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Hepatology International

, Volume 13, Issue 4, pp 454–467 | Cite as

Alteration of splicing factors’ expression during liver disease progression: impact on hepatocellular carcinoma outcome

  • Hualin Wang
  • Bouchra Lekbaby
  • Nadim Fares
  • Jeremy Augustin
  • Tarik Attout
  • Aurelie Schnuriger
  • Anne-Marie Cassard
  • Ganna Panasyuk
  • Gabriel Perlemuter
  • Ivan Bieche
  • Sophie Vacher
  • Janick Selves
  • Jean-Marie Péron
  • Brigitte Bancel
  • Philippe Merle
  • Dina Kremsdorf
  • Janet Hall
  • Isabelle Chemin
  • Patrick SoussanEmail author
Original Article

Abstract

Purpose

Trans-acting splicing factors (SF) shape the eukaryotic transcriptome by regulating alternative splicing (AS). This process is recurrently modulated in liver cancer suggesting its direct contribution to the course of liver disease. The aim of our study was to investigate the relationship between the regulation of SFs expression and liver damage.

Methods

The expression profile of 10 liver-specific SF and the AS events of 7 genes associated with liver disorders was assessed by western-blotting in 6 murine models representing different stages of liver damage, from inflammation to hepatocellular carcinoma (HCC). Relevant SFs (PSF, SRSF3, and SRSF6) and target genes (INSR, SRSF3, and SLK) modulated in mice were investigated in a cohort of 179 HCC patients.

Results

Each murine model of liver disease was characterized by a unique SF expression profile. Changes in the SF profile did not affect AS events of the selected genes despite the presence of corresponding splicing sites. In human HCC expression of SFs, including the tumor-suppressor SRSF3, and AS regulation of genes studied were frequently upregulated in tumor versus non-tumor tissues. Risk of tumor recurrence positively correlated with AS isoform of the INSR gene. In contrast, increased levels of SFs expression correlated with an extended overall survival of patients.

Conclusions

Dysregulation of SF expression is an early event occurring during liver injury and not just at the stage of HCC. Besides impacting on AS regulation, overexpression of SF may contribute to preserving hepatocyte homeostasis during liver pathogenesis.

Keywords

Alternative splicing Splicing factors Liver disease Hepatocellular carcinoma 

Abbreviations

AS

Alternative splicing

SF

Splicing factors

SRSF

Serine/arginine-rich splicing factor

hnRNP

Heterogeneous nuclear ribonucleoprotein

PSF

Proline-rich splicing factor

SF1

Splicing factor 1

La

Lupus autoantigen

HCC

Hepatocellular carcinoma

NAFLD

Non-alcoholic fatty liver disease

ALD

Alcohol liver disease

T

Tumor

NT

Non-tumor

LPS

Lipopolysaccharide

CCl4

Carbon tetrachloride

HFD

High-fat diet

ND

Normal diet

DEN

Diethylnitrosamine

Dgkd

Diacylglycerol kinase, delta

Slk

STE20-like kinase

Fas

TNF receptor superfamily member 6

Col18a1

Collagen, type XVIII, alpha 1

InsR

Insulin receptor

SRSF3

Serine/arginine-rich splicing factor 3

Usp4

Ubiquitin specific peptidase 4

Notes

Acknowledgements

We thank Drs J. Pol, P. De La Grange, G. Wang and M. Dutertre for helpful scientific discussion. We thank animal facilities platform from Pitié and Broussais Universities. We thank P3S platform of Pitié University. We also thank the TCGA Research Network (http://cancergenome.nih.gov/) for HCC data.

Author contributions

Experimental conception and design of these experiments HW, JH, IC, and PS. Conduction the experiments: HW, BL, NF, ACS, GP, JA, IB, SV, and PS. Analysis of the data: HW, NF, TA, AS, GP, DK, JH, IC and PS. Provide biological samples: JS, JMP, BB, PM. Wrote the manuscript: HW, JH, DK and PS.

Funding

This work was supported by grants from INSERM, Sorbonne Université, Fondation ARC (Grant number M17JRAS009) and ANRS (Grant number ECTZ22204). HW was supported by the China Scholarship Council.

Compliance with ethical standards

Conflicts of interest

Hualin Wang, Bouchra Lekbaby, Nadim Fares, Jeremy Augustin, Tarik Attout, Aurelie Schnuriger, Anne-Marie Cassard, Ganna Panasyuk, Gabriel Perlemute, Ivan Bieche, Sophie Vacher, Janick Selves, Jean-Marie Péron, Brigitte Bancel, Philippe, Dina Kremsdorf, Janet Hall, Isabelle Chemin, Patrick Soussan have no conflict of interest to declare.

Informed consent

Signed informed patient consent was obtained before surgery.

Supplementary material

12072_2019_9950_MOESM1_ESM.docx (148 kb)
Supplementary material 1 (DOCX 147 kb)
12072_2019_9950_MOESM2_ESM.pptx (3.9 mb)
Supplementary material 2 (PPTX 4036 kb)
12072_2019_9950_MOESM3_ESM.docx (23 kb)
Supplementary material 3 (DOCX 23 kb)

References

  1. 1.
    Pohl M, Bortfeldt RH, Grutzmann K, Schuster S. Alternative splicing of mutually exclusive exons—a review. Biosystems 2013;114:31–38CrossRefPubMedGoogle Scholar
  2. 2.
    Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 2008;40:1413–1415CrossRefPubMedGoogle Scholar
  3. 3.
    Tress ML, Abascal F, Valencia A. Most alternative isoforms are not functionally important. Trends Biochem Sci 2017;42:408–410CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Tress ML, Abascal F, Valencia A. Alternative splicing may not be the key to proteome complexity. Trends Biochem Sci 2017;42:98–110CrossRefPubMedGoogle Scholar
  5. 5.
    Grosso AR, Gomes AQ, Barbosa-Morais NL, Caldeira S, Thorne NP, Grech G, et al. Tissue-specific splicing factor gene expression signatures. Nucleic Acids Res 2008;36:4823–4832CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Lee BP, Pilling LC, Emond F, Flurkey K, Harrison DE, Yuan R, et al. Changes in the expression of splicing factor transcripts and variations in alternative splicing are associated with lifespan in mice and humans. Aging Cell 2016;15:903–913CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    de la Grange P, Gratadou L, Delord M, Dutertre M, Auboeuf D. Splicing factor and exon profiling across human tissues. Nucleic Acids Res 2010;38:2825–2838CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Berasain C, Goni S, Castillo J, Latasa MU, Prieto J, Avila MA. Impairment of pre-mRNA splicing in liver disease: mechanisms and consequences. World J Gastroenterol 2010;16:3091–3102CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Venables JP. Aberrant and alternative splicing in cancer. Cancer Res 2004;64:7647–7654CrossRefPubMedGoogle Scholar
  10. 10.
    Li S, Hu Z, Zhao Y, Huang S, He X. Transcriptome-wide analysis reveals the landscape of aberrant alternative splicing events in liver cancer. Hepatology 2019;69:359–375CrossRefPubMedGoogle Scholar
  11. 11.
    Karni R, de Stanchina E, Lowe SW, Sinha R, Mu D, Krainer AR. The gene encoding the splicing factor SF2/ASF is a proto-oncogene. Nat Struct Mol Biol 2007;14:185–193CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Sen S, Langiewicz M, Jumaa H, Webster NJ. Deletion of serine/arginine-rich splicing factor 3 in hepatocytes predisposes to hepatocellular carcinoma in mice. Hepatology 2015;61:171–183CrossRefPubMedGoogle Scholar
  13. 13.
    Sen S, Jumaa H, Webster NJ. Splicing factor SRSF3 is crucial for hepatocyte differentiation and metabolic function. Nat Commun 2013;4:1336CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Karni R, Hippo Y, Lowe SW, Krainer AR. The splicing-factor oncoprotein SF2/ASF activates mTORC1. Proc Natl Acad Sci USA 2008;105:15323–15327CrossRefPubMedGoogle Scholar
  15. 15.
    Duriez M, Mandouri Y, Lekbaby B, Wang H, Redelsperger F, Guerrera C, et al. Alternative splicing of Hepatitis B virus: a novel virus/host interaction regulating liver immunity. J Hepatol 2017;67:687–699CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Pol JG, Lekbaby B, Redelsperger F, Klamer S, Mandouri Y, Ahodantin J, et al. Alternative splicing-regulated protein of hepatitis B virus hacks the TNF-alpha-stimulated signaling pathways and limits the extent of liver inflammation. FASEB J 2015;29:1879–1889CrossRefPubMedGoogle Scholar
  17. 17.
    Gustot T, Lemmers A, Moreno C, Nagy N, Quertinmont E, Nicaise C, et al. Differential liver sensitization to toll-like receptor pathways in mice with alcoholic fatty liver. Hepatology 2006;43:989–1000CrossRefPubMedGoogle Scholar
  18. 18.
    Ki SH, Park O, Zheng M, Morales-Ibanez O, Kolls JK, Bataller R, et al.. Interleukin-22 treatment ameliorates alcoholic liver injury in a murine model of chronic-binge ethanol feeding: role of signal transducer and activator of transcription 3. Hepatology 2010;52:1291–1300CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Bertola A, Mathews S, Ki SH, Wang H, Gao B. Mouse model of chronic and binge ethanol feeding (the NIAAA model). Nat Protoc 2013;8:627–637CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Horie Y, Suzuki A, Kataoka E, Sasaki T, Hamada K, Sasaki J, et al. Hepatocyte-specific Pten deficiency results in steatohepatitis and hepatocellular carcinomas. J Clin Invest 2004;113:1774–1783CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Patitucci C, Couchy G, Bagattin A, Caneque T, de Reynies A, Scoazec JY, et al. Hepatocyte nuclear factor 1alpha suppresses steatosis-associated liver cancer by inhibiting PPARgamma transcription. J Clin Invest 2017;127:1873–1888CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Shav-Tal Y, Lee B, Bar-Haim S, Vandekerckhove J, Zipori D. Enhanced proteolysis of pre-mRNA splicing factors in myeloid cells. Exp Hematol 2000;28:1029–1038CrossRefPubMedGoogle Scholar
  23. 23.
    de la Grange P, Dutertre M, Correa M, Auboeuf D. A new advance in alternative splicing databases: from catalogue to detailed analysis of regulation of expression and function of human alternative splicing variants. BMC Bioinform 2007;8:180CrossRefGoogle Scholar
  24. 24.
    Bhate A, Parker DJ, Bebee TW, Ahn J, Arif W, Rashan EH, et al. ESRP2 controls an adult splicing programme in hepatocytes to support postnatal liver maturation. Nat Commun 2015;6:8768CrossRefPubMedPubMedCentralGoogle Scholar
  25. 25.
    Huang CK, Yu T, de la Monte SM, Wands JR, Derdak Z, Kim M. Restoration of Wnt/beta-catenin signaling attenuates alcoholic liver disease progression in a rat model. J Hepatol 2015;63:191–198CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Zhao Y, Gao L, Xu L, Tong R, Lin N, Su Y, et al. Ubiquitin-specific protease 4 is an endogenous negative regulator of metabolic dysfunctions in nonalcoholic fatty liver disease. Hepatology 2018.  https://doi.org/10.1002/hep.29889 CrossRefPubMedPubMedCentralGoogle Scholar
  27. 27.
    Heljasvaara R, Aikio M, Ruotsalainen H, Pihlajaniemi T. Collagen XVIII in tissue homeostasis and dysregulation—lessons learned from model organisms and human patients. Matrix Biol 2017;57–58:55–75CrossRefPubMedGoogle Scholar
  28. 28.
    Aikio M, Elamaa H, Vicente D, Izzi V, Kaur I, Seppinen L, et al. Specific collagen XVIII isoforms promote adipose tissue accrual via mechanisms determining adipocyte number and affect fat deposition. Proc Natl Acad Sci USA 2014;111:3043–3052CrossRefGoogle Scholar
  29. 29.
    Chettouh H, Fartoux L, Aoudjehane L, Wendum D, Claperon A, Chretien Y, et al. Mitogenic insulin receptor-A is overexpressed in human hepatocellular carcinoma due to EGFR-mediated dysregulation of RNA splicing factors. Cancer Res 2013;73:3974–3986CrossRefPubMedGoogle Scholar
  30. 30.
    Sakurai Y, Kubota N, Takamoto I, Obata A, Iwamoto M, Hayashi T, et al. Role of insulin receptor substrates in the progression of hepatocellular carcinoma. Sci Rep 2017;7:5387CrossRefPubMedPubMedCentralGoogle Scholar
  31. 31.
    Kubota T, Kubota N, Kadowaki T. Imbalanced insulin actions in obesity and type 2 diabetes: key mouse models of insulin signaling pathway. Cell Metab 2017;25:797–810CrossRefPubMedGoogle Scholar
  32. 32.
    Paz I, Akerman M, Dror I, Kosti I, Mandel-Gutfreund Y. SFmap: a web server for motif analysis and prediction of splicing factor binding sites. Nucleic Acids Res 2010;38:281–285CrossRefGoogle Scholar
  33. 33.
    Llovet JM, Zucman-Rossi J, Pikarsky E, Sangro B, Schwartz M, Sherman M, et al. Hepatocellular carcinoma. Nat Rev Dis Primers 2016;2:16018CrossRefPubMedGoogle Scholar
  34. 34.
    Kozlovski I, Siegfried Z, Amar-Schwartz A, Karni R. The role of RNA alternative splicing in regulating cancer metabolism. Hum Genet 2017;26:1113–1127CrossRefGoogle Scholar
  35. 35.
    Belfiore A, Frasca F, Pandini G, Sciacca L, Vigneri R. Insulin receptor isoforms and insulin receptor/insulin-like growth factor receptor hybrids in physiology and disease. Endocr Rev 2009;30:586–623CrossRefPubMedGoogle Scholar
  36. 36.
    Chen YW, Boyartchuk V, Lewis BC. Differential roles of insulin-like growth factor receptor- and insulin receptor-mediated signaling in the phenotypes of hepatocellular carcinoma cells. Neoplasia 2009;11:835–845CrossRefPubMedPubMedCentralGoogle Scholar
  37. 37.
    Besic V, Shi H, Stubbs RS, Hayes MT. Aberrant liver insulin receptor isoform a expression normalises with remission of type 2 diabetes after gastric bypass surgery. PLoS One 2015;10:e0119270CrossRefPubMedPubMedCentralGoogle Scholar
  38. 38.
    Braeutigam C, Rago L, Rolke A, Waldmeier L, Christofori G, Winter J. The RNA-binding protein Rbfox2: an essential regulator of EMT-driven alternative splicing and a mediator of cellular invasion. Oncogene 2014;33:1082–1092CrossRefGoogle Scholar
  39. 39.
    Warzecha CC, Jiang P, Amirikian K, Dittmar KA, Lu H, Shen S, et al. An ESRP-regulated splicing programme is abrogated during the epithelial-mesenchymal transition. EMBO J 2010;29:3286–3300CrossRefPubMedPubMedCentralGoogle Scholar
  40. 40.
    Jumaa H, Nielsen PJ. The splicing factor SRp20 modifies splicing of its own mRNA and ASF/SF2 antagonizes this regulation. EMBO J 1997;16:5077–5085.CrossRefPubMedPubMedCentralGoogle Scholar
  41. 41.
    Takayama KI, Suzuki T, Fujimura T, Yamada Y, Takahashi S, Homma Y, et al. Dysregulation of spliceosome gene expression in advanced prostate cancer by RNA-binding protein PSF. Proc Natl Acad Sci USA 2017;114:10461–10466CrossRefPubMedGoogle Scholar
  42. 42.
    Jaafar L, Li Z, Li S, Dynan WS. SFPQ*NONO and XLF function separately and together to promote DNA double-strand break repair via canonical nonhomologous end joining. Nucleic Acids Res 2017;45:1848–1859CrossRefPubMedGoogle Scholar
  43. 43.
    Morozumi Y, Takizawa Y, Takaku M, Kurumizaka H. Human PSF binds to RAD51 and modulates its homologous-pairing and strand-exchange activities. Nucleic Acids Res 2009;37:4296–4307CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Asian Pacific Association for the Study of the Liver 2019

Authors and Affiliations

  • Hualin Wang
    • 1
    • 2
  • Bouchra Lekbaby
    • 1
    • 2
  • Nadim Fares
    • 3
  • Jeremy Augustin
    • 1
    • 2
  • Tarik Attout
    • 1
    • 2
  • Aurelie Schnuriger
    • 1
    • 2
    • 4
  • Anne-Marie Cassard
    • 5
  • Ganna Panasyuk
    • 6
    • 7
  • Gabriel Perlemuter
    • 5
    • 8
  • Ivan Bieche
    • 9
  • Sophie Vacher
    • 9
  • Janick Selves
    • 10
  • Jean-Marie Péron
    • 10
  • Brigitte Bancel
    • 3
  • Philippe Merle
    • 3
  • Dina Kremsdorf
    • 1
    • 2
  • Janet Hall
    • 3
  • Isabelle Chemin
    • 3
  • Patrick Soussan
    • 1
    • 2
    • 4
    Email author
  1. 1.INSERM U1135, Centre d’immunologie et de maladie infectieuseParisFrance
  2. 2.Sorbonne UniversitéParisFrance
  3. 3.Centre de Recherche en Cancérologie de Lyon, UMR INSERM 1052, CNRS 5286Lyon Cedex 03France
  4. 4.Département de Virologie, Hôpitaux Est ParisienParisFrance
  5. 5.Faculté de médecine Paris-SudUniversité Paris-SudKremlin-BicêtreFrance
  6. 6.Institut Necker-Enfants MaladesUniversité Paris DescartesParisFrance
  7. 7.INSERM U1151/CNRS Unité Mixte de Recherche (UMR) 8253ParisFrance
  8. 8.AP-HP, Hôpital Antoine Béclère, Service d’hépato-gastroentérologieClamartFrance
  9. 9.Institut Curie-HôpitalParisFrance
  10. 10.Institut Universitaire de Cancérologie de Toulouse OncopoleUniversité Paul SabatierToulouseFrance

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