{"id":39171,"date":"2025-03-04T00:01:45","date_gmt":"2025-03-03T16:01:45","guid":{"rendered":"https:\/\/17aitech.com\/?p=39171"},"modified":"2025-03-04T00:01:45","modified_gmt":"2025-03-03T16:01:45","slug":"%e7%aa%81%e7%a0%b4%e6%80%a7%e8%bf%9b%e5%b1%95%ef%bc%81%e6%b5%99%e5%a4%a7scniche%e6%a1%86%e6%9e%b6%e7%b2%be%e5%87%86%e8%af%86%e5%88%ab%e7%bb%86%e8%83%9e%e7%94%9f%e6%80%81%e4%bd%8d%ef%bc%8c%e5%8a%a9","status":"publish","type":"post","link":"https:\/\/17aitech.com\/?p=39171","title":{"rendered":"\u7a81\u7834\u6027\u8fdb\u5c55\uff01\u6d59\u5927scNiche\u6846\u67b6\u7cbe\u51c6\u8bc6\u522b\u7ec6\u80de\u751f\u6001\u4f4d\uff0c\u52a9\u529b\u7cbe\u51c6\u533b\u7597"},"content":{"rendered":"

\u6587\u7ae0\u6765\u6e90\u4e8e\u4e92\u8054\u7f51:\u7a81\u7834\u6027\u8fdb\u5c55\uff01\u6d59\u5927scNiche\u6846\u67b6\u7cbe\u51c6\u8bc6\u522b\u7ec6\u80de\u751f\u6001\u4f4d\uff0c\u52a9\u529b\u7cbe\u51c6\u533b\u7597<\/a><\/p>\n

<\/a><\/section>\n

\u7f16\u8f91 | 2049<\/p>\n

\u968f\u7740\u5355\u7ec6\u80de\u7a7a\u95f4\u7ec4\u5b66\u6280\u672f\u7684\u5feb\u901f\u53d1\u5c55\uff0c\u79d1\u7814\u4eba\u5458\u53ef\u4ee5\u5728\u5355\u7ec6\u80de\u5206\u8fa8\u7387\u6c34\u5e73\u4e0a\u7cfb\u7edf\u63a2\u7d22\u7ec4\u7ec7\u4e2d\u7ec6\u80de\u72b6\u6001\u3001\u529f\u80fd\u548c\u76f8\u4e92\u4f5c\u7528\u3002<\/p>\n

\u7136\u800c\uff0c\u5982\u4f55\u4ece\u8fd9\u4e9b\u6d77\u91cf\u7684\u7a7a\u95f4\u7ec4\u5b66\u6570\u636e\u4e2d\u7cbe\u786e\u8bc6\u522b\u548c\u8868\u5f81\u7ec6\u80de\u751f\u6001\u4f4d\uff08cell niche\uff09\u4ecd\u662f\u4e00\u4e2a\u91cd\u5927\u6311\u6218\u3002<\/p>\n

\u8fd1\u65e5\uff0c\u6d59\u6c5f\u5927\u5b66\u836f\u5b66\u9662\u56e2\u961f\u5f00\u53d1\u4e86\u4e00\u4e2a\u540d\u4e3a scNiche \u7684\u8ba1\u7b97\u6846\u67b6\uff0c\u53ef\u4ee5\u4ece\u5355\u7ec6\u80de\u5206\u8fa8\u7387\u7684\u7a7a\u95f4\u7ec4\u5b66\u6570\u636e\u4e2d\u6709\u6548\u8bc6\u522b\u548c\u8868\u5f81\u7ec6\u80de\u751f\u6001\u4f4d\u3002<\/p>\n

\u8be5\u7814\u7a76\u4ee5\u300cIdentification and characterization of cell niches in tissue from spatial omics data at single-cell resolution<\/em>\u300d\u4e3a\u9898\uff0c\u53d1\u8868\u4e8e 2025 \u5e74 2 \u6708 16 \u65e5\u7684\u300aNature Communications<\/em>\u300b\u3002<\/p>\n

<\/a><\/section>\n
\u8bba\u6587\u94fe\u63a5\uff1ahttps:\/\/www.nature.com\/articles\/s41467-025-57029-9<\/em><\/section>\n
\u4ee3\u7801\u5730\u5740\uff1ahttps:\/\/github.com\/ZJUFanLab\/scNiche<\/em><\/section>\n

\u7814\u7a76\u80cc\u666f<\/strong><\/p>\n

\u5f53\u524d\u7a7a\u95f4\u7ec4\u5b66\u6280\u672f\u867d\u80fd\u83b7\u53d6\u5355\u7ec6\u80de\u5206\u8fa8\u7387\u7684\u5206\u5b50\u56fe\u8c31\uff0c\u4f46\u73b0\u6709\u8ba1\u7b97\u65b9\u6cd5\u591a\u57fa\u4e8e\u540c\u8d28\u6027\u5047\u8bbe\uff0c\u96be\u4ee5\u6355\u6349\u7ec6\u80de\u5fae\u73af\u5883\u4e2d\u7684\u5f02\u8d28\u6027\u7279\u5f81\u3002<\/p>\n

\u4f20\u7edf\u65b9\u6cd5\u5982 HMRF \u548c BayesSpace \u91c7\u7528 Potts \u6a21\u578b\u5f3a\u5236\u90bb\u8fd1\u7ec6\u80de\u5171\u4eab\u76f8\u540c\u6807\u7b7e\uff0c\u8fd9\u79cd\u7b80\u5316\u5904\u7406\u5bfc\u81f4\u80bf\u7624-\u514d\u75ab\u754c\u9762\u7b49\u590d\u6742\u5fae\u73af\u5883\u8bc6\u522b\u56f0\u96be\u3002BASS \u7b49\u6539\u8fdb\u65b9\u6cd5\u867d\u5f15\u5165\u5c42\u6b21\u6a21\u578b\uff0c\u4f46\u5728\u591a\u6837\u672c\u6574\u5408\u548c\u5927\u89c4\u6a21\u6570\u636e\u5904\u7406\u4e0a\u4ecd\u663e\u4e0d\u8db3\u3002<\/p>\n

\u7814\u7a76\u56e2\u961f\u53d1\u73b0\uff0c\u7ec6\u80de\u81ea\u8eab\u5206\u5b50\u7279\u5f81\u3001\u90bb\u57df\u5206\u5b50\u7279\u5f81\u548c\u7ec6\u80de\u7ec4\u6210\u7279\u5f81\u8fd9\u4e09\u4e2a\u89c6\u89d2\u7684\u4fe1\u606f\u4e92\u8865\u6027\uff0c\u4e3a\u514b\u670d\u73b0\u6709\u65b9\u6cd5\u7684\u4e0d\u8db3\u63d0\u4f9b\u4e86\u65b0\u601d\u8def\u3002<\/p>\n

scNiche\u6846\u67b6\u7684\u4e09\u7ef4\u89e3\u6790<\/strong><\/p>\n

scNiche \u6846\u67b6\u91c7\u7528\u4e86\u72ec\u7279\u7684\u8bbe\u8ba1\u7406\u5ff5\uff0c\u5c06\u7ec6\u80de\u672c\u8eab\u53ca\u5176\u5fae\u73af\u5883\u7684\u5404\u79cd\u7279\u5f81\u7edf\u4e00\u5b9a\u4e49\u4e3a\u7ec6\u80de\u7684\u4e0d\u540c\u300c\u89c6\u89d2\u300d\u7279\u5f81\u3002\u5177\u4f53\u6765\u8bf4\uff0cscNiche \u9ed8\u8ba4\u5728\u9884\u5b9a\u4e49\u7684 k-nearest neighbors \u8303\u56f4\u5185\u63d0\u53d6\u4e09\u7c7b\u7279\u5f81\uff1a\u7ec6\u80de\u7684\u5206\u5b50\u8868\u8fbe\u8c31\u3001\u5176\u90bb\u57df\u7684\u5206\u5b50\u8868\u8fbe\u8c31\u4ee5\u53ca\u90bb\u57df\u7684\u7ec6\u80de\u7ec4\u6210\u3002<\/p>\n

\u4e0e\u4e4b\u524d\u5927\u591a\u6570\u6df1\u5ea6\u5b66\u4e60<\/mark>\u65b9\u6cd5\u4e0d\u540c\uff0cscNiche \u9996\u5148\u4e3a\u4e0d\u540c\u89c6\u89d2\u7684\u7279\u5f81\u6784\u5efa<\/mark>\u72ec\u7acb\u7684\u56fe\u7f51<\/mark>\u7edc\uff0c\u7136\u540e\u5229\u7528\u56fe\u795e\u7ecf\u7f51\u7edc<\/mark>\u5c06\u8fd9\u4e9b\u591a\u89c6\u89d2\u7279\u5f81\u6574\u5408\u6210\u4e00\u4e2a\u6709\u610f\u4e49\u7684\u8054\u5408\u8868\u793a\u3002<\/p>\n

\u8fd9\u79cd\u6a21\u578b\u67b6\u6784\u5305\u542b\u4e09\u4e2a\u5173\u952e\u7ec4\u4ef6\uff1a\u591a\u56fe\u81ea\u7f16\u7801\u5668\uff08M-GAE\uff09\u3001\u56fe\u878d\u5408\u7f51\u7edc\uff08GFN\uff09\u548c\u591a\u89c6\u56fe\u4e92\u4fe1\u606f\u6700\u5927\u5316\uff08MMIM\uff09\u6a21\u5757\u3002<\/p>\n

M-GAE \u6a21\u578b\u57fa\u4e8e\u56fe\u5377\u79ef\u7f51\u7edc\uff08GCN\uff09\u6784\u5efa\uff0c\u901a\u8fc7\u89c6\u56fe\u7279\u5b9a\u7684 GCN \u7f16\u7801\u5668\u5c42\u7f16\u7801\u591a\u89c6\u56fe\u6570\u636e\u7684\u4e92\u8865\u4fe1\u606f\uff0cGFN \u6355\u83b7\u4e0d\u540c\u89c6\u56fe\u56fe\u4e4b\u95f4\u7684\u5173\u7cfb\u5e76\u751f\u6210\u5305\u542b\u6240\u6709\u89c6\u56fe\u5168\u5c40\u8282\u70b9\u5173\u7cfb\u7684\u4e00\u81f4\u6027\u56fe\u3002<\/p>\n

MMIM \u6a21\u5757\u901a\u8fc7\u63d0\u5347\u4efb\u610f\u89c6\u89d2\u4e2d\u76f8\u90bb\u6837\u672c\u8868\u793a\u4e4b\u95f4\u7684\u76f8\u4f3c\u6027\u6765\u5f15\u5bfc\u66f4\u9002\u5408\u805a\u7c7b<\/mark>\u7684\u8054\u5408\u8868\u793a\u5b66\u4e60\u3002\u8be5\u6a21\u5757\u91c7\u7528\u4e86\u57fa\u4e8e Shannon \u71b5\u7684\u4e92\u4fe1\u606f\u5ea6\u91cf\u65b9\u6cd5\uff0c\u901a\u8fc7\u6700\u5927\u5316\u6837\u672c\u4e0e\u5176\u8fd1\u90bb\u7684\u4e92\u4fe1\u606f\u6765\u589e\u5f3a\u6a21\u578b\u5bf9\u7ec6\u80de\u5fae\u73af\u5883\u7ed3\u6784\u7684\u8bc6\u522b\u80fd\u529b\u3002<\/p>\n

<\/a><\/section>\n
\u56fe\u793a\uff1ascNiche \u6982\u89c8\u3002\uff08\u6765\u6e90\uff1a\u8bba\u6587\uff09<\/section>\n

\u6027\u80fd\u9a8c\u8bc1<\/strong><\/p>\n

scNiche \u7684\u6269\u5c55\u6027\u901a\u8fc7\u5305\u542b 3,698,530 \u4e2a\u7ec6\u80de\u7684\u5c0f\u9f20\u5168\u8111 MERFISH \u6570\u636e\u96c6\u5f97\u5230\u9a8c\u8bc1\u3002<\/p>\n

\u5f97\u76ca\u4e8e\u5176\u521b\u65b0\u7684 subgraph-based batch training strategy\uff08\u901a\u8fc7\u968f\u673a\u91c7\u6837\u6784\u5efa\u5b50\u56fe\u8fdb\u884c\u5206\u6279\u6b21<\/mark>\u8bad\u7ec3\uff09\uff0c\u8be5\u65b9\u6cd5\u80fd\u591f\u51c6\u786e\u8bc6\u522b\u5305\u62ec\u4e18\u8111-\u7eb9\u72b6\u4f53\u8fb9\u754c\u5728\u5185\u7684\u4e0d\u540c\u8111\u533a\u7ed3\u6784\u3002<\/p>\n

\u5728\u57fa\u51c6<\/mark>\u6d4b\u8bd5\u4e2d\uff0cscNiche \u5728\u7a7a\u95f4\u86cb\u767d\u8d28\u7ec4\u5b66\u6570\u636e\u96c6\uff08CODEX\u3001IMC\uff09\u548c\u7a7a\u95f4\u8f6c\u5f55\u7ec4\u6570\u636e\u96c6\uff08STARmap\u3001MERFISH\uff09\u4e0a\u5747\u5b9e\u73b0\u4e86\u6700\u9ad8\u7684 adjusted Rand index (ARI) \u548c macro-F1 \u5206\u6570\uff0c\u663e\u8457\u4f18\u4e8e\u73b0\u6709\u65b9\u6cd5\u3002<\/p>\n

\u5728 10X Visium \u6570\u636e\u5206\u6790<\/mark>\u4e2d\uff0c\u5373\u4f7f\u7528 Cell2location \u7684\u53cd\u5377\u79ef\u7ed3\u679c\u66ff\u4ee3\u539f\u59cb\u7ec6\u80de\u7ec4\u6210\u7279\u5f81\uff0c\u6a21\u578b\u4ecd\u4fdd\u6301\u8f83\u597d\u7684\u8868\u73b0\u3002<\/p>\n

\u5728\u57fa\u56e0\u8868\u8fbe\u968f\u673a\u5f52\u96f6\u7684\u9c81\u68d2\u6027\u6d4b\u8bd5\u4e2d\uff0cscNiche \u5728\u4f4e dropout \u7387\u65f6\u8868\u73b0\u76f8\u5bf9\u7a33\u5b9a\uff0c\u4f46\u5f53 dropout \u7387\u8f83\u9ad8\u65f6\uff0c\u6240\u6709\u65b9\u6cd5\uff08\u5305\u62ec scNiche\uff09\u7684\u6027\u80fd\u90fd\u4f1a\u663e\u8457\u4e0b\u964d\u3002<\/p>\n

<\/a><\/section>\n

\u56fe\u793a\uff1a\u5c0f\u9f20\u5168\u8111 MERFISH \u6570\u636e\u96c6\u7684\u6027\u80fd\u8bc4\u4f30\u3002\uff08\u6765\u6e90\uff1a\u8bba\u6587\uff09<\/p>\n

\u4e34\u5e8a\u5e94\u7528<\/strong><\/p>\n

\u5728 19 \u4f8b\u6df7\u5408\u578b\u4e0e 15 \u4f8b\u533a\u5ba4\u5316\u4e09\u9634\u6027\u4e73\u817a\u764c\u6837\u672c\u4e2d\uff0cscNiche \u63ed\u793a\u4e86\u72ec\u7279\u7684\u514d\u75ab\u5fae\u5730\u7406\u7279\u5f81\u3002<\/p>\n

Niche 6 \u4e2d\u5de8\u566c\u7ec6\u80de\u9ad8\u8868\u8fbe CD11b\uff08p=0.011\uff09\u548c PD-L1\uff08p=0.016\uff09\u7b49\u514d\u75ab\u8c03\u8282\u86cb\u767d\uff0c\u5f62\u6210\u514d\u75ab\u6291\u5236\u5fae\u73af\u5883\uff1b\u800c Niche 12 \u4e2d\u7684\u5de8\u566c\u7ec6\u80de\u5448\u73b0\u51fa\u4e0e\u80bf\u7624\u7ec6\u80de\u7684\u9ad8\u5ea6\u5171\u5b9a\u4f4d\u7279\u5f81\uff08proportion=0.67, p=0.002\uff09\u3002<\/p>\n

\u7814\u7a76\u53d1\u73b0 Keratin+ \u80bf\u7624\u7ec6\u80de\u5728 Niche 5 \u4e0e Niche 11 \u5448\u73b0\u5dee\u5f02\u5316\u5206\u5e03\uff1a\u524d\u8005 CK17 \u8868\u8fbe\u663e\u8457\u9ad8\u4e8e\u540e\u8005\uff08p=0.014\uff09\uff0c\u4e14\u7279\u5f02\u6027\u5bcc\u96c6\u4e8e\u4e0d\u540c\u60a3\u8005\u7fa4\u4f53\uff0c\u8fd9\u4e3a\u4e2a\u4f53\u5316\u6cbb\u7597\u63d0\u4f9b\u4e86\u6f5c\u5728\u9776\u70b9\u3002<\/p>\n

<\/a><\/section>\n

\u56fe\u793a\uff1a\u4e73\u817a\u764c\u5fae\u73af\u5883\u89e3\u6790\u3002\uff08\u6765\u6e90\uff1a\u8bba\u6587\uff09<\/p>\n

\u5728\u809d\u635f\u4f24\u7814\u7a76\u4e2d\uff0cscNiche \u53d1\u73b0\u4e0e\u6b63\u5e38\u809d\u810f\u95e8\u9759\u8109\u5468\u56f4\u533a\u57df\uff08Niche 1\uff09\u76f8\u6bd4\uff0c\u809d\u635f\u4f24\u7ec4\u7ec7\u4e2d\u7684 Niche 10 \u663e\u8457\u4e0a\u8c03\u4e86\u591a\u4e2a\u6297\u6c27\u5316\u57fa\u56e0\uff08\u5982 Gpx3\u3001Gsta1\u3001Gsta2\u3001Gsto1\uff09\u4ee5\u53ca\u7ec4\u7ec7\u7ea4\u7ef4\u5316\u76f8\u5173\u57fa\u56e0\uff08\u5982 Ctsl\u3001Ctsb \u7b49 cathepsins \u7f16\u7801\u57fa\u56e0\uff09\uff0c\u63ed\u793a\u4e86\u809d\u635f\u4f24\u5fae\u73af\u5883\u7684\u9002\u5e94\u6027\u5206\u5b50\u7279\u5f81\u3002<\/p>\n

<\/a><\/section>\n

\u56fe\u793a\uff1a\u75be\u75c5\u7279\u5f02\u6027\u809d\u635f\u4f24\u7684\u5fae\u73af\u5883\u3002\uff08\u6765\u6e90\uff1a\u8bba\u6587\uff09<\/p>\n

\u672a\u6765\u5c55\u671b<\/strong><\/p>\n

scNiche \u901a\u8fc7\u521b\u65b0\u7684\u591a\u89c6\u89d2\u878d\u5408\u67b6\u6784\uff0c\u5728\u4fdd\u6301\u5355\u7ec6\u80de\u5206\u8fa8\u7387\u7684\u540c\u65f6\uff0c\u5b9e\u73b0\u4e86\u8de8\u6837\u672c\u3001\u8de8\u6761\u4ef6\u7684\u5fae\u73af\u5883\u5bf9\u6bd4\u5206\u6790\u3002\u5176\u5728\u809d\u635f\u4f24\u7814\u7a76\u4e2d\u63ed\u793a\u7684 zonation \u6a21\u5f0f\u91cd\u6784<\/mark>\u73b0\u8c61\uff0c\u4e3a\u5668\u5b98\u7ea4\u7ef4\u5316\u673a\u5236\u7814\u7a76\u63d0\u4f9b\u4e86\u65b0\u89c6\u89d2\u3002<\/p>\n

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