Cell Type-specific Weighting-factors to Solve Solid Organs-specific Limitations of Single Cell RNA-sequencing

Overview

Journal PLoS Genet

Specialty Genetics

Date 2024 Nov 18

PMID 39556600

Authors

Kengo Tejima

Satoshi Kozawa

Thomas N Sato

Affiliations

Soon will be listed here.

Abstract

While single-cell RNA-sequencing (scRNA-seq) is a popular method to analyze gene expression and cellular composition at single-cell resolution, it harbors shortcomings: The failure to account for cell-to-cell variations of transcriptome-size (i.e., the total number of transcripts per cell) and also cell dissociation/processing-induced cryptic gene expression. This is particularly a problem when analyzing highly heterogeneous solid tissues/organs, which requires cell dissociation for the analysis. As a result, there exists a discrepancy between bulk RNA-seq result and virtually reconstituted bulk RNA-seq result using its composite scRNA-seq data. To fix this problem, we propose a computationally calculated coefficient, "cell type-specific weighting-factor (cWF)". Here, we introduce a concept and a method of its computation and report cWFs for 76 cell-types across 10 solid organs. Their fidelity is validated by more accurate reconstitution and deconvolution of bulk RNA-seq data of diverse solid organs using the scRNA-seq data and the cWFs of their composite cells. Furthermore, we also show that cWFs effectively predict aging-progression, implicating their diagnostic applications and also their association with aging mechanism. Our study provides an important method to solve critical limitations of scRNA-seq analysis of complex solid tissues/organs. Furthermore, our findings suggest a diagnostic utility and biological significance of cWFs.

References

Schaum N, Lehallier B, Hahn O, Palovics R, Hosseinzadeh S, Lee S . Ageing hallmarks exhibit organ-specific temporal signatures. Nature. 2020; 583(7817):596-602. PMC: 7757734. DOI: 10.1038/s41586-020-2499-y. View

Wang X, Park J, Susztak K, Zhang N, Li M . Bulk tissue cell type deconvolution with multi-subject single-cell expression reference. Nat Commun. 2019; 10(1):380. PMC: 6342984. DOI: 10.1038/s41467-018-08023-x. View

. Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris. Nature. 2018; 562(7727):367-372. PMC: 6642641. DOI: 10.1038/s41586-018-0590-4. View

Pinto A, Ilinykh A, Ivey M, Kuwabara J, DAntoni M, Debuque R . Revisiting Cardiac Cellular Composition. Circ Res. 2015; 118(3):400-9. PMC: 4744092. DOI: 10.1161/CIRCRESAHA.115.307778. View

Raulf A, Horder H, Tarnawski L, Geisen C, Ottersbach A, Roll W . Transgenic systems for unequivocal identification of cardiac myocyte nuclei and analysis of cardiomyocyte cell cycle status. Basic Res Cardiol. 2015; 110(3):33. PMC: 4414935. DOI: 10.1007/s00395-015-0489-2. View

Nie Z, Hu G, Wei G, Cui K, Yamane A, Resch W . c-Myc is a universal amplifier of expressed genes in lymphocytes and embryonic stem cells. Cell. 2012; 151(1):68-79. PMC: 3471363. DOI: 10.1016/j.cell.2012.08.033. View

Anders S, Pyl P, Huber W . HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2014; 31(2):166-9. PMC: 4287950. DOI: 10.1093/bioinformatics/btu638. View

Racle J, de Jonge K, Baumgaertner P, Speiser D, Gfeller D . Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data. Elife. 2017; 6. PMC: 5718706. DOI: 10.7554/eLife.26476. View

Schmidt E, Schibler U . Cell size regulation, a mechanism that controls cellular RNA accumulation: consequences on regulation of the ubiquitous transcription factors Oct1 and NF-Y and the liver-enriched transcription factor DBP. J Cell Biol. 1995; 128(4):467-83. PMC: 2199888. DOI: 10.1083/jcb.128.4.467. View

10.

Zaitsev K, Bambouskova M, Swain A, Artyomov M . Complete deconvolution of cellular mixtures based on linearity of transcriptional signatures. Nat Commun. 2019; 10(1):2209. PMC: 6525259. DOI: 10.1038/s41467-019-09990-5. View

11.

Kozawa S, Sagawa F, Endo S, De Almeida G, Mitsuishi Y, Sato T . Predicting Human Clinical Outcomes Using Mouse Multi-Organ Transcriptome. iScience. 2020; 23(2):100791. PMC: 7033637. DOI: 10.1016/j.isci.2019.100791. View

12.

Joost S, Annusver K, Jacob T, Sun X, Dalessandri T, Sivan U . The Molecular Anatomy of Mouse Skin during Hair Growth and Rest. Cell Stem Cell. 2020; 26(3):441-457.e7. DOI: 10.1016/j.stem.2020.01.012. View

13.

Walsh S, Ponten A, Fleischmann B, Jovinge S . Cardiomyocyte cell cycle control and growth estimation in vivo--an analysis based on cardiomyocyte nuclei. Cardiovasc Res. 2010; 86(3):365-73. DOI: 10.1093/cvr/cvq005. View

14.

Bergmann O, Zdunek S, Felker A, Salehpour M, Alkass K, Bernard S . Dynamics of Cell Generation and Turnover in the Human Heart. Cell. 2015; 161(7):1566-75. DOI: 10.1016/j.cell.2015.05.026. View

15.

Zhurinsky J, Leonhard K, Watt S, Marguerat S, Bahler J, Nurse P . A coordinated global control over cellular transcription. Curr Biol. 2010; 20(22):2010-5. DOI: 10.1016/j.cub.2010.10.002. View

16.

Zhou P, Pu W . Recounting Cardiac Cellular Composition. Circ Res. 2016; 118(3):368-70. PMC: 4755297. DOI: 10.1161/CIRCRESAHA.116.308139. View

17.

Hu Z, Chen K, Xia Z, Chavez M, Pal S, Seol J . Nucleosome loss leads to global transcriptional up-regulation and genomic instability during yeast aging. Genes Dev. 2014; 28(4):396-408. PMC: 3937517. DOI: 10.1101/gad.233221.113. View

18.

Finotello F, Mayer C, Plattner C, Laschober G, Rieder D, Hackl H . Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data. Genome Med. 2019; 11(1):34. PMC: 6534875. DOI: 10.1186/s13073-019-0638-6. View

19.

Hao Y, Hao S, Andersen-Nissen E, Mauck 3rd W, Zheng S, Butler A . Integrated analysis of multimodal single-cell data. Cell. 2021; 184(13):3573-3587.e29. PMC: 8238499. DOI: 10.1016/j.cell.2021.04.048. View

20.

Li Y, Wang H, Muffat J, Cheng A, Orlando D, Loven J . Global transcriptional and translational repression in human-embryonic-stem-cell-derived Rett syndrome neurons. Cell Stem Cell. 2013; 13(4):446-58. PMC: 4053296. DOI: 10.1016/j.stem.2013.09.001. View