Nanoparticle-Enabled Enrichment of Longitudinal Blood Proteomic Fingerprints in Alzheimer's Disease

Advancing personalized medicine: Integrating statistical algorithms with omics and nano-omics for enhanced diagnostic accuracy and treatment efficacy

Medical laboratory services enable precise measurement of thousands of biomolecules and have become an inseparable part of high-quality healthcare services, exerting a profound influence on global health outcomes. The integration of omics technologies into laboratory medicine has transformed healthcare, enabling personalized treatments and interventions based on individuals' distinct genetic and metabolic profiles. Interpreting laboratory data relies on reliable reference values. Presently, population-derived references are used for individuals, risking misinterpretation due to population heterogeneity, and leading to medical errors. Thus, personalized references are crucial for precise interpretation of individual laboratory results, and the interpretation of omics data should be based on individualized reference values. We reviewed recent advancements in personalized laboratory medicine, focusing on personalized omics, and discussed strategies for implementing personalized statistical approaches in omics technologies to improve global health and concluded that personalized statistical algorithms for interpretation of omics data have great potential to enhance global health. Finally, we demonstrated that the convergence of nanotechnology and omics sciences is transforming personalized laboratory medicine by providing unparalleled diagnostic precision and innovative therapeutic strategies.

Nanozymes in Alzheimer's disease diagnostics and therapy

Alzheimer's disease (AD) is a progressive neurodegenerative condition that has become an important public health problem of global concern, and the early diagnosis and etiological treatment of AD are currently the focus of research. In the course of clinical treatment, approved clinical drugs mainly serve to slow down the disease process by relieving patients' clinical symptoms. However, these drugs do not target the cause of the disease, and the lack of specificity of these drugs has led to undesirable side effects in treatment. Meanwhile, AD is mainly diagnosed by clinical symptoms and imaging, which does not have the advantage of early diagnosis. Nanozymes have been extensively investigated for the diagnosis and treatment of AD with high stability and specificity. Therefore, this review summarizes the recent advances in various nanozymes for AD diagnosis and therapy, including with peroxidase-like-activity gold nanozymes, iron nanozymes, superoxide dismutase-like- and catalase-like-activity selenium dioxide nanozymes, platinum nanozymes, and peroxidase-like palladium nanozymes, among others. A comprehensive analysis was conducted on the diagnostic and therapeutic characteristics of nanozyme therapy for AD, as well as the prospects and challenges of its clinical application. Our goal is to advance this emerging topic by building on our own work and the new insights we have learned from others. This review will assist researchers to quickly understand relevant nanozymes' therapeutic and diagnostic information and further advance the field of nanozymes in AD.

Protein Corona Sensor Array Nanosystem for Detection of Coronary Artery Disease

Coronary artery disease (CAD) is the most common type of heart disease and represents the leading cause of death in both men and women worldwide. Early detection of CAD is crucial for decreasing mortality, prolonging survival, and improving patient quality of life. Herein, a non-invasive is described, nanoparticle-based diagnostic technology which takes advantages of proteomic changes in the nano-bio interface for CAD detection. Nanoparticles (NPs) exposed to biological fluids adsorb on their surface a layer of proteins, the "protein corona" (PC). Pathological changes that alter the plasma proteome can directly result in changes in the PC. By forming disease-specific PCs on six NPs with varying physicochemical properties, a PC-based sensor array is developed for detection of CAD using specific PC pattern recognition. While the PC of a single NP may not provide the required specificity, it is reasoned that multivariate PCs across NPs with different surface chemistries, can provide the desirable information to selectively discriminate the condition under investigation. The results suggest that such an approach can detect CAD with an accuracy of 92.84%, a sensitivity of 87.5%, and a specificity of 82.5%. These new findings demonstrate the potential of PC-based sensor array detection systems for clinical use.

Nano-omics: Frontier fields of fusion of nanotechnology

Nanotechnology, an emerging force, has infiltrated diverse domains like biomedical, materials, and environmental sciences. Nano-omics, an emerging fusion, combines nanotechnology with omics, boasting amplified sensitivity and resolution. This review introduces nanotechnology basics, surveys its recent strides in nano-omics, deliberates present challenges, and envisions future growth.

Establishment and clinical application evaluations of a deep mining strategy of plasma proteomics based on nanomaterial protein coronas

Research on plasma proteomics has received extensive attention, because human plasma is an important sample for disease biomarker research due to its easy clinical accessibility and richness in biological information. Plasma samples contain a large number of leaked proteins from different tissues in the body, immune proteins and communication signal proteins. However, MS signal suppression from high-abundance proteins results in a large number of proteins that are present in low abundance in plasma not being detected by the LC-MS method. This situation makes it more difficult to study neurological diseases, where tissue sampling is difficult and body fluid samples such as plasma or cerebrospinal fluid are both affected by signal suppression. A large number of methods have been developed to deeply mine plasma proteomics information; however, their application limitations remain to some extent. Traditional immuno- or affinity-based depletion, fractionation and subproteome enrichment methods cannot meet the challenges of large clinical cohort applications due to limited time efficiency. In this study, a deep mining strategy of plasma proteomics was established by combing the protein corona formed by deep mining beads (DMB beads, hereafter referred to as magnetic covalent organic frameworks Fe3O4@TpPa-1), DIA-MS detection and the DIA-NN library searching method. By optimizing the enrichment step, mass spectrometry acquisition and data processing, the evaluation results of the deep mining strategy showed the following: depth, the strategy identified and quantified results of 2000+ proteins per plasma sample; stability, more than 87% of the enriched low-abundance proteins had CV < 20%; accuracy, good agreement between measured and theoretical values (1.81/2, 8.68/10, 38.36/50) for the gradient addition of E. coli proteins to a plasma sample; time efficiency, the processing time was reduced from >12h in the traditional method to <5h (incubation 30 min, washing 15 min, reductive/alkylation/digestion/desalting 4 h), and more importantly, 96 samples can be processed simultaneously in combination with the magnetic module of the automated device. The optimal strategy enables greater enrichment of neurological disease-related proteins, including SNCA and BDNF. Finally, the deep mining strategy was applied in a pilot study of multiple system atrophy (MSA) for biomarker discovery. The results showed that a total of 215 proteins were upregulated and 184 proteins were downregulated (p < 0.05) in the MSA group compared with the healthy control group. Eighteen proteins of these differentially expressed proteins were reported to be associated with neurological diseases or expressed specifically in brain tissue, 8 and 4 of which have reference concentrations of μg/L and ng/L, respectively. The alterations of ENPP2 and SLC2A1/Glut1 were reanalyzed by ELISA, further supporting the results of mass spectrometry. In conclusion, the results of the evaluation and application of the deep mining strategy showed promise for clinical research applications.

Emerging nanotechnology for Alzheimer's disease: From detection to treatment

Alzheimer's disease (AD), one of the most common chronic neurodegenerative diseases, is characterized by memory impairment, synaptic dysfunction, and character mutations. The pathological features of AD are Aβ accumulation, tau protein enrichment, oxidative stress, and immune inflammation. Since the pathogenesis of AD is complicated and ambiguous, it is still challenging to achieve early detection and timely treatment of AD. Due to the unique physical, electrical, magnetic, and optical properties of nanoparticles (NPs), nanotechnology has shown great potential for detecting and treating AD. This review provides an overview of the latest developments in AD detection via nanotechnology based on NPs with electrochemical sensing, optical sensing, and imaging techniques. Meanwhile, we highlight the important advances in nanotechnology-based AD treatment through targeting disease biomarkers, stem-cell therapy and immunotherapy. Furthermore, we summarize the current challenges and present a promising prospect for nanotechnology-based AD diagnosis and intervention.

Applications of Nanoparticles in Alzheimer's Disease

With the rapid aging of the global population, the prevalence of neurodegenerative diseases has become a significant concern, with Alzheimer's disease (AD) being the most common. However, the clinical trials of many drugs targeting AD have failed due to the challenges posed by the blood-brain barrier (BBB), which makes intracerebral administration of drugs difficult. However, nanoparticles (NPs) may aid in the delivery of such drugs. NPs are materials with sizes between 1-100 nm that offer several advantages, such as improving biocompatibility, prolonging half-life, transporting large molecules, crossing the BBB to deliver to the central nervous system, and exhibiting good targeting ability. In addition to drug delivery, NPs also have excellent diagnostic potential, and multifunctional NPs can integrate the advantages of diagnosis, targeting, and treatment. This mini-review article provides an overview of NPs, including the composition of the carrier, strategies for crossing the BBB, and different targets of AD pathology, with the aim of providing guidance for the development prospects of NPs.

Self-Therapeutic Nanomaterials: Applications in Biology and Medicine

Over past decades, nanotechnology has contributed to the biomedical field in areas including detection, diagnosis, and drug delivery via opto-electronic properties or enhancement of biological effects. Though generally considered inert delivery vehicles, a plethora of past and present evidence demonstrates that nanomaterials also exude unique intrinsic biological activity based on composition, shape, and surface functionalization. These intrinsic biological activities, termed self-therapeutic properties, take several forms, including mediation of cell-cell interactions, modulation of interactions between biomolecules, catalytic amplification of biochemical reactions, and alteration of biological signal transduction events. Moreover, study of biomolecule-nanomaterial interactions offers a promising avenue for uncovering the molecular mechanisms of biology and the evolution of disease. In this review, we observe the historical development, synthesis, and characterization of self-therapeutic nanomaterials. Next, we discuss nanomaterial interactions with biological systems, starting with administration and concluding with elimination. Finally, we apply this materials perspective to advances in intrinsic nanotherapies across the biomedical field, from cancer therapy to treatment of microbial infections and tissue regeneration. We conclude with a description of self-therapeutic nanomaterials in clinical trials and share our perspective on the direction of the field in upcoming years.

Omics-based biomarkers discovery for Alzheimer's disease

Alzheimer's disease (AD) is the most common neurodegenerative disorders presenting with the pathological hallmarks of amyloid plaques and tau tangles. Over the past few years, great efforts have been made to explore reliable biomarkers of AD. High-throughput omics are a technology driven by multiple levels of unbiased data to detect the complex etiology of AD, and it provides us with new opportunities to better understand the pathophysiology of AD and thereby identify potential biomarkers. Through revealing the interaction networks between different molecular levels, the ultimate goal of multi-omics is to improve the diagnosis and treatment of AD. In this review, based on the current AD pathology and the current status of AD diagnostic biomarkers, we summarize how genomics, transcriptomics, proteomics and metabolomics are all conducing to the discovery of reliable AD biomarkers that could be developed and used in clinical AD management.

Synthesis of Surface-Functionalized Molybdenum Disulfide Nanomaterials for Efficient Adsorption and Deep Profiling of the Human Plasma Proteome by Data-Independent Acquisition

Blood is one of the most important clinical samples for protein biomarker discovery, as it provides rich physiological and pathological information and is easy to obtain with low invasiveness. However, the discovery of protein biomarkers in the blood by mass spectrometry (MS)-based proteomic strategies has been shown to be highly challenging due to the particularly large concentration range of proteins and the strong interference by the high-abundant proteins in the blood. Therefore, developing sensitive methods for low-abundant biomarker protein identification is a key issue that has received great attention. Here, we report the synthesis and characterization of surface-functionalized magnetic molybdenum disulfide (MoS₂) for the large-scale adsorption of low-abundant plasma proteins and deep profiling by MS. MoS₂ nanomaterials resulted in the coverage of more than 3400 proteins (including a single-peptide hit) in a single LC-MS analysis without peptide prefractionation using pooled plasma samples, which were five times more than those obtained by the direct analysis of the plasma proteome. A detection limit in the low ng L^-1 range was obtained, which is rare compared with previous reports.

Nano-omics: nanotechnology-based multidimensional harvesting of the blood-circulating cancerome

Over the past decade, the development of 'simple' blood tests that enable cancer screening, diagnosis or monitoring and facilitate the design of personalized therapies without the need for invasive tumour biopsy sampling has been a core ambition in cancer research. Data emerging from ongoing biomarker development efforts indicate that multiple markers, used individually or as part of a multimodal panel, are required to enhance the sensitivity and specificity of assays for early stage cancer detection. The discovery of cancer-associated molecular alterations that are reflected in blood at multiple dimensions (genome, epigenome, transcriptome, proteome and metabolome) and integration of the resultant multi-omics data have the potential to uncover novel biomarkers as well as to further elucidate the underlying molecular pathways. Herein, we review key advances in multi-omics liquid biopsy approaches and introduce the 'nano-omics' paradigm: the development and utilization of nanotechnology tools for the enrichment and subsequent omics analysis of the blood-circulating cancerome.

Combinatorial Power of cfDNA, CTCs and EVs in Oncology

Liquid biopsy is a promising technique for clinical management of oncological patients. The diversity of analytes circulating in the blood useable for liquid biopsy testing is enormous. Circulating tumor cells (CTCs), cell-free DNA (cfDNA) and extracellular vesicles (EVs), as well as blood cells and other soluble components in the plasma, were shown as liquid biopsy analytes. A few studies directly comparing two liquid biopsy analytes showed a benefit of one analyte over the other, while most authors concluded the benefit of the additional analyte. Only three years ago, the first studies to examine the value of a characterization of more than two liquid biopsy analytes from the same sample were conducted. We attempt to reflect on the recent development of multimodal liquid biopsy testing in this review. Although the analytes and clinical purposes of the published multimodal studies differed significantly, the additive value of the analytes was concluded in almost all projects. Thus, the blood components, as liquid biopsy reservoirs, are complementary rather than competitive, and orthogonal data sets were even shown to harbor synergistic effects. The unmistakable potential of multimodal liquid biopsy testing, however, is dampened by its clinical utility, which is yet to be proven, the lack of methodical standardization and insufficiently mature reimbursement, logistics and data handling.

Physiology, pathology and the biomolecular corona: the confounding factors in nanomedicine design

The biomolecular corona that forms on nanomedicines in different physiological and pathological environments confers a new biological identity. How the recipient biological system's state can potentially affect nanomedicine corona formation, and how this can be modulated, remains obscure. With this perspective, this review summarizes the current knowledge about the content of biological fluids in various compartments and how they can be affected by pathological states, thus impacting biomolecular corona formation. The content of representative biological fluids is explored, and the urgency of integrating corona formation, as an essential component of nanomedicine designs for effective cargo delivery, is highlighted.

Nanoparticle protein corona evolution: from biological impact to biomarker discovery

Nanoparticles exposed to biological fluids such as blood, quickly interact with their surrounding milieu resulting in a biological coating that results in large part as a function of the physicochemical properties of the nanomaterial. The large nanoparticle surface area-to-volume ratio further augments binding of biological molecules and the resulting biomolecular or protein corona, once thought of as problematic biofouling, is now viewed as a rich source of biological information that can guide the development of nanomedicines. This review gives an overview of the utility of the protein corona in proteomic profiling and discusses how a better understanding of nano-bio interactions can accelerate the clinical translation of nanomedicines and facilitate the identification of disease-specific biomarkers. With the FDA requirement of the protein corona analysis of nanoparticles in place, it is envisaged that analyzing the protein corona of nanoparticles on a case-by-case basis can provide highly valuable nano-bio interface information that can aid and improve their clinical translation.

Unraveling the Effect of Breast Cancer Patients' Plasma on the Targeting Ability of Folic Acid-Modified Chitosan Nanoparticles

The formation of protein corona (PC) around nanoparticles (NPs) has been reported inside biological conditions. This effect can alter delivery capacity toward the targeted tissues. Here, we synthesized folic acid-modified chitosan NPs (FA-CS NPs) using different concentrations of folic acid (5, 10, and 20%). FA-CS NPs were exposed to plasmas of breast cancer patients and healthy donors to evaluate the possibility of PC formation. We also monitored uptake efficiency in in vitro conditions after incubation with human breast cancer cell line MDA-MB-231 and monocyte/macrophage-like Raw264.7 cells. Data showed that the formation of PC around FA-CS NPs can change physicochemical properties coincided with the rise in NP size and negative surface charge. SDS-PAGE electrophoresis revealed differences in the type and content rate of plasma proteins attached to NP surface in a personalized manner. Based on MTT data, the formation of PC around NPs did not exert cytotoxic effects on MDA-MB-231 cells while this phenomenon reduced uptake rate. Fluorescence imaging and flow cytometry analyses revealed reduced cellular internalization rate in NPs exposed to patients' plasma compared to the control group. In contrast to breast MDA-MB-231 cells, Raw264.7 cells efficiently adsorbed the bare and PC-coated NPs from both sources, indicating the involvement of ligand-receptor-dependent and independent cellular engulfment. These data showed that the PC formed on the FA-CS NPs is entirely different in breast cancer patients and healthy counterparts. PC derived from patients' plasma almost abolishes the targeting efficiency of FA-CS NPs even in different mechanisms, while this behavior was not shown in the control group. Surprisingly, Raw264.7 cells strongly adsorbed the PC-coated NPs, especially when these particles were in the presence of patients' sera. It is strongly suggested that the formation of PC around can affect delivering capacity of FA-CS NPs to cancer cells. It seems that the PC-coated FA-CS NPs can be used as an efficient delivery strategy for the transfer of specific biomolecules in immune system disorders.

Isolation methods commonly used to study the liposomal protein corona suffer from contamination issues

The liposomal protein corona has been the focus of numerous studies, but there is still no consensus regarding its extent and composition. Rather, the literature is full of conflicting reports on the matter. To elucidate whether there could be a methodological explanation for this, we here scrutinize the efficiency of three commonly used liposome isolation methods at isolating stealth liposomes from human plasma. Firstly, we show that size-exclusion chromatography (SEC) in its standard form is prone to isolating unbound protein material together with the liposomes, but also that the method may be optimized to mitigate this issue. Secondly, we demonstrate that SEC in combination with membrane ultrafiltration is no better at removing the unbound protein material than SEC alone. Thirdly, we show that centrifugation is not able to pellet the liposomes. Overall, our results suggest that previous research on the liposomal protein corona may have suffered from significant methodological problems, in particular related to contaminant proteins interfering with the analysis of the protein corona. We believe that the data presented here may help guide future research around this challenge to reach a converging understanding about the properties of the protein corona on liposomes. STATEMENT OF SIGNIFICANCE: Upon administration into the circulatory system, liposomal drug carriers encounter an environment rich in proteins. These proteins may adsorb to the liposomes to form what is known as the protein corona, potentially governing the interactions of the liposomes with tissues and cells. However, despite decades of intense research efforts, there is currently no clear understanding about the extent and composition of the liposomal protein corona, making it impossible to assess its mechanistic importance. Here we report that the methods commonly used to isolate liposomes from blood plasma or serum to study the protein corona are susceptible to protein contamination. This may be the underlying technical reason for the current confusion about the characteristics of the liposomal protein corona.

A Proteomic Study on the Personalized Protein Corona of Liposomes. Relevance for Early Diagnosis of Pancreatic DUCTAL Adenocarcinoma and Biomarker Detection

Due to late diagnosis, high incidence of metastasis, and poor survival rate, pancreatic cancer is one of the most leading cause of cancer-related death. Although manifold recent efforts have been done to achieve an early diagnosis of pancreatic cancer, CA-19.9 is currently the unique biomarker that is adopted for the detection, despite its limits in terms of sensitivity and specificity. To identify potential protein biomarkers for pancreatic ductal adenocarcinoma (PDAC), we used three model liposomes as nanoplatforms that accumulate proteins from human plasma and studied the composition of this biomolecular layer, which is known as protein corona. Indeed, plasma proteins adsorb on nanoparticle surface according to their abundance and affinity to the employed nanomaterial, thus even small differences between healthy and PDAC protein expression levels can be, in principle, detected. By mass spectrometry experiments, we quantified such differences and identified possible biomarkers for PDAC. Some of them are already known to exhibit different expressions in PDAC proteomes, whereas the role of other relevant proteins is still not clear. Therefore, we predict that the employment of nanomaterials and their protein corona may represent a useful tool to amplify the detection sensitivity of cancer biomarkers, which may be used for the early diagnosis of PDAC, with clinical implication for the subsequent therapy in the context of personalized medicine.