Biology subjects

Meyer, D.

Publications and source records attributed to Meyer, D..

31 records · Page 2Linked to original sources

bioRxiv2021

Natural variation in gene expression and Zika virus susceptibility revealed by villages of neural progenitor cells

Variation in the human genome contributes to abundant diversity in human traits and vulnerabilities, but the underlying molecular and cellular mechanisms are not yet known, and will need scalable approaches to accelerate their recognition. Here, we advanced and applied an experimental platform that analyzes genetic, molecular, and phenotypic heterogeneity across cells from very many human donors cultured in a single, shared in vitro environment, with algorithms (Dropulation and Census-seq) for assigning phenotypes to individual donors. We used natural genetic variation and synthetic (CRISPR-Cas9) genetic perturbations to analyze the vulnerability of neural progenitor cells to infection with Zika virus. These analyses identified a common variant in the antiviral IFITM3 gene that regulated IFITM3 expression and explained most inter-individual variation in NPCs susceptibility to Zika virus infectivity. These and other approaches could provide scalable ways to recognize the impact of genes and genetic variation on cellular phenotypes. HIGHLIGHTSO_LIMeasuring cellular phenotypes in iPSCs and hPSC-derived NPCs from many donors C_LIO_LIEffects of donor sex, cell source, genetic and other variables on hPSC RNA expression C_LIO_LINatural genetic variation and synthetic perturbation screens both identify IFITM3 in NPC susceptibility to Zika virus C_LIO_LIA common genetic variant in IFITM3 explains most inter-individual variation in NPC susceptibility to Zika virus C_LI

genomics↗

bioRxiv2021

Population structure in the MHC region

In his 1972 "The apportionment of human diversity", Lewontin showed that, when averaged over loci, genetic diversity is predominantly attributable to differences among individuals within populations. However, selection on specific genes and genomic regions can alter the apportionment of diversity. We examine genetic diversity at the HLA loci, located within the MHC region. HLA genes code for proteins that are critical to adaptive immunity and are well-documented targets of balancing selection. The SNPs within HLA genes show strong signatures of balancing selection on large timescales and are broadly shared among populations, with low FST values. However, when we analyze haplotypes defined by these SNPs (i.e., which define "HLA alleles"), we find marked differences in frequencies between geographic regions. These differences are not reflected in the FST values because of the extreme polymorphism at HLA loci, illustrating challenges in interpreting FST. Differences in the frequency of HLA alleles among geographic regions are relevant to bone-marrow transplantation, which requires genetic identity at HLA loci between patient and donor. We explore the case of Brazils bone-marrow registry, where a deficit of enrolled volunteers with African ancestry reduces the chance of finding donors for individuals with an MHC region of African ancestry.

genetics↗

bioRxiv2021

Effectiveness of the protected areas on the Mornington Peninsula for the common resident shorebird species using citizen science data

In the absence of comprehensive survey data this study used citizen science bird counts, extracted from the Atlas of Living Australia, to assess which species benefit most from protected areas. This was done by fitting temporal models using the Integrated Laplace Approximation (INLA) method. The trends for five resident shorebird species were compared to the Australian Pied Oystercatcher, with significantly steeper upward trends identified for the Black-fronted Dotterel, Red-capped Dotterel and Red-kneed Dotterel. Steeper upward trends were observed in protected than unprotected areas for the Black-fronted Dotterel, Masked Lapwing and Red-kneed Dotterel. This work suggests that, with some limitations, statistical models can be used with citizen science data for monitoring the persistence of resident shorebirds and for investigating factors that are impacting these data. The results for the Dotterel species in protected areas are particularly encouraging.

ecology↗

bioRxiv2021

Single-nucleus sequencing reveals enriched expression of genetic risk factors sensitises Motor Neurons to degeneration in ALS

Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disorder characterised by a progressive loss of motor function. The eponymous spinal sclerosis observed at autopsy is the result of the degeneration of extratelencephalic neurons, Betz cells (ETNs, Cortico-Spinal Motor Neuron). It remains unclear why this neuronal subtype is selectively affected. To understand the unique molecular properties that sensitise these cells to ALS, we performed RNA sequencing of 79,169 single nuclei from cortices of patients and controls. In unaffected individuals, we found that expression of ALS risk genes was significantly enriched in THY1+-ETNs and not in other cell types. In patients, these genetic risk factors, as well as genes involved in protein homeostasis and stress responses, were significantly induced in a wide collection of ETNs, but not in neurons with more superficial identities. Examination of oligodendroglial and microglial nuclei revealed patient-specific changes that were at least in part a response to alterations in neurons: downregulation of myelinating genes in oligodendrocytes and upregulation of a reactive state connected to endo-lysosomal pathways in microglia. Our findings suggest that the selective vulnerability of extratelencephalic neurons is partly connected to their intrinsic molecular properties sensitising them to genetics and mechanisms of degeneration. Graphical abstract and working model O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/452054v2_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@11237fdorg.highwire.dtl.DTLVardef@119f3ceorg.highwire.dtl.DTLVardef@d56c69org.highwire.dtl.DTLVardef@1c087e1_HPS_FORMAT_FIGEXP M_FIG Our study highlights cell type specific changes in premotor/motor cortex of sporadic ALS patients. Specifically, we identify upregulation of synaptic molecules in excitatory neurons of upper cortical layers, interestingly correlating to hyperexcitability phenotypes seen in patients. Moreover, excitatory neurons of the deeper layers of the cortex, that project to the spinal cord and are most affected by the disease, show higher levels of cellular stresses than other neuronal types. Correspondently, oligodendrocytes transition from a highly myelinating state to a more neuronally engaged state, probably to counteract stressed phenotypes seen in excitatory neurons. At the same time, microglia show a reactive state with specific upregulation of endo-lysosomal pathways. C_FIG

neuroscience↗

bioRxiv2020

Whole-genome sequencing of 1,171 elderly admixed individuals from the largest Latin American metropolis (Sao Paulo, Brazil)

As whole-genome sequencing (WGS) becomes the gold standard tool for studying population genomics and medical applications, data on diverse non-European and admixed individuals are still scarce. Here, we present a high-coverage WGS dataset of 1,171 highly admixed elderly Brazilians from a census-based cohort, providing over 76 million variants, of which ~2 million are absent from large public databases. WGS enabled identifying ~2,000 novel mobile element insertions, nearly 5Mb of genomic segments absent from human genome reference, and over 140 novel alleles from HLA genes. We reclassified and curated nearly four hundred variant's pathogenicity assertions in genes associated with dominantly inherited Mendelian disorders and calculated the incidence for selected recessive disorders, demonstrating the clinical usefulness of the present study. Finally, we observed that whole-genome and HLA imputation could be significantly improved compared to available datasets since rare variation represents the largest proportion of input from WGS. These results demonstrate that even smaller sample sizes of underrepresented populations bring relevant data for genomic studies, especially when exploring analyses allowed only by WGS.

genomics↗

bioRxiv2020

Mapping genetic effects on cellular phenotypes with "cell villages"

Tens of thousands of genetic variants shape human phenotypes, mostly by unknown cellular mechanisms. Here we describe Census-seq, a way to measure cellular phenotypes in cells from many people simultaneously. Analogous to pooled CRISPR screens but for natural variation, Census-seq associates cellular phenotypes to donors genotypes by quantifying the presence of each donors DNA in cell "villages" before and after sorting or selection for cellular traits of interest. Census-seq enables population-scale cell-biological phenotyping with low cost and high internal control. We demonstrate Census-seq through investigation of genetic effects on the SMN protein whose deficiency underlies spinal muscular atrophy (SMA). Census-seq quantified and mapped effects of many common alleles on SMN protein levels and response to SMN-targeted therapeutics, including a common, cryptic non-responder allele. We provide tools enabling population-scale cell experiments and explain how Census-seq can be used to map genetic effects on diverse cell phenotypes. O_FIG O_LINKSMALLFIG WIDTH=185 HEIGHT=200 SRC="FIGDIR/small/174383v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@169bf4borg.highwire.dtl.DTLVardef@18dd9c0org.highwire.dtl.DTLVardef@1d30ca5org.highwire.dtl.DTLVardef@e35bf0_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LICensus-seq reveals how inherited genetic variation affects cell phenotypes C_LIO_LIGenetic analysis of cellular traits in cell villages of >100 donors C_LIO_LICharacterizing human alleles that shape SMN protein expression and drug responses C_LIO_LIDevelopment of protocols and software to enable cellular population genetics C_LI

genetics↗

bioRxiv2020

A transcriptome based aging clock near the theoretical limit of accuracy

Aging clocks dissociate biological from chronological age. The estimation of biological age is important for identifying gerontogenes and assessing environmental, nutritional or therapeutic impacts on the aging process. Recently, methylation markers were shown to allow estimation of biological age based on age-dependent somatic epigenetic alterations. However, DNA methylation is absent in some species such as Caenorhabditis elegans and it remains unclear whether and how the epigenetic clocks affect gene expression. Aging clocks based on transcriptomes have suffered from considerable variation in the data and relatively low accuracy. Here, we devised an approach that uses temporal scaling and binarization of C. elegans transcriptomes to define a gene set that predicts biological age with an accuracy that is close to the theoretical limit. Our model accurately predicts the longevity effects of diverse strains, treatments and conditions. The involved genes support a role of specific transcription factors as well as innate immunity and neuronal signaling in the regulation of the aging process. We show that this transcriptome clock can also be applied to human age prediction with high accuracy. This transcriptome aging clock could therefore find wide application in genetic, environmental and therapeutic interventions in the aging process.

bioinformatics↗

bioRxiv2019

Programmed transport and release of nanoscale cargo by immune cells

Transport and delivery of (nanoscale) materials are crucial for many applications in biomedicine. However, controlled uptake, transport and triggered release of such cargo remains challenging. In this study, we use human immune cells (neutrophilic granulocytes, neutrophils) and program them to perform these tasks in vitro. For this purpose, we let neutrophils phagocytose a nanoscale cargo. As an example, we used DNA-functionalized single-walled carbon nanotubes (SWCNT) that fluoresce in the near infrared (980 nm) and serve as sensors for small molecules. Cells still migrate, follow chemical gradients and respond to inflammatory signals after uptake of the cargo. To program release, we make use of neutrophil extracellular trap formation (NETosis), a novel cell death mechanism that leads to chromatin swelling and subsequent rupture of the cellular membrane and release of the cells whole content. By using the process of NETosis we can program the time point of cargo release via the initial concentration of stimuli such as phorbol 12-myristate-13-acetate (PMA) or lipopolysaccharide (LPS). At intermediate stimulation with LPS (100 g/ml), cells continue to migrate, follow gradients and surface cues for around 30 minutes and up to several hundred micrometers until they stop and release their cargo. The transported and released SWCNT sensor cargo is still functional as shown by subsequent detection of the neurotransmitter dopamine and reactive oxygen species (H2O2). In summary, we hijack a biological process (NETosis) and demonstrate how neutrophils can be used for programmed transport and delivery of functional nanomaterials.

biophysics↗

bioRxiv2019

Effect of Adhesion and Substrate Elasticity on Neutrophil Extracellular Trap Formation

Neutrophils are the most abundant type of white blood cells. Upon stimulation, they are able to decondense and release their chromatin as neutrophil extracellular traps (NETs). This process (NETosis) is part of immune defense mechanisms but also plays an important role in many chronic and inflammatory diseases such as atherosclerosis, rheumatoid arthritis, diabetes and cancer. For this reason, much effort has been invested into understanding biochemical signaling pathways in NETosis. However, the impact of the mechanical micro-environment and adhesion on NETosis is not well understood. Here, we studied how adhesion and especially substrate elasticity affect NETosis. We employed polyacrylamide (PAA) gels with distinctly defined elasticities (Youngs modulus E) within the physiologically relevant range from 1 kPa to 128 kPa and coated the gels with integrin ligands (collagen I, fibrinogen). Neutrophils were cultured on these substrates and stimulated with potent inducers of NETosis: phorbol 12-myristate 13-acetate (PMA) and lipopolysaccharide (LPS). Interestingly, PMA-induced NETosis was neither affected by substrate elasticity nor by different integrin ligands. In contrast, for LPS stimulation, NETosis rates increased with increasing substrate elasticity (E > 20 kPa). LPS-induced NETosis increased with increasing cell contact area, while PMA-induced NETosis did not require adhesion at all. Furthermore, inhibition of phosphatidylinositide 3 kinase (PI3K), which is involved in adhesion signaling, completely abolished LPS-induced NETosis but only slightly decreased PMA-induced NETosis. In summary, we show that LPS-induced NETosis depends on adhesion and substrate elasticity while PMA-induced NETosis is completely independent of adhesion.

biophysics↗

bioRxiv2018

Interrelationships among key Reproductive Health indicators in Sub-Saharan Africa

IntroductionIndicators of reproductive health (RH) services, outputs, outcomes and impacts are expected to be related with each other and with key social determinants. As the provision of RH services is usually integrated, the effort expended to improve one component is also expected to affect the other components. There is a lack of evidence-based models demonstrating the interrelationships among these indicators and between RH indicators and social determinants.\n\nObjectiveTo examine interrelationships among key RH indicators and their relationship with key social determinants in Sub-Saharan Africa (SSA).\n\nMethodThis study used data from the most recent demographic and health survey conducted during the period from 2010 to 2016 in 391 provinces of 29 SSA countries. We focused on seven RH indicator -- antenatal care, skilled birth attendance, postnatal care, contraceptive prevalence rate (CPR), ideal number of children, birth interval and total fertility rate (TFR), along with selected socio-demographic indicators. The unit of analysis was sub-national, at provincial level. Structural equation modelling was used to examine the strength of interrelationships among the indicators based on the total standardized effect sizes. Significance tests and 95% confidence intervals for the total effects were presented using a bias-corrected bootstrap method.\n\nResultsWomens literacy rate, at the centre of the model, has direct connections with all the RH indicators included in the final model. The strongest relationship was observed between womens literacy rate and CPR with a total standardized (std.) effect size of 0.79 (95% CI: 0.74, 0.83). RH indicators are interrelated directly and/or indirectly. A strong direct effect was also observed in the relationship between CPR and birth interval ({beta}=0.63, 95%: 0.50, 0.77) and the model suggests that the reported ideal number of children is a key predictor of birth interval (Std. effect size=-0.58, 95% CI: -0.69, -0.48) and TFR (Std. effect size=0.52, 95% CI: 0.38, 0.62).\n\nConclusionRH indicators are strongly interrelated and are all associated with womens literacy. The model of interrelationships developed in this study may guide the design, implementation and evaluation of RH policies and programs.

epidemiology↗

bioRxiv2018

Expression estimation and eQTL mapping for HLA genes with a personalized pipeline

The HLA (Human Leukocyte Antigens) genes are well-documented targets of balancing selection, and variation at these loci is associated with many disease phenotypes. Variation in expression levels also influences disease susceptibility and resistance, but little information exists about the regulation and population-level patterns of expression due to the difficulty in mapping short reads to these highly polymorphic loci, and in accounting for the existence of several paralogues. We developed a computational pipeline to accurately estimate expression for HLA genes based on RNA-seq, improving both locus-level and allele-level estimates. First, reads are aligned to all known HLA sequences in order to infer HLA genotypes, then quantification of expression is carried out using a personalized index. We use simulations to show that expression estimates are not biased due to divergence from the reference genome. We applied our pipeline to GEUVADIS dataset, and compared the quantifications to those obtained with reference transcriptome, and found that a substantial portion of the variation captured by the HLA-personalized index in not captured by the standard index (23%). We describe the impact of the HLA-personalized approach on downstream analyses for seven HLA loci (HLA-A, HLA-B, HLA-C, HLA-DPB1, HLA-DQA1, HLA-DQB1, HLA-DRB1). Although the influence of the HLA-personalized approach is modest for eQTL mapping, the p-values and the causality of the eQTLs obtained are better than when the reference transcriptome is used. Finally, we integrate information on HLA-allele level expression with the eQTL findings to show that the HLA allele is an important layer of variation to understand HLA regulation.

genomics↗

bioRxiv2017

Population Differentiation at the HLA Genes

Balancing selection is defined as a class of selective regimes that maintain polymorphism above what is expected under neutrality. Theory predicts that balancing selection reduces population differentiation, as measured by FST. However, balancing selection regimes in which different sets of alleles are maintained in different populations could increase population differentiation. To tackle this issue, we investigated population differentiation at the HLA genes, which constitute the most striking example of balancing selection in humans. We found that population differentiation of single nucleotide polymorphisms (SNPs) at the HLA genes is on average lower than that of SNPs in other genomic regions. However, this result depends on accounting for the differences in allele frequency between selected and putatively neutral sites. Our finding of reduced differentiation at SNPs within HLA genes suggests a predominant role of shared selective pressures among populations at a global scale. However, in pairs of closely related populations, where genome-wide differentiation is low, differentiation at HLA is higher than in other genomic regions. This pattern was reproduced in simulations of overdominant selection. We conclude that population differentiation at the HLA genes is generally lower than genome-wide, but it may be higher for recently diverged population pairs, and that this pattern can be explained by a simple overdominance regime.

genetics↗

bioRxiv2017

Signatures of long-term balancing selection in human genomes

Balancing selection maintains advantageous diversity in populations through various mechanisms. While extensively explored from a theoretical perspective, an empirical understanding of its prevalence and targets lags behind our knowledge of positive selection. Here we describe the Non-Central Deviation (NCD), a simple yet powerful statistic to detect long-term balancing selection (LTBS) that quantifies how close frequencies are to expectations under LTBS, and provides the basis for a neutrality test. NCD can be applied to a single locus or genomic data, and can be implemented considering only polymorphisms (NCD1) or also considering fixed differences with respect to an outgroup (NCD2) species. Incorporating fixed differences improves power, and NCD2 has higher power to detect LTBS in humans under different frequencies of the balanced allele(s) than other available methods. Applied to genome-wide data from African and European human populations, in both cases using chimpanzee as an outgroup, NCD2 shows that, albeit not prevalent, LTBS affects a sizable portion of the genome: about 0.6% of analyzed genomic windows and 0.8% of analyzed positions. Significant windows (p < 0.0001) contain 1.6% of SNPs in the genome, which disproportionally fall within exons and change protein sequence, but are not enriched in putatively regulatory sites. These windows overlap about 8% of the protein-coding genes, and these have larger number of transcripts than expected by chance even after controlling for gene length. Our catalog includes known targets of LTBS but a majority of them (90%) are novel. As expected, immune-related genes are among those with the strongest signatures, although most candidates are involved in other biological functions, suggesting that LTBS potentially influences diverse human phenotypes.

genomics↗