Barrier epithelia depend upon resident stem cells for homeostasis, defense, and repair. Epithelial stem cells of small and large intestines (ISCs) respond to their local microenvironments (niches) to fulfill a continuous demand for tissue turnover. The complexity of these niches and underlying communication pathways are not fully known. Here, we report a lymphatic network at the intestinal crypt base that intimately associates with ISCs. Employing in vivo loss of function and lymphatic:organoid cocultures, we show that crypt lymphatics maintain ISCs and inhibit their precocious differentiation. Pairing single-cell and spatial transcriptomics, we apply BayesPrism to deconvolve expression within spatial features and develop SpaceFold to robustly map the niche at high resolution, exposing lymphatics as a central signaling hub for the crypt in general and ISCs in particular. We identify WNT-signaling factors (WNT2, R-SPONDIN-3) and a hitherto unappreciated extracellular matrix protein, REELIN, as crypt lymphatic signals that directly govern the regenerative potential of ISCs.

屏障上皮依赖于常驻干细胞来实现体内平衡、防御和修复。小肠和大肠 (ISC) 的上皮干细胞对其局部微环境（生态位）做出反应，以满足组织更新的持续需求。这些利基市场的复杂性和潜在的沟通途径尚不完全清楚。在这里，我们报告了肠隐窝基底处的淋巴网络与 ISC 密切相关。体内雇用功能丧失和淋巴：类器官共培养，我们发现隐窝淋巴管维持 ISC 并抑制其早熟分化。将单细胞和空间转录组学配对，我们应用 BayesPrism 来对空间特征内的表达进行去卷积，并开发 SpaceFold 来以高分辨率稳健地绘制生态位图，将淋巴管暴露为一般隐窝，特别是 ISC 的中央信号中枢。我们确定了 WNT 信号因子（WNT2、R-SPONDIN-3）和迄今为止未被重视的细胞外基质蛋白 REELIN，作为直接控制 ISC 再生潜力的隐窝淋巴信号。