Biology subjects

Ma, J.

Publications and source records attributed to Ma, J..

At least 235 records · Page 13Linked to original sources

bioRxiv2023

Mapping the Organization and Morphology of Calcitonin Gene-Related Peptide (CGRP)-IR Axons in the Whole Mouse Stomach

Nociceptive afferent axons innervate the stomach and send signals to the brain and spinal cord. Peripheral nociceptive afferents can be detected with a variety of markers [e.g., substance P (SP) and calcitonin gene-related peptide (CGRP)]. We recently examined the topographical organization and morphology of SP-immunoreactive (SP-IR) axons in the whole mouse stomach muscular layer. However, the distribution and morphological structure of CGRP-IR axons remain unclear. We used immunohistochemistry labeling and applied a combination of imaging techniques, including confocal and Zeiss Imager M2 microscopy, Neurolucida 360 tracing, and integration of axon tracing data into a 3D stomach scaffold to characterize CGRP-IR axons and terminals in the whole mouse stomach muscular layers. We found that: 1) CGRP-IR axons formed extensive terminal networks in both ventral and dorsal stomachs. 2) CGRP-IR axons densely innervated the blood vessels. 3) CGRP-IR axons ran in parallel with the longitudinal and circular muscles. Some axons ran at angles through the muscular layers. 4) They also formed varicose terminal contacts with individual myenteric ganglion neurons. 5) CGRP-IR occurred in DiI-labeled gastric-projecting neurons in the dorsal root and vagal nodose ganglia, indicating CGRP-IR axons were visceral afferent axons. 6) CGRP-IR axons did not colocalize with tyrosine hydroxylase (TH) or vesicular acetylcholine transporter (VAChT) axons in the stomach, indicating CGRP-IR axons were not visceral efferent axons. 7) CGRP-IR axons were traced and integrated into a 3D stomach scaffold. For the first time, we provided a topographical distribution map of CGRP-IR axon innervation of the whole stomach muscular layers at the cellular/axonal/varicosity scale.

neuroscience↗

bioRxiv2023

Sound-based assembly of three-dimensional cellularized and acellularized constructs

Herein we show an accessible technique based on Faraday waves that assist the rapid assembly osteoinductive {beta}-TCP particles as well as human osteoblast pre-assembled in spheroids. The hydrodynamic forces originating at seabed of the assembly chamber can be used to tightly aggregate inorganic and biological entities at packing densities that resemble those of native tissues. Additionally, following a layer-by-layer assembly procedure, centimeter scaled osteoinductive three-dimensional and cellularised constructs have been fabricated. We showed that the intimate connection between biological building blocks is essential in engineering living system able of localized mineral deposition. Our results demonstrate, for the first time, the possibility to obtain three-dimensional cellularised and acellularised anisotropic constructs using Faraday waves.

bioengineering↗

bioRxiv2023

Centromere Innovations Within a Mouse Species

Mammalian centromeres direct faithful genetic inheritance and are typically characterized by regions of highly repetitive and rapidly evolving DNA. We focused on a mouse species, Mus pahari, that we found has evolved to house centromere-specifying CENP-A nucleosomes at the nexus of a satellite repeat that we identified and term {pi}-satellite ({pi}-sat), a small number of recruitment sites for CENP-B, and short stretches of perfect telomere repeats. One M. pahari chromosome, however, houses a radically divergent centromere harboring [~]6 Mbp of a homogenized {pi}-sat-related repeat, {pi}-satB, that contains >20,000 functional CENP-B boxes. There, CENP-B abundance drives accumulation of microtubule-binding components of the kinetochore, as well as a microtubule-destabilizing kinesin of the inner centromere. The balance of pro and anti-microtubule-binding by the new centromere permits it to segregate during cell division with high fidelity alongside the older ones whose sequence creates a markedly different molecular composition. TeaserChromatin and kinetochore alterations arise in response to evolutionarily rapid changes to underlying repetitive centromere DNA.

genomics↗

bioRxiv2023

Mechanism of ozone alleviation of malignant ascites in hepatocellular carcinoma through inhibition of NETs

Malignant ascites in hepatocellular carcinoma is usually a sign of advanced disease and poor prognosis and is also thought to be associated with chronic inflammation mediated by neutrophil extracellular trap networks (NETs). Whereas ozone, a strong oxidant, has significant antibacterial and anti-inflammatory effects, its effectiveness in treating malignant liver ascites is unclear.cOzone showed significant anti-peritoneal fluid production properties in H22 tumor-bearing mice, and ozone reduced peritoneal fluid production by activating AMPK and up-regulating SR-A phagocytosis damage-associated molecular patterns (DAMPs) to reduce the production of NETs. This suggests that ozone could be used as a new drug for the treatment of malignant ascites in hepatocellular carcinoma.

cancer biology↗

bioRxiv2023

Resistance to abemaciclib is associated with increased metastatic potential and lysosomal protein deregulation in breast cancer cells

Cyclin dependent kinase 4 and 6 inhibitors (CDK4/6i) such as abemaciclib are routinely used to treat metastatic estrogen receptor positive (ER+)/HER2-negative breast cancer. However, adaptive mechanisms inhibit their effectiveness and allow for disease progression. Using murine metastatic ER+ breast cancer cells, we show that acquired resistance to abemaciclib is accompanied by increase in metastatic potential. Mass spectrometry-based proteomics from abemaciclib sensitive and resistant cells showed that lysosomal proteins including CTSD (cathepsin D), CTSA (cathepsin A) and CD68 were significantly increased in resistant cells. Combination of abemaciclib and a lysosomal destabilizer, such as hydroxychloroquine (HCQ) or bafilomycin A1, re-sensitized resistant cells to abemaciclib. Also, combination of abemaciclib and HCQ decreased migration and invasive potential and increased lysosomal membrane permeability (LMP) in resistant cells. Pro-survival BCL2 protein levels were elevated in resistant cells, and a triple treatment with abemaciclib, HCQ, and BCL2 inhibitor, venetoclax, significantly inhibited cell growth compared to treatment with abemaciclib and HCQ. Furthermore, resistant cells showed increased levels of TFEB (Transcription Factor EB), a master regulator of lysosomal-autophagy genes, and siRNA mediated knockdown of TFEB decreased invasion in resistant cells. TFEB gene was found to be mutated in a subset of invasive human breast cancer samples, and overall survival analysis in ER+, lymph node-positive breast cancer showed that increased TFEB expression correlated with decreased survival. Collectively, we show that prolonged exposure to abemaciclib in ER+ breast cancer cells leads to resistance accompanied by an aggressive phenotype that is partly supported by deregulated lysosomal function. Implications: Our data implicate that resistance to abemaciclib is associated with deregulation of lysosomes and augmented metastatic potential, and therefore, the lysosomal pathway could be a therapeutic target in advanced ER+ breast cancer. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=164 SRC="FIGDIR/small/537215v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@1bd5e3aorg.highwire.dtl.DTLVardef@175559borg.highwire.dtl.DTLVardef@473d17org.highwire.dtl.DTLVardef@fbf0bf_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2023

Transcriptomic profiling of nuclei from PFA-fixed and FFPE brain tissues

Formalin-fixed and paraffin-embedded (FFPE) tissue archives are the largest repository of clinically annotated specimens, and FFPE-compatible single cell gene expression workflow had been developed and applied recently. However, for tissues where cells are hard to dissociate or brains with complex neuronal cells, nuclear transcriptomic profiling are desirable. Moreover, the effects of standard pathological practice on the transcriptome of samples obtained from such archived specimens was also largely anecdotal. Here, we performed RNA-seq of nuclei from hippocampal of mice that underwent freezing, paraformaldehyde (PFA) fixation, and paraffin embedding. Then, we comprehensively evaluated the parameters affecting mRNA quality, transcription patterns, functional level and cell states of nuclei, including PFA fixation time and storage time of FFPE tissues. The results showed that the transcriptome signatures of nuclei isolated from fresh PFA-fixed and fresh FFPE tissues were more similar to matched frozen samples. By contrast, the brain fixed for more than 3 days had prominent impacts on the sequencing data, such as the numbers and biotypes of gene, GC content and ratio of reads interval. Commensurately, prolonged fixation time will result in more differentially expressed genes, especially those enriched in spliceosome and synaptic related pathways, affecting the analysis of gene splicing and neuron cells. MuSiC deconvolution results revealed that PFA infiltrating brains for 3 days will destroy the real cell states, and the proportion of neuron, endothelial and oligodendrocytes diminished while that of microglia was reversed. Yet the effect of storage time on cell composition was more neglectable for FFPE samples. In addition, oligodendrocyte precursor cells were most affected in all fixed samples, and their destruction was independent of fixation time and preservation time. The comprehensive results highlighted that fixation time had much more influences on the nuclear transcriptomic profiles than FFPE retention time, and the cliff-like effects appeared to occur over a fixed period of 1-3 days, with no more differences from additional fixation durations.

molecular biology↗

bioRxiv2023

Hippocampal subfield vulnerability to α-synuclein pathology precedes neurodegeneration and cognitive dysfunction

Cognitive dysfunction is a salient feature of Parkinsons disease (PD) and Dementia with Lewy bodies (DLB). The onset of dementia reflects the spread of Lewy pathology throughout forebrain structures. The mere presence of Lewy pathology, however, provides limited indication of cognitive status. Thus, it remains unclear whether Lewy pathology is the de facto substrate driving cognitive dysfunction in PD and DLB. Through application of -synuclein fibrils in vivo, we sought to examine the influence of pathologic inclusions on cognition. Following stereotactic injection of -synuclein fibrils within the mouse forebrain, we measured the burden of -synuclein pathology at 1-, 3-, and 6-months post-injection within subregions of the hippocampus and cortex. Under this paradigm, the hippocampal CA2/3 subfield was especially susceptible to - synuclein pathology. Strikingly, we observed a drastic reduction of pathology in the CA2/3 subfield across time-points, consistent with the consolidation of -synuclein pathology into dense somatic inclusions followed by neurodegeneration. Silver-positive degenerating neurites were observed prior to neuronal loss, suggesting that this might be an early feature of fibril-induced neurotoxicity and a precursor to neurodegeneration. Critically, mice injected with -synuclein fibrils developed progressive deficits in spatial learning and memory. These findings support that the formation of -synuclein inclusions in the mouse forebrain precipitate neurodegenerative changes that recapitulate features of Lewy-related cognitive dysfunction. HighlightsO_LIMice injected with -synuclein fibrils develop hippocampal and cortical - synuclein pathology with a dynamic regional burden at 1-, 3-, and 6-months post-injection. C_LIO_LISilver-positive neuronal processes are an early and enduring degenerative feature of the fibril model, while extensive neurodegeneration of the hippocampal CA2/3 subfield is detected at 6-months post-injection. C_LIO_LIMice exhibit progressive hippocampal-dependent spatial learning and memory deficits. C_LIO_LIForebrain injection of -synuclein fibrils may be used to model aspects of Lewy-related cognitive dysfunction. C_LI

neuroscience↗

bioRxiv2023

Baicalin Ameliorates Defective Decidualization in URSA by Regulating Mitochondrial Fission Induced Necroptosis

Defective decidualization is a significant pathological feature of URSA. And the potential relationship between mitochondrial fission, necroptosis and defective decidualization remains unknown. Baicalin plays an important role in regulating mitochondrial fission and programmed cell death. However, whether baicalin has a protective effect on defective decidualization in URSA has not been reported thus far. This study aims to explore the mechanisms of mitochondrial fission induced necroptosis in defective decidualization in URSA and the regulation of baicalin. First, decidual tissues were collected from URSA and health controls. And then, T-hESC was treated with lipopolysaccharide (LPS), Tyrphostin A9 (TA9), TA9+necrostatin-1(Nec-1) and TA9+baicalin during in vitro decidualization. Besides, URSA mice were established and randomly administrated with low, medium, and high doses of baicalin as well as saline. Results showed that decidualization markers prolactin (PRL) and insulin-like growth factor-binding protein-1 (IGFBP1) in patients with URSA were significantly decreased (P<0.05). The incidence of cell necroptosis was increased, manifested with increased Annexin V and PI positive cells, high level of pRIP3 T231(P<0.01) and pMLKL S358 (P<0.05). Moreover, mitochondrial fission was also hyperactive, featured by elevated level of Fis1 (P<0.01) and Drp1 (P<0.05). In vitro experiments, LPS was induced to trigger necroptosis of T-hESC during induced decidualization, and IGFBP1 and PRL were subsequently decreased (P<0.05). Besides, mitochondrial fission inducer TA9 promoted the level of necroptosis (P<0.05) and induced defective decidualization, which could be rescued by necroptosis inhibitor Nec-1 (P<0.05). In addition, baicalin could reduce mitochondrial fission (P<0.05), necroptosis (P<0.05) and ameliorate defective decidualization in vivo and in vitro (P<0.05). In conclusion, hyperactive mitochondrial fission could promote necroptosis, thus inducing defective decidualization. And baicalin could ameliorates defective decidualization in URSA by regulating mitochondrial fission induced necroptosis.

molecular biology↗

bioRxiv2023

xTrimoGene: An Efficient and Scalable Representation Learner for Single-Cell RNA-Seq Data

AO_SCPLOWBSTRACTC_SCPLOWThe advances in high-throughput sequencing technology have led to significant progress in measuring gene expressions in single-cell level. The amount of publicly available single-cell RNA-seq (scRNA-seq) data is already surpassing 50M records for human with each record measuring 20,000 genes. This highlights the need for unsupervised representation learning to fully ingest these data, yet classical transformer architectures are prohibitive to train on such data in terms of both computation and memory. To address this challenge, we propose a novel asymmetric encoder-decoder transformer for scRNA-seq data, called xTrimoGene, which leverages the sparse characteristic of the data to scale up the pre-training. This scalable design of xTrimoGene reduces FLOPs by one to two orders of magnitude compared to classical transformers while maintaining high accuracy, enabling us to train the largest transformer models over the largest scRNA-seq dataset today. Our experiments also show that the performance of xTrimoGene improves as we increase the model sizes, and it also leads to SOTA performance over various downstream tasks, such as cell classification, perturb-seq effect prediction, and drug combination prediction.

bioinformatics↗

bioRxiv2023

Peripheral detection of viruses shapes brain immunity and behavior in zebrafish

Olfactory sensory neurons (OSNs) are constantly exposed to pathogens, including viruses. However, serious brain infection via the olfactory route rarely occurs. When OSNs detect a virus, they coordinate local antiviral immune responses to stop virus progression to the brain. Despite effective immune control in the olfactory periphery, pathogen-triggered neuronal signals reach the CNS via the olfactory bulb (OB). We hypothesized that neuronal detection of a virus by OSNs initiates neuroimmune responses in the OB that prevent pathogen invasion. Using zebrafish (Danio rerio) as a model, we demonstrate viral-specific neuronal activation of OSNs projecting into the OB, indicating that OSNs are electrically activated by viruses. Further, behavioral changes are seen in both adult and larval zebrafish after viral exposure. By profiling the transcription of single cells in the OB after OSNs are exposed to virus, we found that both microglia and neurons enter a protective state. Microglia and macrophage populations in the OB respond within minutes of nasal viral delivery followed decreased expression of neuronal differentiation factors and enrichment of genes in the neuropeptide signaling pathway in neuronal clusters. Pituitary adenylate-cyclase-activating polypeptide (pacap), a known antimicrobial, was especially enriched in a neuronal cluster. We confirm that PACAP is antiviral in vitro and that PACAP expression increases in the OB 1 day post-viral treatment. Our work reveals how encounters with viruses in the olfactory periphery shape the vertebrate brain by inducing antimicrobial programs in neurons and by altering host behavior.

immunology↗

bioRxiv2023

Phosphorylation of pyruvate dehydrogenase marks the inhibition of in vivo neuronal activity

For decades, the expression of immediate early genes (IEGs) such as c-fos has been the most widely used molecular marker representing neuronal activation. However, to date, there is no equivalent surrogate available for the decrease of neuronal activity (i.e., inhibition). Here, we developed an optogenetic-based biochemical screen in which population neural activities can be controlled by light with single action potential precision, followed by unbiased phosphoproteomic profiling. We identified that the phosphorylation of pyruvate dehydrogenase (pPDH) inversely correlated with the intensity of action potential firing in primary neurons. In in vivo mouse models, monoclonal antibody-based pPDH immunostaining detected neuronal inhibition across the brain induced by a wide range of factors including general anesthesia, sensory experiences, and natural behaviors. Thus, as an in vivo marker for neuronal inhibition, pPDH can be used together with IEGs or other cell-type markers to profile and identify bi-directional neural dynamics induced by experiences or behaviors.

neuroscience↗

bioRxiv2023

Loss of Gasdermin D is protective against influenza virus-induced inflammation and mortality

Influenza virus activates cellular inflammasome pathways, which can be either beneficial or detrimental to infection outcomes. Here, we investigated the role of the inflammasome-activated pore-forming protein gasdermin D (GSDMD) during infection. Ablation of GSDMD in knockout (KO) mice significantly attenuated virus-induced weight loss, lung dysfunction, lung histopathology, and mortality compared with wild type (WT) mice, despite similar viral loads. Infected GSDMD KO mice exhibited decreased inflammatory gene signatures revealed by lung transcriptomics, which also implicated a diminished neutrophil response. Importantly, neutrophil depletion in infected WT mice recapitulated the reduced mortality and lung inflammation observed in GSDMD KO animals, while having no additional protective effects in GSDMD KOs. These findings reveal a new function for GSDMD in promoting lung neutrophil responses that amplify influenza virus-induced inflammation and pathogenesis. Targeting the GSDMD/neutrophil axis may provide a new therapeutic avenue for treating severe influenza.

immunology↗

bioRxiv2023

Rotamer Density Estimator is an Unsupervised Learner of the Effect of Mutations on Protein-Protein Interaction

AO_SCPLOWBSTRACTC_SCPLOWProtein-protein interactions are crucial to many biological processes, and predicting the effect of amino acid mutations on binding is important for protein engineering. While data-driven approaches using deep learning have shown promise, the scarcity of annotated experimental data remains a major challenge. In this work, we propose a new approach that predicts mutational effects on binding using the change in conformational flexibility of the protein-protein interface. Our approach, named Rotamer Density Estimator (RDE), employs a flow-based generative model to estimate the probability distribution of protein side-chain conformations and uses entropy to measure flexibility. RDE is trained solely on protein structures and does not require the supervision of experimental values of changes in binding affinities. Furthermore, the unsupervised representations extracted by RDE can be used for downstream neural network predictions with even greater accuracy. Our method outperforms empirical energy functions and other machine learning-based approaches.

bioinformatics↗

bioRxiv2023

Discovery and characterization of cross-reactive intrahepatic antibodies in severe alcoholic hepatitis

The pathogenesis of antibodies in severe alcoholic hepatitis (SAH) remains unknown. We sought to determine if there was antibody deposition in SAH livers and whether antibodies extracted from SAH livers were cross-reactive against both bacterial antigens and human proteins. We analyzed immunoglobulins (Ig) in explanted livers from SAH patients (n=45) undergoing liver transplantation and tissue from corresponding healthy donors (HD, n=10) and found massive deposition of IgG and IgA isotype antibodies associated with complement fragment C3d and C4d staining in ballooned hepatocytes in SAH livers. Ig extracted from SAH livers, but not patient serum exhibited hepatocyte killing efficacy in an antibody-dependent cell-mediated cytotoxicity (ADCC) assay. Employing human proteome arrays, we profiled the antibodies extracted from explanted SAH, alcoholic cirrhosis (AC), nonalcoholic steatohepatitis (NASH), primary biliary cholangitis (PBC), autoimmune hepatitis (AIH), hepatitis B virus (HBV), hepatitis C virus (HCV) and HD livers and found that antibodies of IgG and IgA isotypes were highly accumulated in SAH and recognized a unique set of human proteins as autoantigens. The use of an E. coli K12 proteome array revealed the presence of unique anti-E. coli antibodies in SAH, AC or PBC livers. Further, both Ig and E. coli captured Ig from SAH livers recognized common autoantigens enriched in several cellular components including cytosol and cytoplasm (IgG and IgA), nucleus, mitochondrion and focal adhesion (IgG). Except IgM from PBC livers, no common autoantigen was recognized by Ig and E. coli captured Ig from AC, HBV, HCV, NASH or AIH suggesting no cross-reacting anti-E. coli autoantibodies. The presence of cross-reacting anti-bacterial IgG and IgA autoantibodies in the liver may participate in the pathogenesis of SAH.

pathology↗

bioRxiv2023

A promising QTL QSns.sau-MC-3D.1 likely superior to WAPO1 for wheat spikelet number per spike shows no adverse effects on yield-related traits

Spikelet number per spike (SNS) is one of the crucial factors determining wheat yield. Thus, improving our understanding of the genes that regulate SNS could help develop higher-yielding wheat varieties. A genetic linkage map constructed using the GenoBaits Wheat 16K Panel and the 660K SNP array contained 5991 polymorphic SNP markers spanning 2813.26 cM. A total of twelve QTL for SNS were detected in the recombinant inbred line (RIL) population msf x Chuannong 16 (MC), and two of them, i.e., QSns.sau-MC-3D.1 and QSns.sau-MC-7A, were stably expressed. QSns.sau-MC-3D.1 had high LOD values ranging from 4.99 to 11.06 and explained 9.71-16.75% of the phenotypic variation. Comparison of QSns.sau-MC-3D.1 with previously reported SNS QTL suggested that it is likely a novel one. A kompetitive allele-specific PCR (KASP) marker, KASP-10, tightly linked to QSns.sau-MC-3D.1 was developed to successfully validate its effect in three segregated populations and a natural population. Genetic analysis indicated that WHEAT ORTHOLOG OFAPO1 (WAPO1) was a candidate gene for QSns.sau-MC-7A. The combined additive effect of QSns.sau-MC-3D.1 and WAP01 had a great additive effect increasing SNS by 7.10%. In addition, our results suggested that SNS is not affected by 1BL/1RS translocations in the MC RIL population. Correlation analysis between two major QTL and other agronomic traits showed that QSns.sau-MC-3D.1 was likely independent of these agronomic traits. However, the H2 haplotype of WAPO1 may affect effective tiller number and plant height. This indicated that the breeding potential of QSns.sau-MC-3D.1 is better than that of WAPO1. The geographical distribution of QSns.nsau-MC-3D.1 showed that QSns.sau-MC-3D.1 positive allele frequency was dominant in most wheat-producing regions of China and it has been positively selected among modern cultivars released in China since the 1940s. Two genes, TraesCS3D03G0222600 and TraesCS3D03G0216800, associated with SNS development were predicted in the physical interval of QSns.sau-MC-3D.1. qRT-PCR results of the two genes showed that only the expression level of TraesCS3D03G0216800 was significantly different between msf and CN16. These results enrich our understanding of the genetic basis of wheat SNS and will be useful for fine mapping and cloning of genes underlying QSns.sau-MC-3D.1, and provide a basis for marker-assisted selection breeding. Author summaryIn this study, we identified two major QTL (QSns.sau-MC-3D.1 and QSns.sau-MC-7A) in a RIL population. WAPO1 was demonstrated to be the candidate gene for QSns.sau-MC-7A. QSns.sau-MC-3D.1 was a novel and stably expressed QTL, and further confirmed in different genetic backgrounds. Our results further demonstrate that QSns.sau-MC-3D.1 has better breeding potential because of its no adverse effect on other agronomic traits than WAPO1, and it has been positively selected during Chinese breeding programs since the 1940s. Taken together, the identification of QSns.sau-MC-3D.1 offers a promising resource to further increase wheat yields.

genetics↗

bioRxiv2023

Structural Optimization of siRNA Conjugates for Albumin Binding Achieves Effective MCL1-Targeted Cancer Therapy

The high potential for therapeutic application of siRNAs to silence traditionally undruggable oncogenic drivers remains largely untapped due to the challenges of tumor cell delivery. Here, siRNAs were optimized for in situ binding to albumin through C18 lipid modifications to improve pharmacokinetics and tumor delivery. Systematic variation of siRNA conjugates revealed a lead structure with divalent C18 lipids each linked through three repeats of hexaethylene glycol connected by phosphorothioate bonds. Importantly, we discovered that locating the branch site of the divalent lipid structure proximally (adjacent to the RNA) rather than at a more distal site (after the linker segment) promotes association with albumin, while minimizing self-assembly and lipoprotein association. Comparison to higher albumin affinity (diacid) lipid variants and siRNA directly conjugated to albumin underscored the importance of conjugate hydrophobicity and reversibility of albumin binding for siRNA delivery and bioactivity in tumors. The lead conjugate increased tumor siRNA accumulation 12-fold in orthotopic mouse models of triple negative breast cancer over the parent siRNA. When applied for silencing of the anti-apoptotic oncogene MCL-1, this structure achieved approximately 80% MCL1 silencing in orthotopic breast tumors. Furthermore, application of the lead conjugate structure to target MCL1 yielded better survival outcomes in three independent, orthotopic, triple negative breast cancer models than an MCL1 small molecule inhibitor. These studies provide new structure-function insights on optimally leveraging siRNA-lipid conjugate structures that associate in situ with plasma albumin for molecular-targeted cancer therapy.

bioengineering↗

bioRxiv2023

Butyrate endows extraocular muscle stem cell-like transcriptomic patterns that ameliorate satellite cell depletion and denervation to slow ALS progression

Amyotrophic lateral sclerosis (ALS) is a fatal neuromuscular disorder characterized by progressive weakness of almost all skeletal muscles, whereas extraocular muscles (EOMs) are comparatively spared. While hindlimb and diaphragm muscles of end-stage SOD1G93A (G93A) mice (a familial ALS mouse model) exhibit severe denervation and depletion of Pax7+ satellite cells (SCs), we found that the pool of SCs and the integrity of neuromuscular junctions (NMJs) are maintained in EOMs. In cell sorting profiles, SCs derived from hindlimb and diaphragm muscles of G93A mice exhibit denervation-related activation, whereas SCs from EOMs of G93A mice display spontaneous (non-denervation-related) activation, similar to SCs from wild-type mice. Specifically, cultured EOM SCs contain more abundant transcripts of axon guidance molecules, including Cxcl12, along with more sustainable renewability than the diaphragm and hindlimb counterparts under differentiation pressure. In neuromuscular co-culture assays, AAV-delivery of Cxcl12 to G93A-hindlimb SC-derived myotubes enhances motor neuron axon extension and innervation, recapitulating the innervation capacity of EOM SC-derived myotubes. G93A mice fed with sodium butyrate (NaBu) supplementation exhibited less NMJ loss in hindlimb and diaphragm muscles. Additionally, SCs derived from G93A hindlimb and diaphragm muscles displayed elevated expression of Cxcl12 and improved renewability following NaBu treatment in vitro. Thus, the NaBu-induced transcriptomic changes resembling the patterns of EOM SCs may contribute to the beneficial effects observed in G93A mice. More broadly, the distinct transcriptomic profile of EOM SCs may offer novel therapeutic targets to slow progressive neuromuscular functional decay in ALS and provide possible "response biomarkers" in pre-clinical and clinical studies.

cell biology↗

bioRxiv2023

The genomic landscape of swine influenza A viruses in Southeast Asia

Swine are a primary source for the emergence of pandemic influenza A viruses. The intensification of swine production, along with global trade, has amplified the transmission and zoonotic risk of swine influenza virus (swIAV). Effective surveillance is essential to uncover emerging virus strains, however gaps remain in our understanding of the swIAV genomic landscape in Southeast Asia. By collecting more than 4,000 nasal swabs and 4,000 sera from pigs in Cambodia, we unmasked the co-circulation of multiple lineages of genetically diverse swIAV of pandemic concern. Genomic analyses revealed a novel European avian-like H1N2 swine reassortant variant with North American triple reassortant internal genes, that emerged approximately seven years before its first detection in pigs in 2021. Using phylogeographic reconstruction, we identified south central China as the dominant source of swine viruses disseminated to other regions in China and Southeast Asia. We also identified nine distinct swIAV lineages in Cambodia, which diverged from their closest ancestors between two to 15 years ago, indicating significant undetected diversity in the region, including reverse zoonoses of human H1N1/2009 pandemic and H3N2 viruses. A similar period of cryptic circulation of swIAVs occurred in the decades before the H1N1/2009 pandemic. The hidden diversity of swIAV observed here further emphasizes the complex underlying evolutionary processes present in this region, reinforcing the importance of genomic surveillance at the human-swine interface for early warning of disease emergence to avoid future pandemics.

microbiology↗