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Bone marrow fibrosis is the most extensive matrix remodeling of the microenvironment and can include de novo formation of bone (osteosclerosis). Spatiotemporal information on the contribution of distinct bone marrow niche populations to this process is incomplete. We demonstrate that fibrosis‐inducing hematopoietic cells cause profibrotic reprogramming of perivascular CXCL12‐abundant reticular (CAR) progenitor cells,resulting in loss of their hematopoiesis‐support and upregulation of osteogenic and pro‐apoptotic programs. In turn,peritrabecular osteolineage cells (OLCs) are activated in an injury‐specific,Wnt‐dependent manner,comparable to skeletal repair. OLCs fuel bone marrow fibrosis through their expansion and skewed differentiation,resulting in osteosclerosis and expansion of Ly6a+ fibroblasts. NCAM1 expression marks peritrabecular OLCs and their expansion into the central marrow is specific for fibrosis in mice and patients. Peritrabecular stromal β‐catenin expression is linked to fibrosis in patients,and inhibition of Wnt signaling reduces bone marrow fibrosis and osteosclerosis,possibly being a clinically relevant therapeutic target. View Publication

Three-dimensional (3D) culture systems that recapitulate the tumor microenvironment are essential for studying cancer cell behavior,drug response,and cell–matrix interactions. Here,we present a detailed protocol for generating 3D spheroid cultures from murine breast cancer cells using methacrylated gelatin (GelMA)-based bioink and a CELLINK BioX bioprinter. This method enables precise deposition of spheroid-laden GelMA droplets into low-attachment plates,facilitating high-throughput and reproducible 3D culture formation. The protocol includes steps for spheroid formation,GelMA preparation,bioprinting,and post-printing analysis using a customized CellProfiler pipeline. The analysis pipeline takes advantage of the functionality of CellProfiler and ImageJ software (version 2.14.0) packages to create a versatile and accessible analysis tool. This approach provides a robust and adaptable platform for in vitro cancer research,including studies of metastasis,drug resistance,cancer cell lipid metabolism,and TME-associated hypoxia. View Publication

Epstein-Barr virus (EBV) causes infectious mononucleosis and contributes to neurodegenerative disorders and malignancies,particularly in immune-compromised hosts. Transplant patients face high risk of post-transplant lymphoproliferative disease,a life-threatening EBV-driven lymphoma. There are no EBV-specific vaccines or treatments; however,neutralizing antibodies against EBV glycoproteins may offer utility as therapeutic agents. EBV entry into B cells involves gp350,which binds complement receptors,and gp42,which engages HLA class II to trigger fusion. Most existing monoclonal antibodies (mAbs) against these antigens are non-human,limiting clinical use. Using a transgenic mouse model,we generate two gp350 and eight gp42 genetically human neutralizing mAbs that block receptor binding. Structural analyses reveal extended sites of vulnerability relevant to vaccine development. Delivery of a gp42 mAb protects humanized mice from EBV challenge,while a gp350 mAb provides partial protection. These mAbs highlight the utility of transgenic mice to produce therapeutic mAbs for preventing EBV-driven disease. Graphical abstract Highlights•Transgenic mice were used to make genetically human EBV mAbs against gp350 and gp42•mAbs potently neutralize EBV infection by blocking receptor-ligand interactions•mAbs prevent EBV infection following EBV challenge in humanized mice Epstein-Barr virus (EBV) can cause serious illness,including cancer,especially in immunocompromised patients. There are no EBV-specific treatments. Chhan et al. leverage a transgenic mouse model to develop human monoclonal antibodies that block EBV entry. These antibodies prevent EBV infection in a murine challenge model offering hope for new therapies. View Publication

Directed differentiation of human induced pluripotent stem cells (iPSCs) into anterior foregut endoderm (AFE) and lung progenitors (LPs) has wide-ranging implications for lung developmental biology,disease modeling,and regenerative medicine. We expand on a previously developed mathematical modeling framework and apply it to the directed differentiation of AFE into LPs. A model-based approach guides experimental design,followed by a multistage model inference process: maximum likelihood estimation based on in vitro data and identifiability analyses to eliminate unidentifiable candidates,thereby guiding model selection. To the authors’ knowledge,this is the first mathematical model of the population dynamics of directed differentiation of AFE into LPs. The model suggests that the overall dynamics are primarily driven by AFE proliferation and differentiation into LPs. In silico experiments predict that daily media change nearly doubles LP yields compared to cultures without media replenishment. Moreover,the model suggests that higher split ratios on day 10 enhance yield per input cell,a measure of differentiation efficiency,by 26%. This work provides a blueprint for refining iPSC-based lung lineage differentiation protocols by combining empirical data and mathematical modeling. View Publication

Cell surface proteins offer significant cancer therapeutic potential attributable to their accessible membrane localization and central roles in cellular signaling,yet their promise remains largely untapped due to technical challenges inherent to profiling them. Here,we employ N-glycoproteomics to analyze 85 patient-derived xenografts (PDXs),constructing Glyco PDXplorer—an in vivo pan-cancer atlas of cancer-derived surface proteins. We develop a target discovery pipeline to prioritize proteins with favorable expression profiles for immunotherapeutic targeting and validate FAT2 as a squamous-cancer-enriched surface protein minimally detected in normal tissue. Functional studies reveal that FAT2 is essential for head and neck squamous cancer (HNSC) cell growth and adhesion through regulation of surface architecture and integrin-PI3K signaling. Chimeric antigen receptor (CAR)-T cells targeting FAT2 demonstrate anti-tumor activity. This work lays the foundation for developing FAT2-targeted therapies and represents a pivotal platform to inform therapeutic target discovery across cancers. Graphical abstract Highlights•Pan-cancer landscape of cancer-derived cell surface proteins detected in vivo•Discovery pipeline to prioritize proteins as immunotherapy target candidates•Validation of FAT2 as an SCC surface protein with minimal normal tissue expression•FAT2 CAR-T cells demonstrate anti-tumor activity in pre-clinical models Govindarajan et al. leverage N-glycoproteomics and PDX models to decode the in vivo cancer cell surfaceome and establish Glyco PDXplorer—a target discovery platform. The identification and validation of FAT2 as a previously undescribed,actionable antigen demonstrates the utility of Glyco PDXplorer for uncovering therapeutic vulnerabilities. View Publication

Baculovirus,an insect virus commonly used for recombinant protein expression in insect cells and gene delivery in mammalian systems,is often generated through bacmid-based engineering. To enable flexible and programmable bacmid engineering,we developed SHOT 2.0,an optimized CRISPR-associated transposon platform that mediates RNA-guided and customized bacmid editing in Escherichia coli. The edited bacmid can be transfected into insect cells to produce recombinant baculoviruses. SHOT 2.0 supported site-specific integration of large DNA cargos (at least 14 kb) into defined loci such as v-cath and ODVe56,with integration at ODVe56 markedly improving transgene stability during serial virus passaging. The system is fully compatible with the Bac-to-Bac® workflow,enabling dual-gene insertion into the bacmid and derived baculovirus. Leveraging this platform,we constructed an all-in-one baculovirus encoding the PE5max prime editor. This vector-mediated prime editing achieves efficiencies up to 85.6% in HEK293T cells and achieves robust prime editing in hard-to-transfect cell types,including iPSCs and liver cancer cells,with efficiencies up to 37.1%. These results demonstrate that SHOT 2.0 substantially expands the baculovirus engineering toolbox,providing a flexible platform for genome editing and future gene delivery. View Publication