Cancer biology functional genomics: From small RNAs to big dreams

Abstract

The year 2021 marks the 20th anniversary of the first publications reporting the discovery of the gene silencing mechanism, RNA interference (RNAi) in mammalian cells. Along with the many studies that delineated the proteins and substrates that form the RNAi pathway, this finding changed our understanding of the posttranscriptional regulation of mammalian gene expression. Furthermore, the development of methods that exploited the RNAi pathway began the technological revolution that eventually enabled the interrogation of mammalian gene function-from a single gene to the whole genome-in only a few days. The needs of the cancer research community have driven much of this progress. In this perspective, we highlight milestones in the development and application of RNAi-based methods to study carcinogenesis. We discuss how RNAi-based functional genetic analysis of exemplar tumor suppressors and oncogenes furthered our understanding of cancer initiation and progression and explore how such studies formed the basis of genome-wide scale efforts to identify cancer or cancer-type specific vulnerabilities, including studies conducted in vivo. Furthermore, we examine how RNAi technologies have revealed new cancer-relevant molecular targets and the implications for cancer of the first RNAi-based drugs. Finally, we discuss the future of functional genetic analysis, highlighting the increasing availability of complementary approaches to analyze cancer gene function.

RNA in Cancer Immunotherapy: Unlocking the Potential of the Immune System

“…Regarding RNAi, hereditary transthyretin amyloidosis and acute hepatic porphyria can already benefit from treatment options ( 137 ). Nevertheless, for the treatment of cancer, RNAi and ncRNA formulations have not yet been approved.…”

Degradome-focused RNA interference screens to identify proteases important for breast cancer cell growth

“…In this work, we performed an RNAi-based genetic screen targeting the entire degradome in two murine breast cancer cell lines for an unbiased identification of proteases important for breast cancer cell proliferation and/or survival. Genetic screens are a widely used tool to efficiently discover cancer drivers, novel cancer-linked genes, and putative therapeutic targets ( 1 , 2 , 31 ), but genome-wide ( 4 – 6 ) or kinase-focused screens ( 7 – 9 ) missed out on proteases so far.…”

“…Short hairpin RNA (shRNA) library-based RNA interference (RNAi) is a widely used method for large-scale genetic loss of function screens, allowing for the unbiased discovery of cancer drivers, putative therapeutic targets, and genes with no previous links to cancer (1)(2)(3). shRNA libraries contain a heterogeneous mixture of different shRNA constructs targeting the whole genome (genome-wide screening) or a subset, i.e., all kinases, in so-called focused libraries.…”

Biotechnological Evolution of siRNA Molecules: From Bench Tool to the Refined Drug

“…Many successful strategies have been developed by rational design using high throughput screenings, especially based on -omics data-integration approaches and genome-wide siRNA screening [ 51 , 52 ]. Furthermore, it is important to highlight that siRNA-based methods are helpful in the context of understanding the complex basis of a number of diseases such as cancer, infection, HIV [ 53 ], neurodegenerative and respiratory diseases. Since 2001, thousands of cancer-based studies have reported the employment of siRNA-based methods to study mammalian gene function, leading to the discovery of many genes with no previous links to cancer biology, for example, and enhanced understanding of the functions of established oncogene and tumor suppressors [ 54 ].…”