- Department of Pathology, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu, China
| | - Chong Liang
- Department of Neurosurgery Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu, China
| | - Lijun Zhao
- Medical Science Liaison, Genetron Health Inc., Beijing, China
| | - Qi Meng
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, China
| | - Jiani C. Yin
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, China
| | - Yuqian Shi
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, China
| | - Fufeng Wang
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, China
| | - Feng Qin
- Cancer Center, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Ji Xuan
- Department of Gastroenterology, Jinling Hospital, Nanjing University, School of Medicine, Nanjing, China
| |
Collapse
|
46
|
Strauss JD, Pursell ZF. Replication DNA polymerases, genome instability and cancer therapies. NAR Cancer 2023; 5:zcad033. [PMID: 37388540 PMCID: PMC10304742 DOI: 10.1093/narcan/zcad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/24/2023] [Accepted: 06/25/2023] [Indexed: 07/01/2023] Open
Abstract
It has been over a decade since the initial identification of exonuclease domain mutations in the genes encoding the catalytic subunits of replication DNA polymerases ϵ and δ (POLE and POLD1) in tumors from highly mutated endometrial and colorectal cancers. Interest in studying POLE and POLD1 has increased significantly since then. Prior to those landmark cancer genome sequencing studies, it was well documented that mutations in replication DNA polymerases that reduced their DNA synthesis accuracy, their exonuclease activity or their interactions with other factors could lead to increased mutagenesis, DNA damage and even tumorigenesis in mice. There are several recent, well-written reviews of replication DNA polymerases. The aim of this review is to gather and review in some detail recent studies of DNA polymerases ϵ and δ as they pertain to genome instability, cancer and potential therapeutic treatments. The focus here is primarily on recent informative studies on the significance of mutations in genes encoding their catalytic subunits (POLE and POLD1), mutational signatures, mutations in associated genes, model organisms, and the utility of chemotherapy and immune checkpoint inhibition in polymerase mutant tumors.
Collapse
Affiliation(s)
- Juliet D Strauss
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, 70118 LA, USA
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, 70118 LA, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, 70118 LA, USA
| |
Collapse
|
47
|
Jensen GL, Pourfarrokh N, Volz M, Morales LL, Walker K, Hammonds KP, El-Ghamry M, Wong L, Hodjat P, Castro E, Rao A, Jhavar SG. Improved Pathologic response to chemoradiation in MGMT methylated locally advanced rectal cancer. Clin Transl Radiat Oncol 2023; 42:100667. [PMID: 37560324 PMCID: PMC10406619 DOI: 10.1016/j.ctro.2023.100667] [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: 11/10/2022] [Revised: 06/11/2023] [Accepted: 07/23/2023] [Indexed: 08/11/2023] Open
Abstract
BACKGROUND AND PURPOSE With the growing interest in total neoadjuvant treatment for locally advanced rectal adenocarcinoma (LARC) there is an urgent unmet need to identify predictive markers of response to long-course neoadjuvant concurrent chemoradiotherapy (LCRT). O6-Methylguanine (O6-MG)-DNA-methyltransferase (MGMT) gene methylation has been associated in some malignancies with response to concurrent chemoradiotherapy. We attempted to find if pathologic response to LCRT was associated with MGMT promoter hypermethylation (MGMTh). MATERIALS AND METHODS Patients were identified with LARC, available pre-treatment biopsy specimens, and at least 1 year of follow-up who received LCRT followed by surgical resection within 6 months. Biopsies were tested for MGMTh using a Qiagen pyrosequencing kit (Catalog number 970061). The primary outcome of LCRT responsiveness was based on tumor regression grade (TRG), with grades of 0-1 considered to have excellent response and grades of 2-3 considered to be non-responders. Secondary outcomes included overall survival (OS) and recurrence free survival (RFS). RESULTS Of 96 patients who met inclusion criteria, 76 had samples which produced reliable assay results. MGMTh corresponded with higher grade and age of the biopsy specimen. The percentage of responders to LCRT was higher amongst the MGMTh patients than the MGMTn patients (60.0% vs 27.5%, p value = 0.0061). MGMTh was not significantly associated with improved OS (2-year OS of 96.0% vs 98.0%, p = 0.8102) but there was a trend for improved RFS (2-year RFS of 87.6% vs 74.2%, p = 0.0903). CONCLUSION Significantly greater tumor regression following LCRT was seen in MGMTh LARC. Methylation status may help identify good candidates for close observation without surgery following LCRT.
Collapse
Affiliation(s)
- Garrett L. Jensen
- Department of Radiation Oncology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Niloufar Pourfarrokh
- Departments of Pathology, Baylor Scott & White Health, 2401 S. 31 St., Temple, TX 76508, USA
| | - Marcus Volz
- Departments of Pathology, Baylor Scott & White Health, 2401 S. 31 St., Temple, TX 76508, USA
| | - Linden L. Morales
- Departments of Pathology, Baylor Scott & White Health, 2401 S. 31 St., Temple, TX 76508, USA
| | - Kimberly Walker
- Departments of Pathology, Baylor Scott & White Health, 2401 S. 31 St., Temple, TX 76508, USA
| | - Kendall P. Hammonds
- Biostatistics, Baylor Scott & White Health, 2401 S. 31 St., Temple, TX 76508, USA
| | - Moataz El-Ghamry
- Radiation Oncology, Baylor Scott & White Health, 2401 S. 31 St., Temple, TX 76508, USA
| | - Lucas Wong
- Medical Oncology, Baylor Scott & White Health, 2401 S. 31 St., Temple, TX 76508, USA
| | - Parsa Hodjat
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston TX, USA
| | - Eduardo Castro
- Departments of Pathology, Baylor Scott & White Health, 2401 S. 31 St., Temple, TX 76508, USA
| | - Arundhati Rao
- Departments of Pathology, Baylor Scott & White Health, 2401 S. 31 St., Temple, TX 76508, USA
| | - Sameer G. Jhavar
- Radiation Oncology, Baylor Scott & White Health, 2401 S. 31 St., Temple, TX 76508, USA
| |
Collapse
|
48
|
Bashir F, Qureshi BM, Minhas K, Tabori U, Bouffet E, Hawkins C, Enam A, Mushtaq N. Pakistan National Guidelines for Pediatric High-Grade Gliomas. Pak J Med Sci 2023; 39:1548-1554. [PMID: 37680835 PMCID: PMC10480739 DOI: 10.12669/pjms.39.5.6300] [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: 03/04/2022] [Revised: 06/15/2022] [Accepted: 05/26/2023] [Indexed: 09/09/2023] Open
Abstract
Pediatric high-grade glioma (pHGG) is highly malignant central nervous system tumor and constitute 10% of the pediatric gliomas. Effective treatment needs a functioning multi-disciplinary team including pediatric neuro oncologist, neurosurgeon, neuroradiologist, neuropathologist and radiation oncologist. Despite surgical resection, radiotherapy and chemotherapy, most HGG will recur resulting in early death. A significant proportion of HGG occurs in context of cancer predisposition syndromes like Constitutional Mismatch Repair Deficiency (CMMRD) also known as Biallelic Mismatch Repair Deficiency (bMMRD) characterized by high mutational burden. The incidence of HGG with CMMRD is one per million patients. bMMRD is caused by homozygous germline mutations in one of the four Mis Match Repair (MMR) genes (PMS2, MLH1, MSH2, and MSH6). The use of TMZ is now avoided in CMMRD related HGG due to its limited response and known ability to increase the accumulation of somatic mutations in these patients, increasing the risk of secondary tumors. HGG should be managed under the care of multidisciplinary team to receive optimum treatment. This is particularly important for low middle-income countries (LMIC) with limited resources like Pakistan.
Collapse
Affiliation(s)
- Farrah Bashir
- Dr. Farrah Bashir, FCPS Aga Khan University Hospital, Karachi, Pakistan
| | | | - Khurram Minhas
- Dr. Khurram Minhas, FCPS Aga Khan University Hospital, Karachi, Pakistan
| | - Uri Tabori
- Dr. Uri Tabori, MD, PHD The Hospital for Sick Children (SickKids), Toronto, Canada
| | - Eric Bouffet
- Dr. Eric Bouffet, MD The Hospital for Sick Children (SickKids), Toronto, Canada
| | - Cynthia Hawkins
- Dr. Cynthia Hawkins, MD The Hospital for Sick Children (SickKids), Toronto, Canada
| | - Ather Enam
- Dr. Ather Enam, MD Aga Khan University Hospital, Karachi, Pakistan
| | - Naureen Mushtaq
- Dr. Naureen Mushtaq, FCPS Aga Khan University Hospital, Karachi, Pakistan
| |
Collapse
|
49
|
Lin Y, Luo S, Luo M, Lu X, Li Q, Xie M, Huang Y, Liao X, Zhang Y, Li Y, Liang R. Homologous recombination repair gene mutations in colorectal cancer favors treatment of immune checkpoint inhibitors. Mol Carcinog 2023; 62:1271-1283. [PMID: 37232365 DOI: 10.1002/mc.23562] [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: 12/11/2022] [Revised: 05/03/2023] [Accepted: 05/06/2023] [Indexed: 05/27/2023]
Abstract
Immune checkpoint inhibitor (ICI) therapy is insensitive for Colorectal cancer (CRC) patients with microsatellite stable (MSS). Genomic data of three CRC cohort, n = 35), and the Cancer Genome Atlas (TCGA CRC cohort, n = 377), were analyzed. A cohort treated with ICIs from Memorial Sloan Kettering Cancer Center (MSKCC CRC cohort, n = 110) and two cases from the local hospital were characterized the impact of the HRR mutation on prognosis of CRC. Homologous recombination repair (HRR) gene mutations were more common in CN and HL cohorts (27.85%; 48.57%) than in TCGA CRC cohort (15.92%), especially in the MSS populations, the frequencies of HRR mutation were higher in CN and HL cohort (27.45%, 51.72%) than in TCGA cohort (6.85%). HRR mutations were associated with high tumor mutational burden (TMB-H). Although HRR mutation uncorrelated with an improved overall survival in the MSKCC CRC cohort (p = 0.97), HRR mutated patients had a significantly improved OS compared to the HRR wildtype population particularly in MSS subgroups (p = 0.0407) under ICI treatment. It probably contributed by a higher neoantigen and increased CD4+ T cell infiltration which found in the TCGA MSS HRR mutated CRC cohort. The similar phenomenon on cases was observed that MSS metastatic CRC patient with HRR mutation seemed more sensitive to ICI after multi-line chemotherapy in clinical practice than HRR wildtype. This finding suggests the feasibility of HRR mutation as an immunotherapy response predictor in MSS CRC, which highlights a potential therapeutic approach for these patients.
Collapse
Affiliation(s)
- Yan Lin
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, People's Republic of China
| | - Shanshan Luo
- Department of Gastrointestinal Gland Surgery, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, People's Republic of China
| | - Min Luo
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, People's Republic of China
| | - Xuerou Lu
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, People's Republic of China
| | - Qian Li
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, People's Republic of China
| | - Mingzhi Xie
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, People's Republic of China
| | - Yu Huang
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, People's Republic of China
| | - Xiaoli Liao
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, People's Republic of China
| | - Yumei Zhang
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, People's Republic of China
| | - Yongqiang Li
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, People's Republic of China
| | - Rong Liang
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, People's Republic of China
| |
Collapse
|
50
|
Wang C, Kuang W, Zeng J, Ren Y, Liu Q, Sun H, Feng M, Liang D. A retrospective study of consistency between immunohistochemistry and polymerase chain reaction of microsatellite instability in endometrial cancer. PeerJ 2023; 11:e15920. [PMID: 37663290 PMCID: PMC10470453 DOI: 10.7717/peerj.15920] [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: 05/12/2023] [Accepted: 07/28/2023] [Indexed: 09/05/2023] Open
Abstract
Objectives Identification of endometrial cancers (EC) with mismatch repair deficiency (dMMR) or microsatellite instability-high (MSI-H) is essential for Lynch syndrome screening and treatment stratification. We aimed to assess the utility of immunohistochemistry (IHC) staining for MMR protein expression and polymerase chain reaction (PCR)-based MSI assays in EC and the correlation between MMR/MSI status and various clinicopathological parameters. Methods We reviewed the clinical and pathological information of 333 patients with EC. MMR protein expression was assessed as retained or lost to determine MMR status by IHC staining, and MSI status was identified by PCR capillary electrophoresis (PCR-CE) testing with a National Cancer Institute (NCI) panel. The correlation of MMR/MSI status with clinicopathological features was determined by statistical analysis. Discrepant results were further analyzed using an alternative PCR-CE MSI (Promega panel) method, MLH1 promoter methylation assays, and next-generation sequencing (NGS). Results Among the EC patients, the overall percentage of dMMR was 25.2%, and the overall percentage of MSI-H was 24%. Among the dMMR patients, 50 (59.5%) showed loss of MLH1 and PMS2 expression, 19 (22.6%) loss of MSH2 and MSH6 expression, and seven (8.3%) and eight (9.5%) loss of PMS2 and MSH6 expression, respectively. The dMMR subgroup was significantly younger than the pMMR subgroup, especially for <60-years-old patients (p = 0.038). In addition, we identified a strong correlation between MMR/MSI status and high-grade endometrioid or nonendometrioid components (p = 0.004 or p = 0.003). IHC staining and PCR-CE assay results showed a high level of overall concordance (98.8%, Cohen's κ = 0.98). Four patients were found to have dMRR/MSS in both examinations. We reanalyzed them with additional methods. One case showed MLH1 promotor methylation, and the other three cases harbored MSH6 germline pathogenic variations. One of the cases with MSH6 deficiency was reanalyzed as MSI-H by alternative PCR-CE assay or NGS testing. Conclusions This study indicates that the combined use of MMR-IHC and PCR-CE MSI analyses may effectively avoid misdiagnoses of EC patients with dMMR/MSI-H. However, use of PCR-CE alone to evaluate MMR/MSI status may lead to missed diagnosis, especially for EC patients with MSH6 deficiency and presenting MSS.
Collapse
Affiliation(s)
- Cheng Wang
- Department of Pathology, West China Second University Hospital of Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Chengdu, Sichuan, China
| | - Wei Kuang
- Department of Pathology, West China Second University Hospital of Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Chengdu, Sichuan, China
| | - Jing Zeng
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Yang Ren
- West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Qianqi Liu
- Department of Pathology, West China Second University Hospital of Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Chengdu, Sichuan, China
| | - Huanxin Sun
- Department of Pathology, West China Second University Hospital of Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Chengdu, Sichuan, China
| | - Min Feng
- Department of Pathology, West China Second University Hospital of Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Chengdu, Sichuan, China
| | - Dongni Liang
- Department of Pathology, West China Second University Hospital of Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Chengdu, Sichuan, China
| |
Collapse
|