Biology subjects

Lin, A.

Publications and source records attributed to Lin, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

MechanoMR microparticle (M3) sensors reveal dynamic stress loading as a driver of epithelial-mesenchymal transition

The dynamic mechanical response of tissues underlies their physiological function, yet direct, quantitative measurement of tissue stress in vivo has remained a major challenge. Here, we introduce the mechanoMR microparticle (M3, "M-cube") sensor, a hybrid soft-matter/nanoparticle probe that integrates directly into tissue mechanical networks while transducing local stress into quantitative magnetic resonance (MR) readouts with single-particle resolution. We demonstrate the utility of this platform across diverse model systems, including tumor spheroids, Xenopus embryos, and mouse xenografts, where the M3 sensor enables noninvasive, spatiotemporally resolved mapping of tissue stress dynamics during cancer development. Using this approach, we reveal that epithelial-mesenchymal transition (EMT) is accompanied by distinctive stress-remodeling patterns observable in vivo. Strikingly, we find that abrupt stress increases, rather than cumulative or peak stress magnitude, are the key determinants of EMT induction in cancer cells within the tumor microenvironment. Transcriptomic profiling under controlled stress-loading dynamics shows that sustained yet gradual stress escalation activates cytoprotective antioxidation pathways (e.g., FOXO/AMPK) that reinforce epithelial stability, whereas acute stress surges overwhelm these defense mechanisms, predisposing cells toward mesenchymal reprogramming. These findings establish the M3 sensor as a broadly applicable technology for linking dynamic mechanical cues to cell-state transitions in development, homeostasis, and disease.

bioengineering↗

bioRxiv2025

Endogenous Osteocyte-Osteoclast Signaling Enables Growth Factor-Free Bone Remodeling, Drug Response, and Cancer Invasion in a Nanoscale Calcified Bone-on-a-Chip Model

Bone homeostasis depends on spatially orchestrated interactions among osteoclasts, osteoblasts, and osteocytes that are embedded within a unique extracellular matrix that is mineralized on the nanoscale. Reconstructing these interactions to enable autonomous cell differentiation and tissue remodeling has remained a significant challenge towards mimicking adequate bone physiology and disease in-vitro. Here, we present an engineered model that spatially defines the paracrine communication of heterogeneous cell populations within bone tissue that supports the rapid maturation of primary osteoblasts into osteocytes, the differentiation of immune cells into osteoclasts, and calcified tissue resorption within a mineralized cell-laden bone-like tissue. We demonstrate that nanoscale mineralization of cell-laden collagen hydrogels on-a-chip enhances osteoblast to osteocyte differentiation, whereas osteocytes in the matrix accelerate osteoclastogenesis and remodeling in a spatially defined manner without the need for exogenous growth factors. Osteocyte-dependent osteoclastogenesis on-a-chip outperformed conventional stimulation with RANKL and M-CSF, reproduced the clinical response of anti-resorptive drugs, and mimicked established tumor-bone interactions observed in invasive oral cancer. By replicating essential aspects of bone composition and function, this system provides a robust, self-regulated microphysiologic model to investigate bone remodeling, cancer-bone crosstalk, and therapeutic interventions.

bioengineering↗

bioRxiv2025

Computational Stabilization of the Human VH Germline Repertoire to Enable Conditional Multi-Specific Therapeutic Development

Protein-based biologic therapies, particularly antibody-like therapeutics, have emerged as a major modality to treat nearly all chronic and infectious diseases. Antagonists have dominated the first wave of antibody and antibody-like biologics, whereas agonism has generally been challenging due to systemic activation leading to issues with therapeutic index and problems with pleiotropic activity. Additionally, agonists that use native proteins such as cytokines can be challenging to produce at scale given these proteins evolved to act locally and are not designed for large scale manufacturing. To address these challenges, we generated a biologics platform comprised of stabilized human VH domains (VH-Select) which encompass the entire human germline repertoire with the goal of building multispecific biologics denoted Tentacles that use avidity-based binding to achieve conditional activity directed to specific cell types or tissues. Stabilizing disulfides and point mutations were identified computationally with Rosetta, evaluated in vitro, and combined into designs with 3-5 amino acid substitutions for each of the seven germline families (VH1-VH7). Computational design was also employed to reduce dimerization from both VL and homotypic VH-VH interactions. Optimization of specific sequences improved expression by greater than 600-fold and thermostability by more than 20{degrees}C. Each of the germline variants were screened for low HLA class II binding and incorporated into a library which demonstrated significant improvements in cellular protein production, thereby increasing sequence diversity for screening campaigns. These VH-Select scaffolds are useful for the discovery of novel binders used to build multispecific Tentacles designed for cis-interactions that achieve cell- and tissue-specific activation. As an example of the utility of the platform, we generated a set of Tentacles that use VH-Select binders to conditionally agonize IL2R{gamma}{beta} and 41BB on PD1+, LAG3+, or CD8+ T cells. These Tentacles demonstrate promising manufacturability, antibody-like exposure in vivo, and strong anti-tumor activity in a humanized tumor model. Overall, we believe the incorporation of VH-Select binders into multispecific Tentacles has the potential to create a host of conditionally active biologics to treat various chronic and acute diseases.

bioengineering↗

bioRxiv2025

Suspended Tissue Engineering with Assemblable Microfluidics (STEAM)

Suspended tissue culture systems enable cellular responses to mechanical forces critical for tissue development and function. Tissues develop in complex environments containing both mechanical and chemical cues that vary spatiotemporally; thus modeling both of these physiochemistries in vitro through integration of spatial patterning with mechanical manipulation simultaneously is an important aspect in microphysiological tissue modeling which has yet to be achieved. Here, we introduce Suspended Tissue Engineering with Assemblable Microfluidics (STEAM), a modular tissue fabrication platform that allows for spatially heterogeneous suspended tissue architectures. With STEAM, we achieve tissue constructs with multiple regions through the addition of capillary pinning features to control hydrogel precursor flow. STEAM tissues can easily be moved from patterning setup to well-plate to microscope slide, which also enables stacking of separately generated layers. Mechanical manipulation post-fabrication is also possible via static stretching, where cell-embedded 3D tissues can be stretched farther apart to induce strain along an axis. To demonstrate the utility of post fabrication strain ability, we showed that myotube alignment increases when strain is applied to STEAM generated engineered muscle tissue containing mouse myoblasts. Finally, by modifying the channel geometry of the fluidic-based patterning rails, we generate complex nonplanar suspended tissues. STEAM leverages microfluidic principles to generate suspended tissues that integrate patterning precision, mechanical functionality, and experimental versatility, providing a suite of construct combinations for modeling tissue behaviors from the interplay of spatial organization and mechanical forces.

bioengineering↗

bioRxiv2025

The Intermediate CA1 and CA3 Subfields of the Hippocampus Differentially Encode Social Recognition

Social recognition requires linking information about others to the spatial contexts in which they are encountered, a computation thought to engage the hippocampus. Although this process depends on coordinated activity across the hippocampal network, how specific subfields differentially contribute to social recognition remains unclear. Of particular interest are the intermediate CA1 (iCA1) and CA3 (iCA3) subfields, which have both been shown to be causally involved in social recognition. Historically, the dense feed-forward projections from CA3 to CA1 led to the view that these subfields form a hierarchical circuit, with CA1 primarily integrating and refining computations from CA3. However, recent causal manipulations of the iCA1 and iCA3 have revealed distinct and separable contributions to approach and avoidance behavior, suggesting functional specialization across the subfields. This functional divergence raises the possibility that iCA1 and iCA3 might differentially encode social recognition information. To test this possibility, we performed one-photon calcium imaging in freely behaving mice to record endogenous activity from the iCA1 and iCA3 during a novel behavioral paradigm that disentangles social identity from spatial position. Notably, we found that iCA3 neurons more robustly discriminated between novel and familiar conspecifics, while iCA1 neurons more strongly encoded spatial position. These results identify the iCA3 as a key locus for social novelty encoding and suggest a functional division of labor within the hippocampus, in which stable spatial frameworks in the iCA1 anchor flexible, context-dependent social representations in the iCA3 that support adaptive social memory.

neuroscience↗

bioRxiv2025

A Feature Learning Model Identifies Predictive Attributes of Mesenchymal Stromal Cell Efficacy

The therapeutic efficacy of human mesenchymal stromal cells (hMSCs) is highly variable, limiting their clinical translation for musculoskeletal diseases and other regenerative medicine applications. There is a poor understanding of the critical quality attributes correlating to therapeutic efficacy of hMSCs. To address this challenge, we analyzed pre-clinical in vitro secretome profiles and in vivo therapeutic efficacy of hMSCs from multiple human donors. hMSCs from different donors showed significant differences between donors in therapeutic efficacy when assessed in a rat post-traumatic osteoarthritis (OA) model. A partial least squares feature learning model was trained to evaluate differences between more and less therapeutic donor hMSCs by examining cytokine secretion profiles, to predict donor-specific therapeutic outcomes. More therapeutic hMSCs exhibited increased secretion of GM-CSF, GRO, IL-4, and PDGF-AA, whereas less therapeutic donors had higher TNF-, IL-6, and MCP-1 secretion. The cytokine profile was accompanied by evaluation of MAPK pathway, which revealed distinct differences in phospho-protein signaling between more and less therapeutic hMSC secretome profiles. Pharmacological inhibition of JNK signaling in more therapeutic donor cells decreased hMSC secretion of the key therapeutic associated cytokines and shifted hMSC secretome towards a less therapeutic profile. Prospective validation of cells from additional donors demonstrated significant correlations between predicted and observed pre-clinical in vivo efficacy to attenuate OA. This approach identifies critical quality attributes enabling consistent prediction of therapeutic potency, thereby addressing a major barrier to scalable and effective cell therapies. These findings advance precision cell-based therapies and offer a framework for standardized donor screening in clinical applications. SummaryA feature learning model was developed, trained, and validated to identify critical quality attributes of MSCs that predict therapeutic potency.

bioengineering↗

bioRxiv2025

Aberrant splicing of MBD1 reshapes the epigenome to drive convergent myeloerythroid defects in MDS

Myelodysplastic neoplasms (MDS) feature hematopoietic deficits driven in part by transcript splicing abnormalities. Thus far, such disease-driving transcripts have been identified in association with specific splicing factor mutations. However, it remains unclear whether there also exists a set of disease-wide conserved pathological transcripts, which drive MDS independently of mutational status. Here, we characterize an MDS-associated long isoform of MBD1 (MBD1-L) as the first described member of this class of transcripts. Overexpression of MBD1-L in healthy human HSPCs recapitulates archetypal defects of MDS including deficits in erythroid differentiation and reconstitution capacity. These defects arise from an isoform-specific switching of MBD1s binding behavior, refocusing its heterochromatin-promoting activity from methylated to unmethylated CpGs and enacting broad downregulation of CpG-rich promoters as well as secondary epigenetic effects mediated by its downstream target BCOR. Remarkably, we also find that directly reversing abnormal MBD1 splicing in primary human MDS using nanoparticle-encapsulated ASOs enhances erythroid differentiation. Key pointsO_LIGlobal mis-splicing of MBD1 represents a novel gain-of-function epigenetic axis driving erythropoietic and proliferative defects in MDS. C_LIO_LIASO based depletion of pathogenic MBD1 transcripts restores erythroid differentiation, advancing RNA-based therapies for MDS. C_LI

cancer biology↗

bioRxiv2025

Sleep Facilitates Pattern Separation through SK Channel-Mediated Sparse Coding

The roles of sleep in priming the brain for associative learning remain unclear. Here, we report that acute sleep deprivation in Drosophila selectively impairs pattern separation--the ability to distinguish between similar stimuli--without affecting classical conditioning. This deficit correlates with disrupted sparse coding in the mushroom body, reflected by an increased number of active Kenyon cells and greater overlap in their odor representations. Electrophysiological analyses reveal that sleep loss enhances small conductance calcium-activated potassium (SK) channel-mediated afterhyperpolarization in GABAergic anterior paired lateral (APL) neurons, leading to reduced levels of feedback inhibition onto Kenyon cells and compromised sparse coding. Targeted knockdown of SK channels in APL neurons reduce their augmented afterhyperpolarization and rescues the pattern separation deficits caused by sleep deprivation. These findings identify a critical role for SK channels in inhibitory interneurons to enable sleep to preserve sparse and decorrelated neural representations, supporting cognitive processes such as pattern separation.

neuroscience↗

bioRxiv2025

Splicing neoepitope prediction is sensitive to methodological differences

MotivationCancer-specific neoepitopes may arise from abnormal splicing in the transcriptomic landscape (alternative splicing neoepitopes, ASNs), leading to divergent proteins with high potential immunogenicity. Predicting candidate ASNs requires a series of algorithmic and parameter choices, but no previous study has investigated the consistency and interpretability of these choices. ResultsWe apply two ASN prediction methods with 35 matched parameter sets to generate candidate ASNs for five breast and ovarian cancer samples from The Cancer Genome Atlas (TCGA). We find that: 1) junction 9-mer peptides generated by two similarly designed pipelines differed by, on average, 68.9% and 76.6% in the BRCA and OV cohorts, respectively, and putatively cancer-specific junction 9-mers from the two pipelines diverged further, by an average of 81.5 % in OV and 84.6 % in BRCA; 2) the most lenient filters in the BRCA cohort show the highest divergence, at 97 %; 3) the rate of mass spectrometry validation of ASNs protein presence in cells is dominated by the size of the input space; and 4) putatively cancer-specific ASNs found by the intersection of both pipelines can be validated when accounting for false discovery with an average of 1.74 and 284.4 candidates in the BRCA and OV cohorts, respectively. Taken together, these results highlight that ASN identification is fragile and difficult to reproduce across analysis platforms, with limited cross-pipeline overlap and strong dependence on parameter choices. Availability and ImplementationPython research code and scripts are available for download at https://github.com/ratschlab/projects2020_ohsu. Contactthompsre@ohsu.edu, raetsch@inf.ethz.ch

bioinformatics↗

bioRxiv2025

BOTany Methods: Accessible Automation for Plant Synthetic Biology

Most members of the synthetic biology community, particularly plant scientists, lack access to liquid handling robots to scale up experiments, enhance reproducibility, and accelerate the Design, Build, Test, Learn cycle. Biofoundries enable high throughput data acquisition to train AI models and to develop new bioproducts, but they are capital-intensive to set up and not widely distributed. Entry-level, 3D-printed robots offer more affordable alternatives, but suffer from a shortage of validated protocols that can be modified without prior coding experience. To enhance access to biological automation, we developed a collection of modular BOTany Methods using Opentrons OT-2 robots to streamline the most common methods for molecular biology research and education. Our comprehensive workflow offers automation for a variety of procedures, ranging from simple but repetitive tasks (such as primer dilution and PCR setup) to more complex operations, including Plant Modular Cloning (MoClo), bacterial transformation, and plasmid extraction. Our BOTany Methods enable undergraduate students and other early career researchers to run designer experiments using table-based inputs, without editing the custom Python scripts. This pipeline enables end-to-end molecular cloning with minimal user intervention, enhancing throughput and traceability for synthetic biology applications. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/671538v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@1b98282org.highwire.dtl.DTLVardef@2727bdorg.highwire.dtl.DTLVardef@a2157borg.highwire.dtl.DTLVardef@1305107_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2025

Expanding the utility of transcriptome analysis for mutation detection in high-risk childhood precision oncology

In precision oncology, whole transcriptome sequencing (RNA-seq) excels at identifying oncogenic fusions. Here, using a cohort of 477 high-risk paediatric tumours, we demonstrate that RNA-seq can identify all mutation classes found previously using whole genome sequencing (WGS) and provides additional functional insights into their pathogenicity. By incorporating reference-guided fusion, and reference-free structural variant (SV) detection algorithms with RNA abundance assessment, RNA-seq identified 96% of SVs and resolved 33 complex SVs that WGS failed to identify. Furthermore, RNA-seq identified 92% of all single nucleotide variants and small insertions and deletions. Importantly RNA-seq informed the pathogenicity assessment in 22% of variants through identification of allele specific expression or the functional consequence of splice-altering variants. The utility of RNA-seq extends beyond fusion identification to the interpretation of mutation pathogenicity and the discovery of important mutations that would otherwise go undetected. We propose that RNA-seq is an indispensable companion to WGS in precision medicine.

genomics↗

bioRxiv2025

High-speed whole-brain imaging in Drosophila

Recent advances in brain-wide recordings of small animals such as worms, fish, and flies have revealed complex activity involving large populations of neurons. In the Drosophila brain, with about 140,000 neurons, brain-wide recordings have been critical to uncovering widespread sensory and motor activity. However, current limitations in volumetric imaging rates hinder the accurate capture of fast neural dynamics. To improve the speed of volumetric imaging in Drosophila, we leverage the recently introduced light beads microscopy (LBM) method. We built a microscope and a LBM module tailored to fly brain experiments and used it to record brain-wide calcium signals in adult behaving flies at either 28 volumes per second or at 60 volumes per second (when selecting the central brain alone). We uncover fast-timescale auditory responses that are missed with standard volumetric imaging. We also demonstrate how temporal super-resolution can be combined with LBM data to uncover responses to single Drosophila courtship song pulses. This establishes LBM as a viable tool for capturing whole-brain activity at high spatial and temporal resolution in the fly.

neuroscience↗

bioRxiv2025

A systemically delivered AAV-CFTR gene therapy for cystic fibrosis

Cystic fibrosis (CF) is the most common monogenic lung disease and results from mutations in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR). There have been over 2000 variants identified in patients that result in loss of function of the CFTR protein leading to systemic disease and respiratory failure in adolescence. While some variants encode proteins with residual activity that can be corrected or potentiated by CFTR modulators, at least 10% of CF individuals cannot tolerate the modulators or have nonsense mutations which fail to make any protein. For all people with CF, a mutation agnostic gene replacement strategy could provide a cure for CF lung disease. Here, we propose using a systemic route of administration to deliver a functional CFTR minigene cargo with a lung tropic AAV capsid. This would serve to reach multiple organs, most importantly the lung epithelium, and would provide a functional CFTR transgene that could be expressed in any cell type with a ubiquitous promoter. To achieve this, we generated the smallest CFTR minigene tested in an AAV delivery to date. We demonstrate its expression and function following transfection in cell-based assays and restoration of function in primary CF airway cells after viral delivery. Furthermore, we identify an AAV capsid that can transduce alveolar and airway epithelium with systemic delivery in non-human primates. These data provide tools for delivering a functional CFTR minigene that fits within the packaging capacity of an AAV and demonstrate lung transduction with an AAV following systemic delivery in a large animal model. This strategy first and foremost can reach target airway cells by circumventing the strong mucosal barrier in CF airways but may also provide a method by which to restore CFTR function in additional CF affected organs.

genetics↗

bioRxiv2025

Leveraging mRNA platform for the development of vaccines against egg allergy

Food allergy has posed a major global health burden due to the rising prevalence and lack of effective prophylactic strategies. During the past decades, allergen-specific immunotherapy (AIT) has been used as a disease-modifying therapy for food allergic conditions, but due to the long-term treatment duration, poor patient compliance and unexpected adverse reactions, only a minority of patients benefit from AIT therapy. In this proof-of-concept study, using well-established mRNA platform, we developed mRNA vaccine candidates encoding for the major egg white allergen Gal d2 (also known as ovalbumin) and comprehensively evaluated the prophylactic efficacy against anaphylaxis in a Gal d2-induced allergic mouse model. Two vaccine formulations, Gal d2 mRNA vaccine and Gal d2-IL-10 mRNA vaccine, both demonstrated effective ability in preventing the onset of allergic disease, which is largely attributed to the versatilities of mRNA vaccine in eliciting allergen-blocking antibody, shifting Th2 towards Th1 immunity, as well as in generating peripheral tolerance.

immunology↗

bioRxiv2025

C9orf50 is a Targetable Spliceosome Regulator for Cancer Immunotherapy

Cancer cells harbor cell-intrinsic programs capable of sculpting immunogenic landscapes, yet molecular brakes that enforce immune evasion remain poorly defined. Here, we identify C9ORF50, a previously uncharacterized intrinsically disordered protein, as a liquid-liquid phase separation-driven regulator of RNA processing and actionable immunotherapy target. Genetic ablation of C9ORF50 induces selective intron retention in spliceosome component transcripts, leading to cytoplasmic accumulation of immunogenic double-stranded RNA (dsRNA). This dsRNA activates type I interferon pathway that in turn orchestrates a chemokine secretory program critical for T cell recruitment. The resultant enhancement of tumor immunogenicity and reprogramming of tumor immune microenvironment drives robust antitumor immunity, effectively converting immunologically "cold" tumors to "hot" phenotypes. Therapeutic targeting of C9ORF50 via RNA interference achieved robust tumor suppression in syngeneic models, suggesting its translational relevance. Notably, C9ORF50 exhibits tumor-predominant expression, with minimal baseline levels detected in healthy tissues or immune cell populations, underscoring its potential safety as a therapeutic target. Our study not only identifies C9ORF50 as a novel LLPS-dependent regulator of RNA splicing but also establishes it as a promising and potentially safe therapeutic target for cancer immunotherapy.

cancer biology↗

bioRxiv2024

Reciprocal links between methionine metabolism, DNA repair and therapy resistance in glioblastoma

Glioblastoma (GBM) is uniformly lethal due to profound treatment resistance. Altered cellular metabolism is a key mediator of GBM treatment resistance. Uptake of the essential sulfur-containing amino acid methionine is drastically elevated in GBMs compared to normal cells, however, it is not known how this methionine is utilized or whether it relates to GBM treatment resistance. Here, we find that radiation acutely increases the levels of methionine-related metabolites in a variety of treatment-resistant GBM models. Stable isotope tracing studies further revealed that radiation acutely activates methionine to S-adenosyl methionine (SAM) conversion through an active signaling event mediated by the kinases of the DNA damage response. In vivo tumor SAM synthesis increases after radiation, while normal brain SAM production remains unchanged, indicating a tumor- specific metabolic alteration to radiation. Pharmacological and dietary strategies to block methionine to SAM conversion slowed DNA damage response and increased cell death following radiation in vitro. Mechanistically, these effects are due to depletion of DNA repair proteins and are reversed by SAM supplementation. These effects are selective to GBMs lacking the methionine salvage enzyme methylthioadenosine phosphorylase. Pharmacological inhibition of SAM synthesis hindered tumor growth in flank and orthotopic in vivo GBM models when combined with radiation. By contrast, methionine depletion does not reduce tumor SAM levels and fails to radiosensitize intracranial models, indicating depleting SAM, as opposed to simply lowering methionine, is critical for hindering tumor growth in intracranial models of GBM. These results highlight a new signaling link between DNA damage and SAM synthesis and define the metabolic fates of methionine in GBM in vivo. Inhibiting radiation-induced SAM synthesis slows DNA repair and augments radiation efficacy in GBM. Using MAT2A inhibitors to deplete SAM may selectively overcome treatment resistance in GBMs with defective methionine salvage while sparing normal brain.

cancer biology↗

bioRxiv2024

Association of oropharyngeal cancer recurrence with tumor-intrinsic and immune-mediated sequelae of reduced genomic instability

BackgroundLimited understanding of the biology predisposing certain human papillomavirus-related (HPV+) oropharyngeal squamous cell carcinomas (OPSCCs) to relapse impedes therapeutic personalization. We aimed to identify molecular traits that distinguish recurrence-prone tumors. Methods50 HPV+ OPSCCs that later recurred (cases) and 50 non-recurrent controls matched for stage, therapy, and smoking history were RNA-sequenced. Groups were compared by gene set enrichment analysis, and select differences were validated by immunohistochemistry. Features discriminating groups were scored in each tumor using gene set variation analysis, and scores were evaluated for recurrence prediction ability. ResultsCases downregulated pathways linked to anti-tumor immunity (FDR-adjusted p<.05) and contained fewer tumor-infiltrating lymphocytes (p<.001), including cytotoxic T-cells (p=.005). Cases also upregulated pathways related to cell division and other aspects of tumor progression. Upregulated and downregulated pathways were respectively used to define a tumor progression score (TPS) and immune suppression score (ISS) for each tumor. Correlation between TPS and ISS (r=.603, p<.001) was potentially explained by observed upregulation of DNA repair pathways in cases, which might enhance their progression directly and by limiting cytosolic DNA-induced inflammation. Accordingly, cases contained fewer double-strand breaks based on staining for phospho-RPA32 (p=.006) and {gamma}-H2AX (p=.005) and downregulated pro-inflammatory components of the cytoplasmic DNA sensing pathway. A combined score derived from TPS and ISS optimized recurrence prediction and stratified survival in a manner generalizable to three external cohorts. ConclusionsWe provide novel evidence that limiting genomic instability makes tumor-intrinsic and immune-mediated contributions to HPV+ OPSCC recurrence risk, opening opportunities to detect and target this treatment-resistant biology.

cancer biology↗

bioRxiv2024

SPP1+ tumor-associated macrophages induce radioresistance of nasopharyngeal carcinoma through crosstalk with the tumor microenvironment

The function and phenotype of tumor-associated macrophages (TAMs) influence the efficacy of radiotherapy. However, the effect of different subsets of TAMs on the radioresistance in nasopharyngeal carcinoma (NPC) still needs to be further explored. This study utilized single-cell RNA sequencing (scRNA-seq) to analyze 120,579 cells obtained from 15 NPC samples. Cell annotation, cell-cell communication analysis, and functional annotation were used to investigate the impact of TAMs on the effectiveness of radiotherapy in NPC patients. Additionally, we employed RNA-seq data and clinical information from many patients, including 24 NPC samples from Zhujiang Hospital, 3,934 samples from patients with a history of radiotherapy, for further validation. We identified a hub TAM subpopulation, SPP1+ TAMs, that induced radioresistance in NPC based on single-cell RNA sequencing (scRNA-seq) data. We combined many public datasets to confirm their prognostic value in radiotherapy patients. We found that SPP1+ TAMs had stronger protumorigenic and immunosuppressive effects in the postradiotherapy recurrent tumor (PRRT) group. SPI1 transcription factor efficiently regulates the expression level of SPP1 in macrophages. In addition, we validated the underlying mechanisms by molecular docking, multiplex immunofluorescence and cellular experiments. In conclusions, by forming an immunosuppressive microenvironment and promoting tumor cell proliferation, SPP1+ TAMs leading to radioresistance and poor clinical prognosis in NPC patients. Targeting SPP1+ TAMs could provide new insights into improving the efficacy of radiotherapy in NPC patients.

cancer biology↗