Biology subjects

Kiel, C.

Publications and source records attributed to Kiel, C..

8 recordsLinked to original sources

bioRxiv2026

DHX30 is a replication stress-responsive R-loop helicase that safeguards genome stability

R-loops are three-stranded nucleic acid structures formed primarily during transcription that can obstruct replication fork progression, leading to replication stress and genome instability. Although RNA helicases are increasingly implicated in R-loop metabolism, how individual helicases safeguard genome integrity remains incompletely understood. Here we identify DHX30, a neurodevelopmental disorder-associated DExH-box RNA helicase, as a replication stress-responsive regulator of R-loops. We show that DHX30 localizes to the nucleus in addition to its known cytoplasmic and mitochondrial pools, and that its nuclear abundance in-creases following aphidicolin or camptothecin treatment. DHX30 deficiency results in RNA:DNA hybrid accumulation in human cells and zebrafish, R-loop-dependent DNA double-strand breaks, micronucleus formation, reduced DNA synthesis, and altered expression of immediate-early stress genes under basal conditions and following replication perturbation. Biochemically, DHX30 binds branched nucleic acid structures and directly unwinds R-loop substrates containing a 3' single-stranded RNA overhang in an ATP- and polarity-dependent manner. Proteomic analyses place DHX30 within a nuclear network of RNA- and R-loop-associated factors, including the RNA helicase DHX9. These findings establish DHX30 as a conserved R-loop-resolving helicase that protects from R-loop-induced replication perturbations, contributes to transcriptional homeostasis, and maintains genome stability, thereby providing a mechanistic framework for understanding DHX30-associated neurodevelopmental disorders.

molecular biology↗

bioRxiv2024

Energetics of the outer retina II: Calculation of a spatio-temporal energy budget in retinal pigment epithelium and photoreceptor cells based on quantification of cellular processes

The outer retina (OR) is highly energy demanding. Impaired energy metabolism combined with high demands are expected to cause energy insufficiencies that make the OR susceptible to complex blinding diseases such as age-related macular degeneration (AMD). Here, anatomical, physiological and quantitative molecular data were used to calculate the ATP expenditure of the main energy-consuming processes in three cell types of the OR for the night and two different periods during the day. The predicted energy demands in a rod dominated (perifovea) area are 1.33 x 1013 ATP/s/mm2 tissue in the night and 6.53 x 1012 ATP/s/mm2 tissue during the day with indoor light conditions. For a cone-dominated foveal area the predicted energy demands are 6.44 x 1012 ATP/s/mm2 tissue in the night and 6.75 x 1012 ATP/s/mm2 tissue with indoor light conditions during daytime. We propose the likely need of for diurnal/circadian shifts in energy demands to efficiently stagger all energy consuming processes. Our data provide insights into vulnerabilities in the aging OR and suggest that diurnal constraints may be important when considering therapeutic interventions to optimize metabolism.

systems biology↗

bioRxiv2024

Energetics of the outer retina I: Estimates of nutrient exchange and ATP generation.

Photoreceptors (PRs) are metabolically demanding and packed at high density, which presents a challenge for nutrient exchange between the associated vascular beds and the tissue. Motivated by the ambition to understand the constraints under which PRs function, in this study we have drawn together diverse physiological and anatomical data in order to generate estimates of the rates of ATP production per mm2 of retinal surface area. With the predictions of metabolic demand in the companion paper, we seek to develop an integrated energy budget for the outer retina. It is known that rod PR number and the extent of the choriocapillaris (CC) vascular network that supports PRs both decline with age. To set the outer retina energy budget in the context of aging we demonstrate how, at different eccentricities, decline CC density is more than matched by rod loss in a way that tends to preserve nutrient exchange per rod. Together these finds provide an integrated framework for the study of outer retinal metabolism and how it might change with age.

systems biology↗

bioRxiv2023

Synergistic effects of predation and parasitism on competition between edible and inedible phytoplankton

Fungi can affect aquatic ecosystems through syntrophic and parasitic interactions with other organisms and organic matter. In pelagic systems, fungal parasites on phytoplankton can control trophic interactions and food-web dynamics, e.g., zooplankton grazing on fungal parasite zoospores creates an alternative energy pathway (termed "mycoloop") from otherwise inedible phytoplankton species. We aim to investigate how the mycoloop influences community dynamics in aquatic food-webs combining experimental and modelling approaches. We assembled an experimental system consisting of an inedible (host) phytoplankton species and its parasitic chytrid, an edible (non-host) phytoplankton species, and a zooplankton grazer. Chytrids parasitizing increased edible phytoplankton abundance, while zooplankton grazing decreased edible phytoplankton abundance. In the presence of zooplankton and chytrids, competition effects between edible and inedible phytoplankton species depended on nutrient levels. At high nutrient levels, competition was balanced by an indirect positive chytrid effect and negative zooplankton grazing effects on edible phytoplankton. In contrast, at low nutrient levels, we found chytrid had a negative impact on edible phytoplankton synergistically with zooplankton. Mathematical investigations suggest that the synergistic effect can be caused by the mycoloop. This indicates that the mycoloop substantially affects predator-prey interactions and phytoplankton competition with yet unknown ecological consequences.

ecology↗

bioRxiv2022

Structure-based prediction of Ras-effector binding affinities and design of 'branchegetic' interface mutations

Ras is a central cellular hub protein controlling multiple cell fates. How Ras interacts with a variety of potential effector proteins is relatively unexplored, with only some key effectors characterized in great detail. Here, we have used homology modelling based on X-ray and AlphaFold2 templates to build structural models for 54 Ras-effectors complexes. These models were used to estimate binding affinities using a supervised learning regressor. Furthermore, we systematically introduced Ras branch-pruning (or branchegetic) mutations to identify 200 interface mutations that affect the binding energy with at least one of the model structures. The impacts of these branchegetic mutants were integrated into a mathematical model to assess the potential for rewiring interactions at the Ras hub on a systems level. These findings have provided a quantitative understanding of Ras-effector interfaces and their impact on systems properties of a key cellular hub.

systems biology↗

bioRxiv2022

Analysis of context-specific KRAS-effectors (sub)complexes in Caco-2 cells

Ras is a key switch controlling cell behavior. In the GTP-bound form, Ras interacts with numerous effectors in a mutually exclusive manner, where individual Ras-effectors are likely part of larger cellular (sub)complexes. The molecular details of these (sub)complexes and their alteration in specific contexts is not understood. Focusing on KRAS, we performed affinity purification (AP)-mass spectrometry (MS) experiments of exogenous expressed FLAG-KRAS WT and three oncogenic mutants ( genetic contexts) in the human Caco-2 cell line, each exposed to 11 different culture media ( culture contexts) that mimic conditions relevant in the colon and colorectal cancer. We identified four effectors present in complex with KRAS in all genetic and growth contexts ( context-general effectors). Seven effectors are found in KRAS complexes in only some contexts ( context-specific effectors). Analyzing all interactors in complex with KRAS per condition, we find that the culture contexts had a larger impact on interaction rewiring than genetic contexts. We investigated how changes in the interactome impact functional outcomes and created a shiny app for interactive visualization. We validated some of the functional differences in metabolism and proliferation. Finally, we used networks to evaluate how KRAS effectors are involved in the modulation of functions by random walk analyses of effector-mediated (sub)complexes. Altogether, our work shows the impact of environmental contexts on network rewiring, which provides insights into tissue-specific signaling mechanisms. This may also explain why KRAS oncogenic mutants may be causing cancer only in specific tissues despite KRAS being expressed in most cells and tissues.

systems biology↗

bioRxiv2019

Genome-wide association meta-analysis for early age-related macular degeneration highlights novel loci and insights for advanced disease

BackgroundAdvanced age-related macular degeneration (AMD) is a leading cause of blindness. While around half of the genetic contribution to advanced AMD has been uncovered, little is known about the genetic architecture of the preceding early stages of the diseases. MethodsTo identify genetic factors for early AMD, we conducted a genome-wide association meta-analysis with 14,034 early AMD cases and 91,214 controls from 11 sources of data including data from the International AMD Genomics Consortium (IAMDGC) and the UK Biobank (UKBB). We ascertained early AMD via color fundus photographs by manual grading for 10 sources and by using an automated machine learning approach for >170,000 images from UKBB. We searched for significant genetic loci in a genome-wide association screen (P<5x10-8) based on the meta-analysis of the 11 sources and via a candidate approach based on 13 suggestive early AMD variants from Holliday et al 2013 (P<0.05/13, additional 3,432 early AMD cases and 11,235 controls). For the novel AMD regions, we conducted in-silico follow-up analysis to prioritize causal genes and pathway analyses. ResultsWe identified 11 loci for early AMD, 9 novel and 2 known for early AMD. Most of these 11 loci overlapped with known advanced AMD loci (near ARMS2/HTRA1, CFH, APOE, C2, C3, CETP, PVRL2, TNFRSF10A, VEGFA), except two that were completely novel to any AMD. Among the 17 genes within the two novel loci, in-silico functional annotation suggested CD46 and TYR as the most likely responsible genes. We found the presence or absence of an early AMD effect to distinguish known pathways of advanced AMD genetics (complement/lipid pathways or extracellular matrix metabolism, respectively). ConclusionsOur data on early AMD genetics provides a resource comparable to the existing data on advanced AMD genetics, which enables a joint view. Our large GWAS on early AMD identified novel loci, highlighted shared and distinct genetics between early and advanced AMD and provides insights into AMD etiology. The ability of early AMD effects to differentiate the major pathways for advanced AMD underscores the biological relevance of a joint view on early and advanced AMD genetics.

genetics↗

bioRxiv2018

VarQ: a tool for the structural analysis of Human Protein Variants

Understanding the functional effect of Single Amino acid Substitutions (SAS), derived from the occurrence of single nucleotide variants (SNVs), and their relation to disease development is a major issue in clinical genomics. Even though there are several bioinformatic algorithms and servers that predict if a SAS can be pathogenic or not they give little or non-information on the actual effect on the protein function. Moreover, many of these algorithms are able to predict an effect that no necessarily translates directly into pathogenicity. VarQ Web Server is an online tool that given an UniProt id automatically analyzes known and user provided SAS for their effect on protein activity, folding, aggregation and protein interactions among others. VarQ assessment was performed over a set of previously manually curated variants, showing its ability to correctly predict the phenotypic outcome and its underlying cause. This resource is available online at http://varq.qb.fcen.uba.ar/.\n\nContact: lradusky@qb.fcen.uba.ar\n\nSupporting Information & Tutorials may be found in the webpage of the tool.

bioinformatics↗