How can we use proteomics to learn more about platelets?

Proteomics tools provide a powerful means to identify, detect, and quantify protein-related details in studies of platelet phenotype and function. Here, we consider how historical and recent advances in proteomics approaches have informed our understanding of platelet biology, and, how proteomics tools can be used going forward to advance studies of platelets. It is now apparent that the platelet proteome is comprised of thousands of different proteins, where specific changes in platelet protein systems can accompany alterations in platelet function in health and disease. Going forward, many challenges remain in how to best carry out, validate and interpret platelet proteomics experiments. Future studies of platelet protein post-translational modifications such as glycosylation, or studies that take advantage of single cell proteomics and top-down proteomics methods all represent areas of interest to profiling and more richly understanding platelets in human wellness and disease.

Extrinsic and intrinsic preanalytical variables affecting liquid biopsy in cancer

Liquid biopsy, through isolation and analysis of disease-specific analytes, has evolved as a promising tool for safe and minimally invasive diagnosis and monitoring of tumors. It also has tremendous utility as a companion diagnostic allowing detection of biomarkers in a range of cancers (lung, breast, colon, ovarian, brain). However, clinical implementation and validation remains a challenge. Among other stages of development, preanalytical variables are critical in influencing the downstream cellular and molecular analysis of different analytes. Although considerable progress has been made to address these challenges, a comprehensive assessment of the impact on diagnostic parameters and consensus on standardized and optimized protocols is still lacking. Here, we summarize and critically evaluate key variables in the preanalytical stage, including study population selection, choice of biofluid, sample handling and collection, processing, and storage. There is an unmet need to develop and implement comprehensive preanalytical guidelines on the optimal practices and methodologies.

Banking of Tumor Tissues: Effect of Preanalytical Variables in the Phase of Pre- and Postacquisition on RNA Integrity

Background: RNA integrity of tumor tissues from 12 common organs was measured, and tumor tissues from liver were found to have the best RNA integrity in our previous study. The effects of preanalytical variables in the phase of pre- and postacquisition on RNA integrity were further assessed in hepatocellular carcinoma (HCC) tissues in this study. Methods: RNA integrity number (RIN) was measured in tissues from 146 HCC patients. First, 42 fresh HCC tumor tissues were newly collected to assess the effect of various preanalytical variables in the phase of preacquisition on RNA integrity. Second, eight paired HCC tumor and normal tissues were newly collected and used in the gradient course study of ex vivo ischemia time and freeze-thaw cycles on RNA integrity. Finally, 96 stock-frozen tumor tissues with various years of frozen storage were used to assess the effect of cryopreservation time. Results: RNA integrity was found to be independent of patient age, sex, clinical stage, tumor location, HBV infection status, tumor diameter, and surgical approach, but affected by tumor grade. Tumor tissues with a greater tumor grade had lower RIN. With the prolongation of ex vivo ischemia time, freeze-thaw cycles, and cryopreservation time, the RIN of HCC tissues showed decreasing trends. Significant decreases in RIN of the tumor and normal tissues were observed at 6 and 2 hours of ex vivo ischemia time, respectively, and significantly decreased RIN of tumor tissues was observed after six freeze-thaw cycles and 6 years of cryopreservation. Conclusions: Preanalytical variables in the phase of preacquisition such as tumor grade, and in the postacquisition phase such as ex vivo ischemia time, freeze-thaw times, and freeze-storage time both have effects on RNA integrity of HCC tissues. Tissue-based translational research should pay attention to preanalytical variables when collecting and utilizing tumor tissues.

Review of coagulation preanalytical variables with update on the effect of direct oral anticoagulants

There are many preanalytical variables (PAV) that are known to affect coagulation testing. The more commonly acknowledged PAV addressed by the clinical laboratory tend to start with their influence on blood collection, but realistically coagulation PAV starts with the patient, where the laboratory has less influence or control. Patient selection and appropriate timing for blood collection may be integral for assuring proper diagnosis and management. Laboratory control and assurance for ideal phlebotomy practice would mitigate most PAVs related to blood collection to minimize suboptimal sample collection. Laboratory oversight of sample transportation, processing and storage will assure sample integrity until testing can be facilitated. The purpose of this document is to review common PAV that should be taken into consideration when ordering, performing and interpreting a coagulation test result, with additional attention to the effect of direct oral anticoagulants (DOACs).

Impact of Preanalytical Factors on the Measurement of Tumor Tissue Biomarkers Using Immunohistochemistry

Analysis of formalin-fixed paraffin-embedded (FFPE) tissue by immunohistochemistry (IHC) is commonplace in clinical and research laboratories. However, reports suggest that IHC results can be compromised by biospecimen preanalytical factors. The National Cancer Institute's Biospecimen Preanalytical Variables Program conducted a systematic study to examine the potential effects of delay to fixation (DTF) and time in fixative (TIF) on IHC using 24 cancer biomarkers. Differences in IHC staining, relative to controls with a DTF of 1 hr, were observed in FFPE kidney tumor specimens after a DTF of ≥2 hr. Reductions in H-score and/or staining intensity were observed for c-MET, p53, PAX2, PAX8, pAKT, and survivin, whereas increases were observed for RCC1, EGFR, and CD10. Prolonged TIF of 72 hr resulted in significantly reduced H-scores of CD44 and c-Met in kidney tumor specimens, compared with controls with 12-hr TIF. An elevated probability of altered staining intensity due to DTF was observed for nine antigens, whereas for prolonged TIF an elevated probability was observed for one antigen. Results reported here and elsewhere across tumor types and antigens support limiting DTF to ≤1 hr when possible and fixing tissues in formalin for 12-24 hr to avoid confounding effects of these preanalytical factors on IHC.

Actual approaches to the transportation of biological samples at low temperatures

Taking into account the impact of shipment method of biosamples is necessary for obtaining high-quality biological samples in biobanking and laboratory research. The impact of liquid nitrogen, dry ice and cold accumulators on the quality of biological markers was considered, as well as recommendations to reduce the impact of these methods of shipment. The liquid nitrogen provides the best preservation of samples, however, dry ice is used much more often during their transportation. When transporting certain types of cells using dry ice, there is the way to use CryoStor CS1 and Cell Banker 1 cryoprotectors. The dry ice has a significant effect on both the pH of liquid biological samples and the coagulological parameters of plasma samples. The penetration of CO2 into the sample leads to changes in the parameters of PTT and APPT, as well as to decrease the protein C and fibrinogen level under certain conditions. Serum and plasma samples exposed to dry ice for more than 16 hours should be thawed open at room temperature, or instead of it should be kept at -80 °C for 24 hours to avoid changes in coagulation parameters, The use of cold accumulators is unacceptable for long-term shipment of serum and plasma containing unstable biomarkers because of insufficiently low temperature (increase over time to -25 °C and above). Besides, metal pellets can be used as cold storage batteries at low temperatures (up to -80 ° C), but they are not as effective as dry ice, since it is able to hold the required temperature for much longer.

Testing the Stability of Plasma Protein and Whole Blood RNA in Archived Blood of Loggerhead Sea Turtles, Caretta caretta

Sample storage conditions can affect accuracy and reproducibility of biological measurements. Storing samples rapidly at the lowest available temperatures is considered ideal but is not always feasible when sampling in remote and logistically challenging field conditions, as is often the case with sea turtles. The objective of this study was to examine the stability of plasma proteins and quality of whole blood RNA from loggerhead sea turtle samples collected as part of an eighteen-year-long curated specimen collection. These biological variables are often used to assess sea turtle health; therefore, it is necessary to maintain the integrity of these components during storage. Protein electrophoresis was conducted on heparinized plasma from individual turtles collected in 2018 (n = 3), 2008 (n = 3), and 2001 (n = 3). Plasma was also pooled from four turtles sampled in 2018 and subjected to various storage temperatures. Whole blood was collected in blood collection tubes containing sodium heparin or PAXgene tubes with an RNA preservative. These were subjected to different storage treatments that can possibly occur during logistically difficult field sampling. Following various treatments, plasma proteins showed minor differences across collection years and no differences among storage treatments were observed, even when exposed to 38°C for three hours. RNA quality was assessed from whole blood using an RNA integrity number (RIN). RINs were poor from sodium heparin tubes that were frozen and from PAXgene tubes after an extended thaw. High-quality RNA was obtained from sodium heparin tubes that were never frozen and from PAXgene tubes with freezing delayed by up to 11 days. Overall, these results indicate that plasma proteins remain stable over time and when exposed to undesirable storage conditions, and RNA degrades rapidly in sea turtle blood after freezing and when not properly preserved. These aspects are important to consider when planning sampling protocols and logistics for optimal long-term sample preservation.

miRNA in prostate cancer: challenges toward translation

Prostate cancer (PCa) represents the most commonly diagnosed neoplasm among men. miRNAs, as biomarkers, could further improve reliability in distinguishing malignant versus nonmalignant, and aggressive versus nonaggressive PCa. However, conflicting data was reported for certain miRNAs, and there was a lack of consistency and reproducibility, which has been attributed to diverse (pre)analytical factors. In order to address current challenges in miRNA clinical research on PCa, a PubMed-based literature search was conducted with the last update in May 2019. After identifying critical variations in designs and protocols that undermined clear-cut evidence acquisition, and reliable translation into clinical practice, we propose guidelines for most critical steps that should be considered in future research of miRNA as biomarkers, especially in PCa.

Utilization of Mobile Application for Better Implementation of Good Clinical Practice in a Biorepository Sample Collection Process: Functions of PancMoBio in Biobanking

Preanalytical variables of biospecimens play a vital role in biobanking. Currently, there is a lack of a convenient and precise methods to document these variables. Paper documentation and computer-based Lab Information Management System software are the most common solutions, but both have clear disadvantages. An application named PancMoBio was newly developed in our pancreas biobank, with the guidance of good clinical practice principles as well as the incorporation of technical support from professional software companies. With portable electronic devices running this application, all data can be precisely collected in a synchronous manner during sample collection and processing. PancMoBio comprises two major modules-recording and searching-and five submodules in the recording module: blood sample collection, solid tumor tissue sample collection, cystic tumor sample collection, plasma sample separation, and serum sample separation. Compared with other methods, our application was found to be more convenient and accurate in recording preanalytical variables and demonstrated improved capability in facilitating real-time quality control and quality assurance. It was apparent that PancMoBio could improve the integrity of biospecimen and biobank quality management. Thus, it should be considered for further utilization in biobanking.

Biological, Medical, and Other Tissue Variables Affecting Biospecimen Utilization

Bioresources are critical resources that support biomedical research because of their ability to appropriately collect, process, store, and distribute a wide range of high-quality biospecimens that meet the needs of specific investigators. Of note, some biorepositories are concerned by their growing inventories and their low rates of tissue utilization. This review discusses the technical characteristics of biospecimens that can cause morphological and molecular variability and/or limit the usefulness of biospecimens in research. This article also describes current challenges related to biospecimen characteristics that may affect biospecimen utilization. These include inadequate awareness of investigators about the availability of biospecimens with specific morphologic and molecular features, donor variability, preanalytical variables, technical problems inherent with an investigator's request for biospecimens, limited tissue availability from a biorepository based on requested sizes and/or numbers of available biospecimens, effects of times of warm and cold ischemia, damage of tissues during surgery, and molecular changes during storage. To ensure maximal biospecimen utilization of all types of biospecimens requires continual education of investigators from diverse fields, particularly on factors that cause variability in the morphological and molecular characteristics of tissues. The investigators' requests for biospecimens and associated data should be reviewed carefully, including by a bioresource-associated pathologist. Queries arising from the request/application form should be resolved by bioresource personnel directly with the investigator.

Sources and solutions for spurious test results in coagulation

In the coagulation laboratory, much emphasis has been placed on rapid and accurate testing; however, spurious results that are inaccurate and do not reflect the actual status of the patient can potentially lead to an incorrect diagnosis and altered intervention. Errors in coagulation results and interpretation can occur at any point of the process from obtaining the specimen to interpretation and use of the result by the clinician. The main sources of error include the patient's biological and preanalytical variation, analytical testing, and postanalytical use of the reported result(s). This article reviews various sources of error leading to spurious results, providing methods to recognize these aberrant results and presenting solutions for minimizing their occurrence.

Effect of preanalytical and analytical variables on the clinical utility of mean platelet volume

BACKGROUND

The study endpoint was to analyze the effect of preanalytical (time, temperature, anticoagulant) and analytical (imprecision, correlation between volume and platelet concentration) variables on mean platelet volume (MPV). A further aim was to calculate in an adult population the reference intervals using the Sysmex XE-5000 analyzer. A critical evaluation was also made of the clinical utility of these parameters.

METHODS

Analyses of the above values were performed in duplicate in 170 healthy adults of both sexes: (1) within 30 min from collection, and (2) after 4 h. To evaluate stability over time, the value of the platelet parameters of 20 subjects were determined, a re-analysis being performed for a period of up to 24 h on samples maintained at room temperature and 4°C using either K2-EDTA or Na-citrate as anticoagulants.

RESULTS

The stability over time of MPV closely depends on the anticoagulant used, storage temperature and time interval between venipuncture and analysis. An inverse, non-linear correlation between MPV and platelet count was also found.

CONCLUSIONS

In view of their effect on MPV and other related indices, the preanalytical and analytical variables make them, little more than experimental.

Application and optimization of minimally invasive cell-free DNA techniques in oncogenomics

The conventional method of measuring biomarkers in malignant tissue samples has already given subversive growth in cancer diagnosis, prognosis, and therapy selection. However, the regression and heterogeneity associated with tumor tissue biopsy have urged for the development of an alternative approach. Considering the limitations, cell-free DNA has emerged as a surrogate alternative, facilitating preoperative chemoradiotherapy (p < 0.0001) treatment response in rectal cancer and detection of biomarker in lung cancer. This potential of cell-free DNA in several other cancers has yet to be explored based on clinical relevance by optimizing the preanalytical factors. This review has highlighted the crucial parameters from blood collection to cell-free DNA analysis that has a significant impact on the accuracy and reliability of clinical data. The quantity of cell-free DNA is also a limiting factor. Therefore, a proper preanalytical factor for blood collection, its stability, centrifugation speed, and plasma storage condition are to be optimized for developing cancer-specific biomarkers useful for clinical purpose. Liquid biopsy-based origin of cell-free DNA has revolutionized the area of cancer research. Lack of preanalytical and analytical procedures may be considered for identification of novel biomarkers through next-generation sequencing of tumor-originated cell-free DNA in contradiction to tissue biopsy for cancer-specific biomarkers.

Deciphering Sources of Variability in Clinical Pathology

The objectives of this session were to explore causes of variability in clinical pathology data due to preanalytical and analytical variables as well as study design and other procedures that occur in toxicity testing studies. The presenters highlighted challenges associated with such variability in differentiating test article-related effects from the effects of experimental procedures and its impact on overall data interpretation. These presentations focused on preanalytical and analytical variables and study design-related factors and their influence on clinical pathology data, and the importance of various factors that influence data interpretation including statistical analysis and reference intervals. Overall, these presentations touched upon potential effect of many variables on clinical pathology parameters, including animal physiology, sample collection process, specimen handling and analysis, study design, and some discussion points on how to manage those variables to ensure accurate interpretation of clinical pathology data in toxicity studies. This article is a brief synopsis of presentations given in a session entitled "Deciphering Sources of Variability in Clinical Pathology-It's Not Just about the Numbers" that occurred at the 35th Annual Symposium of the Society of Toxicologic Pathology in San Diego, California.

Preanalytical study of fetuin-A: effect of sample type, processing speed and freeze-thaw cycles

BACKGROUND

It has been suggested that fetuin-A may be a potential biomarker of cardiometabolic disease. However, few studies have investigated preanalytical factors that might impact the measurement of fetuin-A in the circulation. This pilot study aimed to investigate the preanalytical variables of sample type, timing of sample centrifugation and the impact of freeze-thaw cycles on the concentration of fetuin-A in serum or EDTA-plasma.

METHODS

Blood samples were taken from 19 male or female healthy volunteers, aged 18-70 years, and left at ambient room temperature for 2 h or 48 h. The tubes were then centrifuged, serum and EDTA-plasma separated, and fetuin-A concentrations measured using a commercially available enzyme-linked immunosorbent assay (ELISA).

RESULTS

There was no significant difference between the concentrations of fetuin-A in EDTA-plasma and serum following separation from whole blood at 2 h postcollection (P=0.78). The median (interquartile range) concentrations of fetuin-A in EDTA-plasma separated at 2 h and 48 h postcollection were 589 µg/mL (484-703 µg/mL) and 767 µg/mL (687-942 µg/mL), respectively (P<0.0005). For serum, equivalent concentrations were 606 µg/mL (501-669 µg/mL) at 2 h and 607 µg/mL (564-757 µg/mL) at 48 h postcollection (P=0.06). Fetuin-A concentrations measured in EDTA-plasma and serum showed no significant change following three freeze-thaw cycles in samples separated at 2 h postcollection (EDTA-plasma P=0.16; serum P=0.89).

CONCLUSION

This small pilot study has shown that serum is preferable to EDTA-plasma for the measurement of fetuin-A. It has also shown that fetuin-A appears to be as stable after three freeze-thaw cycles as it is after one.