Whole genome sequencing analysis of high confidence variants of B-cell lymphoma in Canis familiaris.

Alana Sparks,J Paul Woods,Brenda Lynn Coomber,Geoffrey A Wood,Dorothee Bienzle,Silvia Sabattini

doi:10.1371/journal.pone.0238183

Abstract

Lymphoma (lymphosarcoma) is the second most frequent cancer in dogs and is clinically comparable to human non-Hodgkin lymphoma. Factors affecting canine lymphoma progression are unknown and complex, but there is evidence that genetic mutations play an important role. We employed Next Gen DNA sequencing of six dogs with multicentric B-cell lymphoma undergoing CHOP chemotherapy to identify genetic variations potentially impacting response. Paired samples from non-neoplastic tissue (blood mononuclear cells) and lymphoma were collected at the time of diagnosis. Cases with progression free survival above the median of 231 days were grouped as ‘good’ responders and cases below the median were categorized as ‘poor’ responders. The average number of variants found was 17,138 per case. The variants were filtered to examine those with predicted moderate or high impacts. Many of the genes with variants had human orthologs with links to cancer, but the majority of variants were not previously reported in canine or human lymphoma. Seven genes had variants found in the cancers of at least two ‘poor’ responders but in no 'good’ responders: ATRNL1, BAIAP2L2, ZNF384, ST6GALNAC5, ENSCAFG00000030179 (human ortholog: riboflavin kinase RFK), ENSCAFG00000029320, and ENSCAFG00000007370 (human ortholog: immunoglobin IGKV4-1). Two genes had variants found in the cancers of at least two 'good’ responders but in no 'poor’ responders: COX18 and ENSCAFG00000030512. ENSCAFG00000030512 has no reported orthologue in any other species. The role of these mutations in the progression of canine lymphoma requires further functional analyses and larger scale study.

Highlights

Lymphoma originates from poorly controlled lymphocyte clonal expansion, and is the second most frequent canine cancer, accounting for 90% of all hematopoietic cancers in dogs [1,2,3]
At the time of diagnosis, fine needle aspirate (FNA) samples were collected from either the prescapular, submandibular, or popliteal lymph node, and a 3–5 mL blood venipuncture sample was collected from which buffy coat (BC) leukocytes were isolated for this study
There were 11 genes with variants found in both ‘good’ and ‘poor’ responders, but only two of these variants were in genes named in the dog: NEFH and HOXA7

Summary

Introduction

Lymphoma (lymphosarcoma) originates from poorly controlled lymphocyte clonal expansion, and is the second most frequent canine cancer, accounting for 90% of all hematopoietic cancers in dogs [1,2,3]. CL is generally regarded as being highly similar to human non-Hodgkin lymphoma (NHL) [5] Both cancers occur spontaneously, have similar clinical presentation and pathophysiology, along with a closely parallel natural progression and response to chemotherapy [3]. We examine the genomes of six dogs, with paired samples from a non-neoplastic tissue (blood mononuclear cells) and a sample of cancerous tissue (needle aspirate of enlarged peripheral lymph node) to identify significant genetic variations in neoplastic tissue relative to non-neoplastic tissue. We identified multiple genetic changes, both in the tumour samples and in the buffy coat samples relative to the canine reference genome. Several of these gene mutations were previously described, but many are novel and their potential role in CL progression warrants further investigation

Materials and methods

Results

Discussion