Predicting genetic perturbation responses at a single-cell level is central to building models for cell state and disease. However, existing approaches are limited on predicting phenotypic outcomes beyond expression changes and generalizing predictions across genome-scale perturbations in biologically relevant contexts. Here we introduce pertTF, a transformer-based single-cell genetic perturbation model. pertTF was trained from a unique dataset capturing single cell expressions profiles of 30 full gene knockouts across 14 relevant cell types during human pancreatic development and beta-cell differentiation. pertTF outperforms current methods in predicting expression changes of perturbing unseen genes in unseen cellular contexts. In addition, pertTF infers perturbation-induced shifts in cell identity and population composition, an important phenotypic outcome of perturbation in many physiology and disease settings. Through transfer learning, pertTF operates in physiologically relevant systems, including primary human islets, where large-scale perturbation experiments are challenging. The generalizability of pertTF is further demonstrated by in silico pooled and single-cell CRISPR screens, capturing critical regulators of stem cells and early pancreatic cell development. These results establish pertTF as a framework for integrating large-scale single-cell perturbation data with AI models to predict genetic perturbation effects across cellular systems and disease contexts.

Stem cells are critical for the development and maintenance of tissue integrity. An important example is intestinal stem cells (ISCs) that generate all epithelial cell types necessary for formation of the intestinal lining. HAT1, a histone acetyltransferase that acetylates newly synthesized histone H4 molecules on lysine residues 5 and 12 during replication-coupled chromatin assembly, is specifically expressed in intestinal stem and progenitor cells located in intestinal crypts. To determine if HAT1 is important for intestinal stem and progenitor cell function, we generated an inducible deletion of the HAT1 gene in intestinal epithelial cells. Loss of HAT1 resulted in morphological defects in the proximal end of the small intestine. Following loss of HAT1, intestinal crypts became elongated, with an increase in stem and progenitor cell proliferation and an increase in the population of OLFM+ cells. Loss of HAT1 also resulted in alterations in intestinal stem cell differentiation, including an increase in the number of Goblet cells and the mislocalization of Paneth cells into villi. HAT1 is specifically responsible for the acetylation of histone H4 lysine 5 (H4K5ac) in intestinal stem cells. Genome-wide characterization of HAT1-dependent H4K5ac in intestinal crypt cells indicates that the most significant loss of H4K5ac occurs in lamina-associated domains (LADs). Loss of H4K5ac in LADs is accompanied by an increase in histone H3 K9 tri-methylation indicating that HAT1 regulates LAD chromatin structure in intestinal crypt cells. A direct role for HAT1 in intestinal stem cell function was demonstrated using organoids in culture. HAT1 is required for differentiation in organoids and for the maintenance of Lgr5+ stem cells. These results indicate that HAT1 is required for the proper regulation of intestinal stem cell renewal and differentiation.

Maternal obesity is associated with increased risk of sporadic colorectal cancer (CRC) in offspring, suggesting that early-life environmental exposures durably shape disease susceptibility. Intestinal stem cells (ISCs), long-lived drivers of epithelial renewal and tumor initiation, are well poised to mediate this effect; however, how maternal obesity influences ISC programming during development remains poorly understood. Using mouse models of diet-induced obesity, we show that exposure to a maternal high-fat Western diet (mHFD) during pre- and postnatal development stably programs colonic ISCs. Offspring exhibit increased ISC proliferation, enhanced self-renewal, a hypermetabolic state, and altered epithelial lineage composition that persists into adulthood despite dietary normalization. These changes are accompanied by increased tumor burden following loss of Apc heterozygosity. Mechanistically, we identify the pro-inflammatory cytokine IL-17A as a key extrinsic driver and PPARd/a nuclear receptors as intrinsic mediators of the mHFD phenotype, revealing an immune-epithelial axis that programs ISC function during early life. Together, our findings demonstrate that maternal metabolic environments durably enhance stem cell fitness, providing a mechanistic link between developmental exposure and adult disease risk.

To maintain barrier homeostasis, the colonic and intestinal epithelial lining is continually renewed by rapidly proliferating epithelial crypt base columnar (CBC) stem cells that reside at the base of crypts. Using mouse lineage tracing, immunohistochemistry, and single-cell sequencing, we have identified a rare, non-CBC, T-cell factor 4 lineage-negative (Tcf4 Lin-) stem cell population that gives rise to secretory and absorptive precursors. Following endoscopic biopsy-induced injury, Tcf4 Lin- stem cells are recruited to the wound bed and to the site of expanding crypts and function in barrier restoration and wound repair. We show that in a Tcf4-haploinsufficient background, the Tcf4 Lin-, but not the Tcf4 Lin+, cell population represents the cell of origin for colon tumors driven by deletion of Apc. Our results provide a foundation for understanding Apc- allele-specific differences during colon tumorigenesis and identify a new stem-cell population that may prove valuable in the treatment of diseases caused by intestinal barrier homeostasis defects.

Idiopathic pulmonary fibrosis (IPF) is an age-related, progressive, and fatal interstitial lung disease for which effective therapies remain limited. Alveolar type 2 (AT2) epithelial cells serve as facultative stem cells essential for alveolar repair; however, AT2 cell senescence disrupts epithelial regeneration and contributes to fibrotic remodeling in IPF. Syndecan-1 is a transmembrane heparan sulfate proteoglycan predominantly expressed by lung epithelial cells, but its role in AT2 dysfunction during fibrosis is poorly defined. Here, we demonstrate that syndecan-1 is robustly upregulated in AT2 cells in IPF and other fibrotic lung diseases, as well as in murine bleomycin-induced lung fibrosis. Syndecan-1 expression was further enhanced with aging and associated with increased fibrotic burden in aged mice. Using integrated human transcriptomic analyses, mouse genetic models, and epithelial cell-based systems, we show that excess syndecan-1 promotes cell-autonomous epithelial senescence and impairs AT2 progenitor function. Elevated syndecan-1 reduced AT2 renewal capacity, disrupted differentiation, and diminished surfactant protein C level, whereas genetic loss of syndecan-1 attenuated senescence and preserved epithelial function following injury. Together, these findings identify syndecan-1 as a critical epithelial regulator of AT2 senescence and maladaptive repair in pulmonary fibrosis and support targeting syndecan-1-driven epithelial dysfunction as a potential therapeutic strategy.

Diet deeply influences health and disease risk by reshaping cellular metabolism. In the intestine, dietary nutrients directly affect intestinal stem cell (ISC) behavior, yet the regulatory mechanisms linking metabolism to transcriptional control remain poorly defined. Because mitochondria function as central metabolic hubs, we focused on mitochondrial signaling to understand how nutrient utilization governs ISC function. Using the MITO-Tag mouse, we isolated metabolites specifically from ISC mitochondria and found that the sugar-derived metabolite UDP-GlcNAc was reduced in ISCs from mice fed a high-fat diet. Moreover, we identified that reducing O-GlcNAcylation (OGN) rapidly increased stem cell frequency, proliferation, regenerative capacity, and the abundance of PPAR target proteins. Mechanistically, these effects depend on PPAR signaling, as genetic loss of Ppar-d/a blocks the ISC phenotypes induced by reduced OGN. These results reveal an OGN-PPAR signaling axis that translates dietary metabolic cues into transcriptional programs governing fuel utilization and ISC behavior in the intestine. Collectively, our findings highlight that OGN is a previously unrecognized regulator of PPAR signaling in intestinal stem cells.

Single-cell RNA sequencing has transformed our understanding of tissue complexity and heterogeneous cell states, yet provides little information about the subcellular organization of transcriptomes - despite the central role of RNA localization in splicing, translation, and function. Here we introduce single-cell APEX-seq (scAPEX-seq), a proximity labeling-based method for mapping subcellular transcriptomes at single-cell resolution. Improvements in probe design and RNA recovery enable APEX integration with droplet-based RNA-seq to capture endoplasmic reticulum-associated transcripts from thousands of individual cells. Applied to tumor-macrophage co-cultures, ER-targeted scAPEX-seq revealed interaction-dependent cell states and transcriptomic signatures by enriching for cell surface and secretory transcripts that are poorly resolved by conventional scRNA-seq. We further applied scAPEX-seq to short- and long-term co-cultures of HER2+ tumor cells with human chimeric antigen receptor (CAR) T cells, resolving distinct activated CAR T cell states, including populations characterized by upregulated NT5E or CTSW expression. We showed that overexpression of CTSW, a cathepsin protease, in CAR T cells promotes stem-like phenotypes, long-term proliferation, and sustained tumor cell killing. scAPEX-seq provides a powerful and scalable approach for profiling subcellular RNA populations, enabling the discovery of cell-cell interaction regulators missed by conventional approaches.

Keloids and hypertrophic scars are fibroproliferative disorders with high recurrence rates, lacking a definitive treatment standard. This review systematically evaluates current therapies and their effectiveness in treating keloid and hypertrophic scars.

The aim of this study was to compare the immunohistochemical expression of SOX2 and cytokeratins (CKs) 5, 8 and 18 in the lateral periodontal cyst (LPC) and gingival cyst of the adult (GCA) with the more aggressive botryoid odontogenic cyst (BOC), to evaluate diagnostic or prognostic utility.

Articular cartilage injuries present a significant clinical challenge due to the tissue's limited self-repair capacity and the inadequacy of current regenerative strategies. This study aimed to investigate whether bone marrow mesenchymal stem cell-derived extracellular matrix (BM-ECM) enhances cartilage repair and to elucidate the underlying molecular mechanisms involving ubiquitin-specific protease 7 (USP7). Rat BMSCs were isolated and characterized, and decellularized BM-ECM was prepared. Cartilage defects in a rat model were treated with GelMA hydrogel scaffolds loaded with BMSCs and BM-ECM. Histological evaluation demonstrated that the BM-ECM composite scaffold significantly improved cartilage repair. Further mechanistic investigation revealed that BM-ECM promoted chondrogenic differentiation of BMSCs, an effect closely associated with USP7 activity. Overexpression of USP7 enhanced ECM synthesis and chondrogenesis, whereas USP7 knockdown diminished these processes and abolished the prochondrogenic benefits of BM-ECM. In conclusion, BM-ECM facilitates cartilage regeneration, with USP7 playing a central role in mediating its chondro-supportive effects, offering a promising therapeutic target for cartilage repair.

Huntington's disease (HD) is characterized by progressive striatal degeneration associated with mutant huntingtin (mHTT)-related proteostatic disruption and chronic neuroinflammation. Although mHTT-lowering approaches hold therapeutic promise, their capacity to restore the degenerating neural microenvironment remains limited. Here, we evaluated the therapeutic potential of human induced pluripotent stem cell (iPSC)-derived neural precursor cells (s513-NPCs) in two complementary HD models, the acute R6/2 transgenic fragment model and the protracted, full-length YAC128 genomic model. Intrastriatal transplantation of s513-NPCs resulted in sustained functional improvement, including stabilization of motor coordination and attenuation of neuromuscular decline, across both disease contexts. These neuroprotective effects were accompanied by efficient donor cell engraftment and integration within the host striatum. At the molecular level, transplantation was associated with coordinated changes in proteostasis-related pathways, reflected by reduced mHTT aggregate burden and modulation of proteasomal and autophagic markers. In parallel, enhanced local BDNF-TrkB signaling was observed in grafted regions, consistent with improved neuronal support. Notably, transplanted NPCs exhibited context-dependent immunological responses, characterized by attenuation of pro-inflammatory signatures in aggressive disease stages and features of a reparative microenvironment in more protracted settings. Collectively, these findings demonstrate that iPSC-derived neural precursor transplantation confers robust neuroprotective effects in HD models, supporting its potential as a stem cell-based strategy to mitigate striatal pathology and functional decline.

This review systematically evaluates the interactions between traditional Chinese medicine (TCM) polysaccharides and the blood-brain barrier (BBB), positioning BBB modulation as a central mechanistic framework to explain their neurotherapeutic potential. Unlike disease-specific prior works, it identifies BBB dysfunction as a unifying pathological bottleneck in central nervous system (CNS) disorders, offering a cohesive lens to interpret these polysaccharides' multitarget actions. We synthesize evidence on their structural characteristics and bioactivities, focusing on the regulation of tight junction (TJ) proteins, NVU homeostasis, and key signaling pathways. This synthesis elucidates their potential mechanisms in maintaining NVU homeostasis and modulating BBB permeability. Critical limitations are highlighted, including overreliance on preclinical models and the lack of direct evidence for BBB translocation and causal mechanisms. The review also discusses the therapeutic potential of TCM polysaccharides in preclinical models of stroke, AD, and PD, while evaluating current advances in extraction and purification technologies, pharmacokinetic characterization, and emerging nano-delivery strategies. Despite the promising findings, significant challenges persist-including structural heterogeneity, batch-to-batch variability, insufficient pharmacokinetic data, and substantial translational barriers. Collectively, this review aims to provide a systematic and forward-looking reference framework for future mechanistic investigations and translational development of TCM polysaccharides in BBB-related neurological disorders.

Aplastic anemia (AA) is a debilitating disorder marked by bone marrow failure, frequently associated with dysregulated T cell activity. The present study explored the therapeutic potential of anti-CD3 antibody-modified calcium silicate nanoparticles loaded with novel   7H-pyrrolo[2,3-d]pyrimidine derivatives (antiCD3-pCaSiNP@NPDP) for AA treatment. Whole-transcriptome sequencing and bioinformatics analysis identified interleukin-2-inducible T-cell kinase (ITK) as a critical regulator of T cell function in AA. In vitro experiments demonstrated that ITK enhances T cell proliferation and promotes differentiation toward inflammatory subsets, thereby contributing to disease progression. The newly developed NPDP derivatives effectively inhibited ITK activity. Targeted delivery of NPDP via antiCD3-pCaSiNP nanoparticles selectively suppressed ITK expression in T cells, resulting in reduced inflammatory T cell proliferation and increased regulatory T cell populations. In an AA mouse model, administration of antiCD3-pCaSiNP@NPDP nanoparticles markedly improved hematopoietic recovery and immune balance. The findings indicate that nanoparticle-mediated ITK inhibition represents a promising therapeutic strategy for restoring immune and bone marrow function in AA.

Integrins are transmembrane glycoproteins that act as essential adhesion receptors, allowing cells to communicate with the extracellular matrix (ECM). This interaction not only helps cells regulate adhesion, but also transmits signals that guide a variety of cellular processes. Once bound to the ECM, integrins play an important role in the cell differentiation, migration, proliferation, and survival, thereby maintaining tissue homeostasis. However, when integrin signaling becomes dysregulated, it is often associated with tumor development and progression. Abnormal integrin activity promotes uncontrolled cell growth, resistance to apoptosis, and the promotion of angiogenesis in tumors. They also provide resistance to therapies by disrupting growth suppressors. Due to their documented role in the process of tumorigenesis, integrins have become an interesting target for anticancer therapy. In this review, we discuss the function and structure of integrins, emphasizing how altered signaling in integrins consequently leads to cancer formation, progression, and metastasis. In addition, we review existing therapies that target integrins, discuss their limitations, and look at the future of integrin-based therapies. This review deepens our understanding of integrins, their role in cancer, and their possible role as a cancer biomarker.

Restoration of vascular structure and function is pivotal for neurological recovery following spinal cord injury (SCI), yet repairing the blood-spinal cord barrier (BSCB) remains a significant challenge. In this study, we demonstrate that exosomes (Exos) derived from endothelialized human umbilical cord mesenchymal stem cells (E‑UCMSCs) markedly enhance angiogenesis, improve vascular function, and promote neurological recovery. Human umbilical cord mesenchymal stem cells were induced to differentiate into endothelial‑like cells, and RNA‑sequencing revealed upregulation of genes associated with angiogenesis and vascular barrier integrity, alongside activation of relevant signaling pathways. In a co‑culture system, E‑UCMSC‑derived Exos significantly enhanced bEnd.3 cell migration and BSCB stability. To enable targeted delivery to neovasculature, Exos were engineered with RGD peptides (RGD‑E‑UCMSC‑Exos) via lentiviral modification. In vivo, these modified Exos preferentially localized to neovascular endothelial cells, promoted angiogenesis, reinforced BSCB integrity, and improved neurological outcomes in SCI mouse models. Proteomic profiling identified key angiogenic and barrier‑stabilizing factors carried by RGD‑E‑UCMSC‑Exos, including MMP2, FLT1, TIMP1, GAS6, CTHRC1, and NEO1, which likely mediate their therapeutic effects. Collectively, these findings provide novel mechanistic insights and establish a novel strong preclinical foundation for exosome‑based therapies in SCI.

Stem cell therapy has been utilized in the treatment of periodontitis. Recent studies have demonstrated that treatment with apoptotic mesenchymal stem cells (MSCs) exhibits immunomodulatory effects comparable to those of living MSCs. However, the effect of type 2 diabetes mellitus (T2DM) on the efficacy of apoptotic MSCs therapy for periodontitis remains poorly understood. In this study, a ligature-induced experimental periodontitis model was established in wild-type (WT) and db/db mice, followed by the injection of exogenous apoptotic periodontal ligament stem cells (PDLSCs). The results revealed suboptimal therapeutic outcomes with apoptotic PDLSCs in db/db mice. It was observed that the progression of periodontitis was associated with a reduction in the expression of developmental endothelial locus-1 (DEL-1) in experimental periodontitis model. Additionally, the expression of DEL-1 was partially restored during the resolution phase of inflammation. T2DM mice exhibited exacerbated alveolar bone loss and suppressed regeneration, accompanied by the inhibition of DEL-1 expression. In co-culture experiments, impaired macrophage efferocytosis of apoptotic PDLSCs was ameliorated by the addition of exogenous DEL-1 under lipopolysaccharide and high glucose conditions. Moreover, the co-administration of exogenous DEL-1 enhanced the therapeutic efficacy of exogenous apoptotic PDLSCs in db/db mice. In conclusion, diminished DEL-1 expression and impaired macrophage efferocytosis constrain the therapeutic potential of exogenous apoptotic PDLSCs in periodontitis with T2DM. The diminished therapeutic efficacy may be alleviated by the combination of exogenous DEL-1 and apoptotic PDLSCs, offering novel insights into potential therapeutic strategies for periodontitis with T2DM.

Mesenchymal stromal cells (MSCs) of various origins promote regeneration through paracrine signaling, immune modulation, and angiogenesis support. Premature ovarian failure (POF) is an excellent model to study coordinated ovarian and uterine repair, as cytotoxic injury simultaneously depletes ovarian follicles and impairs uterine receptors, resulting in infertility.