Biology subjects

Yan, F.

Publications and source records attributed to Yan, F..

At least 19 recordsLinked to original sources

bioRxiv2026

MINT infers the latent single-cell spatial transcriptome from paired histology

Sequencing-based spatial transcriptomics captures transcriptome-wide molecular information, yet the corresponding cell-resolved tissue map remains incomplete. Histology records dense cellular morphology, tissue architecture and local context. Here, we present MINT (Morphological Integrative Network for Transcriptomics), which combines this latent cellular organisation with sample-specific spatial measurements to infer tissue-wide, cell-resolved transcriptomes without an external single-cell reference. MINT reconstructs expression from sparse Slide-tags profiles across unmatched adjacent sections; its shared nucleus-centred representation also resolves pooled Visium measurements into cell-level profiles. MINT improved Slide-tags alignment and expression recovery under controlled nuclear loss and cross-section perturbation. It also outperformed reference-free Visium disaggregation methods against Xenium ground truth and was validated with Visium HD sequencing. In human lung adenocarcinoma, MINT reconstructed the tumour immune microenvironment cell by cell and resolved tertiary lymphoid structures and their maturity. These results establish paired histology as a quantitative, sample-intrinsic complement to molecularly rich but cellularly incomplete spatial-transcriptomic assays.

bioinformatics↗

bioRxiv2026

TEAD1 signaling modulates adrenal chromaffin maturation

Chromaffin cells synthesize and secrete catecholamines to coordinate systemic stress responses and regulate diverse neuroendocrine and metabolic functions. However, the molecular mechanisms governing chromaffin-cell differentiation and their disruption in pheochromocytoma (PC) remain incompletely understood. Here, through integrated analyses of human developmental atlases, patient-derived transcriptomic datasets, genetically engineered mouse models, and chromaffin organoids, we identify TEAD1 signaling as a critical regulator of chromaffin-cell differentiation and function. In vivo studies using a chromaffin cell-specific TEAD1 overexpression mouse model demonstrated that suppression of TEAD signaling markedly compromises chromaffin-cell differentiation and endocrine function. Additionally, compared with other TEAD family members, TEAD1 transcriptional activities are readily affected by sequences near the binding motif. To identify therapeutically actionable regulators of TEAD1 signaling, we established a TEAD activity-based screening platform and identified the serotonin receptor HTR5A antagonist SB699551 as a potent modulator of chromaffin-cell state. SB699551 suppressed PC-cell proliferation in vivo, and remodeled catecholamines synthesis in primary human PC cells. Additionally, application of SB699551 to human PC tumor revealed a subpopulation of primary chromaffin cells sensitive to this compound. Mechanistically, CXXC5 and L1CAM were identified as downstream SB699551-TEAD1 signaling effectors mediating chromaffin-cell proliferation and differentiation. Overall, we demonstrate that TEAD1 signaling is a fundamental mechanism regulating chromaffin cell differentiation and that modulation of TEAD1 signaling via SB699551 offers a new area of investigation in chromaffin cell biology.

molecular biology↗

bioRxiv2026

Programmed Clonal Expansion Drives an ATM-Dependent Vulnerability Underlying Preferential Lymphocyte Depletion and Myeloid Bias Following DNA Damage

Myeloid bias is a hallmark of aging and genotoxic stress, yet the mechanisms underlying the preferential suppression of lymphopoiesis and the resulting predominance of myeloid cells following DNA damage remain incompletely understood. Here, we systematically characterized the acute hematopoietic response to a clinically relevant 2 Gy dose of ionizing radiation in young adult mice. Forty-eight hours after irradiation, overall bone marrow cellularity was reduced by [~]50-60%, with hematopoietic stem and progenitor cells (HSPCs) and myeloid populations declining proportionally. Strikingly, immature and naive B cells in the bone marrow and developing T cells in the thymus exhibited profound hypersensitivity, declining by [~]90%, thereby recapitulating the preferential vulnerability of lymphocytes to DNA damage. Single-cell RNA sequencing mapped this vulnerability to cells undergoing programmed clonal expansion associated with V(D)J recombination. Specifically, B and T lymphocytes immediately following productive V(D)J recombination at the immunoglobulin heavy-chain (IgH) and T-cell receptor {beta} (TCR{beta}) loci were the most radiosensitive, resulting in the marked depletion of the immediately downstream small pre-B and CD4CD8 double-positive (DP) thymocyte populations. Mechanistically, this stage-specific radiosensitivity was mediated by ATM-dependent DNA damage responses, as Atm deficiency selectively rescued the hypersensitivity of clonally expanding lymphoid progenitors while leaving the global reduction of HSPCs and myeloid cells largely unchanged. Rapidly proliferating S3 erythroblasts also exhibited a similar ATM-dependent hypersensitivity, suggesting that programmed proliferative bursts may represent a general determinant of radiation sensitivity. Together, these findings identify programmed clonal expansion associated with V(D)J recombination as an intrinsic developmental vulnerability that underlies the preferential suppression of lymphopoiesis following DNA damage and provides a mechanistic explanation for the emergence of myeloid bias. Key PointsO_LI2 Gy irradiation preferentially depletes developing mouse B and T cells beyond global hematopoietic loss C_LIO_LIProgrammed clonal expansion drives ATM-dependent DNA damage sensitivity in developing lymphocytes. C_LI

genetics↗

bioRxiv2026

Rabies virus antagonizes interferon signaling by targeting phosphorylated STAT1 tetramers

AO_SCPLOWBSTRACTC_SCPLOWRabies virus phosphoprotein (P protein) antagonizes interferon signalling by selectively targeting activated STAT1 protein, but the structural basis for the selective recognition of activated STAT1 has remained unclear. Here we report cryo-EM structures of tyrosine-phosphorylated STAT1 (pY-STAT1) in complex with the C-terminal domain of P protein (P-CTD). P-CTD engages the pY-STAT1 tetramer through three discrete interfaces, contacting two DNA-binding domains within a pY-mediated STAT1 dimer and the N-terminal domain of a third STAT1 protomer. This binding mode explains how P-CTD selectively recognizes activated STAT1, occludes surfaces required for importin 5 and DNA binding, and stabilizes the compact tetrameric state, thereby restricting the conformational transition required for cooperative DNA binding. Cell-based assays further indicate that distinct P-CTD surfaces differentially contribute to antagonism of type I and type II interferon signalling. Further, by acting as an anchoring molecule, P-CTD also enabled structural elucidation of the complete STAT1 structures in the tetramer. Together, these data reveal critical mechanisms in viral immune evasion and pathogenesis, and fundamental innate immune signaling.

molecular biology↗

bioRxiv2026

CSGDA: A Cell State-Guided Graph Domain Adaptation Network for Single-Cell Drug Response Prediction

Intratumoral heterogeneity drives cancer recurrence and metastasis, yet single-cell drug response prediction faces severe "cross-domain" challenges, such as applying in vitro models to in vivo tissues or inferring metastatic resistance from primary tumors. These scenarios trigger distribution shifts arising from heterogeneous sequencing platforms, distinct tissue microenvironments, and metastatic evolution--problems rarely addressed by existing methods. We introduce CSGDA, a cell state-guided graph domain adaptation framework designed to predict drug responses across these biological heterogeneities. CSGDA incorporates biological priors to map gene expression into functional cell states, guiding a structure learning module to construct robust cell topology. To conquer distribution shifts, the model employs graph domain adaptation combined with a novel overlap penalty mechanism. Extensive benchmarks on five scRNA-seq datasets demonstrate that CSGDA outperforms state-of-the-art methods, achieving an average gain of [~]6% in ACC and AUPR. Beyond prediction accuracy, we employed integrated gradients to effectively pinpoint key genes involved in drug resistance within a challenging cross-metastasis cisplatin dataset. These findings underscore CSGDAs superior performance in single-cell drug response prediction and its potential in resolving single-cell heterogeneity, paving the way for precision medicine.

bioinformatics↗

bioRxiv2026

Azacitidine Response in Myelodysplastic Syndromes is Marked by NK-like CD8 T-Cell Expansion and CXCL12+ Reticular Cell Remodeling

Myelodysplastic syndromes (MDS) are driven by somatic mutations in hematopoietic stem and progenitor cells (HSPCs), leading to clonal expansion and ineffective hematopoiesis. Hypomethylating agents (HMAs; azacitidine or decitabine) are the standard of care for higher-risk MDS. However, their effects on the bone marrow (BM) microenvironment, and the extent to which these changes correlate with clinical response, remain poorly understood. We performed longitudinal analyses of BM aspirates, trephine biopsies, and peripheral blood samples from MDS patients treated with azacitidine in a clinical trial (NCT03493646), integrating CyTOF, 5' single-cell RNA and TCR sequencing, plasma proteomics, and multiplex immunofluorescence microscopy to characterize changes associated with azacitidine response. Clinical responders showed expansion of GzmBCD56CD8 T cells together with increased type I and type II interferon signaling within the T-cell compartment. Responders also exhibited marked alterations in circulating platelet- and myeloid-derived factors with the potential to remodel the BM niche. Spatial analyses revealed expansion of "neighborhoods" enriched for CXCL12-abundant reticular cells and CD8 T cells in responders, whereas HSPC-enriched neighborhoods were largely unchanged. In contrast, several HSPC-enriched neighborhoods expanded in non-responders. These microenvironmental changes were accompanied by evidence of enhanced myelopoiesis in clinical responders. Our findings support a model in which azacitidine response extends beyond direct effects on malignant hematopoietic cells to involve coordinated remodeling of the BM microenvironment which may be reinforced by platelet- and myeloid-derived signals that establish a feed-forward circuit promoting productive hematopoiesis. One Sentence SummaryLongitudinal bone marrow profiling reveals stromal and immune correlates of azacitidine response in myelodysplastic syndrome.

cancer biology↗

bioRxiv2026

Aberrant ciliogenesis induced by enhanced BMP signaling causes heterotopic ossification

Bone morphogenetic protein (BMP) signaling is a principal driver of heterotopic ossification (HO), yet how aberrant BMP activity structurally reprograms cellular signaling machinery to develop HO remains unclear. Here, we identify BMP signaling as a direct upstream regulator of ciliogenesis that coordinates a multi-stage, pro-osteochondrogenic signaling relay during HO. Using a conditional gain-of-function BMP mouse model (Acvr1Q207D/+), we demonstrate that enhanced BMP signaling promotes primary cilium biogenesis and axonemal elongation through canonical Smad1/5/9-dependent transcriptional activation of intraflagellar transport (IFT) Ift20, a core component of the IFT machinery. Rather than operating via a singular downstream cascade, these elongated cilia establish a sensitized signaling hub. Genetic disruption of ciliary Hedgehog (Hh) transduction via Smoothened (Smo) deletion reveals that ciliary Hh signaling is dispensable for initial tissue condemnation but required for the subsequent proliferative expansion and maturation of HO. Conversely, complete genetic ablation of the ciliary structure via Ift20 deletion, or early pharmacological inhibition of ciliogenesis, significantly attenuates HO. Notably, this BMP-IFT20-cilia axis is functionally conserved within injury-responsive, PDGFR-positive fibro-adipogenic progenitor (FAP) populations harboring the clinically authentic Acvr1R206H/+ mutation responsible for fibrodysplasia ossificans progressiva (FOP) in mice. Together, these findings reveal that BMP signaling drives HO by structurally expanding the primary cilium, establishing a novel mechanism for HO development. SignificanceGrowth factor signaling instructs cellular behavior during tissue regeneration, but how they regulate cellular organelles to induce pathological fates remains poorly understood. This study reveals that Bone Morphogenetic Protein (BMP) signaling functions as a direct architectural regulator of the primary cilium, a critical cellular antenna. We show that BMP signaling directly transactivates intraflagellar transport machinery to structurally elongate the cilium, creating a sensitized signaling hub that drives heterotopic ossification. Our findings introduce a novel BMP-driven organelle regulation mechanism and establish a targetable cellular vulnerability to mitigate ectopic bone formation.

developmental biology↗

bioRxiv2026

A Novel Hydrogen Polysulfide Donor Alleviates Neuropathic Pain by Enhancing A-Type Potassium Currents via LIMK1-Cofilin Mediated Interaction between Filamin A and Kv4.2

Hydrogen persulfide (H2S2) is an important endogenous signaling molecule, holding significant therapeutic potential across diverse disease models due to its potent antioxidant and redox-regulating properties. Herein, we report the synthesis, characterization, and in vivo evaluation of an esterase responsive H2S2 donor, HPD1. It reduced mechanical and cold allodynia at 14 mg/kg (i.p.) in chronic constriction injury and paclitaxel-induced neuropathic pain models. Moreover, HPD1 exhibited negligible systemic toxicity and behavioral side effects even at 28 mg/kg. Electrophysiological tests showed that HPD1 suppressed PTX-induced hyperexcitability in dorsal root ganglion (DRG) neurons by specifically potentiating A-type potassium currents (IA). Mechanistically, we demonstrate that HPD1 activates LIMK1, which inactivates cofilin and stabilizes F-actin, thereby promoting the interaction between the actin-binding protein Filamin A and Kv4.2. Furthermore, both the HPD1-induced increase in Filamin A-Kv4.2 co-localization and the subsequent restoration of IA density in DRG neurons, as well as the analgesic effect of HPD1 were dampened by pharmacological inhibition of LIMK1 with BMS-5. This work has developed a new generation of H2S2 donors, demonstrated the analgesic efficacy of HPD1, and uncovered the novel LIMK1-cofilin-Filamin A-Kv4.2 dependent mechanism that restores IA, thus providing a reliable therapeutic strategy for neuropathic pain based on H2S2 donors.

pharmacology and toxicology↗

bioRxiv2026

MNT loss in MYC-driven B lymphoma cells enhances apoptosis, inhibits proliferation and increases sensitivity to cancer drugs.

Our previous mouse genetic studies showed that loss of the transcription repressor MNT enhanced apoptosis of premalignant lymphoid cells over-expressing MYC and inhibited lymphoma development. Here, we have explored the consequences of inducing Mnt deletion in fully malignant lymphoma cells. MNT loss provoked apoptosis of p53 wt and, albeit more slowly, p53 mutant E-Myc lymphoma cells, preceded by elevated levels of major BH3-only proteins BIM and PUMA. By inhibiting apoptosis, we showed that MNT loss also impaired cell cycling and increased senescence. E-Myc lymphoma cells depend on the BCL-2 ortholog MCL-1 for survival and expansion and, importantly, MNT loss enhanced their sensitivity to the MCL-1 inhibitor S63845 and to several chemotherapeutic agents. In BCL-2-overexpressing E-Myc lymphoma cells, which model aggressive human Double Hit Lymphomas, MNT loss enhanced sensitivity to the BCL-2 inhibitor ABT-199, even after BAX loss. Furthermore, MNT deletion improved drug responses of two long-established Burkitt Lymphoma cell lines. SIGNIFICANCEThis study establishing the MNT dependency of E-Myc lymphoma cells and demonstrating that MNT loss enhances their sensitivity to apoptosis induced by conventional chemotherapeutics and BH3 mimetic drugs provides strong proof-of-concept for developing MNT inhibitors to improve treatment of MYC-driven blood cancers.

cancer biology↗

bioRxiv2026

SCIMETAR-seq tracks immunophenotype, demethylation, mutations, and transcriptomes in single cells undergoing HMA therapy

5-azacytidine improves haematopoiesis and delays leukaemic progression in myelodysplastic neoplasms, but responses vary and are complicated by clonal mosaicism and heterogenous demethylation. Using a novel single-cell pipeline ("SCIMETAR-seq"), we found 5-azacytidine induced clonally distinct differentiation responses, with nuclear DNA demethylation occurring primarily in cycling progenitors. Despite the absence of significant nuclear DNA demethylation, quiescent stem cells underwent transcriptional remodelling in vivo, accompanied by 5-azacytidine-induced C*G-to-G*C mutations in mitochondria.

cancer biology↗

bioRxiv2026

Single cell multiomics reveal clonal and functional dynamics of MDS stem/progenitor cells during hypomethylating therapy

Progressive somatic mutations in hematopoietic stem cells (HSCs) drive the development of myelodysplastic neoplasms (MDS). Hypomethylating agents such as azacitidine (AZA) can improve blood counts and reduce blasts, although responses are rarely durable. Determinants of AZA response are complex and incompletely understood, although accumulating evidence suggests that epigenetic rewiring of mutated HSCs underlies improved hematopoietic output. Using single cell multiomics on longitudinal bone marrow samples, we show that AZA responsiveness involves expansion of cells with transcriptomic profiles shared with hematopoietic stem and progenitor cells (HSPCs) from healthy donors. These regenerating cells are depleted of copy number variations and of TP53 mutations. We also identify patient-restricted cell populations, some of which recede through transcriptional restoration or AZA cytotoxicity, and others which expand, regardless of initial clinical response, and dominate at progression. Individual patients carried multiple patient-restricted populations which had unique surface immunophenotypes and were genetically distinct. Strikingly, sorted cells from in vivo progression clones that were AZA-refractive in patients regained AZA-sensitivity when cultured in vitro, suggesting that lack of AZA response at the cellular level can be modulated by cell-extrinsic factors in vivo. Overall, we find that AZA response involves partial hematopoietic regeneration via functional differentiation of mutated, but not cytogenetically abnormal HSPCs, and that persistence of AZA-refractive sub-populations contributes to eventual disease progression.

cancer biology↗

bioRxiv2026

Sex-determination cascade orchestrates male-male pheromone synthesis in the bean bug

Volatile pheromones are vital for insect intraspecific communication, yet the genetic basis of homosexual recognition remains elusive. In the bean bug Riptortus pedestris, we show that two previously identified aggregation pheromone components, (E)-2-hexenyl-(Z)-3-hexenoate (E2HZ3H) and (E)-2-hexenyl-(E)-2-hexenoate (E2HE2H), serve as key chemosensory cues for male-male recognition during mate selection. Their biosynthesis is governed by the sex-determination cascade Rpfmd-Rpdsx. The male-specific isoform Rpdsx_M promotes pheromone production in males and induces ectopic synthesis in females upon knockdown of the feminizing switch gene Rpfmd. Knockdown of Rpdsx_M in males abolishes both compounds, prompting wild-type males to court them as if they were females. Metathoracic gland cells act as the production hub. Behaviourally, E2HZ3H or E2HE2H disrupt mating when applied to females: males avoid such females. E2HZ3H reduces female mobility in the presence of the male-derived primary aggregation pheromone tetradecyl isobutyrate (14:iBu), whereas E2HE2H shows no obvious such effect. These differential effects ensure mating accuracy. The discovery of volatile pheromones functioning in male-male recognition and of their synthesis being governed by the sex-determination cascade updates our understanding of mating accuracy in insect chemical communication.

animal behavior and cognition↗

bioRxiv2026

An agentic framework turns patient-sourced records into a multimodal map of ALS heterogeneity

ALS progression is multidimensional, yet fragmented records and scalar outcomes obscure how patients move through disease states and how those states relate to molecular variation. MEDSTREM converts patient-held medical-record images into standardised longitudinal data, enabling bottom-up cohort construction. Using MEDSTREM-structured records from more than 8,000 AskHelpU participants together with PRO-ACT and Answer ALS, we developed DynaALS, the ALS Disease Dynamics Atlas. DynaALS represents ALS as a dynamic patient-state manifold that captures distinct directions of deterioration and patient movement between them over time. DynaALS retrieved population-referenced future states and decoded them into multidimensional clinical profiles without requiring patient-specific longitudinal histories. Motor-neuron RNA and chromatin profiles linked DynaALS states to developmental and regulatory programs, while neuromuscular-organoid single-cell multi-omics converged on a neural-developmental Netrin-DCC signalling axis across interacting cell types. By coupling MEDSTREM-enabled data construction to dynamic state modelling, DynaALS establishes a transferable patient-state engine for predictive and biologically interpretable disease models.

bioinformatics↗

bioRxiv2025

Robust brain complexity measurement using T2* informed multivariate sample entropy from multi-echo BOLD fMRI

Sample entropy is a useful tool to analyze resting-state fMRI data and evaluate the complexity of neural activity. However, sample entropy computed from conventional BOLD signals is not highly resistant to artifacts. In contrast, T2* may be more sensitive to certain neural-related changes, and directly incorporating T2* information enables the detection of features that are often lost in BOLD-only sample entropy due to noise influences. To further improve the robustness and reliability of complexity estimation, we introduce a multivariate sample entropy approach that incorporates T2* signals derived from multi-echo BOLD signal. We applied this method to compare a cohort of 23 elder adults and 12 younger adults, and observed significant group differences in several brain regions. Notably, the proposed method yielded more pronounced group differences than conventional sample entropy computed without T2* information. Moreover, in regions with reduced neural activity due to ischemia, as well as in ventricular areas, our approach demonstrated superior performance. These results indicate that the proposed method enhances the ability to characterize the complexity of neural activity.

biophysics↗

bioRxiv2025

Aberrant 5-Methylcytosine tRNA Modification Disrupts Proteostasis and Exacerbates Age-Related Osteoporosis

Age-related protein aggregation drives senile osteoporosis. Aberrant tRNA modifications exacerbate the progression, yet mechanisms linking these to bone loss remain unclear. In this study, we identify Nsun2 (m5C methyltransferase) as key regulator: age-dependent Nsun2 downregulation in BMSCs reduces mC levels of tRNAs, destabilizing tRNAs and impairing translation efficiency of specific transcripts. This directly disrupts the protein synthesis of molecular chaperone and pro-osteogenic factors, accelerating misfolded protein aggregates and activating unfolded protein response, inducing BMSCs senescence and impairing osteogenesis. Mice specifically depleted of Nsun2 exhibited reduced bone mass, whereas mice overexpressing Nsun2 alleviated age-associated bone loss. Notably, the exacerbated protein aggregation and bone mass loss in Nsun2-deficient mice were ameliorated following treatment with the molecular chaperone activator-ML346. Remarkably, ML346 administration proved sufficient to reverse age-related functional deficits in aged mice. Overall, our findings demonstrate that aberrant tRNA-m5C modification alters protein synthesis and induces proteostasis collapse, which constitute a novel contributor to the pathogenesis of senile osteoporosis. Additionally, reduction of protein aggregation through the activation of molecular chaperones presents a promising therapeutic strategy for this disease.

cell biology↗

bioRxiv2025

Real-Time Viability Assessment of Ex Vivo Mouse Kidneys for Transplant Applications Using Dynamic Optical Coherence Tomography

Kidney transplantation remains the preferred treatment for patients with end-stage kidney disease. However, the ongoing shortage of donor organs continues to limit the availability of transplant treatments. Existing evaluation methods, such as the kidney donor profile index (KDPI) and pre-transplant donor biopsy (PTDB), have various limitations, including low discriminative power, invasiveness, and sampling errors, which reduce their effectiveness in organ quality assessment and contribute to the risk of unnecessary organ discard. In this study, we explored the dynamic optical coherence tomography (DOCT) as a real-time, non-invasive approach to monitor the viability of ex vivo mouse kidneys during static cold storage over 48 hours. The dynamic metrics logarithmic intensity variance (LIV), early OCT correlation decay speed (OCDSe), and late OCT correlation decay speed (OCDSl) were extracted from OCT signal fluctuations to quantify temporal and spatial tissue activity and deterioration. Our results demonstrate that DOCT provides complementary functional information to morphological assessment offered by conventional OCT imaging, showing potential to improve pre-transplant organ evaluation and clinic decision-making.

bioengineering↗

bioRxiv2025

MF-ProtDisMap: protein real-valued distance prediction with fusion of sequence and coevolutionary features

The precise estimation of protein inter-residue distances is essential for high-accuracy protein structure modeling. Currently, the prediction methods are predominantly based on MSA-derived coevolutionary features or language model-based sequence features. To effectively leverage the strengths of both methods, this study developed MF-ProtDisMap (Multi-Feature Protein Distance Map), an integrative framework that effectively combines both feature types to achieve superior real-valued distance prediction. Briefly, MSA Transformer is employed to extract the coevolutionary features from protein multiple sequence alignments, whereas ESM2 is used to capture long-range interactions and sequence-level features. To reduce the computational cost while maximumly represent fused feature information, we implement group pooling for feature dimensionality reduction and introduce Diff-former--a novel module combining a diffusion model with a triangular attention mechanism to enhance representation learning. MF-ProtDisMap achieved a MAE of 2.20 [A] and an RMSE of 3.40 [A] in the protein real-valued distance prediction task. The predicted distances can be converted into contact results, achieving ROC and PR values of 84.56% and 81.01%, respectively. These results demonstrate that MF-ProtDisMap outperforms state-of-the-art real-valued protein distance methods.

bioinformatics↗

bioRxiv2025

Matrix stiffness-induced IKBKE and MAPK8 signaling drives a phenotypic switch from DCIS to invasive breast cancer

Ductal carcinoma in situ (DCIS) is not life threatening unless it transitions into invasive breast cancer (IBC). However, although breast cancer cell exposure to matrix stiffening in vitro phenotypically mimics the DCIS to IBC switch, the molecular changes driving this switch remains unclear. Here, breast cancer cell kinome activity profiling suggested matrix stiffness-upregulation of 53 kinases, among which 16 kinases were also regulated by integrin {beta}1. Functional validation identified matrix stiffness-activation of inhibitor of nuclear factor kappa-B kinase subunit epsilon (IKBKE) and mitogen-activated protein kinase 8 (MAPK8) signaling as critical for the stiffness-driven IBC phenotype, including for cell proliferation. The IKBKE-inhibitor Amlexanox, clinically utilized for aphthous ulcers, as well as the MAPK8 inhibitor JNK-IN-8, reinstalled the DCIS-like phenotype of breast cancer cells on high matrix stiffness. This suggests that IKBKE and/or MAPK8 inhibitors could enhance the arsenal of treatments to prevent or treat breast cancer.

cancer biology↗