Overview of PAMPs and DAMPs

To comprehend how the host immune system discriminates between physiological safety and pathological distress, it is essential to map the structural and functional organization of the danger surveillance network. This section provides a foundational overview of danger signal biology, delineating their structural attributes, detection mechanisms, and regulatory networks.

Molecular Characterization and Classification

The initiation of immune responses depends on the biochemical classification of the driving ligands. This subsection categorizes danger signals by their origin. Exogenous signals (PAMPs) consist of conserved structural motifs and metabolic intermediates unique to microorganisms. Endogenous signals (DAMPs and alarmins) are normally sequestered intracellular molecules that are released into the extracellular space through active secretion or various cell death pathways. Additionally, bioactive fragments derived from the extracellular matrix function as independent DAMPs. Collectively, these distinct molecules serve as primary alerts for localized or systemic homeostatic perturbations.

PAMPs: The Exogenous Signatures

PAMPs represent highly conserved, evolutionarily stable molecular signatures generated by microorganisms that are intrinsically absent from the host proteome. Although the term “pathogen” implies a restriction to virulent microbes, these motifs are ubiquitously produced by both pathogenic and commensal species [10]. Consequently, the term Microbe‐Associated Molecular Patterns (MAMPs) is often considered a more semantically accurate descriptor [11]. For the sake of readability and consistency with the prevailing literature, however, we retain the original PAMP nomenclature throughout this review.

Several fundamental properties render PAMPs ideally suited for innate immune recognition [12]. First, they represent products of microbial‐specific pathways, providing unambiguous discrimination between self and non‐self for the host. Besides, they are conserved within entire classes of microorganisms, enabling a limited repertoire of germline‐encoded receptors to detect a vast array of potential pathogens. Crucially, they play indispensable roles in microbial physiology and survival, thereby imposing significant constraints on microorganisms' ability to evade innate immune recognition through adaptive evolution.

PAMPs are produced by a broad spectrum of microorganisms, including bacteria, viruses, fungi, and parasites (Figure 2). Bacterial PAMPs predominantly comprise surface‐exposed components such as LPS from Gram‐negative species, lipoteichoic acids (LTA) from Gram‐positive strains, the structural protein flagellin, and bacterial nucleic acids [13]. Beyond these classical structural components, recent research has substantially expanded the PAMP landscape by identifying soluble metabolic intermediates as potent immune agonists. During lipopolysaccharide biosynthesis, Gram‐negative bacteria generate adenosine diphosphate (ADP)‐heptose, a highly conserved metabolic intermediate that functions as a previously unrecognized PAMP, entering the host cell cytosol to activate innate defenses through the cytosolic sensor ALPK1 [14]. Subsequent investigations have identified its derivatives, such as cytidine diphosphate (CDP)‐heptose and uridine diphosphate (UDP)‐heptose, as similarly potent innate immune agonists [15]. Given that functional heptose‐bisphosphate enzymes are distributed across bacteria, archaea, eukaryotes, and even certain viruses, β‐D‐manno‐heptose has been identified as a “cross‐kingdom” small molecule PAMP capable of triggering the ALPK1‐dependent inflammatory signaling cascade [15].

FIGURE 2: Molecular diversity, release mechanism, and the sentinel sensing network of PAMPs and DAMPs. (A) Identification and release dynamics. The PAMP/DAMP axis categorizes molecular danger signatures by their origin, exogenous microbial motifs (bacteria, viruses, fungi, and parasites) versus endogenous alarmins sequestered in intracellular or extracellular matrix (ECM) depots. Intercellular DAMPs are liberated through either active secretion or passive liberation. (B) The sentinel network: Danger perception is orchestrated by a hierarchical cellular network, comprising professional innate/adaptive leukocytes and nonimmune residents (e.g., ISCs, osteocytes), and a topographically organized receptor system. PRRs and non‐PRRs provide spatially partitioned surveillance across diverse subcellular locations.

Because all viral components are synthesized within host cells using host machinery, viral nucleic acids constitute the principal targets for innate immune surveillance. Therefore, viral PAMPs consist primarily of unique nucleic acid motifs generated de novo during active replication cycles. For example, the influenza A virus, a lytic RNA virus, generates Z‐form RNA during its replication cycle; these Z‐RNA structures are recognized by the ZBP1 sensor within the nuclei of infected cells, triggering innate immune responses [16].

Fungal PAMPs are derived primarily from cell wall components. The fungal cell wall comprises two principal layers: the inner wall, composed of chitin and linear β‐glucans, and the outer wall, which consists of heavily glycosylated mannoproteins [17]. Under physiological conditions, this inner core is typically sequestered by the outer mannan layer to avoid immune recognition; however, its exposure during tissue injury or microbial turnover provides a critical signal for the initiation of the antifungal innate response [18]. The fungal cell wall exhibits remarkable compositional diversity, although certain structural elements, notably β‐glucans and chitin, are broadly conserved across fungal genera [18]. Therefore, these conserved components function as PAMPs, representing an inherent vulnerability in the fungal defensive architecture [19].

Beyond the well‐characterized molecular signatures of bacteria, viruses, and fungi, parasite‐derived PAMPs represent a structurally heterogeneous class of innate immune triggers [20]. These motifs are recognized across various developmental stages and exhibit significant biochemical diversity. For instance, during infection with Trypanosomatids such as Trypanosoma cruzi and Leishmania, the innate immune system utilizes Toll‐like receptor (TLR) 2 to detect surface‐associated alkylacylglycerol and lipophosphoglycan, while TLR9 serves as a specialized sensor for parasitic genomic DNA [21]. Furthermore, the host–parasite interface often involves the release of unique molecular assemblies that facilitate immune priming. A sophisticated example is the Lipoxin/Lipocalin complex liberated during Plasmodium midgut invasion [22]. While lipoxins are traditionally recognized for their pro‐resolving properties in vertebrates, this lipid–protein complex acts as a critical signal that heightens the responsiveness of the innate immune compartment, specifically through the activation and differentiation of phagocytic cells, to subsequent challenges.

DAMPs and Alarmins: The Endogenous Danger Signals

DAMPs, namely alarmins, constitute the endogenous mediators of the danger model. Normally restricted to intracellular or extracellular depots, these molecules are unleashed into the surrounding milieu in response to pathological perturbation, thereby exerting their potent immunogenic potential [6]. Their generation is orchestrated by a triad of physical (e.g., excessive mechanical load or ionizing radiation), chemical (e.g., chemotherapy‐induced cytotoxicity), and biological (e.g., microbial invasion or immunosenescence) insults [6].

Intracellular DAMPs originate from multiple subcellular compartments (Figure 2). Nuclear DAMPs include HMGB1 and histones that acquire immunostimulatory properties upon extracellular release [23]. Cytosolic DAMPs encompass molecules like ATP and S100 family proteins [24]. Mitochondrial DAMPs, such as mitochondrial DNA, are particularly potent due to their evolutionary ancestry, containing unmethylated CpG motifs and N‐formylated methionine that function as molecular mimics of bacterial PAMPs [25, 26].

DAMPs exit cells through two fundamentally distinct kinetic routes: active secretion and passive release. Active release involves posttranslational modifications and vesicular trafficking, enabling controlled DAMP export without compromising membrane integrity. Cellular stress induces posttranslational modifications in DAMPs, including acetylation, methylation, phosphorylation, and lactylation, that enable their recognition and sequestration into vesicles [27]. Second‐messenger molecules, secretory autophagy, and metabolic reprogramming further regulate this active export pathway, enabling DAMPs to be packaged into extracellular vesicles that travel to distant organs without enzymatic degradation [28]. For example, lactate drives the acetylation and lactylation of HMGB1 by suppressing the deacetylase SIRT1 through Hippo/YAP signaling and facilitating the GPR81/β‐arrestin2‐mediated nuclear translocation of p300/CBP acetyltransferases, ultimately triggering the exosomal secretion of nuclear HMGB1 from macrophages to the extracellular region [29].

Passive release, conversely, occurs during lytic cell death when plasma membrane rupture allows uncontrolled efflux of intracellular constituents. Necrosis and necroptosis have long been recognized as sources of passive DAMP release [30]. Recent research found that in necroptosis, MLKL not only propagates inflammation through noncell‐autonomous DAMP release but also triggers cell‐autonomous inflammatory signaling by facilitating mitochondrial DNA leakage into the cytoplasm, thereby activating the cGAS‐STING pathway [31]. Beyond these well‐established modalities, recent research has revealed that other regulated cell death pathways contribute to distinct DAMP repertoires. During pyroptosis, inflammatory caspase activation cleaves gasdermin D, generating plasma membrane pores that enable selective efflux of DAMPs while preserving partial membrane integrity [32]. Ferroptosis, defined by iron‐dependent lipid peroxidation and subsequent membrane disruption, similarly creates a conduit for DAMP liberation, which is mediated by NINJ1 [33]. PANoptosis represents an integrated cell death pathway wherein simultaneous activation of multiple death programs, pyroptosis, apoptosis, and necroptosis, converges within a single cell under the coordination of the PANoptosome complex. This multifaceted death modality ensures robust DAMP release while eliminating cells that might otherwise harbor intracellular pathogens [34]. Beyond these immunogenic forms of cell death, emerging research has discovered that even apoptosis, historically considered immunologically silent due to preserved membrane integrity, can contribute to DAMP liberation. It has been found that apoptotic cells expose nuclear constituents on their surface and subsequently release these components into the extracellular environment [23].

In addition to intracellular sources, the extracellular matrix also constitutes an important source of DAMPs through structural rearrangements, such as tenascin‐C and aggrecan 32mer [35] (Figure 2). This process is driven by three primary mechanisms: alternative splicing of ECM components generating tissue‐specific isoforms [36], posttranslational modifications [37], and protease‐mediated degradation that liberates immunostimulatory fragments [38]. These ECM‐derived DAMPs further activate pattern recognition receptors, amplifying local inflammation.

Sensing Mechanism: The Cellular and Molecular Sentinel Network

The transition from physiological homeostasis to pathological inflammation is governed by a highly organized network of sensing platforms. This sensing system comprises diverse cell populations functioning as biological sentinels and an intricate topography of receptors that decode the biochemical language of danger (Figure 2).

Sensing Cells

The detection of danger signals is a collective effort executed by a broad spectrum of cell types, ranging from professional innate sentinels to adaptive lymphocytes and nonimmune tissue residents. Innate immune cells, including macrophages [39], neutrophils [6], and dendritic cells (DCs) [40], constitute the primary defensive line. Besides, natural killer (NK) cells specifically employ receptors like NKp30 (NCR3) [41] and NKp46 [42] as “cytotoxic PRRs” to directly recognize fungal components or stress‐induced ligands. In addition to innate immune cells, adaptive immune cells such as T and B cells utilize TLRs (e.g., TLR2 and TLR5) to modulate their activation thresholds and functional output [43]. Furthermore, the concept of cell‐autonomous immunity has been broadened to include nonimmune populations, such as osteocytes [44], intestinal stem cells [45], and various epithelial cells [46, 47], which independently sense microbial translocation or tissue injury.

Recent advancements in single‐cell technologies have further refined our understanding by identifying highly specialized cell sub‐populations. For example, research identified the “first responder” dendritic cells within conventional DC populations, which are uniquely capable of reaching the activation threshold upon initial PAMP exposure and subsequently orchestrating the immune response through paracrine signaling to mobilize bystander cells [48]. The precision targeting of these “first responders” represents a transformative frontier in vaccine design, offering a means to maximize immunological efficiency while mitigating systemic adverse effects.

Sensing Receptors

Danger perception is mediated by both PRR and non‐PRR sensors [49]. PRRs can bind to both PAMPs and DAMPs, which encompass TLRs and C‐type lectin receptors (CLRs), cytosolic NOD‐like receptors (NLRs), RIG‐I‐like receptors (RLRs), and multiple intracellular DNA sensors. Additionally, DAMPs can interact with non‐PRRs, which include the receptor for advanced glycation end products (RAGE), triggering receptors expressed on myeloid cells (TREMs), G protein‐coupled receptors (GPRs), and ion channels.

These receptors are organized according to distinct subcellular localizations. The TLR family exhibits distinct subcellular topography: TLR1, 2, 4, 5, and 6 are localized on the plasma membrane to monitor the extracellular space, whereas TLR3, 7, 8, and 9 are sequestered within endosomal membranes to survey the endocytic environment [50]. Cytosolic surveillance operates through sensors such as cGAS‐STING recognizing misplaced DNA [51] and ALPK1 detecting bacterial ADP‐heptose [45]. Mitochondria serve as signaling hubs, utilizing MAVS to integrate RNA sensing with bioenergetic adaptation [51]. To achieve optimal sensitivity and specificity, many sensors require specialized adaptor proteins or “two‐factor authentication” strategies to verify transient or low‐abundance signals. For instance, the extracellular co‐factor MD2 is essential for TLR4‐mediated sensing, illustrating that the fidelity of the sentinel network is fundamentally predicated on these intricate molecular docking and verification events [52]. Similarly, the detection of cytoplasmic HIV‐1 DNA, a low‐abundance PAMP, necessitates the adaptor protein PQBP1. Upon infection, PQBP1 decorates the viral capsid to provide primary verification, subsequently recruiting cGAS to the site of PAMP generation to initiate immune responses [53].

Regulation of PAMP and DAMP Signaling

The magnitude and duration of PAMP and DAMP signaling must be precisely calibrated to ensure effective host defense while preventing maladaptive immune responses. This regulatory imperative creates a dynamic tension: pathogens evolve strategies to minimize PAMP recognition and downstream signaling as a means of immune evasion, whereas the host must maintain robust sensing mechanisms to detect microbial invasion and endogenous danger signals while simultaneously avoiding excessive or sustained activation that could lead to tissue damage. The regulatory mechanism governing these pathways operates at multiple levels, from the generation and modification of the signals themselves to the expression and function of their cognate receptors.

Regulation of PAMP Signaling

Pathogenic evolution has yielded an intricate repertoire of tactics designed to minimize the visibility of PAMPs, thereby subverting host surveillance. In Candida albicans, the highly immunostimulatory β‐1,3‐glucan is a potent PAMP that the host is primed to recognize [54]. However, upon sensing host‐derived metabolic cues such as lactate, the fungus initiates an active “shaving” mechanism by inducing the Xog1 exoglucanase [55]. This enzymatic removal of surface‐exposed glucans, co‐regulated by Protein Kinase A signaling, ensures efficient immune concealment and diminishes phagocytic recognition. Similarly, Helicobacter pylori achieves chronic persistence within the gastric mucosa through the structural modification of its LPS. By adding long‐chain fatty acyl groups to the Lipid A moiety, the pathogen renders its LPS largely invisible to TLR4, while simultaneously utilizing specialized flagellin sequences that bypass TLR5 detection [56]. Beyond ligand modification, certain pathogens exert direct sabotage on host intracellular cascades. For instance, specific bacterial toxins hijack host caspase‐3 to cleave the active N‐terminal gasdermin D, thereby suppressing macrophage pyroptosis and preserving a protected intracellular niche for replication [57]. Conversely, clinical interventions can be leveraged to forcibly restore PAMP visibility and enhance pathogen clearance. Tobramycin‐mediated bactericidal activity increases the systemic liberation of bioactive LPS, which in turn amplifies the localized inflammatory milieu and augments antibiotic efficacy through neutrophil‐dependent recruitment [58].

Reciprocally, the host maintains a dynamic sensing threshold by modulating pattern recognition receptors. Lipid mediators, such as epoxyeicosatrienoic acids, can attenuate the inflammatory response to Streptococcus pneumoniae by downregulating the expression of TLR2 and PGLYRP1, illustrating the host's ability to tune innate sensitivity via endogenous metabolites [59]. Furthermore, the overall cellular landscape profoundly dictates PAMP responsiveness. Senescent cells exhibit a hyperinflammatory primed phenotype. When challenged by PAMP motifs such as the SARS‐CoV‐2 spike protein, these senescent cells upregulate viral entry factors and suppress the antiviral defenses of neighboring nonsenescent cells through paracrine signaling cascades [60]. This contextual sensitivity is further calibrated by cytokine environments. For example, IFN‐γ priming utilizes caspase‐8‐dependent pathways to lower the physiological threshold for PAMP‐induced cell death, ensuring a rapid response to imminent threats [61].

Regulation of DAMP Signaling

DAMP activity is regulated at three interconnected levels: generation, clearance, and sensing. These control mechanisms ensure that danger signals accurately reflect genuine tissue injury. However, a disruption in this balance results in persistent inflammation contributing to chronic pathology.

DAMP production is controlled through transcriptional, posttranslational, and cellular mechanisms. At the transcriptional level, DAMP expression is dynamically calibrated rather than constitutive; C/EBPδ drives epigenetic remodeling that governs S100a8 and S100a9 transcription in response to inflammatory signals [62]. Posttranslational modifications further modulate DAMP functionality: circulating FABP5 exists in an oxidized form that exacerbates septic inflammation as a DAMP, whereas its reduced cytoplasmic counterpart actively suppresses pyroptosis, demonstrating how oxidation state converts a benign intracellular protein into a pro‐inflammatory mediator [63]. Cellular stress pathways can influence DAMP liberation. Compound F1929‐1458 engages NF‐κB signaling in stressed tumor cells, triggering release of HMGB1‐genomic DNA complexes, ATP, and oxidized LDL (oxLDL) that activate dendritic cell cGAS‐STING and NLRP3 pathways [64].

To maintain immunological silence, the homeostatic concentration of extracellular DAMPs is regulated by clearance systems and active sequestration [65]. When the rate of cellular death overwhelms these efferocytic pathways, exemplified by liver injury where hepatocyte apoptosis saturates compromised macrophage efferocytic capacity, the resultant accumulation of secondary necrotic debris (originating from uncleared apoptotic cells) fuels a self‐perpetuating inflammatory cycle through the release of DAMPs like HMGB1, oxidized mtDNA, and bioactive phospholipids [66]. This clearance is orchestrated by molecular opsonins such as the apoptosis inhibitor of macrophages (AIM), which anchors to DAMPs via charge‐based and disulfide interactions to facilitate phagocytic uptake [67]. Beyond promoting debris removal, AIM provides a critical layer of immune regulation by sterically hindering DAMP‐receptor engagement, thereby neutralizing pro‐inflammatory signals and restoring immunological homeostasis before they can propagate systemic tissue damage [67].

DAMP detection is dependent on receptor expression. Genetic variation in pattern recognition receptors establishes baseline sensing thresholds: loss‐of‐function mutations compromising DAMP recognition (such as TLR3 defects that disrupt antiviral DAMP detection) increase susceptibility to herpes simplex encephalitis [68]. Conversely, TLR7 gene duplications confer excessive sensitivity to self‐derived DAMPs, precipitating pediatric systemic lupus erythematosus (SLE) and underscoring the need to maintain appropriate recognition thresholds [68].