Biology subjects

Song, F.

Publications and source records attributed to Song, F..

At least 19 recordsLinked to original sources

bioRxiv2026

Impaired glycolysis in bone underlies age-related bone loss in mice

Bone loss and metabolic dysregulation often coexist in older adults, yet the relationship between age-related changes in bone cell metabolism and bone-forming activity remains unclear. By modeling both conditions in aged mice and using in vivo stable-isotope tracing, we demonstrated that age-related decline in bone formation was coupled with an intrinsic impairment of glycolysis within bone tissue. Impaired glycolysis was associated with reduced protein levels of key glycolysis enzymes, and transcriptomics analyses revealed compensatory upregulation of glycolysis genes in aged bone. Metabolic intervention through long-term caloric restriction prevented age-related trabecular bone loss. Furthermore, osteoblast-specific genetic enhancement of glycolysis, via overexpression of HIF1 or the rate-limiting enzyme PFKFB3, significantly improved osteoblast function and increased bone mass in aged mice. Together, the study identifies glycolytic decline as a cell-autonomous driver of osteoblast deficiency and provides proof of principle that reactivating glycolysis can promote bone accrual in aging.

physiology↗

bioRxiv2026

A custom two-in-one HIST and line-scanning confocal excitation module

Fluorescence microscopy applications often require specialized instruments that are optimized for different experimental goals. Here, we present a reconfigurable microscopy module that integrates highly inclined swept tile (HIST) illumination for high-sensitivity single-molecule imaging and line-scanning confocal microscopy for rapid and optically sectioned volumetric acquisition. The system shares major hardware components, including lasers, scanning optics, and detection hardware, while employing unique beam shaping pathways to enable rapid switching between modalities without realignment. We characterize the module performance by measuring the excitation beam profiles, the point spread functions (PSF), and the optical transfer functions (OTF) across 40x, 60x, and 100x magnifications and demonstrate imaging applications including diffraction-limited fixed and live-cell volumetric imaging, fluorescence recovery after photobleaching, and super-resolution DNA-PAINT and single particle tracking (SPT). We also demonstrate the capability to execute multimodal imaging workflows by performing confocal imaging for chromatin density classification correlated with SPT data of nuclear proteins with diverse functions. Together, these results demonstrate a versatile imaging platform capable of supporting complementary fluorescence imaging modalities within a single instrument.

bioengineering↗

bioRxiv2026

Mutational and functional heterogeneity of homology-directed repair deficiency and clinical implications

Homology-directed repair deficiency (HRd) encompasses mutations in multiple genes yet is treated clinically as a single entity. Here, through parallel analyses of isogenic knockouts of multiple HR pathway genes, integrating multi-omic analyses with genome-wide CRISPR-Cas9-dependency and resistance screens, we show that HRd is not a single entity but exists along a molecular and functional continuum. BRCA1, BRCA2, PALB2, RAD51C, and RAD51D mutants shared many HRd-associated mutational signatures, while RAD51B, BRIP1, CDK12 exhibited distinct genomic patterns. Functional heterogeneity was equally apparent: synthetic lethal interactions including CIP2A and a novel dependency on PRDX1 were penetrant across most HRd genotypes, whereas FANCM dependency was linked to HRd subtypes characterized by tandem duplications. PARPi resistance screens in distinct HRd contexts uncovered BRIP1 and RECQL5 as new BRCA2-specific resistance genes. HRd is thus a complex continuum, underscoring why modernizing the molecular taxonomy utilizing all genomic features available per patient is crucial to informing precision interventions.

genomics↗

bioRxiv2026

Reversion mutations define minimal BRCA1/2 requirements for therapy resistance

Although platinum salts or PARP inhibitors are effective in delivering anti-tumor responses in people with BRCA1 or BRCA2 mutated cancers, drug resistance is common and is often caused by secondary BRCA1/2 reversion mutations that restore function. By collating and analyzing 848 BRCA1/2 reversion mutations in 384 cancer patients with drug resistance, we confirm that pathogenic BRCA1/2 mutation type influences the acquisition of reversions, and that large BRCA1/2 deletions are an underappreciated form of reversion. Integrating reversion data with systematic CRISPR-Cas9 screens that delete BRCA1/2 exons, we also show that both proteins contain privileged domains whose structure is essential for drug resistance, including the PALB2 interacting domains of both BRCA1 and BRCA2. Reversions in PALB2 also conserve both BRCA1 and BRCA2 binding domains. Surprisingly, exon 11 of BRCA2, which encodes BRC repeats 1-8, is not essential for resistance. Using this patient and functional information, we estimate the likelihood of pathogenic BRCA2 mutations to revert. We show that risk of reversion correlates with both the presence of clinical reversions and the response to treatment, suggesting that the propensity to revert could be a useful clinical parameter.

cancer biology↗

bioRxiv2026

Sparse mixed codes on shared manifolds for human-like spatial attention in artificial neural networks

Spatial attention is often partitioned into endogenous, exogenous, and social forms, yet it remains unclear whether a single neural circuit can support all three and how their population codes are organized. Here we trained recurrent artificial neural networks (ANNs) with convolutional sensory front-ends on three classic cueing paradigms (central, peripheral, and gaze cues) to reproduce human reaction time (RT) profiles across cue-target onset asynchronies. Despite differences in sensory architecture and visual experience, all ANNs captured the full facilitation-inhibition time course for all three attention types. Model-based targeted dimensionality reduction (mTDR) revealed that cue- and choice-related activity in the advanced cognitive module evolved as rotations within a shared low-dimensional manifold, with angular deflections that mirrored the distinct temporal dynamics of endogenous, exogenous, and social attention. Attentional signals were encoded by highly sparse, distributed population activity: a small subset of recurrent units explained most task-related variance, was sufficient to recover human-like RT patterns after virtual lesioning, and became progressively sparser as training improved performance. At the same time, single unit responses displayed pervasive mixed selectivity, dominated by nonlinear conjunctions of cue type, cue direction, and validity, whose strength and heterogeneity robustly predicted model performance. Together, these results identified low-dimensional geometric rotations, sparse coding, and nonlinear mixed selectivity as core computational principles through which a single recurrent circuit could generate human-like temporal dynamics across endogenous, exogenous, and social orienting, and provided testable predictions for population-level mechanisms of spatial attention in the brain.

neuroscience↗

bioRxiv2026

A single cell atlas defines perinatal factors that drive murine bone marrow development

Processes that direct initial colonization and maturation of the bone marrow remain elusive, despite lifelong importance to hematopoiesis. Bone marrow mesenchymal and stromal cell (BMSC) maturation establishes supportive niches prior to hematopoietic stem cell (HSC) recruitment. We define mouse BMSC progenitor identities and temporal emergence in a developmental single cell atlas spanning fetal life through 18 months of age. We clarify Cxcl12-abundant reticular (CAR) cell and osteoblast development, including temporal emergence of signaling modalities that direct HSC quiescence and regenerative capacity. CAR cells are absent until birth, with a developmental block during fetal maturation related to transcriptional changes during perinatal life. Temporal changes in Early B Cell Factor (Ebf) 1-3 expression and activity correlate with CAR formation and niche establishment, including Ebf2 repression and induction of Ebf3 activities that direct metabolic changes. Changes in systemic physiology underlie these transcriptional changes, including perinatal induction of lipid metabolism, inflammation, and hypoxic signaling. These systemic factors direct CAR cell emergence after birth, providing temporal and developmental resolution underlying the colonization and maturation of the bone marrow environment.

developmental biology↗

bioRxiv2025

Human umbilical cord mesenchymal stromal cells ameliorate ovarian damage and restore function in Premature Ovarian Insufficiency rat model

Premature ovarian insufficiency (POI) is a debilitating condition characterized by infertility and systemic health decline, with limited effective therapeutic options. This study explores the therapeutic potential of human umbilical cord-derived mesenchymal stromal cells (hUC-MSCs) in a cyclophosphamide (CTX)-induced rat model of POI. The POI rats were administered low or high doses of hUC-MSCs via tail vein transplantation. Ovarian function was evaluated through monitoring of the estrous cycle, serum hormone analysis, ovarian histomorphology, follicle counting, and mating assays. Immunohistochemistry was employed to assess the expression of proteins related to apoptosis and angiogenesis. Additionally, in vitro co-culture assays were conducted to evaluate the immunomodulatory capacity of hUC-MSCs. The results indicated that hUC-MSC transplantation restored estrous cyclicity, normalized hormone levels, increased follicle counts, and improved pregnancy outcomes in a dose-dependent manner. Histological analysis indicated a reduction in atretic follicles and an enhancement of ovarian structure. Mechanistically, hUC-MSCs were found to attenuate apoptosis by modulating the expression of Bcl-2 and Caspase-3 and to promote angiogenesis through the upregulation of VEGF. In vitro, hUC-MSCs demonstrated significant immunomodulatory effects, including the suppression of pro-inflammatory cytokine secretion and the promotion of regulatory T cell expression. In conclusion, hUC-MSCs effectively ameliorate CTX-induced ovarian damage, highlighting their promise as a regenerative therapy for POI.

cell biology↗

bioRxiv2025

IGF-1 from bone marrow Adipoq-lineage cells stimulates endocortical bone formation in mature female mice

Insulin-like growth factor 1 (IGF-1) is an anabolic signal promoting growth, differentiation and function of both embryonic and postnatal tissues. Both endocrine and paracrine functions of IGF-1 have been documented to regulate bone growth and bone marrow hematopoiesis. Local production of IGF-1 from various cell types may contribute differently to the overall bioactivity of IGF-1 in bone, but relevant sources and mechanisms are yet to be fully elucidated. Here we report that the Adipoq+ stromal cells are a notable source of IGF-1 in the bone marrow of postnatal mice. Deletion of IGF-1 with Adipoq-Cre diminished endocortical bone formation and cortical bone mass in mature female mice. On the other hand, the trabecular bone parameters or hematopoietic properties were not affected in mutant mice of either sex. The study uncovers a local source of IGF-1 in the bone marrow microenvironment that contributes to bone anabolic regulation in a site-specific manner. Lay SummaryThe insulin-like growth factor 1 (IGF-1) is known to play important roles in promoting bone growth and in regulating blood stem or progenitor cells. The factor is available both through the blood circulation and from the local production by cells in the bone tissue, but the functional contribution of each source is not well understood. Here we discover the non-blood cells in the bone marrow (bone marrow stromal cells) as a notable source of IGF-1 which specifically stimulates bone formation in the bone shaft of the long bone.

developmental biology↗

bioRxiv2025

Droplet-based Random Barcode Transposon-site Sequencing (Droplet RB-TnSeq) to characterize phage-host interactions

Bacteriophages (phages), the most abundant self-replicating entities on Earth, are central to microbial ecology and hold promise as therapies against antibiotic-resistant pathogens. However, the molecular determinants of phage adaptation to hosts remain poorly defined. While bulk genetic screens such as transposon sequencing are high throughput, running all mutants in mixed populations biases outcomes toward phage receptor discovery. Competition among resistant mutants and the escalating multiplicity of infection (MOI) from additional phages released from lysed cells often mask moderately acting host factors--such as inner-membrane and energy-transduction systems supporting DNA entry, surface modifiers, and regulators of host defense. To overcome these limitations, we developed droplet-based random barcode transposon-site sequencing (Droplet RB-TnSeq), which encapsulates single barcoded mutant cells with defined phage titers. Applying this method to Escherichia coli infected with phages T4 and N4, we reproducibly recovered known determinants (ompC for T4 and nfrA/B for N4) and identified additional contributors, including membrane proteins, polysaccharide modifiers, signaling modules, and several uncharacterized genes. Notably, mutations in chbR/C/F, ygaZ/H, and yfbO/L were found to confer resistance to N4, validated by plaque assays and complementation. Droplet RB-TnSeq thus enables genome-wide dissection of host factors beyond receptor-level interactions under well-controlled infection conditions.

microbiology↗

bioRxiv2025

Comprehensive Cross-Domain Taxonomic Classification of Microbiotas using Partitioned Amplification Multiplexed Amplicon Sequencing (PAMA-seq)

Microbial communities encompass diverse bacteria, archaea, and eukaryotes that play vital roles in ecosystems and host health. Comprehensive analysis of these communities requires accurate, quantitative, and cross-domain profiling, yet current sequencing methods--metagenome shotgun sequencing (MGS) and ribosomal RNA (rRNA) amplicon sequencing--struggle to achieve these goals in a single assay. MGS provides broad functional insights but suffers from high cost, computational burden, and reliance on incomplete reference databases. rRNA amplicon sequencing, while more taxonomically targeted, typically profiles either prokaryotes or eukaryotes separately, depending on the chosen primer sets, and thus lacks simultaneous cross-domain resolution. To address these limitations, we developed PAMA-seq, a droplet-digital multiplex PCR technique. PAMA-seq partitions DNA sample from microbial communities into nanoliter droplets, each containing a single template molecule, and independently amplifies both the 16S and 18S rRNA genes, resulting in uniform amplification efficiency and accurate quantification. We validated PAMA-seq on a synthetic microbial community, a stool sample from a patient with colorectal cancer, and a coastal seawater sample. The method provided stable, cross-domain taxonomic profiles at sequencing depths as low as 104 reads--one to two orders of magnitude fewer than comparable shotgun metagenomics approaches--while significantly reducing variability between replicates. By combining comprehensive domain coverage with low sequencing depth requirements, PAMA-seq offers an efficient, cost-effective, and scalable method for monitoring microbial communities across diverse ecosystems, from clinical samples to global marine environments.

microbiology↗

bioRxiv2024

Global invasion history and genomic signatures of adaptation of a highly invasive lace bug

Invasive species cause enormous economic and ecological damage. Climate change has resulted in an unprecedented increase in the number and impact of invaders. The mechanisms underlying invasions, however, are largely unclear. The sycamore lace bug, Corythucha ciliata, is a highly invasive species that originated in North America. Its population has expanded over the Northern Hemisphere since the 1960s. In this study, we assemble the lace bugs genome using high-coverage PacBio, Illumina, and Hi-C sequencing. We identify 15,278 protein-coding genes and expansion of gene families with oxidoreductase and metabolic activities. In-depth resequencing of 402 samples collected from native and nine invasive countries across three continents identified 2.74 million single nucleotide polymorphisms. We resolve two major invasion routes of this lace bug from North America through both Europe and Japan, forming a contact zone in East Asia. Genomic signatures of selection associated with invasion and long-term balancing selection in native ranges are identified. These genomic signatures overlap with each other and the expanded genes, suggesting an improvement in the oxidative stress and thermal tolerance of this species. Our findings offer valuable insights into the genomic architecture and adaptive evolution underlying the invasive capabilities of species in the face of rapid environmental changes.

evolutionary biology↗

bioRxiv2024

Efficient enzyme-free isolation of brain-derived extracellular vesicles

Extracellular vesicles (EVs) have gained significant attention as pathology mediators and potential diagnostic tools for neurodegenerative diseases. However, isolation of brain-derived EVs (BDEVs) from tissue remains challenging, often involving enzymatic digestion steps that may compromise the integrity of EV proteins and overall functionality. Here, we describe that collagenase digestion, commonly used for BDEV isolation, produces undesired protein cleavage of EV-associated proteins in brain tissue homogenates and cell-derived EVs. In order to avoid this effect, we studied the possibility of isolating BDEVs with a reduced amount of collagenase or without any protease. Characterization of the isolated BDEVs revealed their characteristic morphology and size distribution with both approaches. However, we revealed that even minor enzymatic digestion induces artificial proteolytic processing in key BDEV markers, such as Flotillin-1, CD81, and the cellular prion protein (PrPC), whereas avoiding enzymatic treatment completely preserves their integrity. We found no differences in mRNA and protein content between non-enzymatically and enzymatically isolated BDEVs, suggesting that we are purifying the same BDEV populations with both approaches. Intriguingly, the lack of Golgi marker GM130 signal, often referred to as contamination contamination-negative marker in EV preparations, seems to result from enzymatic digestion rather than from its actual absence in BDEV samples. Overall, we show that non-enzymatic isolation of EVs from brain tissue is possible and avoids artificial pruning of proteins while achieving a high BDEV yield and purity. This protocol will help to understand the functions of BDEV in a near-physiological setting, thus opening new research approaches.

neuroscience↗

bioRxiv2023

Cleavage site-directed antibodies reveal the prion protein in humans is shed by ADAM10 at Y226 and associates with misfolded protein deposits in neurodegenerative diseases

Proteolytic cell surface release ( shedding) of the prion protein (PrP), a broadly expressed GPI-anchored glycoprotein, by the metalloprotease ADAM10 impacts on neurodegenerative and other diseases in animal and in vitro models. Recent studies employing the latter also suggest shed PrP (sPrP) to be a ligand in intercellular communication and critically involved in PrP-associated physiological tasks. Although expectedly an evolutionary conserved event, and while soluble forms of PrP are present in human tissues and body fluids, neither proteolytic PrP shedding and its cleavage site nor involvement of ADAM10 or the biological relevance of this process have been demonstrated for the human body thus far. In this study, cleavage site prediction and generation (plus detailed characterization) of sPrP-specific antibodies enabled us to identify PrP cleaved at tyrosin 226 as the physiological and strictly ADAM10-dependent shed form in humans. Using cell lines, neural stem cells and brain organoids, we show that shedding of human PrP can be stimulated by PrP-binding ligands without targeting the protease, which may open novel therapeutic perspectives. Site-specific antibodies directed against human sPrP also detect the shed form in brains of cattle, sheep and deer, hence in all most relevant species naturally affected by fatal and transmissible prion diseases. In human and animal prion diseases, but also in patients with Alzheimers disease, sPrP relocalizes from a physiological diffuse tissue pattern to intimately associate with extracellular aggregates of misfolded proteins characteristic for the respective pathological condition. Findings and research tools presented here will accelerate novel insight into the roles of PrP shedding (as a process) and sPrP (as a released factor) in neurodegeneration and beyond.

neuroscience↗

bioRxiv2023

Causal Role of the Frontal Eye Field in Attention-induced Ocular Dominance Plasticity

Previous research has found that prolonged eye-based attention can bias ocular dominance. If one eye long-termly views a regular movie meanwhile the opposite eye views a backward movie of the same episode, perceptual ocular dominance will shift towards the eye previously viewing the backward movie. Yet it remains unclear whether the role of eye-based attention in this phenomenon is causal or not. To address this issue, the present study relied on both the functional magnetic resonance imaging (fMRI) and transcranial magnetic stimulation (TMS) techniques. We found robust activation of the frontal eye field (FEF) and intraparietal sulcus (IPS) when participants were watching the dichoptic movie while focusing their attention on the regular movie. Interestingly, we found a robust effect of attention-induced ocular dominance shift when the cortical function of vertex or IPS was transiently inhibited by continuous theta burst stimulation (cTBS), yet the effect was significantly attenuated to a negligible extent when cTBS was delivered to FEF. A control experiment verified that the attenuation of ocular dominance shift after inhibitory stimulation of FEF was not due to any impact of the cTBS on the binocular rivalry measurement of ocular dominance. These findings suggest that the fronto-parietal attentional network is involved in controlling eye-based attention in the "dichoptic-backward-movie" adaptation paradigm, and in this network, FEF plays a crucial causal role in generating the attention-induced ocular dominance shift.

neuroscience↗

bioRxiv2023

NRF2 Regulates Contractile Vascular Smooth Muscle Cells Phenotypic Switching In Abdominal Aortic Aneurysm

OBJECTIVEEvidence from previous studies has demonstrated that NRF2 can protect cardiovascular progression,which prompted us to study if NRF2 is involved in AAA development. APPROACH AND RESULTSThe difference and function of NRF2 in AAA were verified on human aortic tissues combined with scRNA-seq samples.We then used angiotensin II (Ang II) infusion mouse model with VSMCs-specific knockout to study the role of NRF2 in AAA formation.Primary cultured VSMCs were used to study how NRF2 regulates contractile VSMCs phenotype.Patient specimens were obtained to investigate the relevance of NRF2 expression to human AAA disease. NRF2 was induced in abdominal aortic VSMCs in both mouse and human AAA tissues. VSMCs-specific NRF2 knockout increased experimental AAA formation. Mechanistically, NRF2 regulates the contractile VSMCs phenotypic through miRNA145, leading to increased classic contractile protein level to prevent the development of AAA. CONCLUSIONSNRF2 is a negative regulator of AAA development, and thus may represent a potentially new therapeutic target to inhibit AAA growth and rupture.

bioinformatics↗

bioRxiv2023

Osteoblast-intrinsic defect in glucose metabolism impairs bone formation in type II diabetic mice

Skeletal fragility is associated with type 2 diabetes mellitus (T2D), but the underlying mechanism is not well understood. Here, in a mouse model for youth-onset T2D, we show that both trabecular and cortical bone mass are reduced due to diminished osteoblast activity. Stable isotope tracing in vivo with 13C-glucose demonstrates that both glycolysis and glucose fueling of the TCA cycle are impaired in diabetic bones. Similarly, Seahorse assays show suppression of both glycolysis and oxidative phosphorylation by diabetes in bone marrow mesenchymal cells as a whole, whereas single-cell RNA sequencing reveals distinct modes of metabolic dysregulation among the subpopulations. Metformin not only promotes glycolysis and osteoblast differentiation in vitro, but also improves bone mass in diabetic mice. Finally, targeted overexpression of Hif1a or Pfkfb3 in osteoblasts of T2D mice averts bone loss. The study identifies osteoblast-intrinsic defects in glucose metabolism as an underlying cause of diabetic osteopenia, which may be targeted therapeutically.

physiology↗

bioRxiv2022

Towards Environmental Control of Microbiomes

Microbial communities have consequential effects on health and the environment yet remain uncontrollable due to their complex dynamics. Ecological modeling offers a platform to overcome their nonlinear and interconnected nature but traditionally does not account for context-dependence. Here, we extend the generalized Lotka-Volterra (gLV) model to accommodate a varying environment by identifying how environmental changes alter species growth rates and interactions in a manner that predicts full community trajectories across environmental gradients. We identify key environment-varying interactions within a synthetic community derived from the Oryzae sativa rhizosphere, and demonstrate how variations in the environment change fixed point compositions and rates of convergence. With our model, we simulate how precise perturbations of the environment can offer improvements in an optimal control problem of driving a community to a target composition. We show that environmental perturbation can minimize the total species input (direct species perturbation) and greatly expand the set of initial states from which a desired target can be reached despite stochasticity. This work demonstrates that a formal perspective on environmental influence of community dynamics is valuable for not only understanding seasonal changes or anthropogenic manipulations, but is critical for improving control of the microbiome.

systems biology↗

bioRxiv2022

MND1 and PSMC3IP control PARP inhibitor sensitivity in mitotic cells

The PSMC3IP-MND1 heterodimer promotes RAD51 and DMC1-dependent D-loop formation during meiosis in yeast and mammalian organisms. For this purpose, it catalyzes the DNA strand exchange activities of the recombinases. Interestingly, in a panel of genome-scale CRISPR-Cas9 mutagenesis and interference screens in mitotic cells, we found that depletion of either PSMC3IP or MND1 caused sensitivity to clinical Poly (ADP-Ribose) Polymerase inhibitors (PARPi). A retroviral mutagenesis screen in mitotic cells also identified PSMC3IP and MND1 as genetic determinants of ionizing radiation sensitivity. The role PSMC3IP and MND1 play in preventing PARPi sensitivity in mitotic cells appears to be independent of a previously described role in alternative lengthening of telomeres (ALT). PSMC3IP or MND1 depleted cells accumulate toxic RAD51 foci in response to DNA damage, show impaired homology-directed DNA repair, and become PARPi sensitive, even in cells lacking both BRCA1 and TP53BP1. Although replication fork reversal is also affected, the epistatic relationship between PSMC3IP-MND1 and BRCA1/BRCA2 suggests that the abrogated D-loop formation is the major cause of PARPi sensitivity. This is corroborated by the fact that a PSMC3IP p.Glu201del D-loop formation mutant associated with ovarian dysgenesis fails to reverse PARPi sensitivity. These observations suggest that meiotic proteins such as MND1 and PSMC3IP could have a greater role in mitotic cells in determining the response to therapeutic DNA damage.

cancer biology↗