Biology subjects

Song, A.

Publications and source records attributed to Song, A..

At least 19 recordsLinked to original sources

bioRxiv2026

CryoSHIELDs: tunable amphipathic peptide additives for cryo-EM

While cryogenic electron microscopy (cryo-EM) has transformed structural biology, sample preparation remains a major determinant of success. Specifically, the air-water interface (AWI) can damage complexes, impose preferred orientation, and reduce particle density. Here, we introduce cryoSHIELDs, a chemically diverse library of peptide additives designed to passivate the AWI and improve cryo-EM grid preparation. Across 24 protein systems spanning GPCRs, ABC and SLC transporters, soluble and Fab-containing complexes, and enzymes, cryoSHIELDs increased the success rate of structure determination. Individual cryoSHIELDs improved particle density, angular sampling, complex stability, and, for routine targets, map quality and resolution. This toolkit enabled the structural characterization of important targets, including the ABCC6 transporter, revealing unique TMD0-mediated stabilization, and DAMGO-bound -opioid receptor-Gi complex using substantially lower protein concentration. CryoSHIELDs provide a simple, tunable, and broadly applicable platform for more reliable cryo-EM in discovery biology and structure-based drug development.

biophysics↗

bioRxiv2026

Somatic DDX41 mutations confer neomorphic splicing activity in the pathogenesis of myelodysplastic neoplasms

Germline mutations in the RNA helicase DDX41 are the most common genetic predisposition to myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML), representing 5-7% of AML. Over 70% of patients acquire a somatic mutation at specific hotspots (R525H/G530D) in the helicase domain of DDX41 in trans, which is linked to disease progression. DDX41 has diverse cellular functions, including RNA splicing, ribosome biogenesis, R-loop resolution and inflammation. However, the mechanisms by which somatic DDX41 mutations drive MDS/AML pathogenesis are yet to be determined. Here, we systematically evaluated the function of pathogenic, missense germline and somatic DDX41 mutations. We report that DDX41 somatic mutations are gain of function alleles and fail to rescue AML cell growth, distinct from germline DDX41 mutations. DDX41 somatic mutations R525H and G530D drive widespread splicing changes in isogenic AML cell lines, consistent in genetically engineered murine bone marrow HSPCs and CD34+ cells from DDX41-mutant MDS/AML patients. Mechanistically, DDX41-R525H exhibits increased RNA binding affinity compared to wildtype, with aberrantly spliced RNA targets overlapping with enriched binding. Strikingly, aberrant splicing of SEPTIN7 is enriched exclusively in CD34+ HSPCs of patients harboring both germline and somatic DDX41 mutations but absent in samples with germline mutation alone or lacking DDX41 mutations altogether. SEPTIN7 mis-splicing introduces a premature stop codon resulting in its downregulation at the protein level. SEPTIN7 is a known regulator of cytokinesis, HSC polarity and repopulation capacity. Our results identify a novel mis-spliced candidate, SEPTIN7, whose deregulation implicates a mechanism by which the DDX41 somatic mutations promote dysplastic hematopoiesis.

cancer biology↗

bioRxiv2026

Endogenous Opioid System Modulates Neural Activation During Emotion Regulation

Emotion regulation is critical for adaptive functioning and mental health. Functional neuroimaging studies have identified distributed frontal, parietal, and limbic networks involved in emotion regulation, particularly during cognitive reappraisal. However, the neurochemical mechanisms underlying individual differences in emotion regulation remain poorly understood. The endogenous opioid system is a promising candidate because -opioid receptor systems acts as a stress buffer and modulates emotional responses to both rewarding and aversive stimuli We used positron emission tomography (PET) and functional magnetic resonance imaging (fMRI) to examine whether baseline -opioid receptor (MOR) availability is associated with haemodynamic responses during emotion regulation through reappraisal. Participants underwent [11C]carfentanil PET imaging to quantify MOR availability and subsequently completed an fMRI task involving passive viewing of emotional images and cognitive reappraisal of their emotions during image viewing As expected, fMRI revealed engagement of the dorsolateral prefrontal cortex and inferior parietal lobule during cognitive reappraisal. Baseline MOR availability predicted blood oxygenation level-dependent (BOLD) responses in frontal, temporal, and parietal regions: individuals with higher MOR availability showed a larger difference between regulation and viewing trials in the temporal pole, angular gyrus, anterior insula, thalamus, and inferior frontal gyrus. These associations were driven primarily by stronger responses during passive viewing, although some regions also showed evidence of reduced responses during active reappraisal. These findings suggest that higher endogenous opioid tone is associated with stronger recruitment of distributed frontal, temporal, and parietal networks during emotional stimulus processing as well as attenuation of activity in some of these regions during cognitive reappraisal. Thus, while higher MOR availability is associated with enhanced neural responsiveness to emotional stimuli, these responses can nevertheless be effectively modulated through deliberate emotion regulation.

neuroscience↗

bioRxiv2026

Granulin loss and TMEM106B risk converge on lysosomal C-terminal fragment pathology in frontotemporal dementia

Frontotemporal dementia (FTD) is the second most common cause of dementia after Alzheimer disease. Mutations in GRN, which encodes progranulin, are a major cause of FTD. Common genetic variants in the TMEM106B gene modify risk of FTD and the effect is especially strong in GRN mutation carriers. Intriguingly, in GRN mutation carriers, being homozygous for the protective TMEM106B haplotype seems to confer near lifetime protection against FTD. Despite the strong genetic link between GRN and TMEM106B, how these two genes interact mechanistically has remained unresolved. Recent studies have revealed that a C-terminal fragment of TMEM106B forms amyloid fibrils and accumulates in the brains of older individuals and patients with neurodegenerative disorders, including FTD. How the production of this fragment connects to granulin deficiency is also unknown. Using lysosome immunoprecipitation, we show that granulin deficiency drives the accumulation of the TMEM106B C-terminal fragment within lysosomes in Grn-knockout mice and GRN-null human iPSC-derived neurons. Recombinant progranulin supplementation reduced TMEM106B C-terminal fragment accumulation. Isogenic neurons carrying the TMEM106B risk allele displayed allele-dose-dependent fragment accumulation that was reversible by progranulin. Structural and genetic analyses demonstrated that TMEM106B dimerization stabilizes the protein and limits C-terminal fragment formation. These findings define a lysosomal pathway linking granulin deficiency to TMEM106B C-terminal fragment accumulation and explain how protective TMEM106B alleles can confer resistance to FTD, even for GRN mutation carriers. One Sentence SummaryGranulin deficiency drives lysosomal accumulation of an amyloidogenic TMEM106B C-terminal fragment, revealing a molecular mechanism that explains how TMEM106B alleles can confer risk or protection from frontotemporal dementia.

genetics↗

bioRxiv2026

Ultrastructural preservation of a whole large mammal brain with a protocol compatible with human physician-assisted death

Building a high-fidelity computational model of the whole human brain will require preservation of the ultrastructure at the level of the entire organ, post-mortem. For such a model to reflect as closely as possible the brain in the living state, artifacts that arise during both the agonal phase and the postmortem interval will need to be minimized. This is potentially feasible if a terminally-ill patient donates their brain for research following physician-assisted death. In this paper, we modify a protocol for aldehyde-stabilized cryopreservation to make it compatible with physician-assisted death. We use pigs as a model, which resemble humans in cardiovascular and brain anatomy. Aldehyde-stabilized cryopreservation was designed to provide superior structural preservation of brains of any size, across all anatomical scales, compatible with diverse analytical assays and long-term storage without ultrastructural degradation. We demonstrate, with light microscopy and volume electron microscopy, that our brain preservation protocol results in connectomically traceable whole brains and propose an economically feasible storage modality that is expected to maintain stability of ultrastructure and macromolecules in the brain even for thousands of years. Most importantly, we establish that 14 min is the approximate length of the perfusability window--the time after the cardiac arrest during which blood washout needs to be initiated so that the brain ultrastructure is preserved.

neuroscience↗

bioRxiv2026

Evolutionary genomics of local adaptation, climate vulnerability, and linarin metabolism in Opisthopappus longilobus

Global climate change and human activities are posing substantial threats to biodiversity. The genus Opisthopappus (O. taihangensis and O. longilobus), endemic to Chinas Taihang Mountains, possesses great ecological, ornamental and medicinal value. However, it is confronted with the pressures of habitat fragmentation and climate change. Here, we present the first haplotype-resolved, chromosome-scale genome assembly of O. longilobus ([~]2.95 Gb) and re-sequence 115 individuals across its range. Comparative analyses show Opisthopappus is sister to Artemisia-Chrysanthemum, with Opisthopappus and Chrysanthemum diverging at 5.15-5.18 million years ago. A profound genetic divergence is evident between O. taihangensis and O. longilobus, resulting in two distinct lineages within each species, driven by geography and climate. Our analyses indicate restricted gene flow, low diversity, and recurrent demographic bottlenecks collectively contribute to their endangerment. By integrating population genomics and environmental variables, we identified 4,437 core adaptive genes linked to water deprivation, and metabolism. Genomic offset predicts higher maladaptation risk in populations under drastic climate change. Furthermore, diverged promoters of two O-methyltransferase genes, OMT250 and OMT310, likely underlie the differential acacetin/linarin accumulation between C. morifolium and O. longilobus. These findings advance understanding of Opisthopappus evolution and climate vulnerability, offering a model for genomics-guided biodiversity conservation.

plant biology↗

bioRxiv2025

Susceptibility of Human Neural Stem Cells to SARS-CoV-2: Entry Mechanisms and Glycocalyx Influence

Previous work demonstrated that ectodermal cells exhibit greater susceptibility to SARS-CoV-2 infection than endodermal and mesodermal cells, raising concerns about potential vulnerability of the developing nervous system. We hypothesized that neural stem cells (NSCs) derived from human ectoderm are susceptible to SARS-CoV-2 infection. Using pseudotyped viral particles representing both wild-type and Omicron spike variants, we confirmed efficient infection of NSCs, with Omicron variants preferentially utilizing endocytosis-mediated entry. Inhibition of endocytosis with filipin and OcTMAB significantly reduced infection across all spike variants. Low glycosylation levels on NSCs facilitated viral entry, and enzymatic removal of glycosylation increased their susceptibility. Ectodermal infection by SARS-CoV-2 raises serious concern for potential teratogenic effects on the nervous system, possibly causing latent or subclinical anomalies not immediately evident at birth. Therefore, future clinical studies and long-term surveillance of infants and children exposed in utero are necessary to investigate and identify potential neurodevelopmental deficits.

developmental biology↗

bioRxiv2025

MDS-associated SF3B1 mutations promote aberrant fate choice of hematopoietic stem cell via mis-splicing of mediator kinase module component CDK8

Mutations in RNA splicing factor SF3B1 are among the most common in MDS and are strongly associated with MDS with ring sideroblasts (MDS-RS). While aberrant splicing of terminal erythroid regulators has been implicated in MDS pathogenesis, the impact of SF3B1 mutations on early hematopoietic progenitor function remains unclear. Here, we identify CDK8, a key kinase of the mediator complex involved in transcriptional regulation, as a recurrent mis-spliced target in SF3B1-mutant MDS. Mutant SF3B1 induces cryptic 3' splice site selection in CDK8, leading to loss of CDK8 mRNA and protein. Using primary human HSPCs, our study identifies CDK8 as an important regulator of HSPC homeostasis and cell fate determination. CDK8 depletion results in expansion of HSPCs and shifts differentiation toward the erythroid and myeloid lineages, mirroring phenotypes observed in SF3B1-mutant MDS. Lastly, functional restoration of CDK8 rescues early erythroid phenotypes in SF3B1-mutant cells. These findings implicate CDK8 mis-splicing as a mechanistic driver of altered progenitor fate and dysplasia in SF3B1-mutant MDS, linking aberrant splicing to transcriptional dysregulation and hematopoietic lineage commitment.

cancer biology↗

bioRxiv2025

Engineering a Juxtamembrane-Targeting CAR T-Cell Against Mesothelin: A Novel Binder Resilient to Shed Antigen in Ovarian and Pancreatic Cancer

Mesothelin is an attractive target for CAR-T therapy on a number of cancer types; however, the efficacy of this therapy is diminished because the bulk of the cell surface-expressed mesothelin is shed through naturally occurring proteolysis leaving behind a short juxtamembrane peptide "stump". The two problems this creates are (1) the bulk of the target protein is no longer on the tumor cell and (2), the free soluble shed mesothelin remains in the tumor microenvironment and becomes present in blood/other body fluids binding to the mesothelin-targeted CAR-T and interfering with their ability to target the mesothelin that remains on the surface of the tumor. These issues have likely contributed at least in part to the lack of desired efficacy of CAR-T cells that target membrane distal regions of mesothelin (i.e., the shed domain) such as those utilizing anti-mesothelin scFvs SS1 and M5. Here we describe CAR T cells that utilize novel antibodies specific for the mesothelin stump domain thus being unaffected by the natural process of mesothelin shedding. Mesothelin "stump" specific CAR T cells (ST4-22) had cytotoxicity and in vivo activity that was comparable to standard anti-mesothelin CAR T cells. Importantly, CAR T cells expressing ST4-22 were effective against tumor cells that were resistant to standard anti-mesothelin CAR T cells.

immunology↗

bioRxiv2025

Rethinking Kalman Filters for Motor Brain-Machine Interface: The Fundamental Limitations and A Perspective Shift

The Kalman filter has been introduced to the motor brain-machine interface (BMI) field for over 20 years and remains one of the most widely used models due to its simple and intuitive nature. However, this paper demonstrates that the application of Kalman filters in the BMI field violates the models own assumptions and numerous neuroscience principles, resulting in six critical limitations: (1) the observation matrix mapping from kinematics to neural activity causes individual neurons to be modeled independently, ignoring neural population activity; aligned kinematic and neural activity sequences fail to capture preparatory information; (3) the presence of behaviorally irrelevant neural activity causes observation weights to be excessively underestimated; (4) noise in the observation matrix renders posterior covariance estimates biased; (5) Kalman gain computation in observation space leads to repeated noise accumulation and (6) computational inefficiency. All these problems can be resolved through a simple perspective shift: separating the decoder from the Kalman filter and treating its predicted kinematics as the Kalman filters observation rather than neural activity. Experiments conducted on CRCNS-recorded monkey dorsal premotor area and primary motor signals performing computer cursor control tasks validate the existence of the six limitations and their violations of neuroscience principles, while demonstrating the superiority of the improved Kalman filter across all evaluated metrics.

neuroscience↗

bioRxiv2025

SARS-CoV-2 Viral Pseudoparticles Preferentially Infect Ectoderm In Human Embryonic Tissues

Early stages in human development are difficult to study in pregnant women. We used a "disease-in-a-dish" model to investigate SARS-CoV-2 infection of human embryonic stem cells and the three germ layers. Ectoderm had a significantly higher infection than the other cell types. This was due to: (1) the use of two entry pathways by the ectoderm (fusion and endocytosis), (2) high levels of TMPRSS2 in the ectoderm, and (3) a much-reduced ectodermal glycocalyx, which facilitated viral attachment to the ACE2 receptor. Our findings provide strong evidence that cells in young postimplantation human embryos are susceptible to SARS-CoV-2 infection, which could be embryo lethal or teratogenic in surviving embryos. The high level of infection in ectoderm is a concern as its derivatives may also be affected by SARS-CoV-2. Future clinical work should investigate the functioning of the nervous system in infants born to mothers who had COVID-19 during pregnancy. HighlightsSARS-CoV-2 pseudoparticles infected human embryonic stem cells, endoderm, mesoderm and ectoderm Ectoderm was significantly more susceptible to infection than the other three cell types Factors accounting for increased susceptibility and tissue tropism were identified SARS-CoV-2 virus can adversely affect early stages of human development

cell biology↗

bioRxiv2025

THA_1941 from Thermosipho africanus: A Thermostable β-1,3-Glucan Phosphorylase for Efficient β-1,3-Glucan Synthesis

{beta}-1,3-Glucan phosphorylases capable of utilizing glucose as a priming substrate are key biocatalysts for the synthesis of functional {beta}-1,3-glucan. In this study, we identified THA_1941 from Thermosipho africanus (Ta{beta}GP) as a GH161 {beta}-1,3-glucan phosphorylase exhibiting robust synthetic activity towards glucose, as confirmed by 13C nuclear magnetic resonance, liquid chromatography-mass spectrometry, and sequence and structural analyses. Ta{beta}GP displayed exceptional thermostability, retaining 93% of its activity at 60 {degrees}C for 180 h, and showed broad pH tolerance ranging from pH 5.0 to 10.0, surpassing the performance of previously reported homologs. In addition, Ta{beta}GP exhibited broad substrate flexibility, accepting both - and {beta}-linked disaccharides, and demonstrated strong resistance to metal ions and lignocellulose-derived inhibitors. In the presence of 150 mM glucose 1-phosphate as the donor substrate, Ta{beta}GP synthesized {beta}-1,3-glucan with a tunable average degree of polymerization (10-32), depending on the concentration of glucose used as the primer. The combination of thermostability, inhibitor resistance, and substrate versatility makes Ta{beta}GP a promising biocatalyst for the economically viable and environmentally sustainable synthesis of {beta}-1,3-glucan from non-food biomass sources.

biochemistry↗

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

Extrinsic Apoptosis and Necroptosis in Telencephalic Development: A Single-Cell Mass Cytometry Study

Regulated cell death is integral to sculpting the developing brain, yet the relative contributions of extrinsic apoptosis and necroptosis remain unclear. Here, we leverage single-cell mass cytometry (CyTOF) to characterize the cellular landscape of the mouse telencephalon in wild-type (WT), RIPK3 knockout (RIPK3 KO), and RIPK3/Caspase-8 double knockout (DKO) mice. Strikingly, combined deletion of RIPK3 and Caspase-8 leads to a 12.6% increase in total cell count, challenging the prevailing notion that intrinsic apoptosis exclusively governs developmental cell elimination. Detailed subpopulation analysis reveals that DKO mice display selective enrichment of Tbr2 intermediate progenitors and endothelial cells, underscoring distinct, cell type-specific roles for extrinsic apoptotic and necroptotic pathways. These findings provide a revised framework for understanding the coordinated regulation of cell number during telencephalic development and suggest potential mechanistic links to neurodevelopmental disorders characterized by aberrant cell death.

developmental biology↗

bioRxiv2025

Amphetamine in Adolescence Induces a Sex-Specific Mesolimbic Dopamine Phenotype in the Adult Prefrontal Cortex

Drugs of abuse in adolescence impact brain maturation and increase psychiatric risk, with differences in sensitivity between males and females. Amphetamine in adolescent male, but not female mice, causes dopamine axons intended to innervate the nucleus accumbens and to grow ectopically to the prefrontal cortex (PFC). This is mediated by drug-induced downregulation of the Netrin-1 receptor DCC. How off-target dopamine axons function in the adult PFC remains to be determined. Here we report that males and females show place preference for amphetamine in adolescence. However, only in males, amphetamine increases PFC dopamine transporter expression in adulthood: leading to aberrant baseline dopamine transients, faster dopamine release, and exaggerated responses to acute methylphenidate. Upregulation of DCC in adolescence, using CRISPRa, prevents all these changes. Mesolimbic dopamine axons rerouted to the PFC in adolescence retain anatomical and functional phenotypes of their intended target, rendering males enduringly vulnerable to the harmful effects of drugs of abuse.

neuroscience↗

bioRxiv2024

Decoding Liver Cancer Prognosis: From Multi-omics Subtypes, Prognostic Models to Single Cell Validation

PurposeHepatocellular carcinoma (HCC) is a highly aggressive tumor characterized by significant heterogeneity and invasiveness, leading to a lack of precise individualized treatment strategies and poor patient outcomes. This necessitates the urgent development of accurate patient stratification methods and targeted therapies based on distinct tumor characteristics. Experimental DesignBy integrating gene expression data from The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC), and Gene Expression Omnibus (GEO), we identified subtypes through a multi-omics consensus clustering approach amalgamated from 10 clustering techniques. Subsequently, we developed a prognostic model, employing machine learning algorithms, based on subtype classification features. Finally, by analyzing single cell sequencing data, we investigated the mechanisms driving prognostic variations among distinct subtypes. ResultsFirst, we developed a novel consensus clustering method that categorizes liver cancer patients into two subtypes, CS1 and CS2. Second, we constructed a prognostic prediction model, which demonstrated superior predictive accuracy compared to several models published in the past five years. Finally, we observed differences between CS1 and CS2 in various metabolic pathways, biological processes, and signaling pathways, such as fatty acid metabolism, hypoxia levels, PI3K-AKT and MIF signaling pathway.

bioinformatics↗

bioRxiv2024

Stabilization of Integrator/INTAC by the small but versatile DSS1 protein

Integrator-PP2A (INTAC) is a highly modular complex orchestrating the transition of paused RNA polymerase II into productive elongation or promoter-proximal premature termination, with its loss resulting in transcription dysregulation and genome instability. Here, we identify human DSS1--a flexible 70-residue protein found in multiple functionally diverse complexes including the 26S proteasome--as an integral subunit of the INTAC backbone. Structural analysis of DSS1-INTAC, both alone and in association with paused polymerase, demonstrates intimate interactions between DSS1 and the INTAC backbone subunit INTS7. We identify tryptophan 39 of DSS1 as being critical for interacting with INTAC and find that mutating this residue disrupts DSS1s interaction with INTAC, while maintaining DSS1s interaction with the proteasome. This substitution not only destabilizes INTAC and therefore INTAC-dependent transcriptional regulation, but also reveals that INTAC is DSS1s major chromatin-bound form. Together, our findings reveal the essential role of the versatile DSS1 protein in the structure and regulatory functions of INTAC.

molecular biology↗

bioRxiv2024

The Drosophila histone methyl-transferase SET1 coordinates multiple signaling pathways in regulating male germline stem cell maintenance and differentiation

Many cell types come from tissue-specific adult stem cells that maintain the balance between proliferation and differentiation. Here, we study how the H3K4me3 methyltransferase, Set1, regulates early-stage male germ cell proliferation and differentiation in Drosophila. Early-stage germline-specific knockdown of set1 results in a temporally progressed defects, arising as germ cell loss and developing to overpopulated early-stage germ cells. These germline defects also impact the niche architecture and cyst stem cell lineage in a non-cell-autonomous manner. Additionally, wild-type Set1, but not the catalytically inactive Set1, could rescue the set1 knockdown phenotypes, highlighting the functional importance of the methyl-transferase activity of the Set1 enzyme. Further, RNA-seq experiments reveal key signaling pathway components, such as the JAK-STAT pathway gene stat92E and the BMP pathway gene mad, that are upregulated upon set1 knockdown. Genetic interaction assays support the functional relationships between set1 and JAK-STAT or BMP pathways, as mutations of both the stat92E and mad genes suppress the set1 knockdown phenotypes. These findings enhance our understanding of the balance between proliferation and differentiation in an adult stem cell lineage. The germ cell loss followed by over-proliferation phenotypes when inhibiting a histone methyl-transferase raise concerns about using their inhibitors in cancer therapy.

developmental biology↗