Biology subjects

Jain, K.

Publications and source records attributed to Jain, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Single molecule Grb2 dynamics reveal spatiomechanical modulation of RTK signaling across length scales

Extracellular matrix (ECM)-mediated cell adhesion and tension regulate development and disease through crosstalk with Receptor Tyrosine Kinases (RTKs). RTKs stimulate proliferation, survival, and metabolic reprogramming via Ras/ERK and PI3K/Akt signaling. Emerging evidence identify the biophysical and biochemical integration of integrin-mediated adhesions with RTK signaling, however, the molecular mechanisms regulating this phenotype remain poorly understood. Here, we demonstrate that ECM stiffness potentiates ligand-mediated epidermal growth factor receptor (EGFR) signaling at scales ranging from the single adaptor protein, Grb2 upward to multicellular spheroids and tissues. We show that ECM stiffness-driven RTK signaling is mediated by integrin adhesions that reshape the membrane to induce the formation of RTK signaling hotspots distributed globally across the cell membrane. A parsimonious computational model and biochemical membrane perturbations causally implicate membrane curvature and topography in tension-dependent integrin-EGFR crosstalk. The results demonstrate how the mechanical properties of the ECM direct molecular recruitment and confinement of signaling molecules to regulate growth factor-dependent RTK signaling. Given that many RTK-driven solid tumors develop a stiff stroma, the findings could explain why many therapeutic tyrosine kinase inhibitors develop clinical resistance. The findings suggest clarifying how tension regulates transmembrane receptor signaling could identify unique force-dependent molecular regulators towards which new antitumor therapies could be applied.

biophysics↗

bioRxiv2026

Unravelling the role of IRX4 variants in non-syndromic and Down syndrome associated congenital heart disease

IRX4 is a TALE- homeodomain transcription factor which is essential for cardiac development. In murine models, Irx4 deficiency leads to impaired ventricular function and results in cardiomyopathy. To elucidate the role of IRX4 in human congenital heart disease (CHD), Sanger sequencing of the IRX4 gene was performed in 205 individuals with non-syndromic CHD, 24 Down syndrome (DS) cases with CHD, 27 DS cases without CHD, and 150 healthy control individuals. Two novel (p.Ser24Asn and p.Thr217Iso) and one reported variant (rs2232376) were identified in non-syndromic CHD. Concurrently, rs2232376 was also detected in DS with CHD. The first novel (p.Ser24Asn) and reported (rs2232376) variants lie in the N-terminal region while the second novel (Thr217Iso) variant lies within the TALE homeodomain. In silico structural modelling suggested that both the novel variants (p.Ser24Asn and Thr217Iso) induce conformational changes in the IRX4 protein, potentially altering its DNA-binding affinity. A significant reduced expression of IRX4 muteins was noted in Western blotting by both variants (p.Ser24Asn and Thr217Iso). Furthermore, luciferase reporter assays demonstrated decline in the activity of Nanog promoter and HEY2 enhancer in response to both the variants which was further corroborated by decrease mRNA expression in qRT-PCR. Additional downstream targets, including Nfyc, Nppa, and Bmp10, also exhibited anomalous expression due to both the variants (p.Ser24Asn and Thr217Iso). Altogether, the aberrant expression of muteins as well as downstream target genes along with compromised activities of promoters substantiate the pathogenic potential of the identified IRX4 variants and underscore the critical role of IRX4 in regulating multiple stages of cardiogenesis.

genetics↗

bioRxiv2026

Gpnmb-positive lipid-associated macrophages contribute to lipid clearance during luteolysis

Macrophages are important regulators of ovarian physiology, yet the complexity in their subpopulations and functions is far from fully understood and is emerging from single-cell analysis of diverse physiological and pathological contexts. One open question in ovarian physiology is how massive lipid loads during structural luteolysis are resolved without inducing inflammation. Here, by integrating single-cell and spatial transcriptomic datasets from mouse and human ovaries with high-resolution immunostaining and whole-mount imaging, we identified a Gpnmb+ subset of macrophages that dynamically expand during luteolysis in the mouse ovary, and a similar GPNMB+ macrophage population is also present in human ovarian scRNA-seq datasets. Transcriptomic profiling revealed that these Gpnmb+ macrophages resemble lipid-associated macrophages (LAMs) in adipose tissues in obesity, displaying strong enrichment in phagocytosis, lysosomal lipid processing, and reverse cholesterol transport. Notably, unlike phagocytic macrophages that only clear cellular debris, Gpnmb+ macrophages represent a distinct, specialized subset dedicated to processing lipid-rich targets: they selectively infiltrate regressing corpora lutea (CL), internalizing lipid droplets and interacting with dying luteal cells via apoptosis (Thbs1-Sdc1/4), efferocytosis (Pros1-Mertk), and cell recruitment (Cxcl12/Cxcr4) signaling axes. Gpnmb+ macrophages also surround oocytes in atretic follicles. Through integrated transcriptomic and imaging analyses, our data suggest that Gpnmb+ macrophages execute a complete cascade of multi-stepped lipid processing, including lipid droplet internalization, lysosomal and lipophagic degradation, and ABCA1/ABCG1-mediated cholesterol efflux. Furthermore, whole-mount imaging revealed close physical interaction between Gpnmb+ macrophages and LYVE1+ lymphatic endothelial cells, supporting a non-inflammatory resolution for lipid clearance via lymphatic circulation. Collectively, our findings establish Gpnmb+ macrophages as specialized LAMs essential for maintaining cyclic ovarian lipid homeostasis. This work redefines the paradigm of LAM biology by demonstrating their vital homeostatic role in normal ovarian physiology, bridging immune-mediated tissue remodeling and reproductive physiology.

physiology↗

bioRxiv2026

Using timescale as a state coordinate reveals the metastable geometry of behavior

Animal behavior unfolds across many timescales, from fast movement patterns to slow changes in internal states such as hunger, arousal, and circadian phase. These slow variables are rarely measured directly and must instead be inferred from their effects on the faster movements that can be observed. Here we propose treating timescale itself as an explicit coordinate of the state representation, constructing a time-frequency state space where fast movements and slow modulations appear simultaneously. We find that slow modes emerge as linear arms radiating from a stationary-weighted hub in the leading non-trivial eigenvectors of the transfer operator, with one arm per metastable basin across three systems of increasing complexity. In a synthetic system, the framework recovers a hidden bistable driver across nearly three decades of dwell time, while a fixed-timescale analysis of the same trajectory finds no separable slow modes. In nematode locomotion, it reproduces the canonical run-pirouette organization. In freely moving fruit flies, where fast leg kinematics are orders of magnitude faster than the behavioral states they compose, the multi-timescale operator identifies four metastable behavioral basins directly from the postural time series, without first decomposing into a sequence of stereotyped actions. We further find that these basins exhibit a broad, heavy-tailed distribution of residence times. Treating timescale as a state coordinate thus exposes a predictable geometric form for the slow organization of behavior, providing a general route for extracting collective modes from partially observed biological time series without first organizing the dynamics into discrete events.

animal behavior and cognition↗

bioRxiv2026

Elimination of senescent cells by mechanical cell competition

Cellular senescence, a hallmark of aging, leads to the accumulation of apoptosis-resistant cells that compromise tissue homeostasis. While senescent cells are known to influence neighboring cells through the senescence-associated secretory phenotype (SASP), the precise nature of the interactions between senescent and normal cells remains elusive. Here we show that progerin-induced senescent cells undergo apoptosis when co-cultured with normal cells. This elimination requires direct cell-cell contact and is mediated by the JNK and p38-MAPK pathways, leading to p53 upregulation and p21 downregulation in progerin-expressing cells. Furthermore, neighboring normal cells exert persistent mechanical compression on progerin-expressing cells prior to their elimination, consistent with mechanical cell competition. In contrast, p16-induced senescent cells resist elimination under the same co-culture conditions, maintaining high p21 levels. Our findings reveal a non-cell-autonomous mechanism for senescent cell clearance, providing new insights into the maintenance of tissue homeostasis during aging.

cell biology↗

bioRxiv2026

Prpf8N1531S homozygous mutant mouse embryos have multiple defects in cardiac development and show aberrant splicing of the cardiac transcription factor Tead1

Mutations in the spliceosomal gene PRPF8 are associated with a range of human diseases. Studies in mouse and zebrafish suggest that Prpf8 also has a developmental function. Here, using a Prpf8 mutant mouse line isolated from a chemical induced mutagenesis screen, we uncover a previously unrecognised and essential role for Prpf8 in heart development, consistent with the embryonic lethality observed in Prpf8N1531S homozygous mutants. Prpf8N1531S mutant embryos display severe defects in ventricular trabeculation and compact zone formation, accompanied by increased cardiomyocyte proliferation specifically in the compact zone. Mutant embryonic hearts also exhibit disrupted cellular organisation, altered cytoskeletal architecture and changes in extracellular matrix protein expression. Notably, these cardiac abnormalities were exacerbated in embryos exhibiting cardiac looping defects. Transcriptomic analysis identified multiple aberrantly spliced transcripts in Prpf8N1531S mutant embryos, among which the cardiac transcription factor Tead1 was selected as a key functional candidate due to it known role in cardiac ventricle wall developemnt. Tead1 mis-splicing generated an in-frame, lower molecular weight protein isoform, associated with reduced overall TEAD1 expression. The Tead1 mis-spliced isoform showed altered nuclear localisation and dysregulation of TEAD1-dependent gene network important for heart development, including known cardiac sarcomeric genes. In addition, we observed reduced levels of the intracellular domain of the NOTCH1 receptor (NICD1), indicating impaired Notch signalling.. These findings suggest that impaired TEAD1-dependent transcription and Notch signalling contribute to abnormal cardiac trabeculation and compact zone development, highlighting a critical role for Prpf8 in maintaining proper heart development through the regulation of cardiac transcription factor expression and associated signalling networks. This study offers new mechanistic insights into congenital heart diseases linked to spliceosomal gene mutations.

developmental biology↗

bioRxiv2025

Organization and triggered release of liposomes with DNA-based synthetic condensates

Cells use a combination of membrane-bound and membrane-less compartments to dynamically orchestrate internal biochemical processes and sustain intracellular communication. Recapitulating the hierarchical integration and interplay between these physically and chemically diverse structures is required to enhance the functionalities of synthetic cells and other advanced biomimetic systems. Here, we describe the use of synthetic DNA condensates to selectively uptake and spatially organize lipid vesicles, interacting with the condensates thanks to cholesterol-DNA anchors. By modulating anchor density, the liposomes can be programmably localized on the surface or interior of the condensates, while base-pairing selectivity can be leveraged to target individual internal domains in multi-phasic condensates. The embedded liposomes can be released by adding a nucleic acid trigger and captured by a second condensate population, thus imitating extracellular vesicles in their ability to support long-range cellular communication. This modular platform demonstrates the potential of DNA-based condensates to program the spatial distribution of membranous subcompartments and to support dynamic cargo-handling capabilities. These features are valuable for engineering cell mimics, microreactors, and delivery systems.

synthetic biology↗

bioRxiv2025

Peptidoglycan turnover promotes active transport of protein through the bacterial cell wall

The bacterial cell wall is a critical load-bearing structure, but is not thought to be an important permeability barrier since proteins freely diffuse through isolated cell wall sacculi and bacteria secrete proteins without the aid of any known channels or transporters in the wall. Using new genetically encoded probes to measure the permeability of the cell in situ at the single-cell level, we discovered that the size threshold determining whether proteins can pass through the Bacillus subtilis sacculus is smaller than was previously thought. We found that transport of small proteins (<10 kDa) through the sacculus was consistent with passive diffusion through discrete pores, while larger proteins (>15 kDa) required the generation of larger pores by inducing peptidoglycan hydrolysis unbalanced by synthesis. These data are consistent with physics-based models of diffusion through a random percolation network of finite thickness. Conversely, the ability of the innate immune factor phospholipase (15.2 kDa) to kill B. subtilis was inhibited by membrane de-polarization. The protective effect of de-polarization was dependent on latent peptidoglycan synthesis (decoupled from cell growth) by PBP1 - highlighting a new role for this enzyme - and on reduced peptidoglycan hydrolysis. These results demonstrate that the rapid peptidoglycan turnover that drives cell growth also promotes movement of phospholipase across the cell wall, identifying a quintessentially bacterial mechanism of active transport. Significance StatementGram-positive bacteria, which include many serious pathogens like Staphylococcus aureus, Listeria monocytogenes, and Clostridium difficile, are defined by their thick peptidoglycan cell wall. Here, we demonstrate that this structure is a critical permeability barrier that blocks antibacterial proteins like those used by the human innate immune system. Furthermore, this barrier function depends on the physiological state of the cell: the wall of non-growing cells is less permeable because peptidoglycan turnover during growth actively promotes transport of specific proteins through the cell wall. This prokaryotic paradigm for molecular transport has important implications for host-pathogen interactions since pathogenic bacteria often assume both non-growing and growing states during infection.

microbiology↗

bioRxiv2025

Dynamics of fixation probability in a population with fluctuating size

In many biological processes, the size of a population changes stochastically with time, and recent work in the context of cancer and bacterial growth have focused on the situation when the mean population size grows exponentially. Here, motivated by the evolutionary process of genetic hitchhiking in a selectively neutral population, we consider a model in which the mean size of the population increases linearly. We are interested in understanding how the fluctuations in the population size impact the first passage statistics, and study the fixation probability that a mutant reaches frequency one by a given time in a population whose size follows a conditional Wright-Fisher process. We find that at sufficiently short and long times, the fixation probability can be approximated by a model that ignores temporal correlations between the inverse of the population size, but at intermediate times, it is significantly smaller than that obtained by neglecting the correlations. Our analytical and numerical study of the correlation functions show that the conditional Wright-Fisher process of interest is neither a stationary nor a Gaussian process; we also find that the variance of the inverse population size initially increases linearly with time t and then decreases as t-2 at intermediate times followed by an exponential decay at longer times. Our work emphasizes the importance of temporal correlations in populations with fluctuating size that are often ignored in population-genetic studies of biological evolution.

evolutionary biology↗

bioRxiv2025

YY1 relieves p300 autoinhibition to promote histone acetylation in advanced prostate cancer, enhancing the oncogenic signaling of Androgen Receptor Splice Variant 7

Genetic and epigenetic aberrations often act in concert to establish oncogenic transcriptomic programs in aggressive cancers. For example, the development of castration-resistant prostate cancer (CRPC), an advanced prostate cancer form, is closely associated with over-expression and/or hyper-activation of transcription factors (TFs) such as Androgen Receptor (AR) and Yin Yang 1 (YY1), as well as p300, a prominent histone acetyltransferase. How exactly these cancer-related lesions are coordinated to generate a malignant cell state remains elusive. Here, we demonstrate that YY1, which is frequently over-expressed in advanced prostate cancers, allosterically stimulates the acetyltransferase activity of p300 in cis, leading to the globally elevated acetylation of histone H3 lysine 18 and 27 (H3K18ac and H3K27ac). Mechanistically, YY1s N-terminal activation domain (AD) directly interacts with p300s TAZ2 domain, relieving the autoinhibition of p300 to facilitate substrate acetylation. Our integrated genome-wide mapping and transcriptomic studies reveal significant co-localization of genomic binding sites of YY1, androgen receptor splice variant 7 (AR-V7, a constitutively active form of AR) and p300 in CRPC cells, where the YY1-mediated p300 activation and resultant histone acetylation increases promote the oncogenic gene-expression programs downstream of YY1 and AR/AR-V7. Both in vitro and in vivo functional assays demonstrate a critical requirement of the above signaling for the advanced disease progression and drug resistance seen in CRPC. Altogether, this study uncovers that YY1 acts to alleviate p300s autoinhibition at target genes co-bound by oncogenic TFs (YY1 and/or AR/AR-V7) in CRPC, thereby sustaining tumorigenicity. Additionally, the blockade of YY1-mediated gene activation resensitizes CRPC to treatment to the clinic anti-AR agent (enzalutamide), which provides a rationale for overcoming the therapeutic resistance often seen in advanced prostate cancers.

cancer biology↗

bioRxiv2025

Circulating Biomarkers for Therapeutic Response to Immune Checkpoint Inhibitor Therapy in Patients with Advanced Lung Cancer

Immune checkpoint inhibitors (ICIs) have demonstrated remarkable efficacy in the treatment of advanced lung cancer (ALC), but not all patients benefit. To identify responders, patient selection, categorization, and the identification of specific predictive biomarkers are crucial. Our research aims to identify circulating metabolites that could be used to stratify patients into potential responders prior to the initiation of ICIs and to monitor clinical response in real-time during treatment. In the discovery phase, plasma samples (n = 25) from ALC patients receiving ICIs were analyzed using unbiased metabolomics and validated in a distinct patient cohort (n = 39). Five potential biomarkers were identified (FC > 1.5, p 0.05, AUC 0.81-1), including Thiourea and a combined metabolite panel (CMP) consisting of sphingosine-1-phosphate, gentisic acid, glutathione, and 4-hydroxybutanone. Early on-treatment high plasma levels of Thiourea were significantly associated with 5-year progression-free survival [Hazard ratio (HR) = 0.038, 95% confidence interval (CI) = 0.013-0.107, p<0.001] and overall survival [HR = 0.048, 95% CI = 0.019-0.120, p<0.001]. Low levels of CMP early on treatment were significantly associated with progression-free survival [HR = 8.119, 95% CI: 3.767-17.501, p<0.001] and overall survival [HR = 7.367, 95% CI: 3.517-15.433, 3.517-15.433, p<0.001]. This predictive plasma metabolite panel could serve as promising circulating biomarkers for predicting the therapeutic response of ICIs in ALC patients.

cancer biology↗

bioRxiv2025

Cytokine profiling identifies circulating IL-2, IL23 and sPD-L1 as prognostic biomarkers for treatment outcomes in Non-Small cell Lung Cancer patients undergoing anti-PD1 therapy

BackgroundThis study investigates the predictive potential of circulating cytokines for response and survival outcomes in patients with advanced non-small cell lung cancer (NSCLC) undergoing immune checkpoint inhibitor (ICI) therapy. Materials and MethodsA cohort of 64 patients with advanced NSCLC receiving ICI therapy were included. Baseline serum samples were collected prior to ICI initiation and profiled using a multiplex cytokine panel. Logistic regression, Cox regression, and Kaplan-Meier survival analysis were employed to assess associations between cytokine levels, therapeutic response, progression-free survival (PFS), and overall survival (OS). Gene expression levels of key cytokines were validated in peripheral blood mononuclear cells (PBMCs) using quantitative real-time PCR. ResultsElevated baseline levels of IL-2, IL-23, and sPD-L1 were significantly associated with clinical response to ICI therapy. Among these, sPD-L1 emerged as an independent predictor of response (AUC = 0.87). Multivariate Cox regression showed IL-2 (HR = 0.67), sPD-L1 (HR = 0.15), and IL-23 (HR = 1.18) were significantly associated with PFS and also predictive of OS. Notably, combined profiling of IL-2 and sPD-L1 enhanced predictive power (AUC = 0.95 for both PFS and OS). RT-PCR analysis of PBMCs corroborated these findings, confirming upregulation of IL-2 in responders and elevated IL-23 expression in non-responders. ConclusionBaseline cytokine profiling particularly of IL-2, sPD-L1, and IL-23 provides important prognostic and predictive information in advanced NSCLC patients undergoing ICI therapy. These biomarkers may facilitate more personalized approaches to immunotherapy and guide clinical decision-making.

cancer biology↗

bioRxiv2025

Optogenetic control of mechanotransduction based on light-induced homodimerization of talin

Integrin-based cell adhesions (IACs) serve as primary sites where piconewton-scale actomyosin-generated mechanical forces are transmitted to the extracellular matrix (ECM), generating traction forces that drive cell-ECM responses including adhesion, migration, and mechano-signaling. Talin, a large (270 kDa) cytosolic adaptor protein, is the principal force-transmission protein in integrin-based adhesions, containing multiple mechanosensitive domains and protein-protein interaction sites that orchestrate molecular events in mechanosensing. As a highly modular multi-domain protein, talin has been identified as an effective target for chemogenetic and optogenetic manipulation of integrin-based mechanotransduction. However, a key limitation of previous approaches is the reliance on heterodimerization modules to control talin function, requiring the expression of two modified talin fragments. In practice, achieving precise expression levels in such a 2-component approach can be challenging, particularly when combined with other genetic tools. Since talin naturally contains a C-terminal dimerization domain that forms part of its actin-binding site, we reasoned that the molecularly engineered talin with a C-terminal optically-controlled homodimerizer could enable single-component optogenetic control of mechanotransduction. This approach would facilitate multiplexing with other molecular perturbations or experimental techniques. Here, we describe an opto-homodimerizable talin based on the pdDronpa1.2 optogenetic module, which enables optogenetic control of talin by a single construct. We demonstrate that light-induced talin dimerization promotes talin recruitment to IACs, adhesion formation, actin retrograde flow engagement, and downstream mechanotransduction signaling. Conversely, light-induced talin monomerization rapidly disassembles focal adhesions, disrupts talin-actin linkages, and accelerates actin retrograde flow, underscoring the critical roles of talin dimerization. Furthermore, our single-construct design allows facile multiplexing of optogenetic modulation of integrin-mediated mechanotransduction with super-resolution single-molecule tracking, revealing the essential role of talin dimerization for integrin v{beta}5 engagement.

cell biology↗

bioRxiv2025

Evolutionary dynamics under demographic fluctuations: beyond the effective population size

It has long been appreciated that changing population size can strongly affect the evolutionary dynamics and genetic diversity, and traditionally, the effects of demographic fluctuations are captured via an effective population size. However, as has been pointed out in previous studies, an effective population size does not always exist and can be defined only when the relevant time scales are well separated. A mechanistic understanding of the non-existence of effective population size is, however, missing, and a very few analytical results have been obtained when the relevant time scales overlap with each other. To address these issues, we consider a neutral, panmictic population whose size fluctuates in time, and for a general demography, we show that the correlations between the population size at different times preclude the existence of an effective population size. We then consider a specific demography in which the population size switches between two fixed values in a stochastic fashion, and formulate a diffusion theory that allows us to obtain exact results for fixation probability, fixation time and mean sojourn time of a mutant for arbitrary switching rates. We find that when the switching time and the time scale for the genetic drift are of the same order, these quantities differ substantially from the corresponding results predicted by a neutral model with an effective population size given by the harmonic mean of the population size, and discuss the implications of these results for neutral genetic diversity in changing environments.

evolutionary biology↗

bioRxiv2025

Alternative Promoters Drive Transcriptomic Reprogramming and Prognostic Stratification in TNBC

Transcriptional regulation frequently involves alternative promoters, yet the distinct regulatory mechanisms governing alternative versus reference promoters remain poorly understood in Triple-Negative Breast Cancer (TNBC), a high-risk breast tumor subtype. It is worth emphasizing that, despite the availability of extensive short-read sequencing data, the impact of alternative promoter usage on TNBC transcriptome dynamics and patient survival remains underexplored. The current study leverages RNA sequencing data from the publicly available TNBC tumor samples (360) and adjacent normal samples (88) to identify TNBC-specific and subtype-specific active alternative promoters (AAPs). To further validate these findings, we integrated H3K4me3 ChIP-seq data, confirming key promoter switching events. We found that HDAC9, RPS14, and EPN1 exhibit tumor-specific AAP expression, while AKAP9 and SEC31A show basal subtype-specific promoter activity in TNBC. Beyond their transcriptional impact, we also explored the prognostic significance of AAPs. The alternative promoters of HUWE1 and FTX were recognized as independent survival predictors in TNBC. Notably, multivariate analysis demonstrated that prognostic AAPs remained significant in predicting relapse-free survival (RFS) even after adjusting for copy number alterations (CNA) and mRNA-based subtypes. Our AAP-based prognostic model achieved C-index of 0.73 in training and 0.72 in validation, with AUROC of 0.72 and integrated Brier score of 0.09 in validation dataset. Our findings indicate that AAP activity serves as a crucial prognostic marker beyond traditional clinical parameters, enhancing patient stratification and risk assessment in TNBC. Understanding promoter switching events may further unveil novel therapeutic targets, paving the way for precision oncology strategies in highly aggressive breast tumors.

genomics↗

bioRxiv2025

Cell-type specific profiling of human entorhinal cortex at the onset of Alzheimer's disease neuropathology

Neurons located in layer II of the entorhinal cortex (ECII) are the primary site of pathological tau accumulation and neurodegeneration at preclinical stages of Alzheimers disease (AD). Exploring the alterations that underlie the early degeneration of these cells is essential to develop therapies that curb the disease before symptom onset. Here we performed cell-type specific profiling of human EC at the onset of AD neuropathology. We identify an early response to amyloid pathology by microglia and oligodendrocytes. Importantly, we provide the first insight into neuronal alterations that coincide with incipient tau pathology: the signaling pathway for Reelin, recently shown to be a major AD resilience gene is dysregulated in ECII neurons, while the secreted synaptic organizer molecules NPTX2 and CBLN4, emerging AD biomarkers, are downregulated in surrounding neurons. By uncovering the complex multicellular landscape of EC at these early AD stages, this study paves the way for detailed characterization of the mechanisms governing NFT formation and opens long-needed novel therapeutic avenues.

neuroscience↗

bioRxiv2024

Histone H3 N-terminal recognition by the PHD finger of PHRF1 is required for proper DNA damage response

Plant homeodomain (PHD) fingers are critical effectors of histone post-translational modifications (PTMs), acting as regulators of gene expression and genome integrity, and frequently presenting in human disease. While most PHD fingers recognize unmodified and methylated states of histone H3 lysine 4 (H3K4), the specific functions of many of the over 100 PHD finger-containing proteins in humans remain poorly understood, despite their significant implications in disease processes. In this study, we undertook a comprehensive analysis of one such poorly characterized PHD finger-containing protein, PHRF1. Using biochemical, molecular, and cellular approaches, we show that PHRF1 robustly binds to histone H3, specifically at its N-terminal region. Through RNA-seq and proteomic analyses, we also find that PHRF1 is intricately involved in transcriptional and RNA splicing regulation and plays a significant role in DNA damage response (DDR). Crucially, mutagenesis of proline 221 to leucine (P221L) in the PHD finger of PHRF1 abolishes histone interaction and fails to rescue defective DDR. These findings underscore the importance of PHRF1-H3 interaction in maintaining genome integrity and provide insight into how PHD fingers contribute to chromatin biology.

biochemistry↗

bioRxiv2024

The acoustic properties, syllable structure, and syllable sequences of ultrasonic vocalizations (USVs) during neonatal opioid withdrawal in FVB/N mouse substrains

Concomitant with the opioid epidemic, there has been a rise in pregnant women diagnosed with opioid use disorder and cases of infants born with neonatal opioid withdrawal syndrome (NOWS). NOWS refers to signs and symptoms following cessation of prenatal opioid exposure that comprise neurological, gastrointestinal, and autonomic system dysfunction. A critical indicator of NOWS severity is excessive, high-pitched crying. However, NOWS evaluation is, in large part, subjective, and additional cry features may not be easily recognized during clinical assessment. Thus, there is a need for more objective measures to determine NOWS severity. We used a third trimester-approximate opioid exposure paradigm to model NOWS traits in genetically similar inbred substrains of FVB/N mice (NJ, NCrl, NHsd, and NTac). Pups were injected twice daily from postnatal day 1 (P1) to P14 with morphine (10 mg/kg, s.c.) or saline (20 ml/g, s.c.). Because there were only very minor substrain differences in spontaneous withdrawal-induced ultrasonic vocalization (USV) profiles, we collapsed across substrains to evaluate the effects of morphine withdrawal on additional USV properties. We identified syllable sequences unique to morphine-withdrawn and saline-control FVB/N pups on P7 and P14. We also observed an effect of spontaneous morphine withdrawal on the acoustic properties of USVs and specific syllables on P7 and P14. Multiple withdrawal traits correlated with some acoustic properties of USVs and syllable type emission in morphine-withdrawn FVB/N pups on P7 and P14. These data provide an in-depth investigation of mouse USV syllable profiles and acoustic features during spontaneous neonatal opioid withdrawal in mice.

animal behavior and cognition↗