Histone Variant MacroH2A1.1 Enhances Nonhomologous End Joining-dependent DNA Double-strand-break Repair and Reprogramming Efficiency of Human IPSCs

Overview

Journal Stem Cells

Publisher Oxford University Press

Specialties Cell Biology
Reproductive Medicine

Date 2022 May 5

PMID 35511867

Authors

Sebastiano Giallongo

Daniela rehakova

Tommaso Biagini

Oriana Lo Re

Priyanka Raina

Gabriela Lochmanova

Zbynek Zdrahal

Igor Resnick

Pille Pata

Illar Pata

Martin Mistrik

Joao Pedro de Magalhaes

Tommaso Mazza

Irena Koutna

Manlio Vinciguerra

Affiliations

Soon will be listed here.

Abstract

DNA damage repair (DDR) is a safeguard for genome integrity maintenance. Increasing DDR efficiency could increase the yield of induced pluripotent stem cells (iPSC) upon reprogramming from somatic cells. The epigenetic mechanisms governing DDR during iPSC reprogramming are not completely understood. Our goal was to evaluate the splicing isoforms of histone variant macroH2A1, macroH2A1.1, and macroH2A1.2, as potential regulators of DDR during iPSC reprogramming. GFP-Trap one-step isolation of mtagGFP-macroH2A1.1 or mtagGFP-macroH2A1.2 fusion proteins from overexpressing human cell lines, followed by liquid chromatography-tandem mass spectrometry analysis, uncovered macroH2A1.1 exclusive interaction with Poly-ADP Ribose Polymerase 1 (PARP1) and X-ray cross-complementing protein 1 (XRCC1). MacroH2A1.1 overexpression in U2OS-GFP reporter cells enhanced specifically nonhomologous end joining (NHEJ) repair pathway, while macroH2A1.1 knock-out (KO) mice showed an impaired DDR capacity. The exclusive interaction of macroH2A1.1, but not macroH2A1.2, with PARP1/XRCC1, was confirmed in human umbilical vein endothelial cells (HUVEC) undergoing reprogramming into iPSC through episomal vectors. In HUVEC, macroH2A1.1 overexpression activated transcriptional programs that enhanced DDR and reprogramming. Consistently, macroH2A1.1 but not macroH2A1.2 overexpression improved iPSC reprogramming. We propose the macroH2A1 splicing isoform macroH2A1.1 as a promising epigenetic target to improve iPSC genome stability and therapeutic potential.

Citing Articles

Lactate accumulation promotes immunosuppression and fibrotic transformation of bone marrow microenvironment in myelofibrosis.

Spampinato M, Giallongo C, Giallongo S, La Spina E, Duminuco A, Longhitano L J Transl Med. 2025; 23(1):69.

PMID: 39810250 PMC: 11734442. DOI: 10.1186/s12967-025-06083-4.

Fish Oil Containing Pro-Resolving Mediators Enhances the Antioxidant System and Ameliorates LPS-Induced Inflammation in Human Bronchial Epithelial Cells.

Distefano A, Orlando L, Giallongo S, Tropea E, Spampinato M, Santisi A Pharmaceuticals (Basel). 2024; 17(8).

PMID: 39204170 PMC: 11360764. DOI: 10.3390/ph17081066.

Integrative Analysis of CUT&Tag and RNA-Seq Data Through Bioinformatics: A Unified Workflow for Enhanced Insights.

Liorni N, Napoli A, Adinolfi M, Vinciguerra M, Mazza T Methods Mol Biol. 2024; 2846:191-213.

PMID: 39141238 DOI: 10.1007/978-1-0716-4071-5_13.

Enhanced Antitumor Activity by the Combination of Dasatinib and Selinexor in Chronic Myeloid Leukemia.

Spampinato M, Zuppelli T, Dulcamare I, Longhitano L, Sambataro D, Santisi A Pharmaceuticals (Basel). 2024; 17(7).

PMID: 39065744 PMC: 11279392. DOI: 10.3390/ph17070894.

Epigenetic and transcriptional control of adipocyte function by centenarian-associated SIRT6 N308K/A313S mutant.

Frohlich J, Liorni N, Mangoni M, Lochmanova G, Pirek P, Kastankova N Clin Epigenetics. 2024; 16(1):96.

PMID: 39033117 PMC: 11265064. DOI: 10.1186/s13148-024-01710-1.

References

Lo Re O, Vinciguerra M . Histone MacroH2A1: A Chromatin Point of Intersection between Fasting, Senescence and Cellular Regeneration. Genes (Basel). 2017; 8(12). PMC: 5748685. DOI: 10.3390/genes8120367. View

Bocchi R, Egervari K, Carol-Perdiguer L, Viale B, Quairiaux C, De Roo M . Perturbed Wnt signaling leads to neuronal migration delay, altered interhemispheric connections and impaired social behavior. Nat Commun. 2017; 8(1):1158. PMC: 5660087. DOI: 10.1038/s41467-017-01046-w. View

Cedeno R, Nakauka-Ddamba A, Yousefi M, Sterling S, Leu N, Li N . The histone variant macroH2A confers functional robustness to the intestinal stem cell compartment. PLoS One. 2017; 12(9):e0185196. PMC: 5608326. DOI: 10.1371/journal.pone.0185196. View

Yamanaka S . Pluripotent Stem Cell-Based Cell Therapy-Promise and Challenges. Cell Stem Cell. 2020; 27(4):523-531. DOI: 10.1016/j.stem.2020.09.014. View

Simara P, Tesarova L, rehakova D, Matula P, Stejskal S, Hampl A . DNA double-strand breaks in human induced pluripotent stem cell reprogramming and long-term in vitro culturing. Stem Cell Res Ther. 2017; 8(1):73. PMC: 5361733. DOI: 10.1186/s13287-017-0522-5. View

Cantarino N, Douet J, Buschbeck M . MacroH2A--an epigenetic regulator of cancer. Cancer Lett. 2013; 336(2):247-52. DOI: 10.1016/j.canlet.2013.03.022. View

Khurana S, Kruhlak M, Kim J, Tran A, Liu J, Nyswaner K . A macrohistone variant links dynamic chromatin compaction to BRCA1-dependent genome maintenance. Cell Rep. 2014; 8(4):1049-62. PMC: 4154351. DOI: 10.1016/j.celrep.2014.07.024. View

Kim J, Sturgill D, Sebastian R, Khurana S, Tran A, Edwards G . Replication Stress Shapes a Protective Chromatin Environment across Fragile Genomic Regions. Mol Cell. 2017; 69(1):36-47.e7. PMC: 5756112. DOI: 10.1016/j.molcel.2017.11.021. View

Barrero M, Sese B, Kuebler B, Bilic J, Boue S, Marti M . Macrohistone variants preserve cell identity by preventing the gain of H3K4me2 during reprogramming to pluripotency. Cell Rep. 2013; 3(4):1005-11. DOI: 10.1016/j.celrep.2013.02.029. View

10.

Gunn A, Stark J . I-SceI-based assays to examine distinct repair outcomes of mammalian chromosomal double strand breaks. Methods Mol Biol. 2012; 920:379-91. DOI: 10.1007/978-1-61779-998-3_27. View

11.

Borghesan M, Fusilli C, Rappa F, Panebianco C, Rizzo G, Oben J . DNA Hypomethylation and Histone Variant macroH2A1 Synergistically Attenuate Chemotherapy-Induced Senescence to Promote Hepatocellular Carcinoma Progression. Cancer Res. 2016; 76(3):594-606. PMC: 4785885. DOI: 10.1158/0008-5472.CAN-15-1336. View

12.

Chadwick B, Willard H . Histone H2A variants and the inactive X chromosome: identification of a second macroH2A variant. Hum Mol Genet. 2001; 10(10):1101-13. DOI: 10.1093/hmg/10.10.1101. View

13.

Kang Y, Yan C . Regulation of DNA repair in the absence of classical non-homologous end joining. DNA Repair (Amst). 2018; 68:34-40. DOI: 10.1016/j.dnarep.2018.06.001. View

14.

Turinetto V, Orlando L, Giachino C . Induced Pluripotent Stem Cells: Advances in the Quest for Genetic Stability during Reprogramming Process. Int J Mol Sci. 2017; 18(9). PMC: 5618601. DOI: 10.3390/ijms18091952. View

15.

Simara P, Tesarova L, rehakova D, Farkas S, Salingova B, Kutalkova K . Reprogramming of Adult Peripheral Blood Cells into Human Induced Pluripotent Stem Cells as a Safe and Accessible Source of Endothelial Cells. Stem Cells Dev. 2017; 27(1):10-22. PMC: 5756468. DOI: 10.1089/scd.2017.0132. View

16.

Lo Re O, Fusilli C, Rappa F, Van Haele M, Douet J, Pindjakova J . Induction of cancer cell stemness by depletion of macrohistone H2A1 in hepatocellular carcinoma. Hepatology. 2017; 67(2):636-650. DOI: 10.1002/hep.29519. View

17.

Giallongo S, Lo Re O, Vinciguerra M . Macro Histone Variants: Emerging Rheostats of Gastrointestinal Cancers. Cancers (Basel). 2019; 11(5). PMC: 6562817. DOI: 10.3390/cancers11050676. View

18.

Braganca J, Lopes J, Mendes-Silva L, Almeida Santos J . Induced pluripotent stem cells, a giant leap for mankind therapeutic applications. World J Stem Cells. 2019; 11(7):421-430. PMC: 6682501. DOI: 10.4252/wjsc.v11.i7.421. View

19.

Pazienza V, Panebianco C, Rappa F, Memoli D, Borghesan M, Cannito S . Histone macroH2A1.2 promotes metabolic health and leanness by inhibiting adipogenesis. Epigenetics Chromatin. 2016; 9:45. PMC: 5078890. DOI: 10.1186/s13072-016-0098-9. View

20.

Takahashi K, Yamanaka S . Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell. 2006; 126(4):663-76. DOI: 10.1016/j.cell.2006.07.024. View