Biology subjects

Dimitriadis, E.

Publications and source records attributed to Dimitriadis, E..

5 recordsLinked to original sources

bioRxiv2024

Comparative analysis of iPSC-derived human kidney organoid and tubuloid models

BackgroundEpithelial kidney organoids (tubuloids) made from kidney biopsies, urine, or iPSC-derived kidney organoids offer new opportunities in experimental and clinical nephrology. Yet, we have limited knowledge of how tubuloid models differ from each other, from iPSC-derived kidney organoids and from the human kidney. New insight is required to guide model selection for studies in kidney physiology and disease. MethodsTubuloids were generated from adult nephrectomy samples (adult tubuloids n=3), iPSC-derived kidney organoids (iTubuloids n=3), and for the first time, from human fetal kidneys (fetal tubuloids n=3). Kidney organoid and tubuloid models were compared to each other and to adult human kidney using bulk RNA sequencing. Tubuloids were subject to hypoxic insults over three passages and profiled with RNA sequencing to assess cumulative injury and repair. ResultsExpression signatures of proximal and distal tubules were stronger in adult kidneys than any organoid or tubuloid model. Comparative analysis between the models revealed that iPSC-derived kidney organoids had the highest expression of proximal tubule markers, even though adult tubuloids were derived from mature kidneys. Collecting duct signatures were enriched in adult and fetal tubuloids. Adult tubuloids showed stronger signatures of ageing and inflammation, while fetal tubuloids had enhanced ureteric tip progenitor signatures. Over 80 genes linked to inherited disorders were expressed in all tubuloid cultures, while a further 54 were expressed at higher levels in either adult, fetal or iTubuloids. Tubuloids subject to a single hypoxic injury effectively recovered by the end of the passage, while iTubuloids exposed to hypoxia over three passages expressed markers of maladaptive repair. ConclusionsThis study provides new transcriptome-wide reference data to aid in the selection and optimization of disease modelling for the human kidney. It defines common and unique opportunities to model inherited disorders in adult, fetal and iTubuloid models and illustrates new potential to model repetitive injury in long-lived tubuloid cultures.

molecular biology↗

bioRxiv2024

PLSKO: a robust knockoff generator to control false discovery rate in omics variable selection

The knockoff framework, combined with variable selection procedure, controls false discovery rate (FDR) without the need for calculating p-values. Hence, it presents an attractive alternative to differential expression analysis of high-throughput biological data. However, current knockoff variable generators make strong assumptions or insufficient approximations that lead to FDR inflation when applied to biological data. We propose Partial Least Squares Knockoff (PLSKO), an efficient and assumption-free knockoff generator that is robust to varying types of biological omics data. We compare PLSKO with a wide range of existing methods. In simulation studies, we show that PLSKO is the only method that controls FDR with sufficient statistical power in complex non-linear cases. In semi-simulation studies based on real data, we show that PLSKO generates valid knockoff variables for different types of biological data, including RNA-seq, proteomics, metabolomics and microbiome. In preeclampsia multi-omics case studies, we combined PLSKO with Aggregation Knockoff to address the randomness of knockoffs and improve power, and show that our method is able to select variables that are biologically relevant.

bioinformatics↗

bioRxiv2024

Perivascular cells function as mechano-structural sensors of vascular capillaries

A wide range of conditions, including chronic inflammatory diseases and cancer, are characterized by the fibrotic microarchitecture and increased stiffness of collagen type I extracellular matrix. These conditions are typically accompanied by altered vascular function, including vessel leakiness, abnormal capillary morphology and stability. The dynamic cell-matrix interactions that regulate vascular function in healthy tissues have been well documented. However, our understanding of how the gradual mechanical and structural alterations in collagen type I affect vascular homeostasis remains elusive, especially as a function of the interactions between endothelial and perivascular cell with the altered matrix. Here we hypothesized that perivascular cells might function as mechano-structural sensors of the microvasculature by mediating the interaction between endothelial cells and altered collagen type I. To test that, we utilized an organotypic model of perivascular cell-supported vascular capillaries in collagen scaffolds of controlled microarchitecture and mechanics. Our results demonstrate that capillaries cultured in soft reticular collagen exhibited consistent pericyte differentiation, endothelial cell-cell junctions, and barrier function. In contrast, capillaries embedded in stiff and bundled collagen fibrils to mimic a more fibrotic matrix induced abluminal migration of perivascular cells, increased leakage, and marked expression of vascular remodeling and inflammatory markers. These patterns, however, were only observed when endothelial capillaries were engineered with perivascular cells. Silencing of NOTCH3, a mediator of endothelial-perivascular cell communication, largely re-established normal vascular morphology and function. In summary, our findings point to a novel mechanism of perivascular regulation of vascular dysfunction in fibrotic tissues which may have important implications for anti-angiogenic and anti-fibrotic therapies in cancer, chronic inflammatory diseases and regenerative medicine. Significance StatementThe fibrotic alterations in extracellular matrix structure and mechanics that are common to many chronic and inflammatory conditions are often associated with a decrease in vascular homeostasis. The mechanisms regulating these abnormalities remain poorly understood. Here, we demonstrate that perivascular cells play a critical role in sensing progressive microarchitectural and mechanical changes occurring in the ECM, drastically altering vascular capillary morphology and barrier function, and exacerbating the production of inflammatory and remodeling markers. These results point to a previously unknown mechano-structural sensory mechanisms mediated by perivascular cells in vascular capillaries that may help elucidate the progression of many profibrotic conditions, and point to possible new targets for antiangiogenic and antifibrotic therapies in cancer, chronic inflammatory conditions and regenerative medicine.

bioengineering↗

bioRxiv2022

Germinal Centers Convergent Evolution and B cell Recirculation in Human Lymph Nodes

Germinal centers (GCs) are specialized compartments within the secondary lymphoid organs where B cells proliferate, differentiate, and mutate their antibody genes in response to the presence of foreign antigens. They play a central role in generating an effective immune response against infectious pathogens, and failures in their regulating mechanisms can lead to the development of autoimmune diseases and cancer. While previous works study experimental systems of the immune response with mouse models that are immunized with specific antigens, our study focuses on a real life situation, with an ongoing GC response in a human lymph node (LN) involving multiple asynchronized GCs reacting simultaneously to unknown antigens. We combined laser capture microdissection (LCM) of individual GCs from human LN with next-generation repertoire sequencing (Rep-seq) to characterize individual GCs as distinct evolutionary spaces. In line with well-characterized GC responses in mice, elicited by immunization with model antigens such as NP-CGG, we observe a relatively low sequence similarity, as well as heterogeneous clonal diversity across individual GCs from the same human LN. Still, we identify shared clones in several individual GCs, and phylogenetic tree analysis combined with paratope modeling suggest the re-engagement and rediversification of B-cell clones across GCs as well as expanded clones exhibiting shared antigen responses across distinct GCs, indicating convergent evolution of the GCs. Finally, our study allows for the characterization of non-functional clones, where frequencies of V(D)J or SHM induced stop codons are quantified.

evolutionary biology↗

bioRxiv2020

Dmp1Cre-directed knockdown of PTHrP in murine decidua is associated with increased bone width and a life-long increase in strength specific to male progeny

Parathyroid hormone related-protein (PTHrP) is a pleiotropic regulator of tissue homeostasis. In bone, knockdown in osteocytes by Dmp1Cre-targeted deletion causes osteopenia and impaired strength. We report that this outcome depends on parental genotype. Adult Dmp1Cre.Pthlhf/f mice from homozygous parents (Dmp1Cre.Pthlhf/f(hom)) have stronger bones, with 40% more trabecular bone mass and 30% greater femoral width than controls. At 12 days old, greater bone width was also found in male and female Dmp1Cre.Pthlhf/f(hom) mice, but not in gene-matched mice from heterozygous parents, suggesting a maternal influence before weaning. Milk PTHrP levels were normal, but decidua from mothers of Dmp1Cre.Pthlhf/f(hom) mice were smaller, with low PTHrP levels. Moreover, Dmp1Cre.Pthlhf/f(hom) embryonic bone was more mineralized and wider than control. We conclude that Dmp1Cre leads to gene recombination in decidua, and that decidual PTHrP influences decidual cell maturation and limits embryonic bone growth. This identifies a maternal-derived developmental origin of adult bone strength.

cell biology↗