hello盼忌，大家好积糯，今天我們來分享一個新的掂墓、很有意思的內(nèi)容，細胞單元看成，在我之前分享的文章里面10X空間轉(zhuǎn)錄組的位點注釋和臨近通訊君编，提到過這個內(nèi)容，但是不夠系統(tǒng)川慌，今天我們就來詳細分析一下什么是細胞單元吃嘿。
先來看一下概念，細胞單元：by employing integrative analysis of single-cell and spatial transcriptomics, we identified novel HSC/MPP（造血干細胞和多能祖細胞） ‘pocket-like’ units（細胞單元） (HSC PLUS), composed of niche cells (hepatoblasts, stromal cells, endothelial cells, and macrophages) and enriched with growth factors.也就是說梦重，一個細胞單元的組成包括目標細胞類型和圍繞在其周圍的細胞類型兑燥，這幾種細胞類型關(guān)系密切，相互合作行使一種重要的生物學功能琴拧，這為我們空間轉(zhuǎn)錄組的發(fā)展提供了很好的機會和借鑒降瞳，畢竟，研究組織并不能割裂的研究蚓胸，而是要放在一個聯(lián)合的背景下進行深入分析挣饥。
當然，細胞單元的部分有些占據(jù)了很大的部分赢织，有的占有的部分比較小亮靴，Unexpectedly, macrophages showed an 11-fold enrichment in the HSC PLUS.這些在細胞單元顯著富集的細胞類型，行使更加重要的生物學功能于置，我們來詳細看看整個的分析過程茧吊。
首先是單細胞的部分，當然八毯，做了很好的個性化分析搓侄，包括細胞注釋和通訊分析，這部分內(nèi)容是基礎话速，需要很大的精力讶踪，基礎的問題也是最根本的問題。
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其中單細胞分析的部分這里有一個部分是對HSC/MPP亞群的一個分析泊交，很值得注意乳讥，需要重點分析一下：
CD93-enriched HSCs/MPPs exhibit enhanced stem cell properties
To further dissect the transcriptome features of HSCs/MPPs, we focused on HSC/MPP 1–3 clusters and explored the underlying differences among them.GO and DEG analyses indicated enrichment of hematopoietic regulation and differentiation, active translation processes, and cell cycle regulation in HSC/MPP 1–3, respectively。（亞群的富集分析）
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In HSC/MPP1, the expression of Mycn, Mecom, and Hlf was enriched; in HSC/MPP2, metabolic and lineage-specific genes were highly expressed; and in HSC/MPP3, cell cycle-related genes showed highly enriched expression（三個群體現(xiàn)了不同的基因表達模式）廓俭。To further evaluate the stem cell properties of heterogeneous HSCs/MPPs, we calculated hscScore(這個地方我們隨后分享) as previously reported,and found that the highest score was seen in HSC/MPP1; meanwhile, trajectory analysis among HSC/MPP subsets and downstream myeloid and lymphoid progenitors revealed that HSC/MPP1 occupied the top of hematopoietic hierarchy. Overall, these results indicate that HSC/MPP1 exhibits the most robust stem cell transcriptome feature, compared to HSC/MPP2–3.（這里大家注意對一種細胞類型干性的研究云石，首先是hscScore，分數(shù)越高研乒，干性越高汹忠，軌跡分析發(fā)現(xiàn)這種細胞類型位于發(fā)育的起點，這些手段都是來輔助證明這種細胞類型的干性很強，值得大家借鑒）宽菜。
我們來科普一下谣膳，什么是hscScore，有機會我們詳細分享一下這個算法铅乡，簡單來講继谚，就是根據(jù)現(xiàn)有的數(shù)據(jù)進行建模，建立一個細胞干性和表達譜的一個數(shù)學模型隆判，以此來預測細胞類型的干性分數(shù)犬庇，這個大家先了解即可。
當然了侨嘀，其中的第一個群高表達CD93臭挽，Given that Cd93 (also known as AA4.1) has been shown to be expressed in hematopoietic progenitors。we asked whether the combination of CD93 and other HSC/MPP markers, such as Lineage–Sca-1+c-Kit+ (LSK), Flt3–LSK, and CD150+CD48–LSK (SLAM-LSK),29,30 can further purify HSCs/MPPs with robust stem cell properties.（當然咬腕，研究也證明欢峰，CD93確實可以提高該細胞類型的干性）。當然之后作者也做了一些其他的驗證涨共，Taken together, CD93 is not only a surface marker for characterizing HSC/MPP heterogeneity, but also functionally required for FL HSC/MPP development.（這個地方是大家最應該關(guān)注的地方）纽帖。
接下來用單細胞數(shù)據(jù)進行細胞通訊分析（CellPhoneDB）,當然，單細胞的通訊分析確實識別了很多重要的細胞交流举反。
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單細胞分析識別的信號交流在空間上是如何分布的懊直？接下來就是單細胞空間的聯(lián)合分析，這部分之前就分享過了火鼻，這里回顧一下室囊。
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接下來我們的重點，Identification of expansion units of HSCs/MPPs（識別細胞單元）
確定細胞間相互作用的架構(gòu)基礎魁索，三種spot的定義融撞，點內(nèi)，點間和其他粗蔚。
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然后對目標細胞類型的三種spot進行細胞類型的富集分析尝偎，發(fā)現(xiàn)點內(nèi)得分最高的 EC 接近 HSC/MPP，hepatoblast and stromal cell with the highest scores respectively for inter-spots and other distant spots were less close to HSCs/MPPs;（方法確實很贊鹏控，很有創(chuàng)新性）致扯，unexpectedly, macrophage with higher scores for intra- and inter-spots than that for other distant spots was considered as a novel niche component spatially close to HSCs/MPPs（巨噬細胞在點內(nèi)和點間都顯示出富集效果），
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To quantitatively compare the interaction between HSCs/MPPs and different niche cells, we defined an enrichment fold based on the ratio of the enrichment score median for each spot type to the enrichment score median for all spots（富集倍數(shù)的定義）当辐，Consequently, we found that macrophage showed a 11.52-fold enrichment in the intra-spots and a 1.31-fold in the inter-spots, EC showed a 1.62-fold enrichment in the intra-spots, while hepatoblast and stromal cell showed less enrichment in the intra-spots（結(jié)果確實顯現(xiàn)了富集效果抖僵，不是隨機出現(xiàn)的）。
Furthermore, to validate the spatial relationship at nearly single-cell resolution, we analyzed the mouse E13.5 FL ST data based on Stereo-seq（這個技術(shù)大家可以關(guān)注一下瀑构，能實現(xiàn)空間的亞細胞精度）, which is a sequencing-based spatially resolved transcriptomic technology with subcellular resolution.As a result, we found that macrophages showed a high enrichment both in intra-spotsStereo-seq and interspotsStereo- seq(多種技術(shù)證明了點內(nèi)和點間的細胞類型富集效果).Finally, the consistent result was validated by CSOmap(這個是張澤民團隊開發(fā)的軟件裆针，依據(jù)單細胞數(shù)據(jù)推斷細胞之間的空間位置，感興趣大家可以看一看), an analytic method to reconstruct the cell spatial organization de novo based on scRNA-seq data寺晌。Taken together, the results from three analytic methods of spatial information support that macrophage serve as an important niche cell with the closest relationship with HSCs/MPPs.（說白了世吨，幾種細胞類型在空間上處于顯著的臨近狀態(tài)）。
At molecular level, we examined the spatial expression of interactive signals predicted by CellPhoneDB analysis, and found that genes encoding ligands, such as MDK and PTN, were highly expressed in niche cells of intra-spots and inter-spots（單細胞識別的顯著配受體在空間上也體現(xiàn)出了很強的共定位現(xiàn)象）呻征。
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and genes related to receptors, such as LRP1 and PTPRS, were enriched in HSCs/MPPs-localized spots.這些結(jié)果表明空間鄰近性促進了功能上支持 HSC/MPP 擴展的信號交互耘婚。 鑒于intra-spots和inter-spots的特點是細胞之間的空間接近性和豐富的交互信號，我們將它們定義為擴展單元陆赋，其中HSCs/MPPs位于斑點的核心并與周圍的小生境細胞斑點相互作用沐祷。 ，我們證明 FL HSCs/MPPs 在許多單位中擴展攒岛，其中巨噬細胞和幾種生長因子赖临，包括 MDK 和 PTN，高度富集灾锯。
怎么樣兢榨，這樣的細胞單元分析，是不是打開了我們的思路呢顺饮？吵聪？后續(xù)作者還做了熒光驗證，證實這個結(jié)果兼雄。
生活很好吟逝，有你更好
