Single-cell epigenetic analysis reveals principles of chromatin states in H3.3-K27M gliomas

Harpaz, Nofar; Mittelman, Tamir; Beresh, Olga; Griess, Ofir; Furth, Noa; Oren, Roni; Fellus-Alyagor, Liat; Harmelin, Alon; Alexandrescu, Sanda; Marques, Joana G.; Filbin, Mariella G.; Ron, G.; Shema, Efrat

doi:10.1016/j.molcel.2022.05.023

Cited by 32 publications

(27 citation statements)

References 66 publications

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“…Taken together, our findings add to an increasing body of evidence indicating that cathepsin L and its nuclear targets play central roles in brain disease ( Fei et al, 2018 ; Harpaz et al, 2022 ; Islam et al, 2022 ). Pharmacological targeting of these processes could have important therapeutic applications, and therefore should be the focus of future studies.…”

Section: Discussionsupporting

confidence: 74%

Cystatin B deficiency results in sustained histone H3 tail cleavage in postnatal mouse brain mediated by increased chromatin-associated cathepsin L activity

Daura

Tegelberg²,

Hakala³

et al. 2022

Front. Mol. Neurosci.

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Cystatin B (CSTB) is a cysteine cathepsin inhibitor whose biallelic loss-of-function mutations in human result in defects in brain development and in neurodegeneration. The physiological function of CSTB is largely unknown, and the mechanisms underlying the human brain diseases remain poorly understood. We previously showed that CSTB modulates the proteolysis of the N-terminal tail of histone H3 (H3cs1) during in vitro neurogenesis. Here we investigated the significance of this mechanism in postnatal mouse brain. Spatiotemporal analysis of H3cs1 intensity showed that while H3cs1 in wild-type (wt) mice was found at varying levels during the first postnatal month, it was virtually absent in adult brain. We further showed that the high level of H3cs1 coincides with chromatin association of de novo synthesized cathepsin L suggesting a role for nuclear cathepsin L in brain development and maturation. On the contrary, the brains of Cstb–/– mice showed sustained H3cs1 proteolysis to adulthood with increased chromatin-associated cathepsin L activity, implying that CSTB regulates chromatin-associated cathepsin L activity in the postnatal mouse brain. As H3 tail proteolysis has been linked to cellular senescence in vitro, we explored the presence of several cellular senescence markers in the maturing Cstb–/– cerebellum, where we see increased levels of H3cs1. While several markers showed alterations in Cstb–/– mice, the results remained inconclusive regarding the association of deficient CSTB function with H3cs1-induced senescence. Together, we identify a molecular role for CSTB in brain with implications for brain development and disease.

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Section: Discussionsupporting

confidence: 74%

Cystatin B deficiency results in sustained histone H3 tail cleavage in postnatal mouse brain mediated by increased chromatin-associated cathepsin L activity

Daura

Tegelberg²,

Hakala³

et al. 2022

Front. Mol. Neurosci.

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“…Using a custom-designed antibody panel for Epigenetic-focused CyTOF (EpiTOF) 80 , 81 (see Table S1 ), we performed high-dimensional phenotypic classification of single cells from five PyMT tumors from 3.5-month-old female mice. Including known markers of cell differentiation and identity 82 – 86 in the CyTOF panel enabled to assign of the tumor epithelial cells to subpopulations representing different phenotypic states: luminal progenitors (“lumP”), mature luminal (“luminal”), and a small but discrete subpopulation displaying molecular features that are commonly associated with a basal-like state (“basal-like”) (Fig S1a ), as well as nonepithelial tumor-associated cells such as fibroblasts and immune cells.…”

Section: Resultsmentioning

confidence: 99%

Breast cancer plasticity is restricted by a LATS1-NCOR1 repressive axis

et al. 2022

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Breast cancer, the most frequent cancer in women, is generally classified into several distinct histological and molecular subtypes. However, single-cell technologies have revealed remarkable cellular and functional heterogeneity across subtypes and even within individual breast tumors. Much of this heterogeneity is attributable to dynamic alterations in the epigenetic landscape of the cancer cells, which promote phenotypic plasticity. Such plasticity, including transition from luminal to basal-like cell identity, can promote disease aggressiveness. We now report that the tumor suppressor LATS1, whose expression is often downregulated in human breast cancer, helps maintain luminal breast cancer cell identity by reducing the chromatin accessibility of genes that are characteristic of a “basal-like” state, preventing their spurious activation. This is achieved via interaction of LATS1 with the NCOR1 nuclear corepressor and recruitment of HDAC1, driving histone H3K27 deacetylation near NCOR1-repressed “basal-like” genes. Consequently, decreased expression of LATS1 elevates the expression of such genes and facilitates slippage towards a more basal-like phenotypic identity. We propose that by enforcing rigorous silencing of repressed genes, the LATS1-NCOR1 axis maintains luminal cell identity and restricts breast cancer progression.

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“…The antibody we have used in our study for the H3K27M mutation is commonly used in a reliable manner in routine diagnostic setting ( 4 ). Moreover, the same antibody, custom-conjugated has been used in a recently published work that, by employing the CyTOF technology, has investigated the epigenetic rearrangements due to H3K27M alteration in a panel of DMG-H3K27M mutant cell lines ( 68 ). Interestingly, Harpaz et al., have demonstrated the existence of two epigenetically distinct subpopulations in DMG-H3K27M mutant cell lines and suggest that these differences mirror the heterogeneous expression of the H3K27M oncohistone ( 68 ).…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, the same antibody, custom-conjugated has been used in a recently published work that, by employing the CyTOF technology, has investigated the epigenetic rearrangements due to H3K27M alteration in a panel of DMG-H3K27M mutant cell lines ( 68 ). Interestingly, Harpaz et al., have demonstrated the existence of two epigenetically distinct subpopulations in DMG-H3K27M mutant cell lines and suggest that these differences mirror the heterogeneous expression of the H3K27M oncohistone ( 68 ). While we confirmed that the antibody anti-H3K27M can be used in a robust manner, unfortunately, the H3.3G34R antibody, which was custom-conjugated and used for CyTOF analysis for the first time in this study, did not prove accurate, due to its poor specificity.…”

Section: Discussionmentioning

confidence: 99%

Inter and intra-tumor heterogeneity of paediatric type diffuse high-grade gliomas revealed by single-cell mass cytometry

et al. 2022

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Paediatric-type diffuse high-grade gliomas (PDHGG) are aggressive tumors affecting children and young adults, with no effective treatment. These highly heterogeneous malignancies arise in different sites of the Central Nervous System (CNS), carrying distinctive molecular alterations and clinical outcomes (inter-tumor heterogeneity). Moreover, deep cellular and molecular profiling studies highlighted the coexistence of genetically and phenotypically different subpopulations within the same tumor mass (intra-tumor heterogeneity). Despite the recent advances made in the field, the marked heterogeneity of PDHGGs still impedes the development of effective targeted therapies and the identification of suitable biomarkers. In order to fill the existing gap, we used mass cytometry to dissect PDHGG inter- and intra-heterogeneity. This is one of the most advanced technologies of the “-omics” era that, using antibodies conjugated to heavy metals, allows the simultaneous measurement of more than 40 markers at single-cell level. To this end, we analyzed eight PDHGG patient-derived cell lines from different locational and molecular subgroups. By using a panel of 15 antibodies, directly conjugated to metals or specifically customized to detect important histone variants, significant differences were highlighted in the expression of the considered antigens. The single-cell multiparametric approach realized has deepened our understanding of PDHGG, confirming a high degree of intra- and inter-tumoral heterogeneity and identifying some antigens that could represent useful biomarkers for the specific PDHGG locational or molecular subgroups.

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Single-cell epigenetic analysis reveals principles of chromatin states in H3.3-K27M gliomas

Cited by 32 publications

References 66 publications

Cystatin B deficiency results in sustained histone H3 tail cleavage in postnatal mouse brain mediated by increased chromatin-associated cathepsin L activity

Cystatin B deficiency results in sustained histone H3 tail cleavage in postnatal mouse brain mediated by increased chromatin-associated cathepsin L activity

Breast cancer plasticity is restricted by a LATS1-NCOR1 repressive axis

Inter and intra-tumor heterogeneity of paediatric type diffuse high-grade gliomas revealed by single-cell mass cytometry

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