The pain matrix encompasses a network of brain regions involved in pain perception and modulation. The S1 and S2 somatosensory cortices play a pivotal role in processing the sensory-discriminative aspects of pain [7]. S1 is responsible for encoding the location and intensity of painful stimuli, while S2 integrates this information and contributes to the perception of pain intensity and the emotional response to pain [7]. These regions collectively contribute to the sensory and affective dimensions of pain perception [7]. A large body of knowledge showed that S1 and S2 somatosensory cortices are important regions in pain matrix framework. Also, Worthen et al. [8] reported a differential role for the S1 and S2 regions in pain with evidence for the involvement for S1 in affective processing. In more detail, the authors recorded magnetoencephalography in male participants during a visceral pain experiment and highlighted the role of S1 in sensory and attentional aspects of pain processing as well as S2 in encoding the characteristics of the stimulus. Remarkably, a recent study revealed that the peripheral immune response mediated by neuropathic pain is correlated with central amygdala and somatosensory cortex via vagal projections to the spleen [9]. Furthermore, current views point to the fact that enhancing cortical excitatory activity can be a valuable way to control neuropathic pain [10]. In more detail, by using patch clamp recording, it was found that the pharmacological or optogenetic enhancement of cortical activity decreased behavioral hypersensitivity that is induced by injury in a neuropathic pain model of transient spinal cord ischemia [10]. Additionally, it was reported that S1 shows paroxysmal discharges and hyperexcitability after the spinal cord injury [10]. All of the aforementioned studies showed that plasticity in the S1 and S2 regions is implicated in pain conditions and the interventions.

The descending pain modulatory system is a critical mechanism in endogenous pain control, involving the periaqueductal gray (PAG), the rostroventromedial medulla (RVM), and the spinal cord. Notably, the PAG integrates input from cortical and subcortical regions to modulate nociceptive transmission through the RVM and the dorsal horn of the spinal cord [11,12]. This pathway facilitates both inhibition and facilitation of pain, underscoring its dual role in modulating the experience of pain [12]. Dysregulation within this system has been implicated in chronic pain conditions, highlighting the importance of understanding its mechanisms for developing targeted therapies [12]. Descending pain modulatory systems have been studied and characterized in animal models and by using brain imaging techniques and deep brain stimulation (DBS), and are implicated in the mechanisms of action of analgesic drugs. It is well-known that there is communication between descending pain modulatory circuits, the cortical and subcortical regions that are responsible for the motivational, emotional, and cognitive processes [13]. Accordingly, dysregulation of descending pain modulation is associated with chronic pain. As such, the treatment or the protection from chronic pain states is linked to descending pain modulatory systems such as serotonin/norepinephrine reuptake inhibitors that enhance the activity of the spinal noradrenergic system [13]. In details, growing evidence depicted that PAG activates a powerful analgesic effect and receives inputs from higher brain centers [14]. It is involved in the descending endogenous pain inhibitory system and is a vital area for pain modulation through its interactions between ascending and descending signals [14]. The PAG influences descending pain modulation primarily through its reciprocal connections with the RVM [15]. Also, the midbrain PAG inhibits nociceptive inputs to neurons in the sacral dorsal horn via alpha 2 (α2) adrenergic and μ-opioid receptors [15].

The NPS is a multivariate pattern of brain activity that serves as a neural biomarker for pain perception. It involves the use of machine learning to distinguish pain-related brain activity from non-pain-related activity. The concept of NPS was introduced in a groundbreaking study published in 2013 by Wager et al. [16]. This study utilized machine learning and pattern-recognition algorithms to analyze functional magnetic resonance imaging (fMRI) data from individuals subjected to controlled painful stimuli. The researchers identified distinct brain regions and activity patterns consistently associated with acute pain, culminating in the formation of the NPS. Importantly, the NPS is crucial for the identification of pain-specific activation in regions such as the insula, ACC, and thalamus, allowing for more precise identification of chronic pain conditions [16]. A plethora of evidence shows that the NPS is characterized by increased activity in several brain regions traditionally associated with pain processing, including the ACC, insula, thalamus, S1, and S2 [16]. Additionally, the NPS is associated with decreased activity in regions such as the ventromedial prefrontal cortex (vmPFC), which may reflect the suppression of competing cognitive or affective states. While the NPS was originally developed for acute pain, its principles can be extended to study chronic pain conditions. Chronic pain involves changes in brain function and connectivity, thus the NPS may help in identifying these alterations [17]. By observing changes in NPS activity, researchers can determine how well a drug reduces pain at the neural level. López-Solà et al. [17] explained how the NPS responds to non-steroidal anti-inflammatory drugs, providing preliminary evidence that fMRI-based measures respond to acute osteoarthritis (OA) pain and are sensitive to naproxen. Taken together, multiple studies underscore the NPS's potential as a reliable and objective biomarker for pain, with applications in clinical diagnosis and personalized pain management strategies.

Several studies revealed that chronic pain affects all aspects of the CNS and profoundly alters both the peripheral and central systems [1]. However, neuroimaging investigations showed structural and functional alterations in given areas connected to pain processing such as the ACC, PFC, and insula [1]. These areas are involved in pain's sensory, emotional, and cognitive aspects and reveal a high level of maladaptive plasticity during chronic pain conditions [1].

It is widely accepted that chronic pain causes structural and functional neuronal plasticity, including synaptic plasticity. Synaptic plasticity is crucial to the progression of chronic pain through the brain structures that are involved in pain processing including the ACC and insular cortex. Regarding structural changes, previous studies elucidated that the brain regions that are involved in pain processing such as the ACC and PFC exhibit gray matter atrophy and cortical thinning, correlated with increased pain duration and intensity [18]. These structural alterations affect the typical brain architecture and are related to impairment in pain modulation. In addition, long-term potentiation (LTP), a process related to learning and memory has been recorded in these areas during chronic pain conditions [3]. In greater detail, LTP enhances pain signals and helps in developing chronic pain [3]. In neuropathic pain, it was reported that spinal dorsal horn changes occur where the synaptic activity increases leading to central sensitization, a state of pain hypersensitivity [19]. Additionally, structural changes in neurons are considered a hallmark of chronic pain. Research studies explained that neuronal loss and reduced dendritic spine pruning in the secondary motor cortex in neuropathic pain are correlated to motor disorders and increased pain sensitivity [18]. Moreover, it was reported that the perineuronal net (PNN), a component of the extracellular matrix surrounding the neuron and regulating synaptic plasticity was involved in developing chronic pain [18]. In mice with chronic inflammatory pain, PNNs of somatosensory cortex and PFC increased due to chronic pain [20]. Furthermore, it was revealed that pain disrupts the mechanisms of signaling within the brain and spinal cord as it progresses to chronicity [20]. For example, several lines of evidences revealed that the deregulation of the gamma-aminobutyric acid (GABAergic) system in the nervous system in neuropathic pain led to the inhibition of pain signals leading to persistence of pain [21]. Also, it was shown that there are neuroplastic changes during chronic pain in the brainstem, which is a center of pain regulation [22]. Additionally, the current fMRI findings revealed a spectrum of changes within the PAG and rostral ventromedial medulla, which are parts of the descending pain inhibition network [21]. Regarding functional changes, it was shown that chronic pain results in changes to resting state networks (RSNs) with the default mode network (DMN) networks such as being involved in self-reflecting activities and emotions [18]. In addition, it was found that reduced connection within the DMN has been associated with increased pain sensitivity and perception of pain [4]. Previous reports shed light on the fact that the brain's functional architecture is disturbed by chronic pain, especially RSNs like the central executive network (CEN), salience network (SN) and DMN [23,24].

The three core networks are the CEN, DMN and SN. The SN plays a pivotal role in the anterior insula that is involved in the regulatory and cognitive, affective functions such as emotional responses, empathic processes, and interoceptive awareness [25]. The ACC and anterior insula, which form part of the SN, segregate the most relevant extrapersonal and internal stimuli to guide behavioral functions [26]. Consistent with this finding, a decrease in the functional connectivity of SN to the right posterior insula was reported in adolescent patients with chronic fatigue syndrome compared to healthy people [25]. Further, pain intensity was correlated with the functional connectivity of the SN to the caudate and left middle insula [25]. Moreover, the right anterior insula plays a causal role in demonstrating competitive interactions during the processing of cognitive information through a switch between the CEN and the DMN [26].

Regarding the CEN, it is crucial for manipulating information in working memory, and for decision-making in the context of goal directed behavior [26]. The CEN encompasses both the lateral posterior parietal cortices and dorsolateral prefrontal cortices (dlPFC). Deficits in this network reflect disturbances in the executive control functions and working memory [25]. Meanwhile, the DMN is anchored in the vmPFC and posterior cingulate cortex (PCC) where alterations in the DMN are associated with deficits in self-referential mental activity [25]. Also, the CEN, anchored by the dlPFC and posterior parietal cortex, is essential for working memory and cognitive control. Meanwhile, the SN network that is centered on the anterior insula and the ACC, detects and prioritizes salient stimuli, including painful ones, facilitating rapid responses to critical events. The DMN, comprising the medial PFC and PCC, is associated with self-referential thought and mind-wandering [27,28]. In fact, chronic pain disrupts the connectivity of the CEN, dLPFC, SN and CEN, leading to impaired cognitive function, emotional dysregulation, and altered pain perception. These disruptions highlight the need for targeted interventions to restore network balance and mitigate chronic pain symptoms [27,28]. Taken together, a remarkable amount of literature has shown that self-referential signal processing, sensory input perception, and affective response modulation depend on these anticipated linkages. These networks' after-connections are reinforced and reorganized in chronic pain, leading to changes that increase pain sensitivity, and diminish cognitive function. Chronic pain and its effect on mental health are exhibited in these changes in connection and network dynamics [23,24].

Astrocytes and microglia describe a class of glial cells that play pivotal roles in establishing chronic pain. Reactive astrogliosis is an aberrant cell response where astrocytes get stimulated, consequent upon injury or chronic pain [29]. In glial cells, pro-inflammatory gliotransmitters and cytokines which modulate nociceptive implication and synaptic plasticity are released [29]. Furthermore, earlier studies described that the cross-talk between neurons and astrocytes initiates pain sensitization and is critical for chronic pain resolution. Thus, its impact on neuropathic pain pathology cannot be ignored [21,29]. Activated glial cells (as markers for neuroinflammation) also contribute to pain by modulating neurons and synapses [21]. In more detail, astrocytes and microglia release pro-inflammatory cytokines such as tumor necrosis factor-alpha and interleukin-1β that, collectively, enhance the excitability of pain–processing neurons [21]. These inflammatory processes are associated with alterations in early synaptic and structural plasticity that generate persistent pain.

Previous studies revealed that epigenetic changes including DNA methylation and histone acetylation play essential roles in governing the plasticity implicated in chronic [30]. Thus, histone deacetylases and DNA methyltransferases epigenetic factors control gene expression in response to pain stimuli [30]. To elaborate, it was found that enhanced DNA (cytosine-5-)-methyltransferase (DNMT3a2) protein expression in the spinal cord contributes to maintaining central sensitization and chronic inflammatory pain [30]. Consequently, new treatment strategies for chronic pain can be established to reverse the epigenetic modifications. Previous studies have demonstrated that suppression of the histone deacetylase 4 (HDAC4) function in spinal neurons decreases sensitization to pain and normalizes the expression of connectivity in neural circuits [30].

For instance, increased expression of DNA (cytosine-5)-methyltransferase 3a2 (DNMT3a2) in the spinal cord has been implicated in the persistence of central sensitization and chronic inflammatory pain. DNMT3a2 is known to hypermethylate promoters of genes involved in anti-nociceptive pathways, effectively silencing their expression and promoting pain sensitization [31]. This discovery highlights the potential of targeting DNMT3a2 to alleviate chronic pain by reversing DNA methylation patterns.

Similarly, histone acetylation has been shown to play an essential role in pain modulation. Histone acetylation typically enhances gene transcription by loosening chromatin structure, whereas histone deacetylation, mediated by HDACs, has the opposite effect. Suppression of HDAC4 activity in spinal neurons has been demonstrated to attenuate pain sensitization and restore normal synaptic connectivity in pain-processing neural circuits [32]. These findings suggest that HDAC4 inhibitors could serve as promising therapeutic agents in the treatment of chronic pain. Several studies have provided additional evidence supporting the role of epigenetic modulation in pain. For example, pharmacological inhibition of HDACs not only reduces pain hypersensitivity but also prevents the development of chronic pain in preclinical models [33]. Similarly, DNMT inhibitors have shown efficacy in reversing established pain phenotypes by reactivating silenced genes involved in nociceptive pathways [34]. Given the accumulating evidence, epigenetic factors such as HDACs and DNMTs represent attractive therapeutic targets for developing novel pain management strategies.

Chronic pain results in consistent modifications of GMV and density in the brain [35,36]. It is related to significant GMV decrease in the PFC, insula, thalamus, and ACC. Structural changes and severe brain atrophy were found in patients with pain lasting for a long duration [35,36]. These outcomes define that chronic pain is coupled with neurodegenerative alteration in which prolonged pain reduces the quality of pain-modulating areas [35]. The changes are noted in various areas involving sensory, affective, and evaluative dimensions of pain such as the ACC, insula, PFC and the thalamus, particularly in patients who have fibromyalgia, chronic back pain, and migraine [36].

GMV reductions in regions such as the PFC, ACC, and thalamus have been linked to pain intensity, emotional dysregulation, and cognitive impairments. These structural alterations underscore the profound impact of chronic pain on brain morphology and its potential as a marker for disease progression and therapeutic efficacy [37]. Nowadays, several studies shed light on the changes in GMV and their correlation with chronic pain and their clinical significance in the diagnosis, and treatment of many diseases. Wang et al. [38] used high-resolution T1 structural scans and voxel-based morphometry, and reported a negative correlation between GMV and the frequency of pain crises in 38 pediatric patients with sickle cell disease similar to other chronic pain conditions such as fibromyalgia and irritable bowel syndrome [38]. Particularly, in the subgroup of sickle cell disease patients with poorer quality of life, a reduction in GMV appeared in the parahippocampus. Accordingly, this matter can be used as an endpoint for the evaluation of pain-directed therapies [38].

These alterations are associated with neuronal atrophy, a reduction in the excitatory neurotransmitters, inflammation, and/or excitotoxicity [38]. Furthermore, Li et al. [39] reported a decrease in GMV in the thalamus in patients suffering from frozen shoulder and highlighted its correlation with pain threshold and intensity by using functional and structural magnetic resonance imaging techniques. Also, the dysfunction in thalamocortical functional connectivity can be used as a neurobiomarker for neuropathic pain [39].