Hypoxia hits APOL1 in the kidney Grampp, Steffen; Krüger, René; Lauer, Victoria ...
Kidney international,
July 2023, 2023-Jul, 2023-07-00, 20230701, Volume:
104, Issue:
1
Journal Article
Peer reviewed
Open access
Individuals of African ancestry carrying two pathogenic variants of apolipoprotein 1 (APOL1) have a substantially increased risk for developing chronic kidney disease. The course of APOL1 nephropathy ...is extremely heterogeneous and shaped by systemic factors such as a response to interferon. However, additional environmental factors operating in this second-hit model have been less well defined. Here, we reveal that stabilization of hypoxia-inducible transcription factors (HIF) by hypoxia or HIF prolyl hydroxylase inhibitors activates transcription of APOL1 in podocytes and tubular cells. An active regulatory DNA-element upstream of APOL1 that interacted with HIF was identified. This enhancer was accessible preferentially in kidney cells. Importantly, upregulation of APOL1 by HIF was additive to the effects of interferon. Furthermore, HIF stimulated expression of APOL1 in tubular cells derived from the urine of an individual carrying a risk variant for kidney disease. Thus, hypoxic insults may serve as important modulators of APOL1 nephropathy.
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Organoids enable in vitro modeling of complex developmental processes and disease pathologies. Like most 3D cultures, organoids lack sufficient oxygen supply and therefore experience cellular stress. ...These negative effects are particularly prominent in complex models, such as brain organoids, and can affect lineage commitment. Here, we analyze brain organoid and fetal single‐cell RNA sequencing (scRNAseq) data from published and new datasets, totaling about 190,000 cells. We identify a unique stress signature in the data from all organoid samples, but not in fetal samples. We demonstrate that cell stress is limited to a defined subpopulation of cells that is unique to organoids and does not affect neuronal specification or maturation. We have developed a computational algorithm, Gruffi, which uses granular functional filtering to identify and remove stressed cells from any organoid scRNAseq dataset in an unbiased manner. We validated our method using six additional datasets from different organoid protocols and early brains, and show its usefulness to other organoid systems including retinal organoids. Our data show that the adverse effects of cell stress can be corrected by bioinformatic analysis for improved delineation of developmental trajectories and resemblance to in vivo data.
Synopsis
Cellular stress in 3D organoids due to insufficient oxygen transport can affect faithful lineage commitment and disease modeling. This work identifies a subpopulation of stressed cells characterized by a distinct gene expression signature that can be removed from scRNAseq datasets for better evaluation of fetal developmental trajectories.
ER‐ and glycolytic stress are found accross organoid protocols.
Stressed cells in 3D organoids form a separate cell state that is not found in vivo and that can be separated bioinformatically.
The presence of stressed cells in organoids does not affect cell‐type specification or the maturation of non‐stressed neurons.
Granular functional filtering (Gruffi) removes stressed cells from the single‐cell datasets but retains cell types found in vivo.
Stress removal leads to clearer developmental trajectories.
A unique stress signature found in in brain organoid samples but not in fetal samples can be quantified and removed from scRNAseq datasets using a new algorithm.
During brain development, neural progenitors expand through symmetric divisions before giving rise to differentiating cell types via asymmetric divisions. Transition between those modes varies among ...individual neural stem cells, resulting in clones of different sizes. Imaging-based lineage tracing allows for lineage analysis at high cellular resolution but systematic approaches to analyse clonal behaviour of entire tissues are currently lacking. Here we implement whole-tissue lineage tracing by genomic DNA barcoding in 3D human cerebral organoids, to show that individual stem cell clones produce progeny on a vastly variable scale. By using stochastic modelling we find that variable lineage sizes arise because a subpopulation of lineages retains symmetrically dividing cells. We show that lineage sizes can adjust to tissue demands after growth perturbation via chemical ablation or genetic restriction of a subset of cells in chimeric organoids. Our data suggest that adaptive plasticity of stem cell populations ensures robustness of development in human brain organoids.
The interplay between genetic and environmental factors influences the course of chronic kidney disease (CKD). In this context, genetic alterations in the kidney disease gene
(Mucin1) predispose to ...the development of CKD. These variations comprise the polymorphism rs4072037, which alters splicing of MUC1 mRNA, the length of a region with variable number of tandem repeats (VNTR), and rare autosomal-dominant inherited dominant-negative mutations in or 5' to the VNTR that causes autosomal dominant tubulointerstitial kidney disease (ADTKD-
). As hypoxia plays a pivotal role in states of acute and chronic kidney injury, we explored the effects of hypoxia-inducible transcription factors (HIF) on the expression of
and its pathogenic variants in isolated primary human renal tubular cells. We defined a HIF-binding DNA regulatory element in the promoter-proximal region of
from which hypoxia or treatment with HIF stabilizers, which were recently approved for an anti-anemic therapy in CKD patients, increased levels of wild-type
and the disease-associated variants. Thus, application of these compounds might exert unfavorable effects in patients carrying
risk variants.
Majoriteten av den ull som produceras av svenska får har under flera år slängts eller bränts upp. Samtidigt importerar svenska textilföretag tonvis med ull för miljoner kronor varje år. Detta problem ...uppmärksammades för några år sedan och ett antal svenska företag har sedandess börjat producera produkter av den svenska ullen. I denna kvalitativa studie har en undersökning gjorts för att sammanställa för- och nackdelar med att producera textilprodukter i svensk ull. Semistrukturerade intervjuer har genomförts med tio olika företag som idag jobbar med materialet. Resultatet av studien visar att det största problemet med ullproduktion inom Sverige är bristen på en strukturerad infrastruktur inom inköp och produktion. Fördelar med att producera textila produkter i svensk ull är att det är ett materialmed goda egenskaper för flera användningsområden. Det är ett hållbart materialval då ullen annars går till spillo. Närheten till materialet underlättar även kontrollen över att helavärdekedjan sköts på ett etiskt och hållbart sätt.
The majority of the wool produced by Swedish sheep has been discarded or burned for several years. At the same time, Swedish textile companies import tons of wool for millions of swedish crowns each year. This problem was brought to attention a few years ago and a number of Swedish companies have since started to produce products from the Swedish wool. In this qualitative study, an investigation was conducted to compile the pros and cons of producing textile products in Swedish wool. Semi-structured interviews have been conducted with ten different companies that are currently working with the material. The results of the study show that the biggest problem with wool production in Sweden is the lack of an organized infrastructure in purchasing and production. The advantage of producing textile products in Swedish wool is that it is a material with good properties for several applications. It is a sustainable choice of material as the wool is otherwise wasted. The proximity to the material also facilitates the control of the entire value chain being managed in an ethical and sustainable way.
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