The intestine plays an important role in nutrient digestion and absorption, microbe defense, and hormone secretion. Although major cell types have been identified in the mouse intestinal epithelium, cell type–specific markers and functional assignments are largely unavailable for human intestine. Here, our single-cell RNA-seq analyses of 14,537 epithelial cells from human ileum, colon, and rectum reveal different nutrient absorption preferences in the small and large intestine, suggest the existence of Paneth-like cells in the large intestine, and identify potential new marker genes for human transient-amplifying cells and goblet cells. We have validated some of these insights by quantitative PCR, immunofluorescence, and functional analyses. Furthermore, we show both common and differential features of the cellular landscapes between the human and mouse ilea. Therefore, our data provide the basis for detailed characterization of human intestine cell constitution and functions, which would be helpful for a better understanding of human intestine disorders, such as inflammatory bowel disease and intestinal tumorigenesis.

Lgr5 ⁺ intestinal stem cells (ISCs) are crucial for the intestinal epithelium renewal and regeneration after injury. However, the mechanism underlying the interplay between Wnt and BMP signaling in this process is not fully understood. Here we report that Bcl11b, which is downregulated by BMP signaling, enhances Wnt signaling to maintain Lgr5 ⁺ ISCs and thus promotes the regeneration of the intestinal epithelium upon injury. Loss of Bcl11b function leads to a significant decrease of Lgr5 ⁺ ISCs in both intestinal crypts and cultured organoids. Mechanistically, BMP suppresses the expression of Bcl11b, which can positively regulate Wnt target genes by inhibiting the function of the Nucleosome Remodeling and Deacetylase (NuRD) complex and facilitating the β-catenin-TCF4 interaction. Bcl11b can also promote intestinal epithelium repair after injuries elicited by both irradiation and DSS-induced inflammation. Furthermore, Bcl11b deletion prevents proliferation and tumorigenesis of colorectal cancer cells. Together, our findings suggest that BMP suppresses Wnt signaling via Bcl11b regulation, thus balancing homeostasis and regeneration in the intestinal epithelium.

BACKGROUND: Chronic thromboembolic pulmonary hypertension is characterized by proximal pulmonary artery obstruction and distal microvasculopathy. However, the mechanisms driving this dual-compartment pulmonary vascular remodeling remain unclear. METHODS: Male Sprague-Dawley rats were injected with gelatin sponge combined with SU5416 as a secondary insult. Hemodynamics, echocardiography, and pulmonary vascular remodeling were evaluated to investigate the development of chronic thromboembolic pulmonary hypertension. Single-cell RNA sequencing of rat lung tissue was conducted to elucidate the molecular mechanisms underlying pulmonary vascular remodeling. The results were validated by immunofluorescence and cell-based experiments. RESULTS: The optimal size range of gelatin sponge for large pulmonary artery obstruction was 710 to 1000 µm, which synergized with a low dose of SU5416 (10 mg/kg) to induce significant increases in right ventricular systolic pressure and right ventricular hypertrophy at 5 weeks. The model exhibited persistent elastic pulmonary artery obstruction and remodeling, along with significant wall thickening and muscularization of pulmonary microvessels. Single-cell transcriptomic analysis revealed a significant reduction in microvascular endothelial cells and an increase in smooth muscle cells in the chronic thromboembolic pulmonary hypertension rats. STAT3 , EGR1 , and HIF1A were identified as key genes driving aberrant smooth muscle cell proliferation. The Sell (encoding L-selectin)- Podxl (encoding PODXL, podocalyxin) ligand-receptor pair was found specifically in diseased rats and mediated immune cell–endothelial cell interactions. L-selectin promoted neutrophil adhesion and dysfunction in pulmonary arterial and microvascular endothelial cells, both of which were reversed by PODXL knockdown. CONCLUSIONS: Our new model recapitulates human chronic thromboembolic pulmonary hypertension pathophysiology and is useful for understanding pulmonary microvasculopathy. Sell-Podxl is a previously unrecognized link between inflammation and vascular remodeling, offering a potential therapeutic target.

BACKGROUND: Pulmonary arterial hypertension (PAH) is a fatal complication of systemic lupus erythematosus (SLE), yet the mechanisms linking autoimmune dysregulation to progressive pulmonary vascular remodeling are poorly defined, leading to inadequate therapies. This study investigated BAFF (B-cell activating factor), a key cytokine in SLE, as a potential driver of SLE-PAH pathogenesis. METHODS: BAFF expression was assessed in patients with SLE-PAH and animal models. Humanized BAFF-transgenic mice were generated to investigate the effects of BAFF elevation on serological, hemodynamic, and histological parameters of SLE and PAH. Single-cell RNA sequencing, flow cytometry, histological analyses, and cell-based experiments were performed to elucidate cellular and molecular mechanisms. The therapeutic efficacy of the BAFF-neutralizing antibody Belimumab was tested in 2 distinct SLE-PAH animal models. RESULTS: BAFF was significantly upregulated in both SLE-PAH patient cohorts and animal models. Humanized BAFF-transgenic mice exhibited systemic B-cell hyperactivation and pulmonary infiltration and spontaneously developed hallmark features of both SLE and PAH. Single-cell transcriptomic analysis of lung tissues revealed that BAFF overexpression drove the increase of a novel, disease-specific S 100a6 ⁺ mature B-cell subset, which orchestrated a pathogenic immune cascade by activating a cytotoxic Gzmk ⁺ CD8 ⁺ T-cell population via MHC-I (major histocompatibility complex class I)-mediated antigen presentation and CD80-CD28 costimulation. This B-T cell crosstalk triggered apoptosis of a susceptible endothelial cell subpopulation through Fas/Fas ligand signaling, ultimately culminating in pulmonary vascular remodeling. The BAFF-neutralizing antibody Belimumab effectively ameliorated both autoimmune and cardiopulmonary manifestations in 2 distinct SLE-PAH animal models, while improving survival. CONCLUSIONS: These findings establish BAFF as a key mediator in SLE-PAH, driving a previously unrecognized pathogenic immune axis connecting dysregulated B cells to T-cell-mediated endothelial injury. BAFF inhibition may represent a therapeutic strategy for SLE-PAH.