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Background The AACC Academy revised the reproductive testing section of the Laboratory Medicine Practice Guidelines: Evidence-Based Practice for Point-of-Care Testing (POCT) published in 2007. Methods A panel of Academy members with expertise in POCT and laboratory medicine was formed to develop guidance for the use of POCT in reproductive health, specifically ovulation, pregnancy, premature rupture of membranes (PROM), and high-risk deliveries. The committee was supplemented with clinicians having Emergency Medicine and Obstetrics/Gynecology training. Results Key recommendations include the following. First, urine luteinizing hormone (LH) tests are accurate and reliable predictors of ovulation. Studies have shown that the use of ovulation predicting kits may improve the likelihood of conception among healthy fertile women seeking pregnancy. Urinary LH point-of-care testing demonstrates a comparable performance among other ovulation monitoring methods for timing intrauterine insemination and confirming sufficient ovulation induction before oocyte retrieval during in vitro fertilization. Second, pregnancy POCT should be considered in clinical situations where rapid diagnosis of pregnancy is needed for treatment decisions, and laboratory analysis cannot meet the required turnaround time. Third, PROM testing using commercial kits alone is not recommended without clinical signs of rupture of membranes, such as leakage of amniotic fluid from the cervical opening. Finally, fetal scalp lactate is used more than fetal scalp pH for fetal acidosis due to higher success rate and low volume of sample required. Conclusions This revision of the AACC Academy POCT guidelines provides recommendations for best practice use of POCT in fertility and reproduction.

Monitoring tacrolimus trough concentrations is important for optimal immunosuppression in solid organ transplant recipients. Available assays generally correlate well with each other but little attention is given to patients in whom tacrolimus metabolite concentrations might be elevated, which could lead to artificially increased tacrolimus concentrations assessed by cross-reacting immunoassays. We addressed this hypothesis by investigating the correlation between four different assays (two immunoassays and two mass-spectrometry assays) in both a population with normal and a population with high dose requirements. Routine blood samples were collected in 37 control (CO) and 72 high dose patients (HD). Tacrolimus was measured with a CMIA, an ECLIA and two LCMS assays. Results were investigated using Deming regression analysis, Pearson correlation coefficients, Bland-Altman plots and by calculating bias. The CMIA demonstrated a positive bias of 23-26% compared with both LCMS assays. The correlation between CMIA and LCMS assays was good for the CO (

Uveal melanoma is a rare melanoma subtype different from cutaneous melanoma, with high incidence of liver metastasis and poor prognosis. Cancer cell–derived extracellular vesicles have been shown to induce proinflammatory and prometastatic signaling in the tumor microenvironment and at distant sites. The characterization of uveal melanoma exosome cargo and its role in metastatic spread is essential to identify targets and intervene in the early stages of metastatic development. Our study characterizes the proteomic content of uveal melanoma exosomes and identified the presence of markers with metastatic properties. We demonstrated that uveal melanoma exosomes induce activation of cell signaling pathways and the release of cytokines and growth factors from hepatocytes. These exosome-stimulated liver cells could in turn induce migration of uveal melanoma cells, confirming that the exosomes have a functional role in the cross-talk between these two cell types. We found that the proinflammatory cytokine macrophage migration inhibitory factor (MIF) was a major player in these mechanisms and its blockade inhibited cell migration in coculture with exosome-stimulated hepatocytes and prevented the development of metastases in vivo. Targeting MIF in the early stages of metastasis may represent a novel adjuvant drug therapy to prevent metastatic spread in uveal melanoma.Implications:This study provides the first in vivo evidence that MIF inhibition may serve as a novel adjuvant drug therapy to prevent metastasis in uveal melanoma.

Supplementary Figure from Uveal Melanoma Exosomes Induce a Prometastatic Microenvironment through Macrophage Migration Inhibitory Factor

Uveal melanoma is a rare melanoma subtype different from cutaneous melanoma, with high incidence of liver metastasis and poor prognosis. Cancer cell–derived extracellular vesicles have been shown to induce proinflammatory and prometastatic signaling in the tumor microenvironment and at distant sites. The characterization of uveal melanoma exosome cargo and its role in metastatic spread is essential to identify targets and intervene in the early stages of metastatic development. Our study characterizes the proteomic content of uveal melanoma exosomes and identified the presence of markers with metastatic properties. We demonstrated that uveal melanoma exosomes induce activation of cell signaling pathways and the release of cytokines and growth factors from hepatocytes. These exosome-stimulated liver cells could in turn induce migration of uveal melanoma cells, confirming that the exosomes have a functional role in the cross-talk between these two cell types. We found that the proinflammatory cytokine macrophage migration inhibitory factor (MIF) was a major player in these mechanisms and its blockade inhibited cell migration in coculture with exosome-stimulated hepatocytes and prevented the development of metastases in vivo. Targeting MIF in the early stages of metastasis may represent a novel adjuvant drug therapy to prevent metastatic spread in uveal melanoma. Implications: This study provides the first in vivo evidence that MIF inhibition may serve as a novel adjuvant drug therapy to prevent metastasis in uveal melanoma.

Circulating cell-free mitochondrial DNA (cf-mtDNA) is an emerging biomarker of psychobiological stress and disease which predicts mortality and is associated with various disease states. To evaluate the contribution of cf-mtDNA to health and disease states, standardized high-throughput procedures are needed to quantify cf-mtDNA in relevant biofluids. Here, we describe MitoQuicLy:Mitochondrial DNAQuantification incell-free samples byLysis. We demonstrate high agreement between MitoQuicLy and the commonly used column-based method, although MitoQuicLy is faster, cheaper, and requires a smaller input sample volume. Using 10 µL of input volume with MitoQuicLy, we quantify cf-mtDNA levels from three commonly used plasma tube types, two serum tube types, and saliva. We detect, as expected, significant inter-individual differences in cf-mtDNA across different biofluids. However, cf-mtDNA levels between concurrently collected plasma, serum, and saliva from the same individual differ on average by up to two orders of magnitude and are poorly correlated with one another, pointing to different cf-mtDNA biology or regulation between commonly used biofluids in clinical and research settings. Moreover, in a small sample of healthy women and men (n=34), we show that blood and saliva cf-mtDNAs correlate with clinical biomarkers differently depending on the sample used. The biological divergences revealed between biofluids, together with the lysis-based, cost-effective, and scalable MitoQuicLy protocol for biofluid cf-mtDNA quantification, provide a foundation to examine the biological origin and significance of cf-mtDNA to human health.

Utilizing biofluids to identify cancer biomarkers has received considerable attention in the past decade. In this regard, serum and urine are convenient biofluids to noninvasively recapitulate information usually indicated by traditional tissue biopsies. In particular, we are interested in exploring the extracellular vesicle (ECV)-containing compartment of these fluids as a targeted source for cancer biomarker discovery. ECVs are membrane-enclosed particles, comprising of various fractions including exosomes, microvesicles, and apoptotic bodies. In both physiological and pathological states such as cancer, ECVs carry a rich load of molecular and protein cargoes, which aid in mediating intercellular communication between cells from various tissue types. Here we successfully enriched ECVs using a simple, low-cost, optimized method that we have developed; it is generalizable for the analysis of ECVs from multiple sample types. Such procedures are necessary as ECVs are nanoparticles that contain a treasure trove of large numbers of biomarkers each present at very low levels. Sample processing procedures can enrich for these vesicles and allow for the enhanced detection of proteins in downstream applications such as comprehensive proteomics methods using data-independent acquisition (DIA) and LC-MS/MS.

Context.— The process for identifying patients with monoclonal gammopathies is complex. Initial detection of a monoclonal immunoglobulin protein (M protein) in the serum or urine often requires compilation of analytical data from several areas of the laboratory. The detection of M proteins depends on adequacy of the sample provided, available clinical information, and the laboratory tests used. Objective.— To develop an evidence-based guideline for the initial laboratory detection of M proteins. Design.— To develop evidence-based recommendations, the College of American Pathologists convened a panel of experts in the diagnosis and treatment of monoclonal gammopathies and the laboratory procedures used for the initial detection of M proteins. The panel conducted a systematic literature review to address key questions. Using the Grading of Recommendations Assessment, Development, and Evaluation approach, recommendations were created based on the available evidence, strength of that evidence, and key judgements as defined in the Grading of Recommendations Assessment, Development, and Evaluation Evidence to Decision framework. Results.— Nine guideline statements were established to optimize sample selection and testing for the initial detection and quantitative measurement of M proteins used to diagnose monoclonal gammopathies. Conclusions.— This guideline was constructed to harmonize and strengthen the initial detection of an M protein in patients displaying symptoms or laboratory features of a monoclonal gammopathy. It endorses more comprehensive initial testing when there is suspicion of amyloid light chain amyloidosis or neuropathies, such as POEMS (polyneuropathy, organomegaly, endocrinopathy, M protein, and skin changes) syndrome, associated with an M protein.

PURPOSE This guideline provides recommendations for available tissue-based prostate cancer biomarkers geared toward patient selection for active surveillance, identification of clinically significant disease, choice of postprostatectomy adjuvant versus salvage radiotherapy, and to address emerging questions such as the relative value of tissue biomarkers compared with magnetic resonance imaging. METHODS An ASCO multidisciplinary Expert Panel, with representatives from the European Association of Urology, American Urological Association, and the College of American Pathologists, conducted a systematic literature review of localized prostate cancer biomarker studies between January 2013 and January 2019. Numerous tissue-based molecular biomarkers were evaluated for their prognostic capabilities and potential for improving management decisions. Here, the Panel makes recommendations regarding the clinical use and indications of these biomarkers. RESULTS Of 555 studies identified, 77 were selected for inclusion plus 32 additional references selected by the Expert Panel. Few biomarkers had rigorous testing involving multiple cohorts and only 5 of these tests are commercially available currently: Onco type Dx Prostate, Prolaris, Decipher, Decipher PORTOS, and ProMark. With various degrees of value and validation, multiple biomarkers have been shown to refine risk stratification and can be considered for select men to improve management decisions. There is a paucity of prospective studies assessing short- and long-term outcomes of patients when these markers are integrated into clinical decision making. RECOMMENDATIONS Tissue-based molecular biomarkers (evaluating the sample with the highest volume of the highest Gleason pattern) may improve risk stratification when added to standard clinical parameters, but the Expert Panel endorses their use only in situations in which the assay results, when considered as a whole with routine clinical factors, are likely to affect a clinical decision. These assays are not recommended for routine use as they have not been prospectively tested or shown to improve long-term outcomes—for example, quality of life, need for treatment, or survival. Additional information is available at www.asco.org/genitourinary-cancer-guidelines .

Background Human immunodeficiency virus (HIV) testing is the first step in the HIV prevention cascade. The Centers for Disease Control and Prevention HIV laboratory diagnostic testing algorithm was developed before preexposure prophylaxis (PrEP) and immediate antiretroviral therapy (iART) became standards of care. PrEP and iART have been shown to delay antibody development and affect the performance of screening HIV assays. Quantitative results from fourth-generation HIV testing may be helpful to disambiguate HIV testing. Methods We retrospectively reviewed 38 850 results obtained at an urban, academic medical center. We assessed signal-to-cutoff (s/co) distribution among positive and negative tests, in patients engaged and not engaged in an HIV prevention program, and evaluated changes in patients with multiple results. Classification and regression tree (CART) analysis was used to determine a threshold cutoff, and logistic regression was used to identify predictors of true positive tests. Results Ninety-seven percent of patients with a negative HIV test had a result that was ≤0.2 s/co. For patients tested more than once, we found differences in s/co values did not exceed 0.2 s/co for 99.2% of results. CART identified an s/co value, 38.78, that in logistic regression on a unique validation cohort remained associated with the likelihood of a true-positive HIV result (odds ratio, 2.49). Conclusions Machine-learning methods may be used to improve HIV screening by automating and improving interpretations, incorporating them into robust algorithms, and improving disease prediction. Further investigation is warranted to confirm if s/co values combined with a patient's risk profile will allow for better clinical decision making for individuals on PrEP or eligible for iART.

Glycosaminoglycans (GAGs), such as heparan sulfate and chondroitin sulfate, are an important component of the tumor microenvironment (TME). These carbohydrates are attached to proteoglycans at the surface of tumor cells and play a vital role in malignant transformation. Heparan sulfate (HS) glycosaminoglycans have been demonstrated to play a pleiotropic role in regulating the activity of important cellular receptors and downstream signaling pathways, and are implicated in cancer cell proliferation, angiogenesis, invasion, and metastasis. Heparinase, an endoglycosidase that specifically cleaves heparan sulfate side chains of heparan sulfate proteoglycans is expressed in several sarcoma subtypes. We measured heparinase activity in several cell lines and found that A673, CHP100, CHLA9 and RD-ES Ewing’s sarcoma cell lines have significantly higher levels of heparinase activity compared to the heparinase-deficient CHO-K1 psgD-677 cell line. Interference with heparinase or heparin sulfate function(s) may represent a therapeutic approach in sarcoma. To this end, we tested these cell lines by measuring cell growth using a cell viability assay, in the presence or absence of GTC3300P, a small molecule inhibitor of protein interaction with glycosaminoglycan. We demonstrate that the Ewing’s sarcoma cell lines exhibit potent and significant inhibition in cell growth in vitro, in the presence of drug. Western blot analysis shows induction of cleaved Poly-ADP Ribose Polymerase (PARP), yH2AX, as well as cleaved caspase-3, known markers of apoptosis and down regulation of mTORC1 targets such as phospho-S6 (p-S6), in Ewing’s sarcoma. Apoptosis was confirmed by the induction of sub-G1 population in Ewing’s sarcoma by cell cycle analysis. Previous reports have indicated that heparinase activity is strongly implicated in cell migration and invasion and is associated with tumor metastasis, angiogenesis and inflammation. This was confirmed by LC-MS/MS proteomics and bioinformatics (gene ontology and gene set enrichment) analysis of these multiple cell lines, which identified alterations in numerous biomarkers in these pathways, including multiple ribosomal protein subunits, spliceosomes components, and complement coagulation cascade. We further conducted a cell migration assay and demonstrate that GTC3300 significantly inhibits cell migration in Ewing’s sarcoma cell lines, but not in heparinase-deficient psg677 cells. Taken together our data strongly suggests that targeting protein interaction with glycosaminoglycans including heparan sulfate in Ewing’s sarcoma represents a novel approach and merits further investigation Citation Format: Tahir N. Sheikh, Elgilda Musi, Alex J. Rai, Gary K. Schwartz. Development of small molecule inhibitors of protein interaction with glycosaminoglycans. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4977.

In biological systems, variable protein expression is a crucial marker for numerous diseases, including cancer. The vast majority of liquid chromatography-triple quadrupole mass spectrometry-based quantitative protein assays use bottom-up methodologies, where proteins are subjected to proteolytic cleavage prior to analysis. Here, the effect of difluoroacetic acid and biological matrices on the developement of a multiple reaction monitoring based top-down reversed-phase liquid chromatography-triple quadrupole mass spectrometry method for analysis of cancer-related intact proteins was evaluated. Seven growth factors (5.5-26.5 kDa; isoelectric points: 4.6-9.9) were analyzed on a wide-pore C4 column. The optimized method was performed at 30°C, using a 0.2 mL/min flow rate, a 10 %B/min gradient slope, and 0.05% v/v difluoroacetic acid as a mobile phase modifier. The increase of mass spectrometry sensitivity due to the difluoroacetic acid (estimated limits of detection in biological matrices 1-500 ng/mL) significantly varied for proteins with lower and higher charge state distributions. Matrix effects, as well as the specificity of the method were assessed for variable biological samples and pretreatment methods. This work demonstrates method development to improve the ability to target intact proteins directly by more affordable triple quadrupole mass spectrometry instrumentation, which could be beneficial in many application fields.

Context.—The performance of laboratory testing has recently come under increased scrutiny as part of important and ongoing debates on regulation and reimbursement. To address this critical issue, this study compares the performance of assay methods, using either commercial kits or assays designed and implemented by single laboratories (“home brews”), including next-generation sequencing methods, on proficiency testing provided by the College of American Pathologists Molecular Oncology Committee.Objective.—To compare the performance of different assay methods on College of American Pathologists proficiency testing for variant analysis of 3 common oncology analytes: BRAF, EGFR, and KRAS.Design.—There were 6897 total responses across 35 different proficiency testing samples interrogating 13 different variants as well as wild-type sequences for BRAF, EGFR, and KRAS. Performance was analyzed by test method, kit manufacturer, variants tested, and preanalytic and postanalytic practices.Results.—Of 26 reported commercial kits, 23 achieved greater than 95% accuracy. Laboratory-developed tests with no kit specified demonstrated 96.8% or greater accuracy across all 3 analytes (1123 [96.8%] acceptable of 1160 total responses for BRAF; 848 [97.5%] acceptable of 870 total responses for EGFR; 942 [97.0%] acceptable of 971 total responses for KRAS). Next-generation sequencing platforms (summed across all analytes and 2 platforms) demonstrated 99.4% accuracy for these analytes (165 [99.4%] acceptable of 166 total next-generation sequencing responses). Slight differences in performance were noted among select commercial assays, dependent upon the particular design and specificity of the assay. Wide differences were noted in the lower limits of neoplastic cellularity laboratories accepted for testing.Conclusions.—These data demonstrate the high degree of accuracy and comparable performance across all laboratories, regardless of methodology. However, care must be taken in understanding the diagnostic specificity and reported analytic sensitivity of individual methods.

IgA nephropathy (IgAN) is an autoimmune disease and the most common primary glomerulonephritis. The four-hit hypothesis describes mechanism of the disease, from synthesis of galactose deficient IgA (GD-IgA), to recognition of GD-IgA by anti-glycan antibodies and deposition of the formed immune complex in the mesangium. Complement and coagulation cascade activation ensues, resulting in mesangial activation and cytokine release, podocyte injury, mesangial sclerosis and tubulointerstitial damage. Currently, there is no disease cure, and 30-40% of patients progress to end stage renal disease.Using complementary bioinformatic approaches, we demonstrate different levels of deviation of the transcriptome of the glomerulus in IgAN from normal, with the aim of identifying therapeutic targets. Approaches used herein include, deconvolution of the transcriptome to estimate immune constitution, co-regulation-based functional analysis of differentially expressed genes, modular co-expression analysis, network analysis of metabolic pathways and differential gene correlation analysis.We describe the immune composition in IgAN and the relatively low fold changes of the abundance of different immune cells and strength of immune signatures compared with control. Additionally, we identify enrichment of the intestinal network for IgA synthesis, repression of expression and dysregulation of networks of amino acid metabolism and PPAR signaling pathways in IgAN glomeruli. We also find loss of correlation between expression of matrix synthesizing and matrix degrading genes in IgAN.We conclude by discussing how therapies based on some nodes in these altered pathways described have been shown to be efficacious in IgAN and/or other inflammatory diseases and the potential of others in effective treatment.

Exosomes are small (30-200nm) membrane-bound vesicles released by all cells. They have been found in many clinical sample types, particularly those that are obtained in minimally-invasive fashion, including serum/plasma, urine, cerebrospinal and other fluids. They serve as an ideal source of biomarkers as their contents reflect the cell of origin and disease status of patients. Exosomes can serve as a "liquid biopsy," a non-invasive means to assess disease/health status in real-time. They can provide insights into disease mechanisms as they carry and transfer important signaling molecules, which may induce changes in the recipient cells. This is particularly relevant for metastatic cancers, as exosomes can prime the pre-metastatic niche. Many different approaches can be used to characterize the effects of the transfer of exosome content into the recipient cells, including global, untargeted approaches and protein-specific, targeted approaches. We describe herein our studies on the use of antibody arrays to probe for protein expression changes in hepatocytes that result from treating these cells with exosomes derived from uveal melanoma cells.

ObjectivesLaboratory testing and the measurement of appropriate biomarkers play a critical role in managing patients with coronavirus disease 2019 (COVID-19), allowing for disease diagnosis, monitoring progression, prognostication, prediction of treatment response, and risk stratification. We sought to characterize these effects on a more detailed, mechanistic level.MethodsWe reviewed the literature and identified a multitude of reports that describe the unique effects of this virus and its devastating consequences to multiple organ systems in COVID-19 patients.ResultsThere are specific alterations in biomarkers related to coagulation, depopulation of T-cell subtypes, the cytokine storm and inflammation, and kidney and cardiac dysfunction.ConclusionsLaboratory measurement of specific parameters and the use of appropriate prognostic, predictive, and monitoring biomarkers afford clinicians the ability to make informed medical decisions and guide therapy for patients afflicted with this dreaded disease.

Current serological immunoassays have inherent limitations for certain infectious diseases such as Lyme disease, a bacterial infection caused by Borrelia burgdorferi in North America. Here we report a novel method of manufacturing high-density multiplexed protein microarrays with the capacity to detect low levels of antibodies accurately from small blood volumes in a fully automated system. A panel of multiple serological markers for Lyme disease are measured using a protein microarray system, Lyme Immunochip, in a single step but interpreted adhering to the standard two-tiered testing algorithm (enzyme immunoassay followed by Western blot). Furthermore, an enhanced IgM assay was supplemented to improve the test’s detection sensitivity for early Lyme disease. With a training cohort (n = 40) and a blinded validation cohort (n = 90) acquired from CDC, the Lyme Immunochip identified a higher proportion of Lyme disease patients than the two-tiered testing (82.4% vs 70.6% in the training set, 66.7% vs 60.0% in the validation set, respectively). Additionally, the Immunochip improved sensitivity to 100% while having a lower specificity of 95.2% using a set of investigational antigens which are being further evaluated with a large cohort of blinded samples from the CDC and Columbia University. This universal microarray platform provides an unprecedented opportunity to resolve a broad range of issues with diagnostic tests, including multiplexing, workflow simplicity, and reduced turnaround time and cost.

Clinical laboratory testing routinely provides actionable results, which help direct patient care in the inpatient and outpatient settings. Since December 2019, a novel coronavirus (SARS-CoV-2) has been causing disease (COVID-19 [coronavirus disease 2019]) in patients, beginning in China and now extending worldwide. In this context of a novel viral pandemic, clinical laboratories have developed multiple novel assays for SARS-CoV-2 diagnosis and for managing patients afflicted with this illness. These include molecular and serologic-based tests, some with point-of-care testing capabilities. Herein, we present an overview of the types of testing available for managing patients with COVID-19, as well as for screening of potential plasma donors who have recovered from COVID-19.

We developed and validated serologic assays to determine SARS-CoV-2 seroprevalence in select patient populations in greater New York City area early during the epidemic. We tested “discarded” serum samples from February 24 to March 29 for antibodies against SARS-CoV-2 spike trimer and nucleocapsid protein. Using known durations for antibody development, incubation period, serial interval, and reproductive ratio for this pandemic, we determined that introduction of SARS-CoV-2 into New York likely occurred between January 23 and February 4, 2020. SARS-CoV-2 spread silently for 4–5 weeks before the first community acquired infection was reported. A novel coronavirus emerged in December 2019 in Wuhan, China1,2 and devasted Hubei Province in early 2020 before spreading to every province within China and nearly every country in the world3. This pathogen, now termed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused a global pandemic, with ~ 10 million cases and over 500,000 deaths reported through June 30, 20203. The first case of SARS-CoV-2 infection in the United States was identified on January 19, 2020 in a man who returned to the State of Washington from Wuhan4. In the ensuing months, the U.S. has become a hotspot of the pandemic, presently accounting for almost one third of the total caseload and over one fourth of the deaths3. The first confirmed case in New York was reported on March 1 in a traveler recently returned from Iran. The first community-acquired SARS-CoV-2 infection was diagnosed on March 3 in a 50-year-old male who lived in New Rochelle and worked in New York City (https://www1.nyc.gov/site/doh/covid/covid-19-data-archive.page.) In the ensuing 18 weeks, New York City has suffered a peak daily infection number of ~ 4,500 (Fig. 1a) and a cumulative caseload of ~ 400,000 to date. The time period when SARS-CoV-2 gained entry into this epicenter of the pandemic remains unclear.

Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin's lymphoma, and it constitutes biologically heterogeneous entities. Standard first-line therapies cure ~60% of patients, the rest being either refractory or experiencing relapse. Currently, there are no robust predictive biomarkers of therapeutic response. Heterogeneity of DLBCL is partly explained by the cell of origin (COO), ie, germinal centre B cell or activated B cell, with the latter exhibiting worse prognosis. While gene expression profiling (GEP) is the gold standard for determining COO, surrogate immunohistochemical algorithms are used clinically, but show significant discordance with GEP. Recently, additional genetic subgroups with different prognoses have been reported. However, the tools/expertise required for analysis prohibit widespread deployment. Liquid biopsy-based assays show promise in providing clinically actionable information, are noninvasive and facilitate serial sampling to assess mechanisms of therapy resistance. Circulating, cell-free DNA analysis has shown enhanced sensitivity for detecting molecular alterations, but this modality cannot determine alterations of the tumor proteome or on signalling pathways. Exosomes are endosomally derived vesicles, are found in high abundance in body fluids and are readily isolated using a variety of methods. Tumour-derived exosomes can yield data regarding genetic, transcriptional, and proteomic changes useful for diagnosis, prognosis, and therapy of DLBCL. At present, standardized techniques for isolating exosomes are lacking and discriminating between exosomes from neoplastic and normal B cells is challenging. Refinements in isolation procedures are required to realize their full potential as precision medicine tools to provide comprehensive information on disease subtypes, identify prognostic factors, allow real-time monitoring of therapy response and delineate novel drug targets.

Background Antibody diagnostics play an important role in disease detection and can potentially aid in monitoring of the immune responses to see if an individual has developed immunity. Developing high throughput diagnostics which does not involve handling of infectious material becomes imperative in the case of pandemics such as the recent outbreak of SARS-CoV2. Methods A protein microarray technology was used to detect the plurality of antibody response to four novel antigens namely S1 glycoprotein, Receptor binding domain (RBD), S2 glycoprotein and Nucleoprotein of the novel coronavirus named SARS-CoV2 using serum samples. A DBS card was additionally used to compare its performance with a venipuncture-based serum separator tube (SST) draw. Results The three main subclasses of antibodies IgM, IgA and IgG were analyzed to see the variations in immune responses in the affected population and compared to their microbial RT-PCR based NP swab results. The clinical sensitivity and specificity were determined to be 99.67% and 99.77%. In the matrix comparison study, which would enable patients to test without risk of transmitting the virus, DBS (Dried Blood Spot) matched with higher than 98% accuracy to a venipuncture-based SST collection. Conclusion Multiplex testing enables higher sensitivity and specificity which is essential while establishing exposure on a population scale. This flexible platform along with a discrete collection methodology would be crucial and broadly useful to scale up testing in current and future pandemics. Minimum sample volume that can be collected using DBS cards can be processed in this multiplex pillar plate format enabling the capacity to provide the reliability of high throughput analyzers while having the ease of collection similar to rapid tests.

Context.— Detection of acquired variants in cancer is a paradigm of precision medicine, yet little has been reported about clinical laboratory practices across a broad range of laboratories. Objective.— To use College of American Pathologists proficiency testing survey results to report on the results from surveys on next-generation sequencing–based oncology testing practices. Design.— College of American Pathologists proficiency testing survey results from more than 250 laboratories currently performing molecular oncology testing were used to determine laboratory trends in next-generation sequencing–based oncology testing. Results.— These presented data provide key information about the number of laboratories that currently offer or are planning to offer next-generation sequencing–based oncology testing. Furthermore, we present data from 60 laboratories performing next-generation sequencing–based oncology testing regarding specimen requirements and assay characteristics. The findings indicate that most laboratories are performing tumor-only targeted sequencing to detect single-nucleotide variants and small insertions and deletions, using desktop sequencers and predesigned commercial kits. Despite these trends, a diversity of approaches to testing exists. Conclusions.— This information should be useful to further inform a variety of topics, including national discussions involving clinical laboratory quality systems, regulation and oversight of next-generation sequencing–based oncology testing, and precision oncology efforts in a data-driven manner.

Exosomes are small (30-200nm) membrane-bound vesicles released by all cells. They have been found in many clinical sample types, particularly those that are obtained in minimally-invasive fashion, including serum/plasma, urine, cerebrospinal and other fluids. They serve as an ideal source of biomarkers as their contents reflect the cell of origin and disease status of patients. Exosomes can serve as a "liquid biopsy," a non-invasive means to assess disease/health status in real-time. They can provide insights into disease mechanisms as they carry and transfer important signaling molecules, which may induce changes in the recipient cells. This is particularly relevant for metastatic cancers, as exosomes can prime the pre-metastatic niche. Many different approaches can be used to characterize the effects of the transfer of exosome content into the recipient cells, including global, untargeted approaches and protein-specific, targeted approaches. We describe herein our studies on the use of antibody arrays to probe for protein expression changes in hepatocytes that result from treating these cells with exosomes derived from uveal melanoma cells.

The performance of laboratory testing has recently come under increased scrutiny as part of important and ongoing debates on regulation and reimbursement. To address this critical issue, this study compares the performance of assay methods, using either commercial kits or assays designed and implemented by single laboratories ("home brews"), including next-generation sequencing methods, on proficiency testing provided by the College of American Pathologists Molecular Oncology Committee.To compare the performance of different assay methods on College of American Pathologists proficiency testing for variant analysis of 3 common oncology analytes:There were 6897 total responses across 35 different proficiency testing samples interrogating 13 different variants as well as wild-type sequences forOf 26 reported commercial kits, 23 achieved greater than 95% accuracy. Laboratory-developed tests with no kit specified demonstrated 96.8% or greater accuracy across all 3 analytes (1123 [96.8%] acceptable of 1160 total responses forThese data demonstrate the high degree of accuracy and comparable performance across all laboratories, regardless of methodology. However, care must be taken in understanding the diagnostic specificity and reported analytic sensitivity of individual methods.

Uveal melanoma (UM) is a rare melanoma subtype with an estimated annual incidence of approximately 2000 in the United States. Despite excellent rates of local disease control with surgery or radiotherapy, nearly 50% of patients will develop metastatic disease, mostly to the liver, with a life expectancy of 12 months. The receptor tyrosine kinase MET is overexpressed in 60-86% of cases and, together with its ligand HGF, it plays a significant role in UM migration and metastasis. In recent years, it has been demonstrated that tumor cells communicate with the microenvironment at distant organs by secreting exosomes, extracellular small vesicles released into body fluids, to support cancer development, immune evasion and metastatic progression. Exosomes are able to stably transfer their unique cargos of proteins and RNA from the primary tumor to distant sites, such as the pre-metastatic “niche”. The functional role of UM exosomes in the tumor microenvironment cross-talk is largely unknown. To get deeper insight into UM exosome biology, we have isolated exosomes from UM cells before and after treatment with the MET inhibitor crizotinib and examined their content by proteomic analysis. Approximately 600 proteins were identified from each of these samples, with 444 proteins in common and 145 and 167 proteins uniquely detected in exosomes from untreated and treated cells, respectively. The expression of several exosome-associated proteins, including MET, were suppressed by crizotinib, suggesting that the exosomal cargo can be pharmacologically manipulated. Exposure of normal hepatocytes to UM-derived exosomes results in activation of MET in a dose dependent fashion, with induction of both the MAPK and AKT/PI3K pathways. Exosomes derived from serum of patients with advanced uveal melanoma also express MET and induced similar effects in hepatocytes. Furthermore, UM-derived exosomes activate the expression of pro-angiogenic and pro-inflammatory factors in normal hepatocytes, while exosomes isolated from crizotinib-treated UM cells reduced these effects. UM-derived exosomes also stimulated immune cells to release cytokines and chemokines, including IL-6, IL-8 CCL2, CCL3, CCL5 and CXCL1. Functionally, we demonstrated that conditioned media from exosome-treated hepatocyte highly stimulated UM cell migration, which could be repressed by the combination of MET and cytokine receptor inhibitors. These findings provide evidence that UM derived exosomes play a role in reprogramming the recipient cells to facilitate the establishment of metastasis, and the inhibition of exosome-mediated signaling may provide a potential therapeutic strategy in the early stages of metastasis. Citation Format: Grazia Ambrosini, Alex J. Rai, Blake Ebert, Gary K. Schwartz. Uveal melanoma exosomes express MET and re-program the recipient cells [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6082.

Amniotic fluid, the fetal-protective liquid that fills the amniotic sac, represents a rich source of biomarkers. The diagnostic utility of amniotic fluid relies on the highly abundant maternal and fetal nucleic acid and proteomic content, which allows for the simultaneous determination of mother and fetal health status. Extracellular vesicles (ECVs) that are released by all cells and found in amniotic fluid could be harnessed to provide substantial clinically actionable data. ECVs are mediators of critical biological functions and reflect the health of the parent cell. Thus, ECVs released from cells in distress may provide important diagnostic information. Here, we describe a straightforward and optimized method for isolating ECVs from amniotic fluid. In addition, we validate our procedure through western blotting using antibodies targeting canonical ECV protein markers and via direct visualization using transmission electron microscopy.

In the prenatal quad screen, the levels of four analytes in maternal serum are used to calculate the risk of serious birth defects. The Beckman Access2 Immunoassay System is an automated analyzer that enables rapid measurement of alpha-fetoprotein, unconjugated estriol, human chorionic gonadotropin, and dimeric inhibin A. The Benetech PRA software package is used to convert maternal serum analyte concentrations to multiples of the median (MoM) and calculates the risks of particular birth defects. The results from this simple and minimally invasive screen determine the need for more sensitive, specific, and usually riskier diagnostic procedures. We present herein some recent data from our experience at Columbia University Medical Center in New York, NY, using the Beckman Access2 immunoassay analyzer and Benetech PRA software package.

Amniotic fluid, the fetal-protective liquid that fills the amniotic sac, represents a rich source of biomarkers. The diagnostic utility of amniotic fluid relies on the highly abundant maternal and fetal nucleic acid and proteomic content, which allows for the simultaneous determination of mother and fetal health status. Extracellular vesicles (ECVs) that are released by all cells and found in amniotic fluid could be harnessed to provide substantial clinically actionable data. ECVs are mediators of critical biological functions and reflect the health of the parent cell. Thus, ECVs released from cells in distress may provide important diagnostic information. Here, we describe a straightforward and optimized method for isolating ECVs from amniotic fluid. In addition, we validate our procedure through western blotting using antibodies targeting canonical ECV protein markers and via direct visualization using transmission electron microscopy.

In the prenatal quad screen, the levels of four analytes in maternal serum are used to calculate the risk of serious birth defects. The Beckman Access2 Immunoassay System is an automated analyzer that enables rapid measurement of alpha-fetoprotein, unconjugated estriol, human chorionic gonadotropin, and dimeric inhibin A. The Benetech PRA software package is used to convert maternal serum analyte concentrations to multiples of the median (MoM) and calculates the risks of particular birth defects. The results from this simple and minimally invasive screen determine the need for more sensitive, specific, and usually riskier diagnostic procedures. We present herein some recent data from our experience at Columbia University Medical Center in New York, NY, using the Beckman Access2 immunoassay analyzer and Benetech PRA software package.

Objectives In the United States, minimum standards for quality control (QC) are specified in federal law under the Clinical Laboratory Improvement Amendment and its revisions. Beyond meeting this required standard, laboratories have flexibility to determine their overall QC program. Methods We surveyed chemistry and immunochemistry QC procedures at 21 clinical laboratories within leading academic medical centers to assess if standardized QC practices exist for chemistry and immunochemistry testing. Results We observed significant variation and unexpected similarities in practice across laboratories, including QC frequency, cutoffs, number of levels analyzed, and other features. Conclusions This variation in practice indicates an opportunity exists to establish an evidence-based approach to QC that can be generalized across institutions.

Purpose.—Clinical use of analytical tests to assess genomic variants in circulating tumor DNA (ctDNA) is increasing. This joint review from the American Society of Clinical Oncology and the College of American Pathologists summarizes current information about clinical ctDNA assays and provides a framework for future research.Methods.—An Expert Panel conducted a literature review on the use of ctDNA assays for solid tumors, including preanalytical variables, analytical validity, interpretation and reporting, and clinical validity and utility.Results.—The literature search identified 1338 references. Of those, 390, plus 31 references supplied by the Expert Panel, were selected for full-text review. There were 77 articles selected for inclusion.Conclusions.—The evidence indicates that testing for ctDNA is optimally performed on plasma collected in cell stabilization or EDTA tubes, with EDTA tubes processed within 6 hours of collection. Some ctDNA assays have demonstrated clinical validity and utility with certain types of advanced cancer; however, there is insufficient evidence of clinical validity and utility for the majority of ctDNA assays in advanced cancer. Evidence shows discordance between the results of ctDNA assays and genotyping tumor specimens, and supports tumor tissue genotyping to confirm undetected results from ctDNA tests. There is no evidence of clinical utility and little evidence of clinical validity of ctDNA assays in early-stage cancer, treatment monitoring, or residual disease detection. There is no evidence of clinical validity or clinical utility to suggest that ctDNA assays are useful for cancer screening, outside of a clinical trial. Given the rapid pace of research, reevaluation of the literature will shortly be required, along with the development of tools and guidance for clinical practice.

Exosomes are RNA and protein-containing nanovesicles secreted by all cell types and found in abundance in body fluids, including blood, urine and cerebrospinal fluid. These vesicles seem to be a perfect source of biomarkers, as their cargo largely reflects the content of parental cells, and exosomes originating from all organs can be obtained from circulation through minimally invasive or non-invasive means. Here we describe an optimized procedure for exosome isolation and analysis using clinical samples, starting from quick and robust extraction of exosomes with Total exosome isolation reagent, then isolation of RNA followed by qRT-PCR. Effectiveness of this workflow is exemplified by analysis of the miRNA content of exosomes derived from serum samples – obtained from the patients with metastatic prostate cancer, treated prostate cancer patients who have undergone prostatectomy, and control patients without prostate cancer. Three promising exosomal microRNA biomarkers were identified, discriminating these groups: hsa-miR375, hsa-miR21, hsa-miR574.

Prostate cancer is a complex disease, with multiple subtypes and clinical presentations. Much progress has been made in recent years to understand the underlying genetic basis that drives prostate cancer. Such mechanistic information is useful for development of novel therapeutic targets, to identify biomarkers for early detection or to distinguish between aggressive and indolent disease, and to predict treatment outcome. Multiple tests have become available in recent years to address these clinical needs for prostate cancer. We describe several of these assays, summarizing test details, performance characteristics, and acknowledging their limitations. There is a pressing unmet need for novel biomarkers that can demonstrate improvement in these areas. We introduce one such candidate biomarker, RAD9, describe its functions in the DNA damage response, and detail why it can potentially fill this void. RAD9 has multiple roles in prostate carcinogenesis, making it potentially useful as a clinical tool for men with prostate cancer. RAD9 was originally identified as a radioresistance gene, and subsequent investigations revealed several key functions in the response of cells to DNA damage, including involvement in cell cycle checkpoint control, at least five DNA repair pathways, and apoptosis. Further studies indicated aberrant overexpression in approximately 45% of prostate tumors, with a strong correlation between RAD9 abundance and cancer stage. A causal relationship between RAD9 and prostate cancer was first demonstrated using a mouse model, where tumorigenicity of human prostate cancer cells after subcutaneous injection into nude mice was diminished when RNA interference was used to reduce the normally high levels of the protein. In addition to activity needed for the initial development of tumors, cell culture studies indicated roles for RAD9 in promoting prostate cancer progression by controlling cell migration and invasion through regulation of ITGB1 protein levels, and anoikis resistance by modulating AKT activation. Furthermore, RAD9 enhances the resistance of human prostate cancer cells to radiation in part by regulating ITGB1 protein abundance. RAD9 binds androgen receptor and inhibits androgen-induced androgen receptor's activity as a transcription factor. Moreover, RAD9 also acts as a gene-specific transcription factor, through binding p53 consensus sequences at target gene promoters, and this likely contributes to its oncogenic activity. Given these diverse and extensive activities, RAD9 plays important roles in the initiation and progression of prostate cancer and can potentially serve as a valuable biomarker useful in the management of patients with this disease.

Importance The debate about the role of the Food and Drug Administration (FDA) in the regulation of laboratory-developed tests (LDTs) has focused attention on the analytical performance of all clinical laboratory testing. This study provides data comparing the performance of LDTs and FDA-approved companion diagnostics (FDA-CDs) in proficiency testing (PT) provided by the College of American Pathologists Molecular Oncology Committee. Objective To compare the analytical performance of LDTs and FDA-CDs on well-characterized PT samples and to compare the practice characteristics of laboratories using these assays. Design, Setting, and Participants This comparison of PT responses examines the performance of laboratories participating in the College of American Pathologists PT for 3 oncology analytes for which both FDA-CDs and LDTs are used: BRAF , EGFR , and KRAS . A total of 6897 PT responses were included: BRAF (n = 2524; 14 PT samples), EGFR (n = 2216; 11 PT samples), and KRAS (n = 2157, 10 PT samples). US Food and Drug Administration companion diagnostics and LDTs are compared for both accuracy and preanalytic practices of the laboratories. Main Outcomes and Measures As per the College of American Pathologists PT standards, results were scored and the percentages of acceptable responses for each analyte were compared. These were also broken down by the specific variants tested, by kit manufacturer for laboratories using commercial reagents, and by preanalytic practices. Results From analysis of 6897 PT responses, this study demonstrates that both LDTs and FDA-CDs have excellent performance overall, with both test types exceeding 97% accuracy for all 3 genes ( BRAF , EGFR , and KRAS ) combined. Rare variant-specific differences did not consistently favor LDTs or FDA-CDs. Additionally, more than 60% of participants using an FDA-CD reported adapting their assay from the approved procedure to allow for a greater breadth of sample types, minimum tumor content, and instrumentation, changing the classification of their assay from FDA-CD to LDT. Conclusions This study demonstrates the high degree of accuracy and comparable performance of both LDTs and FDA-CDs for 3 oncology analytes. More significantly, the majority of laboratories using FDA-CDs have modified the scope of their assay to allow for more clinical practice variety, rendering them LDTs. These findings support both the excellent and equivalent performance of both LDTs and FDA-CDs in clinical diagnostic testing.

TPS3154 Background: Assessing treatment response in castrate resistant prostate cancer (CRPC), remains a challenge due to the limited sensitivity and specificity of existing imaging modalities. Understanding prostate cancer biology with tumor biopsies does not address the issue of tumor heterogeneity or cellular degradation during the decalcification process of bone biopsies. Next generation positron emission tomography (PET) imaging and circulating biomarkers might provide additional insights on treatment responses and inform clinical decision-making earlier in therapy. 18F-DCFPyL (PyL) is a second-generation fluorinated PSMA PET tracer that has superior sensitivity and specificity to detect prostate cancer compared to standard imaging. Its role in assessing tumor response to therapy has not been evaluated. Circulating tumor DNA (ctDNA) in blood can provide tumor genomic information, while exosomes in serum and urine may provide data on the proteomic landscape of tumors. Methods: We are conducting a prospective study of 15 men with metastatic CRPC who are scheduled to start a new systemic therapy for their disease. Upon enrollment, subjects will have baseline assessments with standard cross-sectional imaging, 99mTc bone scan, and blood work. Standard scans will be performed every 8-12 weeks until progression of disease. PyL PET/CT scans and liquid biopsies (ctDNA and exosomes) will occur at baseline, 6 weeks after starting their new therapy, and at disease progression. Lesions seen on PET/CT images will be identified by a certified reader. The maximum standardized uptake value (SUVmax) will be measured and recorded in up to the five hottest lesions and normalized to a background SUVmean measured in the liver, spleen, kidney, mediastinum, and parotid glands. Changes in the normalized SUV from baseline to the 6-week PyL PET scan will be correlated to PSA response by the Pearson’s correlation coefficient. The Kaplan-Meier method will be used to evaluate progression free survival and overall survival dichotomized by the median value of SUV change. Blood for ctDNA and exosomes will be stored for future analysis. The study is open with two patients enrolled at the time of submission. One patient has completed his initial PyL PET/CT scan. Clinical trial information: NCT03585114.

Tumor markers are molecules derived from patient body fluids or tissues that are measured and can provide information useful for the management of cancer patients. Applications include detection of cancer, monitoring of disease progression, and evaluation of the effectiveness of therapeutic regimens, among others. Henry Bence-Jones discovered the first tumor marker in 1846—a protein seen in acidified urine of patients with multiple myeloma (1). Since that time, many more tumor markers have been described for a variety of other cancers. The Food and Drug Administration (FDA) has approved several of these markers (Table 1), and many more are being investigated and evaluated for clinical use. The goal of this chapter is to review how tumor marker assays are evaluated, describe the applications of tumor markers, provide details on the detection of tumor markers using immunoassays, and then list examples of clinically useful tumor markers that are used in the clinical laboratory today. Although the last few years have witnessed a plethora of developments in molecular testing of tumor markers, these will not be discussed here, as we will restrict our discussion to immunoassay-based detection methods.

It is traditionally difficult to incorporate two classes of diagnostic tests into a single platform. In this work, we demonstrate a microfluidic-based smartphone dongle that simultaneously measures concentration of hemoglobin and detects HIV antibodies. Specifically, we demonstrate how a previously published immunoassay device, which measured optical density of silver precipitation on gold colloids, can be expanded to quantitatively measure hemoglobin concentration via a colorimetric assay. By lysing whole blood components with CHAPS detergent, we achieved highly reproducible measurement of hemoglobin concentration with the device. We tested this dual test on 38 patient samples from Columbia University Medical Center. Compared with the Hemocue Hb 201+ analyzer, hemoglobin concentrations from our device were accurate within 1.2 g dL(-1), while the HIV immunoassay (in the presence of CHAPS detergent) showed 95% sensitivity and 95% specificity, comparable to our previous studies. This work demonstrates the feasibility of integrating two classes of diagnostic tests (a colorimetric-based quantitative measurement and an immunoassay based on silver precipitation on gold colloids) into a low-cost, fast, and low-power dongle that works with smartphones, and creates a novel dual panel with clinical utility for antenatal-care settings.

The screening of prostate cancer is usually based on serum prostate-specific antigen (PSA) level. However, PSA is a marker with low specificity and poor sensitivity for early diagnosis and risk stratification of prostate cancer. We performed a systematic review of publications that evaluated the accuracy and reliability of novel exosomal …

Biomarkers have become invaluable tools in the clinical space for cancer detection, diagnosis, patient prognosis and treatment selection. An ideal biomarker should be easily assayed with minimally invasive medical procedures but possess high sensitivity and specificity. Although many candidate biomarkers for various diseases have been proposed in the literature, very few have made their way to clinical use, and for certain types of cancer there are no reliable biomarker options. The use of prostate specific antigen (PSA) has led to a dramatic increase in the diagnosis of prostate cancer - over 230,000 new cases in 2014. However, most of these cases are of low risk disease that is unlikely to cause significant morbidity and mortality, leading to the accepted notion that prostate cancer is overdiagnosed. On the other hand, while it is a sensitive test, less than ¼ of patients undergoing a prostate biopsy based on PSA testing are actually found to have the disease. The identification of biomarkers that are more senstitive and specific predictors for the presence of prostate cancer, as well as for the aggressiveness of the disease, could decrease the complications and morbidity related to prostate biopsies and definitive treatment. The circulating miRNA in blood could potentially fill this void, providing biomarkers suitable for real-time detection and application to the management of prostate cancer patients. The main advantages of miRNAs versus longer molecules (mRNA, lncRNA) include: (i) smaller number of sequences The objective of this project was to develop a set of reagents and tools for efficient recovery and analysis of circulating miRNAs. Our team has built a complete workflow to provide: (1) high throughput isolation of total serum RNA using a new MagMaxTM mirVanaTM reagent kit for the KingFisherTM Flex and Duo instruments, and (2) downstream analysis of microRNA profiles by qRT-PCR using next generation TaqMan® microRNA assays. The effectiveness of this workflow is exemplified by analysis of a panel of miRNAs in samples derived from serum of patients with metastatic prostate cancer versus control groups. Following this fast and easy workflow suitable for serum and other body fluids, disease-specific RNA signatures can be identified and used as biomarkers. TaqMan® is a registered Trademark of Roche Molecular Systems, Inc. used under permission and license. Citation Format: Emily M. Zeringer, Alex J. Rai, Joel DeCastro, Luming Qu, Marie Gonzalez, Laura Chapman, Alexander V. Vlassov, Susan M. Magdaleno, Chunmei Liu, Fangqi Hu, Shoulian Dong, Linda Wong. A complete workflow for high throughput isolation of serum microRNAs and downstream analysis by qRT-PCR: application to cancer biomarker discovery. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3387. doi:10.1158/1538-7445.AM2015-3387