Harmonizing the COVID-19 sample biobanks: Barriers and opportunities for standards, best practices and networks.

The coronavirus disease 2019 (COVID-19) pandemic has highlighted the practice of infectious diseases biobanking, as well as existing challenges and opportunities. Thus, the future of infectious diseases biobanking in the post-pandemic era, shall not be an "entry-level version" of its counterpart in non-communicable diseases and large population cohorts, but incorporate the lessons learned. Biobanks constitute a critical research infrastructure supported by harmonized practices through the implementation of international standards, and perceived within the broader scope of healthcare's intersection with research. This perspective paper considers the barriers in biobanking and standardization of practices, as well as the emerging opportunities in the field.

N_LyST: a simple and rapid screening test for Lynch syndrome.

AIMS: We sought to use PCR followed by high-resolution melting analysis to develop a single closed-tube screening panel to screen for Lynch syndrome. This comprises tests for microsatellite instability (MSI), MLH1 methylation promoter and BRAF mutation. METHODS: For MSI testing, five mononucleotide markers (BAT25, BAT26, BCAT25, MYB, EWSR1) were developed. In addition, primers were designed to interrogate Region C of the MLH1 promoter for methylation (using bisulphite-modified DNA) and to test for mutations in codon 600 of BRAF. Two separate cohorts from Nottingham (n=99, 46 with MSI, 53 being microsatellite stable (MSS)) and Edinburgh (n=88, 45 MSI, 43 MSS) were tested. RESULTS: All the cases (n=187) were blind tested for MSI and all were correctly characterised by our panel. The MLH1 promoter and BRAF were tested only in the Nottingham cohort. Successful blinded analysis was performed on the MLH1 promoter in 97 cases. All MSS cases showed a pattern of non-methylation while 41/44 cases with MSI showed full methylation. The three cases with MSI and a non-methylated pattern had aberrations in MSH2 and MSH6 expression. BRAF mutation was detected in 61% of MSI cases and 11% of MSS cases.Finally, 12 cases were blind screened by using the whole panel as a single test. Of these, five were identified as MSS, four as MSI/non-LS and three as MSI/possible LS. These results were concordant with the previous data. CONCLUSION: We describe the Nottingham Lynch Syndrome Test (N_LyST). This is a quick, simple and cheap method for screening for Lynch syndrome.

Diagnostic Distinction of Malignant Melanoma and Benign Nevi by a Gene Expression Signature and Correlation to Clinical Outcomes.

Background: Histopathologic examination alone can be inadequate for diagnosis of certain melanocytic neoplasms. Recently, a 23-gene expression signature was clinically validated as an ancillary diagnostic test to differentiate benign nevi from melanoma. The current study assessed the performance of this test in an independent cohort of melanocytic lesions against clinically proven outcomes.Methods: Archival tissue from primary cutaneous melanomas and melanocytic nevi was obtained from four independent institutions and tested with the gene signature. Cases were selected according to pre-defined clinical outcome measures. Malignant lesions were defined as stage I-III primary cutaneous melanomas that produced distant metastases (metastatic to sites other than proximal sentinel lymph node(s)) following diagnosis of the primary lesion. Melanomas that were metastatic at the time of diagnosis, all re-excisions, and lesions with <10% tumor volume were excluded. Benign lesions were defined as cutaneous melanocytic lesions with no adverse long-term events reported.Results: Of 239 submitted samples, 182 met inclusion criteria and produced a valid gene expression result. This included 99 primary cutaneous melanomas with proven distant metastases and 83 melanocytic nevi. Median time to melanoma metastasis was 18 months. Median follow-up time for nevi was 74.9 months. The gene expression score differentiated melanoma from nevi with a sensitivity of 93.8% and a specificity of 96.2%.Conclusions: The results of gene expression testing closely correlate with long-term clinical outcomes of patients with melanocytic neoplasms.Impact: Collectively, this provides strong evidence that the gene signature adds valuable adjunctive information to aid in the accurate diagnosis of melanoma. Cancer Epidemiol Biomarkers Prev; 26(7); 1107-13. ©2017 AACR.

Biobanking from the patient perspective.

PLAIN ENGLISH SUMMARY: Biobanks are collections of donations of biological material (DNA, cells, tissue etc.) and related data which are very valuable for research into human diseases. A variety of biobanks exist for example within hospitals, research institutes, pharmaceutical companies and patient organisations. The role of patients in biobanking is changing from being seen simply as donors, to actual collaborators in the design, development and the running of biobanks. In this article, we provide a number of examples of patients acting as partners at the heart of biobanking, where their voice and perspective is being seen and used as a valuable resource for the biobank. Our aim is that these examples can be used by those who work with patients in biobank-based research, to design future strategies for patient and public involvement in all biobanks. ABSTRACT: Biobanks and biobanking research plays an increasingly important role in healthcare research and delivery as health systems become more patient-centred and medicine becomes more personalised. There is also growing acceptance and appreciation of the value that patients, patient advocacy organisations and the public can bring as stakeholders in biobanking and more generally in research. Therefore, the importance of active, early and sustained engagement and involvement of patient and public representatives in biobanks will become increasingly relevant. Organising and facilitating patient and public involvement in biobanking takes considerable time and effort for all stakeholders involved. Therefore, for any biobank operator considering involving patients and the public in their biobanking activities, consideration of best practices, current guidance, ethical issues and evaluation of involvement will be important. In this article, we demonstrate that patients are much more than donors to biobanks-they are collaborators at the heart of biobanking with an important voice to identify perspective, which can be an extremely valuable resource for all biobanks to utilise. The case studies herein provide examples of good practice of patient involvement in biobanking as well as outcomes from these practices, and lessons learned. Our aim is to provide useful insights from these efforts and potential future strategies for the multiple stakeholders that work with patients and the public involved in biobank-based research.

Nottingham Health Science Biobank: a sustainable bioresource.

Nottingham Health Science Biobank (NHSB) was established in 2011 by a 3-year "pump priming" grant from the United Kingdom National Institute of Health Research. Before biobanking operations began, NHSB commissioned a financial report on the full costs of biobanking and worked with key stakeholders and external consultants to develop a business plan with the aim of achieving financial and operational sustainability. The plan included: scanning published information, telephone interviews with commercial companies, Freedom of Information Requests, dialogue with prospective customers, and a market analysis of global trends in the use of human tissue samples in research. Our financial report provided a comprehensive and structured costing template for biobanking and confirmed the absolute requirement to ensure cost-efficient processes, careful staff utilization, and maximization of sample turnover. Together with our external consultants, we developed a business model responsive to global interest in healthcare founded on i) identification of key therapeutic areas that mapped to the strengths of the NHSB; ii) a systematic approach to identifying companies operating in these therapy areas; iii) engagement with noncommercial stakeholders to agree strategically aligned sample collection with the aim of ensuring the value of our tissue resource. By adopting this systematic approach to business modelling, the NHSB has achieved sustainability after less than 3 years of operation.

Retracted article: Quantum dots high fluorescent signal amplification immunoassay using branched DNA and peptide nucleic acid conjugated antibody.

I, Yuan-Cheng Cao, hereby wholly retract this Analyst paper for correction. This article was submitted for publication without the knowledge and approval of the co-authors listed. Signed: Yuan-Cheng Cao, Newcastle University, UK, December 2011. This retraction is endorsed by May Copsey, Editor. Retraction published 16th December 2011.

Identification of SPARC-like 1 protein as part of a biomarker panel for Alzheimer's disease in cerebrospinal fluid.

We have used proteomic fingerprinting to investigate diagnosis of Alzheimer's disease (AD). Samples of lumbar cerebrospinal fluid (CSF) from clinically-diagnosed AD cases (n = 33), age-matched controls (n = 20), and mild cognitive impairment (MCI) patients (n = 10) were used to obtain proteomic profiles, followed by bioinformatic analysis that generated a set of potential biomarkers in CSF samples that could discriminate AD cases from controls. The identity of the biomarker ions was determined using mass spectroscopy. The panel of seven peptide biomarker ions was able to discriminate AD patients from controls with a median accuracy of 95% (sensitivity 85%, specificity 97%). When this model was applied to an independent blind dataset from MCI patients, the intensity of signals was intermediate between the control and AD patients implying that these markers could potentially predict patients with early neurodegenerative disease. The panel were identified, in order of predictive ability, as SPARC-like 1 protein, fibrinogen alpha chain precursor, amyloid-ß, apolipoprotein E precursor, serum albumin precursor, keratin type I cytoskeletal 9, and tetranectin. The 7 ion ANN model was further validated using an independent cohort of samples, where the model was able to classify AD cases from controls with median accuracy of 84.5% (sensitivity 93.3%, specificity 75.7%). Validation by immunoassay was performed on the top three identified markers using the discovery samples and an independent sample cohort which was from postmortem confirmed AD patients (n = 17).

Serum biomarkers which correlate with failure to respond to immunotherapy and tumor progression in a murine colorectal cancer model.

PURPOSE: To advance our understanding of mechanisms involved in tumor progression/regression, a CT26 colorectal mouse model treated intra-tumorally with DISC-herpes simplex virus as immunotherapy was used in the discovery and validation phases to investigate and ultimately identify biomarkers correlating with the failure to respond to immunotherapy. EXPERIMENTAL DESIGN: For the discovery phase, serum protein/peptide profiles of a retrospective sample collection (total n=70) were analyzed using MALDI-TOF-MS combined with artificial neural networks. Following identification of the key predictive peptides using ESI-MS/MS, validation of the identified proteins was carried out on serum and tissues collected in an independent sample set (total n=60). RESULTS: Artificial neural network analysis resulted in four discriminatory peaks with an accuracy of 86%, sensitivity of 90% and specificity of 81% between the progressor/regressor groups. Three of the identified discriminatory markers were upregulated and demonstrated a positive correlation with tumor progression following DISC-herpes simplex virus therapy. Immunovalidation studies corroborated the MALDI-TOF-MS findings. Immunohistochemistry revealed that serum amyloid A-1 and serum amyloid P produced in the liver localized intracellularly in CT26 tumor tissue. CONCLUSIONS: MALDI-TOF-MS and BI analysis of the serum proteome of tumor-bearer mice undergoing immunotherapy, identified biomarkers associating with "failure to respond" and biological arrays confirmed these findings.

Using In silico LD clumping and meta-analysis of genome-wide datasets as a complementary tool to investigate and validate new candidate biomarkers in Alzheimer's disease.

Despite the recent wealth of genome-wide association studies, insufficient power may explain why much of the heritable contribution to common diseases remains hidden. As different SNP panels are genotyped by commercial chips, increasing study power through meta-analysis is made problematic. To address these power issues we suggest an approach which permits meta-analysis of candidate SNPs from multiple GWAS. By identifying correlated SNPs from different platforms (r(2)=1), using PLINK's 'clumping' method, we generated combined p-values (using Fisher's combined and random effects meta-analysis) for each clump. P-values were corrected for the number of clumps (representing the number of independent tests). We also explored to what extent commercial platforms tag HapMap SNPs within these candidate genes. To illustrate this approach, and to serve as 'proof-of-principle', we used 3 late-onset Alzheimer's disease GWAS datasets to explore SNP-disease associations in 4 new candidate genes encoding cerebro-spinal fluid biomarkers for Alzheimer's disease; Fibrinogen γ-chain (FGG), SPARC-like1 (SPARCL1), Contactin-1 (CNTN1) and Contactin-2 (CNTN2). Genes encoding current Alzheimer's biomarkers; APP (Aß), MAPT (Tau) and APOE were also included. This method identified two SNP 'clumps'; one clump in APOE (rs4420638) and one downstream of CNTN2 (which harboured rs7523477 and rs4951168) which were significant following random effects meta-analysis (P < 0.05). The latter was linked to three conserved SNPs in the 3'-UTR of CNTN2. We cannot rule out that this result is a false positive due to the large number of statistical tests applied; nevertheless this approach is easily applied and might well have utility in future '-omics' studies.

The 7th East Midlands Proteomics Workshop 12 November 2008, Nottingham, UK.

Over 200 scientists with a common interest in proteomic techniques and their application to fundamental biological and biomedical problems participated in the 7th East Midlands Proteomics Workshop. This annual one day meeting was held in Nottingham in November 2008 and is a joint venture of colleagues from three local Universities: The University of Nottingham, Nottingham Trent University, and Loughborough University.

Enrichment of low molecular weight serum proteins using acetonitrile precipitation for mass spectrometry based proteomic analysis.

A rapid acetonitrile (ACN)-based extraction method has been developed that reproducibly depletes high abundance and high molecular weight proteins from serum prior to mass spectrometric analysis. A nanoflow liquid chromatography/tandem mass spectrometry (nano-LC/MS/MS) multiple reaction monitoring (MRM) method for 57 high to medium abundance serum proteins was used to characterise the ACN-depleted fraction after tryptic digestion. Of the 57 targeted proteins 29 were detected and albumin, the most abundant protein in serum and plasma, was identified as the 20th most abundant protein in the extract. The combination of ACN depletion and one-dimensional nano-LC/MS/MS enabled the detection of the low abundance serum protein, insulin-like growth factor-I (IGF-I), which has a serum concentration in the region of 100 ng/mL. One-dimensional sodium dodecyl sulfate/polyacrylamide gel electrophoresis (SDS-PAGE) analysis of the depleted serum showed no bands corresponding to proteins of molecular mass over 75 kDa after extraction, demonstrating the efficiency of the method for the depletion of high molecular weight proteins. Total protein analysis of the ACN extracts showed that approximately 99.6% of all protein is removed from the serum. The ACN-depletion strategy offers a viable alternative to the immunochemistry-based protein-depletion techniques commonly used for removing high abundance proteins from serum prior to MS-based proteomic analyses.

The 6(th) East Midlands Proteomics Workshop supported by the BSPR and BMSS 14 November 2007, Nottingham, UK.

Now in its 6(th) year, the East Midlands Proteomics workshop held in November 2007 brought together over 200 scientists with a common interest in proteomic techniques and their application to complex biological and biomedical problems. For the first time, this meeting was jointly supported by the British Society for Proteome Research (BSPR) and British Mass Spectrometry Society (BMSS).

Clinical proteomics: discovery of cancer biomarkers using mass spectrometry and bioinformatics approaches--a prostate cancer perspective.

Prostate cancer (PCa) is an intractable disease, where diagnosis and clinical prediction of the disease course and response to treatment is compromised by the lack of objective and robust biomarker assays. In late stage metastatic disease, treatment options are limited, although it is recognized that some patients may benefit from immunotherapy and in particular vaccine therapy. However, research into biomarkers that correlate with the clinical outcome of immunotherapy has lagged behind vaccine development. Thus, proteomic tools are increasingly being utilized for the discovery of biomarkers which will allow us to make clinical decisions about patient treatment at an earlier stage and should aid in shortening the development time for vaccines. In this review we will summarize the various proteomic platforms used to investigate new biomarkers in PCa for better patient diagnosis, prognosis, patient stratification, treatment monitoring and clinical surrogate endpoints. We will discuss method limitations and highlight the key areas of research required for understanding the etiology of PCa.

Quantitative profiling of epoxyeicosatrienoic, hydroxyeicosatetraenoic, and dihydroxyeicosatetraenoic acids in human intrauterine tissues using liquid chromatography/electrospray ionization tandem mass spectrometry.

A reversed-phase liquid chromatography negative ion electrospray tandem mass spectrometry (LC/ESI-MS/MS) method was developed and validated to quantify a range of physiologically relevant eicosanoids, including 5,6-, 8,9-, 11,12-, and 14,15-epoxyeicosatrienoic acids (EETs); 5-, 8-, 9-, 12-, and 15-hydroxyeicosatetraenoic acids (HETEs), and 5,6-, 8,15-, and 12,20-dihydroxyeicosatetraenoic acids (DiHETEs) in human intrauterine tissues. A solid-phase extraction method was employed to extract the eicosanoids, and gradient LC separation was performed on a Kromasil C(18) column. Mass spectrometric detection was performed by multiple reaction monitoring over a 31-min run time. The calibration curves were linear over the range of 4-400pmol/g tissue, and the intra- and interday precision and accuracy were within a coefficient of variation of 2.0 to 27.4% and 4.6 to 17.9%, respectively. The lower limit of quantitation was 1.0pmol/g tissue. The method was applied successfully to the characterization and quantitation of eicosanoids in the different compartments of human intrauterine tissues. Our results demonstrate significantly greater amounts of HETEs than of either the EETs or DiHETEs (P<0.001), irrespective of tissue type. Specifically, the metabolite 12-HETE was significantly more abundant (P<0.001) than all other HETEs. Of the EET metabolites, 5,6-EET predominated (P<0.001). A significant negative correlation between EETs and HETEs for all tissues (rho=-0.390, P<0.001) was identified, implying a biological feedback mechanism between these two arachidonate metabolite classes.

Diagnostic biomarkers differentiating metastatic melanoma patients from healthy controls identified by an integrated MALDI-TOF mass spectrometry/bioinformatic approach.

The prognosis of advanced metastatic melanoma (American Joint Committee on Cancer (AJCC) stage IV) remains dismal with a 5-year survival rate of 6-18%. In the present study, an integrated MALDI mass spectrometric approach combined with artificial neural networks (ANNs) analysis and modeling has been used for the identification of biomarker ions in serum from stage IV melanoma patients allowing the discrimination of metastatic disease from healthy status with high specificities of 92% for protein ions and 100% for peptide biomarkers. Our ANNs model also correctly classified 98% of a blind validation set of AJCC stage I melanoma samples as nonstage IV samples, emphasizing the power of the newly defined biomarkers to identify patients with late-stage metastatic melanoma. Sequence analysis identified peptides derived from metastasis-associated proteins; alpha 1-acid glycoprotein precursor-1/2 (AAG-1/2) and complement C3 component precursor-1 (CCCP-1). Furthermore, quantitation of serum AAG by an immunoassay showed a significant (p<0.001) increase in AAG serum concentration in stage IV patients in comparison with healthy volunteers; moreover; the quantity of AAG plotted against MALDI-MS peak intensity classified the groups into two distinct clusters. Ongoing studies of other disease stages will provide evidence whether our strategy is sufficiently robust to give rise to stage-specific protein/peptide signatures in melanoma.

The identification of human tumour antigens: Current status and future developments.

The biggest challenge facing us today in cancer control and prevention is the identification of novel biomarkers for detection and improved therapeutic interventions to reduce mortality and morbidity rates. Biomarkers are important indicators to inform us of the physiological state of the cell at a specific time. It is now clear that malignant transformation occurs by changes in cellular DNA and protein expression with subsequent clonal proliferation of the altered cells. The affected genes and their expressed protein products or biomarkers are those involved in the normal growth and maintenance of the cancerous cells. These biomarkers could prove pivotal for the identification of early cancer and people at risk of developing cancer. Altered proteins or changes in gene expression in malignant cells may lead to the expression of tumour antigens recognised by host immune system. In this review we discuss current research into the molecular technologies making possible the global genomic-wide analysis of changes in DNA (genotyping), RNA expression (transcriptomics) and protein expression (proteomics) that have accelerated the rate of new biomarker/tumour antigen discovery. To gain a comprehensive understanding of the physiology and pathophysiology of cancer an approach that harmoniously integrates the various 'omic' platforms are key to unraveling the complexity 'needle-in-a-haystack' quality of biomarker/tumour antigen discovery.

Hydrogen peroxide and superoxide anion modulate pregnant human myometrial contractility.

Reactive oxygen species (ROS) have the propensity to cause macromolecular damage with consequent modification of cellular function. We investigated the effects of two particular oxidants, superoxide (O2(-)) anions and hydrogen peroxide (H2O2), on oxytocin-induced myometrial contractility using biopsies from women undergoing Caesarean section at term gestation. Isometric tension recordings were performed and concentration-response curves derived after addition of test agents. A maximal reduction in myometrial contractility to 27.2 +/- 4.5% of control was observed followed application of H2O2. The enzyme scavenger catalase (CAT) reduced the inhibitory effect of H2O2 but had little effect at 10-fold lower concentrations. Addition of dialysed xanthine oxidase +/- hypoxanthine significantly inhibited contractility to 23.8.0 +/- 4.2% compared with control. Pre-incubation with superoxide dismutase and CAT diminished this effect. The non-specific potassium channel blocker, tetraethylammonium chloride (1 mM), had no effect on myometrial contractility. We conclude that human myometrium is susceptible to the effects of ROS, which may be produced by reperfusion-ischaemic episodes during labour. Our findings could, in part, explain the weak or prolonged depression of contractions characteristic of myometrial dysfunction culminating in difficult labours.

Reduced expression of immunoreactive beta2-adrenergic receptor protein in human myometrium with labor.

A considerable body of evidence exists suggesting that the beta(2)-adrenergic receptor (beta(2)-AR) mediates uterine relaxation. However, little information exists on the localization, distribution, or expression of beta(2)-ARs in the human myometrium during the nonpregnant to labor transition. We have used immunochemical methods to investigate beta(2)-AR localization and expression in the nonpregnant, term pregnant, and term parturient uterus. Myometrial biopsies were obtained from 1) nonpregnant, menstruating women undergoing hysterectomy; 2) singleton term pregnant women undergoing elective cesarean section before the onset of labor; or 3) singleton term pregnant women undergoing emergency cesarean section after spontaneous labor. Tissues were processed for immunohistochemistry, immunofluorescence, and Western blotting and a primary polyclonal antibody specific to the human beta(2)-AR to identify immunoreactive myometrial beta(2)-AR. Protein levels were subsequently quantified by densitometry relative to rat brain protein. Immunohistochemistry and immunofluorescence demonstrated the presence of beta(2)-AR predominantly at the plasma membrane and also in the cytosol of myometrial cells. A 2-fold decrease in protein levels of the beta(2)-AR was apparent in the myometrium of labor compared with that of nonpregnant and pregnant nonlaboring women (P < 0.05). These results demonstrate that down-regulation of beta(2)-AR protein with labor may constitute a contributory mechanism by which uterine quiescence is removed at term.