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Rousseau B, Bieche I, Pasmant E, Hamzaoui N, Leulliot N, Michon L, de Reynies A, Attignon V, Foote MB, Masliah-Planchon J, Svrcek M, Cohen R, Simmet V, Augereau P, Malka D, Hollebecque A, Pouessel D, Gomez-Roca C, Guimbaud R, Bruyas A, Guillet M, Grob JJ, Duluc M, Cousin S, de la Fouchardiere C, Flechon A, Rolland F, Hiret S, Saada-Bouzid E, Bouche O, Andre T, Pannier D, El Hajbi F, Oudard S, Tournigand C, Soria JC, Champiat S, Gerber DG, Stephens D, Lamendola-Essel MF, Maron SB, Diplas BH, Argiles G, Krishnan AR, Tabone-Eglinger S, Ferrari A, Segal NH, Cercek A, Hoog-Labouret N, Legrand F, Simon C, Lamrani-Ghaouti A, Diaz LA, Saintigny P, Chevret S, Marabelle A. PD-1 Blockade in Solid Tumors with Defects in Polymerase Epsilon. Cancer Discov 2022; 12:1435-1448. [PMID: 35398880 PMCID: PMC9167784 DOI: 10.1158/2159-8290.cd-21-0521] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 03/09/2022] [Accepted: 04/04/2022] [Indexed: 11/16/2022]
Abstract
Missense mutations in the polymerase epsilon (POLE) gene have been reported to generate proofreading defects resulting in an ultramutated genome and to sensitize tumors to checkpoint blockade immunotherapy. However, many POLE-mutated tumors do not respond to such treatment. To better understand the link between POLE mutation variants and response to immunotherapy, we prospectively assessed the efficacy of nivolumab in a multicenter clinical trial in patients bearing advanced mismatch repair-proficient POLE-mutated solid tumors. We found that only tumors harboring selective POLE pathogenic mutations in the DNA binding or catalytic site of the exonuclease domain presented high mutational burden with a specific single-base substitution signature, high T-cell infiltrates, and a high response rate to anti-PD-1 monotherapy. This study illustrates how specific DNA repair defects sensitize to immunotherapy. POLE proofreading deficiency represents a novel agnostic biomarker for response to PD-1 checkpoint blockade therapy. SIGNIFICANCE POLE proofreading deficiency leads to high tumor mutational burden with high tumor-infiltrating lymphocytes and predicts anti-PD-1 efficacy in mismatch repair-proficient tumors. Conversely, tumors harboring POLE mutations not affecting proofreading derived no benefit from PD-1 blockade. POLE proofreading deficiency is a new tissue-agnostic biomarker for cancer immunotherapy. This article is highlighted in the In This Issue feature, p. 1397.
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Affiliation(s)
- Benoit Rousseau
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ivan Bieche
- Department of Genetics, Institut Curie, Paris, France
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université de Paris, CARPEM, Paris, France
| | - Eric Pasmant
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université de Paris, CARPEM, Paris, France
- Fédération de Génétique et Médecine Génomique, Hôpital Cochin, AP-HP.Centre-Université de Paris, Paris, France
| | - Nadim Hamzaoui
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université de Paris, CARPEM, Paris, France
- Fédération de Génétique et Médecine Génomique, Hôpital Cochin, AP-HP.Centre-Université de Paris, Paris, France
| | - Nicolas Leulliot
- Cibles Thérapeutiques et Conception de Médicaments, CNRS UMR8015, Université de Paris, UFR de Pharmacie de Paris, Paris, France
| | - Lucas Michon
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Aurelien de Reynies
- Université de Paris, Centre de Recherche des Cordeliers, UMRS1138, AP-HP, SeqOIA-IT, Paris, France
| | | | - Michael B. Foote
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Magali Svrcek
- Pathology department, Saint Antoine Hospital
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité des Microsatellites et Cancer, Equipe labellisée par la Ligue Nationale contre le Cancer, F-75012 Paris, France
| | - Romain Cohen
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité des Microsatellites et Cancer, Equipe labellisée par la Ligue Nationale contre le Cancer, F-75012 Paris, France
- Medical Oncology Department, Hôpital Saint-Antoine, Paris, France
| | - Victor Simmet
- Department of Medical Oncology, Institut de Cancérologie de l’Ouest (ICO), Angers, France
| | - Paule Augereau
- Department of Medical Oncology, Institut de Cancérologie de l’Ouest (ICO), Angers, France
| | - David Malka
- Département d’Innovation Thérapeutique et d’Essais Précoces (DITEP), Gustave Roussy, Université Paris Saclay, Villejuif, France
| | - Antoine Hollebecque
- Département d’Innovation Thérapeutique et d’Essais Précoces (DITEP), Gustave Roussy, Université Paris Saclay, Villejuif, France
| | - Damien Pouessel
- Department of Medical Oncology, Institut Claudius Regaud / IUCT Oncopole, Toulouse, France
| | - Carlos Gomez-Roca
- Department of Medical Oncology, Institut Claudius Regaud / IUCT Oncopole, Toulouse, France
| | | | - Amandine Bruyas
- Department of Medical Oncology, Hôpital de la Croix-Rousse, Lyon, France
| | - Marielle Guillet
- Department of Gastroenterology and Digestive Oncology, Hôpital de la Croix-Rousse, Lyon, France
| | | | - Muriel Duluc
- Dermatology and Oncology, Hôpital de la Timone, Marseille, France
| | | | | | - Aude Flechon
- Department of medical Oncology, Centre Leon Berard, Lyon, France
| | - Frederic Rolland
- Department of Medical Oncology, ICO Institut de Cancerologie de l’Ouest René Gauducheau, Saint-Herblain, France
| | - Sandrine Hiret
- Department of Medical Oncology, ICO Institut de Cancerologie de l’Ouest René Gauducheau, Saint-Herblain, France
| | - Esma Saada-Bouzid
- Medical Oncology, Centre Anticancer Antoine Lacassagne, Nice, France
| | - Olivier Bouche
- Gastroenterology and Digestive Oncology, CHU de Reims - Hôpital Robert Debré, Reims, France
| | - Thierry Andre
- Medical Oncology Department, Hôpital Saint-Antoine, Paris, France
| | | | | | - Stephane Oudard
- Oncology, Hopital Europeen Georges Pompidou, AP-HP, Paris, France
| | | | - Jean-Charles Soria
- Département d’Innovation Thérapeutique et d’Essais Précoces (DITEP), Gustave Roussy, Université Paris Saclay, Villejuif, France
| | - Stephane Champiat
- Département d’Innovation Thérapeutique et d’Essais Précoces (DITEP), Gustave Roussy, Université Paris Saclay, Villejuif, France
| | - Drew G. Gerber
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dennis Stephens
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Steven B. Maron
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bill H. Diplas
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Guillem Argiles
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Asha R. Krishnan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Anthony Ferrari
- Platform of Bioinformatics Gilles Thomas-Synergie Lyon Cancer, Centre Léon Bérard, Lyon
| | - Neil H. Segal
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrea Cercek
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Frederic Legrand
- Research and Innovation, Institut National du Cancer, Boulogne-Billancourt, France
| | | | | | - Luis A. Diaz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pierre Saintigny
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, France
- Department of medical Oncology, Centre Leon Berard, Lyon, France
| | | | - Aurelien Marabelle
- Département d’Innovation Thérapeutique et d’Essais Précoces (DITEP), Gustave Roussy, Université Paris Saclay, Villejuif, France
- U1015 & CIC1428, Institut national de la santé et de la recherche médicale (INSERM), Villejuif, France
- Faculté de Médecine, Université Paris Saclay, Le Kremlin-Bicetre, France
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Favre L, Cohen J, Calderaro J, Pécriaux A, Nguyen CT, Bourgoin R, Larnaudie L, Dupuy A, Ollier M, Lechapt E, Sloma I, Tournigand C, Rousseau B, Pujals A. High prevalence of unusual KRAS, NRAS and BRAF mutations in POLE hypermutated colorectal cancers. Mol Oncol 2022; 16:3055-3065. [PMID: 35624529 PMCID: PMC9441000 DOI: 10.1002/1878-0261.13257] [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: 12/22/2021] [Revised: 04/05/2022] [Accepted: 05/25/2022] [Indexed: 12/04/2022] Open
Abstract
Exonucleasic domain POLE (edPOLE) mutations, which are responsible for a hypermutated tumor phenotype, occur in 1–2% of colorectal cancer (CRC) cases. These alterations represent an emerging biomarker for response to immune checkpoint blockade. This study aimed to assess the molecular characteristics of edPOLE‐mutated tumors to facilitate patient screening. Based on opensource data analysis, we compared the prevalence of edPOLE mutations in a control group of unselected CRC patients (n = 222) vs a group enriched for unusual BRAF/RAS mutations (n = 198). Tumor mutational burden (TMB) and immune infiltrate of tumors harboring edPOLE mutations were then analyzed. In total, 420 CRC patients were analyzed: 11 edPOLE‐mutated tumors were identified, most frequently in microsatellite (MMR)‐proficient young (< 70 years) male patients, with left‐sided tumors harboring noncodon 12 KRAS mutation. The prevalence of edPOLE‐mutated tumors in the control vs the experimental screening group was, respectively, 0.45% (n = 1) vs 5.0% (n = 10). Among the 11 edPOLE‐mutated cases, two had a low TMB, three were hypermutated, and six were ultramutated. EdPOLE‐mutated cases had a high CD8+ tumor‐infiltrating lymphocyte (TIL) infiltration. These clinicopathological and molecular criteria may help to identify edPOLE mutations associated with a high TMB in CRC, and improve the selection of patients who could benefit from immunotherapy.
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Affiliation(s)
- Loetitia Favre
- AP-HP, UHC Henri Mondor, Département de Pathologie, 1 rue Gustave Eiffel, 94010, Créteil, France.,Univ Paris Est Creteil, INSERM, IMRB, 8 rue du général Sarrail, 94010, Creteil, France
| | - Justine Cohen
- AP-HP, UHC Henri Mondor, Département de Pathologie, 1 rue Gustave Eiffel, 94010, Créteil, France
| | - Julien Calderaro
- AP-HP, UHC Henri Mondor, Département de Pathologie, 1 rue Gustave Eiffel, 94010, Créteil, France.,Univ Paris Est Creteil, INSERM, IMRB, 8 rue du général Sarrail, 94010, Creteil, France
| | - Adrien Pécriaux
- AP-HP, UHC Henri Mondor, Département de Pathologie, 1 rue Gustave Eiffel, 94010, Créteil, France
| | - Cong-Trung Nguyen
- Univ Paris Est Creteil, INSERM, IMRB, 8 rue du général Sarrail, 94010, Creteil, France
| | - Rémi Bourgoin
- AP-HP, UHC Henri Mondor, Département de Pathologie, 1 rue Gustave Eiffel, 94010, Créteil, France
| | - Laura Larnaudie
- AP-HP, UHC Henri Mondor, Département de Pathologie, 1 rue Gustave Eiffel, 94010, Créteil, France
| | - Aurélie Dupuy
- Univ Paris Est Creteil, INSERM, IMRB, 8 rue du général Sarrail, 94010, Creteil, France
| | - Marie Ollier
- AP-HP, UHC Henri Mondor, Département de Pathologie, 1 rue Gustave Eiffel, 94010, Créteil, France
| | - Emmanuèle Lechapt
- AP-HP, UHC Henri Mondor, Département de Pathologie, 1 rue Gustave Eiffel, 94010, Créteil, France.,Univ Paris Est Creteil, INSERM, IMRB, 8 rue du général Sarrail, 94010, Creteil, France
| | - Ivan Sloma
- Univ Paris Est Creteil, INSERM, IMRB, 8 rue du général Sarrail, 94010, Creteil, France.,AP-HP, UHC Henri Mondor, Département d'hématologie biologique, 1 rue Gustave Eiffel, 94010, Créteil, France
| | - Christophe Tournigand
- Univ Paris Est Creteil, INSERM, IMRB, 8 rue du général Sarrail, 94010, Creteil, France.,AP-HP, UHC Hopital Henri Mondor, Service d'oncologie médicale, 1 rue Gustave Eiffel, 94010, Creteil, France
| | - Benoit Rousseau
- AP-HP, UHC Hopital Henri Mondor, Service d'oncologie médicale, 1 rue Gustave Eiffel, 94010, Creteil, France.,Memorial Sloan Kettering Cancer Center, Mortimer B. Zuckerman Research Center, 417 E 68th St, New York, NY, 10065, USA
| | - Anaïs Pujals
- AP-HP, UHC Henri Mondor, Département de Pathologie, 1 rue Gustave Eiffel, 94010, Créteil, France.,Univ Paris Est Creteil, INSERM, IMRB, 8 rue du général Sarrail, 94010, Creteil, France
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5
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He J, Ouyang W, Zhao W, Shao L, Li B, Liu B, Wang D, Han-Zhang H, Zhang Z, Shao L, Li W. Distinctive genomic characteristics in POLE/POLD1-mutant cancers can potentially predict beneficial clinical outcomes in patients who receive immune checkpoint inhibitor. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:129. [PMID: 33569431 PMCID: PMC7867935 DOI: 10.21037/atm-20-7553] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Background Mutations in POLE /POLD1 proofreading domain can cause deficiencies in DNA repair, conferring ultramutated cancer phenotypes. Preliminary clinical studies have revealed an association between POLE/POLD1 mutations and beneficial clinical outcomes to immune checkpoint inhibitor (ICI) therapy This study aims to investigate the genomic characteristics of POLE/POLD-mutant tumors and the prognostic value of POLE/POLD mutation for ICI treatment. Methods Genomic data of 21,074 patients with 23 cancer types were retrieved from Burning Rock variant database (BR VarDB). The prevalence and spectra of POLE and POLD1 mutations were assessed and compared with that in The Cancer Genome Atlas (TCGA) samples. The correlations of POLE/POLD1 mutation with tumor mutational burden (TMB) and microsatellite instability (MSI) were investigated. The prognostic value of POLE/POLD1 mutations was also explored in 2,487 ICI-treated patients from published studies. Results BR VarDB samples displayed a similar mutational prevalence of POLE (3.2% vs. 3.2%) and POLD1 (1.4% vs. 1.6%, P=0.248) versusTCGA samples, but a slightly lower frequency of POLE and POLD1 co-mutations (0.21% vs. 0.43%, P<0.001). POLE/POLD1-mutant tumors harbored increased TCT→TAT and TCG→TTG transversions, and genomic signatures associated with DNA mismatch repair (MMR) deficiency and ultra-hypermuation. Furthermore, tumors with POLE/POLD1 proofreading mutation showed a significantly higher TMB than tumors with non-proofreading mutations (P<0.01), although both possessed a higher TMB than POLE/POLD1 wild-type (WT) tumors (P<0.0001 and P<0.0001, respectively). MSI was commonly observed in tumors harboring dominant clone of POLE/POLD1 mutation (10.2%), but occurred rarely in POLE/POLD1 WT tumors (0.5%) and tumors with accumulating sub-cloned POLE/POLD1 mutation (0%). Survival analysis revealed that POLE/POLD1 mutation was not independently correlated with longer survival after adjusting for TMB and other factors (HR =0.86, P=0.372). However, patients harboring POLE/POLD1 mutation demonstrated a higher response rate than patients with POLE/ POLD1 WT tumors (35.2% vs. 19.6%, P=0.0165). Conclusions We delineated distinctive genomic characteristics in POLE/POLD1-mutant tumors, suggesting the potential predictive role of POLE/POLD1 mutations, especially those in the proofreading domain, for beneficial outcomes of immunotherapy. Our results also suggest that MSI caused by a loss-of-function mutation in the MMR pathway tends to result from POLE/POLD1 proofreading deficiency in POLE/POLD1-mutant tumors with MSI.
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Affiliation(s)
- Junjun He
- Key Laboratory of Pancreatic Disease Research of Zhejiang Province, First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Ouyang
- Department of Oncology, Zhuzhou Central Hospital, Xiangya School of Medicine, Central South University, Zhuzhou, China
| | - Wugan Zhao
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lin Shao
- Burning Rock Biotech, Guangzhou, China
| | - Bing Li
- Burning Rock Biotech, Guangzhou, China
| | - Bihao Liu
- Department of Urology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Dejuan Wang
- Department of Urology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | | | | | | | - Wencai Li
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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