Histone Variant macroH2A1.1 Enhances Nonhomologous End Joining-dependent DNA Double-strand-break Repair and Reprogramming Efficiency of Human iPSCs

Giallongo, Sebastiano; Řeháková, Daniela; Biagini, Tommaso; Re, Oriana Lo; Raina, Priyanka; Lochmanová, Gabriela; Zdráhal, Zbyněk; Resnick, Igor B.; Pata, Pille; Pata, Illar; Mistrík, Martin; Magalhães, João Pedro de; Mazza, Tommaso; Koutná, Irena; Vinciguerra, Manlio

doi:10.1093/stmcls/sxab004

Cited by 17 publications

(18 citation statements)

References 82 publications

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“…We analyzed the genome occupancy patterns of 6-His-tagged macroH2A1.1 and macroH2A1.2 in HUVEC at the 4th day of their episomal-driven reprogramming into iPSC (Giallongo et al 2022) by using a CUT&Tag approach. Quality control performed on broad peaks suggested the exclusion of a poor-quality sequencing replicate related to macroH2A1.2 ( Supplemental_Fig_S1 ).…”

Section: Resultsmentioning

confidence: 99%

“…The RNA-seq data (Giallongo et al 2022) was previously deposited into the Gene Expression Omnibus (GEO) with the dataset identifier GSE164396. Reads were quasimapped onto release 36 of the GENCODE human reference transcriptome and counted with Salmon v1.2.1 (Patro et al 2017).…”

Section: Quality-control and Short-read Mappingmentioning

confidence: 99%

“…The RNA-seq data (Giallongo et al 2022) was previously deposited into the Gene Expression Omnibus (GEO) with the dataset identifier GSE164396. Genomics sequences obtained in this study by CUT&Tag have been deposited into the GEO with the dataset identifier GSE214013.…”

Section: Data Accessmentioning

confidence: 99%

“…MacroH2A1 features two exon splicing isoforms: macroH2A1.1 and macroH2A1.2 having common and distinct biological functions in tumorigenesis, cell differentiation and stemness (Bereshchenko et al 2019; Borghesan et al 2016; Giallongo et al 2020, 2021a; Lo Re et al 2018, 2020; Lo Re and Vinciguerra 2017; Pazienza et al 2014, 2016; Podrini et al 2015; Rappa et al 2013; Chiodi et al 2021; Guberovic et al 2022). In particular, we have recently reported that macroH2A1.1, but not macroH2A1.2, is an enhancer of DNA damage repair and iPSC reprogramming from somatic cells, increasing the efficiency of the process (Giallongo et al 2022). Interestingly, while macroH2A1.2 does not impact iPSC differentiation into the 3 major embryonic germ layers (endoderm, mesoderm, and ectoderm), macroH2A1.1-expressing reprogrammed iPSC have a decreased potential to generate ectoderm (Giallongo et al 2022).…”

Section: Introductionmentioning

confidence: 99%

“…In particular, we have recently reported that macroH2A1.1, but not macroH2A1.2, is an enhancer of DNA damage repair and iPSC reprogramming from somatic cells, increasing the efficiency of the process (Giallongo et al 2022). Interestingly, while macroH2A1.2 does not impact iPSC differentiation into the 3 major embryonic germ layers (endoderm, mesoderm, and ectoderm), macroH2A1.1-expressing reprogrammed iPSC have a decreased potential to generate ectoderm (Giallongo et al 2022). Understanding the genome binding and transcriptomic dynamics of macroH2A1.1 could help to improve iPSC production and availability for clinical trials.…”

Section: Introductionmentioning

confidence: 99%

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Integrative CUT&Tag/RNA-Seq analysis of histone variant macroH2A1-dependent orchestration of human iPSCs reprogramming

Liorni

Napoli

Castellana

et al. 2022

Preprint

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Human-induced pluripotent stem cells (iPSCs) can be derived from adult stem cells by forced expression of defined transcription factors. This paves the way for autologous iPSC-derived therapies, which, however, are not yet considered safe. Moreover, reprogramming of somatic cells into iPSCs is an inefficient process, in the range of 0.1%–1%. The epigenetic mechanisms implicated in iPSCs reprogramming are not well understood. The substitution of canonical histone H2A with macroH2A1 histone variant exon-spliced isoforms (macroH2A1.1 and macroH2A1.2) appears as an emerging regulator of iPSCs identity. In particular, we have previously shown that overexpression of macroH2A1.1 led to a more efficient iPSCs reprogramming, by not fully defined mechanisms. Cleavage under targets and tagmentation (CUT&Tag) is a recent methodology used for robust epigenomic profiling of a limited amount of cells. Here, we performed the first integrative CUT&Tag/RNA-Seq analysis of the histone variant macroH2A1-dependent orchestration of iPSCs reprogramming using human umbilical vein endothelial cells (HUVEC) during their reprogramming into iPSC over-expressing tagged macroH2A1.1 or macroH2A1.2. Our results demonstrate a higher and more widespread genome occupancy and a greater number of differentially expressed genes orchestrated by macroH2A1.1 in HUVEC undergoing reprogramming as compared to macroH2A1.2, which involved pervasive functions related to the three embryonic germ layers and increased overlap with CTCF, FOS, GATA2, and POLR2A transcription factor binding sites. In particular, all predicted macroH2A1.1 activating pathways were related to ectoderm/neural processes. As macroH2A1 isoforms have been previously associated with pathologies of the nervous system, our findings may provide relevant molecular insights for modeling neurodegenerative diseases using iPSCs.

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Section: Resultsmentioning

confidence: 99%

Section: Quality-control and Short-read Mappingmentioning

confidence: 99%

Section: Data Accessmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Integrative CUT&Tag/RNA-Seq analysis of histone variant macroH2A1-dependent orchestration of human iPSCs reprogramming

Liorni

Napoli

Castellana

et al. 2022

Preprint

Self Cite

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Subcellular localization of PD‐L1 and cell‐cycle‐dependent expression of nuclear PD‐L1 variants: implications for head and neck cancer cell functions and therapeutic efficacy

Schulz,

Feulner,

Santos Rubenich

et al. 2023

Molecular Oncology

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The programmed cell death 1 ligand 1 (PD‐L1)/programmed cell death protein 1 (PD‐1) axis is primarily associated with immunosuppression in cytotoxic T lymphocytes (CTLs). However, mounting evidence is supporting the thesis that PD‐L1 not only functions as a ligand but mediates additional cellular functions in tumor cells. Moreover, it has been demonstrated that PD‐L1 is not exclusively localized at the cellular membrane. Subcellular fractionation revealed the presence of PD‐L1 in various cellular compartments of six well‐characterized head and neck cancer (HNC) cell lines, including the nucleus. Via Western blotting, we detected PD‐L1 in its well‐known glycosylated/deglycosylated state at 40–55 kDa. In addition, we detected previously unknown PD‐L1 variants with a molecular weight at approximately 70 and > 150 kDa exclusively in nuclear protein fractions. These in vitro findings were confirmed with primary tumor samples from head and neck squamous cell carcinoma (HNSCC) patients. Furthermore, we demonstrated that nuclear PD‐L1 variant expression is cell‐cycle‐dependent. Immunofluorescence staining of PD‐L1 in different cell cycle phases of synchronized HNC cells supported these observations. Mechanisms of nuclear PD‐L1 trafficking remain less understood; however, proximity ligation assays showed a cell‐cycle‐dependent interaction of the cytoskeletal protein vimentin with PD‐L1, whereas vimentin could serve as a potential shuttle for nuclear PD‐L1 transportation. Mass spectrometry after PD‐L1 co‐immunoprecipitation, followed by gene ontology analysis, indicated interaction of nuclear PD‐L1 with proteins involved in DNA remodeling and messenger RNA (mRNA) splicing. Our results in HNC cells suggest a highly complex regulation of PD‐L1 and multiple tumor cell‐intrinsic functions, independent of immune regulation. These observations bear significant implications for the therapeutic efficacy of immune checkpoint inhibition.

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

Liorni,

Napoli,

Adinolfi

et al. 2024

Methods in Molecular Biology

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Histone Variant macroH2A1.1 Enhances Nonhomologous End Joining-dependent DNA Double-strand-break Repair and Reprogramming Efficiency of Human iPSCs

Cited by 17 publications

References 82 publications

Integrative CUT&Tag/RNA-Seq analysis of histone variant macroH2A1-dependent orchestration of human iPSCs reprogramming

Integrative CUT&Tag/RNA-Seq analysis of histone variant macroH2A1-dependent orchestration of human iPSCs reprogramming

Subcellular localization of PD‐L1 and cell‐cycle‐dependent expression of nuclear PD‐L1 variants: implications for head and neck cancer cell functions and therapeutic efficacy

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

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