A multi-omic approach to biomarker discovery for the differential diagnosis of feline IBD and EATL using minimally invasive specimens

Josephine Tsang¹, Karim Mrouj¹, George Courcoubetis¹, Surya Vishnubhatt¹, Chewon Yim², Hyoju Yi², Beeham Lee², Sheena Kapoor¹, Sushmita Sen¹, Jerry Cromarty¹, Sungwon Lim^1,2, Jamin Koo^1,2,3,*, Ilona Holcomb¹*

¹ImpriMed, Inc., 3980 Fabian Way, CA 94303, USA

²ImpriMedKorea, Inc., Seoul 03920, Republic of Korea

³Department of Chemical Engineering, Hongik University, Seoul 04066, Republic of Korea

*Co-correspondence:  

Jamin Koo, PhD (jamin@imprimedicine.com) and Ilona Holcomb, PhD (iholcomb@imprimedicine.com)

Introduction

Differentiating feline IBD from enteropathy-associated T-cell lymphoma (EATL) remains challenging. The stress and cost of invasive methods and overlapping, non-specific clinical signs all present a significant barrier to an accurate diagnosis. We hypothesized that underlying differences in IBD or EATL etiology produce disease-specific molecular signatures and that a multi-omic approach could result in an effective diagnostic.

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Methods

Whole blood, serum, and feces were collected from client-owned cats with histopathologically confirmed IBD (n=15), EATL (n=15), and healthy controls (n=10). We employed sequencing for total RNA (RNA-seq), small RNAs (smRNA-seq), 16S rRNA, and enzymatic methyl sequencing (EM-seq) to identify distinct disease-related signatures.

Results

Multi-omic profiling revealed distinct transcriptomic, epigenetic, and microbiome signatures. Total RNA-seq of whole blood identified 127 differentially expressed genes between IBD and EATL. Fifteen genes, including those associated with inflammatory response, cell adhesion, and migration, were differentially expressed in all three pairwise comparisons.

EM-seq analysis showed that global methylation increased progressively from EATL to IBD to healthy cats, consistent with the general observation that malignant tumors often exhibit global hypomethylation, whereas chronic inflammatory conditions tend to show relatively higher methylation levels. Integration of RNA-seq and EM-seq data showed consistent patterns for six upregulated genes and ten downregulated genes.

16S rRNA sequencing revealed greater microbial diversity in healthy cats than in those with enteropathy (p=0.019), although no microbial signature was specific between the two disease conditions.

Conclusion

Multi-omic evaluation of minimally invasive specimens hold promise for distinguishing feline IBD and EATL. Ongoing work aims to validate putative biomarkers in a prospective study.