Mass Spectrometric Quantification of Histone Post-translational Modifications by a Hybrid Chemical Labeling Method

Mass spectrometry is a powerful alternative to antibody-based methods for the analysis of histone post-translational modifications (marks). A key development in this approach was the deliberate propionylation of histones to improve sequence coverage across the lysine-rich and hydrophilic tails that bear most modifications. Several marks continue to be problematic however, particularly di- and tri-methylated lysine 4 of histone H3 which we found to be subject to substantial and selective losses during sample preparation and liquid chromatography-mass spectrometry. We developed a new method employing a “one-pot” hybrid chemical derivatization of histones, whereby an initial conversion of free lysines to their propionylated forms under mild aqueous conditions is followed by trypsin digestion and labeling of new peptide N termini with phenyl isocyanate. High resolution mass spectrometry was used to collect qualitative and quantitative data, and a novel web-based software application (Fishtones) was developed for viewing and quantifying histone marks in the resulting data sets. Recoveries of 53 methyl, acetyl, and phosphoryl marks on histone H3.1 were improved by an average of threefold overall, and over 50-fold for H3K4 di- and tri-methyl marks. The power of this workflow for epigenetic research and drug discovery was demonstrated by measuring quantitative changes in H3K4 trimethylation induced by small molecule inhibitors of lysine demethylases and siRNA knockdown of epigenetic modifiers ASH2L and WDR5.The field of Epigenetics has become important in drug discovery as many diseases have been linked to aberrations in chromatin and changes of histone post-translational modifications (PTMs)¹ (1, 2). The core histones (H2A, H2B, H3, and H4 and their variants) undergo a multitude of PTMs. Some, like lysine acetylation, lysine mono-, di-, and trimethlyation, and serine/threonine phosphorylation are well documented, with over 100 distinct, albeit generally low abundance, modifications reported for H3 alone (3). Mass spectrometry provides an alternative to antibody-based methods for detecting and quantifying histone PTMs, as the latter are prone to problems of specificity and epitope occlusion (4, 5). The most commonly applied approach to date is known as “bottom-up” mass spectrometry and involves an initial processing of the histones into smaller peptides (6). A key development in histone PTM analysis was the deliberate chemical modification of histone tail lysines by propionic anhydride, preventing digestion of these Lys- and Arg-rich domains into peptides too short or hydrophilic to be detected in reverse-phase liquid chromatography-mass spectrometry experiments (7–9).Despite this advance, some marks like H3K4 di- and tri-methylation remain problematic; in several examples from the recent literature the H3K4me3 mark is detected either only by means of specifically targeted methods (5), with larger quantitative variation than other marks (10), or not reported among detected marks at all (3, 11–13). Alternative approaches include top-down or middle-down mass spectrometry, in which entire histones, or large segments thereof are analyzed directly (14–16), but these techniques still suffer from relatively poor sensitivity in comparison to bottom-up workflows, and must contend with the full combinatorial complexity of histone PTMs (17).The H3K4me3 mark is of low natural abundance, having a very restricted genomic localization strongly associated with active gene promotors and enhancers (18, 19), and aberrant activities of writers and erasers of that mark are associated with a variety of diseases (1, 2). Difficulties in its quantitation thus hinder the investigation of both fundamental biology and the discovery of lifesaving drugs. We therefore undertook a re-evaluation of the bottom-up histone PTM workflow, streamlining sample preparation and investigating sources of bias or sample loss. Alternatives to the standard propionylation technique were also explored, resulting in a new hybrid chemical modification workflow yielding across-the-board improvements in recovery of peptides from the N-terminal tail of histone H3, and dramatically improved detection of hydrophilic peptides with marks like H3K4me2/me3.     

Knotting the NETs: Analyzing histone modifications in neutrophil extracellular traps

Neutrophil extracellular chromatin traps (NETs) are a recently described mechanism of innate immune responses to bacteria and fungi. Evidence indicates that NETs are induced by inflammation, that they contribute to diverse disease pathologies, and that they associate with bactericidal substances. Genomic DNA is released in NETs, leading to a cell death that has been labeled NETosis. Although NETosis clearly differs from apoptosis, the classical form of cell death, recent experiments indicate a connection between NETosis and autophagy. The regulated deployment of NETs may require covalent modification of histones, the basic DNA-binding proteins that organize chromatin in the cell''s nucleus and within NETs. Histone modification by peptidylarginine deiminase 4 (PAD4) is necessary for NET release. The functions of additional histone modifications, however, remain to be tested.Less than a decade since their discovery, neutrophil extracellular traps (NETs) remain in the headlines. Initially, interest focused on the structure of extracellular NET chromatin and its capacity to capture and damage bacteria. Soon, however, researchers began to see the implications of extracellular chromatin for the development of autoimmune diseases. One quintessential autoimmune disease, systemic lupus erythematosus (SLE), is known to arise together with autoantibodies to DNA and chromatin, although the immediate trigger for the production of these autoantibodies is unclear. A connection between NETs and autoimmunity was made by discovering that histones, a set of proteins that act as a structural harness for DNA in chromatin, are modified by peptidylarginine deiminase 4 (PAD4), an enzyme that converts arginines to citrullines. Researchers had long suspected that autoantigen modifications could provide the initial stimuli in autoimmunity because subtle alterations in a protein''s primary sequence can break tolerance. PAD4 is implicated in the development of rheumatoid arthritis (RA) because the most reliable clinical test for RA uses the detection of anti-citrulline antibodies in the sera of patients.In a sophisticated set of experiments reported in the previous issue of Arthritis Research & Therapy, Liu and colleagues [1] accomplished an extensive inventory of post-translational modifications in NET histones. The researchers induced NETs from human neutrophils, as well as two cell lines that assume neutrophil-like characteristics, and used a panel of 40 commercially available antisera to identify histone modifications that arise in parallel with NETs. Stimuli that were used to elicit NET release also induced histone H3 and H4 citrullination in human neutrophils and the EPRO cell line. However, other modifications such as histone H4 lysine 20 methylation and H4 lysine 16 acetylation showed inconsistent results in neutrophils versus the EPRO cells. To survey histone modifications, Liu and colleagues [1] confronted technical difficulties in that histone amino terminal tails contain the highest concentration of histone modifications yet are also highly susceptible to proteases secreted by activated neutrophils [2,3]. The histone tails act as flexible tethers that organize chromatin into higher-order structures. Interestingly, purified NETs failed to induce an immune response in mice, although a subset of SLE sera reacted strongly with citrullinated histone H3 [1]. Therefore, mechanisms that regulate histone modification deserve further attention.Neeli and colleagues [4] were the first to identify citrullinated histone H3 in NETs, a discovery that was confirmed by others [5]. Neeli and colleagues [4] provided a second important insight, namely that PAD4-citrullinated histone H3 is a reliable marker of inflammation. Thus, it became clear that the release of NETs is not an ''accident'' caused by a barrage of proteases and reactive oxygen species unleashed from neutrophils. Instead, production of NETs requires enzymatic activity and input from neutrophil surface receptors and the cytoskeleton [6]. By analyzing PAD4-deficient mice, Li and colleagues [7] demonstrated that PAD4 is essential for the production of NETs in response to bacterial infections. The regulation of PAD4 activity thus moved to the forefront of the research on NETs.It is now clear that NET release takes advantage of NADPH (nicotinamide adenine dinucleotide phosphate) oxidase and the main granule proteases to trigger and construct the extended chromatin network [3,8]. In addition, myeloperoxidase is found in NETs after their release from the cells, and this enzyme and its products are the main components in NETs that kill bacteria [9]. In a notable study from the labs of Banchereau and Pascual [10], it was reported that SLE neutrophils are poised to undergo NETosis upon stimulation with anti-ribonucleo-protein autoantibodies and that NETs released by these neutrophils contain LL37 and HMGB-1, well-known stimulators of immune responses. In subsequent analyses using sera from patients with connective tissue disease, anti-citrullinated histone antibodies were observed in Felty''s syndrome, a rare disorder that shares serologic features with RA and SLE, whereas such autoantibodies were infrequent in SLE and RA [11]. These findings indicate that the process of NETosis is highly relevant to the development of human autoimmune responses, although a direct cause and effect may not connect the release of NETs to the production of autoantibodies.The detailed characterization of NET histone modifications, as accomplished by Liu and colleagues [1], invites speculations about the possible functions of these modifications. Several questions deserve further study: Will NET histone modifications, such as methylation, acetylation, and citrullination, be found to participate in gene regulation that sets the stage for NET release? Will the primary function of histone modifications turn out to be the decondensation of nuclear chromatin that is required for NETs expand to their optimal size and internal structure? Alternatively, NET histone modifications may serve non-traditional purposes. For example, certain modifications may anchor other NET components such as elastase, LL37, or myeloperoxidase to the chromatin meshwork. Unique modifications in NETs may attract phagocytes and stimulate them to ingest the trapped microorganisms. Other histone modifications may activate or dampen the inflammatory response by acting on innate pattern recognition receptors. The answers to these questions will, no doubt, keep research on NETs in leading immunology and microbiology journals for years to come.