Theses Doctoral

Investigation of Novel LncRNAs Harboring Risk SNPs Associated with Celiac and Crohn's Disease

Shearer, Alyssa

Long non-coding RNAs (lncRNAs) have been implicated as important regulators of inflammation through various mechanisms in both the innate and adaptive immune systems of mice and humans. The majority of SNPs identified by GWAS to be associated with autoimmune disorders lie within non-coding areas of the genome, including genes for lncRNAs. To identify lncRNAs with relevancy to inflammation and autoimmunity, a discovery pipeline was used to find lncRNAs differentially expressed in TLR4 activated murine macrophages, conserved between mice and humans, and harboring GWAS identified SNPs associated with autoimmune disorders. Two of the six candidate lncRNAs identified, Lnc15 and Lnc13, are decreased in activated macrophages and are associated with both celiac and Crohn’s disease. To further explore the regulation and influence of these two lncRNAs during inflammation and its resolution, a variety of in vitro and in vivo techniques were utilized, including novel mouse knockout models. An investigation of Lnc15 was conducted in cells of both the innate and adaptive immune system, where the dominant isoform of Lnc15 was identified to be a ~1.4 kb transcript localized to the cytoplasm in both murine macrophages and T cells. Analysis of Lnc15 regulation was conducted in activated murine macrophages, focused on TLR signaling.

Through stimulating macrophages with specific TLR ligands, Lnc15 was found to be decreased by TLR2, TLR3, and TLR4 signaling, likely dependent upon both MYD88 and TRIF. While not dependent upon NF-κB, protein synthesis is required for TLR induced decreases in Lnc15 levels. Conversely, activated neutrophils significantly increase Lnc15 levels, although the mechanism of regulation is not yet known. Mice lacking Lnc15 globally were found to be more susceptible to DSS induced colitis, which is likely dependent upon a defect in the innate immune system. In the adaptive immune system, Lnc15 was found to be specifically upregulated in Tregs compared to other T cell subsets. Lnc15 deficient Tregs had a reduced suppressive capacity in vitro, but not in vivo in a T cell induced model of colitis. These findings suggest Lnc15 plays a role in Treg suppressive capacity under certain conditions, but the exact mechanism influenced remains to be identified. Additionally, overexpression of Lnc15 in a murine T cell line resulted in a decrease in Rorc expression. A Lnc15 RNA pulldown experiment identified USF2, a transcription factor known to regulate Rorc expression, and UBR5, a ubiquitin-protein ligase known to influence RORyt stability, as protein interactors of Lnc15. These data indicate that Lnc15 can influence aspects of RORyt biology, which implicates Lnc15 as a regulator of either the plasticity between Tregs and Th17 cells, or Treg ability to suppress inflammatory Th17 cells.

An investigation into Lnc13 regulation by disease relevant cytokines was conducted with a series of macrophage stimulation experiments. Lnc13 was found to be positively regulated by cytokines with an anti-inflammatory capacity, including IL-6, IL-4 and IL-10. When Lnc13 deficient macrophages were polarized, a higher expression of Il6 was detected in both M1 and M2 macrophages, suggesting a regulatory connection between Lnc13 and IL-6 across macrophage activation states. Previously identified Lnc13 target genes displayed a quicker transcriptional response to LPS stimulation in Lnc13 deficient macrophages. Additionally, when the Lnc13 mouse was crossed with the DQ8 transgenic mouse model and challenged to gluten, the ileum tissue of Lnc13 deficient mice expressed higher amounts of Il12 and Ifng, cytokines directly relevant to celiac disease. These findings provide support for Lnc13 as a novel regulator of macrophage response and cytokine expression in response to disease relevant stimuli.


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More About This Work

Academic Units
Nutritional and Metabolic Biology
Thesis Advisors
Ghosh, Sankar
Ph.D., Columbia University
Published Here
October 12, 2022