Genomic stability is essential for the faithful preservation and error-free transmission of genetic information across generations. This process requires the coordinated maintenance of epigenetic landscapes, precise chromosomal segregation and chromatin structural integrity. As the foundation of species survival and evolutionary adaptability, genomic stability ensures the fidelity of hereditary information transfer and protects cellular homeostasis against mutagenic cascades. The integrity of genetic information flow mechanisms, including DNA replication, transcription, and translation [1], [2], [3] is central to maintaining genomic stability. Disruptions in these processes create error-prone cellular states, leading to accumulated mutations that compromise genome integrity [4], [5].

Clinically, genomic instability is a hallmark of carcinogenesis, promoting malignant transformation through the progressive accumulation of oncogenic alterations [1]. Endogenous metabolic byproducts, such as reactive oxygen species and exogenous genotoxic stressors, including ionizing or ultraviolet radiation and alkylating or oxidizing agents, induce molecular lesions in DNA. These lesions range from base mismatches and bulky adducts to DNA strand breaks [6], [7], [8]. To counteract such threats, evolution has refined a multilayered DNA damage response (DDR) system, that incorporates context-specific repair mechanisms [9]. Base excision repair (BER) corrects small base lesions, mismatch repair (MMR) rectifies replication errors, and nucleotide excision repair (NER) removes helix-distorting damage. In addition, DNA double-strand breaks (DSBs) are resolved through homologous recombination (HR) or non-homologous end joining (NHEJ). When their DNA damage is irreparable, cells activate apoptotic pathways to eliminate potentially neoplastic clones. Incomplete DNA repair and apoptosis evasion, however, allow the propagation of corrupted genetic material across cell divisions. This mutagenic cascade, marked by chromosomal rearrangements, replication stress amplification, and the clonal selection of survival-advantaged mutants, drives the genomic chaos characteristic of tumor evolution. Thus, stringent replication surveillance and precise DDR signaling are critical in safeguarding against oncogenic transformation [10].

Palmitoylation is a dynamic post-translational lipid modification that involves the covalent attachment of saturated C16 fatty acids to cysteine residues via thioester bonds. This modification increases protein hydrophobicity and facilitates membrane localization [11]. It plays critical roles in the regulation of protein stability, subcellular trafficking, membrane interactions, and enzymatic activity. Biochemically, palmitoylation exists in three forms: S-palmitoylation (thioester-linked), N-palmitoylation (amide-linked), and O-palmitoylation (ester-linked). Among these, the predominant variant S-palmitoylation is the predominant and reversible variant. S-palmitoylation (from now on referred to as simply “palmitoylation”) is reversible and dynamically regulated by opposing enzymatic activities: palmitoylation, catalyzed by the aspartate-histidine-histidine-cysteine (DHHC)-type family of palmitoyltransferases (PATs) catalyze palmitoylation, while and depalmitoylation, mediated by acyl-protein thioesterases (APTs) mediate depalmitoylation [12].

First identified over four decades ago, palmitoylation has since been mapped to a wide range of substrates, including signaling hubs, ion channels, scaffolding proteins, and immune regulators [13], [14]. These modifications influence key cellular processes such as neurosynaptic plasticity, immune activation, metabolic reprogramming, and oncogenic signaling [12], [15], [16], [17]. Like phosphorylation and ubiquitination, the reversibility of palmitoylation facilitates its role as a regulatory switch for cellular homeostasis.

Despite its well-documented functions in cancer immunomodulation and metastasis [18], its direct involvement in genomic stability particularly in damage sensing, repair, and DNA replication fidelity, remains largely unexplored. Emerging evidence, however, suggests that palmitoylation cycles contribute to genomic integrity by modulating the stability, localization, or activity of DNA repair effectors, replication fork protectors, and chromatin remodelers. Conversely, the dysregulation of palmitoylation may exacerbate replication stress or impair DNA damage resolution, fostering a mutagenic environment. This review synthesizes the recent progress made in our understanding the contribution of S-palmitoylation to genome stability, focusing on its roles in (1) DDR, including the regulation of sensor kinases, repair machinery, and checkpoint signaling; (2) DNA replication dynamics, through the control of replisome components and replication stress adaptors; (3) the interplay between genomic instability and the innate immune cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) signaling pathway; and (4) human diseases, such as cancer, aging, neurodegenerative disorders and potential therapeutic approaches. Because of its links to lipid metabolism and genome surveillance pathways, S-palmitoylation is emerging as a promising therapeutic target for malignancies driven by genomic instability.

The mediators of S-palmitoylation, the DHHC palmitoyltransferases, are a conserved family of integral membrane proteins that share a cysteine-rich domain harboring a catalytic DHHC motif (Fig. 1) [19]. These enzymes facilitate protein palmitoylation through a tightly controlled nucleophilic acyl transfer mechanism that proceeds via two sequential steps: autopalmitoylation followed by transacylation [19], [20]. Autopalmitoylation initiates when the catalytic cysteine residue of the DHHC enzyme, after being activated by the conserved histidine pair within the DHHC motif, nucleophilically attacks the thioester bond of palmitoyl-CoA to form a palmitoyl-enzyme thioester intermediate. This priming step is indispensable for the enzyme’s activity. Subsequently, the deprotonated thiol group of the substrate protein executes a nucleophilic assault on this intermediate, resulting in transfer of the palmitoyl group and restoration of the enzyme’s active site. This bimolecular nucleophilic substitution (SN2-like) reaction proceeds through a tetrahedral transition state, with the enzyme’s specialized hydrophobic pocket precisely aligning the palmitoyl donor (palmitoyl-CoA) with the protein acceptor to ensure substrate specificity and reaction fidelity (Fig. 2).

Palmitic acid (C16:0) serves as a critical metabolic intermediate and precursor for complex lipid biosynthesis [21]. Its de novo synthesis initiates when glucose is taken up by hepatocytes and glycolytically converted to pyruvate in the cytosol. The pyruvate is then transported to the mitochondrial matrix, where it undergoes oxidative decarboxylation via the pyruvate dehydrogenase complex to yield acetyl-CoA, the fundamental building block for fatty acid synthesis. In the first committed and rate-limiting step in fatty acid biosynthesis, acetyl-CoA is then exported to the cytosol and carboxylated by acetyl-CoA carboxylase (ACACA) to produce malonyl-CoA [22]. Finally, the multifunctional enzyme complex fatty acid synthase (FASN) catalyzes the sequential condensation of one acetyl-CoA primer with seven malonyl-CoA units through a series of decarboxylation, reduction, and dehydration reactions, culminating in palmitic acid synthesis (Fig. 3).

Genomic studies have identified 23 DHHC family members in humans [23] and 24 in mice [19], and functional deficiencies in many of these enzymes have been associated with various diseases [24]. zDHHC3, 7, 9, 13, and 15, involved in certain neurological disorders, critically regulate synaptic protein trafficking and neuronal survival. zDHHC7 and 20 influence oncogenic signaling pathways and tumor microenvironment interactions and are implicated in oncogenesis. Metabolic dysregulation involves zDHHC1, 5, 11, 13, and 21, enzymes that govern lipid metabolism and insulin receptor localization. Additionally, zDHHC2, 3, 6, 7, 8, 15, 19, and 20 contribute to pathogen recognition and viral entry in infectious diseases, highlighting their broad functional significance across multiple disease states.

These enzymes exhibit tissue-specific expression profiles, with their dysregulation frequently triggering compartmentalized pathological cascades, spatially constrained sequences of deleterious biological processes occurring within specialized cellular or tissue microdomains. For instance, zDHHC13 mutations disrupt hippocampal protein palmitoylation, in a manner that correlates with neurodegeneration [18]; AGK palmitoylation by zDHHC2 drives AKT-mTOR signaling activation and promotes sunitinib resistance in Renal Cell Carcinoma [25]; while the zDHHC4-mediated palmitoylation of GSK3β enhances glioblastoma Stem Cell tumorigenicity via the EZH2-STAT3 axis in temozolomide-resistant glioblastoma [26] (Table 1). These findings highlight DHHC-mediated palmitoylation as a spatiotemporally regulated mechanism whose imbalance can drive disease through context-dependent molecular rewiring.

N-palmitoylation is catalyzed by Hedgehog acyltransferase, which irreversibly attaches a palmitoyl group to the N-terminal cysteine or glycine residue of target proteins, such as Hedgehog family morphogens. This modification is essential for Hedgehog protein maturation, secretion, and long-range signaling potency [27]. O-palmitoylation, in contrast, involves the ester bond-mediated covalent linkage of palmitate to serine residues. This reaction is exclusively catalyzed by Porcupine (PORCN) and is crucial for Wnt ligand acylation. O-palmitoylation ensures the proper folding, membrane association, and secretion of Wnt ligands, enabling the activation of downstream signaling cascades (Fig. 1) [28].

Depalmitoylation, the enzymatic reversal of S-palmitoylation, is essential for the spatiotemporal regulation of protein localization and activity. This process is catalyzed by a specialized member of the APT family, each exhibiting distinct substrate selectivity and subcellular compartmentalization. As examples of the compartment-specific regulation of depalmitoylation, the cytoplasmic depalmitoylases APT1/LYPLA1 and APT2/LYPLA2 regulate membrane-proximal signaling hubs by modulating dynamic protein-membrane interactions [17], [75]. In lysosomes, PPT1 and PPT2 function as thioesterases that facilitate palmitate recycling through the hydrolytic degradation of lipidated proteins [17]. To control cellular metabolism, mitochondrial ABHD10 governs the S-depalmitoylation of metabolic enzyme dynamics in respiratory chain complexes [75], while ABHD17 isoforms fine-tune Ras nanoclustering at the plasma membrane and play a role in the termination of oncogenic signaling [76]. Together, this network of enzymes orchestrates the precise spatial and temporal control of protein depalmitoylation across different cellular compartments to maintain a spatially resolved palmitoylation landscape.

Despite their critical roles, APTs remain less well explored than PATs. Emerging evidence suggests that thioesterase dysregulation contributes to certain pathological states. For example, PPT1 mutations have been associated with neuronal ceroid lipofuscinosis [77], while ABHD17C overexpression increases PI3K/AKT pathway activity in hepatocellular carcinoma [78] (Table 2). Explorations of these context-dependent depalmitoylation circuits might reveal novel therapeutic strategies to restore the proteostatic balance in diseases associated with genomic instability.

Cellular responses to genotoxic stress require the balanced maintenance of DNA repair fidelity and survival outcomes. When exposed to endogenous or exogenous DNA-damaging agents, cells lacking competent repair mechanisms may rely on the error-prone translesion synthesis mediated via low-fidelity DNA polymerases or tolerate unrepaired lesions, both of which significantly increase mutagenic risk [9]. These genomic alterations can promote carcinogenesis by inactivating tumor suppressor genes or activating proto-oncogenes. Additionally, unresolved DNA damage can create persistent replication-transcription conflicts, disrupting proteostasis and triggering cell death pathways such as p53-dependent apoptosis [90].

At the molecular level, DNA damage rapidly activates phosphatidylinositol-3 kinase-related kinases, particularly ATM and ATR, which coordinate damage signaling through multiple mechanisms: (i) the γ-H2AX-mediated formation of repair foci containing BRCA1 and MDC1, (ii) CHK1/CHK2-dependent cell cycle arrest via phosphorylation cascades, and (iii) p53 activation to induce apoptosis when repair fails. DDR pathway integrity is crucial for maintaining genomic stability, as evidenced by its frequent dysregulation in malignant cells [90], [91], [92].

Post-translational modifications (PTMs) play a crucial role in regulating protein function and diversity, thus they have been the subject of extensive research, particularly studies focusing on phosphorylation, ubiquitination, and acetylation in the DDR pathway [93]. Emerging evidence is now highlighting the importance of palmitoylation in DDR regulation. The pharmacological inhibition of palmitoylation using 2-bromopalmitate (2-BP) suppresses ATM kinase phosphorylation, impairing downstream p53 activation while simultaneously increasing γ-H2AX levels, a hallmark of DNA damage accumulation[94]. Complementary genetic studies have shown that a loss of zDHHC16 not only disrupts the ATM-p53 signaling axis but also induces G2/M cell cycle arrest [94], mimicking characteristic DDR deficiencies (Fig. 4A). Although these findings established zDHHC16 as essential for DDR progression, the molecular mechanisms underlying its role in ATM activation and the identification of critical palmitoylation substrates in DDR pathways remain unclear. Nevertheless, in mutant epidermal growth factor receptor glioblastoma models, zDHHC16 deficiency was found to disrupt the zDHHC16/SETD2/H3K36me3 signaling axis, leading to p53 pathway inactivation[64]. Mechanistically, zDHHC16-mediated SETD2 palmitoylation enhanced cellular responses to ionizing radiation-induced DNA damage [64], suggesting that this modification might regulate chromatin remodeling through H3K36me3 (Fig. 4A).

As a central regulator of the DDR, p53 functions as a signaling hub downstream of ATM activation, orchestrating cell cycle arrest and genomic stabilization through transcriptional programs [95], [96], [97], [98]. Clinically, p53 mutations are detected in approximately 30 % of glioma cases and are associated with therapeutic resistance and poor prognosis[99]. Mechanistically, mutant p53 acquires oncogenic properties by interacting with the nuclear transcription factor NF-Y, leading to the transcriptional upregulation of zDHHC5 expression [40]. This PAT-driven pathway disrupts the balance between tumor-suppressive phosphorylation and the oncogenic S-palmitoylation of EZH2, a chromatin-modifying enzyme essential for glioma genesis[40]. The observed inverse correlation between EZH2 phosphorylation and S-palmitoylation suggests a novel PMT crosstalk mechanism is involved, highlighting how combinatorial PTM regulation fine-tunes protein functionality in cancer biology.

Collectively, studies are revealing palmitoylation’s role as a master regulator coordinating the DDR and oncogenic transformation. Two pivotal mechanisms are now established: (1) the zDHHC16-ATM/SETD2 axis that governs DDR execution through kinase regulation and H3K36me3-dependent chromatin remodeling, and (2) the mutant p53-zDHHC5-EZH2 cascade that subverts tumor suppression in glioma. These findings position S-palmitoylation as a molecular switch that integrates with other PTMs to control genome stability and cancer progression.

The DDR begins when specialized sensor proteins that recognize DNA damage transmit signals through effector molecules, coordinating processes essential for maintaining genomic integrity [100], [101]. The choice of repair pathway depends on the nature of the DNA lesion. Evolutionarily conserved mechanisms include BER, used for small base modifications, NER for bulky helix-distorting lesions, MMR for replication errors, HR for precise double-strand break repair, and NHEJ for error-prone double-strand break resolution [9], [101], [102], [103]. Notably, emerging evidence suggests that protein palmitoylation plays a regulatory role in modulating these critical DNA repair pathways.

Replication timing regulatory factor 1(RIF1) is a multifunctional protein first identified in budding yeast [104], [105], [106], where it interacts with the telomere-binding protein Rap1 to regulate chromatin dynamics [107], [108]. RIF1 plays critical roles in DNA replication timing, telomere maintenance, mitotic anaphase bridge resolution [109], [110], [111], [112], and the selection of DSB repair pathways [113], [114].

In DSB repair, RIF1 functions through the 53BP1-RIF1-shieldin axis, which is recruited to damaged sites via the ATM-dependent phosphorylation of 53BP1. This axis suppresses HR by blocking DNA end resection [113], [114], stabilizes broken DNA ends, and promotes repair through the NHEJ pathway. Additionally, RIF1 collaborates with the ASF1 histone chaperone complex to mediate chromatin structural reorganization [107], a process regulated by PTMs. Ongoing studies are highlighting palmitoylation as a novel regulatory mechanism for RIF1. Seminal research conducted in Saccharomyces cerevisiae by Park et al. revealed that the palmitoyltransferase Pfa4 catalytically mediates RIF1 palmitoylation, driving heterochromatin assembly and the epigenetic silencing of HM loci through enhanced nuclear membrane anchoring (Fig. 4B) [115], [116]. HM loci (HML and HMR) represent specialized silent chromatin domains where transcriptional repression is achieved via heterochromatin-mediated chromatin condensation, which is a crucial step in mating-type switching, an evolutionarily conserved mechanism for controlling fungal cellular differentiation. Interestingly, palmitoylation also drives the redistribution of RIF1-GFP foci from the nuclear periphery to the nucleoplasm[115], [116], suggesting it has a role in the chromatin dynamics that may facilitate DNA repair [117].

Although palmitoylation does not affect RIF1’s role in replication timing [116], [118], it enhances DSB repair efficiency through two mechanisms: (1) suppressing DNA end resection while promoting NHEJ in a Pfa4-dependent manner (Figs. 4B) and (2) facilitating the compartmentalization of DNA repair processes by modulating the hydrophobicity of proteins, thus strengthening their interactions with membranes, and improving pathway selectivity and repair efficiency [118], [119]. It is likely that this spatial organization mechanism contributes to genomic stability by ensuring the orderly progression of DNA repair.

Parallel investigations have identified PORCN, an endoplasmic reticulum-resident O-acyltransferase, as a novel regulator of the DDR [120]. Beyond its well-established role in Wnt/β-catenin signaling through protein O-palmitoylation, recent studies suggest that nuclear-localized PORCN also possesses S-acyltransferase activity, indicating its dual palmitoylation functionalities. Notably, PORCN depletion impairs NHEJ repair efficiency[120]. Structural analyses revealed that PORCN catalyzed the irradiation-induced S-palmitoylation of XRCC6/Ku70 at five conserved cysteine residues (C66, C150, C389, C398, C585) (Fig. 4C) [120]. The Ku70/Ku80 heterodimer forms the DNA-binding core of DNA-dependent protein kinase catalytic subunit (DNA-PKcs), a master regulator coordinating ATM/ATR-mediated NHEJ activation [121], [122]. These findings established Ku70 palmitoylation as a key post-translational modification governing DNA-PKcs assembly and NHEJ proficiency.

Thus far, research has identified only two proteins whose functional regulation in DNA damage repair is mediated by palmitoylation. This limited number of confirmed palmitoylation targets highlights the need for more extensive explorations of the modification’s role in DNA repair processes. Further investigations are required to (1) systematically identify additional palmitoylation substrates involved in DNA repair pathways, (2) characterize the molecular mechanisms by which palmitoylation regulates these repair factors, and (3) determine how this lipid modification coordinates with other post-translational modifications to maintain genomic stability.

NER is an evolutionarily conserved DNA repair pathway that resolves the helix-distorting lesions caused by bulky DNA adducts, including UV-induced cyclobutene pyrimidine dimers, chemical crosslinks, and oxidative damage [123]. The NER pathway removes genomic lesions in four mechanistically ordered stages. Initially, DNA lesions are identified by the XPC-Rad23B complex, followed by damage verification through coordinated interactions among XPA, XPD helicase, and the DNA-binding protein XPE. These components collectively assemble a pre-incision complex that reshapes the DNA into a distinctive vermiform structure that encircles the lesion. Subsequently, dual incision occurs via the ERCC1-XPF (5′ terminus) and XPG (3′ terminus) endonucleases, which excise a 22–32 nucleotide damage-containing oligonucleotide. Gap filling then proceeds through high-fidelity DNA synthesis catalyzed by polymerases δ/ε, which utilize the undamaged complementary strand as template. Finally, nick sealing by DNA ligase III in transcription-coupled pathways or ligase I in global genome contexts completes the repair and restores genomic integrity [123], [124].

The melanocortin 1 receptor (MC1R), a key mediator of the UV response and melanoma susceptibility, undergoes zDHHC13-mediated palmitoylation at specific cysteines, enhancing its affinity for α-MSH (Fig. 5). This promotes XAB1 recruitment and optimizes NER [59], [125], [126]. Notably, zDHHC13 activity is dynamically regulated. AMPK phosphorylates Ser208 to boost catalytic activity (Fig. 5A), while ATR phosphorylates Ser8 post-UV exposure to strengthen MC1R binding (Fig. 5B) [125], [127]. Conversely, APT2-mediated depalmitoylation counteracts these processes, and inhibiting APT2 with ML349 elevates MC1R palmitoylation and repair capacity [128]. These insights have led to the nomination of MC1R palmitoylation as a therapeutic target for melanoma prevention, particularly in high-risk MC1R variant carriers.

Research has yet to establish a regulatory role for palmitoylation in the BER pathway. This knowledge gap may have arisen due to the spatial discrepancies between the subcellular localization of BER-associated enzymes and zDHHC functionality, as protein activity is intrinsically linked to spatial proteomic organization [129]. The BER pathway is initiated by at least 11 distinct DNA glycosylases, all of which are localized in the nucleus, except for mitochondrial UNG1 [130]. This enzymatic compartmentalization presents a potential mechanistic paradox, as the zDHHC enzymes known as transmembrane PATs primarily reside in the endoplasmic reticulum, Golgi apparatus, and nuclear envelope of the secretory pathway, with limited presence in plasma membranes and endocytic systems [19]. The spatial regulation of DNA glycosylase biogenesis involves mRNA localization to specific subcellular compartments for site-specific translation [131], allowing the precise control of gene expression. Nuclear-targeted DNA glycosylases undergo ribosomal translation followed by nuclear import, mediated by intrinsic nuclear localization signals (NLS), without post-translational membrane anchoring modifications [132]. While palmitoylation enhances protein hydrophobicity to facilitate membrane association, this modification appears nonessential for nuclear enzymes that utilize NLS-dependent translocation through nuclear pores. Nevertheless, considering the multifunctional nature of protein modifications, the potential regulatory role of palmitoylation in BER cannot be entirely ruled out.

Mismatchrepair (MMR), an evolutionarily conserved pathway critical for genomic stability, rectifies base mismatches and insertion-deletion errors during DNA synthesis, enhancing the cell’s replication fidelity 100- to 1000-fold. The mechanistic interplay between palmitoylation and MMR remains poorly defined, due to two fundamental knowledge gaps: (i) the incomplete characterization of eukaryotic MMR machinery beyond core heterotetrameric complexes (MLH1-MSH2-MSH6-PMS2 in mammals) [133], [134], with downstream effectors and regulatory networks yet to be fully elucidated [135]; and (ii) the substrate promiscuity of PATs, which complicates the identification of pathway-specific targets.

Within the dynamic equilibrium of palmitoylation-depalmitoylation cycles, MMR regulation may operate through dual non-exclusive mechanisms: the direct post-translational palmitoylation of core MMR components that modulates their nucleocytoplasmic trafficking via lipid raft partitioning, or their indirect modulation through the palmitoylation-dependent signaling hubs involved in coordinating DNA repair checkpoints. Notably, the transient nature of this reversible modification and our limited understanding of MMR-associated signaling networks pose significant methodological hurdles. Resolving these questions will necessitate multidisciplinary strategies integrating substrate profiling, spatial proteomics, and functional genomics.

DNA replication ensures the faithful transmission of genetic information through semiconservative duplication, a highly regulated process essential for maintaining genome stability. Its precision depends on the coordinated assembly of replication machinery, including origin recognition complexes, which license replication origins, and the sequential execution of initiation, elongation, and termination phases. Replisome components, such as the MCM helicase complex and DNA polymerases work together to promote accurate replication fork progression. Surveillance mechanisms, including the ATR-CHK1 checkpoint, monitor fork integrity to prevent replication stress and incomplete genome duplication [136], [137]. Disruptions in these processes, such as mutations in replication licensing factors or defects in fork protection proteins can trigger genomic instability, leading to carcinogenesis or chromosomal instability syndromes such as Seckel syndrome [136].

Post-translational modifications, including ubiquitination, SUMOylation, and phosphorylation, serve as key regulators of replication dynamics. For example, the ubiquitination of PCNA facilitates translesion synthesis during replication stress, while the SUMOylation of MCM helicases influences replication origin firing. In contrast, S-palmitoylation, a reversible lipid modification analogous to ubiquitination, remains largely unexplored in eukaryotic DNA replication, though emerging evidence suggests it has regulatory potential. The reversible nature of S-palmitoylation, controlled by PATs and APTs enzymes, implies a possible role in replication regulation. Notably, the AAA+ ATPase p97/VCP, a critical regulator of DNA replication processes, including origin licensing, fork restart, and replication termination, undergoes palmitoylation (Fig. 6) [138], [139]. During replication initiation, p97-Ufd1-Npl4 mediates the degradation of Cdt1, ensuring proper origin licensing and activation [140]. In the elongation process, p97/Cdc48-WSS1 and p97/VCP-SPRTN facilitate the removal of DNA-protein crosslinks ahead of the replication fork, enabling bidirectional fork progression [140]. At termination, p97 disassembles the MCM complex (the core component of the Cdc45-MCM-GINS helicase) by extracting ubiquitinated MCM7 in an ATP-dependent manner [141]. However, whether palmitoylation modulates p97’s ATPase activity or alters its interactions with replication-associated proteins and degradation thereby influencing DNA replication remains unclear. The identification of palmitoylation on p97 further suggests that other replication machinery components may also undergo this modification, opening a broad avenue for future research (Fig. 6).

During DNA replication, the progression of replication forks can be disrupted when physical barriers including DNA lesions or stable secondary structures are encountered, leading to fork collapse and subsequent generation of genomic discontinuities. Notably, both endogenous genotoxic stressors (oxidative free radicals and replication errors) and exogenous damaging agents (ranging from ultraviolet irradiation to chemotherapeutic compounds) contribute significantly to DNA fragmentation through distinct molecular mechanisms. When such double-strand breaks fail to undergo faithful repair, the resultant chromatin fragments may undergo cytoplasmic translocation via nuclear envelope defects. This cytosolic DNA dissemination activates pattern recognition receptors, particularly those initiating the cGAS-STING signaling cascade that orchestrates type I interferon-mediated innate immunity[142]. cGAS is a cytosolic DNA sensor that detects aberrant double-stranded DNA (dsDNA) arising from nuclear DNA damage or chromatin instability [143], [144]. Upon binding dsDNA through its nucleotidyltransferase domain, cGAS undergoes dimerization and conformational activation, catalyzing the synthesis of 2′,3′-cyclic GMP-AMP (cGAMP), a second messenger that binds the ER-resident adaptor protein STING [145]. This interaction triggers STING’s transition from a dimeric to an oligomeric state through extensive structural reorganization, leading to TBK1-IRF3 activation and type I interferon production.

The palmitoyltransferase zDHHC18 suppresses cGAS activation by impairing its DNA-binding capacity and dimer stability, whereas zDHHC9 promotes cGAS dimerization and enzymatic activity via site-specific palmitoylation at Cys404/405, enhancing cytosolic DNA sensing [146], [147]. This activation-deactivation cycle is dynamically balanced by lysophospholipase-like 1 (LYPLAL1/APT1)-mediated depalmitoylation, which disrupts cGAS dimers to prevent excessive immune responses (Fig. 7) [147]. Concurrently, STING activation strictly requires palmitoylation, as evidenced by the observation that interferon production was abolished upon pharmacological palmitoylation inhibition (with 2-BP) or genetic ablation (K88/91 mutations) [148]. Therapeutically, 4-octyl itaconate (4-OI) exploits this dependency to inhibit oligomerization and Golgi translocation by alkylating STING at Cys91 to block palmitoylation, a mechanism with significant potential for treating STING-hyperactivation disorders [149]. Collectively, this palmitoylation switch integrates inhibitory (zDHHC18) and activating (zDHHC9) changes to cGAS with LYPLAL1-mediated fine-tuning, while simultaneously governing STING activation, therefore revealing providing druggable targets across cGAS-STING related pathologies.

Palmitoylation dynamically interacts with other post-translational modifications to form an intricate regulatory network that precisely controls protein localization, stability, and function through several key cross-talk mechanisms. Palmitoylation can physically block ubiquitination sites: for example, the palmitoylation of STING impedes its K48-linked polyubiquitination, enhancing its stability and innate immune signaling ability [150]. Palmitoylation can also directly compete with phosphorylation events: the palmitoylation of epidermal growth factor receptor (EGFR) at Cys1025 by zDHHC20 compromises its phosphorylation at Tyr1068, shifting signaling towards PI3K-AKT to promote Myc stability and cell proliferation [70]. In turn, phosphorylation can trigger palmitoylation cascades. The ATR/AMPK-mediated phosphorylation of zDHHC13 enhances its activity towards MC1R, promoting MC1R palmitoylation and subsequently potentiating its nucleotide excision repair capacity [125], [127]. Perturbations to this delicate PTM equilibrium underlie various pathological states, including oncogenesis, neurodegeneration, and immune dysregulation. Consequently, targeting these interconnected modification pathways, particularly through strategic combination therapies, represents a promising frontier for precision medicine.

Emerging research is revealing that dysregulated protein palmitoylation plays critical pathogenic roles in numerous human diseases through distinct mechanisms. In cancer, palmitoylation modulates key oncogenic pathways [151], [152]. For instance, zDHHC9-mediated palmitoylation facilitates Ras membrane localization and activation; while zDHHC9 inhibition results in significant antitumor effects in Ras-driven malignancies [153]. Specific palmitoylation abnormalities are hallmarks of conditions such as Alzheimer's disease (AD) [154], [155], [156], in which the zDHHC7- and zDHHC21-induced palmitoylation of amyloid precursor protein significantly enhances its dimerization. These palmitoylation-stabilized dimers are subject to preferential cleavage by β-secretase within lipid raft microdomains, leading to the elevated production and pathological deposition of Aβ42, a central event in AD pathogenesis [157]. Notably, clinical studies discovered a positive correlation between zDHHC7 expression levels and AD severity, suggesting this palmitoylation-dimerization axis may serve as both a disease biomarker and a potential therapeutic target [158]. Palmitoylation is crucial for immune activation pathways [159], [160], [161]. The zDHHC3/7/15-mediated palmitoylation of STING is essential for its oligomerization and interferon production, and overactivation of this palmitoylation-dependent pathway is implicated in the pathogenesis of lupus erythematosus and related autoimmune conditions [148], [162]. Dopamine transporter palmitoylation modulates synaptic dopamine reuptake, its disruption correlating with neurodevelopmental disorders [163]. The zDHHC8-mediated palmitoylation of glutathione peroxidase 4 (GPX4) enhances the enzyme’s membrane association tendency, protecting hematopoietic/neural stem cells from ferroptosis [164]. Beclin 1 palmitoylation, mediated by zDHHC5, regulates autophagy-dependent organelle clearance, and a decline in zDHHC5 activity has been links linked to mitochondrial dysfunction and inflammation via the RIPK1/necroptosis pathways [165]. The targeted modulation of palmitoylation is emerging as a promising therapeutic strategy. Elucidating its molecular mechanisms and regulatory networks can not only advance our understanding of disease pathogenesis but also help establish a framework for designing novel interventions.