Biology subjects

Mattila, J.

Publications and source records attributed to Mattila, J..

12 recordsLinked to original sources

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

Neutrophils rapidly release nucleoli-stored IFNα during infection

Type I interferons (IFN-I) are critical for antiviral defense but can drive severe pathology when dysregulated. Excess IFN-I is associated with prominent neutrophil accumulation; however, the contribution of neutrophils to IFN-I overproduction remains underexplored. In all cell types previously studied, IFN-I is synthesized de novo following sensing of microbial or host-derived inflammatory stimuli. Contrary to this paradigm, we find that neutrophils express IFN during development and store it in the nucleolus, a membrane-less intranuclear condensate classically functioning in ribosome biogenesis. TLR-mediated bacterial sensing induces a nucleolar stress response in neutrophils that triggers rapid release of nucleoli-stored IFN independent of de novo protein synthesis. These findings reveal that neutrophils have repurposed the nucleolus as a cytokine storage and secretory organelle, identify the first naturally occurring immunoregulatory function of nucleolar stress, and provide insight into the relationship between detrimental IFN-I levels and neutrophil accumulation.

immunology↗

bioRxiv2026

SIV infection disrupts the spatial cellular and communication networks of pulmonary granulomas during SIV/Mtb co-infection

Tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) is the leading infectious cause of death globally. Despite wide use of antiretroviral therapy (ART) by people living with HIV, the risk of TB remains increased. To understand immune interactions within lung granulomas, we compared spatial transcriptomics of Mtb and simian immunodeficiency virus (SIV) in co-infected macaques with or without ART as a model for HIV/Mtb co-infection. Spatially differentiated transcriptional profiles were observed in Mtb-only granulomas, with myeloid cells enriched in metabolic/antimicrobial pathways within the inner ring and T cell costimulatory/activation pathways enriched in the outer ring. These spatially distinct patterns were lost in SIV/Mtb granulomas with higher enrichment in type I IFN pathways compared to Mtb-only granulomas. SIV/ART/Mtb granulomas had an intermediate transcriptional pattern without restoration to Mtb-only granulomas, despite a lack of viral replication. Cell-cell communication was reduced among SIV/Mtb co-infected groups. These data suggest that HIV disrupts spatially organized immune functions of granulomas, which are not fully restored by ART.

immunology↗

bioRxiv2026

Neighborhood-Level Disadvantage Impacts Multiple Measures of Brain Health: An Imaging Epidemiology Study

BackgroundThe relationship between neighborhood-level socioeconomic disadvantage and brain health is an emerging area of research with critical implications for public health and clinical practice, yet its influence on brain structure remains unclear. PurposeTo investigate the epidemiological association between neighborhood-level socioeconomic disadvantage [Area Deprivation Index (ADI)] and morphometric neuroimaging variables in a consecutive, non-disease enriched patient population. Materials and MethodsThis study, conducted at an academic medical center and associated community partners, used consecutive cross-sectional MRI neuroimaging data from 2,826 inpatient and outpatient individuals without radiological evidence of disease from January 2024 to June 2024. ADI, a geospatially determined index of neighborhood-level disadvantage, was calculated for each individual. Linear regressions tested the relationship between ADI and multiple morphometric variables: brain age gap (BAG; estimated - chronological BA), total brain tissue volume (TBV; total gray + white matter), five subcortical region volumes (hippocampus, thalamus, caudate, putamen, and nucleus accumbens) and four cortical region volumes [anterior cingulate cortex, posterior cingulate cortex, medial prefrontal cortex (MPFC), lateral PFC (LPFC)]. Volumetric measures were normalized to intracranial volume. Models controlled for age, sex, and total white matter hyperintensity volume (WMHV). Results2,826 individuals (mean age, 52.7 {+/-} 18.8 [standard deviation]; 1732 women) were evaluated. Residence in the 20% most disadvantaged neighborhoods was associated with a higher BAG ({beta}s > 2.12, Ps < .01) and decreased TBV ({beta}s < -5.12, Ps < .05). Additionally, increased WMHV was higher among those in the most disadvantaged neighborhoods (ts < - 2.50, Ps < .05) and associated with lower volume in most regions. Interaction models showed increased negative associations between WMHV and volumes of the caudate, nucleus accumbens, and lateral prefrontal cortex among those in the most disadvantaged neighborhoods. ConclusionsNeighborhood disadvantage is associated with adverse brain morphometry, including higher BAG, lower TBV, and amplified vascular-related regional volume loss. Key ResultsO_LIIn 2,826 adults (mean age, 53 years {+/-} 19; 1,732 women), residence in the most disadvantaged neighborhoods (national: 116/2,826, 4%; state: 129/2826, 5%) was associated with higher brain age gap at the national ({beta} = 2.12, 95% CI = 0.81 to 3.43, P = .001) and state levels ({beta} = 2.36; 95% CI = 1.10 to 3.61, P < .001). C_LIO_LITotal brain tissue volume was lower at the national ({beta} = -5.12, 95% CI = -10.13 to -0.11, P = .045) and state levels ({beta} = -6.13, 95% CI = -10.90 to -1.37, P = .011). C_LIO_LIWhite matter hyperintensity volume was higher in the most disadvantaged group (national: P = .013; state: P = .003) and demonstrated amplified associations with caudate, nucleus accumbens, and lateral prefrontal cortex volumes in the most disadvantaged group at the national and/or state levels (Ps < .05). C_LI

neuroscience↗

bioRxiv2026

Nuclear Factor Y controls epithelial growth by regulating mTOR in the Drosophila midgut

The intestinal epithelial lining is highly dynamic, with size and cellular composition adapting to nutrient status. This requires regulation of intestinal stem cell (ISC) proliferation and enterocyte (EC) size. How the absorptive area of the intestine matches physiological nutrient conditions remains unclear. Here, we show that the Nuclear Factor Y (NF-Y) transcription factor plays a role in this process. NF-Y loss-of-function (LOF) in ISCs led to high proliferation and cell growth, a phenotype influenced by dietary nutrients. NF-Y LOF also increased nutrient metabolism, shown by more mitochondria and larger lipid droplets in progenitors. Mechanistically, NF-Y restrains mTOR complex 1 (mTORC1) activity in ISC by controlling transcription of mTORC1 signaling components such as Iml1 and Sestrin. Overall, our results demonstrate that NF-Y limits excessive intestinal epithelial growth under nutrient-rich conditions. HighlightsO_LINF-Y is a cell-autonomous regulator of ISC activity C_LIO_LINF-Y restricts ISC proliferation and epithelial growth under nutrient-rich condition C_LIO_LINF-Y regulates mitochondrial biogenesis and lipid storage in progenitors C_LIO_LINF-Y limits mTORC1 activity in progenitors C_LI

physiology↗

bioRxiv2025

Spalt-related is an integrated stress response-activated inhibitor of mTORC1-mediated growth

Anabolic and catabolic processes are coordinated by a conserved regulatory network, which includes the nutrient sensing protein kinase mTOR complex 1 (mTORC1) and the insulin- and stress-responsive transcription factor FoxO. In physiological setting these regulators align growth, storage, reproduction, and aging with nutrient availability. Here, we identify transcription factor Spalt-related (Salr), previously implicated in organogenesis, as a negative regulator of growth and lipid storage. In the Drosophila fat body Salr activates catabolic gene expression and restricts mTORC1-mediated cell growth. The genomic binding of Salr overlaps extensively with that of FoxO and similar convergence is observed between their mammalian homologs SALL1 and FOXO1. Both Salr and FoxO are activated upon fasting but respond to distinct cues: while FoxO displays transient activation and is responsive to AKT inhibition, Salr is activated in a slow and sustained manner through the integrated stress response. Once activated, Salr counters nuclear localization of FoxO. Together, Salr and FoxO are converging transcriptional activators of catabolism during nutrient stress.

cell biology↗

bioRxiv2025

Rapid apical actin filament turnover is required for non-centrosomal microtubule organization in epithelium

Epithelial cells rely on the precise coordination of actin and microtubule cytoskeletons to maintain their polarized structure and function. Within polarized epithelial cells, microtubules form longitudinal non-centrosomal arrays essential for organelle positioning and facilitate directional cargo trafficking whereas the apical actin cytoskeleton supports cell shape and tissue architecture. This study investigates the interplay between disrupted apical actin dynamics and microtubule organization in vivo within Drosophila epithelial tissue. Loss of actin turnover promoting Cyclase-Associated Protein (CAP) results in the excessive accumulation of stable actin structures at the apical cortex. We show that accumulated apical actin sterically excludes microtubules and membrane-bound vesicles. Consequently, non-centrosomal microtubule-dependent processes are impaired, leading to nuclear mispositioning, disrupted apical cargo transport, and defective microvilli formation in CAP mutant cells. Our findings highlight that dense apical actin, due to impaired actin turnover catalyzed by CAP, disrupts the apical organization of non-centrosomal microtubules. This suggests that spatially regulated actin filament turnover is important for microtubule organization and sustaining the polarized functions of epithelial tissues.

cell biology↗

bioRxiv2025

Spatially-distinct programming of macrophage diversity within the granulomas of Mycobacterium tuberculosis infected nonhuman primates

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is defined by granulomas-- immune aggregates that either contain or support bacterial replication. Macrophages, fundamental components of these lesions, are crucial to TB pathogenesis, yet their phenotypic and functional diversity is incompletely understood. Here, we used single-cell RNA sequencing and immunofluorescence to profile macrophages in lung tissue and granulomas from a nonhuman primate model of early TB. We identified distinct subsets, including embryonic-origin tissue-resident alveolar macrophages and monocyte-derived alveolar and interstitial macrophages, with distinct spatial localization in granulomas. Tissue-resident alveolar macrophages and a subset undergoing epithelial-to-mesenchymal transition accounted for the highest frequency of Mtb-infected cells. Infected cells exhibited differential expression of immune- and migration-associated genes compared to uninfected counterparts, suggesting Mtb either induces or exploits these pathways as a survival strategy. These findings highlight macrophage heterogeneity as a major driver of differential susceptibility to Mtb and provide insights relevant to future immunomodulatory strategies.

immunology↗

bioRxiv2025

The immunometabolic topography of tuberculosis granulomas governs cellular organization and bacterial control

Despite being heavily infiltrated by immune cells, tuberculosis (TB) granulomas often subvert the host response to Mycobacterium tuberculosis (Mtb) infection and support bacterial persistence. We previously discovered that human TB granulomas are enriched for immunosuppressive factors typically associated with tumor-immune evasion, raising the intriguing possibility that they promote tolerance to infection. In this study, our goal was to identify the prime drivers for establishing this tolerogenic niche and to determine if the magnitude of this response correlates with bacterial persistence. To do this, we conducted a multimodal spatial analysis of 52 granulomas from 16 non-human primates (NHP) who were infected with low dose Mtb for 9-12 weeks. Notably, each granulomas bacterial burden was individually quantified allowing us to directly ask how granuloma spatial structure and function relate to infection control. We found that a universal feature of TB granulomas was partitioning of the myeloid core into two distinct metabolic environments, one of which is hypoxic. This hypoxic environment associated with pathologic immune cell states, dysfunctional cellular organization of the granuloma, and a near-complete blockade of lymphocyte infiltration that would be required for a successful host response. The extent of these hypoxia-associated features correlated with worsened bacterial burden. We conclude that hypoxia governs immune cell state and organization within granulomas and is a potent driver of subverted immunity during TB.

immunology↗

bioRxiv2024

PROPERMAB: an integrative framework for in silico prediction of antibody developability using machine learning

Selection of lead therapeutic molecules is often driven predominantly by pharmacological efficacy and safety. Candidate developability, such as biophysical properties that affect the formulation of the molecule into a product, is usually evaluated only toward the end of the drug development pipeline. The ability to evaluate developability properties early in the process of antibody therapeutic development could accelerate the timeline from discovery to clinic and save considerable resources. In silico predictive approaches, such as machine learning models, which map molecules to predictions of developability properties could offer a cost-effective and high-throughput alternative to experiments for antibody developability assessment. We developed a computational framework, PROPERMAB, for large-scale and efficient in silico prediction of developability properties for monoclonal antibodies, using custom molecular features and machine learning modeling. We demonstrate the power of PROPERMAB by using it to develop models to predict antibody hydrophobic interaction chromatography retention time and high-concentration viscosity. We further show that structure-derived features can be rapidly and accurately predicted directly from sequences by pre-training simple models for molecular features, thus providing the ability to scale these approaches to repertoire-scale sequence datasets.

bioinformatics↗

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↗

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↗