Biology subjects

Zhang, F.

Publications and source records attributed to Zhang, F..

At least 91 records · Page 5Linked to original sources

bioRxiv2025

Single-cell and Spatial Omics Reveals Region-Specific Plasticity and Therapeutic Vulnerabilities in Metastatic High-Risk Neuroblastoma

Neuroblastoma, a deadly pediatric cancer derived from sympathetic ganglia of the peripheral nervous system, frequently metastasizes, driving poor outcomes. Primary neuroblastomas are well-characterized, but the mechanisms underlying metastasis remain poorly understood. Here, by applying single-cell and spatial multi-omics analyses to primary and metastatic tumors, we found that lymph-node metastases in high-risk neuroblastomas display distinctive cellular heterogeneity and plasticity, marked by mesenchymal-like and stem-like states and heightened epithelial-to-mesenchymal transition activity compared to primary adrenal tumors. Additionally, compared to primary adrenal masses, the metastatic niche display increased immunosuppressive myeloid programs, heightened immune checkpoint signaling, and lymphocyte exhaustion, which are indicative of immune evasion and dysfunction. Notably, metastatic neuroblastomas show elevated eIF4F translation machinery and XPO1 levels. Dual inhibition of eIF4A and XPO1 synergistically halted tumor growth and prolonged survival in xenograft models. Together, our multi-omics studies reveal the molecular and cellular plasticity that contributes to therapy resistance and highlight exploitable therapeutic vulnerabilities in high-risk metastatic neuroblastomas.

cancer biology↗

bioRxiv2025

Oncogenic EGFR rewires STING-TBK1 immune machinery to license DNA damage tolerance

EGFR hotspot mutations (mEGFR), including primary L858R, exon 19 deletion, and secondary T790M, are pivotal oncogenic drivers in human non-small cell lung cancer (NSCLC). Meanwhile, NSCLC resistance to third-generation tyrosine kinase inhibitors (TKIs) is a major clinical challenge and remains mechanistically unresolved. Here, we uncover a previously unrecognized immunological mechanism whereby mEGFR exploits cGAS-STING innate immune signaling, conventionally regarded as tumor-suppressive, to sustain oncogenic signaling and therapeutic resistance. Mechanistically, mutant EGFR kinase aberrantly incorporates into STING signalosomes, directly phosphorylating STING (Y245/Y314) and TBK1 (Y577/Y677), stabilizing and hyperactivating TBK1 proteins, and establishing an unexpected and kinase loop critical for DNA damage repair. Disruption of this mEGFR-STING-TBK1 axis, genetically or pharmacologically, profoundly sensitized resistant patient-derived NSCLC organoids to chemotherapy. Combining TBK1 inhibition with cisplatin notably eradicated mEGFR-driven tumors in spontaneous and immunocompetent NSCLC murine models and patient-derived organoids. Our findings suggest a new function of cGAS-STING in the DNA damage repair program, its paradoxical exploitation by oncogenic driver mutations, and an innate immune therapeutic vulnerability in NSCLC.

cancer biology↗

bioRxiv2025

Engineering Treg-mediated immune tolerance via foxp3a overexpression to evade allograft transplantation barriers in zebrafish

In mammals, regulatory T cells (Treg) cells have been utilized to enhance tolerance in organ transplantation. Although transplanting germline stem cells (GSCs) or gonadal primordia into immunodeficient zebrafish have shown to be an important technique which can bypass the juvenile phase and expedite gamete generation, it remains challenging to raise the immunodeficient fish. Here, we achieved in vivo induction of Tregs by overexpressing the key transcription factor Foxp3a, generating transgenic zebrafish with robust immune tolerance. This was characterized by a significant downregulation of T cell development and homing-related genes, accompanied by a marked upregulation of immunosuppressive factors. Using these immune-tolerant fish as hosts for subcutaneous gonadal primordium transplantation (SGPT) and intraperitoneal GSC transplantation (IGCT), we markedly accelerated germ cell maturation and efficiently established stable transgenic lines. Transcriptomic analyses demonstrated that transgenic hosts demonstrated a phenotypic profile characterized by delayed immune activation, attenuated responsiveness, and enhanced graft survival. Thus, we present a Treg-induction-based approach in fish that resolves the intrinsic conflict between high embryonic transgenesis efficiency and early lethality, while significantly improving overall transgenesis success rates. Moreover, it offers a practical alternative to immunodeficient recipients, avoiding the challenges of complex husbandry and compromised fertility.

genetics↗

bioRxiv2025

Chronic Ethanol Drinking Alters Medial Prefrontal Cortex and Nucleus Accumbens Astrocyte Translatome and Extracellular Matrix Glycosaminoglycans

Alcohol Use Disorder is a leading preventable cause of morbidity and mortality, yet knowledge of mechanisms driving ethanol-related neuroplasticity remains incomplete. While research has traditionally focused on neuronal signaling, emerging evidence implicates astrocytes in addiction-related adaptations. Here, we investigated the astrocyte-specific molecular consequences of chronic ethanol consumption in the prefrontal cortex and nucleus accumbens, two brain regions critical for executive control and reward processing. Using Translating Ribosome Affinity Purification RNA-seq and bulk RNA-seq in Aldh1l1-EGFP/Rpl10a mice, expressing an EGFP tag on astrocyte ribosomes, we identified hundreds of differentially translated astrocytic genes following chronic continuous two-bottle choice ethanol drinking. Sex-specific analyses revealed greater astrocytic changes in the female PFC and male NAc. Pathway enrichment highlighted extracellular matrix remodeling, synaptic signaling, mitochondrial function, and immune-related pathways. Analyses of individual drinking levels further demonstrated distinct correlations between ethanol intake and astrocytic translation. The major components of the brain extracellular matrix are chondroitin sulfate proteoglycans, produced primarily by astrocytes and covalently bound to chondroitin sulfate glycosaminoglycan chains. Complementary mass spectrometry/liquid chromatography analyses of chondroitin sulfate, heparan sulfate, and hyaluronic acid glycosaminoglycan disaccharides revealed ethanol-induced alterations in chondroitin sulfate glycosaminoglycan sulfation patterns, with additional baseline differences identified between selectively bred high- and low-ethanol preference lines. Together, these findings indicate that astrocytes undergo profound sex- and region-specific adaptations to chronic ethanol, implicating extracellular matrix and glycosaminoglycan remodeling as key risk-factors for and mediators of chronic ethanol-related neuroplasticity.

neuroscience↗

bioRxiv2025

Study of Sex Differences in the Whole Brain White Matter Using Diffusion MRI Tractography and Suprathreshold Fiber Cluster Statistics

Sex-specific characteristics demonstrate a substantial influence on the brain white matter (WM), suggesting distinct structural connectivity patterns between females and males. Diffusion MRI (dMRI) tractography is an important tool in assessing WM connectivity and brain tissue microstructure across different populations. Whole brain tractography analysis for group statistical comparison is a challenging task due to the large number of WM connections. This work studies whole-brain WM connectivity differences between females and males using dMRI tractography. We study a large cohort of 707 subjects from the Human Connectome Project Young Adult dataset. By applying a well-established fiber clustering pipeline and a suprathreshold fiber cluster statistical method, we analyze tracts in the cerebral cortex and understudied pathways like those connecting to the cerebellum. We identify several tracts with significant sex differences in terms of their fractional anisotropy and/or mean diffusivity. These include deep tracts like the arcuate fasciculus, corticospinal tract, and corpus callosum, superficial tracts in the frontal lobe, and cerebellar tracts. Finally, correlation analysis reveals that these WM differences are linked to a range of neurobehavioral measures, with the strongest and most consistent associations observed for motor function, suggesting motor circuits as a potential key focus for future research.

neuroscience↗

bioRxiv2025

BCKDK, a novel hypoxia-responsive kinase that exacerbates cerebral ischemia injury

Alterations of circulating amino acid profile have been observed in patients with ischemic stroke. However, whether ischemia disrupts amino acid metabolism in the brain tissue and subsequently potentiates cellular stress and cerebral injury have never been explored. Employing a metabolomics approach combined with metabolic flux analysis, impaired catabolism and significant enrichment of branched-chain amino acids (BCAAs) were identified in mouse primary neuron cells upon oxygen-glucose deprivation. Consistently, BCAA catabolism was also damaged in the brain of mouse with acute ischemic stroke, accompanied with suppressed activity of branched-chain alpha-keto acid dehydrogenase (BCKDH) and upregulation of BCKDH kinase (BCKDK). Furthermore, restoration of BCAA catabolism by suppressing BCKDK via pharmacological inhibitor or silencing RNA dramatically alleviated cerebral ischemia injury in mice. Mechanistically, ischemia induces the expression of BCKDK via hypoxia-inducible factor 1-mediated transcriptional activation and inhibits BCAA conversion into substrates for tricarboxylic acid cycle, contributing to potentiated energy deficiency, glutamate excitotoxicity, and neuronal injury. Collectively, this study identified BCKDK as a novel hypoxia-responsive factor and a promising therapeutic target for cerebral ischemia injury.

molecular biology↗

bioRxiv2025

Antimicrobial Peptides Induce Cell Death in Marginal Zone Lymphoma Models Resistant to Targeted Therapies

Marginal zone lymphoma (MZL) is an indolent yet incurable B-cell malignancy in which targeted agents such as BTK and PI3K inhibitors frequently fail due to resistance or toxicity. Antimicrobial peptides (AMPs), evolutionarily conserved effectors of innate immunity, possess selective cytotoxicity against malignant cells by exploiting tumor-specific membrane alterations. We evaluated the antitumor activity of seven natural AMPs, including Antarctic fish-derived trematocines and chionodracine variants, and amphibian temporins, against MZL cell lines (VL51, Karpas1718) and derivatives resistant to BTK, PI3K{delta}, or PI3K/{delta} inhibitors. Among them, W-trematocine and temporin L demonstrated potent dose-dependent cytotoxicity with IC50 values of 5.7-10 M, maintaining full activity in all resistant models. Other peptides showed moderate activity, while chionodracine-1 was inactive. Notably, W-trematocine displayed minimal toxicity toward non-malignant cells in prior studies, underscoring its selectivity. AMP-mediated killing, driven by membrane disruption and non-apoptotic death pathways, bypassed conventional resistance mechanisms, suggesting therapeutic potential in relapsed/refractory disease. These findings highlight natural AMPs as promising candidates for development in drug-resistant MZL, warranting further optimization and preclinical validation.

cancer biology↗

bioRxiv2025

ATF4 alleviates doxorubicin-induced cardiomyopathy through H2S-mediated antioxidation

BackgroundDoxorubicin (DOX) remains a cornerstone in the treatment of various cancers. However, its clinical utilization is significantly hampered by dose-dependent cardiotoxicity. The generation of reactive oxygen species (ROS) constitutes the central component of the pathogenesis of DOX-induced cardiotoxicity. Activating transcription factor 4 (ATF4) has been demonstrated to exert a cardioprotective effect and augment cardiac antioxidative capacity in settings of heart failure. However, the role of ATF4 in DOX-induced cardiomyopathy (DIC) remains unknown. MethodsTo explore the role of ATF4 in DOX-induced cardiomyopathy, cardiac-specific ATF4 conditional heterozygous mice and AAV9 mediated ATF4 overexpression mouse models were utilized. Cardiac function was assessed by echocardiography. The upstream regulator and downstream mediator of ATF4 were evaluated using RNA-seq analysis and further verified using ChIP assay and luciferase reporter assay. ResultsWe found a substantial decrease in ATF4 expression levels in the heart of DIC mice. ATF4+/- mice exhibited a higher degree of susceptibility to DOX-induced cardiotoxicity in comparison with ATF4flox/flox mice, as evidenced by the manifestation of more severe cardiac dysfunction and a significantly earlier mortality rate. In contrast, cardiacc-specific overexpression ATF4 by AAV9 confers robust cardioprotection against DOX-induced cardiomyopathy. Mechanistically, we identified the upstream regulator of ATF4 as KLF16, which was significantly suppressed during DOX treatment. Further, the decrease of ATF4 led to a reduction in cystathionine {gamma}-lyase (CSE) transcription and hydrogen sulfide (H2S) production in the context of DOX-induced cardiotoxicity. ChIP and luciferase reporter assays revealed that ATF4 functioned as the transcription factor of the CSE gene, which is a key enzyme in the synthesis of H2S to counteract oxidative stress. Consistently, ROS scavengers or H2S donors was shown to mitigate the consequences of ATF4 deficiency. In contrast, the ectopic expression of ATF4 mitigated oxidative stress and apoptosis in DOX-induced cardiotoxicity, both in vivo and in vitro. ConclusionsOur study revealed a novel function of ATF4 in counteracting oxidative stress in DOX cardiotoxicity by promoting the transcription of CSE. ATF4 may represent a promising therapeutic target for the treatment of DOX-induced cardiomyopathy.

pathology↗

bioRxiv2025

RNA helicase Ddx21 safeguards fetal HSPC expansion by recruiting Kdm5a to epigenetically sustain ribosomal and hematopoietic gene transcription

Fetal hematopoietic stem and progenitor cells (HSPCs) require active ribosome biogenesis to sustain their rapid proliferation, yet how non-structural ribosomal factors regulate this process remains unclear. Here, we identify the RNA helicase Ddx21 as a critical determinant of fetal hematopoiesis through its epigenetic role in maintaining active ribosomal transcription. Conditional knockout of Ddx21 in murine fetal hematopoietic cells resulted in severe anemia, fetal liver hypoplasia, and depletion of HSPCs, accompanied by erythroid maturation arrest. Mechanistically, Ddx21 deficiency disrupted ribosomal and hematopoietic gene expressions, impaired translational capacity, and activated p53 pathway, triggering cell cycle arrest and apoptosis. While p53 inhibition partially rescued proliferation defects, it failed to restore rRNA transcription, pointing to p53-independent mechanisms. Multi-omics profiling revealed that Ddx21 interacts with the histone demethylase Kdm5a, co-occupying active promoters marked by H3K4me3. Loss of Ddx21 diminished H3K4me3 levels at ribosomal DNA (rDNA) and hematopoietic genes such as cKit and Gata1, downregulating their transcription. Strikingly, Kdm5a inhibition restored rRNA expression and protein translation in Ddx21-deficient cells, and combined inhibition of Kdm5a and p53 cooperatively rescued HSPC function. These findings demonstrate a paradigm wherein Ddx21 couples ribosome biogenesis to epigenetic regulation by sequestering Kdm5a at active chromatin, thereby preserving transcriptional output essential for fetal hematopoietic expansion.

cell biology↗

bioRxiv2025

Leveraging Large Language Models for Redundancy-Aware Pathway Analysis and Deep Biological Interpretation

Extracting coherent, biologically meaningful insights from vast, complex multi-omics data remains challenging. Currently, pathway enrichment analysis serves as a cornerstone for the functional interpretation of such data. However, conventional approaches often suffer from extensive functional redundancy caused by shared molecular components and overlapping pathway definitions across databases. This redundancy can obscure key biological signals and compromise the interpretability of pathway enrichment results. Here, we present MAPA (Functional Module Identification and Annotation for Pathway Analysis Results Using Large Language Models [LLM]), an open-source computational framework that resolves redundancy and enhances pathway analysis result interpretation. MAPA computes functional similarity between pathways using LLM-based text embeddings, enabling comparison across different databases. It constructs pathway similarity networks and identifies functional modules via community detection algorithms. Crucially, MAPA employs LLMs for automated functional annotation, integrating Retrieval-Augmented Generation (RAG) to generate comprehensive and real-time biological summaries and reduce hallucinations. Benchmarking demonstrated MAPAs superior performance: the biotext embedding similarity showed a large effect size (Cliffs {delta} = 0.96) compared with the Jaccard index ({delta} = 0.73), and module identification achieved high accuracy (Adjusted Rand Index [ARI] = 0.95) versus existing methods (ARI = 0.23-0.33). Human expert evaluation confirmed that MAPAs annotations match expert-quality interpretations. Finally, a multi-omics aging case study illustrates that MAPA uncovers coherent functional modules and generates insights extending beyond conventional pathway analyses. Collectively, MAPA represents a significant advance in redundancy-aware pathway analysis, transforming pathway enrichment results from fragmented lists into biologically coherent narratives. By leveraging the capabilities of LLMs, MAPA offers researchers a robust, scalable tool for deriving deep mechanistic insights from complex and vast multi-omics datasets, marking a new direction for AI-driven bioinformatics.

bioinformatics↗

bioRxiv2025

BioScientist Agent: Designing LLM-Biomedical Agents with KG-Augmented RL Reasoning Modules for Drug Repurposing and Mechanistic of Action Elucidation

Drug discovery is protracted, resource-intensive, and afflicted by attrition rates exceeding 90 %, which leaves most diseases, particularly rare or neglected indications, without effective therapies. Drug repurposing offers a cost effective alternative, yet systematic identification of novel drug indication pairs and mechanistic rationales remains hindered by the scale and heterogeneity of biomedical knowledge. We present BioScientist Agent, an end to end framework that unifies a billion-fact biomedical knowledge graph with (i) a variational graph auto-encoder for representation learning and link prediction driven drug repurposing, (ii) a reinforcement learning module that traverses the graph to recover biologically plausible mechanistic paths, and (iii) A large language model (LLM) multi-agent layer that orchestrates these components, enabling inference of target pathways for a drug disease pair, and automatic generation of coherent causal reports. In all downstream tasks, the BioScientist Agent surpasses existing state of the art baseline models across various metrics and provides mechanistic explanations consistent with the literature. Its open and modular design accelerates hypothesis generation and reduces experimental overhead in early stage discovery.

bioinformatics↗

bioRxiv2025

An improved SIFT algorithm based method for detecting of tumor tissue movement in respiratory motion

BackgroundThis paper intends to make use of the excellent performance of the SIFT algorithm to accurately calculate the displacement of tumor tissues during respiratory movement. Material and methodFirst, we moved phantoms to up,down,right,left respectively to simulate the different directions of movement during respiratory. And rotated phantom to left and right respectively by the angle of 5,10,30,45. Then, used SIFT and cross-correlation algorithms to search the phantoms. Last, use the t-test to check the differences between different directions. ResulThe t-test result proved that there was no significant difference in the detection of moving phantom in all directions. There was no statistical difference between the SIFT of the moving motif and the cross-correlation. The detection results of rotating phantom indicated that the SIFT test results could be used to detect distortion. ConclusionSIFT algorithm can be used to calculate the distortion caused by the thoracic tissue during respiratory movement.

biophysics↗

bioRxiv2025

A fully-open structure-guided RNA foundation model for robust structural and functional inference

RNA language models have achieved strong performances across diverse downstream tasks by leveraging large-scale sequence data. However, RNA function is fundamentally shaped by its hierarchical structure, making the integration of structural information into pre-training essential. Existing methods often depend on noisy structural annotations or introduce task-specific biases, limiting model generalizability. Here, we propose structRFM, a structure-guided RNA foundation model that is pre-trained on millions of RNA sequences and secondary structures data by integrating base pairing interactions into masked language modeling through a novel pair matching operation. We further introduce MUSES (multi-source ensemble of secondary structures) to mitigate model bias, and a dynamic masking ratio to balance the structure-guided mask and nucleotide-level mask. structRFM learns joint knowledge of sequential and structural data, producing versatile representations, including classification-level, sequence-level, and pairwise matrix features, that support a broad spectrum of downstream adaptations. structRFM ranks among the top models in zero-shot homology classification across seventeen biological language models, and sets new benchmarks for secondary structure prediction. structRFM further derives Zfold, which enables robust and reliable tertiary structure prediction, with consistent improvements in estimating 3D structures and their accordingly extracted 2D structures, achieving a pronounced about 20% performance gain compared with baselines and comparable performances with AlphaFold3 on CASP15-natural, CASP16, and RNA-Puzzles datasets. In functional tasks such as internal ribosome entry site identification, structRFM achieves a whopping 48% performance gain in F1 score. Furthermore, state-of-the-art performances in extensive experiments across novel RNA families and long non-coding RNAs indicate the robustness and generalizability of structRFM. These results demonstrate the effectiveness of structure-guided pre-training and highlight a promising direction for developing multi-modal RNA language models in computational biology. To support the broader scientific community, we have made the 21-million sequence-structure dataset and the pre-trained structRFM model fully open-source, facilitating the development of multimodal foundation models in biology.

bioinformatics↗

bioRxiv2025

The superficial white matter in language processing: Broca's area connections are bilaterally associated with individual performance in children and adults

While deeper white matter connections, such as the arcuate fasciculus and frontal aslant tract, are well known for their role in language and show leftward asymmetries in adults, the contribution of the short-range cortico-cortical superficial white matter (SWM) connections remains less understood. In this preregistered study, we examined white matter connections of Brocas area and its right hemisphere homolog in early adolescents and young adults using two large, publicly available datasets: the Adolescent Brain Cognitive Development Study and the Human Connectome Project Young Adult Study, totaling over 10,000 participants. We anatomically curated the ODonnell Research Group (ORG) tractography atlas to identify SWM fiber clusters intersecting Brocas area (pars opercularis and pars triangularis), confirmed through expert visual inspection. We investigated the microstructure, structural connectivity, and lateralization of Brocas area SWM and its relationship with language performance (Picture Vocabulary and Oral Reading Recognition assessments), in comparison to the deeper white matter connections of the frontal aslant tract and arcuate fasciculus. The arcuate fasciculus demonstrated the strongest and most consistent leftward lateralization of both microstructure (fractional anisotropy, FA) and structural connectivity (number of streamlines, NoS), with structure-function associations that were bilateral in adolescents and left-dominant in adults. Interestingly, despite weaker lateralization than the arcuate fasciculus, both the SWM and the frontal aslant tract demonstrated comparable associations with language performance. The frontal aslant tract showed greater leftward lateralization (FA and NoS) with age and was bilaterally associated with language performance, particularly in adolescents. Compared to these deeper tracts, Brocas area SWM demonstrated left-lateralized FA and right-lateralized NoS in both adolescents and adults, with stronger FA lateralization in adults. Bilateral SWM FA and NoS were significantly associated with language performance in both hemispheres and age groups. Overall, these results suggest that Brocas area SWM may support language in a more bilaterally distributed manner and highlight the importance of considering SWM connections in studies of language development and neurosurgical planning.

neuroscience↗

bioRxiv2025

Integrating 12 Spatial and Single Cell Technologies to Characterise Tumour Neighbourhoods and Cellular Interactions in three Skin Cancer Types

Cutaneous squamous cell carcinoma (cSCC), basal cell carcinoma (BCC), and melanoma - the three major skin cancers - collectively comprise over 70% of all cancer cases. Despite their prevalence, much understanding of cellular interactions in the skin cancer microenvironment is needed, both in the outer skin layer where the cancer originates and at the deeper junctional and dermal layers into which it progresses. To address this gap, we integrated 12 complementary spatial and single-cell technologies to generate orthogonally-validated cell signatures, spatial maps, and interactomes for cSCC, BCC, and melanoma. Through comprehensive comparisons and integrating these spatial methods, we provided practical benchmarking guidelines for experimental design and analysis. By identifying keratinocyte cancer cells and melanomas, we found distinct signatures of these cells compared to non-cancer keratinocytes and melanocytes. Spatial integration of transcriptomics, proteomics and glycomics uncovered cancer niches enriched for cancer initiating cells (melanocytes or keratinocytes) and fibroblast and T-cell (MKFT) clusters, with altered tyrosine and pyrimidine metabolism. Ligand-receptor analysis across >700 cell-type combinations and >1.5 million interactions highlighted key roles for CD44, integrins, and collagens, with CD44-FGF2 emerging as a potential therapeutic target. Consistently, melanoma showed strong MFT interactions, validated by Opal Polaris, RNAScope, Proximal Ligation Assay and two additional single-cell spatial platforms (making a total of 14 technologies). For population-scale generalisation, genetic associations from >500,000 individuals were mapped onto spatial skin tissues, identifying SNPs enriched in domains containing melanocytes and T cells and their ligand-receptor pairs, shedding light on functional mechanisms linking genetic heritability to cells within cancer tissue. We built an interactive multiomics resource for exploring spatially-resolved molecular signatures and cellular crosstalk in skin cancer, available at https://skincanceratlas.com.

cancer biology↗

bioRxiv2025

Integrated small and long RNA sequencing in single oocytes reveals piRNA-mediated transposon repression during human oogenesis

The piwi-interacting RNA (piRNA) pathway plays a pivotal role in controlling transposable element (TE) activity, which is crucial for the developmental competence of gametogenesis. Although piRNAs have been studied in golden hamsters and other representative mammals, little is known about the relationship between distinct piRNA populations and their regulatory effects on TEs in human oocytes. In this study, we simultaneously profiled small and long RNA transcriptomes in individual human oocytes across four developmental stages. piRNAs, especially PIWIL3-associated short piRNAs (short-piRNAs), are the predominant small non-coding RNAs during human oogenesis. A marked increase in short-piRNAs after the primordial follicle stage coincided with a global downregulation of TE expression, particularly LINE-1 (L1) and endogenous retroviruses (ERVs). On the other hand, PIWIL1- and PIWIL2-associated long piRNAs (long-piRNAs) were correlated with the silencing of certain specific ERV subfamilies. Genomic-context analyses revealed that highly productive piRNA clusters have evolved asymmetric antisense insertion bias toward L1 and ERVs, contributing to TE families-specific regulation. Our findings highlight the global effect of piRNA-mediated TEs repression, with short-piRNAs acting as the primary and broad-spectrum suppressors, and long-piRNAs providing coordinated ERV-specific silencing. In summary, this study provides a valuable dataset of small and long RNA co-expression landscapes in developing human oocytes and offers insights into the coordinated yet distinct roles of different PIWI/piRNA classes in repressing TEs during human oogenesis.

genomics↗

bioRxiv2025

Activation of PP2A-B56α leads to aberrant EGFR signaling and proliferative phenotypes in PDAC

Pancreatic ductal adenocarcinoma (PDAC) stands to become the second most deadly cancer by 2030. The small GTPase, KRAS, is mutated in over 90% of PDAC patients and considered the primary driver mutation. Despite being an almost ubiquitous event, KRAS mutations have been difficult to target therapeutically, particularly KRASG12D, the most common mutation in PDAC. In addition to these pharmacological challenges, KRAS mutations have been shown to drive signaling plasticity and therapeutic resistance through phosphorylation cascades in most cancers. Protein phosphatases are master regulators of kinase signaling, however the contribution of phosphatase deregulation to mutant KRAS cancer phenotypes is poorly understood. Protein phosphatase 2A (PP2A) inhibits effectors downstream of KRAS, placing this family of enzymes as key regulators of PDAC oncogenic signaling. However, our previous studies utilizing small molecule activating compounds of PP2A show a heterogeneous response in PDAC, with some cell lines displaying increased oncogenic signaling despite induction of phosphatase activity. Similarly, specific PP2A subunits exhibit both tumor suppressive and oncogenic functions depending on the cellular context. Therefore, understanding the role of PP2A in regulating cancer phenotypes is critical for the future development of therapeutic strategies that leverage this phosphatase. Here, we determined the impact of the specific PP2A subunit, B56, on PDAC phenotypes using both genetic and pharmacological activation strategies in human PDAC cell lines and genetic mouse models. We demonstrate that while PP2A-B56 suppresses specific oncogenic pathways, B56 activation exacerbates PDAC proliferative phenotypes and decreases overall survival in vivo, potentially through increased epidermal growth factor receptor (EGFR) signaling. EGFR is a critical signaling node in PDAC as inhibition or loss of EGFR prevents KRAS-driven tumorigenesis and increased EGFR activity is associated with poor patient outcome. The activation of EGFR by PP2A-B56 is in part mediated through increased expression and processing of EGFR ligands, specifically amphiregulin, heparin-binding EGF-like growth factor (HB-EGF), and epiregulin. Furthermore, pharmacological PP2A activation in combination with EGFR inhibitors mitigates this signaling and increases cell death. Together, these studies implicate a previously undescribed non-canonical role for PP2A-B56 in EGFR signaling that contributes to PDAC progression.

cancer biology↗

bioRxiv2025

Pluripotent stem cell-derived siTNK cells attack tumors via a synthetic CD8-CD28 TCR complex

Tumor-associated antigen-specific T cell receptor (TCR)-engineered T cells offer a promising strategy for cancer therapy. Natural killer (NK) cells exhibit broad anti-tumor activity with low side effects but lack the capacity to recognize intracellular antigens. Here, we found that the human pluripotent stem cell (hPSC)-derived iNK cells, unlike tissue-isolated NK cells, expressed all four CD3 subunits at the transcriptome level. We introduced a synthetic gene-expressing complex (SCOTR), encoding a tumor antigen- specific TCR, CD8 coreceptor, and CD28 costimulatory molecule, into hPSCs to generate SCOTR-hPSCs. The SCOTR-hPSCs gave rise to abundant synthetic TCR complex-expressing iNK (siTNK) cells via an organoid induction method. These siTNK cells showed HLA-dependent, antigen-specific cytotoxicity against tumor cells and significantly suppressed tumor growth in tumor xenograft animal models, while also preserving universal non-specific tumor-killing activity. Collectively, siTNK cells, as hPSC-derived hybrid cells with dual features of adaptive T and inherent NK cells, offer an artificial cell source for human immunotherapies.

immunology↗