Transcriptomics Unveil Canonical and Non-Canonical Heat Shock-Induced Pathways in Human Cell Lines

Overview

Journal bioRxiv

Date 2025 Jan 7

PMID 39763846

Authors

Andrew Reinschmidt

Luis Solano

Yonny Chavez

William Drew Hulsy

Nikolas Nikolaidis

Affiliations

Soon will be listed here.

Abstract

The cellular stress response (CSR) is a conserved mechanism that protects cells from environmental and physiological stressors. The heat shock response (HSR), a critical component of the CSR, utilizes molecular chaperones to mitigate proteotoxic stress caused by elevated temperatures. We hypothesized that while the canonical HSR pathways are conserved across cell types, specific cell lines may exhibit unique transcriptional responses to heat shock. To test this, we compared the transcriptomic responses of HEK293, HepG2, and HeLa cells under control conditions immediately following heat shock and after an 8-hour recovery period. RNA sequencing revealed conserved activation of canonical HSR pathways, including the unfolded protein response, alongside enrichment of the non-canonical "Receptor Ligand Activity" pathway across all cell lines. Cell line-specific variations were also observed, with HepG2 cells displaying more uniquely expressed genes and elevated expression levels (fold changes) of shared genes under stress conditions. Validation by qPCR confirmed the activation of key genes within the "Receptor Ligand Activity" pathway across time points. These findings provide insights into conserved and context-specific aspects of the HSR, contributing to a more comprehensive understanding of stress response mechanisms across mammalian cells.

References

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

Mahat D, Salamanca H, Duarte F, Danko C, Lis J . Mammalian Heat Shock Response and Mechanisms Underlying Its Genome-wide Transcriptional Regulation. Mol Cell. 2016; 62(1):63-78. PMC: 4826300. DOI: 10.1016/j.molcel.2016.02.025. View

Kultz D . Evolution of the cellular stress proteome: from monophyletic origin to ubiquitous function. J Exp Biol. 2003; 206(Pt 18):3119-24. DOI: 10.1242/jeb.00549. View

Ciocca D, Cayado-Gutierrez N, Maccioni M, Cuello-Carrion F . Heat shock proteins (HSPs) based anti-cancer vaccines. Curr Mol Med. 2012; 12(9):1183-97. DOI: 10.2174/156652412803306684. View

Hellemans J, Mortier G, De Paepe A, Speleman F, Vandesompele J . qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol. 2007; 8(2):R19. PMC: 1852402. DOI: 10.1186/gb-2007-8-2-r19. View

Danecek P, Bonfield J, Liddle J, Marshall J, Ohan V, Pollard M . Twelve years of SAMtools and BCFtools. Gigascience. 2021; 10(2). PMC: 7931819. DOI: 10.1093/gigascience/giab008. View

Sun S, Zhou J . Molecular mechanisms underlying stress response and adaptation. Thorac Cancer. 2017; 9(2):218-227. PMC: 5792716. DOI: 10.1111/1759-7714.12579. View

Ewels P, Magnusson M, Lundin S, Kaller M . MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016; 32(19):3047-8. PMC: 5039924. DOI: 10.1093/bioinformatics/btw354. View

Subramanian A, Tamayo P, Mootha V, Mukherjee S, Ebert B, Gillette M . Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005; 102(43):15545-50. PMC: 1239896. DOI: 10.1073/pnas.0506580102. View

10.

Morimoto R . Regulation of the heat shock transcriptional response: cross talk between a family of heat shock factors, molecular chaperones, and negative regulators. Genes Dev. 1998; 12(24):3788-96. DOI: 10.1101/gad.12.24.3788. View

11.

Livak K, Schmittgen T . Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. 2002; 25(4):402-8. DOI: 10.1006/meth.2001.1262. View

12.

Radons J . The human HSP70 family of chaperones: where do we stand?. Cell Stress Chaperones. 2016; 21(3):379-404. PMC: 4837186. DOI: 10.1007/s12192-016-0676-6. View

13.

Somu P, Mohanty S, Basavegowda N, Yadav A, Paul S, Baek K . The Interplay between Heat Shock Proteins and Cancer Pathogenesis: A Novel Strategy for Cancer Therapeutics. Cancers (Basel). 2024; 16(3). PMC: 10854888. DOI: 10.3390/cancers16030638. View

14.

Spitzer M, Wildenhain J, Rappsilber J, Tyers M . BoxPlotR: a web tool for generation of box plots. Nat Methods. 2014; 11(2):121-2. PMC: 3930876. DOI: 10.1038/nmeth.2811. View

15.

Richter K, Haslbeck M, Buchner J . The heat shock response: life on the verge of death. Mol Cell. 2010; 40(2):253-66. DOI: 10.1016/j.molcel.2010.10.006. View

16.

Ramilowski J, Goldberg T, Harshbarger J, Kloppmann E, Kloppman E, Lizio M . A draft network of ligand-receptor-mediated multicellular signalling in human. Nat Commun. 2015; 6:7866. PMC: 4525178. DOI: 10.1038/ncomms8866. View

17.

Durinck S, Spellman P, Birney E, Huber W . Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nat Protoc. 2009; 4(8):1184-91. PMC: 3159387. DOI: 10.1038/nprot.2009.97. View

18.

Calderwood S, Khaleque M, Sawyer D, Ciocca D . Heat shock proteins in cancer: chaperones of tumorigenesis. Trends Biochem Sci. 2006; 31(3):164-72. DOI: 10.1016/j.tibs.2006.01.006. View

19.

Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A . Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 2002; 3(7):RESEARCH0034. PMC: 126239. DOI: 10.1186/gb-2002-3-7-research0034. View

20.

Kunachowicz D, Krol-Kulikowska M, Raczycka W, Sleziak J, Blazejewska M, Kulbacka J . Heat Shock Proteins, a Double-Edged Sword: Significance in Cancer Progression, Chemotherapy Resistance and Novel Therapeutic Perspectives. Cancers (Basel). 2024; 16(8). PMC: 11048091. DOI: 10.3390/cancers16081500. View