Single-cell transcriptomic classification of rabies-infected cortical neurons.
Single-cell transcriptomic classification of rabies-infected cortical neurons.
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DOI：
10.1073/pnas.2203677119
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发表时间：
2022-05-31
影响因子：
11.1
通讯作者：
中科院分区：
文献类型：
--
作者：
使用糖蛋白(G)缺失狂犬病病毒的单突触示踪被广泛应用于研究皮质回路的连通性。然而，使用狂犬病病毒进行连接追踪可能受益于更高吞吐量的方法，即将狂犬病标记的输入分配给神经元细胞类型，以及将细胞分配给更精细的基因定义亚型的能力。使用单核RNA测序，我们证明了当使用转录组分析时，狂犬病感染的皮质神经元可以根据已建立的细胞类型进行转录特征描述。此外，我们发现狂犬病感染对不同的宿主基因有不同的影响，这表明某些基因可能比其他基因更容易受到转录调控的影响，这可能会阻碍使用依赖于单个或少数基因检测的方法对狂犬病感染细胞进行分类。使用改进的狂犬病病毒的皮质回路追踪可以识别与感兴趣神经元进行直接单突触连接的输入神经元。然而，在我们确定狂犬病标记的输入神经元的细胞类型身份的能力方面仍然存在挑战。虽然转录切割学可能提供了一种表征输入的途径，但狂犬病诱导的不同神经细胞类型的转录变化的程度仍不清楚，而且这些变化是否排除了根据已建立的转录切割性细胞类型对狂犬病感染的神经元进行表征的可能性尚不清楚。我们使用单核RNA测序来调查狂犬病感染神经元的基因表达谱，并评估它们与已建立的转录转录细胞类型的一致性。我们证明，当使用转录组范围的RNA图谱时，狂犬病感染的皮质神经元可以被转录表征，尽管狂犬病诱导了全局和特定细胞类型的转录变化。值得注意的是，我们发现神经元标记基因表达的差异调节，这表明当试图用单基因或小基因集来描述狂犬病感染细胞时，应该谨慎。
Monosynaptic rabies tracing using glycoprotein (G)-deleted rabies virus is widely applied to study cortical circuit connectivity. However, connectivity tracing using rabies virus could benefit from higher throughput methods of assigning rabies-labeled inputs to neuronal cell types and the ability to assign cells to finer genetically defined subtypes. Using single-nucleus RNA sequencing, we demonstrate that rabies-infected cortical neurons can be transcriptomically characterized according to established cell types when using transcriptome-wide analysis. Furthermore, we find that rabies infection differentially affects distinct host genes, suggesting that some genes may be more vulnerable to transcriptional modulation than others, which may impede the classification of rabies-infected cells when using methods that rely on the detection of single or few genes. Cortical circuit tracing using modified rabies virus can identify input neurons making direct monosynaptic connections onto neurons of interest. However, challenges remain in our ability to establish the cell type identity of rabies-labeled input neurons. While transcriptomics may offer an avenue to characterize inputs, the extent of rabies-induced transcriptional changes in distinct neuronal cell types remains unclear, and whether these changes preclude characterization of rabies-infected neurons according to established transcriptomic cell types is unknown. We used single-nucleus RNA sequencing to survey the gene expression profiles of rabies-infected neurons and assessed their correspondence with established transcriptomic cell types. We demonstrated that when using transcriptome-wide RNA profiles, rabies-infected cortical neurons can be transcriptomically characterized despite global and cell-type-specific rabies-induced transcriptional changes. Notably, we found differential modulation of neuronal marker gene expression, suggesting that caution should be taken when attempting to characterize rabies-infected cells with single genes or small gene sets.
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影响因子：
16.2
作者：
Kim EJ;Juavinett AL;Kyubwa EM;Jacobs MW;Callaway EM
通讯作者：
Callaway EM
影响因子：
25
作者：
Gouwens NW;Sorensen SA;Berg J;Lee C;Jarsky T;Ting J;Sunkin SM;Feng D;Anastassiou CA;Barkan E;Bickley K;Blesie N;Braun T;Brouner K;Budzillo A;Caldejon S;Casper T;Castelli D;Chong P;Crichton K;Cuhaciyan C;Daigle TL;Dalley R;Dee N;Desta T;Ding SL;Dingman S;Doperalski A;Dotson N;Egdorf T;Fisher M;de Frates RA;Garren E;Garwood M;Gary A;Gaudreault N;Godfrey K;Gorham M;Gu H;Habel C;Hadley K;Harrington J;Harris JA;Henry A;Hill D;Josephsen S;Kebede S;Kim L;Kroll M;Lee B;Lemon T;Link KE;Liu X;Long B;Mann R;McGraw M;Mihalas S;Mukora A;Murphy GJ;Ng L;Ngo K;Nguyen TN;Nicovich PR;Oldre A;Park D;Parry S;Perkins J;Potekhina L;Reid D;Robertson M;Sandman D;Schroedter M;Slaughterbeck C;Soler-Llavina G;Sulc J;Szafer A;Tasic B;Taskin N;Teeter C;Thatra N;Tung H;Wakeman W;Williams G;Young R;Zhou Z;Farrell C;Peng H;Hawrylycz MJ;Lein E;Ng L;Arkhipov A;Bernard A;Phillips JW;Zeng H;Koch C
通讯作者：
Koch C
影响因子：
64.5
作者：
Gouwens NW;Sorensen SA;Baftizadeh F;Budzillo A;Lee BR;Jarsky T;Alfiler L;Baker K;Barkan E;Berry K;Bertagnolli D;Bickley K;Bomben J;Braun T;Brouner K;Casper T;Crichton K;Daigle TL;Dalley R;de Frates RA;Dee N;Desta T;Lee SD;Dotson N;Egdorf T;Ellingwood L;Enstrom R;Esposito L;Farrell C;Feng D;Fong O;Gala R;Gamlin C;Gary A;Glandon A;Goldy J;Gorham M;Graybuck L;Gu H;Hadley K;Hawrylycz MJ;Henry AM;Hill D;Hupp M;Kebede S;Kim TK;Kim L;Kroll M;Lee C;Link KE;Mallory M;Mann R;Maxwell M;McGraw M;McMillen D;Mukora A;Ng L;Ng L;Ngo K;Nicovich PR;Oldre A;Park D;Peng H;Penn O;Pham T;Pom A;Popović Z;Potekhina L;Rajanbabu R;Ransford S;Reid D;Rimorin C;Robertson M;Ronellenfitch K;Ruiz A;Sandman D;Smith K;Sulc J;Sunkin SM;Szafer A;Tieu M;Torkelson A;Trinh J;Tung H;Wakeman W;Ward K;Williams G;Zhou Z;Ting JT;Arkhipov A;Sümbül U;Lein ES;Koch C;Yao Z;Tasic B;Berg J;Murphy GJ;Zeng H
通讯作者：
Zeng H
影响因子：
16.2
作者：
Armand EJ;Li J;Xie F;Luo C;Mukamel EA
通讯作者：
Mukamel EA
影响因子：
25
作者：
Pfeffer, Carsten K.;Xue, Mingshan;He, Miao;Huang, Z. Josh;Scanziani, Massimo
通讯作者：
Scanziani, Massimo