Biology subjects

Katajisto, P.

Publications and source records attributed to Katajisto, P..

At least 19 recordsLinked to original sources

bioRxiv2026

mTORC1-dependent control of Hedgehog signaling mediates nutrient-responsive licensing of intestinal stem cell differentiation

How progenitor cells couple their metabolic state to the regulation of fate and differentiation remains a fundamental question in tissue development and regeneration. Here, we identify a nutrient-responsive circuit that links progenitor anabolism to differentiation in the Drosophila midgut. We show that the mTORC1 downstream effector PWP1 is necessary and sufficient for differentiation of intestinal stem cell progeny toward the absorptive lineage in fed animals. In progenitors with high mTORC1 activity, PWP1 controls gene expression to promote Hedgehog (Hh) signaling, which cell autonomously drives progenitor differentiation into enterocytes. This circuit is constrained by feedback regulation, as elevated Hh activity inhibits mTORC1 and consequently excludes PWP1 from the nucleus. Disruption of the mTORC1-PWP1-Hh axis causes a progressive failure of enterocyte turnover during aging and reduced lifespan. While the aged midguts retain their barrier function, defective renewal leads to aging-associated deregulation of intestinal metabolism. Collectively, these observations support the concept of growth-dependent licensing of differentiation, whereby the nutrient-responsive anabolic state of a progenitor cell controls its lineage progression, consequently enabling organ renewal.

physiology↗

bioRxiv2026

Nutrient-responsive midgut turnover is spatially controlled by serotonin signaling

Barrier epithelia undergo rapid turnover, yet how spatial tissue heterogeneity and environmental cues shape turnover rates remains poorly understood. Here, we show that serotonin signaling spatially regulates homeostatic turnover of the Drosophila midgut epithelium in a nutrient-responsive manner. Organ-wide analysis revealed regions of constitutively high and low turnover, as well as areas whose renewal depends on nutrient intake. In rapidly renewing posterior regions, serotonin accumulates in enterocytes undergoing programmed cell death (erebosis) in response to nutrient availability. Serotonin signals through the conserved 5HT7 receptor to promote enteroblast (EB) maturation and migration-associated morphological changes. 5HT7 signaling is both necessary and sufficient for renewal in high-turnover regions, and its sustained disruption leads to epithelial multilayering. Mechanistically, 5HT7 signaling regulates genes involved in metabolic pathways, such as the serine biosynthesis pathway, and in the actin cytoskeleton, which drive EB maturation and morphological change, respectively. Together, our findings establish a signaling mechanism that links nutritional cues to the spatial regulation of barrier epithelium turnover.

physiology↗

bioRxiv2026

Metabolic commitment to human motor neurons is characterized by mitochondrial depletion and pyruvate rewiring

Mitochondrial remodelling is a key feature of neurogenesis in cortical and hippocampal neuronal lineages, yet the temporal control of organellar homeostasis in developing human motor neurons remains poorly understood. Here, we generated a high-resolution temporal resource integrating proteomics, metabolomics, and mitochondrial characterization across human iPSC-to-motor neuron differentiation. This analysis revealed prolonged mitochondrial depletion during early neurogenesis, characterized by reduced mitochondrial content, mitochondrial fragmentation, and lysosome-dependent turnover. This state persisted throughout the neural progenitor stage and was followed by recovery of mitochondrial content during neuronal maturation. During this transition, pyruvate utilization shifted from pyruvate carboxylation towards pyruvate dehydrogenase-dependent oxidation. Pharmacological manipulation of pyruvate partitioning demonstrated that this metabolic switch is required for human neuronal differentiation. Our findings establish a temporal framework for the metabolic control of human motor neuron differentiation and reveal a progenitor-specific state linking mitochondrial depletion to pyruvate metabolism.

cell biology↗

bioRxiv2026

Loss of mitochondrial co-chaperone GRPEL2 protects mice from age- and diet-induced obesity

Mitochondrial protein homeostasis intersects with metabolic control, but the in vivo roles of specific mitochondrial co-chaperones remain unclear. The chaperone mtHSP70 plays a key role in import and folding of nuclear-encoded proteins targeted to mitochondrial matrix. Its protein folding cycle is regulated by the GrpE-like nucleotide exchange factor GRPEL1. Vertebrates also have a GRPEL2 paralog, postulated as the stress-sensitive counterpart, but its physiological relevance is not known. We show here that GRPEL2 is not essential for viability in mice, and its absence does not induce proteotoxic stress responses in stark contrast to GRPEL1. However, we find that GRPEL2 has a role in regulating body weight homeostasis. GRPEL2 knockout mice are protected from age- and diet-induced weight gain and maintain a better metabolic health and insulin sensitivity. Transcriptional profiling revealed minimal changes in liver and skeletal muscle, whereas white adipose tissue from Grpel2-deficient mice lacked the obesity-associated remodeling seen in controls. We propose that GRPEL2 fine-tunes metabolic setpoints without broadly perturbing mitochondrial protein import, thereby maintaining adipose tissue health during nutritional excess. These findings show that subtle alterations in mitochondrial chaperone systems reshape systemic metabolism and could suggest strategies to mitigate obesity and insulin resistance through targeted modulation of mitochondrial proteostasis.

physiology↗

bioRxiv2025

Alanine catabolism of Paneth cells maintains intestinal stem cell function during dietary restriction

Background and aimsPaneth cell niche promotes the function of intestinal stem cells (ISCs) during reduced food intake, but how ISC activity can be boosted when availability of resources is simultaneously reduced remains unknown. MethodsMice were subjected to dietary restriction (DR) and ad libitum (AL) dietary regime. FACS-sorted DR and AL Paneth cells and Lgr5+ stem cells were co-cultured, and organoid formation supportive capacity of Paneth cells was assessed. The role of Gpt2 - a Paneth cell specific mitochondrial alanine transaminase, was investigated by targeting pharmacologically and genetically in the intestinal organoids. By using U-13C labelled Alanine, an intercellular metabolic exchange assay was developed - and a conversion and transport of lactate from Paneth cells to stem cells, was followed by metabolomics. The in vivo role of Gpt2 was investigated in a conditional knock out mouse model. ResultsWe discovered that an increase in ISC function upon dietary restriction (DR) or DR mimicking condition, is dependent on Gpt2 in Paneth cells. Metabolic tracing of alanine directly showed DR boosts Paneth cell alanine catabolism, increasing lactate production via gluconeogenesis. Alanine derived lactate is shuttled from Paneth cells to neighboring stem cells, promoting TCA cycle and enhancing the ISC function during DR. Correspondingly, pharmacologic inhibition in vitro and genetic targeting of Gpt2 in vivo abolished the DR induced capacity of Paneth cells to support ISC function. ConclusionsOur results unravel dynamic intercellular metabolic cooperation in tissue adaptation, where Paneth cells upregulated Gpt2 catabolize increased amount of alanine to generate lactate as a transferable energy source, and to augment stem cell functions under DR.

cell biology↗

bioRxiv2025

High-resolution integrative analysis allows characterization and spatial annotation of normal and cancer-associated colon fibroblasts

Fibroblasts represent key regulators of colon homeostasis, and cancer-associated fibroblasts (CAFs) play pivotal roles in colorectal cancer (CRC). Despite their critical influence, a consensus view of adult human colon fibroblast and CRC CAF heterogeneity, spatial organization, and developmental trajectories is currently lacking. Here, we address this gap by performing a comprehensive characterization of colonic fibroblasts and CRC CAFs. Using large-scale integration of single-cell RNA-sequencing datasets from normal colon and CRC we mapped the fibroblast subpopulations. Spatial transcriptomics, immunohistochemistry, and in situ hybridization were used for validation and computational analyses to predict developmental trajectories and transcription factors underlying CAF activation. Subepithelial myofibroblasts (SEMFs), mucosa-associated fibroblasts (MAFs), and submucosa-associated fibroblasts (SAFs) were identified as the main colon fibroblast subtypes, and in mice, further divided into location-based subclusters. We also identified a novel colon fibroblast subset: muscle-embedded interstitial fibroblasts (MIFs). CRCs contained normal fibroblasts as well as four cancer-specific CAF populations: inflammatory CAFs (iCAFs), matrix CAFs (mCAFs), and two precursor CAF (preCAF) subtypes. Our data suggested that iCAFs originate from SEMFs through a preCAF1 intermediate phenotype, while mCAFs derive from SAFs/MIFs via preCAF2s. Transcription factors PRRX1, MAFB, and TWIST1 were uncovered as potential regulators of CAF identity and CTHRC1 was identified as a specific and sensitive pan-CAF marker in CRC. Our study presents a detailed framework for understanding colon fibroblast and CRC CAF heterogeneity. This work lays the groundwork for future research into the roles and potential therapeutic relevance of different CRC CAF subsets.

cancer biology↗

bioRxiv2024

Tumour-derived LAMA5 is critical for tumour initiation and controls progression and phenotype in luminal breast cancer

Basement membrane (BM) supports and regulates the structural integrity, function and differentiation of epithelial tissues and protects against breast cancer invasion to stroma. Here we show that the BM component LAMA5 is critical for initiation of luminal mammary tumours, and controls tumour progression and phenotype development. LAMA5 is overexpressed in human breast carcinomas and LAMA5 downregulation attenuates growth of human breast cancer cells. Prepubertal luminal deletion of Lama5 in MMTV-PyMT mice results in marked reduction in emergence of early hyperplasias, along with a shift towards luminal progenitor-like phenotype. However, single allele deletion, but not biallelic deletion of Lama5 inhibits growth and progression towards advanced mammary carcinomas. Lama5 deficient luminal epithelial cells collectively display widespread alterations in Fibroblast growth factor (Fgf) signalling genes, including increased expression of Fgf receptor 2 (Fgfr2). Inhibition of Fgf receptors decreases growth and induces apoptosis also in biallelic-Lama5-deleted organoids without affecting wildtype organoids. Our results demonstrate a critical role for the BM component LAMA5 in mammary tumour initiation and reveal mechanisms of ECM-epithelial interplay in breast tumour progression and phenotype maintenance.

cancer biology↗

bioRxiv2024

Aging limits stemness and tumorigenesis in the lung by reprogramming iron homeostasis

Aging is associated with a decline in the number and fitness of adult stem cells1-4. Aging-associated loss of stemness is posited to suppress tumorigenesis5,6, but this hypothesis has not been tested in vivo. Here, using physiologically aged autochthonous genetically engineered mouse models and primary cells7,8, we demonstrate aging suppresses lung cancer initiation and progression by degrading stemness of the alveolar cell of origin. This phenotype is underpinned by aging-associated induction of the transcription factor NUPR1 and its downstream target lipocalin-2 in the cell of origin in mice and humans, leading to a functional iron insufficiency in the aged cells. Genetic inactivation of the NUPR1--lipocalin-2 axis or iron supplementation rescue stemness and promote tumorigenic potential of aged alveolar cells. Conversely, targeting the NUPR1-- lipocalin-2 axis is detrimental to young alveolar cells via induction of ferroptosis. We find that aging-associated DNA hypomethylation at specific enhancer sites associates with elevated NUPR1 expression, which is recapitulated in young alveolar cells by inhibition of DNA methylation. We uncover that aging drives a functional iron insufficiency, which leads to loss of stemness and tumorigenesis, but promotes resistance to ferroptosis. These findings have significant implications for the therapeutic modulation of cellular iron homeostasis in regenerative medicine and in cancer prevention. Furthermore, our findings are consistent with a model whereby most human cancers initiate in young individuals, revealing a critical window for such cancer prevention efforts.

cancer biology↗

bioRxiv2024

Ribosome-binding protein 1, RRBP1, maintains peroxisomal biogenesis

Peroxisomes are single membrane-bound organelles essential for human health, yet the mechanisms of peroxisome biogenesis are not fully understood. Here using a systematic double screening approach, we identified ribosome-binding protein 1, RRBP1, as a novel peroxisome biogenesis factor in human cells. Deletion of RRBP1 in HEK293T cells led to a reduction in both peroxisome number and peroxisomal protein levels as well as in defects in processing of peroxisomal matrix proteins, such as ACOX1 and thiolase. However, cell proliferation and protein translation were not altered in cells lacking RRBP1. RRBP1 depletion did not affect peroxisome-ER contact sites, and pexophagy did not contribute to the reduction of peroxisomes in RRBP1 KO cells. Instead, in the absence of RRBP1, peroxisomal proteins were processed by proteasomal degradation, suggesting that RRBP1 plays a role in the insertion of these proteins into ER membranes and their stabilization. Altogether our results showed that RRBP1 promotes peroxisome biogenesis in human cells highlighting the power of systematic approaches in discovering novel factors of organellar biogenesis.

cell biology↗

bioRxiv2024

Inheritance of old mitochondria controls early CD8+ T cell fate commitment and is regulated by autophagy

T cell immunity is impaired during ageing, particularly in memory responses needed for efficient vaccination. Autophagy and asymmetric cell division (ACD) are cell biological mechanisms key to memory formation, which undergo a decline upon ageing. However, despite the fundamental importance of these processes in cellular function, the link between ACD and in vivo fate decisions has remained highly correlative in T cells and in the field of mammalian ACD overall. Here we provide robust causal evidence linking ACD to in vivo T cell fate decisions and our data are consistent with the concept that initiation of asymmetric T cell fates is regulated by autophagy. Analysing the proteome of first-daughter CD8+ T cells following TCR-triggered activation, we reveal that mitochondrial proteins rely on autophagy for their asymmetric inheritance and that damaged mitochondria are polarized upon first division. These results led us to evaluate whether mitochondria were asymmetrically inherited and to functionally address their impact on T cell fate. For this we used a novel mouse model that allows sequential tagging of mitochondria in mother and daughter cells, enabling their isolation and subsequent in vivo analysis of CD8+ T cell progenies based on pre-mitotic cell cargo. Autophagy-deficient CD8+ T cells showed impaired clearance and symmetric inheritance of old mitochondria, suggesting that degradation events promote asymmetry and are needed to generate T cells devoid of old organelles. Daughter cells inheriting old mitochondria are more glycolytic and upon adoptive transfer show reduced memory potential, whereas daughter cells that have not inherited old mitochondria from the mother cell are long-lived and expand upon cognate-antigen challenge. Proteomic and single-cell transcriptomic analysis of cells inheriting aged mitochondria suggest that their early fate divergence relies on one carbon metabolism as a consequence of poor mitochondrial quality and function. These findings increase our understanding of how T cell diversity is early-imprinted during division and will help foster the development of strategies to modulate T cell function. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=179 SRC="FIGDIR/small/577412v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@526135org.highwire.dtl.DTLVardef@6c04b1org.highwire.dtl.DTLVardef@1a834fforg.highwire.dtl.DTLVardef@2f70f8_HPS_FORMAT_FIGEXP M_FIG The MitoSnap model allows tracking of pre-mitotic and post-mitotic cell cargoes. Both segregation and degradation (autophagy) contribute to the asymmetric inheritance of old mitochondria. Old mitochondria impact cell metabolism and function. Cells devoid of old mitochondria exhibit better memory potential in vivo. C_FIG

cell biology↗

bioRxiv2023

The α-dystroglycan N-terminus is a broad-spectrum antiviral agent against SARS-CoV-2 and enveloped viruses

The COVID-19 pandemic has shown the need to develop effective therapeutics in preparedness for further epidemics of virus infections that pose a significant threat to human health. As a natural compound antiviral candidate, we focused on -dystroglycan, a highly glycosylated basement membrane protein that links the extracellular matrix to the intracellular cytoskeleton. Here we show that the N-terminal fragment of -dystroglycan (-DGN), as produced in E. coli in the absence of post-translational modifications, blocks infection of SARS-CoV-2 in cell culture, human primary gut organoids and the lungs of transgenic mice expressing the human receptor angiotensin I-converting enzyme 2 (hACE2). Prophylactic and therapeutic administration of -DGN reduced SARS-CoV-2 lung titres and protected the mice from respiratory symptoms and death. Recombinant -DGN also blocked infection of a wide range of enveloped viruses including the four Dengue virus serotypes, influenza A virus, respiratory syncytial virus, tick-borne encephalitis virus, but not human adenovirus, a non-enveloped virus in vitro. This study establishes soluble recombinant -DGN as a broad-band, natural compound candidate therapeutic against enveloped viruses.

microbiology↗

bioRxiv2023

Golgi organization is a determinant of stem cell function in the small intestine

Cell-to-cell signalling between niche and stem cells regulates tissue regeneration. While the identity of many mediating factors is known, it is largely unknown whether stem cells optimize their receptiveness to niche signals according to the niche organization. Here, we show that Lgr5+ small intestinal stem cells (ISCs) regulate the morphology and orientation of their secretory apparatus to match the niche architecture, and to increase transport efficiency of niche signal receptors. Unlike the progenitor cells lacking lateral niche contacts, ISCs orient Golgi apparatus laterally towards Paneth cells of the epithelial niche, and divide Golgi into multiple stacks reflecting the number of Paneth cell contacts. Stem cells with a higher number of lateral Golgi transported Epidermal growth factor receptor (Egfr) with a higher efficiency than cells with one Golgi. The lateral Golgi orientation and enhanced Egfr transport required A-kinase anchor protein 9 (Akap9), and was necessary for normal regenerative capacity in vitro. Moreover, reduced Akap9 in aged ISCs renders ISCs insensitive to niche-dependent modulation of Golgi stack number and transport efficiency. Our results reveal stem cell-specific Golgi complex configuration that facilitates efficient niche signal reception and tissue regeneration, which is compromised in the aged epithelium.

cell biology↗

bioRxiv2022

Shared requirement for MYC upstream super-enhancer in tissue regeneration and cancer

Cancer has been characterized as a wound that does not heal. Malignant cells are morphologically distinct from normal proliferating cells, but have extensive similarities to tissues undergoing wound healing and/or regeneration. The mechanistic basis of this similarity has, however, remained enigmatic. Here we show that the genomic region upstream of Myc, which is required for intestinal tumorigenesis, is also required for intestinal regeneration after radiation damage. The region is also critical for growth of adult intestinal cells in 3D organoid culture, indicating that culture conditions that recapitulate most aspects of normal tissue architecture still reprogram normal cells to proliferate using a mechanism similar to that employed by cancer cells. Our results uncover a genetic link between tissue regeneration and tumorigenesis, and establish that normal tissue renewal and regeneration of tissues after severe damage are mechanistically distinct. SummaryMyc regulatory region links regeneration and cancer

cancer biology↗

bioRxiv2022

Flat Clathrin Lattices Nucleate Reticular Adhesions in an Integrin β1 Activity-Dependent Manner

Reticular adhesions (RAs) consist of integrin v{beta}5 and harbor flat clathrin lattices (FCLs), long-lasting structures with similar molecular composition to clathrin mediated endocytosis (CME) carriers. Why FCLs and RAs colocalize is not known. Here, we show that FCLs assemble RAs in a process controlled by fibronectin (FN) and its receptor, integrin v{beta}5. We observed that cells on FN-rich matrices displayed fewer FCLs and RAs. CME machinery inhibition abolished RAs and live-cell imaging showed that RA establishment requires FCL co-assembly. The inhibitory activity of FN was mediated by the activation of integrin 5{beta}1 at Tensin1-positive fibrillar adhesions. Conventionally, endocytosis disassembles cellular adhesions by internalization of their components. Our results present a novel paradigm in the relationship between these two processes by showing that endocytic proteins can actively function in the assembly of cell adhesions. Furthermore, we show this novel adhesion assembly mechanism is coupled to cell migration via a unique crosstalk between cell matrix adhesions.

cell biology↗

bioRxiv2021

Fetal-like reversion in the regenerating intestine is regulated by mesenchymal Asporin

Epithelial tissues undergo fetal-like cellular reprogramming to regenerate after damage1,2. Although the mesenchyme and the extracellular matrix (ECM) play critical roles in tissue homeostasis and regeneration2-5, their role in repurposing developmental programs in epithelium is unknown. To model epithelial regeneration, we culture intestinal epithelium on decellularized small intestinal scaffold (iECM), and identify Asporin (Aspn), an ECM bound proteoglycan, as a critical mediator of cellular reprogramming. Aspn is produced by the mesenchyme, and we show that its effect on epithelial Tgf{beta}-signalling via CD44 is critical for fetal-like conversion. Furthermore, we demonstrate that Aspn is transiently increased upon chemotherapy-induced damage and pivotal for a timely induction of the fetal-like state and tissue regeneration. In summary, we establish a platform for modelling epithelial injury responses ex vivo, and show that the mesenchymal Aspn-producing niche controls tissue repair by regulating epithelial fetal-like reprogramming.

developmental biology↗

bioRxiv2021

Functional, metabolic and transcriptional maturation of stem cell derived beta cells

Transplantation of pancreatic islet cells derived from human pluripotent stem cells is a promising treatment for diabetes. Despite progress in stem cell-derived islet (SC-islet) generation, detailed characterization of their functional properties has not been conducted. Here, we generated functionally mature SC-islets using an optimized protocol and comprehensively benchmarked them against primary adult islets. Biphasic glucose stimulated insulin secretion developed during in vitro maturation, associated with cytoarchitectural reorganization and increased alpha cells. Electrophysiology and exocytosis of SC-islets were comparable to adult islets. Glucose-responsive insulin secretion was achieved despite differences in glycolytic and mitochondrial glucose metabolism. Single-cell transcriptomics of SC-islets in vitro and throughout 6 months of murine engraftment revealed a continuous maturation trajectory culminating in a transcriptional landscape closely resembling that of primary islets. Our thorough evaluation of SC-islet maturation highlights their advanced degree of functionality and supports their use in further efforts to understand and combat diabetes.

developmental biology↗

bioRxiv2021

LAM - an image analysis method for regionally defined organ-wide cellular phenotyping of the Drosophila midgut

Intestine is divided into functionally distinct regions along the anteroposterior (A/P) axis. How the regional identity influences the function of intestinal stem cells (ISCs) and their offspring remain largely unresolved. We introduce an imaging-based method, Linear Analysis of Midgut (LAM), which allows quantitative regionally defined cellular phenotyping of the whole Drosophila midgut. LAM transforms image-derived cellular data from three-dimensional midguts into a linearized representation, binning it into segments along the A/P axis. Through automated multi-variate determination of regional borders, LAM allows mapping and comparing cellular features and frequencies with subregional resolution. Through the use of LAM, we quantify the distributions of ISCs, enteroblasts and enteroendocrine cells in a steady state midgut, and reveal unprecedented regional heterogeneity in the ISC response to a Drosophila model of colitis. Taken together, LAM is a powerful tool for organ-wide quantitative analysis of the regional heterogeneity of midgut cells. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=193 SRC="FIGDIR/small/427422v1_ufig1.gif" ALT="Figure 1"> View larger version (62K): org.highwire.dtl.DTLVardef@4083c0org.highwire.dtl.DTLVardef@189e297org.highwire.dtl.DTLVardef@17b577borg.highwire.dtl.DTLVardef@ac5013_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2020

Polycomb Repressive Complex 2-controlled Essrg regulates intestinal Microfold cell differentiation.

Microfold cells (M cells) are immunosurveillance epithelial cells located in the Peyers patches in the intestine responsible for monitoring and transcytosis of antigens, microorganisms and pathogens. Many transcription factors, e.g., Spi-B and Sox8, necessary to M cell differentiation have been described but the exhaustive set of factors sufficient for differentiation and development of a mature M cell remains elusive. Moreover, the role of polycomb repressive complex 2 (PRC2) as an epigenetic regulator of M cell development has not yet been interrogated. Here, we show that PRC2 regulates a significant set of genes during the M cell differentiation including many transcription factors. Estrogen related receptor gamma (Esrrg) is a novel M cell specific transcription factor acting on a RankL-Rank induced NF-kB pathway, upstream of Sox8 and necessary but not sufficient for a mature M cell marker Gp2 expression. To conclude, with the aid of PRC2 target survey we identified the list of developmental genes specifically implicated in M cell development and Essrg as a necessary factor for Sox8-mediated M cell differentiation.

molecular biology↗