Biology subjects

Christian, M.

Publications and source records attributed to Christian, M..

10 recordsLinked to original sources

bioRxiv2026

Whole slide image analysis of the endometrial decidual reaction reveals multiscale perturbations associated with miscarriage

The inflammatory decidual reaction renders the cycling endometrium transiently permissive for embryo implantation before transforming it into the decidua, the maternal bed accommodating the fetal placenta during pregnancy. Disruptions in decidual tissue remodeling are linked to miscarriage and other pregnancy disorders. However, endometrial assessment is hampered by a lack of affordable technologies capable of mapping the spatiotemporal dysregulation of this dynamic and complex tissue. Employing a graph neural network on whole slide images of 493 CD56-immunostained endometrial samples, Endometronome was developed as a deep learning tool to spatially track the decidual reaction and provide accurate estimates of marker gene expression. When applied to 2,690 additional biopsies, this model consistently identified morphological correlates of prior miscarriage burden, a proxy for future risk. Further, a morphological signature indicative of metabolic glandular impairment discriminated between clinical miscarriage presentations. These findings illustrate how advanced imaging analysis of routine histology can transform miscarriage prevention strategies.

pathology↗

bioRxiv2025

miR-10b-5p regulates adipocyte lineage commitment and adipogenesis via targeting of Gata6 and Tubby.

22.1 BackgroundAdipogenesis is a highly organised series of events that facilitates the healthy expansion of adipose tissue, beginning during embryogenesis and continuing throughout life. White adipogenesis protects against lipotoxicity, influencing insulin resistance and obesity-related comorbidities. Brown adipogenesis enhances energy expenditure, thereby counteracting weight gain, lipotoxicity and insulin resistance. Recently, there has been a significant increase in interest regarding adipocyte differentiation, mainly focusing on the interplay between microRNAs (miRNAs) and the transcriptional cascade that governs adipogenesis and metabolic dysfunction. This study aimed to identify miRNAs regulating white and brown adipocyte differentiation and define miRNA action in a stem cell model of adipogenesis. 2.2 MethodsSmall RNAseq analysis of primary mouse brown and white adipocytes (WAs) identified miR-10b to be upregulated in mature brown adipocytes (BAs). We generated two model systems: 1) immortalized brown pre-adipocytes treated with miRNA inhibitors and 2) CRISPR/Cas9 KO of miR-10b in E14 mouse embryonic stem cells (mESCs). Both cell models were differentiated into mature adipocytes. To unravel the pathways that are affected by miR-10b depletion, a transcriptomic analysis was performed at key time points. 2.3 ResultsBoth cell models showed that miR-10b-5p depletion severely impaired differentiation into mature adipocytes, as indicated by a lack of lipid droplet formation and reduced adipogenic gene expression. Gene expression analysis supports that miR-10b-5p directs embryonic stem (ES) cells towards the mesoderm lineage, promoting commitment to pre-adipocytes by downregulating Gata6 and its downstream target Bmp2. This mechanism appears to be unaffected in BAs. Our study demonstrated that miR-10b-5p regulates the later stages of adipogenesis, at least in part, by downregulating Tub, a direct target of miR-10b-5p. We also confirmed that miR-10b-5p alleviated the halted differentiation phenotypes of adipocytes by supressing the G Protein Signalling pathway mediated by Tubby. 2.4 ConclusionsThese results evidence that miR-10b inhibition plays a dynamic role in adipocyte biology, as its inhibitory effects manifest differently during the stem cell preadipocyte proliferation state and during the maturation phase of adipocytes. Collectively, our study demonstrated that miR-10b-5p may represent a new potential therapeutic target for lipodystrophy and obesity.

molecular biology↗

bioRxiv2025

Ancient origin of an urban underground mosquito

Understanding how life is adapting to urban environments represents an important challenge in evolutionary biology. Here we investigate a widely cited example of urban adaptation, Culex pipiens form molestus, also known as the London Underground Mosquito. Population genomic analysis of [~]350 contemporary and historical samples counter the popular hypothesis that molestus originated belowground in London less than 200 years ago. Instead, we show that molestus first adapted to human environments aboveground in the Middle East over the course of >1000 years, likely in concert with the rise of agricultural civilizations. Our results highlight the role of early human society in priming taxa for contemporary urban evolution and have important implications for understanding arbovirus transmission.

evolutionary biology↗

bioRxiv2024

The exit of naïve pluripotency contains a lipid metabolism-induced checkpoint for genome integrity.

Pluripotent progenitors undergo dramatic cellular and biochemical transformations during peri-implantation development. These large-scale reprogramming events are fundamental for subsequent differentiation, but how they are integrated and co-ordinated with the preservation of genome integrity remain unknown. Here, we uncover a metabolism-induced telomere checkpoint that takes place in pluripotent progenitors as they form rosette-like epithelial structures. We show that the glycolytic switch at the exit of naive pluripotency is preceded by an acceleration of mitochondrial respiration and de novo lipogenesis, fuelling the accumulation of lipid droplets required for morphogenesis. We find that downstream of these CIDEA-promoted metabolic events is the induction of ZSCAN4, a key pluripotency-associated regulator of telomere stability. Surprisingly, the build-up of lipid droplets corresponds to a transient shortening of telomeres, which triggers the activation of an elongation mechanism via ZSCAN4. Thus, telomere homeostasis can be safeguarded as essential lipid metabolic reprogramming unfolds to drive developmental progression.

developmental biology↗

bioRxiv2022

Common risk variants in AHI1 are associated with childhood steroid-sensitive nephrotic syndrome

BackgroundSteroid-sensitive nephrotic syndrome (SSNS) is the most common form of kidney disease in children worldwide. Genome-wide association studies (GWAS) have demonstrated association of SSNS with genetic variation at HLA-DQ/DR and have identified several non-HLA loci that aid in further understanding of disease pathophysiology. We sought to identify additional genetic loci associated with SSNS in children of Sri Lankan and European ancestry. MethodsWe conducted a GWAS in a cohort of Sri Lankan individuals comprising 420 pediatric patients with SSNS and 2339 genetic ancestry matched controls obtained from the UK Biobank. We then performed a trans-ethnic meta-analysis with a previously reported European cohort of 422 pediatric patients and 5642 controls. ResultsOur GWAS confirmed the previously reported association of SSNS with HLA-DR/DQ (rs9271602, p=1.12x10-27, odds ratio[OR]=2.75). Trans-ethnic meta-analysis replicated these findings and identified a novel association at AHI1 (rs2746432, p=2.79x10-8, OR=1.37), which was also replicated in an independent South Asian cohort. AHI1 is implicated in ciliary protein transport and immune dysregulation, with rare variation in this gene contributing to Joubert syndrome type 3. ConclusionsCommon variation in AHI1 confers risk of the development of SSNS in both Sri Lankan and European populations. The association with common variation in AHI1 further supports the role of immune dysregulation in the pathogenesis of SSNS and demonstrates that variation across the allele frequency spectrum in a gene can contribute to disparate monogenic and polygenic diseases. AUTHOR SUMMARYSteroid-sensitive nephrotic syndrome (SSNS) is the most common kidney disease in children worldwide, but the cause of disease is not well understood. Genome-wide association studies (GWAS) in SSNS have shown that genes in the classical HLA region (the human immune centre) and several genes outside of this region are associated with the disease, which has allowed us to further understand the cause of disease. We performed a GWAS of Sri Lankan ancestry that included 420 paediatric patients and 2339 ancestry-matched controls and confirmed association at HLA-DQ/DR with SSNS. We then performed a Sri Lankan-European trans-ethnic meta-analysis and identified a new association with SSNS outside of HLA, in AHI1. This finding further supports the role of immune system involvement in the etiology of SSNS and increases our knowledge of the genetic causes of disease. AHI1 is a gene that can also cause ciliary problems and demonstrates that different genetic variants within the same gene can contribute to both single-gene (Joubert syndrome, a rare disease that causes kidney and neurological problems) and multi-gene diseases (SSNS).

genetics↗

bioRxiv2022

Rapid isolation of respiring skeletal muscle mitochondria using nitrogen cavitation.

BackgroundMethods of isolating mitochondria commonly utilize mechanical force and shear stress to homogenize tissue followed by purification by multiple rounds of ultracentrifugation. Existing protocols can be time-consuming with some physically impairing integrity of the sensitive mitochondrial double membrane. MethodsHere, we describe a method for the recovery of intact, respiring mitochondria from murine skeletal muscle tissue and cell lines using nitrogen cavitation in combination with differential centrifugation. ResultsThis protocol results in high yield, pure and respiring mitochondria without the need for purification gradients or ultracentrifugation. The protocol takes under an hour and requires limited specialised equipment. Our methodology is successful in extracting mitochondria of both cell extracts and skeletal muscle tissue. This represents an improved yield in comparison to many of the existing methods. Western blotting and electron microscopy demonstrate an enrichment of mitochondria with their ultrastructure well-preserved and an absence of contamination from cytoplasmic or nuclear fractions. Using respirometry analysis we show that mitochondria extracted from the murine skeletal muscle cell lines and tibialis anterior have an appropriate respiratory control ratio. These measures are indicative of healthy coupled mitochondria. ConclusionOur method successfully demonstrates the rapid isolation of functional mitochondria and will benefit researchers studying mitochondrial bioenergetics as well as providing greater throughput and application for time-sensitive assays.

molecular biology↗

bioRxiv2021

Sublingual allergen immunotherapy with recombinant dog allergens prevents airway hyperresponsiveness in a model of asthma marked by vigorous TH2 and TH17 cell responses

Allergy to dogs affects around ten percent of the population in developed countries. Immune therapy of allergic patients with dog allergen extracts has shown limited therapeutic benefit. Herein, we established a mouse model of dog allergy and tested the efficacy of a recombinant protein containing Can f 1, f 2, f 4 and f 6 as a sublingual immune therapy (SLIT). Repeated inhalation of dog extracts induced infiltration of the airways by TH2 cells, eosinophils and goblet cells, reminiscent of the house dust mite (HDM) model of asthma. However, dog allergen extracts also induced robust TH17 cell responses, which was associated with a high neutrophilic infiltration of the airways and promoted airway hyperresponsiveness more potently than HDM allergens. scRNA-Seq analysis of T helper cells responding to dog allergens identified several unique clusters with TH17 cells being hallmarked by the expression of several receptors including IL-17RE. Analysis of T cell receptors also depicted a high frequency of clones that were shared between TH17, TH2 and suppressive Treg cells, indicative of the plasticity of T helper cells in this model. Importantly, prophylactic SLIT reduced airway hyperresponsiveness and type 2-mediated inflammation in this model supporting the use of recombinant allergens in immune therapy.

immunology↗

bioRxiv2020

Estimating the timing of HIV infection from unmutated sequences

For HIV, the time since infection can be estimated from sequence data for acutely infected samples. One popular approach relies on the star-like nature of phylogenies generated under exponential population growth, and the resulting Poisson distribution of mutations away from the founding variant. However, real-world complications, such as APOBEC hypermutation and multiple-founder transmission, present a challenge to this approach, requiring data curation to remove these signals before reasonable timing estimates may be obtained. Here we suggest a simple alternative approach that derives the timing estimate not from the entire mutational spectrum but from the proportion of sequences that have no mutations. This can be approximated quickly and is robust to phenomena such as multiple founder transmission and APOBEC hypermutation. Our approach is Bayesian, and we adopt a conjugate prior to obtain closed form posterior distributions at negligible computational expense. Using real data and simulations, we show that this approach provides accurate timing estimates and credible intervals without the inconvenience of data curation and is robust to complicating phenomena that can mislead existing approaches or cause them to fail entirely. For immediate use we provide an implementation via Google Sheets, which offers bulk analysis of multiple datasets, as well as more detailed individual-donor analyses. For inclusion in data processing pipelines we provide implementations in three languages: Julia, R, and Python.

bioinformatics↗

bioRxiv2020

Discriminative Bayesian Serology: Counting Without Cutoffs

During the emergence of a pandemic, we need to estimate the prevalence of a disease using serological assays whose characterization is incomplete, relying on limited validation data. This introduces uncertainty for which we need to account. In our treatment, the data take the form of continuous assay measurements of antibody response to antigens (eg. ELISA), and fall into two groups. The training data includes the confirmed positive or negative infection status for each sample. The population data includes only the assay measurements, and is assumed to be a random sample from the population from which we estimate the seroprevalence. We use the training data to model the relationship between assay values and infection status, capturing both individual-level uncertainty in infection status, as well as uncertainty due to limited training data. We then estimate the posterior distribution over population prevalence, additionally capturing uncertainty due to finite samples. Finally, we introduce a means to pool information over successive time points, using a Gaussian process, which dramatically reduces the variance of our estimates. The methodological approach we here describe was developed to support the longitudinal characterization of the seroprevalence of COVID-19 in Stockholm, Sweden.

immunology↗

bioRxiv2019

KCND3 is a novel susceptibility locus for early repolarization

The presence of an early repolarization pattern (ERP) on the surface electrocardiogram (ECG) is associated with risk of ventricular fibrillation and sudden cardiac death. Family studies have shown that ERP is a highly heritable trait but molecular genetic determinants are unknown. We assessed the ERP in 12-lead ECGs of 39,456 individuals and conducted a two-stage meta-analysis of genome-wide association studies (GWAS). In the discovery phase, we included 2,181 cases and 23,641 controls from eight European ancestry studies and identified 19 genome-wide significant (p<5E-8) variants in the KCND3 (potassium voltage gated channel subfamily D member 3) gene with a p-value of 4.6E-10. Replication of two loci in four additional studies including 1,124 cases and 12,510 controls confirmed the association at the KCND3 gene locus with a pooled odds ratio of 0.82, p=7.7E-12 (rs1545300 minor allele T). A subsequent GWAS meta-analysis combining all samples did not reveal additional loci. The lead SNP of the discovery stage (rs12090194) was in strong linkage disequilibrium with rs1545300 (r2=0.96, D=1). Summary statistics based conditional analysis did not reveal any secondary signals. Co-localization analyses indicate causal effects of KCND3 gene expression levels on ERP in both the left ventricle of the heart and in tibial artery.\n\nIn this study we identified for the first time a genome-wide significant association of a genetic variant with ERP. Our findings of a locus in the KCND3 gene not only provide insights into the genetic determinants but also into the pathophysiological mechanism of ERP, revealing a promising candidate for functional studies.

genetics↗