RNA Interference Library Research Articles

Phenotypic screening reveals a highly selective phthalimide-based compound with antileishmanial activity.

Pharmacophores such as hydroxyethylamine (HEA) and phthalimide (PHT) have been identified as potential synthons for the development of compounds against various parasitic infections. In order to further advance our progress, we conducted an experiment utilising a collection of PHT and HEA derivatives through phenotypic screening against a diverse set of protist parasites. This approach led to the identification of a number of compounds that exhibited significant effects on the survival of Entamoeba histolytica, Trypanosoma brucei, and multiple life-cycle stages of Leishmania spp. The Leishmania hits were pursued due to the pressing necessity to expand our repertoire of reliable, cost-effective, and efficient medications for the treatment of leishmaniases. Antileishmanials must possess the essential capability to efficiently penetrate the host cells and their compartments in the disease context, to effectively eliminate the intracellular parasite. Hence, we performed a study to assess the effectiveness of eradicating L. infantum intracellular amastigotes in a model of macrophage infection. Among eleven L. infantum growth inhibitors with low-micromolar potency, PHT-39, which carries a trifluoromethyl substitution, demonstrated the highest efficacy in the intramacrophage assay, with an EC50 of 1.2 +/- 3.2 μM. Cytotoxicity testing of PHT-39 in HepG2 cells indicated a promising selectivity of over 90-fold. A chemogenomic profiling approach was conducted using an orthology-based method to elucidate the mode of action of PHT-39. This genome-wide RNA interference library of T. brucei identified sensitivity determinants for PHT-39, which included a P-type ATPase that is crucial for the uptake of miltefosine and amphotericin, strongly indicating a shared route for cellular entry. Notwithstanding the favourable properties and demonstrated efficacy in the Plasmodium berghei infection model, PHT-39 was unable to eradicate L. major infection in a murine infection model of cutaneous leishmaniasis. Currently, PHT-39 is undergoing derivatization to optimize its pharmacological characteristics.

The Current Situation and Development Prospect of Whole-Genome Screening.

High-throughput genetic screening is useful for discovering critical genes or gene sequences that trigger specific cell functions and/or phenotypes. Loss-of-function genetic screening is mainly achieved through RNA interference (RNAi), CRISPR knock-out (CRISPRko), and CRISPR interference (CRISPRi) technologies. Gain-of-function genetic screening mainly depends on the overexpression of a cDNA library and CRISPR activation (CRISPRa). Base editing can perform both gain- and loss-of-function genetic screening. This review discusses genetic screening techniques based on Cas9 nuclease, including Cas9-mediated genome knock-out and dCas9-based gene activation and interference. We compare these methods with previous genetic screening techniques based on RNAi and cDNA library overexpression and propose future prospects and applications for CRISPR screening.

Analysis of the Candidate Genes and Underlying Molecular Mechanism of P198, an RNAi-Related Dwarf and Sterile Line.

The genome-wide long hairpin RNA interference (lhRNAi) library is an important resource for plant gene function research. Molecularly characterizing lhRNAi mutant lines is crucial for identifying candidate genes associated with corresponding phenotypes. In this study, a dwarf and sterile line named P198 was screened from the Brassica napus (B. napus) RNAi library. Three different methods confirmed that eight copies of T-DNA are present in the P198 genome. However, only four insertion positions were identified in three chromosomes using fusion primer and nested integrated polymerase chain reaction. Therefore, the T-DNA insertion sites and copy number were further investigated using Oxford Nanopore Technologies (ONT) sequencing, and it was found that at least seven copies of T-DNA were inserted into three insertion sites. Based on the obtained T-DNA insertion sites and hairpin RNA (hpRNA) cassette sequences, three candidate genes related to the P198 phenotype were identified. Furthermore, the potential differentially expressed genes and pathways involved in the dwarfism and sterility phenotype of P198 were investigated by RNA-seq. These results demonstrate the advantage of applying ONT sequencing to investigate the molecular characteristics of transgenic lines and expand our understanding of the complex molecular mechanism of dwarfism and male sterility in B. napus.

Role of ERK1/2 Signaling in Cinnabarinic Acid-Driven Stanniocalcin 2-Mediated Protection against Alcohol-Induced Apoptosis.

We have previously shown that a bona fide aryl hydrocarbon receptor (AhR) agonist, cinnabarinic acid (CA), protects against alcohol-induced hepatocyte apoptosis via activation of a novel AhR target gene, stanniocalcin 2 (Stc2). Stc2 translates to a secreted disulfide-linked hormone, STC2, known to function in cell development, calcium and phosphate regulation, angiogenesis, and antiapoptosis-albeit the comprehensive mechanism by which the CA-AhR-STC2 axis confers antiapoptosis is yet to be characterized. In this study, using RNA interference library screening, downstream antiapoptotic molecular signaling components involved in CA-induced STC2-mediated protection against ethanol-induced apoptosis were investigated. RNA interference library screening of kinases and phosphatases in Hepa1 cells and subsequent pathway analysis identified mitogen-activated protein kinase (MAPK) signaling as a critical molecular pathway involved in CA-mediated protection. Specifically, phosphorylation of ERK1/2 was induced in response to CA treatment without alterations in p38 and JNK signaling pathways. Silencing Stc2 in Hepa1 cells and in vivo experiments performed in Stc2-/- (Stc2 knockout) mice, which failed to confer CA-mediated protection against ethanol-induced apoptosis, showed abrogation of ERK1/2 activation, underlining the significance of ERK1/2 signaling in CA-STC2-mediated protection. In conclusion, activation of ERK1/2 signaling in CA-driven AhR-dependent Stc2-mediated protection represents a novel mechanism of protection against acute alcohol-induced apoptosis. SIGNIFICANCE STATEMENT: Previous studies have shown the role of stanniocalcin 2 (Stc2) in cinnabarinic acid (CA)-mediated protection against alcohol-induced apoptosis. Here, using RNA interference library screening and subsequent in vivo studies, the functional significance of ERK1/2 activation in CA-induced Stc2-mediated protection against acute ethanol-induced apoptosis was identified. This study is thus significant as it illustrates a comprehensive downstream mechanism by which CA-induced Stc2 protects against alcoholic liver disease.

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

Proteases are known to promote or impair breast cancer progression and metastasis. However, while a small number of the 588 human and 672 murine protease genes have been extensively studied, others were neglected. For an unbiased functional analysis of all genome-encoded proteases, i.e., the degradome, in breast cancer cell growth, we applied an inducible RNA interference library for protease-focused genetic screens. Importantly, these functional screens were performed in two phenotypically different murine breast cancer cell lines, including one stem cell-like cell line that showed phenotypic plasticity under changed nutrient and oxygen availability. Our unbiased genetic screens identified 252 protease genes involved in breast cancer cell growth that were further restricted to 100 hits by a selection process. Many of those hits were supported by literature, but some proteases were novel in their functional link to breast cancer. Interestingly, we discovered that the environmental conditions influence the degree of breast cancer cell dependency on certain proteases. For example, breast cancer stem cell-like cells were less susceptible to depletion of several mitochondrial proteases in hypoxic conditions. From the 100 hits, nine proteases were functionally validated in murine breast cancer cell lines using individual knockdown constructs, highlighting the high reliability of our screens. Specifically, we focused on mitochondrial processing peptidase (MPP) subunits alpha (Pmpca) and beta (Pmpcb) and discovered that MPP depletion led to a disadvantage in cell growth, which was linked to mitochondrial dysfunction.

Genome-scale RNA interference profiling of Trypanosoma brucei cell cycle progression defects

Trypanosomatids, which include major pathogens of humans and livestock, are flagellated protozoa for which cell cycle controls and the underlying mechanisms are not completely understood. Here, we describe a genome-wide RNA-interference library screen for cell cycle defects in Trypanosoma brucei. We induced massive parallel knockdown, sorted the perturbed population using high-throughput flow cytometry, deep-sequenced RNAi-targets from each stage and digitally reconstructed cell cycle profiles at a genomic scale; also enabling data visualisation using an online tool (https://tryp-cycle.pages.dev/). Analysis of several hundred genes that impact cell cycle progression reveals >100 flagellar component knockdowns linked to genome endoreduplication, evidence for metabolic control of the G1-S transition, surface antigen regulatory mRNA-binding protein knockdowns linked to G2M accumulation, and a putative nucleoredoxin required for both mitochondrial genome segregation and for mitosis. The outputs provide comprehensive functional genomic evidence for the known and novel machineries, pathways and regulators that coordinate trypanosome cell cycle progression.

Establishing an RNA interference (RNAi) screen for neuroprotection of dopaminergic neurons in Caenorhabditis elegans models of Parkinson’s disease

Parkinson’s disease (PD) is a common neurodegenerative disorder characterized by the selective death of dopaminergic neurons in the substantia nigra of the midbrain, resulting in bradykinesia, tremors, muscle rigidity, and other motor and non‐motor deficits. The prevalence and economic burden of Parkinson’s disease are increasing due to the aging population. Despite this increasing burden, the discovery of clinically useful therapies to halt the progression of the disease remains an unmet need. This is partly because of gaps in our knowledge of the underlying molecular mechanisms of the disease and the lack of accurate disease models. Therefore, understanding the pathobiology and discovery of potential druggable targets remain a priority in PD research. In the current study, we report the development of a high‐throughput assay in the nematode, Caenorhabditis elegans, to monitor neurodegeneration and to probe for genes potentially involved in mediating neuroprotection of dopaminergic neurons using RNA interference (RNAi) technology. Two transgenic strains of C. elegans carrying human PD‐linked genes were used, one expressing mutant (A53T) alpha‐synuclein, and the other expressing mutant (G2019S) leucine‐rich repeat kinase 2 (LRRK2). These strains express the PD‐transgenes and GFP exclusively in their dopaminergic neurons allowing for the monitoring of neurodegeneration via changes in GFP signal intensity. A third control strain was used that lacked the PD‐transgenes genes but expressed GFP in their dopaminergic neurons. We crossed these three strains of worms into neuronal RNAi‐sensitive backgrounds that express mCherry under a pharyngeal promoter thus allowing for accurate quantitation of the worms in liquid cultures within 384‐well microtiter plates. Using a combination of laser cytometry and high content imaging, we have established that these models recapitulate the age‐dependent degeneration of dopaminergic neurons observed in human PD. Neurodegeneration was seen in the SNCA (A53T) and LRRK2 (G2019S) transgenic models, as evidenced by a 30‐50% and 75‐85% loss of GFP intensity, respectively, after 7 days in culture. In preliminary studies, we have found that these worms show susceptibility to RNAi via bacterial feeding as evidenced by a loss of GFP signal from RNAi against GFP or from RNAi against growth factors supporting the differentiation of dopaminergic neurons. Further optimization studies of this RNAi screening assay are currently ongoing. The demonstrated susceptibility of C. elegans to neuronal RNAi in our screening assay, and the availability of chromosomal and genome‐wide RNAi libraries will allow for the interrogation of the entire C. elegans genome in these models. This line of inquiry, if successful, will improve our knowledge of the underlying mechanisms of neurodegeneration and may also identify genes encoding druggable targets for therapeutics directed at slowing the progression of PD.

Genome-wide RNA interference screen in cancer stem cells.

Tumor heterogeneity represents a major hurdle for therapy. This cellular heterogeneity is mainly sustained by different subpopulations of tumorigenic cells, the so-called cancer stem cells (CSCs). CSCs burden is associated with disease progression and patient poor prognosis. In this context, deciphering molecular mechanisms regulating stemness is a key step in the development of new therapeutic strategy. Here, we provide a detailed protocol for high-throughput screening (HTS) strategy to detect modulators of CSC proportion. It is based on a miniaturized ALDEFLUOR-probed CSC assay quantitated by high-content imaging, that allows monitoring the changes in CSC proportions in response to gene silencing. Gene loss-of-function is achieved by transfecting a genome-wide RNA interference library. These genome-wide HTS strategies could lead to the identification of new therapeutic approaches in the treatment of various cancers.

Orthogonal genome-wide screens of bat cells identify MTHFD1 as a target of broad antiviral therapy

Bats are responsible for the zoonotic transmission of several major viral diseases, including those leading to the 2003 SARS outbreak and likely the ongoing COVID-19 pandemic. While comparative genomics studies have revealed characteristic adaptations of the bat innate immune system, functional genomic studies are urgently needed to provide a foundation for the molecular dissection of the viral tolerance in bats. Here we report the establishment of genome-wide RNA interference (RNAi) and CRISPR libraries for the screening of the model megabat, Pteropus alecto. We used the complementary RNAi and CRISPR libraries to interrogate P. alecto cells for infection with two different viruses: mumps virus and influenza A virus, respectively. Independent screening results converged on the endocytosis pathway and the protein secretory pathway as required for both viral infections. Additionally, we revealed a general dependence of the C1-tetrahydrofolate synthase gene, MTHFD1, for viral replication in bat cells and human cells. The MTHFD1 inhibitor, carolacton, potently blocked replication of several RNA viruses, including SARS-CoV-2. We also discovered that bats have lower expression levels of MTHFD1 than humans. Our studies provide a resource for systematic inquiry into the genetic underpinnings of bat biology and a potential target for developing broad-spectrum antiviral therapy.

4E Interacting Protein as a Potential Novel Drug Target for Nucleoside Analogues in Trypanosoma brucei.

Human African trypanosomiasis is a neglected parasitic disease for which the current treatment options are quite limited. Trypanosomes are not able to synthesize purines de novo and thus solely depend on purine salvage from the host environment. This characteristic makes players of the purine salvage pathway putative drug targets. The activity of known nucleoside analogues such as tubercidin and cordycepin led to the development of a series of C7-substituted nucleoside analogues. Here, we use RNA interference (RNAi) libraries to gain insight into the mode-of-action of these novel nucleoside analogues. Whole-genome RNAi screening revealed the involvement of adenosine kinase and 4E interacting protein into the mode-of-action of certain antitrypanosomal nucleoside analogues. Using RNAi lines and gene-deficient parasites, 4E interacting protein was found to be essential for parasite growth and infectivity in the vertebrate host. The essential nature of this gene product and involvement in the activity of certain nucleoside analogues indicates that it represents a potential novel drug target.

RNA Interference (RNAi) Screening in Cultured Drosophila Cells.

Genetic perturbation assays have been crucial to the discovery of molecular pathways that drive diverse biological processes. RNA interference (RNAi)-mediated depletion of gene products represents a powerful means of elucidating gene function, as it allows one to systematically probe the phenotypic effects resulting from the functional loss of specific targets. The relative ease of use of RNAi technologies in cultured cells has allowed the design and implementation of genome-wide investigations to systematically reveal gene function. In this chapter, we describe methods for high-throughput RNAi-mediated loss-of-function studies in cultured cells of Drosophila melanogaster. First, we describe the in vitro synthesis of double stranded RNAs (dsRNAs) from a genome-wide Drosophila RNAi library. Next, we outline the procedures used to carry out high-throughput RNAi screens using a cell bathing approach and high-content screening microscopy, illustrating how these experiments can be utilized to study specific cellular contexts, such as cellular stress. Finally, we illustrate some approaches commonly employed to validate the depletion of identified gene candidates.

Overexpression of FKH-2/FOXG1 is neuroprotective in a C. elegans model of Machado-Joseph disease

Machado-Joseph disease (MJD), also known as spinocerebellar ataxia type 3 (SCA3), is the most common form of dominantly inherited ataxia worldwide. This disease is caused by an expanded CAG repeat in the coding region of ATXN3. Due to our incomplete understanding of mechanisms and molecular pathways related to this disease, there are no therapies that successfully treat core MJD patients. Therefore, the identification of new candidate targets related to this disease is needed.In this study, we performed a large-scale RNA interference (RNAi) screen of 387 transcription factor genes leading to the identification of several modifiers (suppressors and enhancers) of impaired motility phenotypes in a mutant ATXN3 transgenic C. elegans model. We showed that inactivation of one particular gene, fkh-2/FOXG1, enhanced the motility defect, neurodegeneration and reduced longevity in our MJD models. Opposite to genetic inactivation, the overexpression of fkh-2 rescued the impaired motility, shortened-lifespan, and neurodegeneration phenotypes of mutant ATXN3 transgenics. We found that overexpression of FKH-2/FOXG1 in ATXN3 mutant worms is neuroprotective.Using our transgenic ATXN3 C. elegans models and the screening of an RNAi library, we gained insights into the pathways contributing to neurodegeneration, and found that FKH-2/FOXG1 has neuroprotective activity. These findings may aid the development of novel therapeutic interventions for MJD.

A Computational Based Approach for Identification and Validation of Gene Mutations As Surrogate Markers of Gene Essentiality in Acute Myeloid Leukemia

Acute myeloid leukemia (AML) is a hematologic neoplasm characterized by a remarkable phenotypic and genomic heterogeneity. The recent characterization of genomic subtypes of AML based on large sequencing studies has provided the rationale for the development of targeted therapies based on the presence of specific genomic abnormalities. However, long term survival particularly in older patients remains a unmet medicalneed. Additionally, recent studies using RNA interference (RNAi) libraries have determined the existence of genes that are essential for the survival of multiple cancer cells. Understanding the effect of genomic alterations (mutations, deletions, translocations) on gene essentiality could favor the development of targeted therapies for specific subgroups of AML patients. However, current statistical methods such as the Benjamini-Hochberg (BH) procedure have shown limitations for controlling the false discovery rate (FDR) and have suboptimal sensitivity (recall of true positives) because the P-value correction does not include any prior information of individual tests. For this reason, in this study we developed a new large-scale statistical algorithm, which combine the RNAi libraries (more than 17.000 genes) data with mutational profiles, to identify gene essentialities associated with specific genomic mutations in order to explore this approach in AML. We adapted the Independent Hypothesis Weighting (IHW) procedure to the problem of identifying mutations as surrogate markers of gene essentiality, by using the gene mutation state in each cell line as prior information of a IHW problem. This approach was tested in 19 tumor subtypes, of the Cancer Cell Line Encyclopedia (CCLE) showing that it recalls new discoveries that cannot be identified with standard procedures in 17 out of 19 tumors, including the identification of up to 1,000 discoveries in tumor types in which BH recalls no discovery. These results demonstrated the accuracy of the IHW-based approach to identify gene mutations as surrogate markers of gene essentiality in the future. Once validated, we applied this computational model to the15 AMLcell lines of CCLE. The number of discoveries with an FDR of 20% increases from 2 (using the traditional BH correction), to 38 using our procedure, showing NRAS as the top mutation biomarker in the ranking. Interestingly, the algorithm identified one essential gene (NRAS) for NRAS mutated (NRAS-mut) and another essential gene (PTPN11) for NRAS wild type (NRAS-wt) AML cells, covering all samples of AMLs. To validate this hypothesis, we examined the effect of two different specific siRNAs for each gene (siPTPN11 and siNRAS) on cell proliferation of four AML cell lines: two lines with NRAS-mut (HL-60 and OCIAML3) and two with NRAS-wt (MV4-11 and HEL). Downregulation of NRAS expression significantly decreases the cell proliferation only in the 2 NRAS-mutated AML cell lines. Whereas the inhibition of PTPN11expression produced an equivalent effect, but specifically in the 2 NRAS-wt AML cell lines (Figure 1). These results confirmed our predictions and showed the essential role of NRAS or PTNPN11 in AML cell lines either with NRAS mutated or wild type, respectively. These results demonstrate that the application of our algorithm in the context of specific gene mutation not only may allow identification of directed therapies based on the mutation but can also define new gene essentialities amenable for targeted therapies providing new therapeutic strategies in patients with AML and potentially in other tumors. Disclosures Paiva: Amgen, Bristol-Myers Squibb, Celgene, Janssen, Merck, Novartis, Roche and Sanofi: Honoraria, Membership on an entity's Board of Directors or advisory committees; Celgene, Janssen, Sanofi and Takeda: Consultancy. San-Miguel:Amgen, Bristol-Myers Squibb, Celgene, Janssen, MSD, Novartis, Roche, Sanofi, and Takeda: Consultancy, Honoraria.

Enzymatic construction of shRNA library from oligonucleotide library.

Short hairpin RNAs (shRNAs) expressed from vectors have been used as an effective means of exploiting the RNA interference (RNAi) pathway in mammalian cells. Genome-scale screening with shRNA libraries has been used to investigate the relationship between genotypes and phenotypes on a large scale. Although several methods have been developed to construct shRNA libraries, their broad application has been limited by the high cost of constructing these libraries. We develop a new method that efficiently constructs a shRNA library at low cost, using treatments with several enzymes and an oligonucleotide library. The library of shRNA expression cassettes, which were cloned into a lentiviral plasmid, was produced through several enzymatic reactions, starting from a library of 20,000 different short oligonucleotides produced by microarray-based oligonucleotide synthesis. The NGS sequence analysis of the library shows that 99.8% of them (19,956 from 20,000 sequences) were contained in the library: 63.2% of them represent the correct sequences and the rest showed one or two base pair differences from the expected sequences. Considering the ease of our method, shRNA libraries of new genomes and of specific populations of genes can be prepared in a short period of time for genome-scale RNAi library screening.

Lanosterol Synthase Regulates Human Rhinovirus Replication in Human Bronchial Epithelial Cells.

Human rhinovirus (RV) infections are a significant risk factor for exacerbations of asthma and chronic obstructive pulmonary disease. Thus, approaches to prevent RV infection in such patients would give significant benefit. Through RNA interference library screening, we identified lanosterol synthase (LSS), a component of the cholesterol biosynthetic pathway, as a novel regulator of RV replication in primary normal human bronchial epithelial cells. Selective knock down of LSS mRNA with short interfering RNA inhibited RV2 replication in normal human bronchial epithelial cells. Small molecule inhibitors of LSS mimicked the effect of LSS mRNA knockdown in a concentration-dependent manner. We further demonstrated that the antiviral effect is not dependent on a reduction in total cellular cholesterol but requires a 24-hour preincubation with the LSS inhibitor. The rank order of antiviral potency of the LSS inhibitors used was consistent with LSS inhibition potency; however, all compounds showed remarkably higher potency against RV compared with the LSS enzyme potency. We showed that LSS inhibition led to an induction of 24(S),25 epoxycholesterol, an important regulator of the sterol pathway. We also demonstrated that LSS inhibition led to a profound increase in expression of the innate antiviral defense protein, IFN-β. We found LSS to be a novel regulator of RV replication and innate antiviral immunity and identified a potential molecular mechanism for this effect, via induction of 24(S),25 epoxycholesterol. Inhibition of LSS could therefore be a novel therapeutic target for prevention of RV-induced exacerbations.

RNA Interference (RNAi) Screening in Drosophila.

In the last decade, RNA interference (RNAi), a cellular mechanism that uses RNA-guided degradation of messenger RNA transcripts, has had an important impact on identifying and characterizing gene function. First discovered in Caenorhabditis elegans, RNAi can be used to silence the expression of genes through introduction of exogenous double-stranded RNA into cells. In Drosophila, RNAi has been applied in cultured cells or in vivo to perturb the function of single genes or to systematically probe gene function on a genome-wide scale. In this review, we will describe the use of RNAi to study gene function in Drosophila with a particular focus on high-throughput screening methods applied in cultured cells. We will discuss available reagent libraries and cell lines, methodological approaches for cell-based assays, and computational methods for the analysis of high-throughput screens. Furthermore, we will review the generation and use of genome-scale RNAi libraries for tissue-specific knockdown analysis in vivo and discuss the differences and similarities with the use of genome-engineering methods such as CRISPR/Cas9 for functional analysis.

The long noncoding RNA lncR492 inhibits neural differentiation of murine embryonic stem cells.

RNA interference (RNAi) screens have been shown to be valuable to study embryonic stem cell (ESC) self-renewal and they have been successfully applied to identify coding as well as noncoding genes required for maintaining pluripotency. Here, we used an RNAi library targeting >640 long noncoding RNAs (lncRNA) to probe for their role in early cell differentiation. Utilizing a Sox1-GFP ESC reporter cell line, we identified the lncRNA lncR492 as lineage-specific inhibitor of neuroectodermal differentiation. Molecular characterization showed that lncR492 interacts with the mRNA binding protein HuR and facilitates its inhibitory function by activation of Wnt signaling. Thus, lncRNAs modulate the fate decision of pluripotent stem cells.

Loss-of-Function RNAi Screen to Identify Necrosis-Signaling Molecules.

Over the recent years, genome-wide RNA interference (RNAi) library screens have been instrumental in the identification of key regulators of various biological pathways. The prolific use of this technique is attributed to its amenability to a high-throughput format. Here, we present the step-by-step method to conduct a siRNA screen to identify genes involved in necroptosis, a nonapoptotic form of proinflammatory cell death. The method described here uses MTS cell proliferation assay to measure necroptosis, which is compatible with high-throughput format screening on multiwell microtiter plates. This ensures that the screen can be performed in a timely and efficient manner.

CRISPR/Cas9 library screening for drug target discovery.

CRISPR/Cas9-based tools have rapidly developed in recent years. These include CRISPR-based gene activation (CRISPRa) or inhibition (CRISPRi), for which there are libraries. CRISPR libraries for loss of function have been widely used to identify new biological mechanisms, such as drug resistance and cell survival signals. CRISPRa is highly useful in screening for gain of functions, and CRISPRi is a more powerful tool than RNA interference (RNAi) libraries in screening for loss of functions. Positive selection using a CRISPR library can detect survival cells with specific conditions, such as drug treatment, and it can easily clarify drug resistance mechanisms. Negative selection is capable of detecting dead or slow-growing cells efficiently, and it can identify survival-essential genes, which can be promising candidates for molecularly targeted drugs. In addition, negative selection can be applied for synthetic lethality interactions, where the perturbation of both genes simultaneously results in the loss of viability, but that of either gene alone does not affect viability. This mechanism is highly important to identifying the optimal combination of molecularly targeted drugs. Survival-co-essential genes in cancer cells can be identified using new methods, such as the paired guide RNA system and in combination with single-cell RNA sequencing techniques. These efficient methods can clarify interesting biological mechanisms and suggest candidates for molecularly targeted drugs. This review identifies what types of screenings were performed and suggests ideas for the next CRISPR screenings to develop new drugs.

The C. elegans Excretory Canal as a Model for Intracellular Lumen Morphogenesis and In Vivo Polarized Membrane Biogenesis in a Single Cell: labeling by GFP-fusions, RNAi Interaction Screen and Imaging.

The four C. elegans excretory canals are narrow tubes extended through the length of the animal from a single cell, with almost equally far extended intracellular endotubes that build and stabilize the lumen with a membrane and submembraneous cytoskeleton of apical character. The excretory cell expands its length approximately 2,000 times to generate these canals, making this model unique for the in vivo assessment of de novo polarized membrane biogenesis, intracellular lumen morphogenesis and unicellular tubulogenesis. The protocol presented here shows how to combine standard labeling, gain- and loss-of-function genetic or RNA interference (RNAi)-, and microscopic approaches to use this model to visually dissect and functionally analyze these processes on a molecular level. As an example of a labeling approach, the protocol outlines the generation of transgenic animals with fluorescent fusion proteins for live analysis of tubulogenesis. As an example of a genetic approach, it highlights key points of a visual RNAi-based interaction screen designed to modify a gain-of-function cystic canal phenotype. The specific methods described are how to: label and visualize the canals by expressing fluorescent proteins; construct a targeted RNAi library and strategize RNAi screening for the molecular analysis of canal morphogenesis; visually assess modifications of canal phenotypes; score them by dissecting fluorescence microscopy; characterize subcellular canal components at higher resolution by confocal microscopy; and quantify visual parameters. The approach is useful for the investigator who is interested in taking advantage of the C. elegans excretory canal for identifying and characterizing genes involved in the phylogenetically conserved processes of intracellular lumen and unicellular tube morphogenesis.