IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-41855-w.html
   My bibliography  Save this article

Benchmarking strategies for cross-species integration of single-cell RNA sequencing data

Author

Listed:
  • Yuyao Song

    (Wellcome Genome Campus)

  • Zhichao Miao

    (Wellcome Genome Campus
    Guangzhou International Bio Island)

  • Alvis Brazma

    (Wellcome Genome Campus)

  • Irene Papatheodorou

    (Wellcome Genome Campus)

Abstract

The growing number of available single-cell gene expression datasets from different species creates opportunities to explore evolutionary relationships between cell types across species. Cross-species integration of single-cell RNA-sequencing data has been particularly informative in this context. However, in order to do so robustly it is essential to have rigorous benchmarking and appropriate guidelines to ensure that integration results truly reflect biology. Here, we benchmark 28 combinations of gene homology mapping methods and data integration algorithms in a variety of biological settings. We examine the capability of each strategy to perform species-mixing of known homologous cell types and to preserve biological heterogeneity using 9 established metrics. We also develop a new biology conservation metric to address the maintenance of cell type distinguishability. Overall, scANVI, scVI and SeuratV4 methods achieve a balance between species-mixing and biology conservation. For evolutionarily distant species, including in-paralogs is beneficial. SAMap outperforms when integrating whole-body atlases between species with challenging gene homology annotation. We provide our freely available cross-species integration and assessment pipeline to help analyse new data and develop new algorithms.

Suggested Citation

  • Yuyao Song & Zhichao Miao & Alvis Brazma & Irene Papatheodorou, 2023. "Benchmarking strategies for cross-species integration of single-cell RNA sequencing data," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-41855-w
    DOI: 10.1038/s41467-023-41855-w
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-41855-w
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-023-41855-w?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Trygve E. Bakken & Nikolas L. Jorstad & Qiwen Hu & Blue B. Lake & Wei Tian & Brian E. Kalmbach & Megan Crow & Rebecca D. Hodge & Fenna M. Krienen & Staci A. Sorensen & Jeroen Eggermont & Zizhen Yao & , 2021. "Comparative cellular analysis of motor cortex in human, marmoset and mouse," Nature, Nature, vol. 598(7879), pages 111-119, October.
    2. Yuan Liao & Lifeng Ma & Qile Guo & Weigao E & Xing Fang & Lei Yang & Fanwei Ruan & Jingjing Wang & Peijing Zhang & Zhongyi Sun & Haide Chen & Zhongliang Lin & Xueyi Wang & Xinru Wang & Huiyu Sun & Xiu, 2022. "Cell landscape of larval and adult Xenopus laevis at single-cell resolution," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    3. Fei Wang & Peiwen Ding & Xue Liang & Xiangning Ding & Camilla Blunk Brandt & Evelina Sjöstedt & Jiacheng Zhu & Saga Bolund & Lijing Zhang & Laura P. M. H. Rooij & Lihua Luo & Yanan Wei & Wandong Zhao , 2022. "Author Correction: Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level," Nature Communications, Nature, vol. 13(1), pages 1-2, December.
    4. April R. Kriebel & Joshua D. Welch, 2022. "UINMF performs mosaic integration of single-cell multi-omic datasets using nonnegative matrix factorization," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    5. Fei Wang & Peiwen Ding & Xue Liang & Xiangning Ding & Camilla Blunk Brandt & Evelina Sjöstedt & Jiacheng Zhu & Saga Bolund & Lijing Zhang & Laura P. M. H. Rooij & Lihua Luo & Yanan Wei & Wandong Zhao , 2022. "Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    6. Yuan Liao & Lifeng Ma & Qile Guo & Weigao E & Xing Fang & Lei Yang & Fanwei Ruan & Jingjing Wang & Peijing Zhang & Zhongyi Sun & Haide Chen & Zhongliang Lin & Xueyi Wang & Xinru Wang & Huiyu Sun & Xiu, 2022. "Publisher Correction: Cell landscape of larval and adult Xenopus laevis at single-cell resolution," Nature Communications, Nature, vol. 13(1), pages 1-1, December.
    7. Lei Han & Xiaoyu Wei & Chuanyu Liu & Giacomo Volpe & Zhenkun Zhuang & Xuanxuan Zou & Zhifeng Wang & Taotao Pan & Yue Yuan & Xiao Zhang & Peng Fan & Pengcheng Guo & Yiwei Lai & Ying Lei & Xingyuan Liu , 2022. "Cell transcriptomic atlas of the non-human primate Macaca fascicularis," Nature, Nature, vol. 604(7907), pages 723-731, April.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Ruihua Zhang & Qun Liu & Shanshan Pan & Yingying Zhang & Yating Qin & Xiao Du & Zengbao Yuan & Yongrui Lu & Yue Song & Mengqi Zhang & Nannan Zhang & Jie Ma & Zhe Zhang & Xiaodong Jia & Kun Wang & Shun, 2023. "A single-cell atlas of West African lungfish respiratory system reveals evolutionary adaptations to terrestrialization," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    2. Tingting Bo & Jie Li & Ganlu Hu & Ge Zhang & Wei Wang & Qian Lv & Shaoling Zhao & Junjie Ma & Meng Qin & Xiaohui Yao & Meiyun Wang & Guang-Zhong Wang & Zheng Wang, 2023. "Brain-wide and cell-specific transcriptomic insights into MRI-derived cortical morphology in macaque monkeys," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    3. Jia-Ru Wei & Zhao-Zhe Hao & Chuan Xu & Mengyao Huang & Lei Tang & Nana Xu & Ruifeng Liu & Yuhui Shen & Sarah A. Teichmann & Zhichao Miao & Sheng Liu, 2022. "Identification of visual cortex cell types and species differences using single-cell RNA sequencing," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
    4. Jessica M. Vanslambrouck & Sean B. Wilson & Ker Sin Tan & Ella Groenewegen & Rajeev Rudraraju & Jessica Neil & Kynan T. Lawlor & Sophia Mah & Michelle Scurr & Sara E. Howden & Kanta Subbarao & Melissa, 2022. "Enhanced metanephric specification to functional proximal tubule enables toxicity screening and infectious disease modelling in kidney organoids," Nature Communications, Nature, vol. 13(1), pages 1-23, December.
    5. Sungyong Um & Bin Zhang & Sunil Wattal & Youngjin Yoo, 2023. "Software Components and Product Variety in a Platform Ecosystem: A Dynamic Network Analysis of WordPress," Information Systems Research, INFORMS, vol. 34(4), pages 1339-1374, December.
    6. Nelson Johansen & Hongru Hu & Gerald Quon, 2023. "Projecting RNA measurements onto single cell atlases to extract cell type-specific expression profiles using scProjection," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    7. Felix Drost & Yang An & Irene Bonafonte-Pardàs & Lisa M. Dratva & Rik G. H. Lindeboom & Muzlifah Haniffa & Sarah A. Teichmann & Fabian Theis & Mohammad Lotfollahi & Benjamin Schubert, 2024. "Multi-modal generative modeling for joint analysis of single-cell T cell receptor and gene expression data," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    8. Muyesier Maimaitili & Muwan Chen & Fabia Febbraro & Ekin Ucuncu & Rachel Kelly & Jonathan Christos Niclis & Josefine Rågård Christiansen & Noëmie Mermet-Joret & Dragos Niculescu & Johanne Lauritsen & , 2023. "Enhanced production of mesencephalic dopaminergic neurons from lineage-restricted human undifferentiated stem cells," Nature Communications, Nature, vol. 14(1), pages 1-23, December.
    9. Daniel J. Lodge & Hannah B. Elam & Angela M. Boley & Jennifer J. Donegan, 2023. "Discrete hippocampal projections are differentially regulated by parvalbumin and somatostatin interneurons," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    10. Yueli Yang & Wenqi Jia & Zhiwei Luo & Yunpan Li & Hao Liu & Lixin Fu & Jinxiu Li & Yu Jiang & Junjian Lai & Haiwei Li & Babangida Jabir Saeed & Yi Zou & Yuan Lv & Liang Wu & Ting Zhou & Yongli Shan & , 2024. "VGLL1 cooperates with TEAD4 to control human trophectoderm lineage specification," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    11. Ziqi Zhang & Haoran Sun & Ragunathan Mariappan & Xi Chen & Xinyu Chen & Mika S. Jain & Mirjana Efremova & Sarah A. Teichmann & Vaibhav Rajan & Xiuwei Zhang, 2023. "scMoMaT jointly performs single cell mosaic integration and multi-modal bio-marker detection," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    12. Ian Covert & Rohan Gala & Tim Wang & Karel Svoboda & Uygar Sümbül & Su-In Lee, 2023. "Predictive and robust gene selection for spatial transcriptomics," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    13. Thomas M. Goralski & Lindsay Meyerdirk & Libby Breton & Laura Brasseur & Kevin Kurgat & Daniella DeWeerd & Lisa Turner & Katelyn Becker & Marie Adams & Daniel J. Newhouse & Michael X. Henderson, 2024. "Spatial transcriptomics reveals molecular dysfunction associated with cortical Lewy pathology," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    14. Jiao Qu & Fa Yang & Tao Zhu & Yingshuo Wang & Wen Fang & Yan Ding & Xue Zhao & Xianjia Qi & Qiangmin Xie & Ming Chen & Qiang Xu & Yicheng Xie & Yang Sun & Dijun Chen, 2022. "A reference single-cell regulomic and transcriptomic map of cynomolgus monkeys," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    15. Malosree Maitra & Haruka Mitsuhashi & Reza Rahimian & Anjali Chawla & Jennie Yang & Laura M. Fiori & Maria Antonietta Davoli & Kelly Perlman & Zahia Aouabed & Deborah C. Mash & Matthew Suderman & Nagu, 2023. "Cell type specific transcriptomic differences in depression show similar patterns between males and females but implicate distinct cell types and genes," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    16. Shixuan Liu & Camille Ezran & Michael F. Z. Wang & Zhengda Li & Kyle Awayan & Jonathan Z. Long & Iwijn De Vlaminck & Sheng Wang & Jacques Epelbaum & Christin S. Kuo & Jérémy Terrien & Mark A. Krasnow , 2024. "An organism-wide atlas of hormonal signaling based on the mouse lemur single-cell transcriptome," Nature Communications, Nature, vol. 15(1), pages 1-27, December.
    17. Junhao Li & Manoj K. Jaiswal & Jo-Fan Chien & Alexey Kozlenkov & Jinyoung Jung & Ping Zhou & Mahammad Gardashli & Luc J. Pregent & Erica Engelberg-Cook & Dennis W. Dickson & Veronique V. Belzil & Eran, 2023. "Divergent single cell transcriptome and epigenome alterations in ALS and FTD patients with C9orf72 mutation," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
    18. Jing-Ping Lin & Hannah M. Kelly & Yeajin Song & Riki Kawaguchi & Daniel H. Geschwind & Steven Jacobson & Daniel S. Reich, 2022. "Transcriptomic architecture of nuclei in the marmoset CNS," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
    19. Michael Wainberg & Natalie J. Forde & Salim Mansour & Isabel Kerrebijn & Sarah E. Medland & Colin Hawco & Shreejoy J. Tripathy, 2024. "Genetic architecture of the structural connectome," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    20. Ying Lei & Mengnan Cheng & Zihao Li & Zhenkun Zhuang & Liang Wu & Yunong sun & Lei Han & Zhihao Huang & Yuzhou Wang & Zifei Wang & Liqin Xu & Yue Yuan & Shang Liu & Taotao Pan & Jiarui Xie & Chuanyu L, 2022. "Spatially resolved gene regulatory and disease-related vulnerability map of the adult Macaque cortex," Nature Communications, Nature, vol. 13(1), pages 1-20, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-41855-w. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.