H2B Type 1-K Accumulates in Senescent Fibroblasts with Persistent DNA Damage along with Methylated and Phosphorylated Forms of HMGA1

Abstract

Cellular senescence is a state of terminal proliferative arrest that plays key roles in aging by preventing stem cell renewal and by inducing the expression of a series of inflammatory factors including many secreted proteins with paracrine effects. The in vivo identification of senescent cells is difficult due to the absence of universal biomarkers. Chromatin modifications are key aspects of the senescence transition and may provide novel biomarkers. We used a combined protein profiling and bottom-up mass spectrometry approach to characterize the isoforms and post-translational modifications of chromatin proteins over time in post-mitotic human fibroblasts in vitro. We show that the H2B type 1-K variant is specifically enriched in deep senescent cells with persistent DNA damage. This accumulation was not observed in quiescent cells or in cells induced into senescence without DNA damage by expression of the RAF kinase. Similarly, HMGA1a di-methylated and HMGA1b tri-phosphorylated forms accumulated exclusively in the chromatin of cells in deep senescent conditions with persistent DNA damage. H2B type 1-K and modified HMGA1 may thus represent novel biomarkers of senescent cells containing persistent DNA damage.

Progression of irradiated mesenchymal stromal cells from early to late senescence: Changes in SASP composition and anti‐tumour properties

“…The above‐reported results indicated that in our experimental conditions the irradiated quiescent MSC cultures enter progressively into late/deep senescence. This data is in line with other findings showing that deep senescence can be reached within 20–30 days following a genotoxic injury 24–26 . Progression from early to late senescence is associated with SASP enriched in pro‐inflammatory factors.…”

“…This data is in line with other findings showing that deep senescence can be reached within 20–30 days following a genotoxic injury. 24 , 25 , 26 Progression from early to late senescence is associated with SASP enriched in pro‐inflammatory factors. De Cecco and co‐workers identified some factors (IL6, IFNA, IFNB, CCL2, MMP3) whose mRNA levels can be considered as good markers to ascertain passage to the late‐senescence stage.…”

“…This data is in line with other findings showing that deep senescence can be reached within 20-30 days following a genotoxic injury. [24][25][26] Progression from early to late senescence is Panel C: The table reports the mRNA expression level of the indicated genes. The mRNA levels were normalized to GAPDH mRNA expression, which was selected as an internal control.…”

Histone deficiency and hypoacetylation in the aging retinal pigment epithelium

“…In our study, we did not observe significant changes in the expression of H3.3 variant genes ( H3f3a and H3f3b ) between young and aged RPE/choroid (Table S1 ). Other histone variants like H2afy2 , Hist1h2bk , and H1f0 were reported to accumulate in various aging cells and animal models (Contrepois et al., 2021 ; Kreiling et al., 2011 ; Sekeri‐Pataryas & Sourlingas, 2007 ; Zhang et al., 2005 ). Yet, our data demonstrated lower expression of these isoforms in the aged RPE (Figure 2f ).…”

Unraveling Histone Loss in Aging and Senescence

“…Senescent cells, showing γ-H2AX accumulation as a result of persistent DNA damage, were found to regulate p53-dependent senescent growth arrest and senescence-associated extracellular inflammatory signaling [132,133]. Senescent fibroblast cells harbored elevated levels of the H2B type 1-K variant, but the accumulation was exclusive to cells with persistent DNA damage [134]. Thus, DNA damage-associated variant histone exchange within senescent cells likely serves to maintain the genome integrity by nucleosome deposition in damaged chromatin regions.…”