2022单细胞关键意见领袖的关键文章

作者 | 周运来

男，

一个长大了才会遇到的帅哥，

稳健，潇洒，大方，靠谱。

一段生信缘，一棵技能树。

生信技能树核心成员，单细胞天地特约撰稿人，简书创作者，单细胞数据科学家。

生活的细节，靠近了看仿佛散落海滩的贝壳，七零八落，当我们把视角拉长一些，这一颗颗串起来，就是一串串有迹可循的珍珠项链，不可方物。

当我们把2022以春夏秋冬这样铺展开来，历历在目的往事，以某种逻辑连结，2022不再只是一个数字，有了故事也有了温度。2022年单细胞课题怎么样？单细胞技术接下来会往哪个方向发展？更多组学？更高通量？让我们跟随单细胞大佬2022年发表的文章，看未来已来咯~

发育(Atlas)-> 肿瘤(Pan-Cancer) -> 疾病(GWAS)

• 还有哪些组织没有做过单细胞测序？
• 还有哪些癌种没有做过单细胞测序？
• 还有哪些疾病没有做过单细胞测序？
• 还有哪些物种没有做过单细胞测序？
• 还有哪些机构没有做过单细胞测序？
• 还有哪些国家没有做过单细胞测序？

2022明星细胞

中性粒细胞

肿瘤相关成纤维细胞

KOL之图谱鼓手：Aviv Regev

从图谱理解复杂疾病，图谱之下是医者仁心。

Impact of the Human Cell Atlas on medicine. Rood JE, Maartens A, Hupalowska A, Teichmann SA, Regev A. Nat Med. 2022 Dec 8. doi: 10.1038/s41591-022-02104-7. Online ahead of print. PMID: 36482102 Review.

Identifying disease-critical cell types and cellular processes by integrating single-cell RNA-sequencing and human genetics. Jagadeesh KA, Dey KK, Montoro DT, Mohan R, Gazal S, Engreitz JM, Xavier RJ, Price AL, Regev A. Nat Genet. 2022 Oct;54(10):1479-1492. doi: 10.1038/s41588-022-01187-9. Epub 2022 Sep 29. PMID: 36175791

Mostly natural sequencing-by-synthesis for scRNA-seq using Ultima sequencing. Simmons SK, Lithwick-Yanai G, Adiconis X, Oberstrass F, Iremadze N, Geiger-Schuller K, Thakore PI, Frangieh CJ, Barad O, Almogy G, Rozenblatt-Rosen O, Regev A, Lipson D, Levin JZ. Nat Biotechnol. 2022 Sep 15. doi: 10.1038/s41587-022-01452-6. Online ahead of print. PMID: 36109685

Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function. Eraslan G, Drokhlyansky E, Anand S, Fiskin E, Subramanian A, Slyper M, Wang J, Van Wittenberghe N, Rouhana JM, Waldman J, Ashenberg O, Lek M, Dionne D, Win TS, Cuoco MS, Kuksenko O, Tsankov AM, Branton PA, Marshall JL, Greka A, Getz G, Segrè AV, Aguet F, Rozenblatt-Rosen O, Ardlie KG, Regev A. Science. 2022 May 13;376(6594):eabl4290. doi: 10.1126/science.abl4290. Epub 2022 May 13. PMID: 35549429

Spatial components of molecular tissue biology. Palla G, Fischer DS, Regev A, Theis FJ. Nat Biotechnol. 2022 Mar;40(3):308-318. doi: 10.1038/s41587-021-01182-1. Epub 2022 Feb 7. PMID: 35132261

Massively parallel phenotyping of coding variants in cancer with Perturb-seq. Ursu O, Neal JT, Shea E, Thakore PI, Jerby-Arnon L, Nguyen L, Dionne D, Diaz C, Bauman J, Mosaad MM, Fagre C, Lo A, McSharry M, Giacomelli AO, Ly SH, Rozenblatt-Rosen O, Hahn WC, Aguirre AJ, Berger AH, Regev A, Boehm JS. Nat Biotechnol. 2022 Jun;40(6):896-905. doi: 10.1038/s41587-021-01160-7. Epub 2022 Jan 20. PMID: 35058622

KOL之单细胞开拓者：fuchou tang

单细胞三代测序、非编码测序，让2022年的单细胞技术更丰富。

Molecular profiling of human non-small cell lung cancer by single-cell RNA-seq. Li Q, Wang R, Yang Z, Li W, Yang J, Wang Z, Bai H, Cui Y, Tian Y, Wu Z, Guo Y, Xu J, Wen L, He J, Tang F, Wang J. Genome Med. 2022 Aug 13;14(1):87. doi: 10.1186/s13073-022-01089-9. PMID: 35962452

KOL之肿瘤异质性探秘者：zemin zhang

为我们贡献了肿瘤中性粒细胞，这一2022细胞明星。

Liver tumour immune microenvironment subtypes and neutrophil heterogeneity. Xue R, Zhang Q, Cao Q, Kong R, Xiang X, Liu H, Feng M, Wang F, Cheng J, Li Z, Zhan Q, Deng M, Zhu J, Zhang Z, Zhang N. Nature. 2022 Dec;612(7938):141-147. doi: 10.1038/s41586-022-05400-x. Epub 2022 Nov 9. PMID: 36352227

Immune phenotypic linkage between colorectal cancer and liver metastasis. Liu Y, Zhang Q, Xing B, Luo N, Gao R, Yu K, Hu X, Bu Z, Peng J, Ren X, Zhang Z. Cancer Cell. 2022 Apr 11;40(4):424-437.e5. doi: 10.1016/j.ccell.2022.02.013. Epub 2022 Mar 17. PMID: 35303421

KOL之单细胞工具集成者： Satija R

2022年，您的Seurat更新了吗？

Comparison and evaluation of statistical error models for scRNA-seq. Choudhary S, Satija R. Genome Biol. 2022 Jan 18;23(1):27. doi: 10.1186/s13059-021-02584-9. PMID: 35042561

KOL之单细胞调控禅宗：Stein Aerts

SCENIC将基因上下游的调控故事纳入单细胞图谱之中，帮助越多越多同学回答：这个细胞为什么是这个细胞的问题。

SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks

Aerts, S. How regulatory sequences learn cell representations. Nat Methods 19, 1041–1043 (2022). https://doi.org/10.1038/s41592-022-01570-8

Cell type diversity in a developing octopus brain. Styfhals R, Zolotarov G, Hulselmans G, Spanier KI, Poovathingal S, Elagoz AM, De Winter S, Deryckere A, Rajewsky N, Ponte G, Fiorito G, Aerts S, Seuntjens E. Nat Commun. 2022 Nov 30;13(1):7392. doi: 10.1038/s41467-022-35198-1. PMID: 36450803

Decoding gene regulation in the fly brain. Janssens J, Aibar S, Taskiran II, Ismail JN, Gomez AE, Aughey G, Spanier KI, De Rop FV, González-Blas CB, Dionne M, Grimes K, Quan XJ, Papasokrati D, Hulselmans G, Makhzami S, De Waegeneer M, Christiaens V, Southall T, Aerts S. Nature. 2022 Jan;601(7894):630-636. doi: 10.1038/s41586-021-04262-z. Epub 2022 Jan 5. PMID: 34987221

KOL之单细胞自然绘手：guoji guo

在单细胞多物种和跨物种研究中，带领人们领略大自然之美。

Construction of a cross-species cell landscape at single-cell level. Wang R, Zhang P, Wang J, Ma L, E W, Suo S, Jiang M, Li J, Chen H, Sun H, Fei L, Zhou Z, Zhou Y, Chen Y, Zhang W, Wang X, Mei Y, Sun Z, Yu C, Shao J, Fu Y, Xiao Y, Ye F, Fang X, Wu H, Guo Q, Fang X, Li X, Gao X, Wang D, Xu PF, Zeng R, Xu G, Zhu L, Wang L, Qu J, Zhang D, Ouyang H, Huang H, Chen M, Ng SC, Liu GH, Yuan GC, Guo G, Han X. Nucleic Acids Res. 2022 Aug 5:gkac633. doi: 10.1093/nar/gkac633. Online ahead of print. PMID: 35929025

SPEED: Single-cell Pan-species atlas in the light of Ecology and Evolution for Development and Diseases. Chen Y, Zhang X, Peng X, Jin Y, Ding P, Xiao J, Li C, Wang F, Chang A, Yue Q, Pu M, Chen P, Shen J, Li M, Jia T, Wang H, Huang L, Guo G, Zhang W, Liu H, Wang X, Chen D. Nucleic Acids Res. 2022 Oct 28:gkac930. doi: 10.1093/nar/gkac930. Online ahead of print. PMID: 36305818

KOL之推开空间组学之门： Fan Rong

在空间尺度上，逼近单细胞真相。

Spatial profiling of chromatin accessibility in mouse and human tissues . Deng Y, Bartosovic M, Ma S, Zhang D, Kukanja P, Xiao Y, Su G, Liu Y, Qin X, Rosoklija GB, Dwork AJ, Mann JJ, Xu ML, Halene S, Craft JE, Leong KW, Boldrini M, Castelo-Branco G, Fan R. Nature. 2022 Sep;609(7926):375-383. doi: 10.1038/s41586-022-05094-1. Epub 2022 Aug 17. PMID: 35978191

Spatial-CITE-seq: spatially resolved high-plex protein and whole transcriptome co-mapping. Fan R, Liu Y, DiStasio M, Su G, Asashima H, Enninful A, Qin X, Deng Y, Bordignon P, Cassano M, Tomayko M, Xu M, Halene S, Craft J, Hafler D. Res Sq. 2022 Mar 30:rs.3.rs-1499315. doi: 10.21203/rs.3.rs-1499315/v1. Preprint. PMID: 35378748

Single-cell antigen-specific landscape of CAR T infusion product identifies determinants of CD19-positive relapse in patients with ALL. Bai Z, Woodhouse S, Zhao Z, Arya R, Govek K, Kim D, Lundh S, Baysoy A, Sun H, Deng Y, Xiao Y, Barrett DM, Myers RM, Grupp SA, June CH, Fan R, Camara PG, Melenhorst JJ. Sci Adv. 2022 Jun 10;8(23):eabj2820. doi: 10.1126/sciadv.abj2820. Epub 2022 Jun 8. PMID: 35675405

KOL之单细胞微生物见者：David Weitz

以单细胞技术操作单细胞生物，将单细胞测序技术应用到丰富多样的微生物世界。

High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome . Zheng W, Zhao S, Yin Y, Zhang H, Needham DM, Evans ED, Dai CL, Lu PJ, Alm EJ, Weitz DA. Science. 2022 Jun 3;376(6597):eabm1483. doi: 10.1126/science.abm1483. Epub 2022 Jun 3. PMID: 35653470

Large-scale single-cell encapsulation in microgels through metastable droplet-templating combined with microfluidic-integration. Zhang H, Zhang L, An C, Zhang Y, Shao F, Gao Y, Zhang Y, Li H, Zhang Y, Ren C, Sun K, He W, Cheng F, Wang H, Weitz DA. Biofabrication. 2022 Jun 6;14(3). doi: 10.1088/1758-5090/ac7168. PMID: 35593920

KOL之单细胞分析加速神器： Fabian Theis

scanpy 开发者之一，为海量单细胞数据分析提供解决方案。

Palla, G., Spitzer, H., Klein, M. et al. Squidpy: a scalable framework for spatial omics analysis . Nat Methods 19, 171–178 (2022). https://doi.org/10.1038/s41592-021-01358-2

2023的钟声即将敲响，它不是2022+1，也不是2024-1，我们相信2023年会是一个一无二的年份，它也许在历史长河中籍籍无名，但我们每个人都将有着独特的期许和经历。随着单细胞的技术下沉，应用场景也会更加多样化，图谱将不再只是二维的或三维的，单细胞打开的画轴更加绚丽多彩，更高精度，更高分辨率，更多人可及，我们继续重新定义细胞，也会重新认识自己。

*文本仅作学习交流之用，图片来自网路，侵删