A novel canine reference genome resolves genomic architecture and uncovers transcript complexity

Wang, Chao; Wallerman, Ola; Arendt, Maja L.; Sundström, Elisabeth; Karlsson, Åsa; Nordin, Jessika; Mäkeläinen, Suvi; Pielberg, Gerli; Hanson, Jeanette; Ohlsson, Åsa; Saellström, Sara; Rönnberg, Henrik; Ljungvall, Ingrid; Häggström, Jens; Bergström, Tomas F.; Hedhammar, Åke; Meadows, Jennifer R. S.; Lindblad‐Toh, Kerstin

doi:10.1038/s42003-021-01698-x

Cited by 84 publications

(102 citation statements)

References 84 publications

(65 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Finally, it is also possible that the current database of known V(D)J gene segments is incomplete. Modern canine genome assemblies 29 , future annotation work, and de novo analysis of data like ours may identify novel gene segments in the future. Profiling of additional samples will be required to further validate this approach and delineate any technological or biological gaps in V(D)J representation.…”

Section: Discussionmentioning

confidence: 98%

Single Cell T Cell Receptor Repertoire Profiling for Dogs

Skidmore¹,

Rindt

Chu

et al. 2021

Preprint

View full text Add to dashboard Cite

Background: Spontaneous cancers in companion dogs are increasingly recognized as robust models of human disease. This recognition has led to translational clinical trials in companion dogs with osteosarcoma, lymphoma, melanoma, squamous cell carcinoma, and soft tissue sarcoma. The ability to precisely track tumor-specific immune responses in such clinical trials would benefit from reagents to perform species-specific single cell T cell receptor sequencing (scTCRseq). This technology defines clones of T cells reacting to immune interventions and can help identify the specific epitope of response. Single cell gene expression data give insights into the activity and polarization of the T cell. To date, scTCRseq has not been demonstrated for canine samples. Methods: Samples from two responding dogs in a trial of an autologous deglycosylated melanoma vaccine were selected to demonstrate applicability of scTCRseq in a cancer immunotherapy setting. A single-cell suspension of cryopreserved peripheral blood mononuclear cells (PBMC) was prepared for 10X single cell sequencing. Full length 10X cDNA was amplified using a custom-designed nested PCR of the alpha/beta V(D)J region. A library made from this enriched product (scTCRseq) and a 10X gene expression (GEX) library (scRNAseq) were sequenced on the NovaSeq 6000. Results: 1,850-2,172 estimated V(D)J-expressing cells yielded 87-103.7 million reads with 73.8%-75.8% mapped to a V(D)J gene (beta/alpha chains ratio 1.5:1). 43 TRAJ, 29 TRAV, 12 TRBJ, and 22 TRBV gene segments were observed representing 72.9%, 51.8%, 100%, and 62.9% of all known V and J gene segments respectively. A large diversity of clonotypes was captured with 966-1,253 TRA/TRB clonotypes identified. Both dogs also exhibited a small number of highly abundant T cell clonotypes suggesting the presence of an anti-tumor T cell population. GEX enriched libraries successfully defined large clusters of CD8+ and CD4+ T cells that overlapped with V(D)J-expressing cells. Discussion: The developed reagents successfully generated scTCRseq data, for the first time, which allowed the T cell repertoire to be surveyed in dogs responding to anti-tumor immunotherapy. These reagents will allow longitudinal tracking of anti-tumor T cell dynamics in canine cancer immunotherapy trials.

show abstract

Section: Discussionmentioning

confidence: 98%

Single Cell T Cell Receptor Repertoire Profiling for Dogs

Skidmore¹,

Rindt

Chu

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…To date, five long-read-based de novo dog genome assemblies [8][9][10] have been made available at the NCBI genome repository with comparable parameters such as number of genes annotated and number of gaps between the new assemblies. The NCBI has annotated all five genomes and made them available on their genome browser https://www.ncbi.…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, high-quality assemblies are an essential prerequisite for accurate annotation, which is required to assay the potential functional effects of detected variants. Recently, several high-quality genomes from different dogs became available [8][9][10].…”

Section: Introductionmentioning

confidence: 99%

Dog10K_Boxer_Tasha_1.0: A Long-Read Assembly of the Dog Reference Genome

Jagannathan

Hitte

Kidd

et al. 2021

Genes

View full text Add to dashboard Cite

The domestic dog has evolved to be an important biomedical model for studies regarding the genetic basis of disease, morphology and behavior. Genetic studies in the dog have relied on a draft reference genome of a purebred female boxer dog named “Tasha” initially published in 2005. Derived from a Sanger whole genome shotgun sequencing approach coupled with limited clone-based sequencing, the initial assembly and subsequent updates have served as the predominant resource for canine genetics for 15 years. While the initial assembly produced a good-quality draft, as with all assemblies produced at the time, it contained gaps, assembly errors and missing sequences, particularly in GC-rich regions, which are found at many promoters and in the first exons of protein-coding genes. Here, we present Dog10K_Boxer_Tasha_1.0, an improved chromosome-level highly contiguous genome assembly of Tasha created with long-read technologies that increases sequence contiguity >100-fold, closes >23,000 gaps of the CanFam3.1 reference assembly and improves gene annotation by identifying >1200 new protein-coding transcripts. The assembly and annotation are available at NCBI under the accession GCF_000002285.5.

show abstract

“…The comparative aspects of malignant melanoma in dogs have been extensively reviewed, showing both molecular biological similarities and thanks to a spontaneous developing tumor in an immune competent animal, ideal for investigating new treatment modalities, especially immunotherapy (10,11,14,65). Finally, the rapidly increasing resolution of the dog genome sequence makes canine comparative oncology studies easier to perform with high accuracy (66).…”

Section: Discussionmentioning

confidence: 99%

Adenoviral CD40 Ligand Immunotherapy in 32 Canine Malignant Melanomas–Long-Term Follow Up

et al. 2021

View full text Add to dashboard Cite

Malignant melanoma is a serious disease in both humans and dogs, and the high metastatic potential results in poor prognosis for many patients. Its similarities with human melanoma make spontaneous canine melanoma an excellent model for comparative studies of novel therapies and tumor biology. Gene therapy using adenoviruses encoding the immunostimulatory gene CD40L (AdCD40L) has shown promise in initial clinical trials enrolling human patients with various malignancies including melanoma. We report a study of local AdCD40L treatment in 32 cases of canine melanoma (23 oral, 5 cutaneous, 3 ungual and 1 conjunctival). Eight patients were World Health Organization (WHO) stage I, 9 were stage II, 12 stage III, and 3 stage IV. One to six intratumoral injections of AdCD40L were given every seven days, combined with cytoreductive surgery in 20 cases and only immunotherapy in 12 cases. Tumor tissue was infiltrated with T and B lymphocytes after treatment, suggesting immune stimulation. The best overall response based on result of immunotherapy included 7 complete responses, 5 partial responses, 5 stable and 2 progressive disease statuses according to the World Health Organization response criteria. Median survival was 285 days (range 20–3435 d). Our results suggest that local AdCD40L therapy is safe and could have beneficial effects in dogs, supporting further treatment development. Clinical translation to human patients is ongoing.

show abstract

A novel canine reference genome resolves genomic architecture and uncovers transcript complexity

Cited by 84 publications

References 84 publications

Single Cell T Cell Receptor Repertoire Profiling for Dogs

Single Cell T Cell Receptor Repertoire Profiling for Dogs

Dog10K_Boxer_Tasha_1.0: A Long-Read Assembly of the Dog Reference Genome

Adenoviral CD40 Ligand Immunotherapy in 32 Canine Malignant Melanomas–Long-Term Follow Up

Contact Info

Product

Resources

About