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Shaw, P.

Publications and source records attributed to Shaw, P..

At least 19 recordsLinked to original sources

Identification and small molecule rescue of mitochondrial dysfunction phenotype which converges across Leigh Syndrome and Huntington's Disease patient fibroblasts.

Mitochondrial dysfunction is implicated in a variety of complex neurological disorders. Primary mitochondrial diseases are caused directly by mutations in genes encoding mitochondrial proteins, leading to mitochondrial dysfunction and disease. Mitochondrial dysfunction is also a key contributor to pathogenesis in multiple neurodegenerative diseases. Rescue of mitochondrial function is therefore an attractive therapeutic target in both groups of diseases. In this study, we used primary fibroblasts derived from patients with the primary mitochondrial disease Leigh syndrome (LS) and the neurodegenerative disease Huntingtons disease (HD) to investigate mitochondrial phenotypes in these patients. We used these to identify modifiable measures of mitochondrial phenotype using a high content imaging screen. Despite having distinct underlying disease causes, different mitochondrial phenotypes in LS and HD patient derived cells converged on an imbalance between functional and dysfunctional mitochondria. Through multi-parameter screening of the mitochondrial phenotype we identified the AMPK activator A769662 as a small molecule able to rescue this imbalance in both LS and HD patient derived fibroblasts via different pathways. Our findings indicate that high throughput screening for mitochondrial phenotypes could identify novel therapeutic agents to rescue mitochondrial dysfunction in complex neurological disorders. Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSMitochondrial dysfunction is the primary driver of mitochondrial disease and key contributing factor to neurodegenerative disease pathogenesis. Rescuing mitochondrial function is a promising therapeutic strategy, yet strategies to identify mitochondrial modulators in patient cells are limited. Added value of this studyOur in-depth mitochondrial characterisation of Leigh syndrome and Huntingtons disease patient fibroblasts shows the potential for using this methodology to identify mitochondrial therapeutics. We identify a mitochondrial phenotype common across diseases and an AMPK activator capable of rescuing this phenotype. Implications of all the available evidenceOur work extends our understanding of the mitochondrial dysfunction associated with Leigh syndrome and Huntingtons disease and expands the tool set available for identifying modulators of mitochondrial health as potential therapeutics for complex neurological disorders.

neuroscience↗

Cystathionine Beta-Synthase Promotes Anoikis Resistance and Transcoelomic Metastasis in Ovarian Cancer via the SP1-ITGB1 axis

Anoikis resistance is crucial for ovarian cancer (OvCa) transcoelomic metastasis, during which exfoliated OvCa cells survive as spheroids before invading the omentum. Here, we demonstrate that cystathionine {beta}-synthase (CBS), an H2S-producing transsulfuration pathway enzyme, is a key determinant of OvCa spheroidal viability and metastatic potential. Analysis of publicly available patient datasets, as well as an in-house tissue microarray, revealed that high CBS expression positively correlates with both poor progression-free survival and clinically observed peritoneal/omental metastasis. Integrated functional and proteomic analyses indicated that CBS silencing induces apoptosis in 2D monolayers. Consistent with this, CBS silencing in spheroids caused apoptosis and disrupted spheroid architecture. Mechanistically, this phenotype was associated with downregulation of oncogenic stemness and epithelial-mesenchymal transition. Further, through proteomic and bioinformatic analyses, we identified ITGB1 to be the hub protein in OvCa spheroidogenesis. Interestingly, knockdown of CBS led to abrogation of the ITGB1-mediated downstream pathway. Moreover, by proteomic and network analyses, we identified SP1 as a key transcriptional regulator of CBS-induced pro-spheroidal transcriptional programs of stemness and invasiveness. Stabilization of SP1 through persulfidation by H2S supplementation restored spheroidal viability and underlying protein signaling. Further, our results reveal that loss of CBS, through ITGB1 repression, disrupts spheroid architecture, leading to reduced metastatic docking on the murine omental surface in vivo. Collectively, these findings identify CBS as a central regulator of anoikis resistance and OvCa transcoelomic metastasis, highlighting the therapeutic potential of targeting CBS-dependent SP1-ITGB1 regulation to control metastatic spread.

cancer biology↗

C9orf72-ALS mutation drives mitophagy impairments in iNeurons

IntroductionALS is a neurodegenerative disorder characterised by progressive upper and lower motor neuron loss. A GGGGCC hexanucleotide repeat expansion (HRE) in the C9orf72 gene is the most common mutation found in populations of European descent. Mitochondrial dysfunction has been observed in C9orf72-ALS patients and models of the disease, however reports on mitochondrial clearance via mitophagy in C9orf72-ALS are limited. ResultsiNeurons from C9orf72-ALS patients displayed reduced mitochondrial membrane potential and reduced mitophagy, due to reductions in autophagosome production and reduced ULK1 recruitment to mitochondria. No consistent changes to PINK1/Parkin or BNIP3 mitophagy pathways were observed. ConclusionsOur data show that mitochondrial function is impaired in C9orf72-ALS patient iNeurons. An in-depth characterisation of mitophagy suggests that a deficit in autophagosome production is responsible and provides further evidence that toxic gain-of-function mechanisms in C9orf72-ALS are responsible for autophagy deficits.

neuroscience↗

Sex-specific DNA methylation differences in Amyotrophic lateral sclerosis

Sex is an important covariate in all genetic and epigenetic research due to its role in the incidence, progression and outcome of many phenotypic characteristics and human diseases. Amyotrophic lateral sclerosis (ALS) is a motor neuron disease with a sex bias towards higher incidence in males. Here, we report for the first time a blood-based epigenome-wide association study meta-analysis in 9274 individuals after stringent quality control (5529 males and 3975 females). We identified a total of 226 ALS saDMPs (sex-associated DMPs) annotated to a total of 159 unique genes. These ALS saDMPs were depleted at transposable elements yet significantly enriched at enhancers and slightly enriched at 3UTRs. These ALS saDMPs were enriched for transcription factor motifs such as ESR1 and REST. Moreover, we identified an additional 10 genes associated with ALS saDMPs through chromatin loop interactions, suggesting a potential regulatory role for these saDMPs on distant genes. Furthermore, we investigated the relationship between DNA methylation at specific CpG sites and overall survival in ALS using Cox proportional hazards models. We identified two ALS saDMPs, cg14380013 and cg06729676, that showed significant associations with survival. Overall, our study reports a reliable catalogue of sex-associated ALS saDMPs in ALS and elucidates several characteristics of these sites using a large-scale dataset. This resource will benefit future studies aiming to investigate the role of sex in the incidence, progression and risk for ALS.

genomics↗

predicTTE: An accessible and optimal tool for time-to-event prediction in neurological diseases

Time-to-event prediction is a key task for biological discovery, experimental medicine, and clinical care. This is particularly true for neurological diseases where development of reliable biomarkers is often limited by difficulty visualising and sampling relevant cell and molecular pathobiology. To date, much work has relied on Cox regression because of ease-of-use, despite evidence that this model includes incorrect assumptions. We have implemented a set of deep learning and spline models for time-to-event modelling within a fully customizable app and accompanying online portal, both of which can be used for any time-to-event analysis in any disease by a non-expert user. Our online portal includes capacity for end-users including patients, Neurology clinicians, and researchers, to access and perform predictions using a trained model, and to contribute new data for model improvement, all within a data-secure environment. We demonstrate a pipeline for use of our app with three use-cases including imputation of missing data, hyperparameter tuning, model training and independent validation. We show that predictions are optimal for use in downstream applications such as genetic discovery, biomarker interpretation, and personalised choice of medication. We demonstrate the efficiency of an ensemble configuration, including focused training of a deep learning model. We have optimised a pipeline for imputation of missing data in combination with time-to-event prediction models. Overall, we provide a powerful and accessible tool to develop, access and share time-to-event prediction models; all software and tutorials are available at www.predictte.org.

neuroscience↗

ProtEx: A Retrieval-Augmented Approach for Protein Function Prediction

Mapping a protein sequence to its underlying biological function is a critical problem of increasing importance in biology. In this work, we propose ProtEx, a retrieval-augmented approach for protein function prediction that leverages exemplars from a database to improve accuracy and robustness and enable generalization to unseen classes. Our approach relies on a novel multi-sequence pretraining task, and a fine-tuning strategy that effectively conditions predictions on retrieved exemplars. Our method achieves state-of-the-art results across multiple datasets and settings for predicting Enzyme Commission (EC) numbers, Gene Ontology (GO) terms, and Pfam families. Our ablations and analysis highlight the impact of conditioning predictions on exemplar sequences, especially for classes and sequences less well represented in the training data.

bioinformatics↗

Maximising the translational potential of neurophysiology in amyotrophic lateral sclerosis: a study on compound muscle action potentials

Transgenic mouse models of amyotrophic lateral sclerosis, such as the widely used SOD1G93A mouse, enable investigation of disease mechanisms and testing of novel therapeutic interventions. However, treatments that have been considered successful in mice have often failed to translate into human benefit in clinical trials, particularly when relying on the so-called survival read-out. Compound muscle action potentials (CMAPs), are a simple neurophysiological test that measures the summation of muscle fibre depolarisation in response to maximal stimulation of the innervating nerve. CMAPs can be measured in both mice and humans and decline with motor axon loss in ALS, making them a potential translational read-out of disease progression which could help bridge the preclinical and clinical divide. Herein we assess the translational potential of CMAPs and ascertain at what time points human and mouse data aligned most closely. We extracted data from 18 human studies and compared with results generated from SOD1G93A and control mice at different ages across different muscles. We found that the relative CMAP amplitude difference between SOD1G93A and control mice in tibialis anterior and gastrocnemius muscles at 70 days of age was most similar to the relative difference between baseline ALS patient CMAP measurements and healthy controls in the abductor pollicis brevis (APB) muscle. We also found that the relative decline in SOD1G93A tibialis anterior CMAP amplitude between 70-140 days was similar to that observed in 12 month human longitudinal studies in APB. Our findings suggest CMAP amplitudes can provide a translational window, from which to make comparisons between the SOD1G93A model and human ALS patients. CMAPs are easy to perform and can help determine the most clinically relevant starting/end points for preclinical studies and provide a basis for predicting potential clinical effect sizes.

neuroscience↗

Experimentally induced active and quiet sleep engage non-overlapping transcriptomes in Drosophila

Sleep in mammals can be broadly classified into two different physiological categories: rapid eye movement (REM) sleep and slow wave sleep (SWS), and accordingly REM and SWS are thought to achieve a different set of functions. The fruit fly Drosophila melanogaster is increasingly being used as a model to understand sleep functions, although it remains unclear if the fly brain also engages in different kinds of sleep as well. Here, we compare two commonly used approaches for studying sleep experimentally in Drosophila: optogenetic activation of sleep-promoting neurons and provision of a sleep-promoting drug, Gaboxadol. We find that these different sleep-induction methods have similar effects on increasing sleep duration, but divergent effects on brain activity. Transcriptomic analysis reveals that drug-induced deep sleep ( quiet sleep) mostly downregulates metabolism genes, whereas optogenetic active sleep upregulates a wide range of genes relevant to normal waking functions. This suggests that optogenetics and pharmacological induction of sleep in Drosophila promote different features of sleep, which engage different sets of genes to achieve their respective functions.

neuroscience↗

Molecular dynamics analysis of Superoxide Dismutase 1 mutations suggests decoupling between mechanisms underlying ALS onset and progression

Mutations in the superoxide dismutase 1 (SOD1) gene are the second most common known cause of ALS. SOD1 variants express high phenotypic variability and over 200 have been reported in people with ALS. Investigating how different SOD1 variants affect the protein dynamics might help in understanding their pathogenic mechanism and explaining their heterogeneous clinical presentation. It was previously proposed that variants can be broadly classified in two groups, wild-type like (WTL) and metal binding region (MBR) variants, based on their structural location and biophysical properties. MBR variants are associated with a loss of SOD1 enzymatic activity. In this study we used molecular dynamics and large clinical datasets to characterise the differences in the structural and dynamic behaviour of WTL and MBR variants with respect to the wild-type SOD1, and how such differences influence the ALS clinical phenotype. Our study identified marked structural differences, some of which are observed in both variant groups, while others are group specific. Moreover, applying graph theory to a network representation of the proteins, we identified differences in the intramolecular contacts of the two classes of variants. Finally, collecting clinical data of approximately 500 SOD1 ALS patients carrying variants from both classes, we showed that the survival time of patients carrying an MBR variant is generally longer (~6 years median difference, p < 0.001) with respect to patients with a WTL variant. In conclusion, our study highlights key differences in the dynamic behaviour of the WTL and MBR SOD1 variants, and wild-type SOD1 at an atomic and molecular level. We identified interesting structural features that could be further investigated to explain the associated phenotypic variability. Our results support the hypothesis of a decoupling between mechanisms of onset and progression of SOD1 ALS, and an involvement of loss-of-function of SOD1 with the disease progression.

neuroscience↗

Arsenic induced alteration of neuroregulatory gene expression in Macrobrachium lamarrei: a neurotoxicological approach to grooming behaviour

Arsenic is a highly active neuromodulator which can induce neurological disorders in invertebrates. The present study is a neurotoxicological approach to assess the toxicity of arsenic trioxide, where grooming behaviour is considered as a behavioural biomarker of arsenic induced stress in the prawns. Non-lethal exposure to arsenic trioxide, manipulates the expression pattern of neuroregulatory marker genes in a freshwater prawn, Macrobrachium lamarrei and induces symptoms of autism spectrum disorders (ASDs) in a short time.

pharmacology and toxicology↗

MinSNPs: an R package for derivation of resolution-optimised SNP sets from microbial genomic data

2.Here we present the R package - MinSNPs. This is designed to assemble resolution optimised sets of single nucleotide polymorphisms (SNPs) from alignments such as genome wide orthologous SNP matrices. We also demonstrate a pipeline for assembling such matrices from multiple bio-projects, so as to facilitate SNP set derivation from globally representative data sets. MinSNPs can derive sets of SNPs optimised for discriminating any user-defined combination of sequences from all others. Alternatively, SNP sets may be optimised to discriminate all from all, i.e., to maximise diversity. MinSNPs encompasses functions that facilitate rapid and flexible SNP mining, and clear and comprehensive presentation of the results. The MinSNPs running time scales in a linear fashion with input data volume, and the numbers of SNPs and SNPs sets specified in the output. MinSNPs was tested using a previously reported orthologous SNP matrix of Staphylococcus aureus. and an orthologous SNP matrix of 3,279 genomes with 164,335 SNPs assembled from four S. aureus short read genomic data sets. MinSNPs demonstrated efficacy in deriving discriminatory SNP sets for potential surveillance targets and in identifying SNP sets optimised to discriminate isolates from different clonal complexes (CC). MinSNPs was also tested with a large Plasmodium vivax orthologous SNP matrix. A set of five SNPs was derived that reliably indicated the country of origin within 3 south-east Asian countries. In summary, we report the capacity to assemble comprehensive SNP matrices that effectively capture microbial genomic diversity, and to rapidly and flexibly mine these entities for optimised surveillance marker sets. 3. Impact statementWe present the R package "MinSNPs". This derives resolution optimised SNP sets from datasets of genome sequence variation. Such SNP sets can underpin targeted genetic analysis for high throughput surveillance of microbial variants of public health concern. MinSNPs supports considerable flexibility in search methods. The package allows non-specialist bioinformaticians to easily and quickly convert global scale data of intra-specific genomic variation into SNP sets precisely and efficiently directed towards many microbial genetic analysis tasks. 4. Data summaryO_LIThe source code for minSNPs is available from GitHub under MIT Licence (URLs - https://github.com/ludwigHoon/minSNPs and mirrored in https://cran.r-project.org/package=minSNPs) C_LIO_LIStaphylococcus aureus (STARRS data set) Orthologous SNP Matrix; (URL - https://doi.org/10.1371/journal.pone.0245790.s005) C_LIO_LIPlasmodium vivax data set (VCF file); (URL - https://www.malariagen.net/resource/24) C_LIO_LIStaphylococcus aureus short read sequences (fastq) from bioprojects: PRJEB40888 (or STARRS)(https://www.ncbi.nlm.nih.gov/bioproject/PRJEB40888), PRJEB3174 (https://www.ncbi.nlm.nih.gov/bioproject/PRJEB3174), PRJEB32286 (https://www.ncbi.nlm.nih.gov/bioproject/PRJEB32286), and PRJNA400143 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA400143) C_LI

bioinformatics↗

The contribution of Neanderthal introgression and natural selection to neurodegenerative diseases

Humans are thought to be more susceptible to neurodegeneration than equivalently-aged primates. It is not known whether this vulnerability is specific to anatomically-modern humans or shared with other hominids. The contribution of introgressed Neanderthal DNA to neurodegenerative disorders remains uncertain. It is also unclear how common variants associated with neurodegenerative disease risk are maintained by natural selection in the population despite their deleterious effects. In this study, we aimed to quantify the genome-wide contribution of Neanderthal introgression and positive selection to the heritability of complex neurodegenerative disorders to address these questions. We used stratified-linkage disequilibrium score regression to investigate the relationship between five SNP-based signatures of natural selection, reflecting different timepoints of evolution, and genome-wide associated variants of the three most prevalent neurodegenerative disorders: Alzheimers disease, amyotrophic lateral sclerosis and Parkinsons disease. We found no evidence for enrichment of positively-selected SNPs in the heritability of Alzheimers disease, amyotrophic lateral sclerosis and Parkinsons disease,, suggesting that common deleterious disease variants are unlikely to be maintained by positive selection. There was no enrichment of Neanderthal introgression in the SNP-heritability of these disorders, suggesting that Neanderthal admixture is unlikely to have contributed to disease risk. These findings provide insight into the origins of neurodegenerative disorders within the evolution of Homo sapiens and addresses a long-standing debate, showing that Neanderthal admixture is unlikely to have contributed to common genetic risk of neurodegeneration in anatomically-modern humans.

neuroscience↗

Low expression of EXOSC2 protects against clinical COVID-19 and impedes SARS-CoV-2 replication

New therapeutic targets are a valuable resource in the struggle to reduce the morbidity and mortality associated with the COVID-19 pandemic, caused by the SARS-CoV-2 virus. Genome-wide association studies (GWAS) have identified risk loci, but some loci are associated with co-morbidities and are not specific to host-virus interactions. Here, we identify and experimentally validate a link between reduced expression of EXOSC2 and reduced SARS-CoV-2 replication. EXOSC2 was one of 332 host proteins examined, all of which interact directly with SARS-CoV-2 proteins; EXOSC2 interacts with Nsp8 which forms part of the viral RNA polymerase. Lung-specific eQTLs were identified from GTEx (v7) for each of the 332 host proteins. Aggregating COVID-19 GWAS statistics for gene-specific eQTLs revealed an association between increased expression of EXOSC2 and higher risk of clinical COVID-19 which survived stringent multiple testing correction. EXOSC2 is a component of the RNA exosome and indeed, LC-MS/MS analysis of protein pulldowns demonstrated an interaction between the SARS-CoV-2 RNA polymerase and the majority of human RNA exosome components. CRISPR/Cas9 introduction of nonsense mutations within EXOSC2 in Calu-3 cells reduced EXOSC2 protein expression, impeded SARS-CoV-2 replication and upregulated oligoadenylate synthase (OAS) genes, which have been linked to a successful immune response against SARS-CoV-2. Reduced EXOSC2 expression did not reduce cellular viability. OAS gene expression changes occurred independent of infection and in the absence of significant upregulation of other interferon-stimulated genes (ISGs). Targeted depletion or functional inhibition of EXOSC2 may be a safe and effective strategy to protect at-risk individuals against clinical COVID-19.

genetics↗

Sonic Hedgehog Pathway Modulation Normalizes Expression of Olig2 in Rostrally Patterned NPCs with Trisomy 21

The intellectual disability found in people with Down syndrome (DS) is associated with a decrease in white matter in the central nervous system. To study the mechanism of this myelination deficit, we differentiated two isogenic lines of induced pluripotent stem cells (iPSCs) derived from people with DS into brain-like and spinal cord-like neural progenitor cells (NPCs) and promoted a transition towards oligodendroglial fate by activating the Sonic hedgehog (SHH) pathway. In the spinal cord-like trisomic cells, we found no difference in expression of OLIG2 or NKX2.2, two transcription factors essential for commitment to the oligodendrocyte (OL) lineage. However, in the brain-like trisomic NPCs, OLIG2 is significantly upregulated and is associated with reduced expression of NKX2.2. We found that this gene dysregulation and block in NPC transition can be normalized by increasing the concentration of a SHH pathway agonist (SAG) during differentiation. These results underscore the importance of regional and cell type differences in gene expression in DS and demonstrate that modulation of SHH signaling in trisomic cells can rescue an early perturbed step in neural lineage specification in DS.

neuroscience↗

Sleep-drive reprograms clock neuronal identity through CREB-binding protein induced PDFR expression

Neuronal circuits can be re-modeled by Hebbian plasticity, synaptic scaling and, under some circumstances, activity-dependent respecification of cell-surface receptors. Although the impact of sleep on Hebbian plasticity and synaptic scaling are well studied, sleeps role in receptor respecification remains unclear. We demonstrate that high sleep-pressure quickly reprograms the Drosophila wake-promoting large-ventrolateral clock-neurons to express the Pigment Dispersing Factor receptor. The addition of this signaling input into the circuit is associated with increased waking and early mating success. The respecification of Pigment Dispersing Factor receptor in both young and adult large ventrolateral neurons requires two dopamine receptors and activation of the transcriptional regulator nejire (CREB-binding protein). These data identify receptor-respecification as an important mechanism to sculpt circuit function to match sleep levels with demand.

cell biology↗

Dmc1 is a candidate for temperature tolerance during wheat meiosis

We have assessed the effects of high and low temperatures on meiotic chromosome synapsis and crossover formation in the hexaploid wheat (Triticum aestivum L.) variety Chinese Spring. At low temperatures, asynapsis and chromosome univalence have been observed before in Chinese Spring lines lacking the long arm of chromosome 5D (5DL), which led to the proposal that 5DL carries a gene (Ltp1) that stabilises wheat chromosome pairing at low temperatures. In the current study, Chinese Spring wild type and 5DL interstitial deletion mutant plants were exposed to low (13{degrees}C) or high (30{degrees}C) temperatures in controlled environment rooms during a period from premeiotic interphase to early meiosis I. A 5DL deletion mutant was identified whose meiotic chromosomes exhibit extremely high levels of asynapsis and chromosome univalence at metaphase I after seven days at 13{degrees}C. This suggests that the mutant, which we name ttmei1 (temperature tolerance in meiosis 1) has a deletion of a gene that, like Ltp1, normally stabilises chromosome pairing at low temperatures. Immunolocalisation of the meiotic proteins ASY1 and ZYP1 on ttmei1 mutants showed that low temperature results in a failure to complete synapsis at pachytene. After 24 hours at 30{degrees}C, ttmei1 mutants exhibited a reduced number of crossovers and increased univalence, but to a lesser extent than at 13{degrees}C. KASP genotyping revealed that ttmei1 has a 4 Mb deletion in 5DL. Of 41 genes within this deletion region, the strongest candidate for the stabilisation of chromosome pairing at low (and possibly high) temperatures is the meiotic recombination gene Dmc1.\n\nKey messageThe meiotic recombination gene Dmc1 on wheat chromosome 5D has been identified as a candidate for the maintenance of normal chromosome synapsis and crossover at low and possibly high temperatures.

plant biology↗

A co-expression network in hexaploid wheat reveals mostly balanced expression and lack of significant gene loss of homeologous meiotic genes upon polyploidization

Polyploidization has played an important role in plant evolution. However, upon polyploidization the process of meiosis must adapt to ensure the proper segregation of increased numbers of chromosomes to produce balanced gametes. It has been suggested that meiotic gene (MG) duplicates return to a single copy following whole genome duplication to stabilise the polyploid genome. Therefore, upon the polyploidization of wheat, a hexaploid species with three related (homeologous) genomes, the stabilization process may have involved rapid changes in content and expression of MGs on homeologous chromosomes (homeologs). To examine this hypothesis, sets of candidate MGs were identified in wheat using co-expression network analysis and orthology informed approaches. In total, 130 RNA-Seq samples from a range of tissues including wheat meiotic anthers were used to define co-expressed modules of genes. Three modules were significantly correlated with meiotic tissue samples but not with other tissue types. These modules were enriched for GO terms related to cell cycle, DNA replication and chromatin modification, and contained orthologs of known MGs. Overall 74.4 % of genes within these meiosis-related modules had three homeologous copies which was similar to other tissue-related modules. Amongst wheat MGs identified by orthology, rather than co-expression, the majority (93.7 %) were either retained in hexaploid wheat at the same number of copies (78.4 %) or increased in copy number (15.3%) compared to ancestral wheat species. Furthermore, genes within meiosis-related modules showed more balanced expression levels between homeologs than genes in non-meiosis-related modules. Taken together our results do not support extensive gene loss nor changes in homeolog expression of MGs upon wheat polyploidization. The construction of the MG co-expression network allowed identification of hub genes and provided key targets for future studies.\n\nAuthor summaryAll flowering plants have undergone a polyploidization event(s) during their evolutionary history. One of the biggest challenges faced by a newly-formed polyploid is meiosis, an essential event for sexual reproduction and fertility. This process must adapt to discriminate between multiple related chromosomes and to ensure their proper segregation to produce fertile gametes. The meiotic mechanisms responsible for the stabilisation of the extant polyploids remain poorly understood except in wheat, where there is now a better understanding of these processes. It has been proposed that meiotic adaptation in established polyploids could involve meiotic gene loss following the event of polyploidization. To test this hypothesis in hexaploid wheat, we have computationally predicted sets of hexaploid wheat meiotic genes based on expression data from different tissue types, including meiotic anther tissue, and orthology informed approaches. We have calculated homeolog expression patterns and number of gene copies for the predicted meiotic genes and compared them with proper control gene sets. Our findings did not support any significant meiotic gene loss upon wheat polyploidization. Furthermore, wheat meiotic genes showed more balanced expression levels between homeologs than non-meiotic genes.

bioinformatics↗

C/EBPδ demonstrates dichotomous tumor initiation and promotion in high grade serous ovarian carcinogenesis

C/EBP{delta} (CEBPD), a gene part of the highly conserved basic-leucine zipper (b-ZIP) domain of transcriptional factors, is downregulated in 65% of high grade serous carcinoma of the ovary (HGSC). Overexpression of C/EBP{delta} in different tumors as glioblastoma and breast cancer either promotes tumor progression or inhibits growth. Despite these contradictory roles in different cancer types, we show that C/EBP{delta} overexpression has a consistent function of downregulating proliferation and promoting migration in fallopian tube epithelial cells (FTE). We show that the FTE have both mesenchymal and epithelial cell characteristics. Further, our data supports a role for C/EBP{delta} as an early regulatory transcriptional factor that promotes a mesenchymal to epithelial (MET) phenotype by upregulating E-cadherin and downregulating vimentin and N-cadherin in FTE cells. We demonstrate that overexpression of C/EBP{delta} in ovarian and breast cancer cell lines have consistent effects and phenotype as the FTE cells. Our findings suggest a role for C/EBP{delta} in the early events of ovarian serous carcinogenesis which may be used to help further understand how the disease develops from a premalignant cells.

cancer biology↗