Recommendations for clinical biomarker specimen preservation and stability assessments

Biomarkers of food intake and their relevance to metabolic syndrome

Metabolic syndrome (MetS) constitutes a prevalent risk factor associated with non communicable diseases such as cardiovascular disease and type 2 diabetes. A major factor impacting the etiology of MetS is diet. Dietary patterns and several individual food constituents have been related to the risk of developing MetS or have been proposed as adjuvant treatment. However, traditional methods of dietary assessment such as 24 h recalls rely greatly on intensive user-interaction and are subject to bias. Hence, more objective methods are required for unbiased dietary assessment and efficient prevention. While it is accepted that some dietary-derived constituents in blood plasma are indicators for certain dietary patterns, these may be too unstable (such as vitamin C as a marker for fruits/vegetables) or too broad (e.g. polyphenols for plant-based diets) or reflect too short-term intake only to allow for strong associations with prolonged intake of individual food groups. In the present manuscript, commonly employed biomarkers of intake including those related to specific food items (e.g. genistein for soybean or astaxanthin and EPA for fish intake) and novel emerging ones (e.g. stable isotopes for meat intake or microRNA for plant foods) are emphasized and their suitability as biomarker for food intake discussed. Promising alternatives to plasma measures (e.g. ethyl glucuronide in hair for ethanol intake) are also emphasized. As many biomarkers (i.e. secondary plant metabolites) are not limited to dietary assessment but are also capable of regulating e.g. anti-inflammatory and antioxidant pathways, special attention will be given to biomarkers presenting a double function to assess both dietary patterns and MetS risk.

Combination of calretinin, MALAT1, and GAS5 as a potential prognostic biomarker to predict disease progression in surgically treated mesothelioma patients

BACKGROUND

The role of cytoreductive surgery for epithelioid pleural mesothelioma within a multimodal treatment approach remains controversial. Carefully selected patients benefit from cytoreductive surgery and adjuvant chemotherapy, but there is no established biomarker to predict tumor recurrence or progression during the course of the disease. The aim of this study was to identify potential biomarkers to predict therapeutic response in terms of progression-free survival.

METHODS

Between 03/2014 and 08/2022, preoperative blood samples were collected from 76 patients with epithelioid pleural mesothelioma who underwent cytoreductive surgery as part of a multimodal treatment approach. Identification of potential biomarkers was performed by determination of mesothelin and calretinin, as well as specific long non-coding RNAs and microRNAs. Receiver operating characteristic analysis, Kaplan-Meier survival analysis, and Cox regression were used to assess the association between biomarker concentrations and patient recurrence status and survival.

RESULTS

MALAT1, GAS5, and calretinin showed statistically significant increased biomarker levels in patients with recurrence in contrast to recurrence-free patients after surgical treatment (p < 0.0001, p = 0.0190, and p = 0.0068, respectively). The combination of the three biomarkers resulted in a sensitivity of 68 % and a specificity of 89 %.

CONCLUSION

MALAT1, GAS5, and calretinin could be potential biomarkers for the prediction of tumor recurrence, improving the benefit from multimodal treatment including cytoreductive surgery.

OPTIMIZATION OF DRIED BLOOD SPOT ASSAYS FOR HEPATITIS B VIRUS SURFACE ANTIBODY QUANTIFICATION

Dried blood spot (DBS) cards can be used as an alternative sample collection method to plasma, however, there is no optimized elution protocol for DBS cards specifically for hepatitis B surface antibody (anti-HBs) testing. The study aimed to develop a DBS elution protocol for anti-HBs quantification. Our study sought to determine the ideal phosphate-buffered saline (PBS) buffer volume to use by comparing three PBS volumes (300uL, 450uL, and 500uL), and the optimal time to agitate DBS discs on a plate shaker (1hr, 2hrs, 3hrs, and 4hrs) to yield DBS anti-HBs concentrations that are comparable to corresponding plasma anti-HBs concentrations. The optimal DBS storage temperature (25°C, -20°C, and -80°C) was investigated to determine the ideal long-term storage temperature of the cards. Residual samples were used for optimization (2019-2021). A total of 50 DBS-plasma pairs was used throughout the study, with plasma anti-HBs concentrations being used as the golden standard to compare. The analysis of results was carried out by determining the p-values of the Wilcoxon sign rank. A two-way analysis of variance (ANOVA) was also performed to determine the impact of PBS elution volumes, elution time, and storage temperature on the anti-HBs concentration of DBS samples on STATA Version 15.0. No statistically significant difference between the DBS-plasma anti-HBs pairs was observed when using 450 or 500uL of PBS buffer and when samples were agitated for 3 hours (p=0.594, p=0.499 respectively). The optimal storage temperature for DBS cards was 25°C because the results showed no statistically significant difference between DBS-plasma anti-HBs titers (p=0.594). The two-way ANOVA analysis showed that elution volumes and time had no statistically significant impact on the DBS anti-HBs concentrations, p=0.948 and p=0.381 respectively. Storage temperature had a statistically significant impact on the DBS anti-HBs concentrations, p=0.002. The optimized DBS elution protocol for anti-HBs quantification will help monitor vaccine efficacy in infants due to the low sample volumes required compared to plasma and also can be used for anti-HBs testing in resource-limited areas around the country.

Evaluation of Collection and Processing Conditions for Gene Expression Analysis Using Human Myeloid Cells

Background: The population of blast cells among peripheral blood mononuclear cells (PBMCs) obtained from patients is a desirable specimen for analyzing gene expression in diseases including acute myeloid leukemia. Although the enrichment of blast cells often needs to be performed at a central laboratory, acceptable conditions for sample transport from clinical sites remain to be established. Methods: We evaluated storage temperature, duration, and tube type before initiating sample processing for the analysis of cluster of differentiation (CD)33+ myeloid cells among PBMCs as an alternative to CD34+/CD33+ blast cells. Results: CD33+ myeloid cells were successfully purified by MACS. The cell viability and the RNA integrity were sustained during storage up to 48 hours before sample processing. Storage at 4°C had minimal effects on gene expression, whereas storage at room temperature induced the senescence pathway, characterized by the expression of stress-inducible genes. A CPT tube was also better than an ethylenediaminetetraacetic acid tube for minimizing gene expression change. Conclusions: Our study provided important clues for establishing a sample handling approach for gene expression analysis with purified cell fractions from human PBMCs. To keep the variation of gene expression to a minimum, samples should be delivered at 4°C within 48 hours before processing.

Assessment of biomarker stability and assay performance parameters for medical diagnosis: a case study of diagnosis of major depressive disorder

Aim: Assessing the stability profiles and assay performance of 24 biomarker assays in 32 biomarker/body fluid combinations identified as relevant for prediction of major depressive disorder. Materials & methods: Combinations were tested for stability and assay performance with ELISA at different storage and freeze-thaw conditions in pooled samples of 40 patients. Results: Stability and assay performance issues were found in almost all cases except three biomarkers in urine and three in serum. Conclusion: This study shows that, to produce reliable measurement data, assessments of stability and assay performance are essential. In development, other quality assurance parameters might be implemented to increase the level of measurement reliability by increasing assay performance control.

Tasks and Experiences of the Prospective, Longitudinal, Multicenter MoMar (Molecular Markers) Study for the Early Detection of Mesothelioma in Individuals Formerly Exposed to Asbestos Using Liquid Biopsies

Mesothelioma is an aggressive cancer, strongly associated with prior exposure to asbestos. Commonly, tumors are detected at late stages of the disease. Detection at early stages might be meaningful, because therapies might be more effective when the tumor burden is relatively low and the tumor has not spread to distant sites. Circulating biomarkers in blood might be a promising tool to improve the early detection of mesothelioma, but for screening in asymptomatic subjects, candidate biomarkers need to be validated in appropriate studies. This study was conducted to assess the performance of biomarkers in liquid biopsies to detect mesothelioma at early stages. Over a period of 10 years, 2769 volunteers formerly exposed to asbestos were annually examined and liquid biopsies were collected. A follow-up was completed 17 months after the last blood collection. The article provides a detailed overview of our lessons learned and experiences of conducting a prospective, longitudinal, multicenter study. The existing cohort of individuals at risk is highly suitable for the validation of blood-based biomarkers for the early detection of mesothelioma as well as lung cancer.

Blood-based circulating microRNAs as diagnostic biomarkers for subclinical carotid atherosclerosis: A systematic review and meta-analysis with bioinformatics analysis

BACKGROUND

Atherosclerosis in carotid arteries can remain clinically undetected in its early development until an acute cerebrovascular event such as stroke emerges. Recently, microRNAs (miRNAs) circulating in blood have emerged as potential diagnostic biomarkers, but their performance in detecting subclinical carotid atherosclerosis has yet to be systematically researched.

AIM

To investigate the diagnostic performance of circulating miRNAs in detecting subclinical carotid atherosclerosis.

METHODS

We systematically searched five electronic databases from inception to July 23, 2022. Subclinical carotid atherosclerosis was defined using carotid intima-media thickness (CIMT). Diagnostic accuracy parameters and correlation coefficients were pooled. A gene network visualisation and enrichment bioinformatics analysis were additionally conducted to search for potential target genes and pathway regulations of the miRNAs.

RESULTS

Fifteen studies (15 unique miRNAs) comprising 2542 subjects were identified. Circulating miRNAs had a pooled sensitivity of 85% (95% CI 80%-89%), specificity of 84% (95% CI 78%-88%), positive likelihood ratio of 5.19 (95% CI 3.97-6.80), negative likelihood ratio of 0.18 (95% CI 0.13-0.23), diagnostic odds ratio of 29.48 (95% CI 21.15-41.11), and area under the summary receiver operating characteristic curve of 0.91 (95% CI 0.88-0.93), with a strong correlation to CIMT (pooled coefficient 0.701; 95% CI 0.664-0.731). Bioinformatics analysis revealed a major role of the miRNAs, as shown by their relation with CCND1, KCTD15, SPARC, WWTR1, VEGFA genes, and multiple pathways involved in the pathogenesis of carotid atherosclerosis.

CONCLUSION

Circulating miRNAs had excellent accuracy in detecting subclinical carotid atherosclerosis, suggesting their utilisation as novel diagnostic tools.

Clinical Evaluation Based on a New Approach to Improve the Accuracy of 4β-Hydroxycholesterol Measurement as a Biomarker of CYP3A4 Activity

This study examines 4β-Hydroxycholesterol (4β-HC), which is considered to be a potential marker for the CYP3A4 induction of new chemical entities (NCEs) in drug development. To ensure the use of 4β-HC as a practical biomarker, it is necessary to accurately measure 4β-HC and demonstrate that CYP3A4 induction can be appropriately assessed, even for weak inducers. In clinical trials of NCEs, plasma is often collected with various anticoagulants, in some cases, the plasma is acidified, then stored for an extended period. In this study, we examined the effects of these manipulations on the measurement of 4β-HC, and based on the results, we optimized the plasma collection and storage protocols. We also found that a cholesterol oxidation product is formed when plasma is stored, and by monitoring the compound, we were able to identify when plasma was stored inappropriately. After evaluating the above, clinical drug-drug interaction (DDI) studies were conducted using two NCEs (novel retinoid-related orphan receptor γ antagonists). The weak CYP3A4 induction by the NCEs (which were determined based on a slight decline in the systemic exposure of a probe substrate (midazolam)), was detected by the significant increase in 4β-HC levels (more specifically, 4β-HC/total cholesterol ratios). Our new approach, based on monitoring a cholesterol oxidation product to identify plasma that is stored inappropriately, allowed for the accurate measurement of 4β-HC, and thus, it enabled the evaluation of weak CYP3A4 inducers in clinical studies without using a probe substrate.

Differences in Cardiometabolic Biomarkers between Elementary School-Age Latinx Children with Obesity versus Healthy Weight

OBJECTIVES

Low-income Latinx youth are disproportionately affected by obesity, which results in an increased risk of cardiometabolic abnormalities. Biomarker tracking may be useful for the early identification of obesity comorbidities in young Latinx children. Hence, we aimed to compare cardiometabolic biomarkers between age- and sex-matched pairs of elementary school-aged Latinx children with obesity versus healthy weight.

METHODS

This case-control study compared cardiometabolic biomarkers between 13 pairs of age- and sex-matched elementary school-age (median 6.5 years) Latinx children with obesity (body mass index for age ≥ 95th percentile) as compared with their healthy weight (between the 5th and 85th percentiles) counterparts. Anthropometric measures and a fasted venous blood sample were taken for the analysis of lipids, glycemic, inflammatory, endocrine, and hepatic markers. Group differences were tested by the Mann-Whitney U or χ² test.

RESULTS

Cases had higher insulin (P = 0.003), hemoglobin A1c (P = 0.002), triglycerides (P = 0.023), and C-reactive protein (P < 0.001) and lower high-density lipoprotein (P = 0.002). Hepatic markers were similar, with alanine aminotransferase elevated among both groups.

CONCLUSIONS

The aforementioned biomarkers may be more sensitive to higher adiposity risk in this young Latinx population; however, elevated hepatic markers may indicate an ethnic/genetic predisposition to abnormal liver function. Research should be replicated in a larger group to confirm these findings.

Microfluidic Device for Patient-Centric Multiplexed Assays with Readout in Centralized Laboratories

Patient-centric sampling strategies, where the patient performs self-sampling and ships the sample to a centralized laboratory for readout, are on the verge of widespread adaptation. However, the key to a successful patient-centric workflow is user-friendliness, with few noncritical user interactions, and simple, ideally biohazard-free shipment. Here, we present a capillary-driven microfluidic device designed to perform the critical biomarker capturing step of a multiplexed immunoassay at the time of sample collection. On-chip sample drying enables biohazard-free shipment and allows us to make use of advanced analytics of specialized laboratories that offer the needed analytical sensitivity, reliability, and affordability. Using C-Reactive Protein, MCP1, S100B, IGFBP1, and IL6 as model blood biomarkers, we demonstrate the multiplexing capability and applicability of the device to a patient-centric workflow. The presented quantification of a biomarker panel opens up new possibilities for e-doctor and e-health applications.

Molecular biomarker research in periodontology: A roadmap for translation of science to clinical assay validation

The number of studies that aims to apply host‐ or microbe‐derived biochemical biomarkers to periodontal disease diagnosis has increased significantly during the last three decades. The biochemical markers can reflect the presence, severity, and activity of periodontal diseases; however, heterogeneities in applied laboratory methods, data presentation, statistical analysis, and data interpretation prevent the translation of candidate host‐ or microbe‐derived biochemical biomarkers to clinical assay validation. Here, we propose a roadmap for making the research outcomes comparable and re‐analysable with the ultimate goal of translating research to clinical practice. This roadmap presents reporting recommendations for host‐ or microbe‐derived biochemical biomarker studies in periodontology. We aim to make essential elements of the research work (including diagnostic criteria, clinical endpoint definitions, participant recruitment criteria, sample collection and storage techniques, biochemical and microbiological detection methods, and applied statistical analysis) visible and comparable.

Best practices for the development and fit-for-purpose validation of biomarker methods: a conference report

This conference report summarized a full-day workshop, “best practices for the development and fit-for-purpose validation of biomarker methods,” which was held prior to the American Association of Pharmaceutical Scientists (AAPS) PharmSci360 Congress, San Antonio, TX, November 2019. The purpose of the workshop was to bring together thought leaders in biomarker assay development in order to identify which assay parameters and key statistical measures need to be considered when developing a biomarker assay. A diverse group of more than 40 scientists participated in the workshop. The workshop and subsequent working dinner stimulated robust discussion. While a consensus on best practices was not achieved, some common themes and major points to consider for biomarker assay development have been identified and agreed on. The focus of this conference report is to summarize the presentations and discussions which occurred at the workshop. Biomarker assay validation is a complex and an evolving area with discussions ongoing.

Clinical Laboratory Biosafety Gaps: Lessons Learned from Past Outbreaks Reveal a Path to a Safer Future

Patient care and public health require timely, reliable laboratory testing. However, clinical laboratory professionals rarely know whether patient specimens contain infectious agents, making ensuring biosafety while performing testing procedures challenging. The importance of biosafety in clinical laboratories was highlighted during the 2014 Ebola outbreak, where concerns about biosafety resulted in delayed diagnoses and contributed to patient deaths. This review is a collaboration between subject matter experts from large and small laboratories and the federal government to evaluate the capability of clinical laboratories to manage biosafety risks and safely test patient specimens. We discuss the complexity of clinical laboratories, including anatomic pathology, and describe how applying current biosafety guidance may be difficult as these guidelines, largely based on practices in research laboratories, do not always correspond to the unique clinical laboratory environments and their specialized equipment and processes. We retrospectively describe the biosafety gaps and opportunities for improvement in the areas of risk assessment and management; automated and manual laboratory disciplines; specimen collection, processing, and storage; test utilization; equipment and instrumentation safety; disinfection practices; personal protective equipment; waste management; laboratory personnel training and competency assessment; accreditation processes; and ethical guidance. Also addressed are the unique biosafety challenges successfully handled by a Texas community hospital clinical laboratory that performed testing for patients with Ebola without a formal biocontainment unit. The gaps in knowledge and practices identified in previous and ongoing outbreaks demonstrate the need for collaborative, comprehensive solutions to improve clinical laboratory biosafety and to better combat future emerging infectious disease outbreaks.

Andrographolide Against Lung Cancer-New Pharmacological Insights Based on High-Throughput Metabolomics Analysis Combined with Network Pharmacology

Andrographolide (Andro) has known to treat various illnesses such as colds, diarrhea, fever and infectious diseases. However, the effect mechanism of Andro is still unclear. Therefore, we used high-throughput metabolomics analysis to discover biomarkers, metabolic profiles and pathways to reveal the pharmacological action and effective mechanism of Andro against lung cancer. The metabolic effects of Andro on lung cancer animal was explored by ultra-performance liquid chromatography-triple-time of flight/mass spectrometry (UPLC-TOF/MS) analysis. Our results showed that Andro exhibited significant protective effects against lung cancer. Compared with control group, a total of 25 metabolites biomarkers was identified in urine of model animals, which 18 of them were regulated toward the normal direction after Andro treatment, and network pharmacology analysis showed that they were related with 570 proteins. Biological pathways analysis showed that the 11 metabolism pathways were regulated by Andro treatment in lung cancer mouse, and amino acid metabolism and arachidonic acid metabolism have great potential as target pathways for Andro against lung cancer. It revealed that high-throughput metabolomics combined with network pharmacology analysis provides deeply insight into the therapeutic mechanisms of natural product for promoting medicine development and disease treatment.

Suitability and Sufficiency of Telehealth Clinician-Observed, Participant-Collected Samples for SARS-CoV-2 Testing: The iCollect Cohort Pilot Study

BACKGROUND

The severe acute respiratory coronavirus 2 (SARS-CoV-2) pandemic calls for expanded opportunities for testing, including novel testing strategies such as home-collected specimens.

OBJECTIVE

We aimed to understand whether oropharyngeal swab (OPS), saliva, and dried blood spot (DBS) specimens collected by participants at home and mailed to a laboratory were sufficient for use in diagnostic and serology tests of SARS-CoV-2.

METHODS

Eligible participants consented online and were mailed a participant-collection kit to support collection of three specimens for SARS-CoV-2 testing: saliva, OPS, and DBS. Participants performed the specimen collection procedures during a telehealth video appointment while clinical observers watched and documented the suitability of the collection. The biological sufficiency of the specimens for detection of SARS-CoV-2 by reverse transcriptase-polymerase chain reaction and serology testing was assessed by laboratorians using visual inspection and quantification of the nucleic acid contents of the samples by ribonuclease P (RNase P) measurements.

RESULTS

Of the enrolled participants,153/159 (96.2%) returned their kits, which were included in this analysis. All these participants attended their video appointments. Clinical observers assessed that of the samples collected, 147/153 (96.1%) of the saliva samples, 146/151 (96.7%) of the oropharyngeal samples, and 135/145 (93.1%) of the DBS samples were of sufficient quality for submission for laboratory testing; 100% of the OPS samples and 98% of the saliva samples had cycle threshold values for RNase P <30, indicating that the samples contained sufficient nucleic acid for RNA-PCR testing for SARS-CoV-2.

CONCLUSIONS

These pilot data indicate that most participant-collected OPS, saliva, and DBS specimens are suitable and sufficient for testing for SARS-CoV-2 RNA and serology. Clinical observers rated the collection of specimens as suitable for testing, and visual and quantitative laboratory assessment indicated that the specimens were biologically sufficient. These data support the utility of participant-collected and mailed-in specimens for SARS-CoV-2 testing.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)

RR2-10.2196/19054.

A Critical Evaluation of Wet Biomarkers for Huntington's Disease: Current Status and Ways Forward

There is an unmet clinical need for objective biomarkers to monitor disease progression and treatment response in Huntington's disease (HD). The aim of this review is, therefore, to provide practical advice for biomarker discovery and to summarise studies on biofluid markers for HD. A PubMed search was performed to review literature with regard to candidate saliva, urine, blood and cerebrospinal fluid biomarkers for HD. Information has been organised into tables to allow a pragmatic approach to the discussion of the evidence and generation of practical recommendations for future studies. Many of the markers published converge on metabolic and inflammatory pathways, although changes in other analytes representing antioxidant and growth factor pathways have also been found. The most promising markers reflect neuronal and glial degeneration, particularly neurofilament light chain. International collaboration to standardise assays and study protocols, as well as to recruit sufficiently large cohorts, will facilitate future biomarker discovery and development.

Approaching stability challenges for flow cytometry in a regulated bioanalytical environment

Stability of samples for flow cytometry is a critical parameter since storage period of samples is restricted to only a limited period after collection. For most studies, clinical samples have to be shipped to a testing laboratory, in contrast to preclinical samples, which can be analyzed on-site or off-site. Therefore, evaluating stability is critical to provide flexibility on testing of samples to obtain reliable data. A wide variety of factors contributes to establishing stability from sample collection through acquisition. We provided suggestions for experimental and stability parameters to be taken into consideration when designing a flow cytometry method. The case studies presented represent how certain stability issues were overcome to perform flow cytometry assays in a regulated bioanalytical environment.

Specimen Collection for Translational Studies in Hidradenitis Suppurativa

Hidradenitis suppurativa (HS) is a chronic inflammatory disorder characterized by painful nodules, sinus tracts, and scars occurring predominantly in intertriginous regions. The prevalence of HS is currently 0.053-4%, with a predominance in African-American women and has been linked to low socioeconomic status. The majority of the reported literature is  retrospective, population based, epidemiologic studies. In this regard, there is a need to establish a repository of biospecimens, which represent appropriate gender and racial demographics amongst HS patients. These efforts will diminish knowledge gaps in understanding the disease pathophysiology. Hence, we sought to outline a step-by-step protocol detailing how we established our HS biobank to facilitate the formation of other HS tissue banks. Equipping researchers with carefully detailed processes for collection of HS specimens would accelerate the accumulation of well-organized human biological material. Over time, the scientific community will have access to a broad range of HS tissue biospecimens, ultimately leading to more rigorous basic and translational research. Moreover, an improved understanding of the pathophysiology is necessary for the discovery of novel therapies for this debilitating disease. We aim to provide high impact translational research methodology for cutaneous biology research and foster multidisciplinary collaboration and advancement of our understanding of cutaneous diseases.

Advances in biomarker detection: Alternative approaches for blood-based biomarker detection

In the clinical setting, a blood sample is typically the starting point for biomarker search and discovery. Mass spectrometry (MS) is a highly sensitive and informative method for characterizing a very wide range of metabolites and proteins and is therefore a potentially powerful tool for biomarker discovery. However, the physicochemical characteristics of blood coupled with very large ranges of protein and metabolite concentrations present a significant technical obstacle for resolving and quantifying putative biomarkers by MS. Blood fractionation procedures are being developed to reduce the proteome/metabolome complexity and concentration ranges, allowing a greater diversity of analytes, including those at very low concentrations, to be quantified. In this chapter, several strategies for enriching and/or isolating specific blood components are summarized, including methods for the analysis of low and high molecular weight compounds, usually neglected in this type of assays, extracellular vesicles, and peripheral blood mononuclear cells (PBMCs). For each method, relevant practical information is presented for effective implementation.

Unbiased data analytic strategies to improve biomarker discovery in precision medicine

Omics technologies promised improved biomarker discovery for precision medicine. The foremost problem of discovered biomarkers is irreproducibility between patient cohorts. From a data analytics perspective, the main reason for these failures is bias in statistical approaches and overfitting resulting from batch effects and confounding factors. The keys to reproducible biomarker discovery are: proper study design, unbiased data preprocessing and quality control analyses, and a knowledgeable application of statistics and machine learning algorithms. In this review, we discuss study design and analysis considerations and suggest standards from an expert point-of-view to promote unbiased decision-making in biomarker discovery in precision medicine.

Pre-fractionation of Noncirculating Biological Fluids to Improve Discovery of Clinically Relevant Protein Biomarkers

Nowadays, significant difficulties remain in the diagnosis and/or prognosis of many diseases, leading to an unsatisfactory patient management and a counterproductive increase in time and costs. It is therefore crucial to bridge the gap between basic and applied research by complying with clinical requirements, notably from the design stage of the experimental workflow. In this chapter we provide key suggestions for selecting appropriate biological samples and reducing pre-analytical and analytical variabilities to improve the discovery of clinically relevant protein biomarkers.

Integrating exosomal microRNAs and electronic health data improved tuberculosis diagnosis

Background Tuberculosis (TB) is difficult to diagnose under complex clinical conditions as electronic health records (EHRs) are often inadequate in making an affirmative diagnosis. As exosomal miRNAs emerged as promising biomarkers, we investigated the potential of using exosomal miRNAs and EHRs in TB diagnosis.

Methods

A total of 370 individuals, including pulmonary tuberculosis (PTB), tuberculous meningitis (TBM), non-TB disease controls and healthy state controls, were enrolled. Exosomal miRNAs were profiled in the exploratory cohort using microarray and miRNA candidates were selected in the selection cohort using qRT-PCR. EHRs and follow-up information of the patients were collected accordingly. miRNAs and EHRs were used to develop diagnostic models for PTB and TBM in the selection cohort with the Support Vector Machine (SVM) algorithm. These models were further evaluated in an independent testing cohort.

Findings

Six exosomal miRNAs (miR-20a, miR-20b, miR-26a, miR-106a, miR-191, miR-486) were differentially expressed in the TB patients. Three SVM models, "EHR+miRNA", "miRNA only" and "EHR only" were compared, and "EHR + miRNA" model achieved the highest diagnostic efficacy, with an AUC up to 0.97 (95% CI 0.80–0.99) in TBM and 0.97 (0.87–0.99) in PTB, respectively. However, "EHR only" model only showed an AUC of 0.67 (0.46–0.83) in TBM. After 2-month anti-tuberculosis therapy, overexpressed miRNAs presented a decreased expression trend (p= 4.80 × 10⁻⁵).

Interpretation

Our results showed that the combination of exosomal miRNAs and EHRs could potentially improve clinical diagnosis of TBM and PTB.

Fund

Funds for the Central Universities, the National Natural Science Foundation of China.

Pre- and Post-analytical Factors in Biomarker Discovery

The translation of promising biomarkers, which were identified in biomarker discovery experiments, to clinical assays is one of the key challenges in present-day proteomics research. Many so-called "biomarker candidates" fail to progress beyond the discovery phase, and much emphasis is placed on pre- and post-analytical variability in an attempt to provide explanations for this bottleneck in the biomarker development pipeline. With respect to such variability, there is a large number of pre- and post-analytical factors which may impact the outcomes of proteomics experiments and thus necessitate tight control. This chapter highlights some of these factors and provides guidance for addressing them on the basis of examples from previously published proteomics studies.

Evolution of fit-for-purpose biomarker validations: an LBA perspective

Biomarker ligand-binding assays need to be validated for use on clinical studies in the drug development process. There is not one single guidance to cover all types of biomarker assays and their intended uses. Therefore, it is up to the scientist to piece together a validation strategy based on published papers and other sources. Shown here is a summary of what to take into consideration during a validation and how to apply it for use in the drug development process.

2017 White Paper on recent issues in bioanalysis: a global perspective on immunogenicity guidelines & biomarker assay performance (Part 3 – LBA: immunogenicity, biomarkers and PK assays)

The 2017 11th Workshop on Recent Issues in Bioanalysis took place in Los Angeles/Universal City, California, on 3–7 April 2017 with participation of close to 750 professionals from pharmaceutical/biopharmaceutical companies, biotechnology companies, contract research organizations and regulatory agencies worldwide. WRIB was once again a 5-day, week-long event – a full immersion week of bioanalysis, biomarkers and immunogenicity. As usual, it was specifically designed to facilitate sharing, reviewing, discussing and agreeing on approaches to address the most current issues of interest including both small- and large-molecule analysis involving LC–MS, hybrid ligand-binding assay (LBA)/LC–MS and LBA approaches. This 2017 White Paper encompasses recommendations emerging from the extensive discussions held during the workshop, and is aimed to provide the bioanalytical community with key information and practical solutions on topics and issues addressed, in an effort to enable advances in scientific excellence, improved quality and better regulatory compliance. Due to its length, the 2017 edition of this comprehensive White Paper has been divided into three parts for editorial reasons. This publication (Part 3) covers the recommendations for large-molecule bioanalysis, biomarkers and immunogenicity using LBA. Part 1 (LC–MS for small molecules, peptides and small molecule biomarkers) and Part 2 (hybrid LBA/LC–MS for biotherapeutics and regulatory agencies’ inputs) are published in volume 9 of Bioanalysis, issues 22 and 23 (2017), respectively.