We study small RNA-guided gene silencing in cellular homeostasis and human diseases...!!!

CSDE1 interaction with AGO2 regulates microRNA function in the development of cancer

Kakumani PK et al., 2020 and Kakumani PK et al., 2021

Our Research Program - Overview

Small RNAs are essential for cell homeostasis, differentiation and development in animals. They mediate post-transcriptional gene silencing (PTGS) and their dysfunction causes multiple human diseases such as cancer and neurodegeneration. Small RNAs are defined by their length (19-34 nt) and association with Argonaute (AGO) family proteins, classifying them into microRNAs (miRNAs), small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs). miRNAs target messenger RNAs (mRNAs) while siRNAs and piRNAs target mostly transposable elements (TEs) and to a lesser extent, mRNAs. Their distribution and functional relevance during the stages of animal development and disease are yet to be fully explored. Therefore, in our lab, we aim to: 1) dissect the complexities of small RNA-guided gene regulatory mechanisms and 2) delineate the contribution of these pathways to cell differentiation and survival with implications in human diseases.

Theme 1: Dicer-IFN crosstalk regulating dsRNA homeostasis in cells

Double stranded RNAs (dsRNAs, whether exogenous or endogenous) trigger both RNAi and IFN signaling. RNAi and IFN cascades are mutually inhibitory and yet co-exist to clear cellular dsRNAs in stem/progenitor cells. Aside from sharing a common substrate, much remains to be investigated in terms of their interactions towards maintaining cellular dsRNA homeostasis. Since, retrotransposon derived dsRNAs induce abnormal IFN signaling leading to cell death, we stipulate that Dicer mediated processing of dsRNAs is critical to cell survival. To address the issue, we seek to i) explore Dicer mediated processing of dsRNAs and ii) delineate the contribution of dsRNA-Dicer function to cell survival.

Theme 2: AGO2-mediated retrotransposon repression underlying cell fate decisions

Embryonic Stem Cells (ESCs) express siRNAs generated from retrotransposons and these TEs regulate differentiation of stem/progenitor cells. We have identified proteins associated with siRNA Induced Silencing Complexes (siRISCs) in stem/progenitor cells, which have not been characterized for their role in the AGO2-mediated gene silencing. Interestingly,  these AGO2-interacting proteins are critical for stem cell maintenance, by means that remain unknown. Therefore, we aim to explore their regulatory role in AGO2-mediated retrotransposon silencing responsible for stem-like cell characteristics. Here, we primarily focus on i) deciphering the mechanisms of AGO2-interacting partners in retrotransposon repression, and ii) define their role in controlling TE dependent cell fate.

Theme 3: piRNA-guided gene regulation in mammalian somatic cells

PIWI-interacting RNAs (piRNAs) bind specifically to the PIWI subfamily of AGO proteins. PIWI proteins and piRNAs are abnormally expressed in mammalian somatic tissues and during the development of multiple human diseases. Yet, their function in defining the aberrant context remains largely elusive. Therefore, we seek to unveil the mechanisms associated with piRNA reactivation in mammalian somatic cells. Here, we primarily focus on i) elucidating the characteristics of piRNA interacting proteins in somatic retrotransposon silencing and ii) define the contribution of piRNA function to cell death and differentiation with implications in the development and pathogeneis of numerous human diseases.