Biological sample collection for clinical proteomics: existing SOPs

The Role of IL-6, IL-10, and TNF-α in Ocular GVHD Following Allogeneic Transplantation

PURPOSE

To figure out the roles of tear inflammatory cytokines in Ocular graft-versus-host disease (oGVHD) symptoms by analyzing tear cytokine levels and related factors.

METHODS

This prospective study involved 27 post-HSCT patients and 19 controls with dry eye disease. Analyses included tear cytokine (IL-6, IL-10, and TNF-α), ocular surface evaluation, and conjunctival impression cell examination. Tear cytokine levels were evaluated in three grades of corneal epithelial lesions. The study also analyzed the correlation between tear cytokine levels and ocular surface parameters. Tear cytokine levels were then used in a Receiver Operating Characteristic (ROC) curve and linear regression model to predict oGVHD related factors.

RESULTS

IL-6 has good diagnostic efficacy in oGVHD related dry eye. Elevated levels of tear IL-6 and TNF-α were observed in the group with severe corneal epithelial lesions. IL-6 levels were positively correlated with corneal fluorescein staining (CFS), eyelid margin hyperemia, conjunctival lesions, and meibum secretion. IL-6 showed excellent predictive ability with Area Under the Curve (AUC) values all greater than 0.70 (p < 0.05). IL-10 and TNF-α were negatively correlated with the meibomian gland proportion and conjunctival goblet cell (GC) density, while TNF-α was positively correlated with CFS and eyelid margin hyperemia.

CONCLUSION

Dry eye symptoms related to ocular GVHD, can be partly diagnosed and assessed using various tear cytokine level detection methods.

Proteomics and its application in the research of acupuncture: An updated review

As a complementary and alternative therapy, acupuncture is widely used in the prevention and treatment of various diseases. However, the understanding of the mechanism of acupuncture effects is still limited due to the lack of systematic biological validation. Notably, proteomics technologies in the field of acupuncture are rapidly evolving, and these advances are greatly contributing to the research of acupuncture. In this study, we review the progress of proteomics research in analyzing the molecular mechanisms of acupuncture for neurological disorders, pain, circulatory disorders, digestive disorders, and other diseases, with an in-depth discussion around acupoint prescription and acupuncture manipulation modalities. The study found that proteomics has great potential in understanding the mechanisms of acupuncture. This study will help explore the mechanisms of acupuncture from a proteomic perspective and provide information to support future clinical decisions.

Development, Optimization, and Clinical Relevance of Lactoferrin Delivery Systems: A Focus on Ocular Delivery

Lactoferrin (Lf), a multifunctional protein found abundantly in secretions, including tears, plays a crucial role in ocular health through its antimicrobial, immunoregulatory, anti-inflammatory, and antioxidant activities. Advanced delivery systems are desirable to fully leverage its therapeutic potential in treating ocular diseases. The process of Lf quantification for diagnostic purposes underscores the importance of developing reliable, cost-effective detection methods, ranging from conventional techniques to advanced nano-based sensors. Despite the ease and non-invasiveness of topical administration for ocular surface diseases, challenges such as rapid drug elimination necessitate innovations, such as Lf-loaded contact lenses and biodegradable polymeric nanocapsules, to enhance drug stability and bioavailability. Furthermore, overcoming ocular barriers for the treatment of posterior segment disease calls for nano-formulations. The scope of this review is to underline the advancements in nanotechnology-based Lf delivery methods, emphasizing the pivotal role of multidisciplinary approaches and cross-field strategies in improving ocular drug delivery and achieving better therapeutic outcomes for a wide spectrum of eye conditions.

Cerebrospinal Fluid-Basic Concepts Review

Cerebrospinal fluid plays a crucial role in protecting the central nervous system (CNS) by providing mechanical support, acting as a shock absorber, and transporting nutrients and waste products. It is produced in the ventricles of the brain and circulates through the brain and spinal cord in a continuous flow. In the current review, we presented basic concepts related to cerebrospinal fluid history, cerebrospinal fluid production, circulation, and its main components, the role of the blood-brain barrier and the blood-cerebrospinal fluid barrier in the maintenance of cerebrospinal fluid homeostasis, and the utility of Albumin Quotient (Q_Alb) evaluation in the diagnosis of CNS diseases. We also discussed the collection of cerebrospinal fluid (type, number of tubes, and volume), time of transport to the laboratory, and storage conditions. Finally, we briefly presented the role of cerebrospinal fluid examination in CNS disease diagnosis of various etiologies and highlighted that research on identifying cerebrospinal fluid biomarkers indicating disease presence or severity, evaluating treatment effectiveness, and enabling understanding of pathogenesis and disease mechanisms is of great importance. Thus, in our opinion, research on cerebrospinal fluid is still necessary for both the improvement of CNS disease management and the discovery of new treatment options.

Proteomics of Human Biological Fluids for Biomarker Discoveries: Technical Advances and Recent Applications

INTRODUCTION

Biological fluids are routine samples for diagnostic testing and monitoring. Blood samples are typically measured because of their moderate collection invasiveness and high information content on health and disease. Several body fluids, such as cerebrospinal fluid (CSF), are also studied and suited to specific pathologies. Over the last two decades proteomics has quested to identify protein biomarkers but with limited success. Recent technologies and refined pipelines have accelerated the profiling of human biological fluids.

AREAS COVERED

We review proteomic technologies for the identification of biomarkers. Those are based on antibodies/aptamers arrays or mass spectrometry (MS), but new ones are emerging. Advances in scalability and throughput have allowed to better design studies and cope with the limited sample size that had until now prevailed due to technological constraints. With these enablers, plasma/serum, CSF, saliva, tears, urine, and milk proteomes have been further profiled; we provide a non-exhaustive picture of some recent highlights (mainly covering literature from last five years in the Scopus database) using MS-based proteomics.

EXPERT OPINION

While proteomics has been in the shadow of genomics for years, proteomic tools and methodologies have reached a certain maturity. They are better suited to discover innovative and robust biofluid biomarkers.

Separation of Serum and Plasma Proteins for In-Depth Proteomic Analysis

There are probably no biological samples that did more to spur interest in proteomics than serum and plasma. The belief was that comparing the proteomes of these samples obtained from healthy and disease-affected individuals would lead to biomarkers that could be used to diagnose conditions such as cancer. While the continuing development of mass spectrometers with greater sensitivity and resolution has been invaluable, the invention of strategic strategies to separate circulatory proteins has been just as critical. Novel and creative separation techniques were required because serum and plasma probably have the greatest dynamic range of protein concentration of any biological sample. The concentrations of circulating proteins can range over twelve orders of magnitude, making it a challenge to identify low-abundance proteins where the bulk of the useful biomarkers are believed to exist. The major goals of this article are to (i) provide an historical perspective on the rapid development of serum and plasma proteomics; (ii) describe various separation techniques that have made obtaining an in-depth view of the proteome of these biological samples possible; and (iii) describe applications where serum and plasma proteomics have been employed to discover potential biomarkers for pathological conditions.

Review of Liquid Chromatography-Mass Spectrometry-Based Proteomic Analyses of Body Fluids to Diagnose Infectious Diseases

Rapid and precise diagnostic methods are required to control emerging infectious diseases effectively. Human body fluids are attractive clinical samples for discovering diagnostic targets because they reflect the clinical statuses of patients and most of them can be obtained with minimally invasive sampling processes. Body fluids are good reservoirs for infectious parasites, bacteria, and viruses. Therefore, recent clinical proteomics methods have focused on body fluids when aiming to discover human- or pathogen-originated diagnostic markers. Cutting-edge liquid chromatography-mass spectrometry (LC-MS)-based proteomics has been applied in this regard; it is considered one of the most sensitive and specific proteomics approaches. Here, the clinical characteristics of each body fluid, recent tandem mass spectroscopy (MS/MS) data-acquisition methods, and applications of body fluids for proteomics regarding infectious diseases (including the coronavirus disease of 2019 [COVID-19]), are summarized and discussed.

The status of proteomics as we enter the 2020s: Towards personalised/precision medicine

The last decade has seen many major advances in proteomics, with over 70,000 publications in the field since 2010. A comprehensive omics toolbox has been developed facilitating rapid in depth analysis of the human proteome. Such studies are advancing our understanding of the biology of both health and disease. The combination of proteomics with other omics platforms (the omics pipeline), in particular proteogenomics, is giving important insights to the molecular changes leading to disease, covering the spectrum from genotype to phenotype and identifying potential biomarkers for disease detection, surveillance and monitoring, and revealing potential new drug targets. Discovery-based finding are now being translated to clinical application, supporting the rollout of precision/personalised medicine. This perspective has focused on twelve areas of importance that have fuelled the field. Recent exemplars are given to illustrate this and show how, together with some emerging technologies, they are anticipated to lead to further advances in the field. However, hurdles still remain to be overcome, especially in the area of Big Data analysis.

Considerations for mass spectrometry-based multi-omic analysis of clinical samples

Introduction: The role of mass spectrometry in biomolecule analysis has become paramount over the last several decades ranging in the analysis across model systems and human specimens. Accordingly, the presence of mass spectrometers in clinical laboratories has also expanded alongside the number of researchers investigating the protein, lipid, and metabolite composition of an array of biospecimens. With this increase in the number of omic investigations, it is important to consider the entire experimental strategy from sample collection and storage, data collection and analysis.Areas covered: In this short review, we outline considerations for working with clinical (e.g. human) specimens including blood, urine, and cerebrospinal fluid, with emphasis on sample handling, profiling composition, targeted measurements and relevance to disease. Discussions of integrated genomic or transcriptomic datasets are not included. A brief commentary is also provided regarding new technologies with clinical relevance.Expert opinion: The role of mass spectrometry to investigate clinically related specimens is on the rise and the ability to integrate multiple omics datasets from mass spectrometry measurements will be crucial to further understanding human health and disease.

Collection and Analyses of Cerebrospinal Fluid for Pediatric Translational Research

Cerebrospinal fluid sample collection and analysis is imperative to better elucidate central nervous system injury and disease in children. Sample collection methods are varied and carry with them certain ethical and biologic considerations, complications, and contraindications. Establishing best practices for sample collection, processing, storage, and transport will ensure optimal sample quality. Cerebrospinal fluid samples can be affected by a number of factors including subject age, sampling method, sampling location, volume extracted, fraction, blood contamination, storage methods, and freeze-thaw cycles. Indicators of sample quality can be assessed by matrix-associated laser desorption/ionization time-of-flight mass spectrometry and include cystatin C fragments, oxidized proteins, prostaglandin D synthase, and evidence of blood contamination. Precise documentation of sample collection processes and the establishment of meticulous handling procedures are essential for the creation of clinically relevant biospecimen repositories. In this review we discuss the ethical considerations and best practices for cerebrospinal fluid collection, as well as the influence of preanalytical factors on cerebrospinal fluid analyses. Cerebrospinal fluid biomarkers in highly researched pediatric diseases or disorders are discussed.

Proteomic approaches in the discovery of potential urinary biomarkers of mucopolysaccharidosis type II

Mucopolysaccharindosis type II (MPS II) is a rare lysosomal storage disorder caused by deficient or absent activity of the iduronate-2-sulfatase (IDS) enzyme, which leads to pathological accumulation of the glycosaminoglycans(GAGs). The absence of early diagnosis can result in irreversible developmental, neurological, and physiological damage. The lack of clear understanding of the etiology of physiological dysfunction in MPS II has been a major obstacle to the development of new treatment. Therefore, a reliable biomarker for early diagnosis and exploration of pathogenic mechanism are of great importance. Proteomics provides powerful tool for protein expression alterations and study of complicated pathological process. This study was performed to identify the differential protein profile in urine of MPS II patients using two-dimensional gel electrophoresis(2D-PAGE)combining with MALDI-TOF/TOF and a total of 15 differentially expressed proteins were identified. Content of alpha1-antitrypsin, Gm2 activator and lipocalin-type prostaglandin D synthase was measured by ELISA method. The value of urinary α1-AT/Cr in MPS II group was 0.79 ± 0.10 mg/mmol, significantly higher than 0.42 ± 0.05 mg/mmol in healthy control group; whereas the value of GM2A/Cr and L-PGDS/Cr in MPS II group was 1.30 ± 0.12 μg/mmol and 9.86 ± 1.16 ng/mmol respectively, which was significantly lower than 2.19 ± 0.19 μg/mmol and 13.98 ± 1.48 ng/mmol in healthy control group. The proteins can be considered as accessory diagnostic biomarkers for MPS II. This approach helped to discover early diagnostic markers and provided a better understanding of the pathogenic mechanism of MPS II.

Proteomics in Primary Biliary Cholangitis

Primary biliary cholangitis is a chronic cholestatic liver disease characterized by the presence of serum antimitochondrial antibodies and immune-mediated destruction of the small and medium-sized intrahepatic bile ducts. However, the pathophysiology of primary biliary cholangitis has not yet been completely elucidated. In recent years, proteomics has been comprehensively applied in many research fields, including the pathogenesis, prognosis, and diagnosis of disease. Among multiple methods, isobaric tag for relative and absolute quantitation is a powerful analytic method to characterize complex protein mixtures in combination with liquid chromatography-tandem mass spectrometry. In this chapter, we describe a strategy for using isobaric tag for relative and absolute quantitation to discover those differentially expressed proteins in primary biliary cholangitis. The goal is to identify the differences in protein expression between patients with primary biliary cholangitis and healthy controls for defining biomarkers and elucidating molecular mechanisms underlying disease states.

Applications of MALDI-TOF mass spectrometry in clinical proteomics

INTRODUCTION

The development of precision medicine requires advanced technologies to address the multifactorial disease stratification and to support personalized treatments. Among omics techniques, proteomics based on Mass Spectrometry (MS) is becoming increasingly relevant in clinical practice allowing a phenotypic characterization of the dynamic functional status of the organism. From this perspective, Matrix Assisted Laser Desorption Ionization Time of Flight (MALDI-TOF) MS is a suitable platform for providing a high-throughput support to clinics. Areas covered: This review aims to provide an updated overview of MALDI-TOF MS applications in clinical proteomics. The most relevant features of this analysis have been discussed, highlighting both pre-analytical and analytical factors that are crucial in proteomics studies. Particular emphasis is placed on biofluids proteomics for biomarkers discovery and on recent progresses in clinical microbiology, drug monitoring, and minimal residual disease (MRD). Expert commentary: Despite some analytical limitations, the latest technological advances together with the easiness of use, the low time and low cost consuming and the high throughput are making MALDI-TOF MS instruments very attractive for the clinical practice. These features offer a significant potential for the routine of the clinical laboratory and ultimately for personalized medicine.

Evaluation of commonly used tear sampling methods and their relevance in subsequent biochemical analysis

The human precorneal tear film is a special body fluid, since it is a complex mixture of proteins, lipids, small bioactive molecules, and their concentrations and relative distribution represent not only the metabolic state of the ocular surface but also the systemic and local homeostasis of the outer eye and the human body. This suggests that biochemical analysis of the precorneal tear film composition may provide a non-invasive tool for diagnosis and monitoring of disease progression or treatment efficacy in human medicine. However, collecting tears is demanding, and obtaining reproducible and unaltered samples is challenging because of the small sample volumes of tears. Several methods are available for tear collection as a preparatory step of precorneal tear film analysis, and the collection method used has to be assessed since it has a critical impact on the effectiveness of the assays and on the quality of the results. Each sampling method has advantages and disadvantages; therefore, it is not easy to choose the appropriate collecting method for tear collection. To overcome these limitations various methods have been recommended by different authors for special aspects of specific tests. The aim of our review was to evaluate tear sampling methods with regard to our ongoing biochemical analysis.

Urinary proteomics and metabolomics studies to monitor bladder health and urological diseases

Background

Assays of molecular biomarkers in urine are non-invasive compared to other body fluids and can be easily repeated. Based on the hypothesis that the secreted markers from the diseased organs may locally release into the body fluid in the vicinity of the injury, urine-based assays have been considered beneficial to monitoring bladder health and urological diseases. The urine proteome is much less complex than the serum and tissues, but nevertheless can contain biomarkers for diagnosis and prognosis of diseases. The urine metabolome has a much higher number and concentration of low-molecular metabolites than the serum or tissues, with a far lower lipid concentration, yet informs directly about dietary and microbial metabolism.

Discussion

We here discuss the use of mass spectrometry-based proteomics and metabolomics for urine biomarker assays, specifically with respect to the underlying mechanisms that trigger the pathological condition.

Conclusion

Molecular biomarker profiles, based on proteomics and metabolomics studies, reliably distinguish patients from healthy controls, stratify sub-populations with respect to treatment options, and predict therapeutic response of patients with urological disease.

Recent applications of CE- and HPLC-MS in the analysis of human fluids

The present review intends to cover the literature on the use of CE-/LC-MS for the analysis of human fluids, from 2010 until present. It has been planned to provide an overview of the most recent practical applications of these techniques to less extensively used human body fluids, including, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate, tear fluid, breast fluid, amniotic fluid, and cerumen. Potential pitfalls related to fluid collection and sample preparation, with particular attention to sample clean-up procedures, and methods of analysis, from the research laboratory to a clinical setting will also be addressed. While being apparent that proteomics/metabolomics represent the most prominent approaches for global identification/quantification of putative biomarkers for a variety of human diseases, evidence is also provided of the suitability of these sophisticated techniques for the detection of heterogeneous components carried by these fluids.

Proteomic analysis of human follicular fluid from fertile women

Background

Follicular fluid is a unique biological fluid in which the critical events of oocyte and follicular maturation and somatic cell-germ cell communication occur. Because of the intimate proximity of follicular fluid to the maturing oocyte, this fluid provides a unique window into the processes occurring during follicular maturation. A thorough identification of the specific components within follicular fluid may provide a better understanding of intrafollicular signaling, as well as reveal potential biomarkers of oocyte health for women undergoing assisted reproductive treatment. In this study, we used high and low pH HPLC peptide separations followed by mass spectrometry to perform a comprehensive proteomic analysis of human follicular fluid from healthy ovum donors. Next, using samples from a second set of patients, an isobaric mass tagging strategy for quantitative analysis was used to identify proteins with altered abundances after hCG treatment.

Results

A total of 742 follicular fluid proteins were identified in healthy ovum donors, including 413 that have not been previously reported. The proteins belong to diverse functional groups including insulin growth factor and insulin growth factor binding protein families, growth factor and related proteins, receptor signaling, defense/immunity, anti-apoptotic proteins, matrix metalloprotease related proteins, and complement activity. In a quantitative analysis, follicular fluid samples from age-matched women undergoing in vitro fertilization oocyte retrieval were compared and 17 follicular fluid proteins were found at significantly altered levels (p < 0.05) between pre-hCG and post-hCG samples. These proteins belong to a variety of functional processes, including protease inhibition, inflammation, and cell adhesion.

Conclusions

This database of FF proteins significantly extends the known protein components present during the peri-ovulatory period and provides a useful basis for future studies comparing follicular fluid proteomes in various fertility, disease, and environmental exposure conditions. We identified 17 differentially expressed proteins after hCG treatment and together these data showed the feasibility for defining biomarkers that illuminate how the ovarian follicle microenvironment is altered in various infertility-related conditions.

Electronic supplementary material

The online version of this article (doi:10.1186/s12014-015-9077-6) contains supplementary material, which is available to authorized users.