The genomic landscape of canine diffuse large B-cell lymphoma identifies distinct subtypes with clinical and therapeutic implications

Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoid neoplasm in dogs and in humans. It is characterized by a remarkable degree of clinical heterogeneity that is not completely elucidated by molecular data. This poses a major barrier to understanding the disease and its response to therapy, or when treating dogs with DLBCL within clinical trials. We performed an integrated analysis of exome ( n  = 77) and RNA sequencing ( n  = 43) data in a cohort of canine DLBCL to define the genetic landscape of this tumor. A wide range of signaling pathways and cellular processes were found in common with human DLBCL, but the frequencies of the most recurrently mutated genes ( TRAF3 , SETD2 , POT1 , TP53 , MYC , FBXW7 , DDX3X and TBL1XR1 ) differed. We developed a prognostic model integrating exonic variants and clinical and transcriptomic features to predict the outcome in dogs with DLBCL. These results comprehensively define the genetic drivers of canine DLBCL and can be prospectively utilized to identify new therapeutic opportunities. Giannuzzi et al. present an integrated analysis of clinical features and exome and RNA sequencing data in a cohort of dogs with diffuse large B-cell lymphoma to better define the genetic landscape of this tumor and identify multiple mutations associated with the outcome.

[1]  F. Aires-da-Silva,et al.  Immunotherapeutic Strategies for Canine Lymphoma: Changing the Odds Against Non-Hodgkin Lymphoma , 2021, Frontiers in Veterinary Science.

[2]  Shaying Zhao,et al.  Canine tumor mutational burden is correlated with TP53 mutation across tumor types and breeds , 2021, Nature Communications.

[3]  Bin Zhao,et al.  Pan-cancer analysis of SETD2 mutation and its association with the efficacy of immunotherapy , 2021, npj Precision Oncology.

[4]  L. Marconato,et al.  Prognostic Value of PD-L1, PD-1 and CD8A in Canine Diffuse Large B-Cell Lymphoma Detected by RNAscope , 2021, Veterinary sciences.

[5]  R. Neve,et al.  KDM5 inhibition offers a novel therapeutic strategy for the treatment of KMT2D mutant lymphomas. , 2021, Blood.

[6]  K. Noh,et al.  Histone Variant H3.3 Mutations in Defining the Chromatin Function in Mammals , 2020, Cells.

[7]  R. Jarrett,et al.  The prevalence and characterisation of TRAF3 and POT1 mutations in canine B-cell lymphoma. , 2020, Veterinary journal.

[8]  Kui Wu,et al.  Genome-wide mutational signatures revealed distinct developmental paths for human B cell lymphomas , 2020, The Journal of experimental medicine.

[9]  R. Plummer,et al.  Phase I Study of Lysine-Specific Demethylase 1 Inhibitor, CC-90011, in Patients with Advanced Solid Tumors and Relapsed/Refractory Non-Hodgkin Lymphoma , 2020, Clinical Cancer Research.

[10]  Ryan D. Morin,et al.  TBL1XR1 Mutations Drive Extranodal Lymphoma by Inducing a Pro-tumorigenic Memory Fate , 2020, Cell.

[11]  Ryan D. Morin,et al.  A Probabilistic Classification Tool for Genetic Subtypes of Diffuse Large B Cell Lymphoma with Therapeutic Implications. , 2020, Cancer cell.

[12]  A. Avery The Genetic and Molecular Basis for Canine Models of Human Leukemia and Lymphoma , 2020, Frontiers in Oncology.

[13]  Xiaosheng Wang,et al.  Cancer type-dependent correlations between TP53 mutations and antitumor immunity. , 2020, DNA repair.

[14]  K. Young,et al.  Genetic alterations and their clinical implications in DLBCL , 2019, Nature Reviews Clinical Oncology.

[15]  G. Bishop,et al.  TRAF3 regulates the oncogenic proteins Pim2 and c-Myc to restrain survival in normal and malignant B cells , 2019, Scientific Reports.

[16]  W. Schulz,et al.  The histone demethylase UTX/KDM6A in cancer: Progress and puzzles , 2019, International journal of cancer.

[17]  R. Foà,et al.  Biological and clinical implications of BIRC3 mutations in chronic lymphocytic leukemia , 2019, Haematologica.

[18]  Winnie S. Liang,et al.  Canine osteosarcoma genome sequencing identifies recurrent mutations in DMD and the histone methyltransferase gene SETD2 , 2019, Communications Biology.

[19]  Kevin C. Johnson,et al.  Comparative molecular life history of spontaneous canine and human gliomas , 2019, bioRxiv.

[20]  L. Marconato,et al.  Opportunities and challenges of active immunotherapy in dogs with B-cell lymphoma: a 5-year experience in two veterinary oncology centers , 2019, Journal of Immunotherapy for Cancer.

[21]  S. Pileri,et al.  Whole exome sequencing reveals mutations in FAT1 tumor suppressor gene clinically impacting on peripheral T-cell lymphoma not otherwise specified , 2019, Modern Pathology.

[22]  P. Jedlicka,et al.  Biology and targeting of the Jumonji-domain histone demethylase family in childhood neoplasia: a preclinical overview , 2019, Expert opinion on therapeutic targets.

[23]  L. Marconato,et al.  Minimal residual disease in lymph nodes after achievement of complete remission predicts time to relapse in dogs with large B-cell lymphoma. , 2019, Veterinary and comparative oncology.

[24]  Michael R. Green,et al.  Selective inhibition of HDAC3 targets synthetic vulnerabilities and activates immune surveillance in lymphoma , 2019, bioRxiv.

[25]  I. Martincorena,et al.  Cross-species genomic landscape comparison of human mucosal melanoma with canine oral and equine melanoma , 2019, Nature Communications.

[26]  L. Cascione,et al.  New molecular and therapeutic insights into canine diffuse large B-cell lymphoma elucidates the role of the dog as a model for human disease , 2018, Haematologica.

[27]  S. Lowe,et al.  Histone Demethylase LSD1 is required for Germinal Center formation and BCL6-driven lymphomagenesis , 2018, Nature Immunology.

[28]  Winnie S. Liang,et al.  Somatic inactivating PTPRJ mutations and dysregulated pathways identified in canine malignant melanoma by integrated comparative genomic analysis , 2018, PLoS genetics.

[29]  Voichita D. Marinescu,et al.  SETD2 Is Recurrently Mutated in Whole-Exome Sequenced Canine Osteosarcoma. , 2018, Cancer research.

[30]  Ville Mustonen,et al.  The repertoire of mutational signatures in human cancer , 2018, Nature.

[31]  Stefano Monti,et al.  Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes , 2018, Nature Medicine.

[32]  Steven J. M. Jones,et al.  Oncogenic Signaling Pathways in The Cancer Genome Atlas. , 2018, Cell.

[33]  Han Liu,et al.  Histone modifier gene mutations in peripheral T-cell lymphoma not otherwise specified , 2018, Haematologica.

[34]  J. Licht SETD2: a complex role in blood malignancy. , 2017, Blood.

[35]  K. Richards,et al.  Barking up the right tree: advancing our understanding and treatment of lymphoma with a spontaneous canine model , 2017, Current opinion in hematology.

[36]  D. Dunson,et al.  The Genetic Basis of Hepatosplenic T-cell Lymphoma. , 2017, Cancer discovery.

[37]  B. Porse,et al.  EZH2 is a potential therapeutic target for H3K27M-mutant pediatric gliomas , 2017, Nature Medicine.

[38]  G. Bishop,et al.  TRAF3 deficiency promotes metabolic reprogramming in B cells , 2016, Scientific Reports.

[39]  Benjamin J. Raphael,et al.  A weighted exact test for mutually exclusive mutations in cancer , 2016, Bioinform..

[40]  Gerben Duns,et al.  SETD2: an epigenetic modifier with tumor suppressor functionality , 2016, Oncotarget.

[41]  Xiaoyu Chen,et al.  Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications , 2016, Bioinform..

[42]  Eric Talevich,et al.  CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing , 2016, PLoS Comput. Biol..

[43]  E. Mauceli,et al.  Exome sequencing of lymphomas from three dog breeds reveals somatic mutation patterns reflecting genetic background , 2015, Genome research.

[44]  O. Elemento,et al.  The histone lysine methyltransferase KMT2D sustains a gene expression program that represses B cell lymphoma development , 2015, Nature Medicine.

[45]  K. Basso,et al.  Disruption of KMT2D perturbs germinal center B cell development and promotes lymphomagenesis , 2015, Nature Medicine.

[46]  K. Lindblad-Toh,et al.  Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes , 2015, Scientific Reports.

[47]  F. Alt,et al.  An oncogenic role for alternative NF-κB signaling in DLBCL revealed upon deregulated BCL6 expression. , 2015, Cell reports.

[48]  Ryan D. Morin,et al.  Genetic inactivation of TRAF3 in canine and human B-cell lymphoma. , 2015, Blood.

[49]  P. Xie,et al.  Targeting TRAF3 Downstream Signaling Pathways in B cell Neoplasms , 2015, Journal of cancer science & therapy.

[50]  Lu Wang,et al.  DoGSD: the dog and wolf genome SNP database , 2014, Nucleic Acids Res..

[51]  Obi L. Griffith,et al.  SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution , 2014, PLoS Comput. Biol..

[52]  J. Licht,et al.  Molecular Pathways: Deregulation of Histone H3 Lysine 27 Methylation in Cancer—Different Paths, Same Destination , 2014, Clinical Cancer Research.

[53]  M. Drigo,et al.  Minimal residual disease detection by flow cytometry and PARR in lymph node, peripheral blood and bone marrow, following treatment of dogs with diffuse large B-cell lymphoma. , 2014, Veterinary journal.

[54]  Joshua M. Korn,et al.  Pharmacological and genomic profiling identifies NF-κB–targeted treatment strategies for mantle cell lymphoma , 2013, Nature Medicine.

[55]  F. Rossi,et al.  Randomized, Placebo-Controlled, Double-Blinded Chemoimmunotherapy Clinical Trial in a Pet Dog Model of Diffuse Large B-cell Lymphoma , 2013, Clinical Cancer Research.

[56]  V. Valli,et al.  Canine Lymphomas , 2013, Veterinary pathology.

[57]  C. Fan,et al.  Gene profiling of canine B-cell lymphoma reveals germinal center and postgerminal center subtypes with different survival times, modeling human DLBCL. , 2013, Cancer research.

[58]  David T. W. Jones,et al.  Signatures of mutational processes in human cancer , 2013, Nature.

[59]  A. López-Guillermo,et al.  POT1 mutations cause telomere dysfunction in chronic lymphocytic leukemia , 2013, Nature Genetics.

[60]  Stefano Comazzi,et al.  The dog as a possible animal model for human non‐Hodgkin lymphoma: a review , 2013, Hematological oncology.

[61]  A. Sivachenko,et al.  Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples , 2013, Nature Biotechnology.

[62]  David Dunson,et al.  Genetic heterogeneity of diffuse large B-cell lymphoma , 2013, Proceedings of the National Academy of Sciences.

[63]  W. Choi,et al.  Mutational profile and prognostic significance of TP53 in diffuse large B-cell lymphoma patients treated with R-CHOP: report from an International DLBCL Rituximab-CHOP Consortium Program Study. , 2012, Blood.

[64]  David T. W. Jones,et al.  Hotspot mutations in H3F3A and IDH1 define distinct epigenetic and biological subgroups of glioblastoma. , 2012, Cancer cell.

[65]  W. Klapper,et al.  Genetic lesions of the TRAF3 and MAP3K14 genes in classical Hodgkin lymphoma , 2012, British journal of haematology.

[66]  Wendy S. W. Wong,et al.  Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs , 2012, Bioinform..

[67]  S. Pileri,et al.  Alteration of BIRC3 and multiple other NF-κB pathway genes in splenic marginal zone lymphoma. , 2011, Blood.

[68]  Heng Li,et al.  A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data , 2011, Bioinform..

[69]  C. Cole,et al.  COSMIC: the catalogue of somatic mutations in cancer , 2011, Genome Biology.

[70]  Steven J. M. Jones,et al.  Frequent mutation of histone modifying genes in non-Hodgkin lymphoma , 2011, Nature.

[71]  Raul Rabadan,et al.  Analysis of the Coding Genome of Diffuse Large B-Cell Lymphoma , 2011, Nature Genetics.

[72]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[73]  H. Hakonarson,et al.  ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data , 2010, Nucleic acids research.

[74]  J. Keats,et al.  Classical and/or alternative NF-kappaB pathway activation in multiple myeloma. , 2010, Blood.

[75]  C. Khanna,et al.  Response evaluation criteria for peripheral nodal lymphoma in dogs (v1.0)--a Veterinary Cooperative Oncology Group (VCOG) consensus document. , 2010, Veterinary and comparative oncology.

[76]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[77]  L. Bruhn,et al.  Promiscuous mutations activate the noncanonical NF-kappaB pathway in multiple myeloma. , 2007, Cancer cell.

[78]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[79]  P. Srivastava,et al.  Immunotherapy of tumors with autologous tumor-derived heat shock protein preparations. , 1997, Science.

[80]  Rafael Rosales,et al.  signeR: an empirical Bayesian approach to mutational signature discovery , 2017, Bioinform..