IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-39627-7.html
   My bibliography  Save this article

Single-cell profiling of lncRNA expression during Ebola virus infection in rhesus macaques

Author

Listed:
  • Luisa Santus

    (Barcelona Supercomputing Center
    The Barcelona Institute for Science and Technology)

  • Maria Sopena-Rios

    (Barcelona Supercomputing Center)

  • Raquel García-Pérez

    (Barcelona Supercomputing Center)

  • Aaron E. Lin

    (Harvard University
    Broad Institute of MIT and Harvard
    Harvard Medical School)

  • Gordon C. Adams

    (Harvard University
    Broad Institute of MIT and Harvard)

  • Kayla G. Barnes

    (Broad Institute of MIT and Harvard
    Harvard University
    Liverpool School of Tropical Medicine)

  • Katherine J. Siddle

    (Harvard University
    Broad Institute of MIT and Harvard)

  • Shirlee Wohl

    (Harvard University
    Broad Institute of MIT and Harvard
    The Scripps Research Institute, Department of Immunology and Microbiology)

  • Ferran Reverter

    (Microbiology and Statistics University of Barcelona)

  • John L. Rinn

    (University of Colorado Boulder)

  • Richard S. Bennett

    (National Institutes of Health)

  • Lisa E. Hensley

    (National Institutes of Health)

  • Pardis C. Sabeti

    (Harvard University
    Broad Institute of MIT and Harvard
    Harvard Medical School
    Howard Hughes Medical Institute)

  • Marta Melé

    (Barcelona Supercomputing Center)

Abstract

Long non-coding RNAs (lncRNAs) are involved in numerous biological processes and are pivotal mediators of the immune response, yet little is known about their properties at the single-cell level. Here, we generate a multi-tissue bulk RNAseq dataset from Ebola virus (EBOV) infected and not-infected rhesus macaques and identified 3979 novel lncRNAs. To profile lncRNA expression dynamics in immune circulating single-cells during EBOV infection, we design a metric, Upsilon, to estimate cell-type specificity. Our analysis reveals that lncRNAs are expressed in fewer cells than protein-coding genes, but they are not expressed at lower levels nor are they more cell-type specific when expressed in the same number of cells. In addition, we observe that lncRNAs exhibit similar changes in expression patterns to those of protein-coding genes during EBOV infection, and are often co-expressed with known immune regulators. A few lncRNAs change expression specifically upon EBOV entry in the cell. This study sheds light on the differential features of lncRNAs and protein-coding genes and paves the way for future single-cell lncRNA studies.

Suggested Citation

  • Luisa Santus & Maria Sopena-Rios & Raquel García-Pérez & Aaron E. Lin & Gordon C. Adams & Kayla G. Barnes & Katherine J. Siddle & Shirlee Wohl & Ferran Reverter & John L. Rinn & Richard S. Bennett & L, 2023. "Single-cell profiling of lncRNA expression during Ebola virus infection in rhesus macaques," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-39627-7
    DOI: 10.1038/s41467-023-39627-7
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-39627-7
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-023-39627-7?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. Anamaria Necsulea & Magali Soumillon & Maria Warnefors & Angélica Liechti & Tasman Daish & Ulrich Zeller & Julie C. Baker & Frank Grützner & Henrik Kaessmann, 2014. "The evolution of lncRNA repertoires and expression patterns in tetrapods," Nature, Nature, vol. 505(7485), pages 635-640, January.
    2. Orit Rozenblatt-Rosen & Michael J. T. Stubbington & Aviv Regev & Sarah A. Teichmann, 2017. "The Human Cell Atlas: from vision to reality," Nature, Nature, vol. 550(7677), pages 451-453, October.
    3. Adam T. Waickman & Kaitlin Victor & Tao Li & Kristin Hatch & Wiriya Rutvisuttinunt & Carey Medin & Benjamin Gabriel & Richard G. Jarman & Heather Friberg & Jeffrey R. Currier, 2019. "Dissecting the heterogeneity of DENV vaccine-elicited cellular immunity using single-cell RNA sequencing and metabolic profiling," Nature Communications, Nature, vol. 10(1), pages 1-16, December.
    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. Christoph Ziegenhain & Rickard Sandberg, 2021. "BAMboozle removes genetic variation from human sequence data for open data sharing," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    2. Aiko Sekita & Hiroshi Kawasaki & Ayano Fukushima-Nomura & Kiyoshi Yashiro & Keiji Tanese & Susumu Toshima & Koichi Ashizaki & Tomohiro Miyai & Junshi Yazaki & Atsuo Kobayashi & Shinichi Namba & Tatsuh, 2023. "Multifaceted analysis of cross-tissue transcriptomes reveals phenotype–endotype associations in atopic dermatitis," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    3. Yingxin Lin & Yue Cao & Elijah Willie & Ellis Patrick & Jean Y. H. Yang, 2023. "Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    4. Emily Kirby & Alexander Bernier & Roderic Guigó & Barbara Wold & Fabiana Arzuaga & Mayumi Kusunose & Ma’n Zawati & Bartha M. Knoppers, 2024. "Data sharing ethics toolkit: The Human Cell Atlas," Nature Communications, Nature, vol. 15(1), pages 1-7, December.
    5. Rongbo Shen & Lin Liu & Zihan Wu & Ying Zhang & Zhiyuan Yuan & Junfu Guo & Fan Yang & Chao Zhang & Bichao Chen & Wanwan Feng & Chao Liu & Jing Guo & Guozhen Fan & Yong Zhang & Yuxiang Li & Xun Xu & Ji, 2022. "Spatial-ID: a cell typing method for spatially resolved transcriptomics via transfer learning and spatial embedding," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    6. Raphael Lutz & Florian Grünschläger & Malte Simon & Mohamed H. S. Awwad & Marcus Bauer & Schayan Yousefian & Niklas Beumer & Lea Jopp-Saile & Anastasia Sedlmeier & Llorenç Solé-Boldo & Bogdan Avanesya, 2024. "Multiple myeloma long-term survivors exhibit sustained immune alterations decades after first-line therapy," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    7. Dongqing Li & Zhuang Liu & Letian Zhang & Xiaowei Bian & Jianmin Wu & Li Li & Yongjian Chen & Lihua Luo & Ling Pan & Lingzhuo Kong & Yunting Xiao & Jiating Wang & Xiya Zhang & Wang Wang & Maria Toma &, 2024. "The lncRNA SNHG26 drives the inflammatory-to-proliferative state transition of keratinocyte progenitor cells during wound healing," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    8. Andrew Jones & Diana Cai & Didong Li & Barbara E. Engelhardt, 2024. "Optimizing the design of spatial genomic studies," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    9. Erping Long & Montserrat García-Closas & Stephen J. Chanock & M. Constanza Camargo & Nicholas E. Banovich & Jiyeon Choi, 2022. "The case for increasing diversity in tissue-based functional genomics datasets to understand human disease susceptibility," Nature Communications, Nature, vol. 13(1), pages 1-4, December.
    10. Rafael dos Santos Peixoto & Brendan F. Miller & Maigan A. Brusko & Gohta Aihara & Lyla Atta & Manjari Anant & Mark A. Atkinson & Todd M. Brusko & Clive H. Wasserfall & Jean Fan, 2025. "Characterizing cell-type spatial relationships across length scales in spatially resolved omics data," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
    11. Abhishek Nagaraj, 2022. "T he P rivate I mpact of P ublic D ata: L andsat S atellite M aps I ncreased G old D iscoveries and E ncouraged E ntry," Management Science, INFORMS, vol. 68(1), pages 564-582, January.
    12. Claudia Ctortecka & Natalie M. Clark & Brian W. Boyle & Anjali Seth & D. R. Mani & Namrata D. Udeshi & Steven A. Carr, 2024. "Automated single-cell proteomics providing sufficient proteome depth to study complex biology beyond cell type classifications," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    13. Chang Hoon Cho & Ilana Vasilisa Deyneko & Dylann Cordova-Martinez & Juan Vazquez & Anne S. Maguire & Jenny R. Diaz & Abigail U. Carbonell & Jaafar O. Tindi & Min-Hui Cui & Roman Fleysher & Sophie Molh, 2023. "ANKS1B encoded AIDA-1 regulates social behaviors by controlling oligodendrocyte function," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
    14. Katharina T. Schmid & Barbara Höllbacher & Cristiana Cruceanu & Anika Böttcher & Heiko Lickert & Elisabeth B. Binder & Fabian J. Theis & Matthias Heinig, 2021. "scPower accelerates and optimizes the design of multi-sample single cell transcriptomic studies," Nature Communications, Nature, vol. 12(1), pages 1-18, December.
    15. Matthew P. Morrow & Elisabeth Gillespie & Albert Sylvester & Milan R. Amin & Peter C. Belafsky & Simon R. Best & Aaron D. Friedman & Adam M. Klein & David G. Lott & Ted Mau & Randal C. Paniello & Seth, 2025. "DNA immunotherapy for recurrent respiratory papillomatosis (RRP): phase 1/2 study assessing efficacy, safety, and immunogenicity of INO-3107," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
    16. Wei Vivian Li & Yiling Chen & Jingyi Jessica Li, 2017. "TROM: A Testing-Based Method for Finding Transcriptomic Similarity of Biological Samples," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 9(1), pages 105-136, June.
    17. Ajita Shree & Musale Krushna Pavan & Hamim Zafar, 2023. "scDREAMER for atlas-level integration of single-cell datasets using deep generative model paired with adversarial classifier," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    18. Licai Huang & Paul Little & Jeroen R. Huyghe & Qian Shi & Tabitha A. Harrison & Greg Yothers & Thomas J. George & Ulrike Peters & Andrew T. Chan & Polly A. Newcomb & Wei Sun, 2021. "A Statistical Method for Association Analysis of Cell Type Compositions," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 13(3), pages 373-385, December.
    19. Shuo Feng & Liangfeng Huang & Anna Vathrakokoili Pournara & Ziliang Huang & Xinlu Yang & Yongjian Zhang & Alvis Brazma & Ming Shi & Irene Papatheodorou & Zhichao Miao, 2024. "Alleviating batch effects in cell type deconvolution with SCCAF-D," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    20. Lindsay A. Rutter & Henry Cope & Matthew J. MacKay & Raúl Herranz & Saswati Das & Sergey A. Ponomarev & Sylvain V. Costes & Amber M. Paul & Richard Barker & Deanne M. Taylor & Daniela Bezdan & Nathani, 2024. "Astronaut omics and the impact of space on the human body at scale," Nature Communications, Nature, vol. 15(1), pages 1-13, 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_s41467-023-39627-7. 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.