Unbiased interrogation of functional lysine residues in human proteome

Functional profiling of serine, threonine and tyrosine sites

Systematic perturbation of amino acids at endogenous loci provides diverse insights into protein function. Here, we performed a genome-wide screen to globally assess the cell fitness dependency of serine, threonine and tyrosine residues. Using an adenine base editor, we designed a whole-genome library comprising 817,089 single guide RNAs to perturb 584,337 S, T and Y sites. We identified 3,467 functional substitutions affecting cell fitness and 677 of them involving phosphorylation, including numerous phosphorylation-mediated gain-of-function substitutions that regulate phosphorylation levels of itself or downstream factors. Furthermore, our findings highlight that specific substitution types, notably serine to proline, are crucial for maintaining domain structure broadly. Lastly, we demonstrate that 309 enriched hits capable of initiating cell overproliferation might be potential cancer driver mutations. This study represents an extensive functional profiling of S, T and Y residues and provides insights into the distinctive roles of these amino acids in biological mechanisms and tumor progression.

dsDAP: An efficient method for high-abundance DNA-encoded library construction in mammalian cells

DNA-encoded libraries are invaluable tools for high-throughput screening and functional genomics studies. However, constructing high-abundance libraries in mammalian cells remains challenging. Here, we present dsDNA-assembly-PCR (dsDAP), a novel Gibson-assembly-PCR strategy for creating DNA-encoded libraries, offering improved flexibility and efficiency over previous methods. We demonstrated this approach by investigating the impact of translation initiation sequences (TIS) on protein expression in HEK293T cells. Both CRISPR-Cas9 and piggyBac systems were employed for genomic integration, allowing comparison of different integration methods. Our results confirmed the importance of specific nucleotides in the TIS region, particularly the preference for adenine at the -3 position in high-expression sequences. We also explored the effects of library dilution on genotype-phenotype correlations. This Gibson-assembly-PCR strategy overcomes limitations of existing methods, such as restriction enzyme dependencies, and provides a versatile tool for constructing high-abundance libraries in mammalian cells. Our approach has broad applications in functional genomics, drug discovery, and the study of gene regulation.

Multiplexed in vivo base editing identifies functional gene-variant-context interactions

Human genome sequencing efforts in healthy and diseased individuals continue to identify a broad spectrum of genetic variants associated with predisposition, progression, and therapeutic outcomes for diseases like cancer1-6. Insights derived from these studies have significant potential to guide clinical diagnoses and treatment decisions; however, the relative importance and functional impact of most genetic variants remain poorly understood. Precision genome editing technologies like base and prime editing can be used to systematically engineer and interrogate diverse types of endogenous genetic variants in their native context7-9. We and others have recently developed and applied scalable sensor-based screening approaches to engineer and measure the phenotypes produced by thousands of endogenous mutations in vitro 10-12. However, the impact of most genetic variants in the physiological in vivo setting, including contextual differences depending on the tissue or microenvironment, remains unexplored. Here, we integrate new cross-species base editing sensor libraries with syngeneic cancer mouse models to develop a multiplexed in vivo platform for systematic functional analysis of endogenous genetic variants in primary and disseminated malignancies. We used this platform to screen 13,840 guide RNAs designed to engineer 7,783 human cancer-associated mutations mapping to 489 endogenous protein-coding genes, allowing us to construct a rich compendium of putative functional interactions between genes, mutations, and physiological contexts. Our findings suggest that the physiological in vivo environment and cellular organotropism are important contextual determinants of specific gene-variant phenotypes. We also show that many mutations and their in vivo effects fail to be detected with standard CRISPR-Cas9 nuclease approaches and often produce discordant phenotypes, potentially due to site-specific amino acid selection- or separation-of-function mechanisms. This versatile platform could be deployed to investigate how genetic variation impacts diverse in vivo phenotypes associated with cancer and other genetic diseases, as well as identify new potential therapeutic avenues to treat human disease.

Mapping functional elements of the DNA damage response through base editor screens

Maintaining genomic stability is vital for cellular equilibrium. In this study, we combined CRISPR-mediated base editing with pooled screening technologies to identify numerous mutations in lysine residues and protein-coding genes. The loss of these lysine residues and genes resulted in either sensitivity or resistance to DNA-damaging agents. Among the identified variants, we characterized both loss-of-function and gain-of-function mutations in response to DNA damage. Notably, we discovered that the K494 mutation of C17orf53 disrupts its interaction with RPA proteins, leading to increased sensitivity to cisplatin. Additionally, our analysis identified STK35 as a previously unrecognized gene involved in DNA damage response (DDR) pathways, suggesting that it may play a critical role in DNA repair. We believe that this resource will offer valuable insights into the broader functions of DNA damage response genes and accelerate research on variants relevant to cancer therapy.

Protocol for high-throughput screening of functional lysine residues in cell fitness

Amino acid residues are crucial to protein structure and function and have links to various human diseases. Here, we present a protocol for screening functional lysine residues across the human genome. We describe steps for designing lysine codon-targeting single-guide RNAs (sgRNAs), constructing an sgRNA library, conducting cell fitness screenings, and acquiring screening results. This approach leverages base editing and high-throughput screening techniques to systematically examine functional amino acid residues. For complete details on the use and execution of this protocol, please refer to Bao et al.1.

Covalent fragment-based drug discovery for target tractability

An important consideration in drug discovery is the prioritization of tractable protein targets that are not only amenable to binding small molecules, but also alter disease biology in response to small molecule binding. Covalent fragment-based drug discovery has emerged as a powerful approach to aid in the identification of such protein targets. The application of irreversible binding mechanisms enables the identification of fragment hits for challenging-to-target proteins, allows proteome-wide screening in a cellular context, and makes it possible to determine functional effects with modestly potent ligands without the requirement for extensive compound optimization. Here, we provide an overview of recent approaches to covalent fragment-based screening and discuss how these have been applied to establish the tractability of unexplored binding sites on protein targets.

CRISPR screens in mechanism and target discovery for AML

CRISPR-based screens have discovered novel functional genes involving in diverse tumor biology and elucidated the mechanisms of the cancer pathological states. Recently, with its randomness and unbiasedness, CRISPR screens have been used to discover effector genes with previously unknown roles for AML. Those novel targets are related to AML survival resembled cellular pathways mediating epigenetics, synthetic lethality, transcriptional regulation, mitochondrial and energy metabolism. Other genes that are crucial for pharmaceutical targeting and drug resistance have also been identified. With the rapid development of novel strategies, such as barcodes and multiplexed mosaic CRISPR perturbation, more potential therapeutic targets and mechanism in AML will be discovered. In this review, we present an overview of recent progresses in the development of CRISPR-based screens for the mechanism and target identification in AML and discuss the challenges and possible solutions in this rapidly growing field.

Deconstructing cancer with precision genome editing

Recent advances in genome editing technologies are allowing investigators to engineer and study cancer-associated mutations in their endogenous genetic contexts with high precision and efficiency. Of these, base editing and prime editing are quickly becoming gold-standards in the field due to their versatility and scalability. Here, we review the merits and limitations of these precision genome editing technologies, their application to modern cancer research, and speculate how these could be integrated to address future directions in the field.

Detection and Analysis of Short Linear Motif-Based Protein-Protein Interactions with SLiMAn2 Web Server

Interactomics is bringing a deluge of data regarding protein-protein interactions (PPIs) which are involved in various molecular processes in all types of cells. However, this information does not easily translate into direct and precise molecular interfaces. This limits our understanding of each interaction network and prevents their efficient modulation. A lot of the detected interactions involve recognition of short linear motifs (SLiMs) by a folded domain while others rely on domain-domain interactions. Functional SLiMs hide among a lot of spurious ones, making deeper analysis of interactomes tedious. Hence, actual contacts and direct interactions are difficult to identify.Consequently, there is a need for user-friendly bioinformatic tools, enabling rapid molecular and structural analysis of SLiM-based PPIs in a protein network. In this chapter, we describe the use of the new webserver SLiMAn to help digging into SLiM-based PPIs in an interactive fashion.

The case of the missing Ks: Base editor screen to assess cellular fitness at single lysines

In this issue of Molecular Cell, Bao et al.1 set out to elucidate "functional lysines" in the genome using adenine base editors. The study reveals several cases of alteration of functions that previous canonical CRISPR-Cas9 screens were unable to detect.