Biology subjects

Yuan, X.

Publications and source records attributed to Yuan, X..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Divergent Minimum Inhibitory Concentrations of Clarithromycin and Azithromycin Against Clinical Isolates of Mycobacterium abscessus Complex

Current treatment guidelines for Mycobacterium abscessus complex (MAB) infections recommend macrolides (clarithromycin/CAM and azithromycin/AZM) as cornerstone therapies, considering them clinically interchangeable without distinction. This study evaluated the comparative in vitro activity of clarithromycin (CAM) and azithromycin (AZM) against 146 clinical isolates of Mycobacterium abscessus complex organisms. MIC distributions revealed significantly higher resistance to AZM (94.5% resistant at [≥]8 g/mL) compared to CAM (77.4% resistant at [≥]8 g/mL), with only 4.8% of isolates susceptible to both drugs. Notably, 26 strains (17.8% of total) showed AZM resistance despite being non-resistant to CAM (MIC <8 g/mL) among 146 clinical isolates. Among the 33 CAM-non-resistant isolates (including susceptible and intermediate strains), 78.8% (26/33) were AZM-resistant, demonstrating frequent discordance in susceptibility profiles. These findings contrast with current treatment guidelines that recommend using CAM and AZM interchangeably without distinction. Subspecies analysis showed three distinct susceptibility profiles: isolates susceptible to both antibiotics (n=3, M. massiliense), isolates resistant to both antibiotics (n=3, M. massiliense), and M. bolletii with CAM-susceptible/AZM-resistant phenotypes (n=2). This differential resistance pattern suggests that while both drugs face substantial resistance challenges, CAM retains meaningful activity against certain strains that are AZM-resistant--particularly in M. bolletii. These findings indicate that AZM and CAM should not be used interchangeably to treat MAB infections and emphasize the need to prioritize CAM over AZM in treatment regimens.

microbiology↗

bioRxiv2025

Metabolic modulation of intratumoral cholesterol with gut microbiota for the treatment of colorectal cancer

Excess cholesterol is positively correlated with colorectal cancer (CRC). Current therapeutic strategies for modulating cholesterol levels in CRC are limited and often come with complications. Here, we demonstrated that microbiome shunting of intestinal cholesterol to anticancer metabolites is a safe and applicable therapeutic approach for CRC. By screening major microbial metabolic products of cholesterol, we found that 4-cholesten-3-one (4-C-3) was selectively depleted in fecal samples and tumor tissues of patients with CRC. 4-C-3 exhibits strong antitumor effects on human CRC cell lines, patient-derived organoids, and patient-derived xenograft (PDX) models. Mechanistically, 4-C-3 suppresses CRC tumorigenesis by dually targeting the epidermal growth factor receptor (EGFR) and Kirsten rat sarcoma viral oncogene homologue (KRAS). 4-C-3 directly binds to EGFR, blocking its signal transduction by inhibiting the binding of EGFR ligands. Additionally, 4-C-3 inhibits oncogenic KRAS variants, such as KRASG12D, by suppressing nucleotide exchange activity and effector engagement. By targeting both EGFR and KRAS, 4-C-3 reduces primary resistance to anti-EGFR therapies caused by KRAS mutations in CRC. As a proof-of-concept study, we showed that delivery of 4-C-3 by Oscillibacter ruminantium, a 4-C-3- producing commensal bacterium that is reduced in CRC patients, or a nonpathogenic Escherichia coli strain engineered to specifically convert intestinal cholesterol into 4-C-3, removed intratumoral cholesterol and led to rapid tumor regression in multiple models of CRC. These results suggest that microbial therapies for restoring intestinal cholesterol homeostasis represent a new therapeutic avenue for CRC.

cancer biology↗

bioRxiv2025

Anti-CSF-1R therapy with combined immuno- chemotherapy coordinate an adaptive immune response to eliminate macrophage enriched Triple Negative Breast Cancers

Patients diagnosed with metastatic triple negative breast cancer (mTNBC) have limited treatment options, are more prone to develop resistance and are associated with high mortality. A cold tumor immune microenvironment (TIME) characterized by low T cells and high tumor associated macrophages (TAMs) in mTNBC is associated with the failure of standard-of-care chemotherapy and immune checkpoint blockade (ICB) treatment. We demonstrate that the combination of immunomodulatory metronomic Cyclophosphamide (CTX) coupled with anti-CSF-1R antibody targeted therapy (SNDX-ms6352) and anti-PD-1 (ICB), was highly effective against aggressive metastatic syngeneic Trp53 null TNBC genetically engineered mouse models (GEMMs) that present with high macrophage infiltration. Mechanistically, CSF-1R inhibition along with CTX disrupted the M-CSF/CSF-1R axis which upregulated IL-17, IL-15 and type II interferon resulting in elevated B- and T cell infiltration. Addition of an anti-PD-1 maintenance dose helped overcome de novo PD-L1 intra-tumoral heterogeneity (ITH) associated recurrence in lung and liver mTNBC.

cancer biology↗

bioRxiv2025

Tnfrsf10 Signaling is Required to Maintain the Stem Cell Niche in the Zebrafish Lateral Line

Regenerative capacity varies significantly among species and across different organs. In mammals, the inner ear exhibits a limited ability to regenerate hair cells, whereas the lateral line sensory organ of zebrafish demonstrates apparently limitless capability to spontaneously regenerate hair cells following injury. However, the specific cell populations representing the stem cells in the neuromast and the mechanism of stem cell self-renewal remain unclear. In this study, we show that a mutation in tnfrsfa led to the depletion of neuromast sensory organs and impairment of hair cell regeneration in zebrafish. The decrease of cells peripheral to the neuromasts in tnfrsfa mutants indicates that these peripheral cells, particularly cells called "mantle cells", serve as the stem cells within the neuromast. Furthermore, our findings indicate that the ligands Tnfsf10 and Tnfsf10l3 (TRAIL) act through Tnfrsfa activating the NF-{kappa}B signaling pathway in the mantle cells in a non-cell-autonomous manner. NF-{kappa}B signaling is crucial for maintaining the stem cell identity of the mantle cells through activation or maintenance of sox2 expression. These findings demonstrate a critical role for TNF superfamily signaling in stem cell maintenance. HighlightsO_LIZebrafish tnfrsfa maintains the stem cell niche in neuromasts and is necessary for hair cell regeneration of the lateral line C_LIO_LITnfrsfa is essential for mantle cell proliferation during lateral line development and hair cell regeneration C_LIO_LITnfsf10 and Tnfsf10l3 signal through Tnfrsfa, activating NF-{kappa}B signaling and Sox2 expression in the mantle cells in a non-cell-autonomous manner C_LIO_LITnfrsfa regulates the development of neuromast independently of the Notch signaling pathway C_LI

developmental biology↗

bioRxiv2025

Identification of Novel Mutations Causing Clofazimine Resistance in Mycobacterium intracellulare

Clofazimine (CFZ) is a promising repurposed drug for treating Mycobacterium avium-intracellulare complex pulmonary disease (MAC-PD), but its resistance mechanisms in M. intracellulare remain poorly understood. In this study, we generated 36 CFZ-resistant M. intracellulare mutants in vitro and identified various mutations in the marR gene (WP_009952290.1) in 61% of resistant mutants through whole-genome sequencing. Mutations were identified in additional genes encoding flavin-dependent oxidoreductase (ssuD, C67A), membrane lipoprotein (lppI, C207 deletion), glucose-methanol-choline oxidoreductase (G157 deletion), MASE1 domain-containing protein (C62G), and PPE family protein (222C deletion). Gene complementation experiments demonstrated that introducing the wild-type marR in CFZ-resistant strains (L72 and L74) with marR mutations reduced CFZ minimum inhibitory concentrations (MICs) from 1 g/mL to the susceptible baseline (0.25 g/mL), confirming its critical role in CFZ resistance. Notably, the M. intracellulare MarR lacks homology to M. tuberculosis MarR family protein Rv0678 (MmpR) whose mutations are involved in CFZ and bedaquiline (BDQ) resistance and is flanked by non-efflux pump genes (dhmA and doxX), and unlike M. tuberculosis, its mutation does not cause bedaquiline cross-resistance, indicating a different MarR and distinct regulatory mechanism for CFZ resistance in M. intracellulare. This work highlights marR as a key determinant of CFZ resistance in M. intracellulare and underscores the need for further mechanistic studies with implications for clinical diagnostics and therapeutic strategies.

microbiology↗

bioRxiv2025

Extracellular loops of the β-barrel domain catalyze rapid folding for function of self-associating autotransporters

Bacterial aggregation is a phenotype associated with disease pathogenesis. Aggregate formation enhances biofilm development, host colonization, and resistance to antibiotics and host defenses. Antigen 43 (Ag43) is a surface-located autotransporter produced by pathogenic Escherichia coli that mediates cell aggregation in biofilms. Two Ag43 molecules, each from neighboring bacterial cells, fold into elongated {beta}-helical passenger domains that associate in a head-to-tail manner while being anchored to the cell surface by their outer membrane-embedded {beta}-barrels. In this study, we conduct mutational analyses on Ag43 to show that the {beta}-hairpin structure of the fourth and fifth extracellular loops of the {beta}-barrel domain have a crucial role for passenger domain folding and subsequent formation of bacterial aggregates. This work provides mechanistic insight into the role of the autotransporter {beta}-barrel domain to nucleate the rapid folding of the passenger domain into the {beta}-helix that enables bacterial interactions during infection.

biochemistry↗

bioRxiv2025

High-throughput Monoclonal Antibody Screening from Immunized Rabbits via Droplet Microfluidics

The discovery of monoclonal antibodies (mAbs) is critical to advancing therapeutics, diagnostics, and biomedical research. While mouse-derived mAbs dominate current applications, their limitations--short serum half-life, human immunogenicity, and restricted recognition of human-specific antigens--underscore the need for alternative sources. Rabbit-derived mAbs have been gaining significant traction with their superior antigen-binding affinity, broader epitope diversity, and higher yield potential. However, the absence of well-defined surface markers on rabbit B cells has hindered efficient enrichment strategies, limiting the exploration of this valuable antibody repertoire. In this study, we present an integrated workflow that combines magnetic negative selection with high-throughput droplet microfluidics to overcome these barriers. By optimizing a pan B cell enrichment protocol using a tailored antibody cocktail, we achieved a notable boost in IgG secretion and B cell enrichment. Through two complementary droplet-encapsulated assays using particle aggregation for soluble antigens and reporter cells for membrane-bound antigens, we identified target cells capable of secreting high-affinity IgGs. Subsequent sequencing, in vitro antibody production and characterization confirmed the high affinity rate of the discovered antibodies, outperforming rates previously reported. The use of droplet microfluidics streamlines the analysis of rabbit IgG repertoires, providing a robust platform for rabbit single B cell antibody discovery with promising applications in precision medicines and diagnostics.

molecular biology↗

bioRxiv2025

Obesity Increases Atherosclerosis Susceptibility via Inter-tissue miR-30e-SLC7A11 Axis

BackgroundWith obesity as a risk factor for atherosclerotic disease, recent research suggests that adipose tissue in obese animal models and humans can generate endocrine-like molecules that affect arterial health later on. Previous studies showed that microRNA-30e (miR-30e) level is elevated in atherosclerosis and solute carrier family 7 member 11 (SLC7A11), a cystine/glutamate transporter, is involved in atherogenesis. However, whether an endocrine-like link between the adipose-derived miR-30e-5p and SLC7A11 in the vascular endothelium can lead to obesity-caused atherosclerosis is unknown. MethodsMiRNA data mining and RT-PCR validations were used to demonstrate the positive association among serum level of miR-30e-5p, obesity, and coronary arterial disease in human patients. Transcriptomics (RNA-seq and single-nucleus RNA-seq), metabolomics, and in silico analysis were used to establish a miR-30e-5p-SLC7A11 regulation of central carbon metabolism, mitochondrial and endothelial cell (EC) function. Mouse models with EC-specific Slc7a11 knockout (EC-Slc7a11-/-) and gain or loss of function of miR-30e-5p were used to elucidate the detrimental role of this endocrine-like axis in obesity-related atherosclerosis. ResultsThe level of adipocyte-derived miR-30e-5p was significantly upregulated in obese humans with coronary artery disease and obese and atherosclerotic mice. Via serum exosomes, the adipocyte-generated miR-30e-5p targeted SLC7A11 mRNA in vascular ECs. SLC7A11 deficiency due to miR-30e-5p targeting dysregulated glutamate/cystine metabolism increased glycolysis, reduced oxidative phosphorylation, and impaired mitochondrial function. The EC dysfunction could be rectified by SLC7A11 overexpression or miR-30e-5p antagonism. Exogenously delivered miR-30e-5p phenocopied the increased atherosclerosis in EC-Slc7a11-/- mice. In contrast, miR-30e-5p antagomir treatment reduced atherosclerosis in Apoe-/- and ob/ob mice. ConclusionOur multi-omics approaches demonstrates that the adipose-derived miR-30e-5p downregulated SLC7A11 mRNA in ECs via tissue crosstalk. The resulting EC dysfunction led to obesity-related atherosclerosis in mice. These findings underscore a causality between obesity and atherosclerosis in the context of cardiovascular-kidney-metabolic syndrome.

molecular biology↗

bioRxiv2025

Designer DX-tile DNAns hydrogels

Pure deoxyribonucleic acid (DNA) hydrogels synthesized via the hybridization of multi-arm DNA tiles are uniquely programmable and functionalizable biomaterials suitable for applications ranging from biosensing to cell-free protein production and soft tissue engineering. However, the full potential of the design flexibility and functionalization offered by DNA molecules has not yet been leveraged for pure DNA hydrogels, thereby limiting their range of mechanical properties and reducing their versatility and broader use. In this study, we introduce multi-arm double-crossover (DX)-tile motifs, often used in DNA nanoparticle design, to enable greater control over the hydrogels mechanical properties and facilitate functionalization. Specifically, we demonstrate that modifying structural design parameters, such as the arm geometry, length, valency, and linker design, allows fine control of the elastic modulus and viscoelastic properties of the hydrogels. We also show that functionalization can be performed without compromising the hydrogels physical properties and exhibit enhanced mechanical strength and tunable properties, compared to simple duplex-based DNA hydrogels. Furthermore, these DNA hydrogels demonstrated printability and scalability, which pave the way towards the development of novel formulations and bioinks for the rational design of soft tissue engineering scaffolds and broaden the use of DNA hydrogels for other biomedical applications.

bioengineering↗

bioRxiv2025

Investigation of the Mechanism of Action of JinHuangJieDu against SARS-CoV-2 Infection and Inflammation Based on Network Pharmacology and Experimental Validation

Withdrawal StatementThe authors have withdrawn this manuscript because additional experiments are required to enhance the completeness and clarity of the study. Therefore, the authors do not wish this work to be cited as a reference for any project. If you have any questions, please contact the corresponding author at lcchenlong@163.com.

cell biology↗

bioRxiv2025

Clinical and Taxonomic Characterization of a Novel Urinary Tract Pathogen Providencia lanzhouensis

BackgroundThe genus Providencia includes species of ecological and clinical significance, with some acting as opportunistic pathogens in hospital-acquired infections such as urinary tract infection (UTI). However, overlapping phenotypic traits and genetic similarities pose challenges for accurate species characterization. This study exemplifies this challenge by identifying a novel Providencia isolate through genomic analysis. ResultsIn this study, strain PAZ2 was isolated from the urine sample of a hospitalized patient in Lanzhou, Gansu Province, China. Initial mass spectrometry analysis identified the strain as Providencia alcalifaciens. It exhibits a resistance profile against antibiotics including ampicillin, tetracycline, tigecycline, polymyxin B, colistin, trimethoprim-sulfamethoxazole, and ciprofloxacin. However, whole-genome sequence analysis indicated that this strain is a novel species with an average nucleotide identity (ANI) values ranging from 79.92% to 94.73% and digital DNA-DNA hybridization (dDDH) values between 21.2% and 57.6% when compared with all known Providencia species. Furthermore, strain PAZ2 exhibited unique biochemical properties that differentiated it from all previously described species within the genus. ConclusionsGenomic and biochemical evidence supports PAZ2 as a novel Providencia species, which we named Providencia lanzhouensis sp. nov. This finding enhances the taxonomy of Providencia and underscores its clinical relevance, notably in UTIs and other nosocomial infections. Accurate identification is crucial for guiding effective treatment and preventing misdiagnosis. Further studies should investigate its pathogenicity, antimicrobial resistance, and epidemiology to inform infection control measures.

microbiology↗

bioRxiv2025

AAVone: A Cost-Effective, Single-Plasmid Solution for Efficient AAV Production with Reduced DNA Impurities

Currently, the most common approach for manufacturing GMP-grade adeno-associated virus (AAV) vectors involves transiently transfecting mammalian cells with three plasmids that carry the essential components for production. The requirement for all three plasmids to be transfected into a single cell and the necessity for high quantities of input plasmid DNA, limits AAV production efficiency, introduces variability between production batches, and increases time and labor costs. Here, we developed an all-in-one, single-plasmid AAV production system, called AAVone. In this system, the adenovirus helper genes (E2A, E4orf6, and VA RNA), packaging genes (rep and cap), and the vector transgene cassette are consolidated into a single compact plasmid with a 13-kb backbone. The AAVone system achieves a two- to four-fold increase in yields compared to the traditional triple-plasmid system. Furthermore, the AAVone system exhibits low batch-to-batch variation and eliminates the need for fine-tuning the ratios of the three plasmids, simplifying the production process. In terms of vector quality, AAVs generated by the AAVone system show similar in vitro and in vivo transduction efficiency, but a substantial reduction in sequences attributed to plasmid backbones and a marked reduction in non-functional snap-back genomes. In Summary, the AAVone platform is a straightforward, cost-effective, and highly consistent AAV production system - making it particularly suitable for GMP-grade AAV vectors.

bioengineering↗

bioRxiv2024

Local Gradients of Functional Connectivity Enable Precise Fingerprinting of Infant Brains During Dynamic Development

Brain functional connectivity patterns exhibit distinctive, individualized characteristics capable of distinguishing one individual from others, like fingerprint. Accurate and reliable depiction of individualized functional connectivity patterns during infancy is crucial for advancing our understanding of individual uniqueness and variability of the intrinsic functional architecture during dynamic early brain development, as well as its role in neurodevelopmental disorders. However, the highly dynamic and rapidly developing nature of the infant brain presents significant challenges in capturing robust and stable functional fingerprint, resulting in low accuracy in individual identification over ages during infancy using functional connectivity. Conventional methods rely on brain parcellations for computing inter-regional functional connections, which are sensitive to the chosen parcellation scheme and completely ignore important fine-grained, spatially detailed patterns in functional connectivity that encodes developmentally-invariant, subject-specific features critical for functional fingerprinting. To solve these issues, for the first time, we propose a novel method to leverage the high-resolution, vertex-level local gradient map of functional connectivity from resting-state functional MRI, which captures sharp changes and subject-specific rich information of functional connectivity patterns, to explore infant functional fingerprint. Leveraging a longitudinal dataset comprising 591 high-resolution resting-state functional MRI scans from 103 infants, our method demonstrates superior performance in infant individual identification across ages. Our method has unprecedentedly achieved 99% individual identification rates across three age-varied sub-datasets, with consistent and robust identification rates across different phase encoding directions, significantly outperforming atlas-based approaches with only around 70% accuracy. Further vertex-wise uniqueness and differential power analyses highlighted the discriminative identifiability of higher-order functional networks. Additionally, the local gradient-based functional fingerprints demonstrated reliable predictive capabilities for cognitive performance during infancy. These findings suggest the existence of unique individualized functional fingerprints during infancy and underscore the potential of local gradients of functional connectivity in capturing neurobiologically meaningful and fine-grained features of individualized characteristics for advancing normal and abnormal early brain development.

neuroscience↗

bioRxiv2024

Complex opioid driven modulation of glutamatergic and cholinergic neurotransmission in a GABAergic brain nucleus associated with emotion, reward and addiction.

The medial habenula (mHb)/interpeduncular nucleus (IPN) circuitry is resident to divergent molecular, neurochemical and cellular components which, in concert, perform computations to drive emotion, reward and addiction behaviors. Although housing one of the most prominent mu opioid receptor (mOR) expression levels in the brain, remarkably little is known as to how they impact mHb/IPN circuit function at the granular level. In this study, our systematic functional and pharmacogenetic analyses demonstrate that mOR activation attenuates glutamatergic signaling whilst producing an opposing potentiation of glutamatergic/cholinergic co-transmission mediated by mHb substance P and cholinergic neurons, respectively. Intriguingly, this latter non-canonical augmentation is developmentally regulated only emerging during later postnatal stages. In addition, we reveal that specific potassium channels act as a molecular brake on nicotinic receptor signaling in the IPN with the opioid mediated potentiation of this arm of neurotransmission being operational only following attenuation of Kv1 function. Thus, mORs play a complex role in shaping the salience of distinct afferent inputs and transmitter modalities that ultimately influences synaptic recruitment of downstream GABAergic IPN neurons. Together, these observations provide a framework for future investigations aimed at identifying the neural underpinnings of maladaptive behaviors that can emerge when opioids, including potent synthetic analogs such as fentanyl, modulate or hijack this circuitry during the vulnerable stages of adolescence and in adulthood.

neuroscience↗

bioRxiv2024

Stage-specific CAR-mediated signaling generates naive-like, TCR-null CAR T cells from induced pluripotent stem cells

Genetically modified, induced pluripotent stem cells (iPSCs) offer a promising allogeneic source for the generation of functionally enhanced, chimeric antigen receptor (CAR) T cells. However, the signaling of CARs during early T cell development and the removal of the endogenous T cell receptor required to prevent alloreactivity pose significant challenges to the production of mature conventional CAR T cells from iPSCs. Here, we show that TCR-null, CD8{beta} CAR T cells can be efficiently generated from iPSCs by engineering stage-specific onset of CAR expression and signaling to both permit conventional T cell development and to induce efficient positive selection. CAR T cells produced using this approach displayed a uniform, naive T cell phenotype and demonstrated superior antigen-specific cytotoxicity compared to iPSC-derived effector memory CAR T cells. Multimodal sequencing revealed CAR-mediated positive selection induced the persistent upregulation of key transcription factors involved in naive T cell development. Achieving precise control of CAR expression and signaling in developmentally sensitive T precursors will be critical to realizing the full potential for "off-the-shelf", iPSC-derived cellular therapies.

bioengineering↗

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

Functional diversification of the BBSome: Insights from honey bee trypanosomatid parasite, Lotmaria passim

The BBSome is an octameric protein complex crucial for ciliary transport, though it also participates in multiple other cellular processes. These diverse functions may result from the co-option of its ancestral roles. Studying the BBSome in flagellated protists can provide insights into these ancestral functions and their subsequent adaptations. Here, we examine the function of the BBSome in Lotmaria passim, a monoxenous trypanosomatid parasite infecting honey bee. Parasites deficient in LpBBS2 are smaller and less motile compared to wild-type. Although intraflagellar transport of a marker membrane protein is only mildly impaired, its association with lipid rafts is significantly disrupted in the mutants. This suggests that the BBSome is essential for maintaining lipid raft integrity in L. passim. Transcriptomic comparisons between wild-type and LpBBS2-deficient parasites reveal that the BBSome may also influence processes related to metabolism, membrane localization of specific proteins, DNA repair, microtubules, and mitochondria. In contrast to Leishmania mexicana, the BBSome in L. passim is crucial for efficient infection of the honey bee gut, demonstrating that its cellular functions vary between related trypanosomatid species. The BBSome is likely an adaptor that links multiple proteins in a species-specific manner under various cellular contexts.

cell biology↗

bioRxiv2024

Spatial multi-omics reveal intratumoral humoral immunity niches associated with tertiary lymphoid structures in pancreatic cancer immunotherapy pathologic responders

Pancreatic adenocarcinoma (PDAC) is a rapidly progressing cancer that responds poorly to immunotherapies. Intratumoral tertiary lymphoid structures (TLS) have been associated with rare long-term PDAC survivors, but the role of TLS in PDAC and their spatial relationships within the context of the broader tumor microenvironment remain unknown. We generated a spatial multi-omics atlas encompassing 26 PDAC tumors from patients treated with combination immunotherapies. Using machine learning-enabled H&E image classification models and unsupervised gene expression matrix factorization methods for spatial transcriptomics, we characterized cellular states within TLS niches spanning across distinct morphologies and immunotherapies. Unsupervised learning generated a TLS-specific spatial gene expression signature that significantly associates with improved survival in PDAC patients. These analyses demonstrate TLS-associated intratumoral B cell maturation in pathological responders, confirmed with spatial proteomics and BCR profiling. Our study also identifies spatial features of pathologic immune responses, revealing TLS maturation colocalizing with IgG/IgA distribution and extracellular matrix remodeling. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=188 SRC="FIGDIR/small/613714v1_ufig1.gif" ALT="Figure 1"> View larger version (69K): org.highwire.dtl.DTLVardef@d5e1a5org.highwire.dtl.DTLVardef@1d14012org.highwire.dtl.DTLVardef@c57c6corg.highwire.dtl.DTLVardef@16baa56_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIIntegrated multi-modal spatial profiling of human PDAC tumors from neoadjuvant immunotherapy clinical trials reveal diverse spatial niches enriched in TLS. C_LIO_LITLS maturity is influenced by tumor location and the cellular neighborhoods in which TLS immune cells are recruited. C_LIO_LIUnsupervised machine learning of genome-wide signatures on spatial transcriptomics data characterizes the TLS-enriched TME and associates TLS transcriptomes with survival outcomes in PDAC. C_LIO_LIInteractions of spatially variable gene expression patterns showed TLS maturation is coupled with immunoglobulin distribution and ECM remodeling in pathologic responders. C_LIO_LIIntratumoral plasma cell and immunoglobin gene expression spatial dynamics demonstrate trafficking of TLS-driven humoral immunity in the PDAC TME. C_LI SignificanceWe report a spatial multi-omics atlas of PDAC tumors from a series of immunotherapy neoadjuvant clinical trials. Intratumorally, pathologic responders exhibit mature TLS that propagate plasma cells into malignant niches. Our findings offer insights on the role of TLS-associated humoral immunity and stromal remodeling during immunotherapy treatment.

cancer biology↗