Results 1-25 of about 1,000
  1. Background: To manipulate particular locations in the bacterial genome, researchers have recently resorted to a group of unique sequences in bacterial genomes that are responsible for safeguarding bacteria against bacteriophages. Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) are two such systems, each of which consists of an RNA component and an enzyme component. Methods and Results: This review focuses primarily on how CRISPR/Cas9 technology can be used to make models to study human diseases in mice. Creating RNA molecules that direct endonucleases to a specific position in the genome are crucial for achieving a specific genetic modification. CRISPR/Cas9 technology has allowed scientists to edit the genome with greater precision than ever before. Researchers can use knock-in and knock-out methods to model human diseases like Neurological, cardiovascular disease, and cancer. Conclusions: : In terms of developing innovative methods to discover ailments for diseases/disorders, improved CRISPR/Cas9 technology will provide easier access to valuable novel animal models.
    Date: 2022-09-27
    Authors: SOWBHAGYA R, MUKTHA H, RAMAKRISHNAIAH TN, SURENDRA AS, TANVI Y, NIVITHA K, RAJASHEKARA S.
    Ref: Research Square
  2. Highly efficient generation of deletions, substitutions, and small insertions (up to ~150 bp) into the C. elegans genome by CRISPR/Cas9 has been facilitated by use of single-stranded oligonucleotide donors as repair templates. However, efficient insertion of larger sequences such as fluorescent markers and other functional proteins remains inefficient due to lack of standardized methods for generating repair templates and labor intensive or cost prohibitive synthesis. We have optimized the simple and efficient generation of long single-stranded DNA for use as donors in CRISPR/Cas9 using a standard PCR followed by an enzymatic digest by lambda exonuclease. Comparison of long single-stranded DNA donors to previously described methods using double-stranded DNA yields orders of magnitude increased efficiency for single-stranded DNA donors. This efficiency can be leveraged to simultaneously generate multiple large insertions as well as successful edits without use of selection or co-conversion (coCRISPR) markers when necessary. Our approach complements the CRISPR/Cas9 toolkit for C. elegans to enable highly efficient insertion of longer sequences with a simple, standardized and labor-minimal protocol.
    Date: 2022-09-27
    Authors: Eroglu M, Yu B, Derry WB.
    Ref: bioRxiv
  3. Activin and inhibin are both dimeric proteins sharing the same β subunits that belong to the TGF-β superfamily. They are well known for stimulating and inhibiting pituitary FSH secretion, respectively, in mammals. In addition, activin also acts as a mesoderm-inducing factor in frogs. However, their functions in development and reproduction of other species are poorly defined. In this study, we disrupted all three activin/inhibin β subunits (βAa, inhbaa; βAb, inhbab; and βB, inhbb) in zebrafish using CRISPR/Cas9. The loss of βAa/b but not βB led to a high mortality rate in the post-hatching stage. Surprisingly, the expression of fshb but not lhb in the pituitary increased in the female βA mutant together with aromatase (cyp19a1a) in the ovary. The single mutant of βAa/b showed normal folliculogenesis in young females; however, their double mutant (inhbaa-/-;inhbab-/-) showed delayed follicle activation, granulosa cell hypertrophy, stromal cell accumulation and tissue fibrosis. The ovary of inhbaa-/- deteriorated progressively after 180 dpf with reduced fecundity and the folliculogenesis ceased completely around 540 dpf. In addition, tumor- or cyst-like tissues started to appear in the inhbaa-/- ovary after about one year. In contrast to females, activin βAa/b mutant males showed normal spermatogenesis and fertility. As for activin βB subunit, the inhbb-/- mutant exhibited normal folliculogenesis, spermatogenesis and fertility in both sexes; however, the fecundity of mutant females decreased dramatically at 270 dpf with accumulation of early follicles. In summary, the activin-inhibin system plays an indispensable role in fish reproduction, in particular folliculogenesis and ovarian homeostasis.
    Date: 2022-09-26
    Authors: Zhao C, Zhai Y, Geng R, Wu K, Song W, Ai N, Ge W.
    Ref: bioRxiv
  4. Despite many successful preclinical treatment studies to improve neurocognition in the Ts65Dn mouse model of Down syndrome (DS), translation to humans has failed. This raises critical questions about the appropriateness of the Ts65Dn mouse as the gold standard for DS research given that it carries, in addition to Mmu16 orthologous genes, triplication of 50 Mmu17 non-orthologous genes that might contribute to the observed brain and behavioral phenotypes. We used the novel Ts66Yah mouse that carries both an extra mini chromosome and the identical segmental Mmu16 trisomy as Ts65Dn, but in which the Mmu17 non-orthologous region was removed using CRISPR/Cas9 technology. We demonstrate that the Ts65Dn exhibits a more severe phenotype throughout the lifespan compared to the Ts66Yah mouse. Several Mmu17 non-orthologous genes were uniquely overexpressed in Ts65Dn embryonic forebrain; this produced major differences in dysregulated genes and pathways. Despite these genome-wide differences, the primary Mmu16 trisomic effects were highly conserved in both models, resulting in several commonly dysregulated disomic genes and pathways. During the neonatal period, delays in motor development, communication and olfactory spatial memory were observed in both Ts66Yah and Ts65Dn pups but were more pronounced in Ts65Dn. Adult Ts66Yah mice showed working memory deficits and sex-specific effects in exploratory behavior and spatial hippocampal memory, while long-term memory was preserved. Like the neonates, adult Ts66Yah mice exhibited fewer and milder behavioral deficits when compared to Ts65Dn mice. Our findings suggest that trisomy of the non-orthologous Mmu17 genes significantly contributes to the phenotype of the Ts65Dn mouse and may be one major reason why preclinical trials that used this model have unsuccessfully translated to human therapies.
    Date: 2022-09-26
    Authors: Guedj F, Kane E, Bishop L, Pennings JLA, Herault Y, Bianchi DW.
    Ref: bioRxiv
  5. Genome-wide recessive genetic screens using lentiviral CRISPR-guide RNA libraries are widely performed in mammalian cells to functionally characterise individual genes and for the discovery of new anti-cancer therapeutic targets. As the effectiveness of such powerful and precise tools for cancer pharmacogenomic is emerging, reference datasets for their quality assessment and the validation of the underlying experimental pipelines are becoming increasingly necessary. Here, we provide a dataset, an R package, and metrics for the assessment of novel experimental pipelines upon the execution of a single calibration viability screen of the HT-29 human colon cancer cell line, employing a commercially available genome-wide library of single guide RNAs: the Human Improved Genome-wide Knockout CRISPR (Sanger) Library. This dataset contains results from screening the HT-29 in multiple batches with the Sanger library, and outcomes from several levels of quality control tests on the resulting data. Data and accompanying R package can be used as a toolkit for benchmarking newly established experimental pipelines for CRISPR-Cas9 recessive screens, via the generation of a final quality-control report.
    Date: 2022-09-25
    Authors: Iannuzzi R, Manipur I, Pacini C, Behan FM, Guarracino MR, Garnett MJ, Savino A, Iorio F.
    Ref: bioRxiv
  6. To maintain genome integrity, cells must avoid DNA damage by ensuring the accurate duplication of the genome and by having efficient repair and signaling systems that counteract the genome-destabilizing potential of DNA lesions. To uncover genes and pathways that suppress DNA damage in human cells, we undertook genome-scale CRISPR/Cas9 screens that monitored the levels of DNA damage in the absence or presence of DNA replication stress. We identified 160 genes in RKO cells whose mutation caused high levels of DNA damage in the absence of exogenous genotoxic treatment. This list was highly enriched in essential genes, highlighting the importance of genomic integrity for cellular fitness. Furthermore, the majority of these 160 genes are involved in a limited set of biological processes related to DNA replication and repair, nucleotide biosynthesis, RNA metabolism and iron sulfur cluster biogenesis, suggesting that genome integrity may be insulated from a wide range of cellular processes. Among the many genes identified and validated in this study, we discovered that GNB1L, a schizophrenia/autism-susceptibility gene implicated in 22q11.2 syndrome, protects cells from replication catastrophe promoted by mild DNA replication stress. We show that GNB1L is involved in the biogenesis of ATR and related phosphatidylinositol 3-kinase-related kinases (PIKKs) through its interaction with the TTT co-chaperone complex. These results implicate PIKK biogenesis as a potential root cause for the neuropsychiatric phenotypes associated with 22q11.2 syndrome. The phenotypic mapping of genes that suppress DNA damage in human cells therefore provides a powerful approach to probe genome maintenance mechanisms.
    Date: 2022-09-24
    Authors: Zhao Y, Tabet D, Rubio Contreras D, Kousholt AN, Weile J, Melo H, Hoeg L, Cote AG, Lin Z, Setiaputra D, Jonkers J, Gingras A, Gomez Herreros F, Roth FP, Durocher D.
    Ref: bioRxiv
  7. Individuals with Cystic Fibrosis (CF) suffer from severe respiratory disease due to a genetic defect in the Cystic Fibrosis Transmembrane conductance Regulator ( CFTR ) gene, which impairs airway epithelial ion and fluid secretion. New CFTR modulators that restore mutant CFTR function have been recently approved for a large group of people with CF (pwCF), but ∼19% of pwCF cannot benefit from CFTR modulators [1]. Restoration of epithelial fluid secretion through non-CFTR pathways might be an effective treatment for all pwCF. Here we developed a medium-throughput 384-wells screening assay using nasal CF airway epithelial organoids, with the aim to repurpose FDA-approved drugs as modulators of non-CFTR dependent epithelial fluid secretion. From a ∼1400 FDA-approved drug library, we identified and validated 12 FDA-approved drugs that induced CFTR-independent fluid secretion. Among the hits were several cAMP-mediating drugs, including β2-adrenergic agonists. The hits displayed no effects on chloride conductance measured in Ussing chamber, and fluid secretion was not affected by TMEM16A as demonstrated by knockout (KO) experiments in primary nasal epithelial cells. Altogether, our results demonstrate the use of primary nasal airway cells for mediumscale drug screening, target validation with a highly efficient protocol for generating CRISPR-Cas9 KO cells and identification of compounds which induce fluid secretion in a CFTR- and TMEM16A-indepent manner.
    Date: 2022-09-23
    Authors: Rodenburg LW, Delpiano L, Railean V, Centeio R, Pinto MC, Smits SM, van der Windt IS, van Hugten CF, van Beuningen SF, Rodenburg RN, van der Ent CK, Amaral MD, Kunzelmann K, Gray MA, Beekman JM, Amatngalim GD.
    Ref: bioRxiv
  8. Purpose: Existing biomarkers for diagnosing and predicting the metastasis of lung adenocarcinoma (LUAD) may not meet the demands of clinical practice. Risk prediction models based on multiple markers may provide better prognostic factors for accurate diagnosis and prediction of metastatic LUAD. Methods: : An animal model of LUAD metastasis was constructed using CRISPR library technology, and genes related to LUAD metastasis were screened by mRNA sequencing of normal and metastatic tissues. The immune characteristics of different subtypes were analyzed, and the differential genes were subjected to survival and Cox regression analysis to identify the specific genes for metastasis. The biological function of RFLNA was first verified by analyzing cck-8, migration, invasion and apoptosis in LUAD cell lines. Results: : We identified 108 differential genes related to metastasis, and classified LUAD samples into two subtypes according to their expression levels. Subsequently, a prediction model composed of 8 metastasis-related genes (RHOBTB2, KIAA1524, CENPW, DEPDC1, RFLNA, COL7A1, MMP12 and HOXB9) was constructed. The AUC values of the logistic regression and neural network were 0.946 and 0.856, respectively. Moreover, the model can effectively classify patients into low- and high-risk groups. We found a better prognosis in the low-risk group both in the training cohort and test cohort, indicating that the prediction model has good diagnosis and predictive power. Up-regulation of RFLNA expression successfully promoted cell proliferation, migration, invasion, and attenuated apoptosis, suggesting that RFLNA plays a role in promoting LUAD development and metastasis. Conclusion: The model has important diagnostic and prognostic value for metastatic LUAD, and may serve as a novel biomarker for LUAD patients in clinic.
    Date: 2022-09-22
    Authors: Shao F, Ling L, Li C, Huang X, Ye Y, Zhang M, Huang K, Pan J, Chen J, Wang Y.
    Ref: Research Square
  9. The highly phosphorylated nucleotide, guanosine tetraphosphate (ppGpp), functions as a secondary messenger in bacteria and chloroplasts. The accumulation of ppGpp alters plastidial gene expression and metabolism, which are required for proper photosynthetic regulation and robust plant growth. However, because four plastid-localized ppGpp synthases/hydrolases function redundantly, the impact of the loss of ppGpp-dependent stringent response on plant physiology remains unclear. We used the CRISPR/Cas9 technology to generate an Arabidopsis thaliana mutant lacking all four ppGpp synthases/hydrolases, and characterized its phenotype. The mutant showed 20-fold less ppGpp levels than the wild type (WT) under normal growth conditions, and exhibited leaf chlorosis and increased expression of defense-related genes as well as salicylic acid and jasmonate levels upon transition to nitrogen-starvation conditions. These results demonstrate that proper levels of ppGpp in plastids are required for controlling not only plastid metabolism but also phytohormone signaling, which is essential for plant defense.
    Date: 2022-09-22
    Authors: Inazu M, Nemoto T, Suzuki S, Ono S, Kanno Y, Seo M, Oikawa A, Masuda S.
    Ref: bioRxiv
  10. Bitter taste receptors (T2Rs) are G protein-coupled receptors identified on the tongue but expressed all over the body, including in airway cilia and macrophages, where T2Rs serve an immune role. T2R isoforms detect bitter metabolites (quinolones and acyl-homoserine lactones) secreted by gram negative bacteria, including Pseudomonas aeruginosa , a major pathogen in cystic fibrosis (CF). T2R activation by bitter bacterial products triggers calcium-dependent nitric oxide (NO) production. In airway cells, the NO increases mucociliary clearance and has direct antibacterial properties. In macrophages, the same pathway enhances phagocytosis. Because prior studies linked CF with reduced NO, we hypothesized that CF cells may have reduced T2R/NO responses. Using qPCR, immunofluorescence, and live cell imaging of air-liquid interface cultures, we found primary nasal epithelial cells from both CF and non-CF patients exhibited similar T2R expression, localization, and calcium signals. However, CF cells exhibited reduced NO production also observed in immortalized CFBE41o-CF cells and non-CF 16HBE cells CRISPR modified with CF-causing mutations in the CF transmembrane conductance regulator (CFTR). NO was restored by VX-770/VX-809 corrector/potentiator pretreatment, suggesting reduced NO in CF cells is due to loss of CFTR function. In nasal cells, reduced NO correlated with reduced ciliary and antibacterial responses. In primary human macrophages, inhibition of CFTR reduced NO production and phagocytosis during T2R stimulation. Together, these data suggest an intrinsic deficiency in T2R/NO signaling caused by loss of CFTR function that may contribute to intrinsic susceptibilities of CF patients to P. aeruginosa and other gram-negative bacteria that activate this pathway.
    Date: 2022-09-22
    Authors: Carey RM, Palmer JN, Adappa ND, Lee RJ.
    Ref: bioRxiv
  11. SARS-CoV-2 primarily infects the respiratory tract, but pulmonary and cardiac complications occur in severe COVID-19. To elucidate molecular mechanisms in the lung and heart, we conducted paired experiments in human stem cell-derived lung alveolar type II (AT2) epithelial cell and cardiac cultures infected with SARS-CoV-2. With CRISPR- Cas9 mediated knock-out of ACE2, we demonstrated that angiotensin converting enzyme 2 (ACE2) was essential for SARS-CoV-2 infection of both cell types but further processing in lung cells required TMPRSS2 while cardiac cells required the endosomal pathway. Host responses were significantly different; transcriptome profiling and phosphoproteomics responses depended strongly on the cell type. We identified several antiviral compounds with distinct antiviral and toxicity profiles in lung AT2 and cardiac cells, highlighting the importance of using several relevant cell types for evaluation of antiviral drugs. Our data provide new insights into rational drug combinations for effective treatment of a virus that affects multiple organ systems. One-sentence summary Rational treatment strategies for SARS-CoV-2 derived from human PSC models
    Date: 2022-09-21
    Authors: Rudraraju R, Gartner MJ, Neil JA, Stout ES, Chen J, Needham EJ, See M, Mackenzie-Kludas C, Yang Lee LY, Wang M, Pointer H, Karavendzas K, Abu-Bonsrah D, Drew D, Sun YBY, Tan JP, Sun G, Salavaty A, Charitakis N, Nim HT, Currie PD, Tham W, Porrello E, Polo J, Humphrey SJ, Ramialison M, Elliott DA, Subbarao K.
    Ref: bioRxiv
  12. ABSTRACT Interleukin 1α (IL-1α) and IL-1β are the founding members of the IL-1 cytokine family, and these innate immune inflammatory mediators are critically important in health and disease. Early studies on these molecules suggested that their expression was interdependent, with an initial genetic model of IL-1α depletion, the IL-1α KO mouse ( Il1a -KO line1 ), showing reduced IL-1β expression. However, studies using this line in models of infection and inflammation resulted in contrasting observations. To overcome the limitations of this genetic model, we have generated and characterized a new line of IL-1α KO mice ( Il1a -KO line2 ) using CRISPR-Cas9 technology. In contrast to cells from the Il1a -KO line1 , where IL-1β expression was drastically reduced, bone marrow-derived macrophages (BMDMs) from Il1a -KO line2 mice showed normal induction and activation of IL-1β. Additionally, Il1a -KO line2 BMDMs showed normal inflammasome activation and IL-1β expression in response to multiple innate immune triggers, including both pathogen-associated molecular patterns and pathogens. Moreover, using Il1a -KO line2 cells, we confirmed that IL-1α, independent of IL-1β, is critical for the expression of the neutrophil chemoattractant KC/CXCL1. Overall, we report the generation of a new line of IL-1α KO mice and confirm functions for IL-1α independent of IL-1β. Future studies on the unique functions of IL-1α and IL-1β using these mice will be critical to identify new roles for these molecules in health and disease and develop therapeutic strategies.
    Date: 2022-09-21
    Authors: Malireddi RS, Bynigeri R, Kancharana B, Sharma BR, Burton AR, Pelletier S, Kanneganti T.
    Ref: bioRxiv
  13. Ras proteins are GTPases that regulate a wide range of cellular processes. The activity of Ras is dependent on its nucleotide-binding status, which is modulated by guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). Previously, we demonstrated that mutation of lysine 104 to glutamine (K104Q) attenuates the transforming capacity of oncogenic K-Ras by interrupting GEF induced nucleotide exchange. To assess the effect of this mutation in vivo , we used CRISPR/Cas9 to generate mouse models carrying the K104Q point mutation in wild-type and conditional K-Ras LSL-G12D alleles. Consistent with our previous findings from in vitro studies, the oncogenic activity of K-Ras G12D was significantly attenuated by mutation at K104 in vivo . These data demonstrate that lysine at position 104 is critical for the full oncogenic activity of mutant K-Ras and suggest that modification at K104, for example acetylation, may also regulate its activity. In addition, animals homozygous for K104Q were viable, fertile, and arose at Mendelian frequency, indicating that K104Q is not a complete loss of function mutation. Using biochemical and structural analysis, we found that the G12D and K104Q mutations cooperate to suppress GEF-mediated nucleotide exchange, explaining the preferential effect of K104Q on oncogenic K-Ras. Finally, we discovered an allosteric regulatory network consisting of K104 and residues including G75 on switch II (SWII) that is the key for regulating the stability of the α helix on SWII. In this allosteric network, K104-G75 interaction might be primary for keeping stabilization of SWII. Given the high frequency of KRAS mutations in human cancers, modulation of this network may provide a unique therapeutic approach.
    Date: 2022-09-21
    Authors: Yang MH, Tran TH, Hunt B, Agnor R, Johnson CW, Waybright TJ, Nowak JA, Stephen AG, Simanshu DK, Haigis KM.
    Ref: bioRxiv
  14. The antigen presenting molecule, MR1, presents microbial metabolites to MAIT cells, a population of innate-like, anti-microbial T cells. It also presents an unidentified ligand to MR-1 restricted T cells in the setting of cancer. The cellular co-factors that mediate MR1 antigen presentation have yet to be fully defined. We performed a mass spectrometry-based proteomics screen to identify MR1 interacting proteins and identified the selective autophagy receptor SQSTM1/p62. CRISPR-Cas9-mediated knock out of SQSTM1/p62 increased MAIT cell activation in the presence of E.coli but not the synthetic ligand 5-OP-RU whereas depletion of Atg5 and Atg7, key autophagy proteins, increased MAIT activation irrespective of the ligand used. This regulation appears to occur at an early step in the trafficking pathway. This data implicates distinct roles for autophagy associated proteins in the regulation of MR1 activity and highlights the autophagy pathway as a key regulator of cellular antigen presentation.
    Date: 2022-09-21
    Authors: Phalora P, Ussher J, Hester S, Marchi E, Mak JYW, Fairlie DP, Klenerman P.
    Ref: bioRxiv
  15. Background: The mammalian retina contains an autonomous circadian clock that controls many physiological functions within this tissue. Our previous studies have indicated that disruption of this circadian clock by removing Bmal1 from the retina affects the visual function, retinal circuitry, and cone photoreceptor viability during aging. In the present study, we employed a mouse-derived cone photoreceptor‒like cell, 661W, to investigate which molecular mechanisms of the circadian clock may modulate cone photoreceptor viability during aging. Methods: Bmal1 knockout (BKO) cells were generated from 661W cells using the CRISPR/Cas9 gene editing tool. Deletion of Bmal1 from 661W was verified by western blot and monitoring Per2-luc bioluminescence circadian rhythms. To investigate the effect of Bmal1 removal on an oxidative stress challenge, cells were treated with hydrogen peroxide (H 2 O 2 ,1 mM) for two hours and then cell viability was assessed. Cells were also cultured and harvested for gene expression analysis and antioxidant assay. Results: Our data indicated that 661W cells contain a functional circadian clock that mediates the response to an oxidative stress challenge in vitro and that such a response is no longer present in the BKO cell. We also hypothesized that the effect was due to the circadian regulation of the intracellular antioxidant defense mechanism. Our results indicated that in 661W cells, the antioxidant defense mechanism is under circadian control, whereas in BKO cells, there is an overall reduction in this antioxidant defense mechanism, and it is no longer under circadian control. Conclusions: Our work supported the notion that the presence of a functional circadian clock and its ability to modulate the response to an oxidative stress is the underlying mechanism that may protect cones during aging.
    Date: 2022-09-20
    Authors: Baba K, Suen T, Goyal V, Stowie A, Davidson A, DeBruyne J, Tosini G.
    Ref: F1000Res
  16. Rationale The most significantly associated atrial fibrillation (AF) risk loci in humans map to a noncoding gene desert upstream of the evolutionarily conserved left-right (LR) transcription factor Pitx2 , a master regulator of LR asymmetric organ development. Pitx2 dosage is fundamentally linked to the development of sinus node dysfunction (SND) and AF, the most common cardiac arrhythmia affecting adults, but the mechanistic basis for this remains obscure. We identified a conserved long noncoding RNA (lncRNA), Playrr , which is exclusively transcribed on the embryo’s right side, opposite to Pitx2 on the left, that participates in mutually antagonistic transcriptional regulation with Pitx2 . Objective The objective of this study was to investigate a role of Playrr in regulating Pitx2 transcription and protecting against the development of cardiac rhythm disturbances. Methods and Results Playrr expression in the developing heart was analyzed with RNA in situ hybridization. Playrr was expressed asymmetrically (on the right) to Pitx2 (on the left) in developing mouse embryos, including in mouse embryonic sinoatrial node cells. We utilized CRISPR/Cas9 genome editing in mice to target Playrr , generating mice lacking Playrr RNA transcript ( Playrr Ex1sj allele). Using qRT-PCR we detected upregulation of the cardiac isoform, Pitx2c , during visceral organ morphogenesis in Playrr Ex1sj mutant embryos. Surface ECG (AliveCor®) and 24-hour telemetry ECG detected bradycardia and irregular interbeat (R-R) intervals suggestive of SND in Playrr Ex1sj mutant adults. Programmed stimulation of Playrr Ex1sj mutant adults resulted in pacing-induced AF. Within the right atrium of Playrr Ex1sj mutant hearts, Masson’s trichrome stain revealed increased collagen deposition indicative of fibrosis, and immunofluorescence demonstrated mis-localization of Connexin 43 in atrial cardiomyocytes. These findings suggested an altered atrial substrate in Playrr Ex1sj adult mice. Finally, transcriptomic analysis by chromatin run-on and sequencing (ChRO-seq) in atria of Playrr Ex1sj mutant mice compared to wild type controls revealed differential expression of genes involved in cell-cell adhesion and motility, fibrosis, and dysregulation of the key cardiac genes Tbx5 and Hcn1 . Conclusions Adult mice lacking functional Playrr lncRNA transcript have baseline bradyarrhythmia and increased susceptibility to AF. These cardiac phenotypes are similar to those observed in Pitx2 heterozygous mice. Interactions between Pitx2 and Playrr may provide a genetic mechanism for modulating Pitx2 dosage and susceptibility to SND and AF.
    Date: 2022-09-20
    Authors: Chen FL, Oxford EM, Chou S, Li N, Leach JP, Perry SK, Sanketi BD, Cong C, Kupiec-Weglinski SA, Dubowitz R, Daugherity E, Martin JF, Danko CG, Kurpios NA.
    Ref: bioRxiv
  17. Chickpea is considered recalcitrant to in vitro tissue culture. The Clustered, Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 (CRISPR/Cas9) based genome editing in chickpea can remove the bottleneck of limited genetic variation in this cash crop rich in nutrients and protein. However, the generation of stable mutant lines using CRISPR/Cas9 requires efficient and highly reproducible transformation approaches. We modified a binary vector pPZP200 by introducing a codon-optimized Cas9 gene for chickpea and the promoters of Medicago truncatula U6 snRNA for expressing guide RNA targeted to the Phytoene Desaturase (PDS) gene. The dissected single cotyledons with half embryo of chickpea were used as explants for genetic transformation. A single gRNA was found sufficient to achieve high efficiency (42%) editing with the generation of PDS mutants with albino phenotypes. A simple, rapid, highly reproducible, stable transformation and CRISPR/Cas9-based genome editing system for chickpea was established. For the first time, this study aimed to demonstrate this system’s applicability by performing a gene knockout of the chickpea phytoene desaturase gene ( CaPDS ) in stable shoots using an improved chickpea transformation protocol.
    Date: 2022-09-20
    Authors: Gupta SK, Vishwakarma NK, Malakar P, Vanaspati P, Sharma NK, Chattopadhyay D.
    Ref: bioRxiv
  18. Background CRISPR-Cas based diagnostic assays provide a portable solution which bridges the benefits of qRT-PCR and serological assays in terms of portability, specificity and ease of use. CRISPR-Cas assays are rapidly fieldable, specific and have been rigorously validated against a number of targets, including HIV and vector-borne pathogens. Recently, CRISPR-Cas12 and CRISPR-Cas13 diagnostic assays have been granted FDA approval for the detection of SARS-CoV-2. A critical step in utilizing this technology requires the design of highly-specific and efficient CRISPR RNAs (crRNAs) and isothermal primers. This process involves intensive manual curation and stringent parameters for design in order to minimize off-target detection while also preserving detection across divergent strains. As such, a single, streamlined bioinformatics platform for rapidly designing crRNAs for use with the CRISPR-Cas12 platform is needed. Here we offer PrimedSherlock, an automated, computer guided process for selecting highly-specific crRNAs and primers for targets of interest. Results Utilizing PrimedSherlock and publicly available databases, crRNAs were designed against a selection of Flavivirus genomes, including West Nile, Zika and all four serotypes of Dengue. Using outputs from PrimedSherlock in concert with both wildtype A.s Cas12a and Alt-R Cas12a Ultra nucleases, we demonstrated sensitive detection of nucleic acids of each respective arbovirus in in-vitro fluorescence assays. Moreover, primer and crRNA combinations facilitated the detection of their intended targets with minimal off-target background noise. Conclusions PrimedSherlock is a novel crRNA design tool, specific for CRISPR-Cas12 diagnostic platforms. It allows for the rapid identification of highly conserved crRNA targets from user-provided primer pairs or PrimedRPA output files. Initial testing of crRNAs against arboviruses of medical importance demonstrated a robust ability to distinguish multiple strains by exploiting polymorphisms within otherwise highly conserved genomic regions. As a freely-accessible software package, PrimedSherlock could significantly increase the efficiency of CRISPR-Cas12 diagnostics. Conceptually, the portability of detection kits could also be enhanced when coupled with isothermal amplification technologies.
    Date: 2022-09-20
    Authors: Mann JG, Pitts RJ.
    Ref: bioRxiv
  19. An elevated level of low-density lipoprotein (LDL) in the bloodstream is a causal risk factor for atherosclerotic cardiovascular disease (ASCVD). The low-density lipoprotein receptor (LDLR) is a critical regulator of circulating LDL, and increasing LDLR activity is an effective therapeutic approach to reduce circulating LDL cholesterol levels. In this study, we characterize PROX1 and CHD7 , two genes we previously identified in a genome-scale CRISPR screen as positive regulators of LDL uptake in HuH7 cells. We found that although disruption of either PROX1 or CHD7 significantly reduced LDL uptake, only PROX1 disruption significantly reduced the cellular levels of LDLR mRNA and surface-displayed LDLR protein. Consistent with a direct role for PROX1 in LDLR gene regulation, we also observed in publicly available data sets the presence of two liver-specific PROX1 binding sites near the LDLR locus, one of which colocalized with biochemical hallmarks of enhancer activity in hepatic tissue. Both PROX1 LDLR binding sites contained predicted PROX1 transcription factor binding motifs and colocalized with binding sites for HNF4α, a known interactor for PROX1 and regulator of hepatic lipid metabolism and LDL uptake. In contrast to PROX1, no CHD7 binding sites were detected near the LDLR locus. Together, our results support a model in which both PROX1 and CHD7 promote cellular LDL uptake through distinct mechanisms, with PROX1 directly promoting LDLR gene expression and CHD7 functioning through an LDLR-independent pathway.
    Date: 2022-09-20
    Authors: Serrano-Zayas C, Holding ML, Khan TG, Tang VT, Skidmore JM, Martin DM, Ginsburg D, Emmer BT.
    Ref: bioRxiv
  20. Novel versions of Cas12a, together with optimised guide architecture led to barley target genes being mutagenised in around 90% of transgenic lines. This system also functioned in Brassica oleracea.
    Date: 2022-09-19
    Authors: Lawrenson T, Hinchliffe A, Forner M, Harwood W.
    Ref: Research Square
  21. In genome engineering, integration of incoming DNA has been dependent on enzymes produced by dividing cells which has been a bottle neck towards increasing DNA-insertion frequencies and accuracy. RNA-guided transposition with CRISPR-associated transposase (CAST) was shown to be highly effective and specific in Escherichia coli . Here we developed Golden-Gate vectors to test this approach in filamentous cyanobacteria and show that CAST is effective in Anabaena sp. strain PCC 7120. The comparatively large plasmids containing the CAST and the engineered transposon were successfully transferred into Anabaena via conjugation using either suicide or replicative plasmids. Single guide RNA that target the leading, but not the reverse complement strand were effective with the protospacer associated motif (PAM) sequence included in the single guide RNA. In four out of six cases analyzed over two distinct target loci, the insertion site was exactly 63 bases after the PAM. CAST on a replicating plasmid was toxic which could be used to cure the plasmid. In all six cases analyzed, only the transposon defined by the sequence ranging from left and right elements was inserted at the target loci, therefore, RNA-guided transposition resulted from cut and paste. No endogenous transposons were remobilized by exposure to CAST enzymes. This work is foundational for genome editing by RNA-guided transposition in filamentous cyanobacteria, whether in culture or in complex communities.
    Date: 2022-09-19
    Authors: Arévalo S, Rico DP, Abarca MD, Dijkhuizen LW, Lindblad P, Flores E, Nierzwicki-Bauer S, Schluepmann H.
    Ref: bioRxiv
  22. Substance use disorder is a debilitating chronic disease and a leading cause of disability around the world. The nucleus accumbens (NAc) is a major brain hub that mediates reward behavior. Studies demonstrate exposure to cocaine is associated with molecular and functional imbalance in two NAc medium spiny neuron subtypes (MSNs), dopamine receptor 1 and 2 enriched D1-MSNs and D2-MSNs. Our previous reports showed that repeated cocaine exposure induced transcription factor early growth response 3 (Egr3) mRNA in NAc D1-MSNs, while reducing it in D2-MSNs. Here, we report our findings of repeated cocaine exposure inducing cell subtype specific bidirectional expression of the Egr3 corepressor NGFI-A-binding protein 2 (Nab2). Using CRISPR activation and interference (CRISPRa and CRISPRi) tools combined with Nab2 or Egr3 targeted sgRNAs, we mimicked these bidirectional changes in Neuro2a cells. Furthermore, we investigated D1-MSN and D2-MSN subtype specific expressional changes of histone lysine demethylases Kdm1a, Kdm6a and Kdm5c in NAc after repeated cocaine exposure. Since Kdm1a showed bidirectional expression patterns in D1-MSNs and D2-MSNs, like Egr3, we developed a light inducible Opto-CRISPR-KDM1a system. We were able to downregulate Egr3 and Nab2 transcripts and cause bidirectional expression changes in D1-MSNs and D2-MSNs similar to cocaine exposure in Neuro2A cells. In contrast, our Opto-CRISPR-p300 activation system induced the Egr3 and Nab2 transcripts and caused bidirectional transcription regulations in D1-MSNs and D2-MSNs. Our study sheds light on the expression patterns of Nab2 and Egr3 in specific NAc MSN subtypes in cocaine action and uses CRISPR tools to further mimic these expression patterns.
    Date: 2022-09-19
    Authors: Choi EY, Franco D, Stapf CA, Gordin M, Chow A, Cover KK, Chandra R, Lobo MK.
    Ref: bioRxiv
  23. The generation of haploids is one of the most powerful means to accelerate the plant breeding process. In most crop species, an efficient haploid technology is not yet available or only applicable to a limited set of genotypes. Recent results published for Arabidopsis thaliana and major cereal crops like maize and wheat about successful haploid induction by CRISPR/Cas9-mediated editing of the centromeric histone H3 gene (CENH3) suggest that this novel method for the production of haploid plants might also be applicable to vegetable species like carrot. Here, we report and summarize the different experimental and genetic approaches that have been focused in the past few years on CRISPR/Cas9-based editing of the carrot CENH3 gene. We also describe the discovery of a second CENH3 locus in the carrot genome, which complicates the attempts to generate and to analyse putative haploid inducer genotypes. We show that three different CRISPR/Cas9 target constructs, used alone or in combinations, could successfully target carrot CENH3. Promising mutants such as in-frame indel or deletion mutants were found, but their successful usage as putative haploid inducer is uncertain yet. Next generation sequencing of amplicons spanning CRISPR target sites and transcript-based amplicon sequencing seemed to be appropriate methods to select promising mutants, to estimate mutation frequencies, and to allow a first prediction which gene was concerned. Since a serious amount of allelic variability within CENH3 genes of different carrot cultivars appeared to be present, future carrot CENH3 research should consider cloning and sequencing of further full-length CENH3 genes. Another aim of this study was the simultaneous knockout and complementation of the endogenous carrot CENH3 gene by an alien CENH3 gene. Co-transformation of a CRISPR/Cas9-based carrot CENH3 knockout construct together with a CENH3 gene cloned from ginseng ( Panax ginseng ) was performed by using Rhizobium rhizogenes . It is shown, that ginseng CENH3 protein is accumulated inside the kinetochore region of carrot chromosomes, indicating that PgCENH3 might be a good candidate for this approach. However, presently it is unclear, if this gene is fully functioning during the meiotic cell divisions and able to complement lethal gametes. Challenges and future prospects to develop a CENH3-based HI system for carrot are discussed.
    Date: 2022-09-19
    Authors: Dunemann F, Krüger A, Maier K, Struckmeyer S.
    Ref: bioRxiv
  24. Jumbo bacteriophages of the ⌽KZ-like family are characterized by large genomes (>200 kb) and the remarkable ability to assemble a proteinaceous nucleus-like structure. The nucleus protects the phage genome from canonical DNA-targeting immune systems, such as CRISPR-Cas and restriction-modification. We hypothesized that the failure of common bacterial defenses creates selective pressure for immune systems that target the unique jumbo phage biology. Here, we identify the “ ju mbo phage k iller” (Juk) immune system that is deployed by a clinical isolate of Pseudomonas aeruginosa to resist ⌽KZ. Juk immunity rescues the cell by preventing early phage transcription, DNA replication, and nucleus assembly. Phage infection is first sensed by JukA (formerly YaaW), which localizes rapidly to the site of phage infection at the cell pole, triggered by ejected phage factors. The effector protein JukB is recruited by JukA, which is required to enable immunity and the subsequent degradation of the phage DNA. JukA homologs are found in several bacterial phyla and are associated with numerous other putative effectors, many of which provided specific anti-⌽KZ activity when expressed in P. aeruginosa . Together, these data reveal a novel strategy for immunity whereby immune factors are recruited to the site of phage protein and DNA ejection to prevent phage progression and save the cell.
    Date: 2022-09-18
    Authors: Li Y, Guan J, Hareendranath S, Crawford E, Agard DA, Makarova KS, Koonin EV, Bondy-Denomy J.
    Ref: bioRxiv
  25. PICKLES ( https://pickles.hart-lab.org ) is an updated web interface to a freely available database of genome-scale CRISPR knockout fitness screens in human cell lines. Using a completely rewritten interface, researchers can explore gene knockout fitness phenotypes across cell lines and tissue types and compare fitness profiles with fitness, expression, or mutation profiles of other genes. The database has been updated to include data from three CRISPR libraries (Avana, Score, and TKOv3), and includes information from 1,162 whole-genome screens probing the knockout fitness phenotype of 18,959 genes. Source code for the interface and the integrated database are available for download.
    Date: 2022-09-18
    Authors: Novak LC, Chou J, Colic M, Bristow CA, Hart T.
    Ref: bioRxiv
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