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Xu, J.

Publications and source records attributed to Xu, J..

At least 235 records · Page 13Linked to original sources
bioRxiv2025

Microbes regulate glomerular filtration rate in health and chronic kidney disease in mice

Microbes are implicated in a variety of host physiological and pathophysiological processes. In this study, we tested the hypothesis that microbes modulate glomerular filtration rate (GFR). Microbiota were depleted in mice using oral antibiotics (ABX; a mixture of ampicillin, neomycin, and vancomycin). GFR was significantly increased in ABX-treated mice. To confirm that the increase in GFR was due to decreased microbes, we also measured GFR in germ-free (GF) mice. GFR was increased in GF mice as compared to both conventional and conventionalized GF (CGF) mice. We next used the murine adenine diet model to ask if suppressing gut microbes with ABX also increases GFR in a setting of chronic kidney disease (CKD), where GFR is impaired. In females on an adenine diet, ABX increased GFR versus adenine alone on weeks 4 and 6. In males, ABX elevated GFR on week 2. Adenine diet significantly increased plasma creatinine and kidney fibrosis; this was suppressed by ABX in both sexes. To explore the mechanism of this increase, we tested the hypothesis that altered tubuloglomerular feedback (TGF) contributes to elevated GFR using the sodium-glucose cotransporter 2 (SGLT2) inhibitor empagliflozin (EMPA); EMPA impairs Na+ reabsorption in the proximal tubule, altering TGF. We found that EMPA impaired ABX-induced GFR increases on week 3 but not week 5, suggesting that altered TGF contributes to the initial increase in GFR. In conclusion, the microbiome plays a key role in setting baseline GFR by a mechanism which partially involves TGF, and, suppressing gut microbes can elevate GFR even in CKD. Translational StatementThis study reports that GFR is elevated when gut microbes are absent or suppressed in mice, indicating a role for commensal microbes to help establish baseline GFR in health. Likewise, suppressing gut microbes also elevates GFR in a chronic kidney disease model. These data suggest a future possibility of modulating the commensal microbes to elevate GFR in a clinical setting.

physiology↗
bioRxiv2025

Cold-activated hepatocyte derived exosomes promote BAT thermogenesis through miR-293-5p

The liver-adipose axis serves as a fundamental regulatory network governing systemic lipid homeostasis, with hepatic-derived signals orchestrating adipose tissue plasticity through multimodal mechanisms. Comprehensive elucidation of these bidirectional crosstalk mechanisms may reveal novel therapeutic strategies for metabolic disorders. Our investigation demonstrates that cold exposure induces hepatic secretion of exosomes that potentiate adipose thermogenic activation in both in vitro and in vivo models. This thermogenic potentiation is mechanistically linked to cold-induced upregulation of hepatocyte-derived exosomal miR-293-5p. Notably, pharmacological administration of miR-293-5p agomir significantly attenuates diet- induced obesity and associated metabolic dysregulation in murine models. Through mechanistic interrogation, we identified Tet1 as a direct downstream target of miR- 293-5p, where ectopic Tet1 expression disrupts brown adipose tissue (BAT) thermogenic programming independently of miR-293-5p modulation. Our findings establish cold-activated hepatocyte exosomes as endocrine signaling mediators containing thermogenic microRNA cargos, with miR-293-5p emerging as a regulatory nexus coordinating mitochondrial bioenergetics and systemic energy equilibrium through liver-adipose cross-talk.

genetics↗
bioRxiv2025

Tracing the stemness and malignant transition in a heritable colorectal cancer Lynch Syndrome by single-cell RNA-seq analysis

BackgroundLynch Syndrome (LS) is an autosomal dominant disease characterized by germline heterozygous mutations in DNA mismatch repair (MMR) genes. High-risk LS patients may proceed to colorectal cancer (CRC). However, the drivers or biomarkers of LS benign colon tissue approaching malignant CRC are not completely understood. The similarity and difference between LS-related and nonLS-related CRC are also not well interrogated (LS-CRC vs. nonLS-CRC). This study aimed to understand the cellular changes during malignant transition in LS. MethodsSingle-cell RNA sequencing (scRNA-seq) was used to analyze paired biopsy samples from 3 patients with LS (cancer tissues vs. adjacent normal tissues, n=3). Single-nuclear RNA sequencing (snRNA-seq) was used to analyze a frozen biopsy sample from a patient with LS (n=1). scRNA-seq or snRNA-seq datasets from CRC were downloaded from the open source. Integrative computational analysis was performed to conclude the distinct pattern in the single-cell atlas. Immuno-histo-fluorescence staining (IHF) were also performed for three key markers. ResultsIn the single-cell atlas, we observed an increase in primitive cancer stem-cell-like cells with high expression of a general cancer biomarker CarcinoEmbryonic Antigen-related Cell Adhesion Molecule 5 (CEACAM5) in the epithelium of the LS. Infiltration of immune cells and DNA repair biological activity are dramatically increased in LS carcinoma. The burden in LS is fundamentally elevated compared to that in CRC or healthy donors when the mutations are in the coding-sequence-wide range. Furthermore, T cell and macrophage-related tumor immunity is readily mobilized in carcinomas compared to paraCArcinomas. ConclusionsThis study provides single-cell transcriptomic resource using affected tissues from patients with Lynch Syndrome and describes an integrative profile covering the alterations (cancer stem cell markers, mutation burden, and tumor immunity) during the malignant transition from healthy to Lynch Syndrome and to colorectal cancer at the single-cell level. Highlights and Figure/Table Index (Take-Home Messages)O_LIColon tissues from HD (n=4), patients with LS (n=6) and with CRC (n=3) were collected for snRNA-seq or scRNA-seq analysis; Diagnosis of the 6 LS patients are clearly supported by our pedigree documentations (Fig. 1 and Supp. Fig. 1) and briefed in Table 1; C_LIO_LIAmong the 6 patients with LS, 1 for snRNA-seq analysis (a carcinoma tissue only), 3 for scRNA-seq analysis (3 paired para-carcinoma and carcinoma tissues) and 3 for experimental validations; (Fig. 1) C_LIO_LIFollowing studies are focused on the comparisons between HD, LS and CRC; In addition, comparisons between paired carcinoma and para-carcinoma tissues from patients with LS were also performed; (Fig. 2-7) C_LIO_LIWhen HD and LS are compared, a cancer stem cell marker CEACAM5 is readily detected by snRNA-seq analysis; (Fig. 5) C_LIO_LIWhen carcinoma and para-carcinoma from LS patients are compared, increased immune cell infiltration of and enhanced DNA repair activity in the malignant tissues is readily detected by scRNA-seq analysis; in addition, three upregulated markers in LS carcinoma (BACE2, GRPC5A and OLFM4) were identified and validated by immunohistoinfloresnce; (Fig. 3 and Fig. 4) C_LIO_LISComatic algorithm-based mutation calling analysis suggests a comparable mutation burden between carcinoma and para-carcinoma from LS patients, but such mutation burdens are grossly greater than that from HD or that from patients with CRC; (Fig. 6) C_LI O_FIG O_LINKSMALLFIG WIDTH=170 HEIGHT=200 SRC="FIGDIR/small/647495v1_fig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@174af7dorg.highwire.dtl.DTLVardef@1ad3e71org.highwire.dtl.DTLVardef@dea1e4org.highwire.dtl.DTLVardef@568f91_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 1C_FLOATNO Enrollment of LS patients and overall design of the study. (A) Three family pedigrees of the LS patients (LS-CRC) who donated the samples for single-cell transcriptomic analysis. Cropped pedigree information is provided in the Main text. See the Supp. Fig. 1 for the complete pedigree information. (B) Two different platforms were used in the study: snRNA-seq and scRNA-seq. (C) Various types of comparison were performed to characterize the malignant transition of LS. C_FIG O_TBL View this table: org.highwire.dtl.DTLVardef@eb8e4eorg.highwire.dtl.DTLVardef@cbafaaorg.highwire.dtl.DTLVardef@79ca83org.highwire.dtl.DTLVardef@1de7544org.highwire.dtl.DTLVardef@1e4fcbc_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 1.C_FLOATNO O_TABLECAPTIONClinical information of enrolled patients with LS. An Excel version of the table is provided in the Supp. Material C_TABLECAPTION C_TBL O_FIG O_LINKSMALLFIG WIDTH=160 HEIGHT=200 SRC="FIGDIR/small/647495v1_fig2.gif" ALT="Figure 2"> View larger version (56K): org.highwire.dtl.DTLVardef@8cd71corg.highwire.dtl.DTLVardef@7e75b3org.highwire.dtl.DTLVardef@61757eorg.highwire.dtl.DTLVardef@68ca5f_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 2C_FLOATNO snRNA-seq analysis of a frozen colon biopsy sample from a LS patient reveals a cluster of cancer stem cells (A) Frozen colon biopsy samples were subjected for snRNA analysis (Healthy donors, N=4; Lynch Syndrome, N=1) and epithelial cells were filtered out for further study. Data were integrated by the Seurat and Harmony standard procedure. Clusters 0-9 were identified in a total of 11,353 cells (the Healthy Controls have 7,373 cells; the LS patient has 3,980 cells). The malignancy of the epithelial cells was inferred by the inferCNV and SCEVAN algorithm (two major compartments: tumor and no-tumor). The portion of tumor or non-tumor cells in each cluster was also illustrated (right panel). Note that the major contributor in Cluster 4, 6, and 7 is the tumor-like cells from the LS patient. (B) Each cluster of the epithelial cells was further annotated according to the combination of Seurat cluster identity and SCEVAN malignant identity. Mix_1 to 5 contain both tumor-like cells and non-tumor-like cells; Other clusters are marked as BEST4+-Enterocytes, Enterocytes and Goblet cells where much fewer tumor-like cells were assigned. Note that the epithelial cells from the LS patient are mainly classified into Mix_2, 4, and 5 tumor-like cells. (C) Three clones were inferred by SCEVAN algorithm. In the phylogenetic tree, Clone_1 and Clone_2 are closer and probably originated from Clone_3. (D) A Sankey plot showing overall belonging relationships in the epithelial snRNA-seq dataset. Note that the Mix_2 pool is dominated by cells from Lynch_01 and that in the Mix_2 pool Clone_3 is the most dominant clone. (E) The Mix_2 cells specifically express numerous colon epithelial stem cells signature markers such as SMOC2, RGBM, OLFM4, AXIN2 and LGR5. Of note, all these intestine stem cell signature genes were reported as marker genes for cancer stem cells, especially LGR5. (F) Pseudotime trajectory analysis of the Lynch Syndrome epithelium cells indicates the Mix_2 cells are the most primitive in development. (G) Top 36 differentially expressed genes (DEGs, both upregulated and downregulated) were highlighted when the non-tumor-like cells were compared with tumor-like cells in the Mix2. (H) The Mix_2, 4, 5 epithelial cells all have enriched signaling pathways involved in DNA repair response and MYC targets (fonts in red) while Mix_4 and 5 manifest Interferon alpha or gamma response (fonts in blue). C_FIG O_FIG O_LINKSMALLFIG WIDTH=158 HEIGHT=200 SRC="FIGDIR/small/647495v1_fig7.gif" ALT="Figure 7"> View larger version (54K): org.highwire.dtl.DTLVardef@1be2c6aorg.highwire.dtl.DTLVardef@55f267org.highwire.dtl.DTLVardef@9d60fborg.highwire.dtl.DTLVardef@4a2d37_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 7C_FLOATNO Distinct tumor immunity microenvironment profiles in LS carcinoma (A) T cells from LS-CA and LS-paraCA patients were filtered for further annotation. The LS-paraCA group had 1410 T cells, whereas the Lynch CA group had 2125 T cells. Six major T cell subtypes were identified: Naive CD4-T, NKT, Treg, IL7R+CD8_T, GZMA+CD8_T, and GZMK+CD8_T. Note that GZMA+CD8_T cells appear to be more abundant in Lynch CA (arrows). (B) The pseudotime trajectory indicating the T cells developed towards two branches: the Naive CD4-T and Treg branches, and GZMA+CD8_T and GZMK+CD8_T branches. GZMA+CD8_T cells appear to be more mature in LS-CA than in LS-paraCA (arrows). (C-F) Biological function-instructed scoring of the paired single-cell datasets of T cells from the three LS patients, including T cell cytotoxicity (B), T cell exhaustion (C), T cell immune escape (D), and T cell surveillance (E). (G) Circle plots showing interaction profiles across indicated cells in the paired LS samples. The direction of the lines indicates the direction of the cell-cell communication, the width of the lines indicates the interaction strength, and the color of the lines indicates the cell types of the senders. (H) Summary of the Study. In this study, we profiled Lynch Syndrome biopsy samples using single-cell or single-nucleus RNA-seq analysis. Paired carcinoma and adjacent para-carcinoma samples were included to facilitate the analysis, including tracing tumor clones, calculating mutation burden, identifying biomarkers for cancer stem cells, and tumor immune microenvironment changes during the transition from pre-carcinoma to carcinoma in the inheritable cancer Lynch Syndrome. See the text in the Discussion section for further detail. C_FIG O_FIG O_LINKSMALLFIG WIDTH=148 HEIGHT=200 SRC="FIGDIR/small/647495v1_fig5.gif" ALT="Figure 5"> View larger version (44K): org.highwire.dtl.DTLVardef@1de7f42org.highwire.dtl.DTLVardef@74e8ddorg.highwire.dtl.DTLVardef@1642847org.highwire.dtl.DTLVardef@907a23_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 5C_FLOATNO Distinct pre-cancer signs in epithelial and immune cells of LS para-carcinoma (A) The scRNA-seq datasets of LS-paraCA were integrated with those of the colons from healthy donors (HD) (N=3, respectively; the HD group had 7885 cells in total, whereas the LS-paraCA group had 4766 cells). A dominance of CEACAM5high epithelial cells were identified in LS-paraCA. The sample from the patient with relapsed LS is marked with an arrow in the bar plot (left panel). (B) The portion of CEACAM5high epithelial cells, infiltrated CD8_T cells and macrophages was quantified. The sample from the relapsed LS patient is marked with arrows. (C, E) Top marker genes co-expressed in CEACAM5high epithelial cells and the enriched pathways are illustrated in the gene expression heatmap. Cells from the Enterocytes, Tufts, and Goblet subtypes were used as controls. (D, F) Quantification of the expression of CEACAM5 in epithelial cells of HD and LS-paraCA cells. C_FIG O_FIG O_LINKSMALLFIG WIDTH=178 HEIGHT=200 SRC="FIGDIR/small/647495v1_fig3.gif" ALT="Figure 3"> View larger version (48K): org.highwire.dtl.DTLVardef@142c991org.highwire.dtl.DTLVardef@1bf5d99org.highwire.dtl.DTLVardef@99edd5org.highwire.dtl.DTLVardef@1cd5c15_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 3C_FLOATNO Distinct infiltration of immune cells in carcinoma and para-carcinoma tissues of LS (A) Fresh paired carcinoma (LS-CA) and adjacent para-carcinoma (LS-paraCA) biopsies of colon tissue was subjected to scRNA-seq analysis (N=3). Colorectal cancer (nonLS-CRC, they are not diagnosed as LS) tumor samples from the public dataset were also included as controls (N=4). Cells were first grossly annotated as stromal, epithelial, or immune cells. Note that the LS-CA group showed increased infiltration of myeloid cells compared with LS-paraCA group, but T cell infiltration was comparable between the two groups. (B) Expression of classic markers for annotating the major 5 cell types. (C) Detailed annotations of 16 cell types in paired LS-CA and LS-paraCA samples. (D) Stacked bar plot showing the contribution of sample sources in each cell type. (E) Quantification of immune cell infiltration in LS-CA compared with LS-paraCA. Although no significant differences were observed, the fold-changes were approximately 2-10. Although the overall T cell infiltration was comparable, infiltration of GZMA+CD8_T and GZMK+CD8_T cells appeared to be higher in LS-CA than in LS-paraCA. Of the three LS patients enrolled in the study, one was a relapsed patient (gray dashed line, surgery treatment performed; whose son donated the frozen sample in Figure 2), while the other two were treatment-naive (gray solid lines). (F) Boxplots show DNA repair score quantification per sample (above) or per epi-cell. (bottom). C_FIG O_FIG O_LINKSMALLFIG WIDTH=152 HEIGHT=200 SRC="FIGDIR/small/647495v1_fig4.gif" ALT="Figure 4"> View larger version (51K): org.highwire.dtl.DTLVardef@1588458org.highwire.dtl.DTLVardef@58db3borg.highwire.dtl.DTLVardef@1a12084org.highwire.dtl.DTLVardef@15de70e_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 4C_FLOATNO Prioritizing novel epithelial biomarkers for tracing the transition between para-carcinoma and carcinoma in LS (LS-paraCA vs. LS-CA) (A) Epithelial cells were filtered out for further analysis and annotated as clusters 0-9 in the UMAP plot. (B, C) Bar and pie plots show the contribution of sources to epithelial clusters. Cluster 0 contained cells largely from Lynch CA_02, whereas Cluster 9 was composed of Lynch paraCA_02. The patient who donated Lynch CA_02 and paraCA_02 is identified as a relapsed LS. (D) KEGG enrichment analysis showing the enriched bioprocesses in the four epithelial cell clusters. (E) Five genes with upregulated expression in LS carcinoma epithelial cells were prioritized based on the scRNA-seq and snRNA-seq datasets. (F) Expression of BACE2, GPRC5A and OLFM4 in the paired LS-paraCA and LS-CA groups. Epithelial cells are circled by dashed lines. Note that the expression of genes in epithelial cells from nonLS-CRC samples was also very strong. (G) Verification of the low-to-high transition in the expression of BACE2, GPRC5A and OLFM4. Paraffin sections from paired LS-paraCA and LS-CA samples were prepared, and immunohistochemical (IHF) staining was performed. The expression of the indicated proteins is labeled in green, whereas the nuclei are stained with DAPI in blue. In total, biopsy samples from 4 patients with LS were used for IHF verification. C_FIG O_FIG O_LINKSMALLFIG WIDTH=148 HEIGHT=200 SRC="FIGDIR/small/647495v1_fig6.gif" ALT="Figure 6"> View larger version (28K): org.highwire.dtl.DTLVardef@1ec5210org.highwire.dtl.DTLVardef@1ffd6f9org.highwire.dtl.DTLVardef@17a7a8forg.highwire.dtl.DTLVardef@4819e_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 6C_FLOATNO Increased mutation burden in the colon tissues from Lynch Syndrome (A) The schematic diagram for calculating mutation burden based on the scRNA-seq datasets using the SComatic algorithm. Only single-base substitutions (SBS) were called in this study. Once mutation calls were achieved, the mutation burden value was quantified by normalizing the total mutation calls to the total cell number in the samples or cell types (See Methods section for details). (B) The total SBS mutation burden in the four groups of samples was indicated. (C) The six different SBS mutation burdens in the four groups of samples as indicated. (D) The SBS mutation burden in the cell types of the four groups is indicated. Note that the The mutation burden appears to be higher in mast, epithelial, plasma, myeloid, and Treg cells in the LS-CA group than in that the LS-paraCA group. C_FIG

cancer biology↗
bioRxiv2025

A global P-Process map to avoid P-value abuse

P-abuse is serious in difference identification analysis of data. How to avoid P-abuse is a huge challenge. Here, we evolve P-value (a single value) to P-Process (a global landscape of P-values under different sample size) to help researchers correctly recognize and use p-value. We observed -ln(P-Process) after rotation has very similar morphology with Wiener Process (or Brownian motion). Based on this property, for any sample size, we estimated the 95% fluctuation range of P-value and further estimated how many samples (N95()) could make sure 95% of P-values less than the given significant level . Tests proved that the estimation obtains a good performance with only a small number of samples in each group. For broader accessibility, a free web-service, P-Process Map, is available online to show the whole landscape of P-Process. At the end of the article, we explained 10 of the most typical P-abuse problems which can be easily voided by using P-Process. This "rethinking" of P-value from a higher position, which is profoundly different from the way we have seen this for the past century, would yield a new era - 2P era in which hypothesis testing is strongly required to evolve from P-value to P-Process.

bioinformatics↗
bioRxiv2025

Context-dependent Interactors Regulate TDP-43 Dysfunction in ALS/FTLD

TDP-43 mislocalization, aggregation, and loss of splicing function are neuropathological hallmarks in over 97% of Amyotrophic Lateral Sclerosis (ALS), 45% of Frontotemporal Lobar Degeneration (FTLD), and 60% of Alzheimers Disease, which has been reclassified as LATE-NC. However, the mechanisms underlying TDP-43 dysfunction remain elusive. Here, we utilize APEX2-driven proximity labeling and mass spectrometry to characterize the context-dependent TDP-43 interactome in conditions of cytoplasmic mislocalization, impaired RNA-binding contributing to aggregation, and oxidative stress. We describe context-dependent interactors, including disrupted interactions with splicing-related proteins and altered biomolecular condensate (BMC) associations. By integrating ALS and FTLD snRNA-seq data, we uncover disease-relevant molecular alterations and validate our dataset through a functional screen that identifies key TDP- 43 regulators. We demonstrate that disrupting nuclear speckle integrity, particularly through the downregulation of the splicing factor SRRM2, promotes TDP-43 mislocalization and loss of function. Additionally, we identify NUFIP2 as an interactor associated with mislocalization that sequesters TDP-43 into cytoplasmic aggregates and co-localizes with TDP-43 pathology in patient tissue. We also highlight HNRNPC as a potent TDP-43 splicing regulator, where precise modulation of TDP-43 or HNRNPC can rescue cryptic exon splicing. These findings provide mechanistic insights and potential therapeutic targets for TDP-43 dysfunction.

molecular biology↗
bioRxiv2025

Topoisomerase IIα orchestrates secretion of IL-6 and IL-8 with human papillomavirus replication

High-risk human papillomavirus (HPV) replication requires deregulation of host DNA damage response (DDR) and inflammatory pathways. DNA topoisomerase 2{beta} (Top2{beta}) was previously shown to promote HPV replication, while the function of its paralog Top2 in the viral life cycle remains unknown. Elevated levels of Top2 are consistently observed in cervical intraepithelial lesions and the related carcinomas, as well as in HPV-positive cell lines. Silencing Top2 with shRNA severely suppresses HPV genome maintenance and amplification, but in a DDR-independent manner. Instead, Top2 facilitates secretion of interleukin (IL)-6 and IL-8, which are necessary for HPV replication. Mechanistically, this manipulation is regulated by toll-like receptor 4 (TLR4). Top2 binds to the TLR4 promoter to transcriptionally induce TLR4 expression. Blockade of TLR4 signaling by the specific inhibitor TAK-242 significantly reduces the secreted IL-6/IL-8 levels and HPV replication. Overall, our results reveal a novel role of Top2 to shape the inflammatory microenvironment that benefits HPV replication, making it a promising therapeutic target for HPV-associated diseases. IMPORTANCEHuman papillomaviruses (HPVs) are oncogenic pathogens responsible for many HPV-related diseases such as cervical cancer. HPV replication depends on the subversion of host cellular machineries, particularly pathways governing DNA damage response (DDR) and inflammation. However, the roles of enzymes that directly introduce DNA nicks or mediate strand rejoining remain poorly characterized. Here we highlight a novel role of DNA topoisomerase 2 (Top2) in promoting HPV genome maintenance and amplification but in a DDR-independent manner. Unlike its previously studied paralog Top2{beta}, Top2 supports HPV replication by driving the secretion of inflammatory molecules interleukin (IL)-6 and IL-8, which are critical for the viral genome persistence and copy number expansion. To our knowledge, this is the first evidence that a DDR-associated protein manipulates cytokine secretion, rather than expression, to support HPV replication. Furthermore, blocking toll-like receptor 4 (TLR4) activities significantly reduced Top2-dependent IL-6/IL-8 secretion and impaired HPV replication. These findings establish Top2 as a crucial player in HPV pathogenesis, with a therapeutic potential for treating HPV-associated malignancies.

microbiology↗
bioRxiv2025

Enhanced FLI1 accessibility mediates STAG2-mutant leukemogenesis

Chromatin architecture governs transcriptional output and cell identity; however, how its disruption promotes leukemic transformation remains incompletely understood. Here, we show that loss of the cohesin subunit STAG2 creates a hyper-accessible chromatin landscape that amplifies FLI1 activity and extends its binding to ectopic loci. Using multi-omic analyses in human AML samples, cell lines, and mouse models, we identify chromatin-dependent co-occupancy of FLI1 and Menin, accompanied by amplification of Menin occupancy at non-canonical loci beyond its HOXA/MEIS1 targets. Therapeutically, the aberrant expansion of Menin binding drives an altered response towards Revumenib and activates interferon response pathways, creating a therapeutic vulnerability to Menin inhibition. Functionally, STAG2/NPM1c co-mutation drives a stem cell-like immunophenotype and a fully penetrant leukemia in vivo. Collectively, these findings define a model in which cohesin loss rewires transcription factor occupancy to amplify oncogenic chromatin programs and expose context-specific therapeutic dependencies.

cancer biology↗
bioRxiv2025

Corticospinal excitability during timed interception depends on the speed of the moving target

Successfully intercepting a moving object requires precisely timing the optimal moment to act by integrating information about the targets visual motion properties. Neurophysiological evidence indicates that activity in the primary motor cortex (M1) during interception preparation is sensitive to both the targets kinematic features and motor planning. However, how visual motion signals are integrated within M1 to guide interception timing is unclear. In the present study, we applied single-pulse transcranial magnetic stimulation (TMS) over M1 to examine how a targets kinematics influence corticospinal excitability during interception preparation. Participants were instructed to abduct their right index finger to intercept a target moving horizontally at a constant speed toward a fixed interception zone. Target speed (Fast or Slow) and travel distance (Far or Close) were manipulated while controlling motion duration across conditions. Motor-evoked potentials (MEPs) were elicited at five latencies before target arrival at the interception zone. Consistent with previous behavioral findings, movement initiation occurred earlier for faster targets and was delayed when TMS was applied closer to the targets arrival. Though MEPs were generally suppressed relative to baseline at earlier timepoints and facilitated closer to movement initiation, we observed that target speed--but not distance--influenced the time course of MEP modulation. When adjusting for movement initiation times, there was an overall reduced suppression and increased facilitation for faster-moving targets, possibly reflecting a heightened urgency to move. These results suggest M1 activity during interception preparation integrates internal estimates of target motion, which may serve to optimize interception timing and performance. New & NoteworthyWhen intercepting a moving object, like catching a ball, we need to continuously combine visual motion signals to predict the objects future location and enable accurate movement. Here, we show that preparatory suppression and facilitation of corticospinal excitability depends on the speed, but not the distance, of the moving target. These findings reveal that differences in interception timing are closely linked to changes in motor system excitability.

neuroscience↗
bioRxiv2025

Spermatogonia derived RpS13 non-autonomously regulates the cyst cell differentiation via Rho1-mediated adhesion junctions in Drosophila testis

ObjectiveIn the testis of Drosophila, spermatogonia transit-amplification (TA) divisions are necessary for germline proliferation and differentiation. Both the germline and the surrounding somatic cyst cells (SCCs) have a significant influence on these processes. However, the underlying mechanism is largely unknown. MethodsFlies were used to generate tissue-specific gene knockdown. Immunofluorescence was used to determine protein localization and expression pattern. Small interfering RNAs were used to knockdown genes in S2 cells. qRT-PCR was used to examine the relative mRNA expression level. ResultsOur findings indicate that spermatogonial RpS13 regulates cyst cell growth through a non-autonomous manner. In terms of mechanism, RpS13 may regulate the adhesion junctions of the soma-germline via the DE-cad and Arm proteins in addition to dpERK, which is found in SCCs. Interestingly, Rho1 and RpS13 mutually inhibit each other in Drosophila S2 cells. Additionally, Rho1 controlled cell adhesions that rely on DE-cad, Arm, and dpERK and imitated the actions of RpS13 in Drosophila testis. ConclusionAll of these findings implied that during spermatogonia TA-divisions in the testis of Drosophila, RpS13 regulates the development of cyst cells via Rho1-mediated adhesion junctions.

developmental biology↗
bioRxiv2025

A novel enterococcus phage endolysin Lys22 with a wide host range against mixed biofilm of Enterococcus faecalis, Staphylococcus aureus and Acinetobacter baumannii

The global surge in multidrug-resistant (MDR) bacterial pathogens has created an urgent imperative for innovative antimicrobial strategies. Enterococcus faecalis, Staphylococcus aureus, and Acinetobacter baumannii demonstrate remarkable antibiotic resistance and dominate hospital-acquired infections. These bacteria often form biofilms, a complex community structure that shields them from immune system phagocytosis, resists antibiotic penetration, and enhances their survival in harsh environments. In clinical cases, these bacteria often form mixed biofilms and lead to treatment failures. Phages and their derivatives have emerged as promising candidates in the fight against drug-resistant bacteria. Lys22, an endolysin derived from an enterococcus phage, has been cloned and demonstrated to possess a broad host range, effectively targeting E. faecalis, various Staphylococcus species, and A. baumannii. When applied to the biofilms formed by these bacteria, Lys22 was found to significantly inhibit both simple and complex biofilms in vitro. Virulent genes, including agrA, sarA, and icaA in S. aureus; asa1, cylA, and hyl in E. faecalis; and OmpA and lpsB in A. baumannii were also downregulated by Lys22. Notably, Lys22 also exhibited a robust protective effect against dual or triple infections involving E. faecalis, S. aureus, and A. baumannii in a zebrafish eggs model, highlighting its potential as a therapeutic agent in combatting multi-bacterial infections.

microbiology↗
bioRxiv2025

Deciphering the Pathogenic Landscape of Amyloid Light-Chain Cardiomyopathy

Amyloid light-chain cardiomyopathy (ALCA) is an infiltrative disorder marked by misfolded immunoglobulin light-chain deposition in the myocardium, ultimately leading to cardiac dysfunction. Despite its clinical severity, the underlying mechanisms remain poorly understood. Here, we integrated multi-omics analyses of human cardiac samples to construct a comprehensive cellular and spatial atlas of the ALCA heart. We observed a marked expansion of PTX3+ fibroblasts (FB), which undergo a distinct phenotypic transition into pro-fibrotic POSTN+ FB regulated by EGR1.Concurrently, SPP1+ macrophages (Mac) emerged as major drivers of fibrosis, interacting robustly with PTX3+ FB via APP-CD74, GAS6-MERTK, and TGF-{beta}1-TGF-{beta}1/2 pathways. Endothelial cell (EC) profiling revealed substantial vascular remodeling characterized by the emergence of specialized capillary-like immune endothelial cells expressing chemokines CXCL1, CXCL3, and CCL2, alongside depletion of functional capillary EC. Immunologically, elevated cytotoxic CD8+ T cells and reduced NK cells contributed to an imbalanced inflammatory milieu, with NF{kappa}B2 orchestrating both fibrotic and immune pathways across multiple cell types. These findings highlight the pivotal role of fibroblast-immune crosstalk, particularly the SPP1+ Mac-PTX3+ FB axis, in driving ALCA pathogenesis. Targeting these pathological cellular interactions may offer a promising therapeutic avenue to mitigate fibrosis, restore immune homeostasis, and improve cardiac function in ALCA.

bioinformatics↗
bioRxiv2025

On interactive spatial visualisation of pathogenicity predictions

The past few years have revolutionised the utility of protein structural information in assessing disease risk. Such efforts have been pioneered by the DeepMind and Meta teams, who initially developed accurate protein prediction tools AlphaFold and ESMFold, respectively. More recently, both have been readapted to create AlphaMissene and ESM1b, through which, the pathogenicity potential of all possible missense mutations within the human proteome has been predicted. Similarly, VESPA was created as an alignment-agnostic predictor, which infers conservation from protein-language model embeddings to assign an effect for each variant. To facilitate their utility, we present a unified dashboard, MissenseViewer, which permits direct predictor comparison, and visualisation within the protein 3-dimensional structural context. Our interactive resource is freely available at: https://biosig.lab.uq.edu.au/missenseviewer/.

bioinformatics↗
bioRxiv2025

MAIS: an in-vitro sandbox enables adaptive neuromodulation via scalable neural interfaces

Brain-machine interfaces (BMIs) predominantly rely on static digital architectures to decode biological neuronal networks, a paradigm that is incompatible with natural neural coding in the human brain1-4. Bridging this gap is a critical step in combating neuronal dysfunction, enhancing brain functionality, and refining the precision of neuroprosthetics5. The integration of brain organoids with microelectrode array (MEA), as a class of BMIs, offers a humanized in vitro platform with unique biological compatibility advantages for dynamic neuronal decoding. This study resolves the biological-electronic encoding incompatibility of brain organoid-MEA Integration through three progressive breakthroughs. First, a human-machine hybrid agent is developed as a newly proposed bioengineered platform that couples brain organoids together with high-density MEAs and computational chips, enabling closed-loop perturbation of biological neuronal networks via exogenous signals. Second, through plasticity-driven real-time tracking of neuronal activity, we establish dynamically reconfigurable stimulation nodes that self-align with the electrophysiological states of the organoids. This resolves the exogenous-endogenous encoding mismatch by implementing plasticity-driven adaptation principles that ensure biological compatibility through spatially adaptive coordination. Finally, through shared plasticity rules rather than centralized control, we construct the first scalable multi-agent interactive system (MAIS) and demonstrate its real-world applications. Through designed scenarios of pathological/normal neuronal network interaction, we validate that MAIS achieves stable cross-network coordination. MAIS embodies a self-evolving neural coding sandbox in which plasticity-driven dynamic decoding bridges the compatibility gaps between biological and digital systems, providing a scalable and foundational infrastructure for human-centered neural interfaces.

bioengineering↗
bioRxiv2025

RamEx: An R package for high-throughput microbial ramanome analyses with accurate quality assessment

Microbial single-cell Raman spectroscopy (SCRS) has emerged as a powerful tool for label-free phenotyping, enabling rapid characterization of microbial diversity, metabolic states, and functional interactions within complex communities. However, high-throughput SCRS datasets often contain spectral anomalies from noise and fluorescence interference, which obscure microbial signatures and hinder accurate classification. Robust algorithms for outlier detection and microbial ramanome analysis remain underdeveloped. Here, we introduce RamEx, an R package specifically designed for high-throughput microbial ramanome analyses with robust quality control and phenotypic classification. At the core of RamEx is the Iterative Convolutional Outlier Detection (ICOD) algorithm, which dynamically detects spectral anomalies without requiring predefined thresholds. Benchmarking on both simulated and real microbial datasets--including pathogenic bacteria, probiotic strains, and yeast fermentation populations--demonstrated that ICOD achieves an F1 score of 0.97 on simulated datasets and 0.74 on real datasets, outperforming existing approaches by at least 19.8%. Beyond anomaly detection, RamEx provides a modular and scalable workflow for microbial phenotype differentiation, taxonomic marker identification, metabolic fingerprinting, and intra-population heterogeneity analysis. It integrates Raman-based species-specific biomarkers, enabling precise classification of microbial communities and facilitating functional trait mapping at the single-cell level. To support large-scale studies, RamEx incorporates C++ acceleration, GPU parallelization, and optimized memory management, enabling the rapid processing of over one million microbial spectra within an hour. By bridging the gap between high-throughput Raman-based microbial phenotyping and computational analysis, RamEx provides a comprehensive toolkit for exploring microbial ecology, metabolic interactions, and antibiotic susceptibility at the single-cell resolution. RamEx is freely available under the MIT license at https://github.com/qibebt-bioinfo/RamEx.

bioinformatics↗
bioRxiv2025

A multi-modal whole-slide image processing pipeline for quantitative mapping of tissue architecture, histopathology, and tissue microenvironment

Multi-modal, multiscale imaging is crucial for quantitative high-content spatial profiling. We present an integrated image processing pipeline for comprehensive tissue analysis that combines quantitative phase microscopy for tissue architecture mapping, hyper-plex fluorescence imaging for immune microenvironment profiling, and whole-slide histopathology. This approach enables detailed morphological mapping of tissue architecture and cell morphology, while simultaneously linking them to the functional states of individual cells across the entire slide. By analyzing tissue biopsies from patients with ulcerative colitis, we demonstrate the potential of this pipeline for quantitative spatial analysis of molecular markers related to mucosal healing. Open-source and compatible with conventional microscopy systems, this pipeline provides a powerful tool for research and clinical applications through its comprehensive integration of quantitative, high-content, and histological imaging modalities.

bioinformatics↗
bioRxiv2025

Correlative In Situ Cryo-ET Reveals Cellular and Viral Remodeling Associated with Selective HIV-1 Core Nuclear Import

Lentiviruses like HIV-1 infect non-dividing cells by traversing the nuclear pore, but studying this process has been challenging due to its scarcity and dynamic nature in infected cells. Here, we developed a robust cell-permeabilization system that recapitulates HIV-1 nuclear import and established an integrated cryo-correlative workflow combining cryo-CLEM, cryo-FIB, and cryo-ET for targeted imaging of this process. These advancements enabled the successful capture of 1,899 HIV-1 cores at various stages of nuclear import. Statistical and structural analyses of native wild-type and mutant cores revealed that HIV-1 nuclear import depends on both capsid elasticity and nuclear pore adaptability, as well as nuclear factors such as CPSF6. Brittle cores fail to enter the nuclear pore complex (NPC), while CPSF6-binding-deficient cores stall inside the NPC, resulting in impaired nuclear import. Intriguingly, nuclear pores function as selective filters favoring the import of smaller, tube-shaped cores. Our study opens new avenues for dissecting the biochemistry and structural biology of HIV-1 nuclear import as well as downstream events including core uncoating and potentially integration, with unprecedented detail.

microbiology↗
bioRxiv2025

sedimix: A workflow for the analysis of hominin nuclear DNA sequences from sediments

SummarySediment DNA--the ability to extract DNA from archaeological sediments-- is an exciting new frontier in ancient DNA research, offering the potential to study individuals at a given archaeological site without destructive sampling. In recent years, several studies have demonstrated the promise of this approach by recovering hominin DNA from prehistoric sediments, including those dating back to the Middle or Late Pleistocene. However, a lack of open-source workflows for analysis of hominin sediment DNA samples poses a challenge for data processing and reproducibility of findings across studies. Here we introduce a snakemake workflow, sedimix, for processing genomic sequences from archaeological sediment DNA samples to identify hominin sequences and generate relevant summary statistics to assess the reliability of the pipeline. By performing simulations and comparing to published studies, we show that sedimix has high sensitivity and precision. sedimix offers a reliable and adaptable framework to aid in the analysis of sediment DNA datasets and improve reproducibility across studies. Availability and Implementationsedimix is available as an open-source software with the associated code and user manual available at https://github.com/jierui-cell/sedimix ContactJierui Xu (jierui.xu@berkeley.edu) Supplementary informationSupplementary data are available at Bioinformatics online

genetics↗
bioRxiv2025

Fast, accurate parsing of antibody structures and antibody-antigen interactions enables a comprehensive structural antibody database

Antibody (Ab) structures and antibody-antigen interactions (AAIs) are essential for understanding immune recognition and designing Ab therapeutics. While existing structural Ab databases provide valuable insights, they still have notable limitations. Here, we present SAAINT-parser, an computational workflow for rapid, accurate, and robust extraction of Ab and AAI information from the Protein Data Bank (PDB). SAAINT-parser features precise detection of Ab chains, accurate pairing of Ab chains, and reliable identification of AAIs. The resulting SAAINT-DB contains 18,031 data entries from 9,373 PDB structures, offering a comprehensive and up-to-date resource. Detailed analyses of SAAINT-DB reveals its advantages over the most widely used SAbDab database, particularly in terms of data accuracy and completeness. Furthermore, SAAINT-DB provides nearly twice as many nonredundant, manually curated Ab-Ag binding affinity data compared to SAbDab. Both SAAINT-parser and SAAINT-DB are available as open-source resources, aimed at advancing Ab-related research and benefiting the broader scientific community.

bioinformatics↗