Paired Plasma Research Articles

BIOM-19. PLASMA EXTRACELLULAR VESICLE SAMPLING FROM HIGH GRADE GLIOMA PATIENTS DEMONSTRATES A SMALL RNA SIGNATURE INDICATIVE OF DISEASE AND IDENTIFIES LNCRNA RPPH1 AS A HIGH GRADE GLIOMA BIOMARKER

Abstract High grade gliomas (HGGs) and cells of the tumour microenvironment (TME) secrete extracellular vesicles (EVs) into the plasma that contain genetic and protein cargo which function in paracrine signaling. Isolation of these EVs and their cargo from plasma could lead to a simplistic tool that can inform on diagnosis and disease course of HGG. In the present study, plasma extracellular vesicles (EVs) were captured utilizing a peptide affinity method (Vn96 peptide) from high grade glioma (HGG) patients and normal controls followed by next generation sequencing (NovaSeq6000) to define a small RNA (sRNA) signature unique to HGG. Over 750 differentially expressed sRNA (miRNA, snoRNA, lncRNA, tRNA, mRNA fragments and non-annotated regions) were identified between HGG and controls. MiEAA 2.0 pathway analysis of the miRNA in the sRNA signature revealed miRNA highly enriched in both EV and HGG pathways demonstrating the validity of results in capturing a signal from the TME. Also revealed were several novel HGG plasma EV sRNA biomarkers including lncRNA RPPH1 (Ribonuclease P Component H1), RNY4 (Ro60-Associated Y4) and RNY5 (Ro60-Associated Y5). Furthermore, in paired longitudinal patient plasma sampling, RPPH1 informed on surgical resection (decreased on resection) and importantly RPPH1 increased again on clinically defined progression. The present study supports the role of plasma EV sRNA sampling (and particularly RPPH1) as part of a multi-pronged approach to HGG disease course surveillance.

Acoramidis produces near-complete TTR stabilization in blood samples from patients with variant transthyretin amyloidosis that is greater than that achieved with tafamidis

Abstract Introduction Transthyretin (TTR) amyloidosis (ATTR) is a progressive, fatal disease caused by destabilizing TTR variants (TTRv) and age-related factors. Dissociation of tetrameric TTR initiates protein misfolding, aggregation, and tissue deposition which constitutes the mechanism of disease. More destabilizing variants drive more severe clinical phenotypes. TTR stabilizers have demonstrated clinical benefits for neuropathic and cardiovascular outcomes correlated with the extent of TTR stabilization. Acoramidis (AG10) is a novel TTR stabilizer in development for the treatment of TTR amyloid cardiomyopathy. Hypothesis: Acoramidis achieves near-complete in vitro TTR stabilization, exceeding levels achieved with clinically relevant concentrations of tafamidis (a TTR stabilizer in clinical use), when added to blood samples from ATTRv patients across a spectrum of destabilizing TTR variants. Methods Two established assays assessed TTR stabilization: fluorescent probe exclusion (FPE; measures binding site occupancy), and Western blot (WB; quantifies tetrameric TTR persistence under conditions of accelerated dissociation). Over 60 individual patient samples representing 18 unique TTRv across a spectrum of intrinsic instability and clinical phenotypes were assayed. Acoramidis was added at its target clinical trough concentration (10 µM) and compared to tafamidis added at its clinical peak (26 µM) and trough (16 µM) concentrations reported for its maximal approved dose. Results Acoramidis bound serum TTR to a greater extent (103 ± 13%) than either peak (87 ± 14%) or trough (71 ± 14%) concentrations of tafamidis. WB assays showed that addition of acoramidis resulted in significantly greater and more durable TTR stabilization (93 ± 14%) than adding tafamidis (peak: 49 ± 14%, trough: 36 ± 13%) in all paired individual patient plasma samples tested (Figure 1, p < 0.0001). Rare variants (A97S, D38A, F64L, L58H, P24S, Y114C) also demonstrated near complete stabilization upon in vitro addition of acoramidis. Conclusions At its target therapeutic trough concentration, acoramidis achieved near-complete TTR stabilization across 18 unique genotypes; in the subset of paired samples, the stabilization was significantly greater for acoramidis than for tafamidis even at its peak clinical concentration. This observation held across a range of destabilizing mutations, including a∼2-fold greater stabilization than tafamidis for the prevalent cardiomyopathic V122I variant. Based on the mechanism of disease and the association between TTR destabilization and severity of clinical outcomes, these data suggest that acoramidis has the potential to be a clinically differentiated and efficacious treatment option for patients with ATTRv, independent of variant genotype.

Resistance to osimertinib in advanced EGFR-mutated NSCLC: a prospective study of molecular genotyping on tissue and liquid biopsies.

Resistance to osimertinib in advanced EGFR-mutated non-small cell lung cancer (NSCLC) constitutes a significant challenge for clinicians either in terms of molecular diagnosis and subsequent therapeutic implications. This is a prospective single-centre study with the primary objective of characterising resistance mechanisms to osimertinib in advanced EGFR-mutated NSCLC patients treated both in first- and in second-line. Next-Generation Sequencing analysis was conducted on paired tissue biopsies and plasma samples. A concordance analysis between tissue and plasma was performed. Sixty-five advanced EGFR-mutated NSCLC patients treated with osimertinib in first- (n = 56) or in second-line (n = 9) were included. We managed to perform tissue and liquid biopsies in 65.5% and 89.7% of patients who experienced osimertinib progression, respectively. Acquired resistance mechanisms were identified in 80% of 25 patients with post-progression samples, with MET amplification (n = 8), EGFR C797S (n = 3), and SCLC transformation (n = 2) the most frequently identified. The mean concordance rates between tissue and plasma for the EGFR activating mutation and for the molecular resistance mechanisms were 87.5% and 22.7%, respectively. Resistance to osimertinib demonstrated to be highly heterogeneous, with MET amplification the main mechanism. Plasma genotyping is a relevant complementary tool which might integrate tissue analysis for the study of resistance mechanisms.

Abstract 13263: Utilization of Proteomic Surrogates for Early Detection of Unexpected Drug Benefits

Introduction: Detection of benefits and adverse effects of therapies in early clinical trial phases could improve the safety, efficiency, and cost of clinical trials. For example, while SGLT2i and GLP-1 RA drugs are recognized success stories, earlier identification of their benefits beyond improved diabetic control may have had the potential to save loss of patients’ lives and years of sales. Hypothesis: Using the EXSCEL and SUGAR-DM-HF trials as examples to study GLP1-RA and SGLT2i responses, we hypothesized that previously validated proteomic surrogates of cardiovascular (CV) events, and kidney health could have enabled detection of these unexpected drug benefits earlier in development in a smaller number of participants over a shorter follow-up period. Methods: CV risk and kidney prognosis SomaSignal tests (each derived from ~5000 plasma proteins measurements using SomaScan® assay) were applied to paired plasma samples at baseline and 9-months (SUGAR-DM-HF) or 1-year (EXSCEL) in intervention (EXSCEL n=1840; SUGAR-DM-HF n=45) and control (EXSCEL n=1833; SUGAR-DM-HF n=52) participants. Power calculations were performed to determine the minimum number of samples needed to detect a significant change within the treatment period with alpha = 0.05, 80% power using a t-test comparing two-sample means. Results: We demonstrated that the cardiovascular benefits of exenatide were detectable with a proteomic surrogate within 1-year (p=0.002), with power analysis indicating a significant 1-year change is observable with group sizes of n=1368 compared with >7000 participants for up to 6.8 years follow-up. Additionally, kidney protection (p=0.037) and CV protection (p=0.06) impacts of empagliflozin within 36 weeks were detectable using proteomic surrogates in small sample sizes (n ~ 50) compared to published outcomes studies requiring thousands of participants followed for >2 years. Conclusions: SomaSignal tests were able to predict cardiometabolic benefits of GLP-1 RA and SGLT2i drugs within a significantly shortened interval and fewer participants than in the outcome trials. Proteomics may provide a powerful tool for improving the efficacy, and cost of drug development by predicting effects of novel therapeutics in smaller, shorter studies.

Dimethyl fumarate treatment in relapsing remitting MS changes the inflammatory CSF protein profile by a prominent decrease in T-helper 1 immunity

BackgroundDimethyl fumarate (DMF) is a common treatment for multiple sclerosis (MS), but its mechanisms of action are not fully understood. Targeted proteomics offers insights into effects of DMF and biomarkers for treatment responses. ObjectivesTo assess influence of DMF on inflammation- and neuro-associated proteins in plasma and cerebrospinal fluid (CSF) in MS and to reveal biomarkers for predicting treatment responses. MethodsUsing the high-sensitivity and high-specificity method of proximity extension assay (PEA), we measured 182 inflammation- and neuro-associated proteins in paired plasma (n = 28) and CSF (n = 12) samples before and after one year of DMF treatment. Disease activity was evaluated through clinical examination and MRI. Statistical tests, network analysis, and regression models were used. ResultsSeveral proteins including T-helper 1 (Th1)-associated proteins (CXCL10, CXCL11, granzyme A, IL-12p70, lymphotoxin-alpha) were consistently decreased in CSF, while IL-7 was increased after one year of treatment. The changes in plasma protein levels did not follow the same pattern as in CSF. Logistic regression models identified potential biomarker candidates (including plexins and neurotrophins) for prediction of treatment response. ConclusionsDMF treatment induced prominent changes in CSF proteins, consistently reducing Th1-associated pro-inflammatory proteins. Neurodegeneration-related CSF proteins were able to predict treatment response. Protein biomarkers hold promise for personalized medicine.

Applicability of the cobas 6800 System for Epstein-Barr viral load quantitation using whole-blood specimens.

This study aimed to evaluate the analytical performance of the cobas 6800 System (Roche Diagnostics) and assess the feasibility of using whole-blood specimens instead of plasma. The analytical performance of the cobas EBV test (Roche Diagnostics) was evaluated. Thereafter, 120 clinical samples were collected to compare the cobas EBV test and the artus EBV RG PCR Kit (Qiagen). The results of the cobas EBV test conducted using paired plasma as well as 5× and 10× diluted whole-blood specimens were compared with those of the artus EBV RG PCR Kit performed using whole blood. The precision of the cobas EBV test was acceptable, and its linearity was confirmed to be within the range of 2.85 to 6.89 log IU/mL. Cross-reactivity was not observed. The best qualitative agreement (Cohen κ = 0.733) was observed using 5× diluted whole blood; the best quantitative correlation (Spearman correlation coefficient = 0.6865) was observed using 10× diluted whole blood. A significant discrepancy was observed in the results obtained from the 2 assays because of the different specimens used. We observed, however, that diluting whole blood before conducting the cobas EBV test effectively resolved polymerase chain reaction inhibition and viscosity issues, leading to an acceptable correlation with the results from the artus EBV RG PCR Kit conducted using whole blood.

Observed Variability in Gene Expression in Individuals with Sickle Cell Disease during Baseline Health and Acute Pain

Background: Acute pain episodes are the most common complication of sickle cell disease (SCD). There is wide variability in frequency and presentation of pain between patients despite inheritance of the same genetic defect. The underlying biology that accounts for this variability is still unknown. Prior data support cytokine profiles change in individuals with SCD during acute pain as opposed to baseline health and may contribute to SCD pain biology. We therefore hypothesized that there would be differences in gene expression profiles within a patient between baseline health and acute pain ( intraindividual variability). Further, due to the variability in pain expression between individuals with SCD, we also hypothesized that gene expression profiles would show interindividual variability between patients with SCD. Methods: Our study included a convenience sample of individuals with SCD and healthy Black controls recruited from tertiary care facilities. Paired plasma samples were collected from individuals with SCD during baseline health and acute pain. We conducted a cross-sectional analysis in 2 independent datasets (i.e., one single center, one multicenter - “The Magnesium for Children in Crisis trial”) of these paired samples. We used a novel plasma-based transcription bioassay to assess gene transcription in a peripheral blood mononuclear cell (PBMC) that served as a sensor to plasma-borne factors. Patient plasma was co-cultured with cryopreserved PBMCs from a healthy donor to induce transcription. We identified informative transcripts that differentiated individuals with SCD from healthy controls thereby defining the disease-specific plasma-induced signature and retained transcripts differentially expressed between individuals with SCD and controls that exhibit a fold change >1.4, ANOVA p-value of <0.05 and an FDR <10%. For further data reduction, we also retained the top 25% of transcripts with the highest intensity signals and retained the top 5000 genes with the highest mean absolute deviation (MAD) in both analyses. The intersection of genes identified by these two analyses (i.e., top 25% and MAD) was used as an input gene list for Weighted Gene Correlation Network Analysis (WGCNA). WGCNA was used to extract the genes that were most closely associated with pain. To this end, we retained all genes that had a correlation of ≥0.3 and p-value of <0.05 between the gene and the number of acute care visits for pain in the prior 3 years. This gene list was designated as the final SCD pain-specific list. Heatmaps of gene expression of those in the SCD pain-specific list were created using Genesis. Results: We analyzed paired samples from 149 individuals with SCD (median age 13.6, IQR 9.3-17.1) during baseline health and acute pain (27 from single center cohort, 122 from multicenter cohort). The data reduction filtering analyses identified 1177 genes of interest. Figure 1 shows both mean gene expression in the single center cohort and paired gene expression for each individual. As depicted, overall mean gene expression does not appear to differ between baseline health and acute pain. When evaluating each individual as a paired set we observe that in the majority of individuals gene expression does not change substantially between the two states of health, suggesting minimal intraindividual variability. However, a minority of individuals do exhibit more substantial changes between states of health. When considering the same state of health, wide interindividual variability among patients is observed. These findings were reproducible in a larger, multicenter cohort, as shown in Figure 2. Conclusion: Our findings suggest low intraindividual variability in most individuals with SCD, signifying fixed gene expression that may not change within an individual between baseline health and acute pain. Wide interindividual variability in gene expression was observed which might be responsible for the differences in phenotypic pain expression despite inheritance of the same hemoglobin S mutation. These data suggest pain endotypes within SCD may exist that need further investigation. If identified, these SCD pain endotypes could be leveraged for tailored analgesia or early intervention with higher risk treatments such as curative therapy. Further investigation of groups of genes that show the most variability could be investigated as potential targets for pain treatment.

Rapid serum tubes reduce transport hemolysis and false positive rates for high-sensitivity troponin T

IntroductionHemolysis in the emergency department (ED) can significantly delay results and appropriate action. We evaluated the main sources of hemolysis during sample collection, and to evaluate the use of rapid serum tubes (RST) as a transport hemolysis-mitigating measure for high-sensitivity troponin T (hs-cTnT) testing. MethodsWe examined the effect of tube type, tube fill, types of sample draw and collection methods on hemolysis and hs-cTnT in samples (n = 158) from ED patients. We also compared hs-cTnT values in paired RST and plasma separate tube (PST) samples that were hemolysis-free. ResultsThe primary source of hemolysis in samples collected in the ED was underfilling tubes. In both tube types, PST and RST, filled tubes showed a median reduction in hemolysis of 69.1 % (p < 0.0001). Blood collected in RST also experienced less hemolysis compared to PST. In hemolysis-free samples, false positive results in PST were noted in patients with hs-cTnT values < 50 ng/l. ConclusionWe suggest that proper tube filling during sample collection and use of RST tubes can significantly reduce the effects of hemolysis. In addition, laboratories should be aware that PST tubes have a non-trivial rate of false positives when hs-cTnT < 50 ng/l.

Three doses of COVID-19 mRNA vaccine induce class-switched antibody responses in inflammatory arthritis patients on immunomodulatory therapies.

Patients with inflammatory arthritis (IA) are at increased risk of severe COVID-19 due to medication-induced immunosuppression that impairs host defenses. The aim of this study was to assess antibody and B cell responses to COVID-19 mRNA vaccination in IA patients receiving immunomodulatory therapies. Adults with IA were enrolled through the Johns Hopkins Arthritis Center and compared with healthy controls (HC). Paired plasma and peripheral blood mononuclear cell (PBMC) samples were collected prior to and 30 days or 6 months following the first two doses of mRNA vaccines (D2; HC=77 and IA=31 patients), or 30 days following a third dose of mRNA vaccines (D3; HC=11 and IA=96 patients). Neutralizing antibody titers, total binding antibody titers, and B cell responses to vaccine and Omicron variants were analyzed. Anti-Spike (S) IgG and S-specific B cells developed appropriately in most IA patients following D3, with reduced responses to Omicron variants, and negligible effects of medication type or drug withholding. Neutralizing antibody responses were lower compared to healthy controls after both D2 and D3, with a small number of individuals demonstrating persistently undetectable neutralizing antibody levels. Most IA patients respond as well to mRNA COVID-19 vaccines as immunocompetent individuals by the third dose, with no evidence of improved responses following medication withholding. These data suggest that IA-associated immune impairment may not hinder immunity to COVID-19 mRNA vaccines in most individuals.

Detection of Tumor DNA in Bronchoscopic Fluids in Peripheral NSCLC: A Proof-of-Concept Study

IntroductionDNA genotyping from plasma is a useful tool for molecular characterization of NSCLC. Nevertheless, the false-negative rate justifies the development of methods with higher sensitivity, especially in difficult-to-reach peripheral lung tumors. MethodsWe aimed at comparing molecular analysis from the supernatant of guide sheath flush fluid collected during radial-EndoBronchial UltraSound (r-EBUS) bronchoscopy with plasma sampling and tumor biopsies in patients with peripheral NSCLC. The DNA was genotyped using high-throughput sequencing or the COBAS mutation test. There were 65 patients with peripheral lung tumors subjected to concomitant sampling of guide sheath flush supernatant, plasma tumor DNA, and tumor biopsy and cytology using r-EBUS. There were 33 patients (including 24 newly diagnosed with having NSCLC) with an identifiable tumor mutation in the primary lesion selected for the comparative analysis. ResultsGuide sheath flush-based genotyping yielded a mutation detection rate of 61.8% (17 of 24 mutated EGFR, one of two ERBB2, one of one KRAS, one of one MAP2K, one of four MET, and zero of one STK11), compared with 33% in plasma-based genotyping (p = 0.0151). Furthermore, in eight of 34 r-EBUS without tumor cells on microscopic examination, we were able to detect the mutation in four paired guide sheath flush supernatant, compared with only two in paired plasma. ConclusionThe detection of tumor DNA in the supernatant of guide sheath flush fluid collected during r-EBUS bronchoscopy represents a sensitive and complementary method for genotyping NSCLC.

Plasma hepatocyte growth factor as a noninvasive biomarker in small cell lung cancer

BackgroundHepatocyte growth factor (HGF) is a peptide-containing multifunctional cytokine, which is overexpressed and/or activated in multiple malignancies and is reported to be associated with tumor development and inferior survival. At present, the role of HGF in small cell lung cancer (SCLC) has not been fully explored yet.Materials and methodsThe expression of HGF and its value in predicting survival in SCLC were explored from GEO database and in pan-cancer analysis. Furthermore, we detected the expression of HGF using tumor tissue and paired plasma samples from a validation cohort of 71 SCLC patients at our institute. Correlation between tumor and plasma HGF expression and the prognostic values were analyzed.ResultsGEO database analysis revealed that tumor tissue had lower HGF expression than paired normal tissue in SCLC. At our institute, immunohistochemical staining showed negative expression of HGF in tumor tissue of SCLC at our institute (47/47, 100%). The average baseline plasma HGF was 1.28 (range,0.42–4.35) ng/ml. However, plasma HGF was higher in SCLC patients with patients with N3, M1, liver metastasis (LM) and bone metastasis (BM) disease compared with those N0 − 2 (1.25 vs. 1.75 ng/mL, P = 0.000), M0 (1.26 vs. 1.63 ng/mL, P = 0.003), non-LM (1.32 vs. 2.06 ng/mL, P = 0.009), and non-BM (1.35 vs. 1.77 ng/mL, P = 0.047), respectively. Multivariate analysis revealed plasma HGF was an independent predictor for LM and prognostic factor of OS.ConclusionOur results revealed that plasma HGF rather than tumor HGF exhibited a potential role in predicting metastasis and survival in SCLC. Plasma HGF might be used as a non-invasive detecting and monitoring tool for SCLC.

Investigations of leukocyte and inflammatory markers in pregnancies complicated by preeclampsia

ObjectivesPreeclampsia is a frequent and potentially fatal pregnancy complication. It can be challenging to make a timely diagnosis. Identifying clinically useful biochemical markers would be a remedying tool to support the diagnosis of preeclampsia. The aim was to investigate differential cell counts and acute phase reactants as diagnostic markers of preeclamptic third-trimester pregnancies and in relation to pregnancy term, gravidity and the severity of hypertension. MethodsBased on a cohort of 421 pregnant women, we included 174 participants (case n = 84, control n = 90) during the third trimester. Peripheral blood was sampled to measure differential white blood cell counts and acute phase reactants on the day of inclusion. ResultsThe neutrophil-to-lymphocyte ratio and plasma haptoglobin levels were significantly increased in healthy pregnancies compared with preeclamptic pregnancies. Plasma ferritin levels and albumin levels were respectively increased and decreased in cases of preeclampsia compared with controls. Albumin was specific among multigravida. Plasma transferrin and high-sensitivity C-reactive protein (hs-CRP) levels were significantly decreased and increased, respectively, in cases with preterm preeclampsia compared with term preeclampsia. ConclusionPlasma ferritin and albumin levels reflected higher inflammation in cases with preeclampsia compared with healthy pregnancies; the same did plasma transferrin and hs-CRP levels in preterm versus term preeclampsia. When considering the normal ranges plasma albumin and hs-CRP levels identified preeclamptic from healthy third-trimester pregnancies and preterm from term preeclampsia cases, respectively, with near-acceptable diagnostic performances. Further validation of the diagnostic value will require larger sample-sized studies with paired plasma and serum samples.

Human immunodeficiency virus 1 5'-leader mutations in plasma viruses before and after the development of reverse transcriptase inhibitor-resistance mutations.

Human immunodeficiency virus 1 (HIV-1) reverse transcriptase (RT) initiation depends on interaction between viral 5'-leader RNA, RT and host tRNA3Lys. Therefore, we sought to identify co-evolutionary changes between the 5'-leader and RT in viruses developing RT-inhibitor resistance mutations. We sequenced 5'-leader positions 37-356 of paired plasma virus samples from 29 individuals developing the nucleoside RT inhibitor (NRTI)-resistance mutation M184V, 19 developing a non-nucleoside RT inhibitor (NNRTI)-resistance mutation and 32 untreated controls. 5'-Leader variants were defined as positions where ≥20 % of next-generation sequencing (NGS) reads differed from the HXB2 sequence. Emergent mutations were defined as nucleotides undergoing a ≥4-fold change in proportion between baseline and follow-up. Mixtures were defined as positions containing ≥2 nucleotides each present in ≥20 % of NGS reads. Among 80 baseline sequences, 87 positions (27.2 %) contained a variant; 52 contained a mixture. Position 201 was the only position more likely to develop a mutation in the M184V (9/29 vs 0/32; P=0.0006) or NNRTI-resistance (4/19 vs 0/32; P=0.02; Fisher's exact test) groups than the control group. Mixtures at positions 200 and 201 occurred in 45.0 and 28.8 %, respectively, of baseline samples. Because of the high proportion of mixtures at these positions, we analysed 5'-leader mixture frequencies in two additional datasets: five publications reporting 294 dideoxyterminator clonal GenBank sequences from 42 individuals and six National Center for Biotechnology Information (NCBI) BioProjects reporting NGS datasets from 295 individuals. These analyses demonstrated position 200 and 201 mixtures at proportions similar to those in our samples and at frequencies several times higher than at all other 5'-leader positions. Although we did not convincingly document co-evolutionary changes between RT and 5'-leader sequences, we identified a novel phenomenon, wherein positions 200 and 201 immediately downstream of the HIV-1 primer binding site exhibited an extraordinarily high likelihood of containing a nucleotide mixture. Possible explanations for the high mixture rates are that these positions are particularly error-prone or provide a viral fitness advantage.

Diagnostic miRNA Signatures in Paired Tumor, Plasma, and Urine Specimens From Renal Cell Carcinoma Patients.

The incidence of patients diagnosed with renal cell carcinoma (RCC) is increasing. There are no approved biofluid biomarkers for routine diagnosis of RCC patients. This retrospective study aims to identify cell-free microRNA (cfmiR) signatures in urine samples that can be utilized as biomarkers for early diagnosis of sporadic RCC patients. Tissue, plasma, and urine samples (n = 221) from 56 sporadic RCC patients and respective normal healthy donors were profiled for 2083 microRNAs (miRs) using the next-generation sequencing-based HTG EdgeSeq miR Whole Transcriptome Assay. DESeq2 (FC |1.2|, false discovery rate <0.05) was performed to identify differentially expressed miRs. Data from RCC tissue samples of The Cancer Genome Atlas database were used for miR validation. We found a 10-miR signature that distinguished RCC tissues from remote normal kidney tissue or benign kidney lesion samples. Additionally, we identified subtype-specific miRs (miR-122-5p, miR-210-3p, and miR-21-3p) and miRs specific for all RCC subtypes (miR-106b-3p, miR-629-5p, and miR-885-5p). We observed that miR-155-5p was associated with tumor size. Using The Cancer Genome Atlas data sets, we validated the miRs found in RCC tissue samples. In plasma or urine analysis, we found cfmiRs that were consistently and significantly upregulated in RCC tissue samples. A 15-cfmiR signature was proposed in urine samples of RCC patients, of which miR-1275 was consistently upregulated in tissue, plasma, and urine samples. This integrative study found diagnostic miRs/cfmiRs for RCC patients, which were validated using The Cancer Genome Atlas data sets. Distinctive cfmiR signatures found in urine may have clinical utility for the diagnosis of RCC.

Annihilation-gamma-based diagnostic techniques for magnetically confined electron–positron pair plasma

Efforts are underway to magnetically confine electron–positron pair plasmas to study their unique behaviour, which is characterized by significant changes in plasma time and length scales, supported waves and unstable modes. However, use of conventional plasma diagnostics presents challenges with these low-density and annihilating matter–antimatter plasmas. To address this problem, we propose to develop techniques based on the distinct emission provided by annihilation. This emission exhibits two spatial correlations: the distance attenuation of isotropic sources and the back-to-back propagation of momentum-preserving 2 $\gamma$ annihilation. We present the results of our analysis of the $\gamma$ emission rate and the spatial profile of the annihilation in a magnetized pair plasma from direct pair collisions, from the formation and decay of positronium as well as from transport processes. In order to demonstrate the effectiveness of annihilation-based techniques, we tested them on annular $\gamma$ emission profiles produced by a $\beta ^+$ radioisotope on a rotating turntable. Direct and positronium-mediated annihilation result in overlapping volumetric $\gamma$ sources, and the 2 $\gamma$ emission from these volumetric sources can be tomographically reconstructed from coincident counts in multiple detectors. Transport processes result in localized annihilation where field lines intersect walls, limiters or internal magnets. These localized sources can be identified by the fractional $\gamma$ counts on spatially distributed detectors.

Non-Small Cell Lung Cancer: Targetable Variants in Concurrent Tissue and Liquid Biopsy Testing in a North Indian Cohort.

Testing for EGFR, ALK, ROS1 and MET alterations in paired tissue and plasma samples of treatment-naïve patients of NSCLC and correlating their status with overall survival. One hundred treatment-naïve patients were recruited after obtaining informed consent. Ten ml of blood was collected within a period of two weeks from histological diagnosis, prior to the start of any treatment. DNA & RNA extraction was done from formalin-fixed paraffin embedded (FFPE) tissue and total cell-free nucleic acid extraction was done from plasma samples. EGFR mutation, ALK, ROS1 and MET rearrangements were tested by ARMS (Amplification Refractory Mutation System) PCR. All statistical analyses were conducted in R version 4.1.1. A total of 61 cases showed molecular alterations in tissue samples which included EGFR mutations (47), ALK rearrangements (12), ROS1 fusion (2). MET alteration was not detected. Forty-three cases showed EGFR mutations in plasma, 26 of which were concurrently positive in tissue. Concordance observed was 62%. ALK-EML4 rearrangement, ROS1 fusion and MET were not detected in plasma samples. Sensitivity and specificity for detection of EGFR mutation in plasma were 55.3% and 67.9% respectively. Univariate Cox regression analysis showed a positive association between EGFR mutation in tissue and overall survival (HR = 0.4; 95% CI: 0.2-0.7; p = 0.003) and improved overall survival in those who received targeted therapy (HR = 0.29; 95% CI: 0.1-0.8; p = 0.02). Concurrent testing in tissue and liquid biopsy in NSCLC increased the detection of EGFR mutations (47% to 64%). This has substantial implications in deciding treatment and administration targeted therapy and the consequent overall survival.

Relaxation of relativistic pair plasma in a massive photon field

The relaxation of relativistic hot electron–positron plasma is investigated by incorporating the effect of non-zero photon mass, and a quadruple Beltrami (QB) relaxed state for the magnetic vector potential is derived. The QB state is a linear superposition of four single force-free fields and is characterized by four self-organized structures of different length scales. The analysis of QB states shows that for certain values of generalized helicities at lower relativistic temperatures, plasma shows diamagnetic behaviour. It is also noteworthy that the inclusion of non-zero photon mass naturally provides the possibility of multiscale structure formation in the relaxed state. In this scenario, one of the field structures is significantly larger than the Compton wavelength of photons, while the other three structures are on the scale of the electron skin depth. The potential implications of this QB state for astrophysical environments are also discussed.

Preexisting immunity restricts mucosal antibody recognition of SARS-CoV-2 and Fc profiles during breakthrough infections.

Understanding mucosal antibody responses from SARS-CoV-2 infection and/or vaccination is crucial to develop strategies for longer term immunity, especially against emerging viral variants. We profiled serial paired mucosal and plasma antibodies from COVID-19 vaccinated only vaccinees (vaccinated, uninfected), COVID-19-recovered vaccinees (recovered, vaccinated), and individuals with breakthrough Delta or Omicron BA.2 infections (vaccinated, infected). Saliva from COVID-19-recovered vaccinees displayed improved antibody-neutralizing activity, Fcγ receptor (FcγR) engagement, and IgA levels compared with COVID-19-uninfected vaccinees. Furthermore, repeated mRNA vaccination boosted SARS-CoV-2-specific IgG2 and IgG4 responses in both mucosa biofluids (saliva and tears) and plasma; however, these rises only negatively correlated with FcγR engagement in plasma. IgG and FcγR engagement, but not IgA, responses to breakthrough COVID-19 variants were dampened and narrowed by increased preexisting vaccine-induced immunity against the ancestral strain. Salivary antibodies delayed initiation following breakthrough COVID-19 infection, especially Omicron BA.2, but rose rapidly thereafter. Importantly, salivary antibody FcγR engagements were enhanced following breakthrough infections. Our data highlight how preexisting immunity shapes mucosal SARS-CoV-2-specific antibody responses and has implications for long-term protection from COVID-19.

Plasma microRNAs as potential biomarkers in diagnosis of acute venous thromboembolism.

To assess the potential use of plasma microRNAs (miRNAs) in diagnosis of acute venous thromboembolism (VTE). Using BGISEQ-500 sequencing technology, we analyzed the miRNA profile of paired plasma samples from the acute and chronic phases of four patients with unprovoked VTE. Using real-time quantitative polymerase chain reaction (RT-qPCR), we verified nine upregulated named miRNAs in the acute phase in the plasma samples of 54 patients with acute VTE and 39 controls. We then compared the relative expression of the 9 candidate miRNAs between the acute VTE and control group, and plotted the receiver operating characteristic (ROC) curves of the differentially expressed miRNAs. We chose the miRNA with the greatest area under curve (AUC) to evaluate the effect of miRNA on coagulation and platelet function in the plasma samples of 5 healthy volunteers. The plasma levels of miR-374b-3p, miR-660-5p, miR-378a-3p, miR-425-5p, miR-3613-5p, miR-130b-3p, miR-183-5p, and miR-103b were higher in patients with acute VTE than in the controls, with AUCs of 0.6776, 0.6614, 0.6648, 0.6885, 0.8048, 0.6871, 0.7298, and 0.7498, respectively, and P values of 0.0036, 0.0081, 0.0069, 0.0020,<0.0001, 0.0022, 0.0002, and < 0.0001, respectively. There were no significant differences in miR-193b-5p level between the acute VTE group and the control group. Fibrinogen (Fib), thrombin- antithrombin complex (TAT), tissue plasminogen activator-inhibitor complex (t-PAIC), and TAT/plasmin-α2-plasmin inhibitor complex (PIC) were decreased in the miR-3613-5p group when compared with the control group (P < 0.05). miRNAs can be potential biomarkers for diagnosing acute VTE, and miR-3613-5p may be involved in the formation, coagulation, and platelet functions in acute VTE.

Therapeutic plasma exchange decreases plasma anti-SARS-CoV-2 spike IgG without increasing the proximate incidence of COVID-19.

Therapeutic plasma exchange (TPE) removes both pathologic and protective immunoglobulins (Ig). SARS-CoV-2 immunity is partially mediated by anti-SARS-CoV-2 spike antibodies (SAb), which impair viral host-cell invasion. Nonetheless, the systematic effect of TPE on SAb concentration and SARS-CoV-2 immunity is unknown. Paired plasma waste specimens from the first (first-TPE) and last (last-TPE) TPE treatment were collected from 9 patients between July 21, 2021 and March 1, 2022. The effects of TPE on Ig levels were assessed by quantitatively comparing the SAb, total IgG, and total IgM levels first-/last-TPE treatment. Complementary qualitative assessment for these changes was achieved via protein electrophoresis (PEP) and immunofixation (IFE). A retrospective review was performed to investigate the incidence of new SARS-CoV-2 infections following TPE v. other treatment at the same outpatient apheresis/infusion center during the same time frame. Median SAb levels between the first- and last-TPE waste specimens decreased significantly from 424.6 AU/mL to 17.0 AU/mL (P = 0.004). Concordantly, PEP and IFE analysis demonstrated broad Ig decreases. Cumulative incidence of subsequent COVID-19 diagnosis at 30, 90, and 180 days post-procedure did not differ between the TPE v. other treatment groups (n = 709 total patients). TPE significantly reduced SAb levels, a marker of SARS-CoV-2 immunity, but did not appear to provoke increased incidence of COVID-19 infections. Further investigation of the kinetics of TPE-mediated SAb decrease and post-TPE recovery are warranted.