Biology subjects

Korzelius, J.

Publications and source records attributed to Korzelius, J..

6 recordsLinked to original sources

bioRxiv2024

The transcription factor Chronophage/BCL11A/B promotes intestinal stem cell proliferation and endocrine differentiation in the Drosophila intestine

Tissue-resident Adult Stem Cells (ASCs) need to continuously adapt their rate of division and differentiation based on their tissue environment. However, the gene regulatory networks that govern these decisions in ASCs and how they respond to challenges such as infection are often not fully understood. We identify a novel role for the transcription factor (TF) Chronophage (Cph) in ISC proliferation and entero-endocrine (EE) cell differentiation. Cph is a Z2H2 zinc TF orthologous to mammalian BCL11A/B that are involved in regulating adult stem cell fate in various contexts. We show here that Cph is expressed in ISCs and EEs in the Drosophila intestine. Increased levels of Cph correlates with increased ISC proliferation and EE differentiation. cph loss-of-function leads to impaired ISC proliferation. Cph levels are elevated during tumourigenesis as well as in ageing and infection conditions. Knockdown of Cph in a Notch-mutant tumour model reduces tumour size and incidence and extends lifespan. Mechanistically, Cph overexpression leads to an increase in enteroendocrine (EE) cells and DamID DNA-binding and qRT-PCR analysis reveals that Cph directly regulates the levels of key EE regulatory genes such as Prospero (pros) and Phyllopod (phyl). In addition, Cph directly regulates core cell cycle regulators such as E2F1 as well as the TF Nerfin-1 that controls ISC proliferation and maintenance. Together, these data support a role for Cph in finetuning the balance between differentiation and proliferation during entero-endocrine differentiation.

developmental biology↗

bioRxiv2023

Stem cell growth directs region-specific cell fate decisions during intestinal nutrient adaptation

The adult intestine is a regionalized organ, whose size and cellular composition is adjusted in response to nutrient status. This involves dynamic regulation of intestinal stem cell (ISC) proliferation and differentiation. How nutrient signaling controls cell fate decisions to drive regional changes in cell type composition remains unclear. Here we show that nutrient adaptation involves region-specific control of intestinal cell size, number and differentiation. We uncovered that activation of mTOR complex 1 increases ISC size in a region-specific manner. This promotes Delta expression to direct cell fate towards the absorptive enteroblast lineage, while inhibiting secretory enteroendocrine cell differentiation. The observed coupling between nutrient sensing and cell fate enabled mitigation of aging-induced ISC misdifferentiation through intermittent fasting. In conclusion, ISC size acts as an early fate determinant allowing regional control of intestinal cell differentiation in response to nutrition with relevance to maintenance of tissue integrity during aging. HighlightsO_LImTORC1 signaling regulates ISC size in a region-specific manner C_LIO_LImTORC1 signaling is activated in the S and G2 phase of the ISC cell cycle C_LIO_LIISC size directs differentiation towards absorptive vs. secretory lineage C_LIO_LIIntermittent fasting mitigates aging induced deregulation of ISC differentiation C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=184 SRC="FIGDIR/small/537654v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@1205ebforg.highwire.dtl.DTLVardef@2c4e2corg.highwire.dtl.DTLVardef@c0664aorg.highwire.dtl.DTLVardef@17b88c3_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2019

Prioritization of genes driving congenital phenotypes of patients with de novo genomic structural variants

BackgroundGenomic structural variants (SVs) can affect many genes and regulatory elements. Therefore, the molecular mechanisms driving the phenotypes of patients with multiple congenital abnormalities and/or intellectual disability carrying de novo SVs are frequently unknown.\n\nResultsWe applied a combination of systematic experimental and bioinformatic methods to improve the molecular diagnosis of 39 patients with de novo SVs and an inconclusive diagnosis after regular genetic testing. In seven of these cases (18%) whole genome sequencing analysis detected disease-relevant complexities of the SVs missed in routine microarray-based analyses. We developed a computational tool to predict effects on genes directly affected by SVs and on genes indirectly affected due to changes in chromatin organization and impact on regulatory mechanisms. By combining these functional predictions with extensive phenotype information, candidate driver genes were identified in 16/39 (41%) patients. In eight cases evidence was found for involvement of multiple candidate drivers contributing to different parts of the phenotypes. Subsequently, we applied this computational method to a collection of 382 patients with previously detected and classified de novo SVs and identified candidate driver genes in 210 cases (54%), including 32 cases whose SVs were previously not classified as pathogenic. Pathogenic positional effects were predicted in 25% of the cases with balanced SVs and in 8% of the cases with copy number variants.\n\nConclusionsThese results show that driver gene prioritization based on integrative analysis of WGS data with phenotype association and chromatin organization datasets can improve the molecular diagnosis of patients with de novo SVs.

genomics↗

bioRxiv2019

The WT1-like transcription factor Klumpfuss maintains lineage commitment in the intestine

Stem cell (SC) lineages in barrier epithelia exhibit a high degree of plasticity. Mechanisms that govern the precise specification of SC daughter cells during regenerative episodes are therefore critical to maintain homeostasis. One such common mechanism is the transient activation of the Notch (N) signaling pathway. N controls the choice between absorptive and entero-endocrine cell fates in both the mammalian small intestine and the Drosophila midgut, yet how precisely N signaling promotes lineage restriction in progenitor cells remains unclear. Here, we describe a role for the WT1-like transcription factor Klumpfuss (Klu) in restricting the fate of Drosophila enteroblasts (EBs) downstream of N activation. Klu is transiently induced in Notch-positive EBs and its transient activity restricts cell fate towards the enterocyte (EC) lineage. Transcriptomics and DamID profiling show that Klu suppresses enteroendocrine (EE) cell fates by repressing E(Spl)m8-HLH and Phyllopod, both negative regulators of the proneural gene Scute, which is essential for EE differentiation. At the same time, Klu suppresses cell cycle genes, committing EBs to differentiation. Klu-mediated repression of its own transcription further sets up a negative feedback loop that ensures temporal restriction of Klu-mediated gene regulation, and is essential for subsequent differentiation of ECs. Our findings define a transient cell state in which EC lineage restriction is cemented, and establish a hierarchy of transcriptional programs critical in executing a differentiation program downstream of initial induction events governed by N signaling.

developmental biology↗

bioRxiv2018

Mutational impact of culturing human pluripotent and adult stem cells

Genetic changes acquired during in vitro culture pose a potential risk for the successful application of stem cells in regenerative medicine. To assess mutation accumulation risks induced by culturing, we determined genetic aberrations in individual human induced pluripotent stem cells (iPS cells) and adult stem cells (ASCs) by whole genome sequencing analyses. Individual iPS cells, intestinal ASCs and liver ASCs accumulated 3.5{+/-}0.5, 7.2{+/-}1.0 and 8.4{+/-}3.6 base substitutions per population doubling, respectively. The annual in vitro mutation accumulation rate of ASCs adds up to [~]1600 base pair substitutions, which is [~]40-fold higher than the in vivo rate of [~]40 base pair substitutions per year. Mutational analysis revealed a distinct in vitro induced mutational signature that is irrespective of stem cell type and distinct from the in vivo mutational signature. This in vitro signature is characterized by C to A changes that have previously been linked to oxidative stress conditions. Additionally, we observed stem cell-specific mutational signatures and differences in transcriptional strand bias, indicating differential activity of DNA repair mechanisms between stem cell types in culture. We demonstrate that the empirically defined mutation rates, spectra, and genomic distribution enable risk assessment by modelling the accumulation of specific oncogenic mutations during typical in vitro expansion, manipulation or screening experiments using human stem cells. Taken together, we have here for the first time accurately quantified and characterized in vitro mutation accumulation in human iPS cells and ASCs in a direct comparison. These results provide insights for further optimization of culture conditions for safe in vivo utilization of these cell types for regenerative purposes.

genomics↗

bioRxiv2017

Mapping And Phasing Of Structural Variation In Patient Genomes Using Nanopore Sequencing

Structural genomic variants form a common type of genetic alteration underlying human genetic disease and phenotypic variation. Despite major improvements in genome sequencing technology and data analysis, the detection of structural variants still poses challenges, particularly when variants are of high complexity. Emerging long-read single-molecule sequencing technologies provide new opportunities for detection of structural variants. Here, we demonstrate sequencing of the genomes of two patients with congenital abnormalities using the ONT MinION at 11x and 16x mean coverage, respectively. We developed a bioinformatic pipeline - NanoSV - to efficiently map genomic structural variants (SVs) from the long-read data. We demonstrate that the nanopore data are superior to corresponding short-read data with regard to detection of de novo rearrangements originating from complex chromothripsis events in the patients. Additionally, genome-wide surveillance of SVs, revealed 3,253 (33%) novel variants that were missed in short-read data of the same sample, the majority of which are duplications < 200bp in size. Long sequencing reads enabled efficient phasing of genetic variations, allowing the construction of genome-wide maps of phased SVs and SNVs. We employed read-based phasing to show that all de novo chromothripsis breakpoints occurred on paternal chromosomes and we resolved the long-range structure of the chromothripsis. This work demonstrates the value of long-read sequencing for screening whole genomes of patients for complex structural variants.

genomics↗