今年1月发表在Cell Reports (IF: 9.995) 的文章，张抒扬老师和卞修武老师分别是第一和第二通讯。
1. Spatial proteome architecture of the resolved human hearts
新冠患者常常伴随着心脏的损伤，见SARS-CoV-2受体ACE2在人类心脏的细胞特异性表达。
Figure S1：新冠患者心脏四个腔组织的HE。可以看到有心肌细胞坏死、血管周淋巴和单核细胞浸润。D图中可以看到毛细血管中有微血栓形成（毛细血管中的均质红染）。
Fig 1a：为了进一步探究SARS-CoV-2感染对心脏的影响，作者对28例HC和17例新冠患者心脏的4个解剖部位(LA, LV, RA, and RV)进行了蛋白组学检测，一共监测到4,143个蛋白。
Fig 1b：四个解剖部位的心脏在两组间都有显著差异。（LA, LV, RA, 和 RV的差异性表达基因分别是228, 347, 338, 和 219 个。）
Fig 1c,d：与免疫反应相关的蛋白在4个区域都出现了显著上调，尤其是在RA。
2. Spatial proteome architecture of the resolved human hearts
Fig 2a：作者使用激光捕获显微切割技术分离了COVID-19心脏组织中的炎性微血管和有周围炎症浸润的心肌。
Fig 2b-d：微血管组织一共检测出2376种蛋白，炎症浸润心肌一共检测出2494种蛋白。
Fig 2e：通过不同组样本（4个心腔的微血管样本和4个心腔的心肌样本）的相关性分析，发现聚为两组，心肌一组，微血管一组。（参考基因表达相关性绘图corrplot）
Fig 2f：细胞组分分析提示myocardia相关蛋白主要与myelin sheath, focal adhesion, mitochondria, sarcomere, Z disc, actin cytoskeleton, sarcolemma 和 neuromuscular junction有关；而心脏微血管的蛋白则主要与ECM, actin cytoskeleton, basement membrane (BM) 和 neuron projection相关。此外，微血管中还包括了与myelin sheath, focal adhesion, mitochondria等相关的蛋白。
Fig 2g：随后作者根据蛋白表达的intensity将蛋白分为4类(quantile [Q] 1: 25%, Q2: 50%, Q3: 75%, Q4: 100%)，以确定不同区域中特异性高表达的蛋白。结果显示：
心肌四个区域的高表达蛋白(in Q1 or Q2)包括actins (ACTB and ACTA2), muscle myosins (MYH7, MYL4, and TPM1), troponins (TNNT2), creatine kinase (CKM), myoglobin (MB), 和 atrial natriuretic peptide (NPPA)，基本都属于肌细胞的标志或调节蛋白。而 troponins (TNNC1), desmosome (DSP), titin (TTN), thyroid hormone-binding protein (TTR), and 和 component of a calcium channel (RYR2) 则表达相对较低 (in Q3 or Q4)。
Fig 2h：在血管组织中，四个区域的高表达蛋白 (in Q1 or Q2) 包括spermatogenesis associated (SPATA20), actins (ACTB 和 ACTA2), type I collagens (COL1A2 和 COL1A1), 和 vimentin (VIM)。而 type IV collagens (COL4A1 and COL4A2), proteoglycans (HSPG2 and LUM), elastin and elastin microfibril (ELN and EMILIN3), nidogens (NID1 and NID2), hemidesmosome (PLEC and ITGB4) 和 integrins (ITGA3 and ITGB1) 则表达相对较低 (in Q3 or Q4)。
Intensity的概念参考：蛋白组学定量值的比较说明
A region- resolved proteome profiling system is established, and the specific components of myocardium and microvessel from the four regions are identified, enabling the investigation of the specific functions of human heart in different regions.
3. Region-resolved functional characteristics of human myocardia
Fig 3a：随后通过hierarchical clustering analysis (HCA)和GO分析，作者鉴定出每个解剖学部位特异的蛋白cluster，这些cluster的蛋白具有不同的功能。
不分是正常还是新冠的样本，直接进行蛋白聚类。
Fig 3b：模块1代表LA，其蛋白主要参与protein assembly, response to oxygen levels, microvilli assembly, and transmembrane transport。
模块2代表LV，主要参与small-molecule metabolism, energy metabolism, protein assembly, cytoskeleton, myocardial contraction, myocardial tissue development, and transmembrane transport。
模块3代表RA，主要参与process of small-molecule metabolism, myocardial contraction, macromolecular metabolism, cell junction, circulation, immune effector, and immune responses, including monocyte-mediated immunity, complement activation, humoral immunity, innate immunity, phagocytosis, and wound healing。
模块4代表RV，主要参与energy metabolism, cytoskeleton, myocardial contraction, myocardial tissue development, and circulation process。
Fig 3c：为了验证蛋白组学的结果，作者对一个transferrin受体 (TFRC; 特异性的在RA中高峰度表达)进行了免疫组化染色。结果显示TFRC特异性的在RA_MC的胞浆和胞膜表达。
These results suggest that highly expressed proteins in the myocardia from all four heart regions are involved in small molecule metabolism, energy metabolism, and cytoskeleton. Highly enriched proteins in the myocardia of both ventricles (RV and LV) are involved in additional biological processes such as myocardial tissue development. Highly enriched proteins in the myocardia of RA are involved in the most specific functions.
4. Characteristics of inflammatory myocardia in COVID-19 hearts
主要是差异分析探究两组间的转录改变
Fig 4a：新冠患者的心肌出现了炎症反应相关基因的上调，主要是RA。如急性反应期蛋白(SERPINA3, FN1, and LBP) 和固有免疫反应相关蛋白 (KRT16, KRT1, DEFA1, SAMHD1, TUBB4B, and CLU) 在COVID-19 RA myocardia高表达。心脏也出现了病毒反应性蛋白的上调，以RA最为显著，与RA的高炎性反应相一致。四个部位的心脏代谢通路都出现显著下调。除LV以外，其他区域的心肌收缩功能也下调。神经系统和心脏传导系统也出现了多种蛋白的下调。
Fig 4b：炎症反应相关蛋白出现上调，心脏传导蛋白出现显著下调。（Cardiac conduction abnormalities have been regarded as sequelae of COVID-19; 10% of the patients with COVID-19 presented with heart palpitations, and 16.7% presented with cardiac arrhythmia）
Fig 4c：和a图的意思差不多（a图主要描述不同部位多的差异，c图说的是不同区域也有共性）
Together, these results demonstrate that COVID-19 myocardium injuries commonly affect several biological processes and functions of the heart not only with region specificity but also with commonality.
5. Region-resolved functional characteristics of microvessels in COVID-19 hearts
和Fig3一样，不过换成了血管。
These results suggest that highly expressed proteins in the microvessels from four heart regions are all involved in the function of material metabolism. The highly enriched proteins in RA and RV microvessels are also involved in additional biological processes, such as myocyte growth and energy metabolism. However, most of the biological processes of the highly enriched proteins in the four regions of microvessels are specific, which may be related to the functional differences of microvessels in different regions.
6. Characteristics of inflammatory microvessels in COVID- 19 hearts
和Fig4一样，不过换成了血管。值得注意的是，LA出现了很明显的炎症反应，而且LA的viral process通路相关基因出现了非常显著的上调。提示LA可能是心脏中最早受到病毒感染的部位（肺脏的血液汇聚回LA）
7. Effect of SARS-CoV-2 proteins on microvessel function in different heart regions
Fig 7a：为了探究SARS-CoV-2对微血管的影响，作者对新冠患者和HC的微血管差异表达蛋白和病毒蛋白构建了integrated interactome network。结果显示病毒蛋白对四个解剖学部位心脏的微血管都造成了影响。
8. Inflammation-driven ECM characteristics in different regions of the COVID-19 hearts
SARS-CoV-2 感染可以引起患者心衰。心衰通常是由于ECM沉积引起的心脏纤维化所致。为了进一步探究感染的心肌和微血管如何引起新冠患者心脏四个区域的 ECM 改变，作者使用了 ‘‘Matrisome’’ 数据库去分析SARS-CoV-2感染后的心脏ECM 特征。
Fig S6a：结果显示一共125 ECMs（包括53个 myocardia和72个microvessels）在新冠患者心脏中出现了差异表达。
Fig S6b：多种ECM相关蛋白在微血管组织中出现更显著的上调，尤其是LA和LV。在心肌则出现下调，提示心肌受损。
These results suggest that the dysregulation of ECM may also be an important reason for the inflammation mediated severe injury of COVID-19 hearts.
Fig S6. Dysregulated extracellular matrix of four heart regions of patients
with COVID-19, related to Figure 4 and Figure 6
Next, we used differentially expressed proteins between COVID-19 sera and hearts for correlation analysis. Results showed that several ECM proteins that were identified in the sera proteome profile and can be used to predict the prognosis of COVID-19 pneumonia were consistent with those differently expressed between COVID-19 and normal hearts, including in myocardia and microvessels.
Fig S7. Circos diagram shows the correlation of dysregulated proteins from four regions of myocardia (A) and microvessels (B) between COVID-19 hearts
These results indicate that the differentially expressed ECMs identified in the inflammatory myocardium and microvessels of patients with COVID-19 can also be detected in sera of patients with COVID-19; thus, these ECM proteins could be considered as potential markers for heart injury.
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