Biology subjects

Nguyen, P.

Publications and source records attributed to Nguyen, P..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Voluntary Exercise Attenuates Tumor Growth in a Preclinical Model of Castration-Resistant Prostate Cancer

PurposeTo examine the effects of voluntary exercise training on tumor growth and explore the underlying intratumoral molecular pathways and processes responsible for the beneficial effects of VWR on tumor initiation and progression in a mouse model of Castration-Resistant Prostate Cancer (CRPC). MethodsMale immunodeficient mice (SCID) were castrated and subcutaneously inoculated with human CWR-22RV1 cancer cells to construct CRPC xenograft model before randomly assigned to either voluntary wheel running (VWR) or sedentary (SED) group (n=6/group). After three weeks, tumor tissues were collected. Tumor size was measured and calculated. mRNA expression of markers of DNA replication, Androgen Receptor (AR) signaling, and mitochondrial dynamics was determined by RT-PCR. Protein expression of mitochondrial content and dynamics was determined by western blotting. Finally, RNA-sequencing analysis was performed in the tumor tissues. ResultsVoluntary wheel running resulted in smaller tumor volume at the initial stage and attenuated tumor progression throughout the time course (P < 0.05). The reduction of tumor volume in VWR group was coincided with lower mRNA expression of DNA replication markers (MCM2, MCM6, and MCM7), AR signaling (ELOVL5 and FKBP5) and regulatory proteins of mitochondrial fission (Drp1 and Fis1) and fusion (MFN1 and OPA1) when compared to the SED group (P<0.05). More importantly, RNA sequencing data further revealed that pathways related to pathways related to angiogenesis, extracellular matrix formation and endothelial cell proliferation were downregulated. ConclusionsThree weeks of VWR was effective in delaying tumor initiation and progression, which coincided with reduced transcription of DNA replication, AR signaling targets and mitochondrial dynamics. We further identified reduced molecular pathways/processes related to angiogenesis that may be responsible for the delayed tumor initiation and progression by VWR.

cancer biology↗

bioRxiv2024

SGLT2 inhibitors protect against diabetic cardiomyopathy and atrial fibrillation through a CaMKII independent mechanism

Ca2+/calmodulin-dependent protein kinase II (CaMKII) has been implicated as an important mediator of the increasingly evident cardioprotective benefits exerted by sodium- glucose transport protein 2 channel inhibitors (SGLT2i). However, the exact nature of the relationship between CaMKII and SGLT2i remains unclear. Here, we find that empagliflozin but not dapagliflozin attenuated susceptibility to atrial fibrillation (AF) in a type 2 diabetic (T2D) mouse model. However, both empagliflozin and dapagliflozin protected from diabetic cardiomyopathy in T2D mice. We then used real-time microscopy of neonatal rat ventricular cardiomyocytes (NRVMs) with the CaMKII biosensor - CaMKAR to demonstrate that direct inhibition of CaMKII is not essential for the effects of SGLT2i in these cells. Therefore, we conclude that the benefits of SGLT2i in heart disease likely occur through indirect modulation of CaMKII activity, or possibly through an alternative pathway altogether.

molecular biology↗

bioRxiv2024

Therapeutic targeting of Syndecan-1 axis overcomes acquired resistance to KRAS-targeted therapy in gastrointestinal cancers

The therapeutic benefit of recently developed mutant KRAS (mKRAS) inhibitors has been limited by the rapid onset of resistance. Here, we aimed to delineate the mechanisms underlying acquired resistance to mKRAS inhibition and identify actionable targets for overcoming this clinical challenge. Previously, we identified Syndecan-1 (SDC1) as a key effector for pancreatic cancer progression whose surface expression is driven by mKRAS. By leveraging both pancreatic and colorectal cancer models, we found that surface SDC1 expression was initially diminished upon mKRAS inhibition, but recovered in tumor cells that bypass mKRAS dependency. Functional studies showed that these tumors depended on SDC1 for survival, further establishing SDC1 as a driver for the acquired resistance to mKRAS inhibition. Mechanistically, we revealed that the YAP1-SDC1 axis was the major driving force for bypassing mKRAS dependency to sustain nutrient salvage machinery and tumor maintenance. Specifically, YAP1 activation mediated the recovery of SDC1 localization on cell surface that sustained macropinocytosis and enhanced the activation of multiple RTKs, promoting resistance to KRAS-targeted therapy. Overall, our study has provided the rationale for targeting the YAP-SDC1 axis to overcome resistance to mKRAS inhibition, thereby revealing new therapeutic opportunities for improving the clinical outcome of patients with KRAS-mutated cancers.

cancer biology↗

bioRxiv2024

Polyommatine blue butterflies reveal unexpected integrity of the W sex chromosome amid extensive chromosome fragmentation

Chromosomal rearrangements are crucial in speciation, acting as barriers to gene flow. Holocentric chromosomes, such as those in Lepidoptera, can facilitate karyotype changes. Despite chromosome fusions being more common, speciation events are mostly linked to fissions. Notable karyotypic variation is observed in three clades of the subfamily Polyommatinae (Lycaenidae), with chromosome numbers ranging from n = 10 to n = 225. This study used flow cytometry and molecular cytogenetic analyses to investigate genome sizes and karyotypes in several species of the genera Polyommatus and Lysandra with derived and modal chromosome numbers. The findings show no support for polyploidy, supporting karyotypic diversification via fragmentation of chromosomes. Species with high chromosome numbers have larger genomes, which indicates a potential role of mobile elements but contradicts the hypothesis of holocentric drive. Telomeric signals were detected at the ends of fragmented chromosomes. No interstitial telomeric sequences were detected on autosomes. Interstitial telomeric signals on sex chromosomes, however, revealed multiple sex chromosome systems in Polyommatus dorylas and Polyommatus icarus, with two karyotype races differing in sex chromosome constitution in the latter. Pool-seq and coverage analyses indicated shared fusion of sex chromosomes with an autosome bearing the rDNA locus, followed by a fusion with chromosome 20 in the Czech population. Notably, the W chromosome resists fragmentation, likely due to epigenetic silencing protecting it from activity of mobile elements.

genomics↗

bioRxiv2024

Perturbation-Specific Transcriptional Mapping facilitates unbiased target elucidation of antibiotics

The rising prevalence of antibiotic resistance threatens human health. While more sophisticated strategies for antibiotic discovery are being developed, target elucidation of new chemical entities remains challenging. In the post-genomic era, expression profiling can play an important role in mechanism-of-action (MOA) prediction by reporting on the cellular response to perturbation. However, the broad application of transcriptomics has yet to fulfill its promise of transforming target elucidation due to challenges in identifying the most relevant, direct responses to target inhibition. We developed an unbiased strategy for MOA prediction, called Perturbation-Specific Transcriptional Mapping (PerSpecTM), in which large-throughput expression profiling of wildtype or hypomorphic mutants, depleted for essential targets, enables a computational strategy to address this challenge. We applied PerSpecTM to perform reference-based MOA prediction based on the principle that similar perturbations, whether chemical or genetic, will elicit similar transcriptional responses. Using this approach, we elucidated the MOAs of three new molecules with activity against Pseudomonas aeruginosa by comparing their expression profiles to those of a reference set of antimicrobial compounds with known MOAs. We also show that transcriptional responses to small molecule inhibition resemble those resulting from genetic depletion of essential targets by CRISPRi by PerSpecTM, demonstrating proof-of-concept that correlations between expression profiles of small molecule and genetic perturbations can facilitate MOA prediction when no chemical entities exist to serve as a reference. Empowered by PerSpecTM, this work lays the foundation for an unbiased, readily scalable, systematic reference-based strategy for MOA elucidation that could transform antibiotic discovery efforts. Significance StatementNew antibiotics are critically needed in the face of increasing antibiotic resistance. However, mechanism-of-action (MOA) elucidation remains challenging and imposes a major bottleneck in antibiotic discovery and development. Building on the principle that molecules with similar MOAs elicit similar transcriptional responses, we have developed a highly scalable strategy for MOA prediction in the important bacterial pathogen Pseudomonas aeruginosa based on correlations between the expression profiles of new molecules and known perturbations, either small molecule inhibition by known antibiotics or transcriptional repression of essential targets by CRISPRi. By rapidly assigning MOAs to three new molecules with anti-pseudomonal activity, we provide proof-of-concept for a rapid, comprehensive, systematic, reference-based approach to MOA prediction with the potential to transform antibiotic discovery efforts.

genomics↗

bioRxiv2024

Cytosolic Ribosomal Protein Haploinsufficiency affects Mitochondrial Morphology and Respiration

The interplay between ribosomal protein composition and mitochondrial function is essential for sustaining energy homeostasis. Precise stoichiometric production of ribosomal proteins is crucial to maximize protein synthesis efficiency while reducing the energy costs to the cell. However, the impact of this balance on mitochondrial ATP generation, morphology and function remains unclear. Particularly, the loss of a single copy ribosomal protein gene is observed in Mendelian disorders like Diamond Blackfan Anemia and is common in somatic tumors, yet the implications of this imbalance on mitochondrial function and energy dynamics are still unclear. In this study, we investigated the impact of haploinsufficiency for four ribosomal protein genes implicated in ribosomopathy disorders (rps-10, rpl-5, rpl-33, rps-23) in Caenorhabditis elegans and corresponding reductions in human lymphoblast cells. Our findings uncover significant, albeit variably penetrant, mitochondrial morphological differences across these mutants, alongside an upregulation of glutathione transferases, and SKN-1 dependent increase in oxidative stress resistance, indicative of increased ROS production. Specifically, loss of a single copy of rps-10 in C. elegans led to decreased mitochondrial activity, characterized by lower energy levels and reduced oxygen consumption. A similar reduction in mitochondrial activity and energy levels was observed in human leukemia cells with a 50% reduction in RPS10 transcript levels. Importantly, we also observed alterations in the translation efficiency of nuclear and mitochondrial electron transport chain components in response to reductions in ribosomal protein genes expression in both C. elegans and human cells. This suggests a conserved mechanism whereby the synthesis of components vital for mitochondrial function are adjusted in the face of compromised ribosomal machinery. Finally, mitochondrial membrane and cytosolic ribosomal components exhibited significant covariation at the RNA and translation efficiency level in lymphoblastoid cells across a diverse group of individuals, emphasizing the interplay between the protein synthesis machinery and mitochondrial energy production. By uncovering the impact of ribosomal protein haploinsufficiency on the translation efficiency of electron transport chain components, mitochondrial physiology, and the adaptive stress responses, we provide evidence for an evolutionarily conserved strategy to safeguard cellular functionality under genetic stress.

genetics↗

bioRxiv2024

Sex chromosome turnover in African annual killifishes of the genus Nothobranchius

Sex chromosomes of teleost fishes often have low levels of differentiation and undergo frequent turnovers. Annual Nothobranchius killifishes comprise representatives with male-heterogametic XY or X1X2Y sex chromosome systems, scattered across their phylogeny, nested within species lacking cytologically detectable sex chromosomes. They thus provide a suitable system to study sex chromosome evolution and turnover. Here, we combined molecular cytogenetics and genomic analyses to examine several multiple sex chromosome systems in Nothobranchius spp. and their outgroup Fundulosoma thierryi. We used fluorescence in situ hybridization with three sex chromosome-specific painting probes and bacterial artificial chromosomes (BAC) bearing eight orthologues of genes found to be repeatedly co-opted as master sex determining (MSD) genes in fishes. Our results suggest at least four independent origins of sex chromosomes in the genus Nothobranchius. The synteny block carrying amhr2 gene was shared by X1X2Y systems of N. brieni, N. guentheri and N. lourensi, but the autosomal additions and the overall neo-Y chromosome structure differed among these species. On the other hand, gdf6 gene was localized to neo-Y of F. thierryi. None of the mapped MSD gene candidates seems to determine sex in N. ditte. We further sequenced genomes of F. thierryi female and N. guentheri male by long-read platforms and performed analyses of male and female Pool-seq data and coverage to delimit their non-recombining regions, determine degree of their differentiation, and thus complement the cytogenetic data in assessing potential MSD genes. We found low level of sex chromosomes differentiation in F. thierryi. In N. guentheri, however, we identified two distinct evolutionary strata on neo-Y. The amhr2 gene resides in the younger stratum and has low allelic variation, which questions its role in sex determination.

evolutionary biology↗

bioRxiv2024

Effects of electroconvulsive shock on the function, circuitry, and transcriptome of dentate gyrus granule neurons

Therapeutic use of electroconvulsive shock (ECS) is particularly effective for treatment-resistant depression. Like other more common forms of antidepressant treatment such as SSRIs, ECS has been shown to increase neurogenesis in the hippocampal dentate gyrus of rodent models. Yet the question of how ECS-induced neurogenesis supports improvement of depressive symptoms remains unknown. Here, we show that ECS-induced neurogenesis is necessary to improve depressive-like behavior of mice exposed to chronic corticosterone (Cort). We then use slice electrophysiology to show that optogenetic stimulation of adult-born neurons produces a greater hyperpolarization in mature granule neurons after ECS vs Sham treatment. We identify that this hyperpolarization requires the activation of group II metabotropic glutamate receptors. Consistent with this finding, we observe reduced expression of the immediate early gene cFos in the granule cell layer of ECS vs Sham subjects. Using single nucleus RNA sequencing, we reveal major transcriptomic shifts in granule neurons after treatment with ECS+Cort or fluoxetine+Cort vs Cort alone. We identify a population of immature cells which has greater representation in both ECS+Cort and fluoxetine+Cort treated samples vs Cort alone. We also find global differences in ECS-vs fluoxetine-induced transcriptomic shifts. Together, these findings highlight a critical role for immature granule cells in the antidepressant action of ECS.

neuroscience↗

bioRxiv2024

A Novel Therapeutic Approach using CXCR3 Blockade to Treat Immune Checkpoint Inhibitor-mediated Myocarditis

BackgroundImmune checkpoint inhibitors (ICIs) are successful in treating many cancers but may cause immune-related adverse events. ICI-mediated myocarditis has a high fatality rate of up to 40%, with severe cardiovascular consequences. Targeted therapies for ICI myocarditis are currently lacking. MethodsWe used a genetic mouse model of PD-1 deletion (MRL/Pdcd1-/-) along with a novel drug-treated ICI myocarditis mouse model to recapitulate the disease phenotype. We performed single-cell RNA-sequencing (scRNAseq), single-cell T-cell receptor sequencing (scTCR-seq), and cellular indexing of transcriptomes and epitopes (CITE-seq) on immune cells isolated from MRL and MRL/Pdcd1-/- mice at serial timepoints. We assessed the impact of macrophage deletion in MRL/Pdcd1-/- mice, then inhibited CXC chemokine receptor 3 (CXCR3) in ICI-treated mice to assess therapeutic effect on myocarditis phenotype. Furthermore, we delineated functional effects of CXCR3 blockade on T-cell and macrophage interactions in a transwell assay. We then correlated the results in human single-cell multi-omics data from blood and heart biopsy data from patients with ICI myocarditis. ResultsSingle-cell multi-omics demonstrated expansion of CXCL9/10+CCR2+ macrophages and CXCR3hi CD8+ effector T-lymphocytes in the hearts of MRL/Pdcd1-/- mice correlating with onset of myocarditis development. Both depletion of CXCL9/10+CCR2+ macrophages and CXCR3 blockade respectively led to decreased CXCR3hiCD8+ T-cell infiltration into the heart and significantly improved survival. A transwell assay showed that selective blockade of CXCR3 and its ligand, CXCL10 decreased CD8+ T-cell migration towards macrophages, implicating this interaction in T-cell cardiotropism towards cardiac macrophages. Cardiac biopsies from patients with confirmed ICI myocarditis demonstrated infiltrating CXCR3+ lymphocytes and CXCL9+/CXCL10+ macrophages. Both mouse cardiac immune cells and patient peripheral blood immune cells revealed expanded TCRs correlating with CXCR3hi CD8+ T-cells in ICI myocarditis samples. ConclusionsThese findings bring forth the CXCR3-CXCL9/10 axis as an attractive therapeutic target for ICI myocarditis treatment, and more broadly, as a druggable pathway in cardiac inflammation.

cell biology↗

bioRxiv2023

An interactive web application for exploring human plasma and fibroblast metabolomics data from patients with inborn errors of metabolism

Metabolomic profiling is instrumental in understanding the systemic and cellular impact of inborn errors of metabolism (IEMs), monogenic disorders caused by pathogenic genomic variants in genes involved in metabolism. This study encompasses untargeted metabolomics analysis of plasma from 474 individuals and fibroblasts from 67 subjects, incorporating healthy controls, patients with 65 different monogenic diseases, and numerous undiagnosed cases. We introduce a web application designed for the in-depth exploration of this extensive metabolomics database. The application offers a user-friendly interface for data review, download, and detailed analysis of metabolic deviations linked to IEMs at the level of individual patients or groups of patients with the same diagnosis. It also provides interactive tools for investigating metabolic relationships and offers comparative analyses of plasma and fibroblast profiles. This tool emphasizes the metabolic interplay within and across biological matrices, enriching our understanding of metabolic regulation in health and disease. As a resource, the application provides broad utility in research, offering novel insights into metabolic pathways and their alterations in various disorders.

bioinformatics↗

bioRxiv2023

Formation of hemiclonal reproduction and hybridogenesis in Pelophylax water frogs studied with species-specific cytogenomic probes

Meiosis is a conservative process in all sexual organisms which ensures fertility and is central for producing genetic diversity by recombination and random segregation of parental chromosomes. Yet unexplored mechanisms may disrupt it and cause loss of sex followed by the emergence of clonal modes of reproduction. Interspecific hybridization is the primary trigger for this process, but mechanistic basis of the transition to asexuality remains still unknown for most vertebrate animals. To study these processes in water frogs, we performed reciprocal mating between two sexual species, Pelophylax ridibundus and P. lessonae, and produced vital F1 progeny (P. esculentus). The RepeatExplorer2 analysis of low-coverage genomic data of the two parental species identified the P. lessonae-specific minisatellite marker PlesSat01-48 (44 bp), which hybridized to (peri)centromeric regions of two chromosome pairs in P. lessonae - the acrocentric chromosome 8 and the chromosome 10 (a carrier of nucleolar organizer region; NOR). Chromosomal mapping combining the novel hybridization probe with the previously designed marker for P. ridibundus-specific centromeric satellite DNA showed that the P. esculentus progeny do not reproduce sexually. Instead, the F1 generation of P. esculentus instantly modified its gametogenesis and established asexual reproduction via hybridogenesis. Gametogenic modifications included premeiotic elimination of one of the parental genomes and clonal propagation of the remaining genome via endoreplication followed by standard meiotic division. The origin of DNA elimination and hybridogenesis in laboratory-produced hybrids supports a hypothesis that P. esculentus arises recurrently in nature whenever parental species come into reproductive contact. Based on the observed pattern of DNA elimination in the F1 progeny we discuss the origin and evolution of population systems in water frogs and the applicability of a newly designed chromosomal probe for other Pelophylax taxa.

evolutionary biology↗

bioRxiv2023

Ghost W chromosomes and unique genome architecture in ghost moths of the family Hepialidae

The classical model of sex chromosome evolution has been recently challenged in moths and butterflies (Lepidoptera). According to the current hypothesis, the adoption of a supernumerary chromosome may have driven the transition from the Z0 to the WZ sex chromosome system in females. However, the evolutionary history of the W chromosome remains enigmatic, especially in the early-diverging lepidopteran lineages. In ghost moths of the family Hepialidae, one of the most basal lepidopteran clades, there is conflicting evidence regarding their sex chromosomes. In this study, we aimed to clarify the status of the hepialid W chromosome. Using cytogenetics and genomics, we investigated the karyotype, sex chromosomes, genome size and repeatome of multiple ghost moth species and reconstructed basic phylogenetic relationships in the group. Our data show that Hepialidae have unusually large genomes (reaching up to 1C = 3 Gb) and are the oldest known lepidopteran clade with a W chromosome. However, the W does not form a typical heterochromatin body in polyploid nuclei, known as sex chromatin, previously employed to detect the presence of W chromosomes across Lepidoptera. Moreover, in some species, the W does not exhibit distinct repeat content and can escape detection via methods that rely on W-specific sequences. Analysis of the Z chromosome confirmed highly conserved gene content, arguing for a possible origin of the hepialid W chromosome from a B chromosome. We hypothesize that the mechanism underlying the formation of sex chromatin could be used in future research to study the origin of the W chromosome.

genomics↗

bioRxiv2023

Orb2 enables rare-codon-enriched mRNA expression during Drosophila neuron differentiation

Regulation of codon optimality is an increasingly appreciated layer of cell- and tissue-specific protein expression control. Here, we use codon-modified reporters to show that differentiation of Drosophila neural stem cells into neurons enables protein expression from rare-codon-enriched genes. From a candidate screen, we identify the cytoplasmic polyadenylation element binding (CPEB) protein Orb2 as a positive regulator of rare-codon-dependent expression in neurons. Using RNA sequencing, we reveal that Orb2-upregulated mRNAs in the brain with abundant Orb2 binding sites have a rare-codon bias. From these Orb2-regulated mRNAs, we demonstrate that rare-codon enrichment is important for expression control and social behavior function of the metabotropic glutamate receptor (mGluR). Our findings reveal a molecular mechanism by which neural stem cell differentiation shifts genetic code regulation to enable critical mRNA and protein expression.

developmental biology↗

bioRxiv2023

Multiple sex chromosomes of Yponomeuta ermine moths suggest a role of sexual antagonism in sex chromosome turnover in Lepidoptera

Sex chromosome-autosome fusions give rise to neo-sex chromosomes, which provide an insight into early evolution of sex chromosomes and drivers of chromosomal fusions. While sex chromosome-autosome fusions are scarce in vertebrates with female heterogamety ([female]ZW/[male]ZZ), they are common in moths and butterflies (Lepidoptera), the most species rich group with heterogametic females. This contradicts theoretical model that assumes chromosome fusions to be random and predicts them to be rare in taxa with high chromosome number such as Lepidoptera. In the present study we analyzed sex chromosomes in nine ermine moths of the genus Yponomeuta (Yponomeutidae) and their two outgroups, Teinoptila gutella (Yponomeutidae) and Plutella xylostella (Plutellidae). We employed genomic in situ hybridization to identify sex chromosomes and used a custom designed microarray to identify Z-linked genes. Our results confirmed a multiple sex chromosome system Z1Z2W to be present in T. gutella and all Yponomeuta spp. except for Y. tokyonella. The multiple sex chromosome system resulted from a fusion between the W chromosome and autosome homeologous to the Bombyx mori chromosome 2 (BmChr2). The BmChr2 bears a cluster of genes with ovary-specific expression which suggests that sexually antagonistic selection could have driven fixation of the fusion in a common ancestor of Yponomeuta and Teinoptila genera. We hypothesize that sex chromosome turnover in Lepidoptera could be driven by sexual antagonism.

evolutionary biology↗

bioRxiv2023

Estimating receptive fields of simple and complex cells in early visual cortex: A convolutional neural network model with parameterized rectification

Neurons in the primary visual cortex respond selectively to simple features of visual stimuli, such as orientation and spatial frequency. Simple cells, which have phase-sensitive responses, can be modeled by a single receptive field filter in a linear-nonlinear model. However, it is challenging to analyze phase-invariant complex cells, which require more elaborate models having a combination of nonlinear subunits. Estimating parameters of these models is made additionally more difficult by cortical neurons trial-to-trial response variability. We develop a simple convolutional neural network method to estimate receptive field models for both simple and complex visual cortex cells from their responses to natural images. The model consists of a spatiotemporal filter, a parameterized rectifier unit (PReLU), and a two-dimensional Gaussian "map" of the receptive field envelope. A single model parameter determines the simple vs. complex nature of the receptive field, capturing complex cell responses as a summation of homogeneous subunits, and collapsing to a linear-nonlinear model for simple type cells. The convolutional method predicts simple and complex cell responses to natural image stimuli as well as grating tuning curves. The fitted models yield a continuum of values for the PReLU parameter across the sampled neurons, showing that the simple/complex nature of cells can vary in a continuous manner. We demonstrate that complex-like cells respond less reliably than simple-like cells - compensation for this unreliability reveals good predictive performance on novel sets of natural images, with predictive performance for complex cells proportionately closer to that for simple cells. Most spatial receptive field structures are well fit by Gabor functions, whose parameters confirm well-known properties of cat A17/18 receptive fields. Author summaryMethods for recording increasingly many visual cortex neurons are advancing rapidly, demanding new approaches to characterize diverse receptive fields. We present a compact convolutional neural network model of early cortical neurons, which is uniformly applicable to simple and complex cells, and whose parameters are straightforwardly interpretable and readily estimated from responses to natural image stimuli. This novel approach introduces a single estimated model parameter to capture the simple/complex nature of a neurons receptive field, revealing a continuum of simple vs complex-like behaviour. We show that almost all complex-like cells exhibit a lower response reliability to repeated presentations of the same stimuli, compared to more reliable responses from simple-like cells. Accounting for this "noise ceiling" brings predictive performance for complex cells proportionately closer to that for simple cells. Using this model estimation approach with natural images, we evaluate findings from previous approaches that were restricted to simple-type cells and the use of grating or white noise stimuli, revealing a diversity of Gabor-like spatial receptive field shapes, which lie along a continuum of spatial bandwidths.

neuroscience↗

bioRxiv2023

Fast centromeric repeat turnover provides a glimpse into satellite DNA evolution in Nothobranchius annual killifishes

Satellite DNA (satDNA) is rapidly evolving class of tandem repeats with some motifs being involved in centromere organization and function. Rapid co-evolution of centromeric satDNA and associated proteins has been mostly attributed to the so-called centromere drive. To identify repeats associated with centromeric regions and test for the role of meiotic drive in their evolution, we investigated satDNA across Southern and Coastal clades of African annual killifishes of the genus Nothobranchius. C-banding showed expansion of (peri)centromeric heterochromatin regions in the Southern-clade killifishes. Molecular cytogenetic and bioinformatic analyses further revealed that two previously identified satellites, Nfu-SatA and Nfu-SatB, are associated with centromeres only in one lineage of the Southern clade. Nfu-SatB was, however, detected outside centromeres also in other members of the Coastal clade, which is consistent with the "library" hypothesis of satDNA evolution. We also identified a novel satDNA, Cl-36, associated with (peri)centromeres in N. foerschi, N. guentheri and N. rubripinnis from the Coastal clade. Our findings could be explained by centromere drive shaping karyotype change and centromeric repeat turnover in Nothobranchius species with possible reversal of spindle polarity within the Southern clade.

genetics↗

bioRxiv2023

Generation of Schwann cell derived melanocytes from hPSCs identifies pro-metastatic factors in melanoma

Summary/AbstractThe neural crest (NC) is highly multipotent and generates diverse lineages in the developing embryo. However, spatiotemporally distinct NC populations display differences in fate potential, such as increased gliogenic and parasympathetic potential from later migrating, nerve-associated Schwann cell precursors (SCPs). Interestingly, while melanogenic potential is shared by both early migrating NC and SCPs, differences in melanocyte identity resulting from differentiation through these temporally distinct progenitors have not been determined. Here, we leverage a human pluripotent stem cell (hPSC) model of NC temporal patterning to comprehensively characterize human NC heterogeneity, fate bias, and lineage development. We captured the transition of NC differentiation between temporally and transcriptionally distinct melanogenic progenitors and identified modules of candidate transcription factor and signaling activity associated with this transition. For the first time, we established a protocol for the directed differentiation of melanocytes from hPSCs through a SCP intermediate, termed trajectory 2 (T2) melanocytes. Leveraging an existing protocol for differentiating early NC-derived melanocytes, termed trajectory 1 (T1), we performed the first comprehensive comparison of transcriptional and functional differences between these distinct melanocyte populations, revealing differences in pigmentation and unique expression of transcription factors, ligands, receptors and surface markers. We found a significant link between the T2 melanocyte transcriptional signature and decreased survival in melanoma patients in the cancer genome atlas (TCGA). We performed an in vivo CRISPRi screen of T1 and T2 melanocyte signature genes in a human melanoma cell line and discovered several T2-specific markers that promote lung metastasis in mice. We further demonstrated that one of these factors, SNRPB, regulates the splicing of transcripts involved in metastasis relevant functions such as migration, cell adhesion and proliferation. Overall, this study identifies distinct developmental trajectories as a source of diversity in melanocytes and implicates the unique molecular signature of SCP-derived melanocytes in metastatic melanoma.

developmental biology↗

bioRxiv2022

Optimized CRISPR guide RNA library cloning reduces skew and enables more compact genetic screens

The development of CRISPR genetic screening tools has improved functional genomics, as these tools enable precise genomic editing, provide broad access to genomic regions beyond protein-coding genes, and have fewer off-target effects than other functional genomics modalities, allowing for novel applications with smaller library sizes compared to prior technologies. Pooled functional genomics screens require high cellular coverage per perturbation to accurately quantify phenotypes and average out phenotype-independent variability across the population. While more compact libraries have decreased the number of cells needed for a given screen, the cell coverage required for large-scale CRISPR screens still poses technical hurdles to screen in more challenging systems, such as iPSC-derived and primary cells. A major factor that influences cell coverage is screening library uniformity, as larger variation in individual guide RNA abundance requires higher cell coverage to reliably measure low-abundance guides. In this work, we have systematically optimized guide RNA cloning procedures to decrease bias. We implement these protocols to demonstrate that CRISPRi screens using 10-fold fewer cells than the current standard provides equivalent statistically significant hit-calling results to screens run at higher coverage, opening the possibility of conducting genome-wide and other large-scale CRISPR screens in technically challenging models.

genomics↗