Biology subjects

Szemes, T.

Publications and source records attributed to Szemes, T..

10 recordsLinked to original sources

bioRxiv2024

Novel insights into Emx2 and Dmrta2 cooperation during cortex development and evidence for Dmrta2 function in choroid plexus

Early dorsal telencephalon development is coordinated by an interplay of transcription factors that exhibit a graded expression pattern in neural progenitors. How they function together to orchestrate cortical development remains largely unknown. The Emx2 and Dmrta2 genes encode TFs that are expressed in a similar caudomedialhigh/ rostrolaterallowgradient in the ventricular zone of the developing dorsal telencephalon with, in the medial pallium, Dmrta2 but not Emx2 expressed in the developing choroid plexus. Their constitutive loss has been shown to impart similar cortical abnormalities, and their combined deletion exacerbates the phenotypes, suggesting possible cooperation during cortex development. In this study, we utilized molecular and genetic approaches to dissect how Emx2 functions with Dmrta2 during cortical development. Our results show that while they regulate a similar set of genes, their common direct targets are limited but include key regulators of cortical development. Identification of the interaction partners of Emx2 suggests that it coordinates with the LIM-domain binding protein Ldb1 to execute the activation and repression of some of its downstream targets. Finally, while Emx2 is known to suppress choroid plexus development, we also provide evidence that Dmrta2 is in contrast required for choroid plexus since in its absence in medial telencephalic progenitors, mice develop hydrocephalous postnatally, a phenotype that appears to be due to a compromised cytoarchitecture. Together, these data indicate that Emx2 and Dmrta2 have similar but also distinct functions in telencephalon development and provide the first insights into Emx2 mechanism of action. SIGNIFICANCE STATEMENTEmx2 and Dmrta2 encode transcription factors that generate similar phenotypes upon their loss in the developing cortex suggesting possible cooperation. Here we explored how Emx2 functions with Dmrta2 during cortical development. Results obtained indicate that Emx2 directly regulates with Dmrta2 only a few genes, some coding for key cortical determinants and that Emx2 utilizes the Ldb1 cofactor for the regulation of some of its targets. Results also suggest that, unlike Emx2 which suppresses choroid plexus development, Dmrta2 is required for choroid plexus as its loss in medial telencephalic progenitors leads to hydrocephalus. Together, our results reveal that Emx2 and Dmrta2 have similar but also distinct functions during telencephalon development and provide novel insights into the mechanism of action of Emx2.

neuroscience↗

bioRxiv2024

Evidence that Dmrta2 acts as a transcriptional repressor of Pax6 in murine cortical progenitors and identification of a mutation crucial for DNA recognition associated with microcephaly in human

Dmrta2 (also designated Dmrt5) is a transcriptional regulator expressed in cortical progenitors in a caudomedialhigh/rostrolaterallow gradient with important roles at different steps of cortical development. Dmrta2 has been suggested to act in cortex development mainly by differential suppression of Pax6 and other homeobox transcription factors such as the ventral telencephalic regulator Gsx2, which remains to be fully demonstrated. Here we have addressed the epistatic relation between Pax6 and Dmrta2 by comparing phenotypes in mutant embryos or embryos overexpressing both genes in various allelic combinations. We showed that Dmrta2 cooperates with Pax6 in the maintenance of cortical identity in dorsal telencephalic progenitors and that it acts as a transcriptional repressor of Pax6 to control cortical patterning. Mechanistically, we show that in P19 cells, Dmrta2 can act as a DNA-binding dependent repressor on the Pax6 E60 enhancer and that a point mutation that affects its DNA binding properties leads to agenesis of the corpus callosum, pachygyria, and the absence of the cingulate gyrus. Finally, we provide evidence that Dmrta2 binds to the Zfp423 zinc finger protein and that it enhances its ability to recruit the NurD repressor complex. Together, our results highlight the importance and conserved function of Dmrta2 in cortical development and provide novel insights into its mechanism of action. SIGNIFICANCE STATEMENTCorticogenesis is controlled by an array of transcription factors that coordinate neural progenitor self-renewal and differentiation to generate correct cortical cell number and diversity. However, how this complex array of transcription factors works in concert to regulate this delicate process remains largely unknown. Here we provide important insights into the mechanism of action of Dmrta2 by demonstrating that it cooperates with the transcription factor Pax6 to define the pallium-subpallium boundary and that it acts by repressing it, likely via the recruitment of Zfp423 and the NurD repressor complex, to control cortical patterning. Our data also reveal that a point mutation that affects its DNA binding causes cortical abnormalities in human, further highlighting its importance in cortex development.

neuroscience↗

bioRxiv2024

The temporal refinement of Dach1 is a key step in the functional maturation of primary somatosensory neurons

During somatosensory neurogenesis, neurons are born in an unspecialized transcriptional state, with several transcription factors following a broad-to-restricted expression dynamic as development proceeds, supporting neuron subtype identities. The relevance of this temporal refinement remains however unclear, these broad-to-restricted transcription factors being selectively involved in neurons in which they are ultimately maintained. Here we found that Dach1 encodes for a bona fide broad-to-restricted transcription factor retained and required in tactile somatosensory neurons. Within developing nociceptors, we demonstrate that Prdm12 contributes to Dach1 extinction. Using genetic approaches to prevent its temporal restriction during somatosensory development, we reveal that Dach1 refinement is a prerequisite for the appropriate transcriptional maturation of somatosensory subtypes from which it becomes ultimately excluded. These findings highlight the essential role played by Dach1 during somatosensory neuron development. They further demonstrate that the broad-to-restricted temporal pattern followed by several transcription factors is physiologically relevant to achieve appropriate transcriptional maturation of somatosensory neurons.

neuroscience↗

bioRxiv2022

Combination of Expert Guidelines-based and MachineLearning-based Approaches Leads to Superior Accuracy ofAutomated Prediction of Clinical Effect of Copy Number Variations

Clinical interpretation of copy number variants (CNVs) is a complex process that requires skilled clinical professionals. General recommendations have been recently released to guide the CNV interpretation based on predefined criteria to uniform the decision process. Several semiautomatic computational methods have been proposed to recommend appropriate choices, relieving the clinicians from the tedious search in vast genomic databases. We have developed and evaluated such a tool called MarCNV and tested it on CNV records collected from the ClinVar database. Alternatively, the emerging machine learning-based tools, such as the recently published ISV (Interpretation of Structural Variants), showed promising ways of even fully automated predictions using wider characterization of affected genomic elements. Such tools utilize features that are additional to ACMG criteria, thus, they have the potential to significantly improve and/or provide supportive evidence for accurate CNV classification. Since both approaches contribute to evaluation of CNVs clinical impact, we propose a combined solution in the form of a decision support tool based on automated ACMG guidelines (MarCNV) supplemented by a machine learning-based pathogenicity prediction (ISV) for classification of CNVs. We provide evidence that such a combined approach is able to reduce the number of uncertain classifications and reveal potentially incorrect classifications using automated guidelines. CNV interpretation using MarCNV, ISV, and combined approach is available for non-commercial use at https://predict.genovisio.com/.

bioinformatics↗

bioRxiv2020

Varlock: privacy preserving storage and dissemination of sequenced genomic data

IntroductionCurrent and future applications of genomic data may raise ethical and privacy concerns. Processing and storing these data introduces a risk of abuse by a potential adversary since a human genome contains sensitive personal information. For this reason, we developed a privacy preserving method, called Varlock, for secure storage of sequenced genomic data. Materials and methodsWe used a public set of population allele frequencies to mask personal alleles detected in genomic reads. Each personal allele described by the public set is masked by a randomly selected population allele with respect to its frequency. Masked alleles are preserved in an encrypted confidential file that can be shared, in whole or in part, using public-key cryptography. ResultsOur method masked personal variants and introduced new variants detected in a personal masked genome. Alternative alleles with lower population frequency were masked and introduced more often. We performed a joint PCA analysis of personal and masked VCFs, showing that the VCFs between the two groups can not be trivially mapped. Moreover, the method is reversible and personal alleles can be unmasked in specific genomic regions on demand. ConclusionOur method masks personal alleles within genomic reads while preserving valuable non-sensitive properties of sequenced DNA fragments for further research. Personal alleles may be restored in desired genomic regions and shared with patients, clinics, and researchers. We suggest that the method can provide an additional layer of security for storing and sharing the raw aligned reads.

bioinformatics↗

bioRxiv2020

Automated prediction of the clinical impact of structural copy number variations

Introduction: Copy number variants (CNVs) play an important role in many biological processes, including the development of genetic diseases, making them attractive targets for genetic analyses. The interpretation of the effect of structural variants is a challenging problem due to highly variable numbers of gene, regulatory or other genomic elements affected by the CNV. This led to the demand for the interpretation tools that would relieve researchers, laboratory diagnosticians, genetic counselors, and clinical geneticists from the laborious process of annotation and classification of CNVs. Materials and Methods: We designed a classifier method based on the annotations of CNVs from several publicly available databases. The attributes take into account gene elements, regulatory elements affected by the CNV, as well as other CNVs with known clinical significance that overlap the candidate CNV. We also describe the process of model selection and the construction of training, validation, and test set. Results: The presented approach achieved more than 98% prediction accuracy on both copy number loss and copy number gain variants and can be improved by imposing probability thresholds to eliminate low confidence predictions. Discussion: Method has shown considerable performance in predicting the clinical impact of CNVs and therefore has a great potential to guide users to more precise conclusions. The CNV annotation and pathogenicity prediction can be fully automated, relieving users of tedious interpretation processes. Availability and Implementation: The results can be reproduced by following instructions at {{https://github.com/tsladecek/isv}}.

bioinformatics↗

bioRxiv2020

PHERI - Phage Host Exploration tool.

Antibiotic resistance is becoming a common problem in medicine, food, and industry, with multi-resistant bacterial strains occurring in all world regions. One of the possible future solutions is the use of bacteriophages in therapy. Bacteriophages are the most abundant form of life in the biosphere, so we can highly likely purify a specific phage against each target bacterium. The identification and consistent characterization of individual phages was a common form of phage work and included determining bacteriophages host-specificity. With the advent of new modern sequencing methods, there was a problem with the detailed characterization of phages in the environment identified by metagenome analysis. The solution to this problem may be to use a bioinformatic approach in the form of prediction software capable of determining a bacterial host based on the phage whole-genome sequence. The result of our research is the machine learning algorithm based tool called PHERI. PHERI predicts suitable bacterial host genus for purification of individual viruses from different samples. Besides, it can identify and highlight protein sequences that are important for host selection. PHERI is available at https://hub.docker.com/repository/docker/andynet/pheri. The source code for the model training is available at https://github.com/andynet/pheri_preprocessing, and the source code for the tool is available at https://github.com/andynet/pheri.

bioinformatics↗

bioRxiv2019

Non-invasive prenatal testing by low coverage genomic sequencing: Detection limits of screened chromosomal microdeletions

ObjectiveTo study the detection limits of chromosomal microaberrations in non-invasive prenatal testing with aim for five target microdeletion syndromes, including DiGeorge, Prader-Willi/Angelman, 1p36, Cri-Du-Chat, and Wolf-Hirschhorn syndromes.\n\nMethodWe used known cases of pathogenic deletions from ISCA database to specifically define regions critical for the target syndromes. Our approach to detect microdeletions, from whole genome sequencing data, is based on sample normalization and read counting for individual bins. We performed both an in-silico study using artificially created data sets and a laboratory test on mixed DNA samples, with known microdeletions, to assess the sensitivity of prediction for varying fetal fractions, deletion lengths, and sequencing read counts.\n\nResultsThe in-silico study showed sensitivity of 79.3% for 10% fetal fraction with 20M read count, which further increased to 98.4% if we searched only for deletions longer than 3Mb. The test on laboratory-prepared mixed samples was in agreement with in-silico results, while we were able to correctly detect 24 out of 29 control samples.\n\nConclusionOur results suggest that it is possible to incorporate microaberration detection into basic NIPT as part of the offered screening/diagnostics procedure, however, accuracy and reliability depends on several specific factors.\n\nWhats already known about this topic?Microdeletion detection accuracy, similarly to most common trisomies detection, was found to be dependent mostly on technical and biological parameters of the test and tested samples, such as coverage of target region, fetal fraction, size and positions of the deletions.\n\nWhat does this study add?Estimation of relevant regions for five chosen microdeletion syndromes. Confirmation and improvement upon previous methods. Systematic evaluation of sensitivity of microdeletion detection with read counts from 10M to 20M.

bioinformatics↗

bioRxiv2018

Innovative method for reducing uninformative calls in non-invasive prenatal testing

MotivationNon-invasive prenatal testing or NIPT is currently among the top researched topic in obstetric care. While the performance of the current state-of-the-art NIPT solutions achieve high sensitivity and specificity, they still struggle with a considerable number of samples that cannot be concluded with certainty. Such uninformative results are often subject to repeated blood sampling and re-analysis, usually after two weeks, and this period may cause a stress to the future mothers as well as increase the overall cost of the test.\n\nResultsWe propose a supplementary method to traditional z-scores to reduce the number of such uninformative calls. The method is based on a novel analysis of the length profile of circulating cell free DNA which compares the change in such profiles when random-based and length-based elimination of some fragments is performed. The proposed method is not as accurate as the standard z-score; however, our results suggest that combination of these two independent methods correctly resolves a substantial portion of healthy samples with an uninformative result. Additionally, we discuss how the proposed method can be used to identify maternal aberrations, thus reducing the risk of false positive and false negative calls.\n\nAvailability and ImplementationA particular implementation of the proposed methods is not provided with the manuscript.\n\nContactCorrespondence regarding the manuscript should be directed at Frantisek Duris (fduris@dcs.fmph.uniba.sk).\n\nSupplementary InformationNo additional supplementary information is available.

bioinformatics↗

bioRxiv2018

Non-invasive prenatal testing as a valuable source of population specific allelic frequencies

Low-coverage massively parallel genome sequencing for non-invasive prenatal testing (NIPT) of common aneuploidies is one of the most rapidly adopted and relatively low-cost DNA tests. Since aggregation of reads from a large number of samples allows overcoming the problems of extremely low coverage of individual samples, we describe the possible re-use of the data generated during NIPT testing for genome scale population specific frequency determination of small DNA variants, requiring no additional costs except of those for the NIPT test itself. We applied our method to a data set comprising of 1,548 original NIPT test results and evaluated the findings on different levels, from in silico population frequency comparisons up to wet lab validation analyses using a gold-standard method. The revealed high reliability of variant calling and allelic frequency determinations suggest that these NIPT data could serve as valuable alternatives to large scale population studies even for smaller countries around the world.

genomics↗