Genome-wide DNA methylation analysis in canine gastrointestinal lymphoma

Use of genome-wide DNA methylation analysis to identify prognostic CpG site markers associated with longer survival time in dogs with multicentric high-grade B-cell lymphoma

BACKGROUND

DNA methylation analysis might identify prognostic CpG sites in CHOP-treated dogs with multicentric high-grade B-cell lymphoma (MHGL) with heterogenous prognosis.

OBJECTIVE

To identify prognostic CpG sites of MHGL through genome-wide DNA methylation analysis with pyrosequencing validation.

ANIMALS

Test group: 24 dogs. Validation group: 100 dogs. All client-owned dogs were diagnosed with MHGL and treated with CHOP chemotherapy.

METHODS

Cohort study. DNA was extracted from lymph node samples obtained via FNA. Genome-wide DNA methylation analysis using Digital Restriction Enzyme Analysis of Methylation (DREAM) was performed on the test group to identify differentially methylated CpG sites (DMCs). Bisulfite pyrosequencing was used to measure methylation status of candidate DMCs in the validation group. Median survival times (MST) were analyzed using Kaplan-Meier (log-rank) product limit method.

RESULTS

DREAM analyzed 101 576 CpG sites. Hierarchical clustering of 16 262 CpG sites in test group identified group with better prognosis (MST = 55-477 days vs 10-301 days, P = .007). Volcano plot identified 1371 differentially methylated CpG sites (DMCs). DMC near the genes of FAM213A (DMC-F) and PHLPP1 (DMC-P) were selected as candidates. Bisulfite-pyrosequencing performed on validation group showed group with methylation level of DMC-F < 40% had favorable prognosis (MST = 11-1072 days vs 8-1792 days, P = .01), whereas group with the methylation level combination of DMC-F < 40% plus DMC-P < 10% had excellent prognosis (MST = 18-1072 days vs 8-1792 days, P = .009).

CONCLUSION AND CLINICAL IMPORTANCE

Methylation status of prognostic CpG sites delineate canine MGHL cases with longer MST, providing owners with information on expectations of potential improved treatment outcomes.

Diverse genome-wide DNA methylation alterations in canine hepatocellular tumours

BACKGROUND

Canine hepatocellular tumours (HCTs) are common primary liver tumours. However, the exact mechanisms of tumourigenesis remain unclear. Although some genetic mutations have been reported, DNA methylation alterations in canine HCT have not been well studied.

OBJECTIVES

In this study, we aimed to analyse the DNA methylation status of canine HCT.

METHODS

Tissues from 33 hepatocellular carcinomas, 3 hepatocellular adenomas, 1 nodular hyperplasia, 21 non-tumour livers from the patients and normal livers from 5 healthy dogs were used. We analysed the DNA methylation levels of 72,367 cytosine-guanine dinucleotides (CpG sites) in all 63 samples.

RESULTS AND CONCLUSIONS

Although a large fraction of CpG sites that were highly methylated in the normal liver became hypomethylated in tumours from most patients, we also found some patients with less remarkable change or no change in DNA methylation. Hierarchical clustering analysis revealed that 32 of 37 tumour samples differed from normal livers, although the remaining 5 tumour livers fell into the same cluster as normal livers. In addition, the number of hypermethylated genes in tumour livers varied among tumour cases, suggesting various DNA methylation patterns in different tumour groups. However, patient and clinical parameters, such as age, were not associated with DNA methylation status. In conclusion, we found that HCTs undergo aberrant and diverse patterns of genome-wide DNA methylation compared with normal liver tissue, suggesting a complex epigenetic mechanism in canine HCT.

Epigenetic Alterations in Canine Malignant Lymphoma: Future and Clinical Outcomes

Canine malignant lymphoma is a common neoplasia in dogs, and some studies have used dogs as a research model for molecular mechanisms of lymphomas in humans. In two species, chemotherapy is the treatment of choice, but the resistance to conventional anticancer drugs is frequent. The knowledge of molecular mechanisms of development and progression of neoplasia has expanded in recent years, and the underlying epigenetic mechanisms are increasingly well known. These studies open up new ways of discovering therapeutic biomarkers. Histone deacetylases and demethylase inhibitors could be a future treatment for canine lymphoma, and the use of microRNAs as diagnosis and prognosis biomarkers is getting closer. This review summarises the epigenetic mechanisms underlying canine lymphoma and their possible application as treatment and biomarkers, both prognostic and diagnostic.

Genome-wide DNA methylation profile in feline haematological tumours: A preliminary study

Although DNA methylation has been analysed in few studies for a limited number of loci in cats with diseases, genome-wide profile of DNA methylation has never been addressed. The hypothesis for this study is that next-generation sequencing with sequential digestion of genomic DNA with SmaI and XmaI enzymes could provide highly quantitative information on methylation levels in cats. Using blood from four healthy control cats and two disease cats as well as three feline lymphoma/leukemia cell lines, approximately 74-94 thousand CpG sites across the cat genome could be analysed. CpG sites in CpG island (CGI) were broadly either methylated or unmethylated in normal blood, while CpG sites in non-CpG islands (NCGI) are largely methylated. Lymphoma cell lines showed thousands of CpG sites with gain of methylation at normally unmethylated CGI sites and loss of methylation at normally methylated NCGI sites. Hypermethylated CpG sites located at promoter regions included genes annotated with 'developmental process' and 'anatomical structure morphogenesis' such as HOXD10. This highly quantitative method would be suitable for studies of DNA methylation changes not only in cancer but also in other common diseases in cats.