Biology subjects

Jackson, S.

Publications and source records attributed to Jackson, S..

At least 19 recordsLinked to original sources

bioRxiv2026

A Compact Regulatory Logic Governs Fibroblast Cell State Plasticity in Fibrosis

Fibroblast activation drives organ failure across human diseases, yet its regulatory basis remains largely undefined. Here, we repressed 280 conserved disease-activated enhancers using CRISPR droplet sequencing (CROP-seq) in ~550,000 fibroblasts, constructing a regulome of 15 gene programs governing the profibrotic state. Systematic TF perturbation converged on MEOX1 as a central regulator, and fibroblast-specific Meox1 deletion in mice improved cardiac function, reduced fibrosis, and rewired profibrotic fibroblasts toward quiescence in heart failure. Effector gene perturbation in human cardiac fibroblasts revealed distinct regulators of contractility, migration, and inflammatory signaling, and these programs were conserved across profibrotic states in human lung, liver, and skin. Simultaneous repression of just six enhancers using a multiplexed dCas12a-KRAB system collapsed the profibrotic network, suppressed migration and contraction, and rewired fibroblast paracrine signaling to attenuate macrophage inflammation. These findings define the regulatory logic of fibroblast plasticity and establish a new framework for reprogramming profibrotic cell states in disease.

genomics↗

bioRxiv2026

Collateral Immune Cell Signaling Compromises the Efficacy of T-cell Engaging Therapies for Cardiac Fibrosis

Cardiac fibrosis is causally linked to heart failure progression and survival. Currently, there are no approved treatments that directly target cardiac fibrosis. Recent studies have identified a subset of activated cardiac fibroblasts distinct from myofibroblasts that are marked by fibroblast activation protein (FAP) expression, emerge in the injured and diseased heart through inflammatory signaling, and contribute to fibrosis. Using a genetic mouse model, we demonstrate the potential benefits of FAP+ fibroblast depletion following myocardial infarction. Unexpectedly, while FAP targeted bispecific T-cell engaging antibodies (BiTE(R) molecules) effectively eliminate FAP+ fibroblasts from the heart, they surprisingly lead to accelerated deterioration of cardiac function, enhanced remodeling, and increased scar size. FAP BiTE(R) molecules elicit a robust cytokine response within the heart with prominent activation of interferon gamma (IFNg) and CD40 ligand pathways. Target cell killing was independent of IFNg; and CD40L signaling and blockade of these pathways was sufficient to unmask the protective therapeutic effects of FAP+ fibroblast depletion. Mechanistically, we reveal that IFNg; signaling to fibroblasts drives the differentiation of an independent lineage of activated fibroblasts not typically found in the infarcted heart, which are responsible for the harmful effects of FAP BiTE(R) molecules. Collectively, these findings highlight a previously unrecognized cardiac liability of BiTE(R) molecules and inform the design of the next generation of therapeutics.

immunology↗

bioRxiv2026

Complementary cytotoxicity of GD2-targeted photoimmunotherapy and 5-aminolevulinic acid photodynamic therapy in neuroblastoma and osteosarcoma

Phototherapy, a light-activated anticancer treatment, enables localized tumor-cell killing with distinct mechanisms of action. Photoimmunotherapy (PIT) produces immunogenic tumor cell death upon near-infrared light activation of a photoabsorber through antigen-specific targeting. Photodynamic therapy (PDT) produces reactive oxygen species through red-light activation of intracellular protoporphyrin IX generated from 5-aminolevulinic acid uptake and metabolism. PIT may have limited activity in antigen-low cells, whereas PDT has less precise tumor selectivity. We combined these modalities to define their interaction, broaden cytotoxicity, and determine whether dual treatment could reduce light-dose requirements. We conjugated dinutuximab, which targets the GD2 antigen, to IRDye 700DX and characterized plasma-membrane localization by confocal and widefield microscopy. PIT and PDT monotherapies were evaluated across agent and light doses in neuroblastoma (NB) and osteosarcoma (OS) cell lines. Combination matrices were tested using interaction, highest-single-agent, and Bliss analyses. Both monotherapies demonstrated significant light-dose-dependent effects in NB and OS. PIT produced no measurable cytotoxicity in antigen-blunted control cells, whereas PDT remained effective, confirming antigen-dependence of PIT and antigen-independence of PDT. The combination interaction was significant in SK-N-BE(2) but not LM7. At selected combinations, however, dual treatment produced greater killing than the more effective matched monotherapy in both SK-N-BE(2) and LM7 (Padj<0.022). Notably, lowest combination of PIT 10 J/cm2 plus PDT 10 J/cm2 achieved 90.3% killing in SK-N-BE(2), exceeding higher light-dose PIT or PDT monotherapy, suggesting a light-dose sparing effect. These findings establish potent and complementary PIT-PDT activity, supporting dual phototherapy to broaden cytotoxicity and reduce light-dose requirements in GD2-expressing tumor phototherapy.

cancer biology↗

bioRxiv2026

Genomic signatures of selection in the mound-building mouse Mus spicilegus

The steppe mouse Mus spicilegus is distinguished by several unusual phenotypes: animals of this species build complex mounds from brush and dirt, and this behavior as well as the pace of development is regulated by season of birth. The genetic and evolutionary basis of species-defining traits in Mus spicilegus is unknown. To discover genomic clues to the mechanisms at play, we took a molecular-evolution approach. Sequence-based tests of protein-coding exons, and of brain-active cis-regulatory regions, revealed a striking excess of evidence for evolutionary acceleration in the M. spicilegus genome relative to those of closely related species. Transcriptional analyses also revealed unique expression programs in the M. spicilegus brain, which could be traced in part to cis-regulatory sequence variation. Hit loci from our molecular-evolution tests tended to be active in the cerebral cortices and hypothalamus and have annotated functions in neuronal development, neural plasticity, or endocrine signaling. In many cases, their orthologs in other animal systems had been implicated in neoteny/the pace of maturation, unusual building behaviors, and autism. Together, our data indicate that M. spicilegus has undergone divergence in brain-active genes to an extent far more than its relatives. We interpret the affected genes under a model in which they mediate the seasonal capacity by M. spicilegus for protracted maturation and mound-building. Thus our work provides an evolutionary interpretation of, and catalog of candidate determinants for, shifts in motivated behavior and development in this intriguing mouse species.

evolutionary biology↗

bioRxiv2026

The impact of intermittent palatable food consumption on microbiota structure in male and female rats

The gut microbiome plays a vital role in metabolism, behavior, and overall health, with diet being a key factor shaping its composition. This study examines the impact of intermittent palatable food (PF) consumption on microbiota structure in male and female rats, focusing on feeding preferences and sex differences. Rats were characterized as high preferring (HP) or low preferring (LP) based on PF intake, and microbial analyses were conducted across different gastrointestinal regions, including the colon, feces, cecum, and cecal contents. However, microbiota composition varied with significant differences in Firmicutes, Bacteroidetes, and Actinobacteria abundances. Sex-based differences were evident particularly in fecal and cecal samples, where Proteobacteria and Actinobacteria populations varied between males and females within the same feeding groups. Our findings support the notion that dietary habits and microbiota composition may form a feedback loop, reinforcing food preferences through gut-brain axis signaling. While alpha diversity remained unchanged, beta diversity analysis indicated subtle, but significant differences in microbial community structures based on sex and feeding behavior. This research provides novel insights into the interplay between diet, gut microbiota, and behavior, while emphasizing the importance of considering sex as a variable in microbiome studies. Understanding these relationships may inform dietary interventions aimed at optimizing microbiota composition to improve metabolic and mental health outcomes linked to diet-induced microbiota shifts. ImportanceThe gut microbiome plays a critical role in various bodily functions, from the brains protective mechanisms to dietary behaviors and food choices. In this study, we sought to broaden the understanding of how various levels of high fat and high carbohydrate diet consumption alter gut microbiota, and ultimately, shape food preference behaviors. We assessed preference behaviors by categorizing rats into high-preference and low-preference groups based on their consumption of high calorie, palatable food, then analyzed their gut bacterial composition, comparing diet preference groups and examining whether sex differences were reflected in the results. The findings from this research hold significant implications for understanding the complex interplay between diet, microbiota, and behavior. Understanding the bidirectional relationship between feeding behavior and microbiota may provide novel insights into the mechanisms underlying eating disorders and metabolic dysregulation.

microbiology↗

bioRxiv2025

B7-H3 upregulation in ischemic stroke: friend or foe?

B7-H3 (CD276) is an immune checkpoint co-signaling molecule expressed on immune and non-immune cells. It is best known for suppressing T-cell responses but can also promote inflammation depending on the microenvironment. In neuroinflammatory models such as experimental autoimmune encephalomyelitis, B7H3 expression increases concomitantly with the inflammatory response, and its inhibition is associated with reduced disease progression. Although its role in ischemic stroke remains unclear, we hypothesized that cerebral ischemia/reperfusion (I/R) would upregulate B7-H3 expression in the ischemic brain and that increased B7-H3 expression would positively correlate with pro-inflammatory cytokine expression. Young and aged male and female rodents, including normotensive and spontaneously hypertensive rats to model comorbid hypertension, underwent transient middle cerebral artery occlusion (MCAO) followed by reperfusion. Brain tissue was collected on post-ischemic days 1, 3, 5, or 7. B7-H3 mRNA was analyzed by real-time PCR, whereas protein expression was assessed by Western blotting and immunohistochemistry at selected time points. B7-H3 expression was significantly upregulated in the ischemic brain across sexes, age groups, and species. The extent of B7-H3 degradation in the ischemic brain was influenced by species, sex, age, and time after cerebral I/R. Upregulation of B7-H3 was observed at both the mRNA and protein levels, and increased expression was localized primarily to the somatosensory cortex and caudate putamen in the ipsilateral hemisphere, the main regions affected in this MCAO model. Elevated B7-H3 expression in the ischemic brain positively correlated with the pro-inflammatory mediator TNF. The temporal profile of B7-H3 expression observed in rats paralleled the early inflammatory phase associated with secondary tissue damage following ischemic stroke. These findings identify B7-H3 as an ischemia-induced immune checkpoint molecule in the brain that may modulate post-stroke immune responses and support further investigation into its beneficial versus detrimental roles in neuroinflammation, as well as its potential as a therapeutic target following cerebral I/R.

neuroscience↗

bioRxiv2025

Automated filtering of particle images in single particle cryoEM

Continued exponential growth in the number of structures resolved by single particle cryoEM, as seen in the last decade, requires ever more effective data analysis workflows. Datasets are rarely homogeneous, demanding a multistep procedure for discarding outliers. Since individual particles are very noisy, either 2D or 3D averages are normally used for discrimination. This becomes challenging when the 2D classes themselves are heterogeneous, leading to selection of contaminants or discarding useful rare views/poses. The 3D model-based discrimination requires trustworthy 3D maps and a correct assignment of Euler angles, which in turn depends on the quality of the initial data and might not be available at the very early stages of the analysis. We propose a novel deep-learning approach for improving quality of single particle datasets. The two-stage procedure consists of denoising single particle images using Variational AutoEncoder framework followed by particle quality filtering based on the score inferred for every particle by Domain Adaptation Neural Network trained on a large data set of categorised 2D averages. This approach allows an automated scoring of noisy raw images using data patterns learned from the high signal-to-noise ratio, externally derived 2D classes. Consequently, a higher quality data set enters computationally expensive steps of the data analysis, reducing the need for protracted and expensive calculations. Importantly, our method does not require any prior knowledge about the data or existence of a 3D model, making it universally applicable. Tests on publicly available datasets demonstrated that our approach largely outperformed 2D class-based particle discrimination. Smaller subsets of the top-scoring particles selected with our method were required to obtain the author-reported 3D model resolution. When applied to the user data in the automated on-the-fly data processing pipeline, the method rescued 30% of cases, which otherwise would not reach confidence threshold required for making decision to proceed to the 3D model refinement. It also led to general improvements in the quality of the 3D models for many datasets which were selected for the high-resolution processing.

biophysics↗

bioRxiv2025

Angulin-1/LSR inhibition transiently disrupts the blood-tumor barrier to enhance doxil permeability and impair malignant glioma progression

The blood-tumor barrier (BTB) prevents effective central nervous system (CNS) drug delivery, especially in malignant gliomas. Brain endothelium predominates the BTB and connects through bicellular and tricellular tight junctions (TJ). Angulin-1/LSR, is a highly expressed endothelial tricellular TJ. Our studies explore the role of Angubindin-1, an Angulin-1/LSR binder, to disrupt tricellular TJ integrity, increase drug entry and hamper glioma progression. Using rat brain endothelial cells (RBMVEC) we tracked Angulin-1/LSR localization and expression to the membrane; binding tightest to Angubindin-1 2-8 hours post-treatment (p < 0.05). Angubindin-1 dose-dependently reduced bicellular and tricellular TJs 1-4 hours post treatment (p < 0.05), returning to baseline by 24 hours (p < 0.05). In human and rat-derived glioma cells, Angubindin-1 transiently reduced Angulin-1/LSR expression between 2-8 hours (p < 0.05), with return to baseline by 24 hours (p < 0.001). Silenced Angulin-1/LSR expression on endothelium resulted in decreased mRNA levels of bicellular (occludin, claudin-5, ZO-1) and tricellular (tricellulin/MARVELD2, angulin-1/LSR) TJs compared to control (p < 0.01). Angubindin-1 treatment also inhibited efflux transporter P-gp in both RBMVECs and glioma cells with high P-gp expression only. Orthotopic rat glioma models were treated with Doxil (3 mg/kg), Angubindin-1 (10 mg/kg), or combination to evaluate BTB permeability/drug accumulation, and overall survival. Combination therapy enhanced Doxil tumor accumulation by 20% (p < 0.001), reduced tumor volume by day 14 (77.5% vs. 81.6%, p < 0.05), and significantly extended survival compared to Doxil alone (24 days vs. 18 days, p < 0.0001). These findings demonstrate the effects of tricellular tight junction inhibition on disrupting the BTB, enhancing CNS drug delivery, and improving rodent glioma survival. SignificanceThis study demonstrates that Angubindin-1, a targeted modulator of tricellular tight junction protein Angulin-1/LSR, transiently disrupts BTB integrity to enhance chemotherapy delivery and prolong survival in glioma-bearing rats. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=145 SRC="FIGDIR/small/667901v1_ufig1.gif" ALT="Figure 1"> View larger version (76K): org.highwire.dtl.DTLVardef@b1b46corg.highwire.dtl.DTLVardef@bc552dorg.highwire.dtl.DTLVardef@7c1a74org.highwire.dtl.DTLVardef@1ace101_HPS_FORMAT_FIGEXP M_FIG C_FIG Angubindin-1 targets both bicellular tight junctions and the tricellular tight junction protein, Angulin-1/LSR, in brain endothelial and glioma cells leading to transient disruption of the blood-tumor barrier (BTB) and inhibition of P-glycoprotein towards enhanced Doxil penetration and reduced tumor burden.

cell biology↗

bioRxiv2025

Targeting RUNX1 in Macrophages Facilitates Cardiac Recovery

Despite advances in disease treatment, our understanding of how damaged organs recover and the mechanisms governing this process remain poorly defined. Here, we mapped the transcriptional and regulatory landscape of human cardiac recovery using single cell multiomics. Macrophages emerged as the most reprogrammed cell type. Deep learning identified the transcription factor RUNX1 as a key regulator of this process. Macrophage-specific Runx1 deletion recapitulated the human cardiac recovery phenotype in a chronic heart failure model. Runx1 deletion reprogrammed macrophages to a reparative phenotype, reduced fibrosis, and promoted cardiomyocyte adaptation. RUNX1 chromatin profiling revealed a conserved regulon that diminished during recovery. Mechanistically, the epigenetic reader BRD4 controlled Runx1 expression in macrophages. Chromatin activity mapping, combined with CRISPR perturbations, identified the precise regulatory element governing Runx1 expression. Therapeutically, small molecule Runx1 inhibition was sufficient to promote cardiac recovery. Our findings uncover a druggable RUNX1 epigenetic mechanism that orchestrates recovery of heart function.

immunology↗

bioRxiv2025

miRNA Mimic Optimization: Chemical Structure - Activity - Targetome Relationship to Engineer Selective Anti-Tumor Immunity in T cells

MicroRNA (miRNA) mimic therapies act through a broad and complex targetome in disease contexts. However, both the composition of these targetomes and the impact of chemical modifications on them remain poorly understood. In this study, we investigate eight fully chemically modified miRNA scaffolds across three miRNA sequences in a model immune disorder, graft-versus-host-disease (GvHD), which is an off-tumor effect of allogeneic T cell therapy. We demonstrate that conventional silencing assays fail to predict the functional performance of miRNA mimics in GVHD and graft-versus-leukemia (GvL), the on-tumor effect of allogeneic T cells. Moreover, we find that chemical scaffolds influence the duration of silencing mediated by miRNA mimics. We identify a miR-374b version as a lead miRNA candidate that not only inhibits GVHD but also enhances GVL--an unprecedented and desired improvement in on-versus-off-tumor selectivity of clinical relevance. Further analysis reveals distinct responder and non-responder groups to miR-374b therapy. While responders exhibit significant transcriptomic shifts, non-responders show virtually no changes, despite intact miRNA pathway function, underscoring a strong correlation between transcriptome reprogramming and therapeutic efficacy. RNA sequencing reveals that miR-374b acts via metabolic reprogramming of T cells and induces partially distinct transcriptional programs in GVHD and GVL. Collectively, our findings demonstrate that fully chemically modified miRNA mimic therapies are feasible to rewrite the T-cell transcriptome, profoundly improving on-versus-off-tumor specificity in T-cell-mediated cancer therapies.

bioengineering↗

bioRxiv2025

A systematic review of climate-change driven range shifts in mosquito vectors

As global temperatures rise, concerns about shifting mosquito ranges--and accompanying changes in the transmission of malaria, dengue, and other diseases--are mounting. However, systematic evidence for climate-driven changes in mosquito ranges remains limited. We conducted a systematic review of studies documenting expansions or contractions in medically important mosquito species. In total, 178 studies on six continents identified range expansions in 118 mosquito species. While over a third of these studies cited warming as a driver, fewer than 10% performed statistical tests of the role of climate. Instead, most expansions were linked to human-aided dispersal (e.g., trade, travel), land-use changes, and urbanization. Although several studies reported poleward or upward expansions consistent with climate warming, none demonstrated warm-edge contractions driven by rising temperatures, which are theoretically predicted in some settings. Rather than expanding into newly suitable areas, many expansions appear to be filling preexisting thermally suitable habitats. Our findings highlight the need for long-term mosquito monitoring, rigorous climate-attribution methods, and better documentation of confounding factors like land-use change and vector control efforts to disentangle climate-driven changes from other anthropogenic factors.

ecology↗

bioRxiv2025

Targeting Modulated Vascular Smooth Muscle Cells in Atherosclerosis via FAP-Directed Immunotherapy

Vascular smooth muscle cell (VSMC) and immune cell diversification play a central role in driving atherosclerotic coronary artery disease (CAD)1-3. However, the molecular mechanisms governing cell state transitions within the neo-intima in human CAD remain poorly understood, and no lipid-independent therapies are currently approved for its treatment. Here, we performed multi-omic single-cell gene expression profiling, epitope mapping, and spatial transcriptomics from 27 human coronary arteries. Our analysis identified fibroblast activation protein (FAP) as a marker of modulated VSMCs within the neo-intima. Genetic lineage tracing in mice confirmed that FAP cells in the plaque originate from medial VSMCs. Additionally, non-invasive positron emission tomography (PET) imaging in patients with CAD revealed focal FAP uptake in atherosclerotic lesions. Spatial transcriptomics further delineated the distinct localization of VSMC and immune cell subsets within plaques, with FAP states enriched in the neo-intima. To explore the therapeutic potential of targeting de-differentiated VSMCs, we developed an anti-FAP bispecific T-cell engager (BiTE) and demonstrated that it significantly reduced the plaque burden in multiple mouse models of atherosclerosis. Collectively, our study provides the first single-cell and spatially resolved map of human CAD, establishes FAP as a marker of modulated smooth muscle cells, and demonstrates the broader potential of immunotherapeutics for lipid independent targets in atherosclerotic CAD.

genomics↗

bioRxiv2024

ENDOTHELIAL PROX1 INDUCES BLOOD-BRAIN BARRIER DISRUPTION IN THE CENTRAL NERVOUS SYSTEM

The central nervous system (CNS) parenchyma has conventionally been believed to lack lymphatic vasculature, likely due to a non-permissive microenvironment that hinders the formation and growth of lymphatic endothelial cells (LECs). Recent findings of ectopic expression of LEC markers including Prospero Homeobox 1 (PROX1), a master regulator of lymphatic differentiation, and the vascular permeability marker Plasmalemma Vesicle Associated Protein (PLVAP), in certain glioblastoma and brain arteriovenous malformations (AVMs), has prompted investigation into their roles in cerebrovascular malformations, tumor environments, and blood-brain barrier (BBB) abnormalities. To explore the relationship between ectopic LEC properties and BBB disruption, we utilized endothelial cell-specific Prox1 overexpression mutants. When induced during embryonic stages of BBB formation, endothelial Prox1 expression induces hybrid blood-lymphatic phenotypes in the developing CNS vasculature. This effect is not observed when Prox1 is overexpressed during postnatal BBB maturation. Ectopic Prox1 expression leads to significant vascular malformations and enhanced vascular leakage, resulting in BBB disruption when induced during both embryonic and postnatal stages. Mechanistically, PROX1 downregulates critical BBB-associated genes, including {beta}-catenin and Claudin-5, which are essential for BBB development and maintenance. These findings suggest that PROX1 compromises BBB integrity by negatively regulating BBB-associated gene expression and Wnt/{beta}-catenin signaling.

developmental biology↗

bioRxiv2024

py_ped_sim - A flexible forward genetic simulator for complex family pedigree analysis

BackgroundLarge-scale family pedigrees are commonly used across medical, evolutionary, and forensic genetics. These pedigrees are tools for identifying genetic disorders, tracking evolutionary patterns, and establishing familial relationships via forensic genetic identification. However, there is a lack of software to accurately simulate different pedigree structures along with genomes corresponding to those individuals in a family pedigree. This limits simulation-based evaluations of methods that use pedigrees. ResultsWe have developed a python command-line-based tool called py_ped_sim that facilitates the simulation of pedigree structures and the genomes of individuals in a pedigree. py_ped_sim represents pedigrees as directed acyclic graphs, enabling conversion between standard pedigree formats and integration with the forward population genetic simulator, SLiM. Notably, py_ped_sim allows the simulation of varying numbers of offspring for a set of parents, with the capacity to shift the distribution of sibship sizes over generations. We additionally add simulations for events of misattributed paternity, which offers a way to simulate half-sibling relationships. We validated the accuracy of our software by simulating genomes onto diverse family pedigree structures, showing that the estimated kinship coefficients closely approximated expected values. Conclusionspy_ped_sim is a user-friendly and open-source solution for simulating pedigree structures and conducting pedigree genome simulations. It empowers medical, forensic, and evolutionary genetics researchers to gain deeper insights into the dynamics of genetic inheritance and relatedness within families.

bioinformatics↗

bioRxiv2024

The J-Like Protein ARC6 Regulates Chloroplast FtsZ-Ring Assembly through Fine-tuning ARC3 Activity in Arabidopsis

Chloroplast division is initiated by the establishment of the stromal FtsZ ring (Z ring). Assembly and positioning of the Z ring are governed by the chloroplast Min system, which inhibits Z-ring formation everywhere but the middle of the chloroplast. ACCUMULATION AND REPLICATION OF CHLOROPLASTS3 (ARC3), the core component of this system, is a direct inhibitor of Z-ring assembly. Regulation of ARC3 activity is vital thus for chloroplast division. Here, we report that ARC6, which localizes on the chloroplast inner envelope membrane, interacts with ARC3 and acts upstream of ARC3 during chloroplast division. We show that the C-terminal MORN domain of ARC3, demonstrated previously to prevent ARC3-FtsZ interaction, binds to the J-like domain (JLD) of ARC6, enabling full-length ARC3 to interact with FtsZ proteins and activating the inhibitory activity of ARC3 on the assembly of FtsZ filaments. Overexpression of a JLD-deleted version of ARC6 causes disruption of Z-ring formation in an ARC3-dependent manner. Finally, we reveal that ARC6 recruits ARC3 to the middle of the chloroplast. Our findings suggest a model whereby ARC6 regulates the assembly and positioning of the Z ring through fine-tuning the inhibitory activity of ARC3 at the chloroplast division site. One Sentence SummaryThe chloroplast membrane protein ARC6 recruits ARC3 to the chloroplast division site and regulates the assembly of the FtsZ ring by fine-tuning ARC3 activity through its J-like domain. The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (https://academic.oup.com/plcell/pages/General-Instructions) is: Cheng Chen (cgchen@sjtu.edu.cn).

plant biology↗

bioRxiv2023

Translational mapping of spatially resolved transcriptomes in human and mouse pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease with poor prognosis and limited treatment options. Efforts to identify effective treatments are thwarted by limited understanding of IPF pathogenesis and poor translatability of available preclinical models. To address these limitations, we generated spatially resolved transcriptome maps of human IPF and bleomycin-induced mouse lung fibrosis. We uncovered distinct fibrotic niches in the IPF lung, characterized by aberrant alveolar epithelial cells in a microenvironment dominated by TGF{beta} signaling alongside factors such as p53 and ApoE. We also identified a clear divergence between the arrested alveolar regeneration in the IPF fibrotic niches, and the active tissue repair in the acutely fibrotic mouse lung. Our study offers in-depth insights into the IPF transcriptional landscape and proposes alveolar regeneration as a promising therapeutic strategy for IPF.

molecular biology↗

bioRxiv2023

The potential of Senicapoc, a KCNN4 inhibitor, for the prevention and treatment of breast cancer

BackgroundGenome-wide association studies have identified a breast cancer risk locus at 19q13.31. The candidate causal variants at this locus are located in the first exon of KCNN4. KCNN4, which regulates membrane potential and Ca2+ signaling, is a good candidate for drug repositioning because its inhibitor, Senicapoc, has been shown to be well tolerated in Phase-II and -III clinical trials for asthma and sickle cell anemia. MethodsWe evaluated public mRNA expression data to determine whether the allele at 19q13.31 associated with increased breast cancer risk was associated with KCNN4 expression. We also used immunohistochemistry to evaluate the relationship between KCNN4 protein expression and breast cancer survival. We then used Senicapoc in two murine mammary tumor models to determine if it would delay tumor development. We also treated mice bearing 4T1 mammary tumors with Senicapoc, by subcutaneous injection and by oral gavage. Finally we used gene editing to make deletions within Kcnn4 in 4T1 to determine whether Senicapoc had off-target effects on tumor growth. ResultsAnalysis of the Genotype-Tissue Expression Project showed that the allele at 19q13.31 associated with increased breast cancer risk is associated with increased KCNN4 expression, suggesting that inhibiting KCNN4 might reduce breast cancer risk. Using immunohistochemistry in a large breast cancer cohort, we found that membrane and cytoplasmic expression is a marker of poor prognosis in triple negative breast cancer. We then tested the efficacy of Senicapoc to prevent and treat breast cancer. This showed that it delays the development of mammary tumors in two murine models, and slows growth of a syngeneic (4T1) model of triple negative breast cancer. Senicapoc monotherapy showed similar efficacy to anthracycline/taxane-based chemotherapy in these studies, with a stronger effect when they were combined. ConclusionsThese results provide a rationale for clinical testing of Senicapoc for treating, and even preventing, breast cancer.

cancer biology↗

bioRxiv2023

Cognitive relevance of an evolutionarily new and variable prefrontal structure

Identifying structure-function correspondences is a major goal among biologists, cognitive neuroscientists, and brain mappers. Recent studies have identified relationships between performance on cognitive tasks and the presence or absence of small, shallow indentations, or sulci, of the human brain. Building on the previous finding that the presence of one such sulcus in the left anterior lateral prefrontal cortex (aLPFC) was related to reasoning task performance in children and adolescents, we tested whether this relationship extended to a different sample, age group, and reasoning task. As predicted, the presence of this aLPFC sulcus--the ventral para-intermediate frontal sulcus--was also associated with higher reasoning scores in young adults (ages 22-36). These findings have not only direct developmental, but also evolutionary relevance--as recent work shows that the pimfs-v is exceedingly rare in chimpanzees. Thus, the pimfs-v is a novel developmental, cognitive, and evolutionarily relevant feature that should be considered in future studies examining how the complex relationships among multiscale anatomical and functional features of the brain give rise to abstract thought.

neuroscience↗