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Fernandes, T.

Publications and source records attributed to Fernandes, T..

11 recordsLinked to original sources

Stem-cell modeling of cerebellar dysfunction of Angelman syndrome

Angelman syndrome (AS) is a severe neurodevelopmental disorder caused by the loss of function of the maternal allele of the neuron-specific imprinted gene UBE3A. Although AS presents with developmental delay, ataxia, epilepsy, and speech impairment, the distinct roles of various brain regions in its pathology remain unclear, hindering the design of effective therapeutic strategies. Of all brain regions, the nature and impact of dysfunction of the cerebellum in AS remain elusive. To start addressing this, we leveraged our optimized stem cell-based model of regionally patterned human cerebellar organoids (hCerOs) capable of producing major cerebellar neuronal subtypes, including Purkinje and granule cells, further matured in a two-dimensional (2D) culture system. We modeled AS using induced pluripotent stem cell (iPSC) lines carrying the common class II deletion and unaffected controls previously validated in our system. hCerOs from both backgrounds recapitulate lineage commitment and neuron-specific UBE3A imprinting. AS hCerOs consistently show reduced size, impaired neuroepithelial expansion, and diminished expression of glutamatergic and GABAergic progenitor markers. Transcriptomic profiling and functional assays assessing neuronal activity during the maturation stage uncovered delayed maturation, abnormal firing and increased neuronal excitability in AS cultures. These results position our hCerO model as a robust platform for future mechanistic studies and therapeutic screening aimed at targeting cerebellar dysfunction in AS.

developmental biology↗

Lipid droplet dysmetabolism affects cell homeostasis in an in vitro model of Alzheimer disease

Lipid droplets (LD) are dynamic organelles involved in neutral lipid storage, energy homeostasis, and can prevent lipotoxicity and oxidative distress. LD dysmetabolism has been considered a pathological hallmark in neurodegenerative disorders, including Alzheimers disease (AD). In this study, we investigated the alterations in LD metabolism and their impact on mitochondria-associated membranes (MAM) in an in vitro model of AD, namely the mouse neuroblastoma cell (N2A) line overexpressing the amyloid precursor protein with the familial Swedish mutation (APPswe). In APPswe cells, we found depletion of LD associated with an accumulation of free fatty acids that can be related with the observed LD degradation by chaperone-mediated autophagy. In these cells we also found decreased levels of seipin, which might contribute to triacylglycerol accumulation. These lipid alterations are associated with increased levels of ROS and lipid peroxidation in APPswe cells. The pharmacological modulation of DGAT1, that mediates triacylglycerol synthesis, normalized LD size and improved ER-mitochondria contacts and mitochondrial function in APPswe cells. In summary, these observations suggest the involvement of altered LD metabolism in AD pathophysiology, which impact on MAM and mitochondria function leading to cell dyshomeostasis. Our findings also support the idea that LD are relevant therapeutic targets in AD. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/658644v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@de3fc6org.highwire.dtl.DTLVardef@12d1f2forg.highwire.dtl.DTLVardef@15a5185org.highwire.dtl.DTLVardef@9e1655_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

OsbHLH089 and OsbHLH094 Modulate OsSLR1 Levels to Maintain Male Reproductive Fitness in Rice

DELLA proteins are a unique class of transcriptional regulators in plants, playing critical roles in diverse biological processes. Far from being only negative regulators of the Gibberellin (GA) signalling pathway, DELLAs act as central signalling hubs due to their versatile binding capacity and responsiveness to GA fluctuations. This adaptability allows DELLAs to interact with a wide array of proteins but also makes their functional study challenging: disruptions in DELLA function lead to pleiotropic effects across multiple pathways. To address this complexity, understanding DELLA interactors provides valuable insights into DELLAs nuanced functions and regulation. Building on this approach, we investigated novel OsSLR1 interactors, OsbHLH089 and OsbHLH094, members of the basic-helix-loop-helix transcription factor family. Our findings reveal that OsbHLH089 and OsbHLH094 are expressed in mature pollen grains, with the Osbhlh089/94 double mutant displaying smaller, indehiscent anthers and non-viable pollen, indicating their redundant role in pollen development during its late stages. Through ChIP-Seq and RNA-Seq analyses, we identified five target genes repressed by OsbHLH089 and OsbHLH094 (OsTDL1A, OsSPS1, OsDGD2{beta}, OspPGM, and OsDPE2) that are essential for pollen and anther development. Interestingly, we also observed the binding of these TFs to the OsSLR1 promoter. Notably, while other target genes were repressed, OsSLR1 was induced, with a significant protein accumulation in the double mutant compared to the Kitaake background in the late stages of pollen development. This suggests that OsSLR1 accumulation may compromise pollen viability, further highlighting the critical regulatory role of OsbHLH089 and OsbHLH094 in repressing OsSLR1 levels for proper pollen and anther development.

plant biology↗

Comparative transcriptomics of Lathyrus sativus reveals accession-specific resistance responses against Erysiphe pisi

Lathyrus sativus (grass pea) is a valuable crop for sustainable agriculture, offering both dietary benefits and desirable agronomic traits. However, its yield stability is limited by different diseases such as powdery mildew caused by Erysiphe pisi. Frequent fungal resistance to pesticides and growing environmental concerns highlight the need for research investment to develop resistant crop varieties. Four L. sativus accessions, exhibiting varying levels of resistance to E. pisi (resistant, partially resistant, partially susceptible, and susceptible), were analysed using dual RNA-seq to identify key defence mechanisms and effector genes involved in this plant-pathogen interaction. The dual transcriptomic analysis highlighted a host biphasic response, characterised by an initial burst of gene expression, followed by a quiescent phase, and a second wave of intense gene expression at 72 hours after inoculation. Common L. sativus defence mechanisms, including antifungal protein expression, cell wall reinforcement, reactive oxygen species-mediated defence were activated by all accessions compared to susceptible accession. Unique responses in the resistant accession integrate early reinforcement of structural barriers with sustained chemical defences and stress responses. Overall, the partially resistant accession exhibited a front-loaded defence response, focused on biotic stimuli and interspecies interactions at early infection stages. In contrast, partial susceptible accessions exhibited a weaker baseline defence system, with a slower and less robust response specifically targeting pathogen infection. We identified potential E. pisi effectors, including genes involved in cell wall hydrolysis, nutrient acquisition, and virulence, with a higher diversity of effectors identified in the susceptible accession. This study identifies novel targets within the complex defence mechanisms of the Lathyrus sativus-Erysiphe pisi interaction that will support to future breeding programs aimed at enhancing resistance to E. pisi in L. sativus and other related species.

plant biology↗

Transcriptional repression of SOX2 by p53 in cancer cells regulates cell identity and migration

During cancer development and progression, many genetic alterations lead to the acquisition of novel features that confer selective advantage to cancer cells and that resemble developmental programs. SOX2 is one of the key pluripotency transcription factors, expressed during embryonic development and active in adult stem cells. In cancer, SOX2 is frequently dysregulated and associated with tumor stemness and poor patient survival. SOX2 expression is suppressed in differentiated cells by tumor suppressor proteins that form a transcriptional repressive complex. We previously identified some of these proteins and found that their absence combined with deficiency in Trp53, leads to maximal dysregulated expression of Sox2. Using cancer cell lines of different origin and with different p53 status, we show here that manipulating TP53 to restore or decrease its activity results in repression or induction of SOX2, respectively. Mechanistically, we observed that the regulation of SOX2 expression by TP53 is transcriptional and identified Trp53 bound to the promoter region and the SRR2 enhancer of Sox2. Forcing high levels of SOX2 in cancer cells leads to morphological changes that molecularly correspond to the acquisition of a more mesenchymal phenotype correlating with an increased migratory capacity. Finally, the analysis of human breast cancer samples shows that this correlation between TP53 status, levels of expression of SOX2 and a more metastatic phenotype is also observed in cancer patients. Our results support the notion that lack of TP53 in tumor cells results in deregulated expression of developmental gene SOX2 with phenotypic consequences related with increased malignization. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=198 HEIGHT=200 SRC="FIGDIR/small/623640v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@15e8df8org.highwire.dtl.DTLVardef@baa5e5org.highwire.dtl.DTLVardef@1e181aaorg.highwire.dtl.DTLVardef@7c3f0_HPS_FORMAT_FIGEXP M_FIG C_FIG Novelty and ImpactOur work demonstrates that TP53 regulates transcriptionally SOX2 through binding to its promoter and the SRR2 enhancer. Increased expression of SOX2 promotes an EMT and increased migration. Breast cancer patients with genetic alteration of TP53 show increased levels of SOX2 and a more metastatic phenotype. This work is a key demonstration of an additional effect of genetic alterations of TP53, leading to de-repression of SOX2 and alteration of cancer cell plasticity with important phenotypic consequences.

cancer biology↗

Optimised in-solution enrichment of over a million ancient human SNPs

In-solution hybridisation enrichment of genetic markers is a method of choice in paleogenomic studies, where the DNA of interest is generally heavily fragmented and contaminated with environmental DNA, and where the retrieval of genetic data comparable between individuals is challenging. Here, we benchmarked the commercial "Twist Ancient DNA" reagent from Twist Biosciences using sequencing libraries from ancestrally diverse ancient human samples with low to high endogenous DNA content (0.1-44%). For each library, we tested one and two rounds of enrichment, and assessed performance compared to deep shotgun sequencing. We find that the "Twist Ancient DNA" assay provides robust enrichment of [~]1.2M target SNPs without introducing allelic bias that may interfere with downstream population genetics analyses. Additionally, we show that pooling up to 4 sequencing libraries and performing two rounds of enrichment is both reliable and cost-effective for libraries with less than 27% endogenous DNA content. Above 38% endogenous content, a maximum of one round of enrichment is recommended for cost-effectiveness and to preserve library complexity. In conclusion, we provide researchers in the field of human paleogenomics with a comprehensive understanding of the strengths and limitations of different sequencing and enrichment strategies, and our results offer practical guidance for optimising experimental protocols.

genomics↗

PCBP1 regulates alternative splicing of AARS2 in congenital cardiomyopathy

Alanyl-transfer RNA synthetase 2 (AARS2) is a nuclear encoded mitochondrial tRNA synthetase that is responsible for charging of tRNA-Ala with alanine during mitochondrial translation. Homozygous or compound heterozygous mutations in the Aars2 gene, including those affecting its splicing, are linked to infantile cardiomyopathy in humans. However, how Aars2 regulates heart development, and the underlying molecular mechanism of heart disease remains unknown. Here, we found that poly(rC) binding protein 1 (PCBP1) interacts with the Aars2 transcript to mediate its alternative splicing and is critical for the expression and function of Aars2. Cardiomyocyte-specific deletion of Pcbp1 in mice resulted in defects in heart development that are reminiscent of human congenital cardiac defects, including noncompaction cardiomyopathy and a disruption of the cardiomyocyte maturation trajectory. Loss of Pcbp1 led to an aberrant alternative splicing and a premature termination of Aars2 in cardiomyocytes. Additionally, Aars2 mutant mice with exon-16 skipping recapitulated heart developmental defects observed in Pcbp1 mutant mice. Mechanistically, we found dysregulated gene and protein expression of the oxidative phosphorylation pathway in both Pcbp1 and Aars2 mutant hearts; these date provide further evidence that the infantile hypertrophic cardiomyopathy associated with the disorder oxidative phosphorylation defect type 8 (COXPD8) is mediated by Aars2. Our study therefore identifies Pcbp1 and Aars2 as critical regulators of heart development and provides important molecular insights into the role of disruptions in metabolism on congenital heart defects.

developmental biology↗

Magnetic Resonance Fingerprinting based Thermometry (MRFT): application to ex vivo imaging near DBS leads

The purpose of this study is to demonstrate the first work of T1-based magnetic resonance thermometry using magnetic resonance fingerprinting (dubbed MRFT). We compared temperature estimation of MRFT with proton resonance frequency shift (PRFS) thermometry on ex vivo bovine muscle. We demonstrated MRFTs feasibility in predicting temperature on ex vivo bovine muscles with deep brain stimulation (DBS) lead. B0 maps generated from MRFT were compared with gold standard B0 maps near the DBS lead. All experiments were performed on a 3 Tesla whole-body GE Premier system equipped with a 21-channel receive head coil (GE Healthcare, Milwaukee, WI). Four fluoroptic probes were used to measure the temperature at the center of a cold muscle (probe 1), the room temperature water bottle (probe 2), and the center and periphery of the heated muscle (probes 3 and 4). We selected regions of interest (ROIs) around the location of the probes and used simple linear regression to generate the temperature sensitivity calibration equations that convert T1 maps and {Delta}s maps to temperature maps. We then repeated the same setup and compared MRFT, PRFS thermometry temperature estimation with gold standard probe measurements. For the MRFT experiment on DBS lead, we taped the probe to the tip of the DBS lead and used a turbo spin echo (TSE) sequence to induce heating near the lead. We selected ROIs around the tip of the lead to compare MRFT temperature estimation with probe measurements. Vendor-supplied B0 mapping sequence was acquired to compare with MRFT-generated B0 maps. We found strong linear relationships (R2>0.958) between T1 and temperature and {Delta}s and temperatures in our temperature sensitivity calibration experiment. MRFT and PRFS thermometry both accurately predict temperature (RMSE<1.55 {degrees}C) compared to probe measurements. MRFT estimated temperature near DBS lead has a similar trend as the probe temperature. Both B0 maps show inhomogeneities around the lead.

bioengineering↗

The boundaries of State-Space Granger Causality Analysis applied to BOLD simulated data: a comparative modelling and simulation approach

BackgroundThe analysis of connectivity has become a fundamental tool in human neuroscience. Granger Causality Mapping is a data-driven method that uses Granger Causality (GC) to assess the existence and direction of influence between signals, based on temporal precedence of information. More recently, a theory of Granger causality has been developed for state-space (SS-GC) processes, but little is known about its statistical validation and application on functional magnetic resonance imaging (fMRI) data. New MethodWe implemented a new heuristic, focusing on the application of SS-GC with a distinct statistical validation technique - Time Reversed Testing - to generative synthetic models and compare it to classical multivariate computational frameworks. We also test a range of experimental parameters, including block structure, sampling frequency, noise and system mean pairwise correlation, using a statistical framework of binary classification. ResultsWe found that SS-GC with time reversed testing outperforms other frameworks. The results validate the application of SS-GC to generative models. When estimating reliable causal relations, SS-GC returns promising results, especially when considering synthetic data with an high impact of noise and sampling rate. ConclusionsSS-GC with time reversed testing offers a possible framework for future analysis of fMRI data in the context of data-driven causality analysis. HighlightsO_LIState-Space GC was combined with a statistical validation step, using a Time Reversed Testing. C_LIO_LIThis novel heuristic overpowers classical GC, when applied to generative models. C_LIO_LICorrectly identified connections between variables increase with the increase of number of blocks and number of points per block. C_LIO_LISNR and subsampling have a significant impact on the results. C_LI

neuroscience↗

SUMOylation of rice DELLA SLR1 modulates transcriptional responses and improves yield under salt stress

DELLA proteins modulate GA signalling and are major regulators of plant plasticity to endure stress. DELLAs are mostly regulated at the post-translational level, and their activity relies on the interaction with upstream regulators and transcription factors (TFs). SUMOylation is a post-translational modification (PTM) capable of changing protein interaction and found to influence DELLA activity in Arabidopsis. We determined that SUMOylation of the single rice DELLA SLENDER RICE1 (SLR1) occurs in a lysine residue different from the one previously identified in Arabidopsis REPRESSOR OF GA (RGA). Remarkably, artificially increasing SUMOylated SLR1 (SUMO1SLR1) levels attenuated the penalty of salt stress on plant yield. Gene expression analysis revealed that the overexpression of SUMOylated SLR1 regulates key dioxygenases that modulate active GA levels, namely GA20ox2 and GA2ox3, which could partially explain the sustained productivity upon salt stress imposition. Besides, SLR1 SUMOylation blocked the interaction with the growth regulator YAB4, which may fine-tune GA20ox2 expression. Mechanistically, we propose that SLR1 SUMOylation disrupts the interaction with members of several transcription factor families to modulate gene expression. We found that SLR1 SUMOylation represents a novel mechanism modulating DELLA activity, which attenuates the impact of stress on plant performance. One sentence summaryRice plants show increased yield under salt stress when its gibberellin transcriptional regulator DELLA protein is artificially SUMOylated.

plant biology↗

Winter in water: Differential responses and the maintenance of biodiversity

The ecological consequences of winter in freshwater systems are an understudied but rapidly emerging research area. Here, we argue that winter periods of reduced temperature and light (and potentially oxygen and resources) could play an underappreciated role in mediating the coexistence of species. This may be especially true for temperate and subarctic lakes, where seasonal changes in the thermal environment might fundamentally structure species interactions. With climate change already shortening ice-covered periods on temperate and polar lakes, consideration of how winter conditions shape biotic interactions is urgently needed. Using freshwater fishes in northern temperate lakes as a case study, we demonstrate how physiological trait differences (e.g., thermal preference, light sensitivity) drive differential behavioral responses to winter among competing species. Specifically, some species have a higher capacity for winter activity than others. Existing and new theory is presented to argue that such differential responses to winter can promote species coexistence. Importantly, if winter is a driver of niche differences that weaken competition between relative to within species, then shrinking winter periods could threaten coexistence by tipping the scales in favor of certain sets of species over others.

ecology↗