Lethal Gene Research Articles

A blueprint to discovering synthetic lethal gene interactions for precision oncology.

A blueprint to discovering synthetic lethal gene interactions for precision oncology.

Generation of viable hypomorphic and null mutant plants via CRISPR-Cas9 targeting mRNA splicing sites.

Genetic analysis is important for modern plant molecular biology, and in this regard, the existence of specific mutants is crucial. While genome editing technologies, particularly CRISPR-Cas9, have revolutionized plant molecular biology by enabling precise gene disruption, knockout methods are ineffective for lethal genes, necessitating alternatives like gene knockdown. This study demonstrates the practical generation of a hypomorphic mutant allele, alongside severe null mutant alleles, via the targeting of mRNA splicing sites using CRISPR-Cas9. The Arabidopsis HIGH PLOIDY 2 (HPY2) encodes a yeast NSE2 ortholog, part of the conserved eukaryotic SMC5/6 complex, with SUMO E3 ligase activity essential for cell cycle progression and plant development. Loss-of-function HPY2 mutants exhibit severe dwarfism and seedling lethality, making functional analysis challenging. To overcome these limitations, we created HPY2 knockdown mutants as novel tools to investigate gene function. Of the three mutant alleles, the hpy2-cr1 and hpy2-cr2 mutants resembled the existing severe hpy2-1 allele, both harboring a single base pair insertion in one exon, causing significant root shortening and seedling lethality. In contrast, the hypomorphic mutant hpy2-cr3, which has a five bp deletion at an intron-exon junction, showed relatively longer root growth and survived until the reproductive stage. RT-PCR analysis of hpy2-cr3 revealed atypical mRNAs producing truncated polypeptides that retained some HPY2 function, explaining the milder phenotype. These results establish the successful generation of novel hypomorphic mutant alleles critical for studying the lethal gene HPY2, and demonstrate the usefulness of CRISPR-Cas9 for producing viable hypomorphic mutants for investigating complex genetic interactions.

Critical role of Spatio-Temporally Regulated Maternal RNAs in Zebrafish Embryogenesis.

Differentially distributed marginal maternal RNAs have a critical role in early embryogenesis.Cas13d complements the Cas9 limitation to study the functions of embryonic lethal genes. Cth1 is essential for gametogenesis and early embryonic development. Cth1 is a maternal RNA decay factor required for spatio-temporal RNA regulation. 3'UTR of Cth1 drives its spatio-temporal RNA dynamics.

RNA interference protocols for gene silencing in the spittlebug Philaenus spumarius, vector of Xylella fastidiosa

RNA interference (RNAi) is double stranded RNA (dsRNA)-based gene silencing mechanism. Exogenous dsRNAs application to crops has raised as a powerful tool to control agricultural pests. In particular, several sap-feeder are important plant pathogens vectors, such as Philaenus spumarius, known as main vector of Xylella fastidiosa (Xf), causal agent of olive quick decline syndrome (OQDS) in southern Italy. Here, dsATP synthase beta (dsATP), dsLaccase (dsLacc) and dsGreen Fluorescent Protein (dsGFP) as control, were provided to spittlebug adults by microinjection or to nymphs fed on dsRNA-treated plant shoots. Treated insects were collected at different time points to monitor silencing efficiency over time, describing significant reduction of transcript levels from 8 to 24 days post treatment. Downregulation of target genes ranged from 2- to 16-fold compared to the corresponding dsGFP controls, where highest silencing effects were generally noticed for ATP synthase beta. Sequencing of libraries obtained from total smallRNA (sRNA) showed the generation of dsRNA-derived sRNAs by RNAi pathway, with majority of reads mapping exclusively on the correspondent dsRNA. Also, we characterized components of a functional RNAi machinery in P. spumarius. Further research is needed to clarify such mechanism, screen effective target lethal genes to reduce vector population and improve delivery strategies.

Analysis of potential genotoxicity of deicing material in the test for induction of dominant lethal mutations in germ cells of male Drosophila

Introduction. Long-term use of deicing materials (DM) is one of the significant factors causing the active distribution of various chemical compounds that are part of multicomponent deicing mixtures in the environment. In this regard, the expansion of methodological approaches to assessing their biological hazard remains important. Materials and methods. The DM used for research based on a mixture of urea with magnesium and ammonium nitrates. The DM was tested in the form of an aqueous solution and added to the soil to obtain an aqueous extract. The analysis includes test for induced dominant lethal mutations in Drosophila male germ cells. Results. All samples tested significantly reduced the fertility of Drosophila males. The frequencies of early dominant lethal mutations (EDLM) significantly exceeded the levels of the controls, and the effects of the soil extract appeared at the lowest concentration – 5 g/L and of the DM solution – 10 g/L. The trend in the rate of late dominant lethal mutations (LDLM) indicates to the death of sperm or a decrease in mating potency. Limitations. The method of inducing dominant lethal mutations in Drosophila melanogaster and the genotoxic effects assessment of DM in the germ cells of male flies within the study has no restrictions. Conclusion. The conducted test is so far the only one in the field of research into the genetic safety of multicomponent DMs using a method for induced dominant lethal mutations in Drosophila male germ cells. The results prove the high informative rate of the methodological approach which involves analyzing soil extracts to identify and assess a genotoxicity of DM component composition when it enters the soil which can become as a transit layer for migration of DM components and their products transformation into groundwater.

Characterization of CYP303A1 and its potential application based on ZIF-8 nanoparticle-wrapped dsRNA in Nilaparvata lugens (Stål).

RNA interference (RNAi) technology has been put forward as a promising method for pest control and resistance management. Mining highly efficient lethal genes and constructing stable double-stranded RNA (dsRNA) delivery systems are of great significance to improve the application potential of RNAi technology. In this study, we characterized a molting-related gene, NlCYP303A1, in Nilaparvata lugens that was highly expressed in the cuticle and at the end stages of each instar in nymphs. Silencing the expression of NlCYP303A1 in N. lugens resulted in a deformed phenotype and a significant increase in mortality. Furthermore, interfering with NlCYP303A1 changed the relative expression of key genes in the chitin synthesis and degradation pathway. Finally, we used the nanocarrier zeolitic imidazolate framework-8 (ZIF-8) to load dsNlCYP303A1, forming a complex denoted as dsNlCYP303A1@ZIF-8. The results of both feeding and rice-seedling dip experiments indicated that the expression of NlCYP303A1 was dramatically and persistently suppressed by the dsNlCYP303A1@ZIF-8 treatment, compared with treatment with dsNlCYP303A1, suggesting that ZIF-8 can enhance the interference efficiency as well as the stability of dsNlCYP303A1. Our results demonstrate that the lethal gene NlCYP303A1 can be employed as an excellent target for RNAi technology by loading onto a nano-delivery system, and provide new insights into the creation of innovative pest control approaches. © 2024 Society of Chemical Industry.

Harnessing the power of AI in precision medicine: NGS-based therapeutic insights for colorectal cancer cohort.

Developing innovative precision and personalized cancer therapeutics is essential to enhance cancer survivability, particularly for prevalent cancer types such as colorectal cancer. This study aims to demonstrate various approaches for discovering new targets for precision therapies using artificial intelligence (AI) on a Polish cohort of colorectal cancer patients. We analyzed 71 patients with histopathologically confirmed advanced resectional colorectal adenocarcinoma. Whole exome sequencing was performed on tumor and peripheral blood samples, while RNA sequencing (RNAseq) was conducted on tumor samples. We employed three approaches to identify potential targets for personalized and precision therapies. First, using our in-house neoantigen calling pipeline, ARDentify, combined with an AI-based model trained on immunopeptidomics mass spectrometry data (ARDisplay), we identified neoepitopes in the cohort. Second, based on recurrent mutations found in our patient cohort, we selected corresponding cancer cell lines and utilized knock-out gene dependency scores to identify synthetic lethality genes. Third, an AI-based model trained on cancer cell line data was employed to identify cell lines with genomic profiles similar to selected patients. Copy number variants and recurrent single nucleotide variants in these cell lines, along with gene dependency data, were used to find personalized synthetic lethality pairs. We identified approximately 8,700 unique neoepitopes, but none were shared by more than two patients, indicating limited potential for shared neoantigenic targets across our cohort. Additionally, we identified three synthetic lethality pairs: the well-known APC-CTNNB1 and BRAF-DUSP4 pairs, along with the recently described APC-TCF7L2 pair, which could be significant for patients with APC and BRAF variants. Furthermore, by leveraging the identification of similar cancer cell lines, we uncovered a potential gene pair, VPS4A and VPS4B, with therapeutic implications. Our study highlights three distinct approaches for identifying potential therapeutic targets in cancer patients. Each approach yielded valuable insights into our cohort, underscoring the relevance and utility of these methodologies in the development of precision and personalized cancer therapies. Importantly, we developed a novel AI model that aligns tumors with representative cell lines using RNAseq and methylation data. This model enables us to identify cell lines closely resembling patient tumors, facilitating accurate selection of models needed for in vitro validation.

The Drosophila maternal-effect gene abnormal oocyte (ao) does not repress histone gene expression.

The abnormal oocyte (ao) gene of Drosophila melanogaster is a maternal-effect lethal gene previously identified as encoding a transcriptional regulator of core histones. However, background genetic mutations in existing ao mutant strains could compromise their utility in manipulating histone levels. To distinguish the true ao phenotype from background effects, we created two new ao reagents: a CRISPR/Cas9-mediated knockout of the ao allele for genetic and molecular analyses and an epitope-tagged ao allele for cytological experiments. Using these reagents, we confirm previous findings that ao exhibits maternal-effect lethality, which can be rescued by either a decrease in the histone gene copy number or by Y chromosome heterochromatin. We also confirm that the Ao protein localizes to the histone locus bodies in ovaries. Our data also suggest that ao genetically interacts with the histone genes and heterochromatin, as previously suggested. However, contrary to prior findings, we find that ao does not repress core histone transcript levels. Thus, the molecular basis for ao-associated maternal-effect lethality remains unknown.

BioPathNet: Enhancing Link Prediction in Biomedical Knowledge Graphs through Path Representation Learning.

Understanding complex interactions in biomedical networks is crucial for advancements in biomedicine, but traditional link prediction (LP) methods are limited in capturing this complexity. Representation-based learning techniques improve prediction accuracy by mapping nodes to low-dimensional embeddings, yet they often struggle with interpretability and scalability. We present BioPathNet, a novel graph neural network framework based on the Neural Bellman-Ford Network (NBFNet), addressing these limitations through path-based reasoning for LP in biomedical knowledge graphs. Unlike node-embedding frameworks, BioPathNet learns representations between node pairs by considering all relations along paths, enhancing prediction accuracy and interpretability. This allows visualization of influential paths and facilitates biological validation. BioPathNet leverages a background regulatory graph (BRG) for enhanced message passing and uses stringent negative sampling to improve precision. In evaluations across various LP tasks, such as gene function annotation, drug-disease indication, synthetic lethality, and lncRNA-mRNA interaction prediction, BioPathNet consistently outperformed shallow node embedding methods, relational graph neural networks and task-specific state-of-the-art methods, demonstrating robust performance and versatility. Our study predicts novel drug indications for diseases like acute lymphoblastic leukemia (ALL) and Alzheimer's, validated by medical experts and clinical trials. We also identified new synthetic lethality gene pairs and regulatory interactions involving lncRNAs and target genes, confirmed through literature reviews. BioPathNet's interpretability will enable researchers to trace prediction paths and gain molecular insights, making it a valuable tool for drug discovery, personalized medicine and biology in general.

Population suppression by release of insects carrying a dominant sterile homing gene drive targeting doublesex in Drosophila

CRISPR homing gene drives can suppress pest populations by targeting female fertility genes, converting wild-type alleles into drive alleles in the germline of drive heterozygotes. fsRIDL (female-specific Release of Insects carrying a Dominant Lethal) is a self-limiting population suppression strategy involving continual release of transgenic males carrying female lethal alleles. Here, we propose an improved pest suppression system called “Release of Insects carrying a Dominant-sterile Drive” (RIDD), combining performance characteristics of homing drive and fsRIDL. We construct a split RIDD system in Drosophila melanogaster by creating a 3-gRNA drive disrupting the doublesex female exon. Drive alleles bias their inheritance in males, while drive alleles and resistance alleles formed by end-joining cause dominant female sterility. Weekly releases of RIDD males progressively suppressed and eventually eliminated cage populations. Modeling shows that RIDD is substantially stronger than SIT and fsRIDL. RIDD is also self-limiting, potentially allowing targeted population suppression.

Population suppression with dominant female-lethal alleles is boosted by homing gene drive

BackgroundMethods to suppress pest insect populations using genetic constructs and repeated releases of male homozygotes have recently been shown to be an attractive alternative to older sterile insect techniques based on radiation. Female-specific lethal alleles have substantially increased power, but still require large, sustained transgenic insect releases. Gene drive alleles bias their own inheritance to spread throughout populations, potentially allowing population suppression with a single, small-size release. However, suppression drives often suffer from efficiency issues, and the most well-studied type, homing drives, tend to spread without limit.ResultsIn this study, we show that coupling female-specific lethal alleles with homing gene drive allowed substantial improvement in efficiency while still retaining the self-limiting nature (and thus confinement) of a lethal allele strategy. Using a mosquito model, we show the required release sizes for population elimination in a variety of scenarios, including different density growth curves, with comparisons to other systems. Resistance alleles reduced the power of this method, but these could be overcome by targeting an essential gene with the drive while also providing rescue. A proof-of-principle demonstration of this system in Drosophila melanogaster was effective in both biasing its inheritance and achieving high lethality among females that inherit the construct in the absence of antibiotic.ConclusionsOverall, our study shows that substantial improvements can be achieved in female-specific lethal systems for population suppression by combining them with various types of gene drive.

Synthetic lethality of combined ULK1 defection and p53 restoration induce pyroptosis by directly upregulating GSDME transcription and cleavage activation through ROS/NLRP3 signaling

BackgroundHigh expression of ubiquitin ligase MDM2 is a primary cause of p53 inactivation in many tumors, making it a promising therapeutic target. However, MDM2 inhibitors have failed in clinical trials due to p53-induced feedback that enhances MDM2 expression. This underscores the urgent need to find an effective adaptive genotype or combination of targets.MethodsKinome-wide CRISPR/Cas9 knockout screen was performed to identify genes that modulate the response to MDM2 inhibitor using TP53 wild type cancer cells and found ULK1 as a candidate. The MTT cell viability assay, flow cytometry and LDH assay were conducted to evaluate the activation of pyroptosis and the synthetic lethality effects of combining ULK1 depletion with p53 activation. Dual-luciferase reporter assay and ChIP-qPCR were performed to confirm that p53 directly mediates the transcription of GSDME and to identify the binding region of p53 in the promoter of GSDME. ULK1 knockout / overexpression cells were constructed to investigate the functional role of ULK1 both in vitro and in vivo. The mechanism of ULK1 depletion to activate GSMDE was mainly investigated by qPCR, western blot and ELISA.ResultsBy using high-throughput screening, we identified ULK1 as a synthetic lethal gene for the MDM2 inhibitor APG115. It was determined that deletion of ULK1 significantly increased the sensitivity, with cells undergoing typical pyroptosis. Mechanistically, p53 promote pyroptosis initiation by directly mediating GSDME transcription that induce basal-level pyroptosis. Moreover, ULK1 depletion reduces mitophagy, resulting in the accumulation of damaged mitochondria and subsequent increasing of reactive oxygen species (ROS). This in turn cleaves and activates GSDME via the NLRP3-Caspase inflammatory signaling axis. The molecular cascade makes ULK1 act as a crucial regulator of pyroptosis initiation mediated by p53 activation cells. Besides, mitophagy is enhanced in platinum-resistant tumors, and ULK1 depletion/p53 activation has a synergistic lethal effect on these tumors, inducing pyroptosis through GSDME directly.ConclusionOur research demonstrates that ULK1 deficiency can synergize with MDM2 inhibitors to induce pyroptosis. p53 plays a direct role in activating GSDME transcription, while ULK1 deficiency triggers upregulation of the ROS-NLRP3 signaling pathway, leading to GSDME cleavage and activation. These findings underscore the pivotal role of p53 in determining pyroptosis and provide new avenues for the clinical application of p53 restoration therapies, as well as suggesting potential combination strategies.

Development of an agroinfiltration-based transient hairpin RNA expression system in pak choi leaves (Brassica rapa ssp. chinensis) for RNA interference against Liriomyza sativae

The vegetable leafminer (Liriomyza sativae) is a devastating invasive pest of many vegetable crops and horticultural plants worldwide, causing serious economic loss. Conventional control strategy against this pest mainly relies on the synthetic chemical pesticides, but widespread use of insecticides easily causes insecticide resistance development and is harmful to beneficial organisms and environment. In this context, a more environmentally friendly pest management strategy based on RNA interference (RNAi) has emerged as a powerful tool to control of insect pests. Here we report a successful oral RNAi in L. sativae after feeding on pak choi (Brassica rapa ssp. chinensis) that transiently express hairpin RNAs targeting vital genes in this pest. First, potentially lethal genes are identified by searching an L. sativae transcriptome for orthologs of the widely used V-ATPase A and actin genes, then expression levels are assessed during different life stages and in different adult tissues. Interestingly, the highest expression levels for V-ATPase A are observed in the adult heads (males and females) and for actin in the abdomens of adult females. We also assessed expression patterns of the target hairpin RNAs in pak choi leaves and found that they reach peak levels 72 h post agroinfiltration. RNAi-mediated knockdown of each target was then assessed by letting adult L. sativae feed on agroinfiltrated pak choi leaves. Relative transcript levels of each target gene exhibit significant reductions over the feeding time, and adversely affect survival of adult L. sativae at 24 h post infestation in genetically unmodified pak choi plants. These results demonstrate that the agroinfiltration-mediated RNAi system has potential for advancing innovative environmentally safe pest management strategies for the control of leaf-mining species.

Using gene and gene-set association tests to identify lethal prostate cancer genes.

Recent advances in the detection and treatment of prostate cancer (PCa) have reduced morbidity and mortality from this common cancer. Despite these improvements, PCa remains the second leading cause of cancer death in men in the United States. Further understanding of the genetic underpinnings of lethal PCa is required to drive risk detection and prevention and ultimately reduce mortality. We therefore set out to identify germline variants associated with cases of lethal prostate cancer (LPCa). Using a two-stage study design, we compared whole-exome sequencing data of 550 LPCa patients to 488 healthy male controls. Men were classified as having LPCa based on medical record review. Candidate genes were identified using gene- and gene-set-based rare truncating variant association tests. Case-control burden testing through Firth's penalized logistic regression and case-gnomAD allelic burden testing through a one-sided mid-p Fisher's exact test were conducted. Each gene's p-values from these tests were combined into an omnibus p-value for candidate gene selection. In the subsequent validation stage, genes were assessed using the UK Biobank and Firth's penalized logistic regression for each ancestry, combined through meta-analysis. Gene-based rare variant association tests identified 12 genes nominally associated with LPCa. Rare-variant association tests identified a gene set with a significantly higher burden of truncating germline mutations in LPCa patients than controls. Combining gene- and gene-set test results, four nominally significant genes (PPP1R3A, TG, PPFIBP2, and BTN3A3) were selected as candidates. Subsequent validation using the UK Biobank found that PPP1R3A was significantly associated with LPCa risk (odds ratio 2.34, CI 1.20-4.59). Specifically, pGln662ArgfsTer7 was identified as the predominant variant in PPP1R3A among LPCa patients in our dataset. Both individual gene and gene-set analyses identified candidates associated with LPCa. The novel association of PPP1R3A and LPCa risk merits further investigation.

Evaluation of safety of Bifidobacterium and Lactobacillus strains and their synbiotic combination with isomalto-oligosaccharides against LPS-induced inflammation in murine macrophages

In this study, the safety of Bifidobacterium longum Bif10, Bifidobacterium breve Bif11, Lacticaseibacillus rhamnosus LAB3, and Lactiplantibacillus plantarum LAB39 was evaluated using in-vitro, genomics, and in-vivo approaches. In the in-vitro safety studies, mucin degradation, biogenic amine production and cytotoxicity on HEK-293 cells by these strains were evaluated. Whole genome sequencing and bioinformatics analysis were carried out to identify the genes responsible for mucin degradation, biogenic amine production, antibiotic resistance, and virulence factors. In-vivo safety was assessed after acute, subacute, and sub-chronic oral feeding with respective strains to the mice as per revised OECD guidelines. Histopathological examination, gut permeability, hematological, blood biochemistry, and oxidative stress were evaluated after sacrificing the animals. Further, the compatibility of the four strains was assessed and their synbiotic combination with isomaltooligosaccharides (IMOs) was evaluated for its potential in alleviating lipopolysaccharide (LPS) induced inflammation in murine macrophages. In-vitro studies indicated that the strains do not produce biogenic amines and were non-cytotoxic to HEK-293 cells. Whole genome analysis suggested a lack of transferable antibiotic-resistance genes or potentially lethal virulence factors and genes for biogenic amines. In vivo studies showed that the bacterial strains did not affect the health parameters related to blood or induce histological alterations in the vital organs. The four strains were compatible with each other and their synbiotic blend efficiently curtailed LPS-induced oxidative stress, inducible nitric oxide and proinflammatory cytokine production. Given these observations, Bif10, Bif11, LAB3, and LAB39 can be deemed safe and their synbiotic blend with IMOs could impart anti-inflammatory effects.

Path-based reasoning for biomedical knowledge graphs with BioPathNet.

Understanding complex interactions in biomedical networks is crucial for advancements in biomedicine, but traditional link prediction (LP) methods are limited in capturing this complexity. Representation-based learning techniques improve prediction accuracy by mapping nodes to low-dimensional embeddings, yet they often struggle with interpretability and scalability. We present BioPathNet, a novel graph neural network framework based on the Neural Bellman-Ford Network (NBFNet), addressing these limitations through path-based reasoning for LP in biomedical knowledge graphs. Unlike node-embedding frameworks, BioPathNet learns representations between node pairs by considering all relations along paths, enhancing prediction accuracy and interpretability. This allows visualization of influential paths and facilitates biological validation. BioPathNet leverages a background regulatory graph (BRG) for enhanced message passing and uses stringent negative sampling to improve precision. In evaluations across various LP tasks, such as gene function annotation, drug-disease indication, synthetic lethality, and lncRNA-mRNA interaction prediction, BioPathNet consistently outperformed shallow node embedding methods, relational graph neural networks and task-specific state-of-the-art methods, demonstrating robust performance and versatility. Our study predicts novel drug indications for diseases like acute lymphoblastic leukemia (ALL) and Alzheimer's, validated by medical experts and clinical trials. We also identified new synthetic lethality gene pairs and regulatory interactions involving lncRNAs and target genes, confirmed through literature reviews. BioPathNet's interpretability will enable researchers to trace prediction paths and gain molecular insights, making it a valuable tool for drug discovery, personalized medicine and biology in general.

Molecular detection and association of 12.1kb deletion within the high mobility AT-hook 2 gene in the Netherlands dwarf rabbit (Oryctolagus Cuniculus).

Rabbits are mainly bred for human consumption and medical research. However, it has been recently showed that several rabbit breeds are also kept as pets for human leisure. The Netherlands dwarf rabbit is currently in the immense interest of many Vietnamese customers due to its personality and miniature stature. However, 12.1kb deletion from position 44,709,089 to 44,721,236bp in the high mobility AT-hook 2 (HMGA2) gene on chromosome 4 was identified as the structural variant causing dwarfism and altered craniofacial development in this breed. It has been documented that HMGA2 plays an important role in regulating growth and individuals with genotype HMGA2 del/del are fatal several days after birth. Despite the economically high value of the Netherlands dwarf rabbit, there has been no study on the genetic survey of lethal alleles in this breed in Vietnam. The aim of this study is to develop a fast and reliable method to screen the frequency of lethal alleles of HMGA2 in the South of Vietnam. Rabbit saliva was collected, and DNA extraction was followed. Multiplex polymerase chain reaction (PCR) with three primers was optimized and performed to detect the presence of 12.1kb deletion within the HMGA2 sequence. Our data showed that the 12.1kb deletion in the Netherlands dwarf rabbit population was detected by our optimized multiplex PCR. In 100 rabbit animals, 34 and 16 individuals were homozygous wild type (+/+) and homozygous mutant (del/del), respectively, while 50 rabbits were heterozygous. The frequency of HMGA2 lethal allele carrier was 66% (66/100 individuals). Our results indicated that we successfully developed a fast, accurate multiplex PCR to detect carrier individuals. Verification of the genotypes was followed by sequencing. We recommend implementing our multiplex PCR procedure in genetic selection for carrier and homozygous wild-type animals in the mating scheme to prevent the lethality of the rabbit offspring. Additionally, awareness should be raised among rabbit breeders to monitor the genetic makeup of the Netherlands dwarf rabbit populations. However, due to the limitation of the sample size, more samples should be taken in future studies to obtain the genetic frequency of the HMGA2 lethal allele more accurately.

Identifying actionable synthetically lethal cancer gene pairs using mutual exclusivity.

Mutually exclusive loss-of-function alterations in gene pairs are those that occur together less frequently than may be expected and may denote a synthetically lethal relationship (SSL) between the genes. SSLs can be exploited therapeutically to selectively kill cancer cells. Here, we analysed mutation, copy number variation, and methylation levels in samples from The Cancer Genome Atlas, using the hypergeometric and the Poisson binomial tests to identify mutually exclusive inactivated genes. We focused on gene pairs where one is an inactivated tumour suppressor and the other a gene whose protein product can be inhibited by known drugs. This provided an abundance of potential targeted therapeutics and repositioning opportunities for several cancers. These data are available on the MexDrugs website, https://bioinformaticslab.sussex.ac.uk/mexdrugs.

Effects of a blood-free mosquito diet on fitness and gonotrophic cycle parameters of laboratory reared Anopheles gambiae sensu stricto

BackgroundThe current rise of new innovative tools for mosquito control, such as the release of transgenic mosquitoes carrying a dominant lethal gene and Wolbachia-based strategies, necessitates a massive production of mosquitoes in the insectary. However, currently laboratory rearing depends on vertebrate blood for egg production and maintenance. This practice raises ethical concerns, incurs logistical and cost limitations, and entails potential risk associated with pathogen transmission and blood storage. Consequently, an artificial blood-free diet emerges as a desirable alternative to address these challenges. This study aims to evaluate the effects of a previously formulated artificial blood-free diet (herein referred to as BLOODless) on Anopheles gambiae (An. gambiae s.s.; IFAKARA) gonotrophic parameters and fitness compared with bovine blood.MethodsThe study was a laboratory-based comparative evaluation of the fitness, fecundity and fertility of An. gambiae s.s. (IFAKARA) reared on BLOODless versus vertebrate blood from founder generation (F0) to eighth generation (F8). A total of 1000 female mosquitoes were randomly selected from F0, of which 500 mosquitoes were fed with bovine blood (control group) and the other 500 mosquitoes were fed with BLOODless diet (experimental group). The feeding success, number of eggs per female, hatching rate and pupation rate were examined post-feeding. Longevity and wing length were determined as fitness parameters for adult male and female mosquitoes for both populations.ResultsWhile blood-fed and BLOODless-fed mosquitoes showed similar feeding success, 92.3% [95% confidence interval (CI) 89.7–94.9] versus 93.6% (95% CI 90.6–96.6), respectively, significant differences emerged in their reproductive parameters. The mean number of eggs laid per female was significantly higher for blood-fed mosquitoes (P < 0.001) whereas BLOODless-fed mosquitoes had significantly lower hatching rates [odds ratio (OR) 0.17, 95% CI 0.14–0.22, P < 0.001]. Wing length and longevity were similar between both groups.ConclusionsThis study demonstrates the potential of the BLOODless diet as a viable and ethical alternative to vertebrate blood feeding for rearing An. gambiae s.s. This breakthrough paves the way for more efficient and ethical studies aimed at combating malaria and other mosquito-borne diseases.Graphical

Identification of the polymorphism of the &lt;i&gt;APAF1&lt;/i&gt; gene and its association with economically useful traits of Holstein cattle

A decrease in the reproductive ability of cows leads to losses in dairy farming, as dairy production decreases due to the lack of a lactation period in cows. Haplotype HH1 is responsible for a mutation in the protein apoptotic protease-activating factor 1 (APAF1), as a result of which its structure is shortened, resulting in a decrease in fertility, an increase in the number of embryonic mortality and abortions in Holstein dairy cattle. To study the polymorphism of the APAF1 gene (SNP p.Q579X [c.1741C&gt;T]) and its associations with economically traits, we used data and DNA from 254 cows of Holstein population of indigenous selection of Breeding Farm Integrated Agricultural Production Center of the Republic of Tatarstan. As a result, 2 alleles (Q and X) and 2 genotypes (QQ and QX) were identified in the APAF1 – BstC8 I gene locus in cattle. It was established that the dominant population is represented by carriers of the homozygous QQ genotype of the APAF1 gene - 98.0 %, and the frequency of the Q allele reached 0.990. The percentage of QX-type animals is minimal - 2.0 % of the total number of cows subjected to the study, as a result of which the occurrence of the X allele was only 0.010. An assessment of the influence of APAF1 gene polymorphism on economically significant traits showed that, depending on the genotype, such reproduction traits as the age of the first fertile insemination, the duration of the dry period and the Doha fertility index vary statistically significantly. Analysis of dairy productivity traits that cows with the QQ genotype are significantly superior to individuals with the QX genotype in all compared positions, with the exception of the content of the mass fraction of fat. Through selection using genetic marking, damage to livestock farms can be reduced by reducing the frequency of carriers of lethal alleles in the parent generation. This research was supported by FASO Russia project, registration number 122011800138-7.