Altered histone acetylation patterns in pancreatic cancer cell lines induce subtype‑specific transcriptomic and phenotypical changes

Zhou,Quan; Zhou,Quan; Zhou,Quan; Zhou,Quan; Zhou,Quan; Zhou,Quan; Zhou,Quan; Zhou,Quan; Pichlmeier,Svenja; Pichlmeier,Svenja; Pichlmeier,Svenja; Pichlmeier,Svenja; Pichlmeier,Svenja; Pichlmeier,Svenja; Pichlmeier,Svenja; Pichlmeier,Svenja; Denz,Anna Maria; Denz,Anna Maria; Denz,Anna Maria; Denz,Anna Maria; Denz,Anna Maria; Denz,Anna Maria; Denz,Anna Maria; Denz,Anna Maria; Schreiner,Nicole; Schreiner,Nicole; Schreiner,Nicole; Schreiner,Nicole; Schreiner,Nicole; Schreiner,Nicole; Schreiner,Nicole; Schreiner,Nicole; Straub,Tobias; Straub,Tobias; Straub,Tobias; Straub,Tobias; Straub,Tobias; Straub,Tobias; Straub,Tobias; Straub,Tobias; Benitz,Simone; Benitz,Simone; Benitz,Simone; Benitz,Simone; Benitz,Simone; Benitz,Simone; Benitz,Simone; Benitz,Simone; Wolff,Julia; Wolff,Julia; Wolff,Julia; Wolff,Julia; Wolff,Julia; Wolff,Julia; Wolff,Julia; Wolff,Julia; Fahr,Lisa; Fahr,Lisa; Fahr,Lisa; Fahr,Lisa; Fahr,Lisa; Fahr,Lisa; Fahr,Lisa; Fahr,Lisa; Del Socorro Escobar Lopez,Maria; Del Socorro Escobar Lopez,Maria; Del Socorro Escobar Lopez,Maria; Del Socorro Escobar Lopez,Maria; Del Socorro Escobar Lopez,Maria; Del Socorro Escobar Lopez,Maria; Del Socorro Escobar Lopez,Maria; Del Socorro Escobar Lopez,Maria; Kleeff,Jörg; Kleeff,Jörg; Kleeff,Jörg; Kleeff,Jörg; Kleeff,Jörg; Kleeff,Jörg; Kleeff,Jörg; Kleeff,Jörg; Mayerle,Julia; Mayerle,Julia; Mayerle,Julia; Mayerle,Julia; Mayerle,Julia; Mayerle,Julia; Mayerle,Julia; Mayerle,Julia; Mahajan,Ujjwal Mukund; Mahajan,Ujjwal Mukund; Mahajan,Ujjwal Mukund; Mahajan,Ujjwal Mukund; Mahajan,Ujjwal Mukund; Mahajan,Ujjwal Mukund; Mahajan,Ujjwal Mukund; Mahajan,Ujjwal Mukund; Regel,Ivonne; Regel,Ivonne; Regel,Ivonne; Regel,Ivonne; Regel,Ivonne; Regel,Ivonne; Regel,Ivonne; Regel,Ivonne

doi:10.3892/ijo.2024.5614

Altered histone acetylation patterns in pancreatic cancer cell lines induce subtype‑specific transcriptomic and phenotypical changes

Authors:
- Quan Zhou
- Svenja Pichlmeier
- Anna Maria Denz
- Nicole Schreiner
- Tobias Straub
- Simone Benitz
- Julia Wolff
- Lisa Fahr
- Maria Del Socorro Escobar Lopez
- Jörg Kleeff
- Julia Mayerle
- Ujjwal Mukund Mahajan
- Ivonne Regel
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Affiliations: Department of Medicine II, University Hospital, LMU Munich, D‑81377 Munich, Germany, Bioinformatic Unit, Biomedical Center, Faculty of Medicine, LMU Munich, D‑82152 Planegg‑Martinsried, Germany, Department of Surgery, Henry Ford Health System, Detroit, MI 48208, USA, Department of Surgery, Martin‑Luther University Halle‑Wittenberg, D‑06120 Halle (Saale), Germany
Published online on: January 16, 2024 https://doi.org/10.3892/ijo.2024.5614
Article Number: 26
Copyright: © Zhou et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

Pancreatic ductal adenocarcinoma (PDAC) is often diagnosed at advanced tumor stages with chemotherapy as the only treatment option. Transcriptomic analysis has defined a classical and basal‑like PDAC subtype, which are regulated by epigenetic modification. The present study aimed to determine if drug‑induced epigenetic reprogramming of pancreatic cancer cells affects PDAC subtype identity and chemosensitivity. Classical and basal‑like PDAC cell lines PaTu‑S, Capan‑1, Capan‑2, Colo357, PaTu‑T, PANC‑1 and MIAPaCa‑2, were treated for a short (up to 96 h) and long (up to 30 weeks) period with histone acetyltransferase (HAT) and histone deacetylase (HDAC) inhibitors. The cells were analyzed using gene expression approaches, immunoblot analysis, and various cell assays to assess cell characteristics, such as proliferation, colony formation, cell migration and sensitivity to chemotherapeutic drugs. Classical and basal‑like PDAC cell lines showed pronounced epigenetic regulation of subtype‑specific genes through acetylation of lysine 27 on Histone H3 (H3K27ac). Moreover, classical cell lines revealed a significantly decreased expression of HDAC2 and increased total levels of H3K27ac in comparison with the basal‑like cell lines. Following HAT inhibitor treatment, classical cell lines exhibited a loss of epithelial marker gene expression, decreased chemotherapy response gene score and increased cell migration in vitro, indicating a tumor‑promoting phenotype. HDAC inhibitor treatment, however, exerted minimal reprogramming effects in both subtypes. Epigenetic reprogramming of classical and basal‑like tumor cells did not have a major impact on gemcitabine response, although the gemcitabine transporter gene SLC29A1 (solute carrier family 29 member 1) was epigenetically regulated.

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1	Connor AA and Gallinger S: Pancreatic cancer evolution and heterogeneity: Integrating omics and clinical data. Nat Rev Cancer. 22:131–142. 2022. View Article : Google Scholar
2	Regel I, Mayerle J and Mahajan UM: Current Strategies and future perspectives for precision medicine in pancreatic cancer. Cancers (Basel). 12:10242020. View Article : Google Scholar : PubMed/NCBI
3	Chan-Seng-Yue M, Kim JC, Wilson GW, Ng K, Figueroa EF, O'Kane GM, Connor AA, Denroche RE, Grant RC, McLeod J, et al: Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution. Nat Genet. 52:231–240. 2020. View Article : Google Scholar : PubMed/NCBI
4	Williams HL, Dias Costa A, Zhang J, Raghavan S, Winter PS, Kapner KS, Ginebaugh SP, Väyrynen SA, Väyrynen JP, Yuan C, et al: Spatially resolved single-cell assessment of pancreatic cancer expression subtypes reveals co-expressor phenotypes and extensive intratumoral heterogeneity. Cancer Res. 83:441–455. 2023. View Article : Google Scholar :
5	Bailey P, Chang DK, Nones K, Johns AL, Patch AM, Gingras MC, Miller DK, Christ AN, Bruxner TJ, Quinn MC, et al: Genomic analyses identify molecular subtypes of pancreatic cancer. Nature. 531:47–52. 2016. View Article : Google Scholar : PubMed/NCBI
6	Lomberk G, Blum Y, Nicolle R, Nair A, Gaonkar KS, Marisa L, Mathison A, Sun Z, Yan H, Elarouci N, et al: Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes. Nature communications. 9:19782018. View Article : Google Scholar : PubMed/NCBI
7	Shvedunova M and Akhtar A: Modulation of cellular processes by histone and non-histone protein acetylation. Nat Rev Mol Cell Biol. 23:329–349. 2022. View Article : Google Scholar : PubMed/NCBI
8	Aghdassi A, Sendler M, Guenther A, Mayerle J, Behn CO, Heidecke CD, Friess H, Büchler M, Evert M, Lerch MM and Weiss FU: Recruitment of histone deacetylases HDAC1 and HDAC2 by the transcriptional repressor ZEB1 downregulates E-cadherin expression in pancreatic cancer. Gut. 61:439–448. 2012. View Article : Google Scholar
9	von Burstin J, Eser S, Paul MC, Seidler B, Brandl M, Messer M, von Werder A, Schmidt A, Mages J, Pagel P, et al: E-cadherin regulates metastasis of pancreatic cancer in vivo and is suppressed by a SNAIL/HDAC1/HDAC2 repressor complex. Gastroenterology. 137:361–371. 371.e1–e5. 2009. View Article : Google Scholar : PubMed/NCBI
10	Roca MS, Moccia T, Iannelli F, Testa C, Vitagliano C, Minopoli M, Camerlingo R, De Riso G, De Cecio R, Bruzzese F, et al: HDAC class I inhibitor domatinostat sensitizes pancreatic cancer to chemotherapy by targeting cancer stem cell compartment via FOXM1 modulation. J Exp Clin Cancer Res. 41:832022. View Article : Google Scholar : PubMed/NCBI
11	Lee HS, Park SB, Kim SA, Kwon SK, Cha H, Lee DY, Ro S, Cho JM and Song SY: A novel HDAC inhibitor, CG200745, inhibits pancreatic cancer cell growth and overcomes gemcitabine resistance. Sci Rep. 7:416152017. View Article : Google Scholar : PubMed/NCBI
12	Edderkaoui M, Chheda C, Soufi B, Zayou F, Hu RW, Ramanujan VK, Pan X, Boros LG, Tajbakhsh J, Madhav A, et al: An inhibitor of GSK3B and HDACs kills pancreatic cancer cells and slows pancreatic tumor growth and metastasis in mice. Gastroenterology. 155:1985–1998.e5. 2018. View Article : Google Scholar : PubMed/NCBI
13	Cai MH, Xu XG, Yan SL, Sun Z, Ying Y, Wang BK and Tu YX: Depletion of HDAC1, 7 and 8 by histone deacetylase inhibition confers elimination of pancreatic cancer stem cells in combination with gemcitabine. Sci Rep. 8:16212018. View Article : Google Scholar : PubMed/NCBI
14	Hessmann E, Johnsen SA, Siveke JT and Ellenrieder V: Epigenetic treatment of pancreatic cancer: Is there a therapeutic perspective on the horizon? Gut. 66:168–179. 2017. View Article : Google Scholar
15	Diaferia GR, Balestrieri C, Prosperini E, Nicoli P, Spaggiari P, Zerbi A and Natoli G: Dissection of transcriptional and cisregulatory control of differentiation in human pancreatic cancer. EMBO J. 35:595–617. 2016. View Article : Google Scholar : PubMed/NCBI
16	Suarez-Arnedo A, Torres Figueroa F, Clavijo C, Arbeláez P, Cruz JC and Muñoz-Camargo C: An image J plugin for the high throughput image analysis of in vitro scratch wound healing assays. PLoS One. 15:e02325652020. View Article : Google Scholar : PubMed/NCBI
17	Pfaffl MW: A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 29:e452001. View Article : Google Scholar : PubMed/NCBI
18	Kopylova E, Noé L and Touzet H: SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics. 28:3211–3217. 2012. View Article : Google Scholar : PubMed/NCBI
19	Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M and Gingeras TR: STAR: Ultrafast universal RNA-seq aligner. Bioinformatics. 29:15–21. 2013. View Article : Google Scholar
20	Love MI, Huber W and Anders S: Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15:5502014. View Article : Google Scholar : PubMed/NCBI
21	Wu T, Hu E, Xu S, Chen M, Guo P, Dai Z, Feng T, Zhou L, Tang W, Zhan L, et al: clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. Innovation (Camb). 2:1001412021.PubMed/NCBI
22	Yu G, Wang LG, Han Y and He QY: clusterProfiler: An R package for comparing biological themes among gene clusters. OMICS. 16:284–287. 2012. View Article : Google Scholar : PubMed/NCBI
23	Gröger CJ, Grubinger M, Waldhör T, Vierlinger K and Mikulits W: Meta-analysis of gene expression signatures defining the epithelial to mesenchymal transition during cancer progression. PLoS One. 7:e511362012. View Article : Google Scholar : PubMed/NCBI
24	Nicolle R, Gayet O, Duconseil P, Vanbrugghe C, Roques J, Bigonnet M, Blum Y, Elarouci N, Armenoult L, Ayadi M, et al: A transcriptomic signature to predict adjuvant gemcitabine sensitivity in pancreatic adenocarcinoma. Ann Oncol. 32:250–260. 2021. View Article : Google Scholar
25	Collisson EA, Sadanandam A, Olson P, Gibb WJ, Truitt M, Gu S, Cooc J, Weinkle J, Kim GE, Jakkula L, et al: Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy. Nat Med. 17:500–503. 2011. View Article : Google Scholar : PubMed/NCBI
26	Fujisawa T and Filippakopoulos P: Functions of bromodomain-containing proteins and their roles in homeostasis and cancer. Nat Rev Mol Cell Biol. 18:246–262. 2017. View Article : Google Scholar : PubMed/NCBI
27	Maréchal R, Bachet JB, Mackey JR, Dalban C, Demetter P, Graham K, Couvelard A, Svrcek M, Bardier-Dupas A, Hammel P, et al: Levels of gemcitabine transport and metabolism proteins predict survival times of patients treated with gemcitabine for pancreatic adenocarcinoma. Gastroenterology. 143:664–674.e6. 2012. View Article : Google Scholar : PubMed/NCBI
28	Greenhalf W, Ghaneh P, Neoptolemos JP, Palmer DH, Cox TF, Lamb RF, Garner E, Campbell F, Mackey JR, Costello E, et al: Pancreatic cancer hENT1 expression and survival from gemcitabine in patients from the ESPAC-3 trial. J Natl Cancer Inst. 106:djt3472014. View Article : Google Scholar
29	Bird NTE, Elmasry M, Jones R, Psarelli E, Dodd J, Malik H, Greenhalf W, Kitteringham N, Ghaneh P, Neoptolemos JP and Palmer D: Immunohistochemical hENT1 expression as a prognostic biomarker in patients with resected pancreatic ductal adenocarcinoma undergoing adjuvant gemcitabine-based chemotherapy. Br J Surg. 104:328–336. 2017. View Article : Google Scholar : PubMed/NCBI
30	Fritsche P, Seidler B, Schüler S, Schnieke A, Göttlicher M, Schmid RM, Saur D and Schneider G: HDAC2 mediates therapeutic resistance of pancreatic cancer cells via the BH3-only protein NOXA. Gut. 58:1399–1409. 2009. View Article : Google Scholar : PubMed/NCBI
31	Lehmann A, Denkert C, Budczies J, Buckendahl AC, Darb-Esfahani S, Noske A, Müller BM, Bahra M, Neuhaus P, Dietel M, et al: High class I HDAC activity and expression are associated with RelA/p65 activation in pancreatic cancer in vitro and in vivo. BMC Cancer. 9:3952009. View Article : Google Scholar : PubMed/NCBI
32	Mees ST, Mardin WA, Wendel C, Baeumer N, Willscher E, Senninger N, Schleicher C, Colombo-Benkmann M and Haier J: EP300-a miRNA-regulated metastasis suppressor gene in ductal adenocarcinomas of the pancreas. Int J Cancer. 126:114–124. 2010. View Article : Google Scholar
33	Zhong Z, Harmston N, Wood KC, Madan B and Virshup DM: A p300/GATA6 axis determines differentiation and Wnt dependency in pancreatic cancer models. J Clin Invest. 132:e1563052022. View Article : Google Scholar : PubMed/NCBI
34	Ono H, Basson MD and Ito H: P300 inhibition enhances gemcitabine-induced apoptosis of pancreatic cancer. Oncotarget. 7:51301–51310. 2016. View Article : Google Scholar : PubMed/NCBI
35	Krauß L, Urban BC, Hastreiter S, Schneider C, Wenzel P, Hassan Z, Wirth M, Lankes K, Terrasi A, Klement C, et al: HDAC2 facilitates pancreatic cancer metastasis. Cancer Res. 82:695–707. 2022. View Article : Google Scholar
36	Silverman BR and Shi J: Alterations of epigenetic regulators in pancreatic cancer and their clinical implications. Int J Mol Sci. 17:21382016. View Article : Google Scholar : PubMed/NCBI
37	Raghavan S, Winter PS, Navia AW, Williams HL, DenAdel A, Lowder KE, Galvez-Reyes J, Kalekar RL, Mulugeta N, Kapner KS, et al: Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer. Cell. 184:6119–6137.e26. 2021. View Article : Google Scholar : PubMed/NCBI
38	Neoptolemos JP, Kleeff J, Michl P, Costello E, Greenhalf W and Palmer DH: Therapeutic developments in pancreatic cancer: Current and future perspectives. Nat Rev Gastroenterol Hepatol. 15:333–348. 2018. View Article : Google Scholar : PubMed/NCBI
39	Ono H, Kato T, Murase Y, Nakamura Y, Ishikawa Y, Watanabe S, Akahoshi K, Ogura T, Ogawa K, Ban D, et al: C646 inhibits G2/M cell cycle-related proteins and potentiates anti-tumor effects in pancreatic cancer. Sci Rep. 11:100782021. View Article : Google Scholar : PubMed/NCBI
40	Maietta I, Martínez-Pérez A, Álvarez R, De Lera ÁR, González-Fernández Á and Simón-Vázquez R: Synergistic antitumoral effect of epigenetic inhibitors and gemcitabine in pancreatic cancer cells. Pharmaceuticals (Basel). 15:8242022. View Article : Google Scholar : PubMed/NCBI
41	Hamdan FH and Johnsen SA: Epigenetic targeting of aberrant transcriptional modulation in pancreatic cancer. Epigenomes. 2:82018. View Article : Google Scholar