Neurodegenerative diseases result from a complex interplay of genetic, environmental, and aging factors. These conditions entail progressive dysfunction and gradual loss of specific neuronal subsets, leading to the accumulation of misfolded proteins, heightened oxidative stress, mitochondrial dysfunction, compromised bioenergetics, and neuroinflammatory processes [1]. The overall process of neurodegeneration is illustrated in Figure 1. Neurodegenerative disorders have a profound impact on an individual’s quality of life, marked by a gradual decline in cognitive and physical functions [2, 3]. The prevalence of such diseases, exemplified by Alzheimer’s disease (AD), is anticipated to rise with increasing life expectancy, posing a substantial clinical and economic burden for the US and other nations, surpassing the costs associated with cancer [4]. By 2037, Parkinson’s disease (PD) is projected to affect 1.6 million people in the USA [5], while AD is expected to surge by approximately 130 million by 2050 [6].

Therapeutic approaches for neurodegenerative diseases encompass a spectrum of strategies, ranging from physical therapy and medications to surgical interventions. Currently, however, there is a scarcity of drugs for many neurodegenerative conditions, and available treatments are often limited to managing symptoms and slowing disease progression. The precise mechanism for identifying neurodegenerative diseases remains elusive, presenting a significant challenge for clinicians [7–9]. Consequently, there is an unmet need to develop diagnostic kits capable of identifying biomarkers for early detection. The utilization of biomarkers holds substantial promise in advancing the diagnosis and treatment of central nervous system (CNS) diseases. Biomarkers offer the potential for early detection, improved diagnostic accuracy, and the development of personalized patient-specific treatment options [10]. In the context of the CNS, biomarkers are measurable indicators that convey information about normal or pathological processes within the brain and spinal cord. These biomarkers can be identified in diverse biological samples, including blood, cerebrospinal fluid (CSF), and through imaging studies [11, 12]. Biomarkers play a crucial role in enhancing diagnostic processes in clinical settings and are instrumental in the development and monitoring of effective disease-modifying treatments [13]. Their application extends to the diagnosis, monitoring, and assessment of treatment efficacy in a range of neurological diseases and disorders, including AD, multiple sclerosis (MS), and PD [2, 14–16]. Various body fluids, such as blood, CSF, urine, and saliva, contain detectable biomarkers that can be analyzed using diverse molecular approaches. This underscores the versatility and potential of biomarkers in advancing the understanding and management of neurological conditions (Figure 2).

In recent years, the exploration of biomarkers has emerged as a promising avenue for gaining a deeper understanding of neurodegenerative disorders. microRNAs (miRNAs) and protein biomarkers have garnered significant attention due to their intricate involvement in the molecular mechanisms underlying neurodegeneration. Proteins, acting as pivotal players in cellular functions, are implicated in various physiological and pathological processes within the CNS. Alterations in their expression, post-translational modifications, or aggregation can lead to synaptic dysfunction, neuronal cell death, and the progression of neurodegenerative disorders [17] making them valuable candidates for biomarker discovery. In addition to proteins, miRNAs, a class of small RNA molecules, play a crucial role as regulators of gene expression. Dysregulation of miRNAs has been implicated in neurodegenerative processes [18], offering a unique perspective on the intricate molecular landscape of these disorders. The exploration of both proteins and miRNAs as biomarkers provides a multifaceted approach to understanding and potentially diagnosing neurodegenerative conditions.

The CNS, comprised of the brain and spinal cord, constitutes a complex and sophisticated system responsible for regulating and coordinating body activities. CNS diseases encompass a broad spectrum of disorders wherein the functioning of the brain or spinal cord is compromised, leading to diminished motor, sensory, or cognitive capabilities [19]. These conditions may arise from various factors such as infection [20], injury [21], degeneration, or structural defects [22]. Common CNS diseases include stroke, MS, PD, and AD.

Biomarkers play a crucial role in diverse settings for identifying and managing individuals at high risk of developing various diseases, including AD, PD, Huntington’s disease (HD), dementia, and different types of cancers such as lung cancer, colorectal cancer, breast cancer, liver cancer, and esophageal cancer [23, 24]. Within the context of CNS disorders, a variety of biomarkers can be employed, encompassing genetic, molecular, functional, and image-based biomarkers [11, 25]. This multifaceted approach underscores the potential for biomarkers to contribute significantly to the understanding and management of CNS-related conditions.

Biomarkers serve as measurable biological molecules or factors that can indicate normal or disease states. Extensive research over the past decades has aimed at developing reliable biomarkers for neurodegenerative diseases. These biomarkers can be employed independently or in conjunction with other factors to enhance the reliability and precision of diagnosis, prognosis, and treatment planning in CNS diseases [26–28]. The exploration of biomarkers through miRNA expression holds immense clinical potential due to the non-invasive nature of studying gene expression using plasma samples, facilitated by advancements in microarray and high-throughput sequencing technology. miRNAs are being investigated as early biomarkers and diagnostic tools for various diseases, including cancer and Alzheimer’s, gaining strong interest in recent years [29]. They play a significant role in regulating processes such as cell proliferation, differentiation, maturation, apoptosis, and other developmental activities [30]. Numerous studies have demonstrated that miRNA dysregulation is associated with various diseases, suggesting their potential for diagnosis and treatment [29, 31, 32]. More recently, serum miRNAs and blood cell-derived miRNAs are being explored as non-invasive diagnostic biomarkers for PD, glioblastoma, and other diseases [33–35].

In addition to miRNAs, long noncoding RNAs (lncRNAs) have been implicated in the pathogenesis of neurodegenerative diseases, suggesting that their dysregulation could trigger neuronal death through unexplored RNA-based regulatory mechanisms [36, 37]. Studies have reported on the involvement of lncRNAs in various molecular processes that regulate gene expression in the CNS, ranging from neural stem cell differentiation, predominantly through chromatin remodeling, to the control of neuronal activities [38, 39].

Another class of noncoding RNAs, circulating miRNAs (cimiRNAs), holds promise as biomarkers for CNS disorders. These miRNAs are found in various body fluids, including CSF, blood, urine, breast milk, tears, and saliva [40, 41]. cimiRNAs originate in the nucleus, transfer to the cytoplasm, and are either actively released into body fluids or passively released without requiring any energy [42]. They exhibit exceptional stability, lacking loose ends that are accessible to canonical RNA decay pathways [43]. Abundant in the brain, cimiRNAs display cell- and tissue-specific expression and often remain unaltered, in contrast to proteins that undergo various post-translational modifications. This stability makes them readily detectable using laboratory techniques such as RT-PCR [42]. Moreover, cimiRNAs can endure harsh environmental conditions, including high temperature, pH levels, long-term storage, and repeated defrost cycles, showcasing greater resistance to degradation through endogenous RNA activity [44]. Their quantitative evaluation can be performed using various approaches, including next-generation sequencing (NGS), microarrays, and qRT-PCR. A notable study by Dube et al. [45] recently identified a significant correlation between circular RNA (circRNA) expression and the diagnosis, clinical dementia severity, and neuropathological severity in AD patient brain tissue samples. This highlights the potential utility of cimiRNAs as valuable biomarkers in understanding and diagnosing CNS disorders.

The past few decades have witnessed a rapid expansion in the discovery and application of protein biomarkers for neurological disorders. The complex network of protein interactions within the nervous system provides a nuanced framework for comprehending underlying pathophysiology, encompassing synaptic plasticity, cognition, and long-term potentiation [46]. Exploring protein biomarkers not only unveils molecular signatures associated with neurological disorders but also holds the potential to revolutionize clinical approaches by enabling early detection, accurate prognosis, and the development of targeted treatments [47]. The discovery of protein biomarkers for neurological disorders has seen promising developments, especially concerning the use of neurofilament proteins (NFPs) and neurogranin (Ng), amyloid-beta 42/40 (Aβ42/40), and tau. Examples of some miRNA and protein biomarkers are summarized in Tables 1 and 2. The comparatively slower progress of biomarkers for CNS disorders, compared to other areas of research, can be attributed to intricate processes, challenges in obtaining CNS tissue samples, and the complexities of the brain’s structure and functions [48, 49]. Additionally, numerous external factors can influence the design and outcomes of studies, including the interplay between genes and the environment, the diversity of CNS disorders, and variations in patient populations.

miRNAs are short non-coding RNA molecules, typically 22–24 nucleotides in length, playing a crucial role in diverse biological processes, including cellular proliferation, differentiation, cell cycling, and the maintenance of immune homeostasis [88, 89]. Abundantly expressed in neurons, miRNAs are essential for various neurobiological functions, such as synaptogenesis, neural patterning, neuronal differentiation, the formation and maintenance of cell identity, and neuronal plasticity [90]. miRNAs have been implicated in various human diseases, including neurological disorders like AD, PD, and MS. They have the potential to serve as biomarkers for different neurological disorders and are released as circulating molecules into body fluids such as CSF, blood, and urine, making them valuable for early detection of neurodegenerative disorders [91].

miRNAs can be collected from various sources, including CSF, blood, and other biofluids like serum, plasma, and urine, and utilized as diagnostic biomarkers for neurological disorders [74, 92–94]. Ideal biomarkers need to be easily accessible and extracted through liquid biopsies from different bodily fluids [95]. The circulating levels of miRNAs from these fluids can be characterized and used as non-invasive diagnostic biomarkers [96, 97]. Various specific and sensitive methods, including qRT-PCR, microarray, and NGS, are employed to detect miRNAs. For example, in a study on PD and multiple system atrophy (MSA), miRNA biomarkers were collected from CSF, and their expression levels were quantified using quantitative PCR [98]. Recently, dysregulation of miRNA and non-coding RNA expression has been reported in diverse neurological diseases, such as AD, PD, and HD [99, 100]. The role of miRNA biomarkers has been particularly emphasized in the early stages of AD [51, 101]. Novel plasma miRNAs (miR134-3p, miR-22-5p, miR-1185-2-3p, miR-1909-3p, and miR-107) have been identified as potential therapeutic targets for AD at the prodromal stage [102].

The investigation of specific miRNAs in the context of AD and PD has provided insights into their potential roles and therapeutic implications:

miR-98 in AD: This effect was mediated via the Notch signaling pathway through binding to hairy and enhancer of split-related with YRPW motif protein 2 (HEY2). It was found that miR-98 decreased the production of Aβ-protein and significantly increased oxidative stress while modifying mitochondrial functioning in scopolamine-treated AD mice. Detection of miR-98 and the protein levels of HEY2 and β-amyloid precursor protein (APP) was performed in brain tissues using RT-PCR and western blot analyses [103].

miR-153 in AD: miR-153 expression was reported to be downregulated in the brains of individuals with advanced-stage AD. This miRNA was found to obstruct the expression of Aβ-precursor protein in cultured human fetal brain cells [104].

miR-128 in AD: The expression of miR-128 was upregulated, and peroxisome proliferator-activated receptor gamma (PPAR-gamma) expression was downregulated in the plasma of AD patients. miR-128 was shown to suppress Aβ-mediated neurotoxic effects by binding to PPAR-gamma and blocking the intracellular NF-κB pathway [105]. miR-128 directly inhibits the expression of tau phosphorylation by targeting glycogen synthase kinase 3β (GSK3β), modulators APP binding protein 2 (APPBP2) and the mammalian target of rapamycin (mTOR). Upregulation of miR-128 in the hippocampus of five familial AD (5XFAD) mice ameliorates learning and memory impairments, tau phosphorylation, Aβ secretion, and enhances autophagic flux. While downregulation of miR-128 in the late stage of AD increases the concentration of Aβ in brain [106].

miR-7 in PD: miR-7, a brain-enriched miRNA, plays a significant role in brain development and neurological disorders, including PD [107, 108]. It directly downregulates α-synuclein expression in dopaminergic neurons, providing cellular protection [109]. Abnormal aggregation and expression of the α-synuclein protein in the brain are key features of PD [110–112]. miR-7 regulates α-synuclein expression by interacting with the 3’-untranslated region (UTR) region of the synuclein alpha non A4 component of amyloid precursor (SNCA) gene, blocking the conversion of the gene’s information into a protein. Reduced levels of miR-7 in the substantia nigra have been observed in PD patients, emphasizing its role in regulating α-synuclein expression and suggesting its potential as a therapeutic target for PD [113].

miR-124 is one of the most widely expressed miRNAs in the brain and is implicated in various crucial processes, including neurogenesis, synaptic architecture, apoptosis, inflammation, neurotransmission, and mitochondrial function [114, 115]. In the context of PD, chronic inflammation in the CNS driven by microglial cells plays a vital role in disease progression. Studies have suggested the following roles for miR-124 in neuroinflammation and neurodegenerative diseases. Overexpression of miR-124 in the brain has been associated with protection of SH-SY5Y cells from apoptosis induced by microglial activation triggered by lipopolysaccharide exposure. This finding suggests a potential key role for miR-124 in inhibiting neuroinflammation in the context of PD [116]. Downregulation of miR-124 expression has been linked to increased Aβ deposition, angiogenesis, and microvascular dysfunction in the hippocampus and cerebral cortex of AD mice. This effect is mediated by the control of complement C1q-like protein 3 [117]. Brain-specific miR-124 has been implicated in inhibiting neuroinflammation during the development of PD by targeting p38, p62, and autophagy. This suggests that miR-124 may serve as an effective therapeutic target for controlling the inflammatory response in PD patients [116]. Furthermore, a clinical study has demonstrated that small extracellular vesicles (sEVs) loaded with miR-124-3p protect dopaminergic neurons in the substantia nigra and striatal fibers, counteracting motor behavior symptoms in a PD model, and induce neuronal differentiation under physiological conditions in vitro. These findings suggest that miR-124-3p-enriched sEVs could offer a promising therapeutic strategy for halting PD neurodegeneration and improving motor function [118]. The multifaceted roles of miR-124 underscore its significance in various processes relevant to neurodegenerative diseases, particularly PD and AD.

HIV-associated neurocognitive disorders (HAND) impact a significant percentage of people living with HIV (PLWH), ranging from 15% to 60% of individuals with HIV infection. PLWH refers to individuals who have been diagnosed with HIV and are living with the virus. These individuals may be receiving treatment and care for their HIV infection. Though effective therapy for HAND is currently lacking, management strategies involve a combination of antiviral drugs, cognitive therapy, and other supportive therapies. Identifying biomarkers for cognitive health in PLWH is crucial for effective interventions to prevent and delay the onset of HAND. Substance abuse and comorbid conditions can complicate the detection of these biomarkers in PLWH [119, 120]. Several studies have explored the potential of miRNAs as biomarkers for HAND. Microarray-based analysis of plasma samples from two cohorts of HIV-positive patients, with and without HAND, identified three upregulated miRNAs (miR-3665, miR-4516, and miR-4707-5p) in patients with HAND. This suggests that plasma miRNA profiling holds potential for predicting and understanding HAND [121]. Investigation of miRNAs isolated from the CSF of HIV-positive patients indicated that 11 miRNAs were significantly upregulated in HIV encephalitis [122]. HIV-1-encoded viral proteins of HIV-1 transactivator of transcription (Tat), has attracted significant attention due to its toxicity to many CNS cells [123]. A study investigated the effects of HIV-1 Tat and cocaine co-exposure on two miRNAs (hsa-miR-2355 and hsa-miR-4726-5p), finding that their expression was significantly downregulated in human primary astrocytes exposed to both substances [124].

HIV-1 Tat-mediated upregulation of miR-34a targets the 3’-UTR of NOD-like receptor family CARD domain-containing 5 (NLRC5) in microglial cells. Dysregulated NLRC5 inflammasome leads to decreased activation of the NF-κB p65 signaling axis, resulting in increased expression of pro-inflammatory cytokines [125]. miR-34a and miR-138 negatively regulated the expression of astrocytic SIRT1 in astrocytes exposed to HIV-1 Tat, leading to astrogliosis, a characteristic feature of aging in the CNS [126]. Seventeen miRNAs were differentially expressed in the brain tissue of HAND patients. Some of these miRNAs were predicted to target peroxisome biogenesis factors, suggesting a new mechanism by which HIV-1 may cause neurocognitive dysfunction [127]. The advantages of using miRNAs as biomarkers include their early detection potential, stability in various bodily fluids, and the ability to enable larger studies and retrospective analyses [128].

lncRNAs are a class of non-coding RNA molecules longer than 200 nucleotides, located in the nucleus or cytoplasm [129]. They play various roles in cellular processes, including transcriptional regulation, chromatin modification, and post-transcriptional regulation. lncRNAs can mediate pathogenesis through mechanisms such as decoy, scaffold, histone modifiers, miRNA sequestration, and transcriptional interference [130, 131]. Their levels can be determined using techniques like qRT-PCR, NGS, and microarray, making them potential non-invasive prognostic and diagnostic markers [100, 130]. In the context of AD, several of the following lncRNAs have been implicated.

Aβ accumulation in the brain, associated with neurodegeneration in AD, is linked to altered expression levels of the lncRNA beta-site APP cleaving enzyme1-antisense (BACE1-AS). Higher expression of BACE1-AS is observed in both APP mouse models and Alzheimer’s patients, suggesting its potential as a diagnostic biomarker for AD and a therapeutic target [132]. Knockdown of early B cell factor 3 antisense (EBF3-AS) was shown to inhibit apoptosis induced by Aβ25–35 and okadaic acid in SH-SY5Y human cells. This suggests that EBF3-AS could be a potential therapeutic target for AD treatment [133]. Small nucleolar RNA host gene 1 (SNHG1) expression was found to be upregulated in an in vitro model of AD cells. SNHG1 may contribute to cell damage by controlling the miR-361-3p/zinc-finger protein 217 (ZNF217) pathway, providing a potential conceptual framework for AD treatment [134]. The expression of lncRNA 51A was found to be upregulated in AD-affected brain tissues compared to control tissues. 51A, originating from the initial intron of the Sortilin-related receptor 1 (SORL1) gene (a recognized risk factor for AD), facilitates alternative splicing of SORL1, enhancing the formation of Aβ [135]. These findings highlight the diverse roles of lncRNAs in the pathogenesis of AD and their potential as diagnostic markers and therapeutic targets.

lncRNAs have been identified as potential diagnostic markers and therapeutic targets for PD, with aberrant expression detected in brain tissues, peripheral blood, and CSF of PD patients [136–138]. lncRNAs are widely expressed in the brain and play various roles in biological functions such as cell transcription, histone modification, and DNA methylation [139]. In the context of PD, significant changes in the expression of lncRNAs have been observed in the substantia nigra of PD patients [140]. In the substantia nigra of PD patients, non-coding RNA AL049437 was found to be upregulated, while lncRNA AK021630 was downregulated compared to normal tissues. Knockdown of AL049437 increased cell viability, mitochondrial mass, mitochondrial transmembrane potential, and tyrosine hydroxylase secretion in a cell model of parkinsonism, while AK021630 had the opposite effect. This suggests that lncRNA AK021630 might inhibit the occurrence of PD, while lncRNA AL049437 may contribute to the risk of PD [140]. lncRNA GAS5 has been shown to stimulate microglial inflammation by activating the NLRP3 pathway by sponging miR-223-3p in a PD mouse model [141]. Elevated levels of lncRNA HAGLROS have been found in both SH-SY5Y cells and a mouse model of PD. HAGLROS has been linked to the inhibition of cell death and autophagy through the stimulation of the phosphoinositide-3 kinase/protein kinase-B/mTOR (PI3K/Akt/mTOR) pathway and regulation of the miR-100/ATG10 pathway [142]. Suppressing lncRNA NEAT1 prevents 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) from inducing autophagy in vivo through regulating the PTEN-induced kinase 1 (PINK1) protein. Additionally, lncRNA LINC-PINT through RNA interference results in higher cell death in cultures exposed to oxidative stress, suggesting a potential neuroprotective role in PD pathogenesis [143]. Up-regulated lncRNA-p21 indirectly increases α-synuclein expression by sponging miR-1277-5p, inhibiting viability, and promoting apoptosis in SH-SY5Y cells. This indicates that lncRNA-p21 might be a novel therapeutic target in the context of PD [144]. lncRNA GAS5 has been linked with inflammatory effects in LPS-treated microglial cells and rotenone-treated PD mice, activating NLRP3 expression by sponging miR-223-3p, thus suggesting a role in the progression of PD [141, 145]. The major advantages of lncRNAs include their association with disease pathogenicity, diverse mechanisms of action, and tissue-specific expression, making them valuable for identifying specific neurological disorders [100, 146]. The exploration of lncRNAs in PD may provide insights into disease mechanisms and potential therapeutic strategies.

Early diagnosis of CNS disorders using cimiRNAs holds significant promise for providing patients with more specialized and efficient therapy choices [147, 148]. One particular miRNA family, the miR-29 family, consisting of miR-29a, miR-29b, and miR-29c, plays a crucial role in neuronal maturation and dendritic spine morphology [149, 150]. The downregulation of miR-29 has implications in aging and various neurological disorders, including AD [151], HD [152], and MS [153]. The expression of the miR-29 family, particularly miR-29a and miR-29c, is significantly downregulated in the blood serum of patients with PD compared to healthy controls [154]. Upregulation of miR-29a contributes to axonal outgrowth and neurological recovery through targeting PTEN/PI3K/Akt pathway after intracerebral hemorrhage insults in rats and cortical neurons [155]. A novel cimiRNA, cimiRNA-132, has been identified to regulate crucial pathways related to neuronal plasticity, including long-term potentiation and DNA methylation. It was found to be upregulated in the serum of AD patients, suggesting its potential as a biomarker for diagnosis [156]. Increased expression of miR-221-3p was found to activate the Akt/mTOR pathway, indicating a protective effect in PD. This miRNA could be considered a target for PD treatment [157]. The major advantages of miRNA biomarkers include their potential for use in multimarker models for accurate diagnosis, guided treatment, and monitoring the course of a disease. miRNA biomarkers offer high specificity and sensitivity, low baseline variability, and their non-invasive nature makes them cost-effective for use in personalized patient profiles, allowing for more specific therapeutic interventions [95]. cimiRNAs are stable in biofluids and their expression levels may not be significantly affected by basic characteristics like gender, age, and smoking status, making them reliable for monitoring and early diagnosis of diseases. Additionally, miRNAs can identify a relatively early response to toxic exposure, even in benign situations [158, 159]. In summary, the use of miRNAs in various diseases, including CNS disorders, holds significant potential as biomarkers due to their remarkable tissue specificity, early appearance, and stability in biological fluids.

In the realm of CNS biomarker research, several challenges are anticipated in the future. A primary obstacle is the development of biomarkers with heightened sensitivity and specificity. Many existing biomarkers exhibit limitations in these aspects, posing difficulties in accurately diagnosing and monitoring certain CNS disorders. The intricate and multifaceted nature of CNS disorders adds to the complexity, making it challenging to pinpoint and validate biomarkers that genuinely encapsulate the underlying pathophysiology of these conditions. Moreover, addressing the heterogeneity of CNS disorders proves to be another intricate challenge, as it is difficult to identify biomarkers that can be consistently applied across various subtypes of the disorder. The diverse manifestations within CNS disorders necessitate a nuanced understanding for effective biomarker development and application. To overcome these challenges, longitudinal studies and the integration of big data will be indispensable in validating biomarkers and assessing their utility in the clinical setting. These approaches will enable researchers to gather comprehensive insights into the dynamic nature of CNS disorders and enhance the reliability and applicability of identified biomarkers [180, 223].

While numerous biomarkers have emerged from preclinical studies, their validation in larger and more diverse patient populations is a critical next step. Transitioning from preclinical validation to clinically useful tests presents a significant challenge, demanding the development of assays that are not only sensitive and specific but also user-friendly [31, 224]. Reproducibility and standardization emerge as major stumbling blocks in the field, with many RNA signatures entering clinical trials but failing to progress to practical clinical applications. The development and validation of miRNA biomarkers can be financially burdensome, necessitating a careful consideration of costs versus benefits to justify their implementation in terms of improved diagnosis and treatment of diseases [225]. In addition to financial considerations, the expansive data generated in miRNA biomarker research poses challenges related to data sharing and collaboration. Balancing the imperative for collaborative efforts with concerns surrounding patient privacy and data security is essential for maximizing the potential of data-driven biomarker discovery. Overcoming these challenges is pivotal for translating promising preclinical findings into clinically relevant applications and advancing the field of miRNA biomarker research [226].

The field of image-based biomarkers is rapidly advancing, driven by recent technological breakthroughs. Various imaging techniques are currently being employed to gather valuable insights into biological processes and disease states. These include different imaging techniques are currently being utilized such as functional MRI (fMRI), quantitative MRI (qMRI), PET, and single photon emission computed tomography (SPECT) [8, 227, 228]. The utilization of these advanced imaging techniques offers a non-invasive and highly detailed view of biological structures and functions. These image-based biomarkers have the potential to enhance early detection, diagnosis, and monitoring of various diseases, providing valuable information for personalized medicine and treatment planning. Continued technological advancements in imaging modalities are expected to further broaden the scope and impact of image-based biomarkers in medical research and clinical practice [229, 230]. Addressing these challenges requires careful attention to standardizing imaging protocols, implementing correction techniques, and employing advanced imaging technologies that minimize the impact of patient-related factors. Quality control measures and standardized imaging procedures can also help enhance the reliability and reproducibility of imaging biomarkers. As technology advances, efforts to develop imaging techniques that minimize patient discomfort, reduce radiation exposure, and account for potential sources of variability [227, 231, 232]. Additionally, ongoing research and improvements in imaging protocols aim to mitigate the impact of these factors, ensuring that imaging biomarkers remain a valuable tool in medical diagnosis and research.

Tissue biopsies in the CNS are typically acquired through neurosurgical removal or stereotactic tissue biopsy procedures. While these methods are valuable for diagnosing various CNS conditions, they come with inherent risks and limitations due to their invasive nature [233]. Brain biopsy, for example, involves collecting small pieces of brain tissue for microscopic examination to diagnose abnormalities such as tumors, inflammation, AD, infections, and other brain disorders. However, this approach poses several challenges [234]. Neurosurgical removal or stereotactic tissue biopsy is inherently invasive, carrying risks for the patient. This invasiveness can result in pain, discomfort, and a small but notable risk of complications such as bleeding or infection. This method is only feasible when the targeted tissue is accessible. In the case of certain diseases or specific regions of the body, especially within the CNS, obtaining a biopsy may be challenging or impractical. The amount of tissue that can be obtained through biopsy may be restricted, impacting the ability to conduct multiple tests or replicate results. This limitation is particularly relevant in cases where larger samples are required for comprehensive analysis. The process of obtaining and isolating tissue for analysis can be costly and time-consuming. This makes it difficult to perform multiple tests efficiently and may hinder the rapid replication of results.

Given these challenges, the development and utilization of non-invasive or minimally invasive diagnostic methods, such as imaging and liquid biopsy techniques, are gaining prominence. These approaches aim to provide valuable diagnostic information while minimizing the risks and limitations associated with traditional tissue biopsies, especially in the sensitive and critical context of the CNS [235, 236].

Stereotactic brain biopsy is indeed a minimally invasive procedure designed to extract tissue samples from specific areas within the brain suspected of harboring infections or tumors. This procedure involves the utilization of a stereotactic device, which employs a coordinate-based navigation system integrated with the patient’s brain images, typically obtained through MRI or computed tomography (CT) [237, 238]. This technique has become a valuable diagnostic tool, providing important information for treatment planning while minimizing the impact on the patient.

The ethical considerations surrounding tissue sample collection, particularly in the context of neurodegenerative disease research, are indeed critical and multifaceted [239]. Proper storage and handling of biopsy samples are vital for maintaining the integrity of biomarkers. Challenges arise in preventing contamination or degradation of samples, especially during long-term storage. Robust protocols for sample preservation, including temperature control and adequate labeling, are crucial to ensure the reliability of biomarker analyses [240, 241]. At present, the development of economically viable biomarkers for widespread use in the early diagnosis of neurodegenerative diseases is a persistent challenge [13, 25, 242]. While many CNS biomarkers show promise in preclinical studies, transitioning them to clinical practice remains a significant hurdle. Biomarkers for disease prognosis, treatment, and outcome assessment often undergo extensive preclinical evaluation, but their translation into practical clinical applications requires rigorous validation and approval processes [243].

A mounting body of evidence supports the application of biomarkers in diagnosing and treating CNS disorders. Nevertheless, additional research is imperative to comprehensively grasp the clinical efficacy of these markers and to pinpoint novel biomarkers. It is pivotal to underscore that the biomarker discovery process should unfold concurrently with clinical validation. Specifically, the validation of biomarkers ought to transpire in both retrospective and prospective manners, utilizing independent sample cohorts, ideally procured by multiple hospitals. Exploring and elucidating the regulatory mechanisms of miRNAs, lncRNAs, and cimiRNAs in neurodegenerative disorders is essential to enhance the applicability and accuracy of these molecules as biomarkers for clinical diagnoses. To augment the sensitivity and specificity of protein detection in biological samples, advancements in testing methods, such as mass spectrometry and immunoassays, are imperative. Additionally, there remains much to unravel about the dynamics of protein levels in the body, encompassing genetic and environmental factors, and how these levels evolve over time in both healthy individuals and those with neurological disorders. In conclusion, the integration of biomarkers into CNS research holds the potential to revolutionize the field by enhancing diagnostic precision, predicting disease progression and treatment response, ultimately culminating in the development of more effective therapies.