Diagnostic Panel Research Articles

Immunohistochemical expression of transcription factors PAX5, OCT2, BCL6 and transcription regulator P53 in Non-Hodgkin lymphomas: A diagnostic cross-sectional study

BackgroundNon-Hodgkin lymphoma represents a heterogeneous group of tumors that constitute the seventh most common malignancy. Immunohistochemistry plays a major role in the detection of specific cell receptors. Transcription factors are a heterogeneous group of genes that play a critical role in the commitment, differentiation, and proliferation of specific cell types. MethodsParaffin-embedded tissue sections of non-Hodgkin lymphoma cases were selected, classified, and evaluated before staining with immunohistochemical markers (PAX5, OCT2, BCL6, and P53). Expression of the aforementioned markers was compared with histological subtypes and grades of lymphoma cases. Means of expression were also compared among histological subtypes. ResultsA total of 55 cases of NHL including 26 cases of low-grade lymphomas and 29 cases of high-grade lymphomas were included in the study. DLBCL and FL were the most common subtypes of high-grade and low-grade lymphomas respectively. Both PAX5 and OCT2 were positive in 44 cases of NHL (80%) including all cases of B-cell lymphomas. BCL6 and P53 demonstrated positive expression in 29.1% and 67.3% respectively. Interestingly, we found a significant association between the histological subtypes and the aforementioned markers (P-value<0.05). DiscussionExpression of PAX5, OCT2, BCL, and P53 played a major role in the diagnosis and grading of non-Hodgkin lymphomas in our study. Both PAX5 and OCT2 provided more accuracy and specificity in the diagnosis of B-cell neoplasms compared to the classical B-cell markers. BCL6 expression reflected its role in germinal center formation in normal and malignant lymphoid tissues, and expression of P53 mirrored the accumulation of gene mutations in more aggressive lymphoma subtypes. ConclusionIn this manuscript, we aimed to present a unique study that highlights the immunohistochemical expression of all the aforementioned factors among various histological subtypes of non-Hodgkin lymphomas with disparities in histological aggressiveness, highlighting a promising diagnostic and prognostic panel for non-Hodgkin lymphomas.

Assessment of the Safety and Efficacy of an Oral Probiotic-Based Vaccine Against Aspergillus Infection in Captive-Bred Humboldt Penguins (Spheniscus humboldti).

Aspergillosis is a fungal infection caused mainly by Aspergillus fumigatus that often results in respiratory disease in birds. Aspergillosis is a major cause of morbidity and mortality in captive-bred penguin species. Currently, there is no registered vaccine to prevent aspergillosis. Recent research demonstrated that oral administration of gram-negative bacteria expressing high levels of galactose-α-1,3-galactose (α-Gal) modulates anti-α-Gal immunity and protects turkeys from clinical aspergillosis caused by experimental A. fumigatus infection. The role of anti-α-Gal immunity in penguins has not been studied. Here, we tested the distribution of α-1,3-galactosyltransferase (α1,3GT) genes in the fecal microbiome of Humboldt penguins (Spheniscus humboldti). The occurrence of natural anti-α-Gal antibodies (Abs) in sera and eggs of healthy Humboldt penguins was also assessed. A trial was then conducted to test whether oral administration of Escherichia coli Nissle, expressing high α-Gal levels, modulates anti-α-Gal immunity in a colony of Humboldt penguins. Animals in the vaccination and placebo groups were evaluated before the trial and followed for one year for aspergillosis detection using a diagnostic panel including computed tomography scans, capillary zone electrophoresis, 3-hydroxybutyrate levels, and anti-A. fumigatus Abs. Anti-α-Gal Abs were detected in sera (IgM and IgY) and eggs (IgY) of healthy penguins. Microbiota analysis and functional predictions revealed the presence of α1,3GT genes in the microbiota of Humboldt penguins and other penguin species. A strong decrease in anti-α-Gal IgM levels was observed in all animals in the placebo group three months after vaccination protocol. This decrease was not observed in E. coli Nissle-treated penguins. After the vaccination protocol, we found a positive correlation between anti-E. coli IgY and anti-α-Gal IgY in the E. coli Nissle group, suggesting a correlation between the presence of the bacteria and these Abs. During the study period, three penguins exhibited respiratory signs consistent with aspergillosis. Two were from the placebo group whose symptoms resolved with specific treatments, while a single vaccinated individual developed fatal respiratory aspergillosis eight months after the trial. We conclude that E. coli Nissle represents a safe potential probiotic with a protective effect against aspergillosis in Humboldt penguins that deserves to be further explored for therapeutic uses in these animals.

Analysis of possible markers of effective antitumor cellular immune response before starting therapy with immune check-point inhibitors

The aim of the study. to analyse possible markers of an effective antitumor cellular immune response.Material and methods. using the keywords «checkpoint inhibitors, immunotherapy, t-lymphocytes, exhausted t-lymphocytes, anti-tumor immune response», review and original articles (n=34) published from 2005 to 2020 in the Pubmed, Web Of Science, Elsevier databases were selected.Results. the study revealed possible markers reflecting a high activity of an adaptive immune response based on effective recognition of tumor antigens through MHC molecules, a sufficient number of T-lymphocytes and a predominance of T-cytotoxic cells, as well as a low level of expression of inhibitory receptors and small molecules. the presence of single nucleotide polymorphisms in the HLA-I and HLA-II genes encoding MHC-I and MHC-II proteins, respectively, a high level of lymphocytes, among which the most important is the predominance of CD8+ t cells and a low level of T-regulatory cells (T-reg), as well as the presence of single nucleotide polymorphisms in the genes encoding FcγR receptors of T-lymphocytes showed their predictive significance. the diagnostic significance of determining the expression of inhibitory receptors for T-lymphocytes (TIM3, LAG3, TIGIT), especially in combination with the determination of PD-1 expression, was also revealed.Conclusion. the results obtained may be relevant for applying new methods for the assessment of the functional activity of the T-cell immune response before starting therapy with checkpoint inhibitors, as well as for the development of new diagnostic panels, which may be of interest to employees of clinical diagnostic laboratories and research centers.

MO275: A Biomarker of Acute Kidney Injury from Proven Renal Origin

Abstract BACKGROUND AND AIMS Acute kidney injury (AKI) is a threatening, multi-aetiological syndrome encompassing a variety of forms and damage patterns. AKI lacks sufficiently specific diagnostic tools to evaluate the distinct combination of pathophysiological events underlying each case, which limits personalized and optimized handling. Therefore, a pathophysiological diagnosis based on new urinary biomarkers is sought for practical (readiness and non-invasiveness) and conceptual reasons, as the urine is a direct product of the kidneys. However, biomarkers found in the urine may also have extra-renal origin, thus conveying pathophysiological information from other organs or tissues. In fact, very few biomarkers of AKI have been proven to have a renal origin. Urinary plasminogen activator inhibitor 1 (PAI-1) has been associated to AKI in experimental models, although its origin and traffic to the urine are not known. The aim of this study was to investigate whether the urinary PAI-1 found in the urine following AKI is shed directly by renal structures or has a blood-borne origin. A further objective was to study whether urinary PAI-1 also associates to human AKI. METHOD AKI was induced in male Wistar rats by a single dose of cisplatin or by ischemia-reperfusion to study the blood or renal origin of urinary PAI-1. Blood and urine samples were collected on day 0 (basal) and on the day of maximal damage. The kidneys were collected at sacrifice (i.e. the day of maximal damage). The origin of urinary PAI-1 was studied with the in situ renal perfusion method. At maximal damage time, the right kidney was ligated, and the left kidney was perfused with Krebs-dextran solution. Urine was collected during perfusion. If PAI-1 was secreted by tubule cells directly to the urine, it should be detected in the urine during perfusion. If PAI-1 had a blood borne origin, PAI-1 should disappear from the urine during perfusion. The level of PAI-1 was also analyzed in the urine of AKI patients. RESULTS Our results show that urinary PAI-1 levels increase after AKI and correlate with an increased expression in kidney tissue. During in situ renal perfusion with Krebs–dextran solution, PAI-1 remained in the urine of AKI rats, suggesting that renal cells shed this protein directly to the urine. PAI-1 is also significantly increased in the urine of AKI patients. Its low correlation with other urinary markers such as neutrophil gelatinase-associated lipocalin or NAG suggests that PAI-1 provides complementary and distinct pathophysiological information. CONCLUSION Urinary PAI-1 is produced by the kidneys after AKI and secreted directly to the urine providing specific pathological information, which needs to be explored further. Urinary PAI-1 is one of the few biomarkers of AKI with proven renal origin and therefore a potentially valuable tool for a prospective pathophysiological diagnostic panel.

Diagnosis of Congenital Toxoplasmosis: No Benefit of IgA Antibody Detection by Platelia ELISA in a Tricentric Evaluation.

The diagnostic accuracy of a commercial Toxoplasma gondii IgA antibody enzyme-linked immunosorbent assay (ELISA) was evaluated in the context of routine practice on 289 newborns with congenital toxoplasmosis (CT) and 220 healthy controls. The performance of this assay was compared to that of the current gold-standard test for anti-Toxoplasma IgM detection, an immunosorbent agglutination assay (ISAGA). IgM and IgA sensitivity and specificity were assessed in cord and postnatal samples. The sensitivity of IgA detection by ELISA on all serum and peripheral blood samples was 60.56% and 56.52%, respectively, which is low compared with the sensitivity of IgM detection by ISAGA (73.26% on serum samples, 82.35% on peripheral blood). Adding the T. gondii IgA antibody ELISA to the diagnostic panel did not significantly increase the overall performance of the serological diagnosis based on IgM detection.

Омиксные технологии в диагностике Mycobacterium tuberculosis

Tuberculosis, caused by Mycobacterium tuberculosis, remains a global burden on our country and entire world. According to the World Health Organization, 10 million incident cases of tuberculosis were registered in 2019. A steady increase in the drug-resistant tuberculosis aggravates the situation and appears to be the major obstacle to the fight against the disease. A thorough understanding of the pathogen physiology and virulence properties is extremely important for the development of new diagnosis methods and treatment strategies. Multiomics approaches to studying the infectious agents are indispensable in understanding the nature of the disease. Despite the availability of sufficient genomic and transcriptomic data, pathogenic potential, survival rate, persistence, immunomodulation, mechanisms underlying drug resistance and host–pathogen interaction remain poorly understood. The use of proteomic approaches has been more informative, and provides more information about the true state of the cell in various conditions. Proteomic and bioinformatic approaches helped considerably in identification and characterization of target proteins that could be used for the development of new therapeutic options. Nevertheless, OMICs data integration with simultaneous use of the system approach to studying various clinically significant mycobacterial strains makes it possible to increase knowledge about the disease mechanisms and infection control methods. The review outlines various OMICs technologies and their role in the development of the M. tuberculosis diagnostic panels.

Study on plasma amino acids and piperonamide as potential diagnostic biomarkers of non-small cell lung cancer.

BackgroundThe value of plasma threonine, cysteine, and piperonamide as diagnostic biomarkers for non-small cell lung cancer (NSCLC) has been rarely explored. The lack of a validation set containing confounders is common to most previous metabolomics studies. The purpose of this study was to explore and validate the value of plasma amino acids and piperonamide as diagnostic biomarkers for NSCLC using liquid chromatography-tandem mass spectrometry (LC-MS/MS).MethodsA total of 250 participants were included in this study, including 167 patients with pathologically confirmed NSCLC and 83 healthy controls (HCs). These participants were divided into training set, validation set 1, and validation set 2 in chronological order and in a certain proportion. The plasma levels of 22 amino acids and 1 piperonamide in these pre-treatment NSCLC patients and HCs were measured by LC-MS/MS. Metabolic biomarkers were identified after multivariate analysis, univariate analysis, receiver operating characteristic (ROC) analysis. Furthermore, these biomarkers and transcriptomic data were subjected to joint pathway analysis.ResultsThe area under the ROC curve (AUC) values for threonine, piperonamide, arginine, alanine, cysteine, methionine, and histidine in the integrated data set were 0.911, 0.848, 0.909, 0.869, 0.786, 0.597 and 0.637, respectively. This panel composed of these 7 metabolites showed good diagnostic capability for NSCLC (the AUC of this diagnostic panel in each data set was greater than 0.9). The specificity of this diagnostic panel in validation set 2, which included confounders, was 0.970, similar to that of the other datasets. The presence of confounding factors had little effect on the diagnostic accuracy of this panel. The ROC analysis of this diagnostic panel between all stage I NSCLC patients and HCs showed AUC, sensitivity, and specificity of 1.000, 1.000, and 0.988, respectively. Moreover, PSAT1, SHMT2, AOC3, and MAOB were found to be involved in the metabolism of threonine and cysteine.ConclusionsPlasma amino acids and piperonamide have potential as diagnostic biomarkers in NSCLC. This metabolic biomarker panel appears useful for the diagnosis and screening of NSCLC. In addition, metabolomic and transcriptomic integration pathway analysis may help elucidate the mechanism of NSCLC occurrence and development and even reveal new treatment vulnerabilities.

Изменение аминокислотного профиля в системе «мать–плод» при COVID-19

Systemic nature of the human body response to SARS-CoV-2 requires dedicated analysis at the molecular level. COVID-19 during pregnancy affects maternal health and may entail complications in the early neonatal period and possibly long-term consequences for the offspring. The aim of the study was to assess the impact of COVID-19 on amino acid profiles in maternal venous blood, amniotic fluid and umbilical cord blood in order to develop a diagnostic panel accounting for possible consequences. The main group included 29 pregnant patients with a confirmed diagnosis of COVID-19 and the control group included 17 somatically healthy pregnant women. Amino acid profiles of the biological fluids were measured by high-performance liquid chromatography combined to mass spectrometry (HPLC-MS) and assessed in logistic regression models. The analysis revealed altered content of certain amino acids, their biosynthetic precursors and metabolites in the biological fluids collected from patients with COVID-19 possibly reflecting the development of systemic inflammatory reaction and associated changes in gene expression profiles. These findings may guide further research into health outcomes for neonates born from mothers infected with SARS-CoV-2 during pregnancy. The study may help to develop advanced recommendations and differential care protocols for pregnant women and newborns diagnosed with COVID-19.

Posttreatment Gene Scores Support Histologic and Endoscopic Response Thresholds in Eosinophilic Esophagitis.

The correlation between clinical and molecular treatment response thresholds in eosinophilic esophagitis (EoE) is not well understood. We evaluated posttreatment EoE diagnostic panel gene expression profiles across histologic and endoscopic thresholds (EREFS) in a prospective adult EoE cohort. We observed a strong inverse correlation between posttreatment gene score and eosinophil count (R = -0.66; P &lt; 0.001); biopsies with &lt;15 eos/hpf had higher gene scores (≥425) vs those with ≥15 eos/hpf. Findings for EREFS were similar; EREFS ≤2 was associated with EoE diagnostic panel scores ≥395. Molecular signatures support the use of posttreatment response thresholds &lt;15 eos/hpf and EREFS ≤2 in clinical practice and trials.

The predictive potential of different molecular markers linked to amikacin susceptibility phenotypes in Pseudomonas aeruginosa.

Informed antibiotic prescription offers a practical solution to antibiotic resistance problem. With the increasing affordability of different sequencing technologies, molecular-based resistance prediction would direct proper antibiotic selection and preserve available agents. Amikacin is a broad-spectrum aminoglycoside exhibiting higher clinical efficacy and less resistance rates in Ps. aeruginosa due to its structural nature and its ability to achieve higher serum concentrations at lower therapeutic doses. This study examines the predictive potential of molecular markers underlying amikacin susceptibility phenotypes in order to provide improved diagnostic panels. Using a predictive model, genes and variants underlying amikacin resistance have been statistically and functionally explored in a large comprehensive and diverse set of Ps. aeruginosa completely sequenced genomes. Different genes and variants have been examined for their predictive potential and functional correlation to amikacin susceptibility phenotypes. Three predictive sets of molecular markers have been identified and can be used in a complementary manner, offering promising molecular diagnostics. armR, nalC, nalD, mexR, mexZ, ampR, rmtD, nalDSer32Asn, fusA1Y552C, fusA1D588G, arnAA170T, and arnDG206C have been identified as the best amikacin resistance predictors in Ps. aeruginosa while faoAT385A, nuoGA890T, nuoGA574T, lptAT55A, lptAR62S, pstBR87C, gidBE126G, gidBQ28K, amgSE108Q, and rplYQ41L have been identified as the best amikacin susceptibility predictors. Combining different measures of predictive performance together with further functional analysis can help design new and more informative molecular diagnostic panels. This would greatly inform and direct point of care diagnosis and prescription, which would consequently preserve amikacin functionality and usefulness.

What is the Clinical Impact of a Multiplex Gastrointestinal Panel in Children?

Because pediatric gastroenteritis is often self-limited, guidelines do not routinely recommend routine stool testing, although early identification of organisms may lead to expeditious treatment and optimal infection control. Nucleic acid amplification multiplex diagnostic panels are highly sensitive and rapid, detecting the nucleic acid of bacteria, parasites, and viruses simultaneously. The objective of this study was to compare the results of stool testing in children pre- and post-introduction of a molecular multiplex gastrointestinal panel (GIP). This is a multicenter cross-sectional cohort study of inpatient and outpatient children who had stool testing performed in the Children’s Hospital Colorado microbiology laboratory between 2013 and 2017. The 2 years before the introduction of the GIP in November 2015 functioned as historical controls. Testing options in each era are described below: In total, 8720 patient encounters with 12 222 stool tests were assessed. Patients hospitalized with community-acquired diarrhea were used to evaluate primary...

Lipid Alterations in Early-Stage High-Grade Serous Ovarian Cancer.

Epithelial ovarian cancer (OC) ranks first in the number of deaths among diseases of the female reproductive organs. Identification of OC at early stages is highly beneficial for the treatment but is highly challenging due to the asymptomatic or low-symptom disease development. In this study, lipid extracts of venous blood samples from 41 female volunteers, including 28 therapy-naive patients with histologically verified high-grade serous ovarian cancer at different stages (5 patients with I-II stages; 23 patients with III-IV stages) and 13 apparently healthy women of reproductive age, were profiled by high-performance liquid chromatography mass spectrometry (HPLC-MS). Based on MS signals of 128 differential lipid species with statistically significant level variation between the OC patients and control group, an OPLS-DA model was developed for the recognition of OC with 100% sensitivity and specificity R 2 = 0.87 and Q2 = 0.80. The second OPLS-DA model was developed for the differentiation between I-II OC stages and control group with R 2 = 0.97 and Q2 = 0.86 based on the signal levels of 108 differential lipid species. The third OPLS-DA model was developed for the differentiation between I-II OC stages and III-IV stages based on the signal levels of 99 differential lipid species. Various lipid classes (diglycerides, triglycerides, phosphatidylchlorines, ethanolamines, sphingomyelins, ceramides, phosphatidylcholines and phosphoinositols) in blood plasma samples display distinctly characteristic profiles in I-II OC, which indicates the possibility of their use as marker oncolipids in diagnostic molecular panels of early OC stages. Our results suggest that lipid profiling by HPLC-MS can improve identification of early-stage OC and thus increase the efficiency of treatment.

Identification of potential plasma markers for hepatitis B virus-related chronic hepatitis and liver fibrosis/cirrhosis.

The aim of this study was to identify potential plasma biomarkers for hepatitis B virus (HBV)-related liver diseases. High-throughput transcriptome sequencing analysis was performed on five patients with chronic hepatitis B (CHB), five patients with HBV-associated liver fibrosis/liver cirrhosis (LF/LC), and four healthy participants. By short time-series expression miner and functional analysis, aquaporin 1 (AQP1), dystroglycan 1 (DAG1), and hemoglobin subunit beta (HBB) were identified as potential biomarkers. Immunohistochemical analysis revealed that the expression levels of AQP1, DAG1, and HBB were upregulated in the three groups. Subsequent enzyme-linked immunosorbent assay tests on the training cohort (n = 150) indicated that the plasma levels of AQP1 and DAG1 were highest in LF/LC patients, followed by those in CHB patients, and the lowest in healthy controls. APAD model, a diagnostic panel incorporating age, platelet, AQP1, and DAG1 levels, exhibited the strongest stratification ability to distinguish LF/LC patients from CHB patients, and to differentiate CHB patients from healthy controls. Furthermore, the diagnostic accuracies of the biomarkers and APAD model were verified in an independent cohort consisting of 230 participants. In conclusion, both AQP1 and DAG1 have good diagnostic values and APAD model greatly enhances the diagnostic accuracy for HBV-related hepatic diseases.

PanelDesign: Integrating Epidemiological Information into the Design of Diagnostic NGS Gene Panels

We report upon PanelDesign, a framework to support the design of diagnostic next generation DNA sequencing panels with epidemiological information. Two publicly available resources, namely Genomics England PanelApp and Orphadata, were combined into a single data set to allow genes in a given NGS panel to be ranked according to the frequency of the associated diseases, thereby highlighting potential core genes as defined by the Eurogenetest/ESHG guidelines for diagnostic next generation DNA sequencing. In addition, PanelDesign can be used to evaluate the contribution of different genes to a given disease following ACMG (American College of Medical Genetics) technical standards.

Shotgun lipidomics combined targeted MRM reveals sphingolipid signatures of coronary artery disease

Sphingolipids (SPLs) are bioactive lipids that manifest structural diversity and complexity in eukaryotes. However, the distributions and functions of these molecules in mammalian tissues/cells have not been systematically investigated. Herein, we integrated shotgun lipidomics with targeted LC-MRM/MS approach to comprehensively analyze SPL species in various biological samples with high accuracy. Preliminarily, 1311 SPL molecules were identified in 18 kinds of mammalian samples, including 3 groups of human sera, 10 mouse tissues and 5 cell lines via 26 sphingoid long-chain bases scanning. The sphingolipidome compositions and distributions were systematically characterized and distinct qualitative and quantitative profiles were clearly exhibited in various samples, indicating unique biological functions of the sphingolipidomes. Next, targeted SPLs analysis by LC-MRM/MS with critical criteria monitoring two characteristic fragments of one precursor was applied to human serum samples from 24 coronary artery disease (CAD) patients and 12 healthy controls, which successfully quantified 170 SPL molecules. Ten novel SPL molecules were discovered as a potential diagnostic panel for CAD patients via multivariate exploratory receiver operating characteristic curve-based biomarker analysis. The diagnostic panel with the 10 SPL molecules achieved 97.2% accuracy, with a favorable auxiliary diagnostic value (AUC = 1.000), for the detection of CAD. These results clearly support the sphingolipidomic approach in application to discovering disease biomarker panel as well as deep investigation of biological functions of complex SPLs in mammalian samples.

Analysis of microsatellite aberrations and loss of heterozygosity in follicular lymphoma, diffuse large B-cell lymphoma, and high-grade B-cell lymphoma patients

Background . The study of genetic predictors of non-Hodgkin’s lymphomas prognosis is one of the most relevant areas of oncohematology. It is extremely interesting to search for integral markers that reflect the most important stages of tumor pathogenesis. DNA repair system plays one of the key roles in genomic instability. Aberrations of microsatellite repeats such as microsatellite instability (MSI), in particular elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) is characteristic for mismatch repair system and loss of heterozygosity (LOH) is an integral feature of genomic instability. Objective . Analysis of MSI, EMAST, LOH significance in follicular lymphoma (FL), diffuse large B-cell lymphoma (DLBCL), and high-grade B-cell lymphoma (HGBL) patients. Materials and methods . The study was performed by multiplex PCR and fragment analysis with diagnostic panels COrDIS Plus and COrDIS MSI in 85 FL patients, 32 DLBCL patients, and 37 HGBL patients. Results . The frequency of LOH in the general FL group was 40/81 (49.4 %), MSI – 10/82 (12.2 %), EMAST – 15/81 (18.5 %). The frequency of LOH in the HGBL group was 21/31 (67.8 %), MSI – 11/37 (29.7 %), EMAST – 13/31 (41.9 %). The frequency of LOH in the DLBCL group was 18/29 (62.0 %), MSI – 5/32 (15.6 %), EMAST – 14/32 (43.8 %). When considering the morphological types of FL, it was noted that a higher frequency of genetic aberrations was characteristic of lymphomas with a more aggressive morphology (p &lt;0.05). LOH identifies FL and HGBL patients with an unfavorable prognosis. The EMAST analysis allows identifying additional patients in the LOH+ cohort with early events and low EFS. Conclusion . LOH and EMAST have a prognostic value for FL and HGBL. No associations of LOH and EMAST with the survival were observed in DLBCL. Changes in mononucleotide repeats in FL, DLBCL and HGBL did not correspond to the MSI-H characteristic of solid tumors. For this reason, the clinical consequences of MSI-H in solid neoplasms, in particular the efficacy of immune checkpoint inhibitors, in lymphomas cannot be expected to be replicated solely on the basis of microsatellite aberrations detection.

Surrogate markers in non-alcoholic steatohepatitis.

Hepatic steatosis with inflammation, inflated hepatocytes, and potential fibrosis defines non-alcoholic steatohepatitis (NASH), which can possibly lead to liver cirrhosis. Although liver biopsy is still the gold standard for diagnosing NASH, numerous non-invasive surrogate markers have been investigated to reduce the need for this invasive technique. In this review we present several currently assessed biomarkers, scores, and indexes in assessing NASH. A search in the main medical literature databases was conducted. We searched for observational studies evaluating non-invasive markers, scores, and panels in predicting NASH. Several proinflammatory markers, inflammation and apoptosis biomarkers, as well as complex models have been studied in predicting NASH. Proinflammatory markers include C-reactive protein, ferritin, tumor necrosis factor-α, interleukin-6, pentraxin-3, and neutrophil extracellular traps. Inflammation and apoptosis biomarkers include cytokineratin-18, adipocytokines, lipid oxidation panels, plasminogen activator inhibitor-1, and products of free radical-mediated oxidation of linoleic acid. Moreover, several studied complex models such as NashTest, NashTest-2, pairing CK18 fragments with other biomarkers such as ALT and the presence of MetS, the HAIR model, acNASH, NAFIC score, Visceral Adiposity Index have also been studied. A variety of diagnostic panels have shown good predictive values for diagnosing NASH. Nevertheless, non-invasive surrogate markers are currently unable to replace liver biopsy. However, their clinical significance is mainly in triaging patients for liver biopsy, reducing the financial burden associated with the procedure.

LC-MS biomarker diagnostics for neuroinflammatory disorders.

In a pilot study published in eBioMedicine, Bandodkar and colleagues aimed to develop and validate a diagnostic panel of inflammatory biomarkers for neuroinflammatory diseases by use of LC-MS/MS.1 The adopted methodology is meticulously substantiated and the CSF-based panel of nine tryptophan-kynurenine and four nitric oxide pathway metabolites performs well in terms of sensitivity and accuracy to discriminate patients with acute encephalitis from healthy individuals.

Profiling PI3K-AKT-MTOR variants in focal brain malformations reveals new insights for diagnostic care.

Focal malformations of cortical development including focal cortical dysplasia, hemimegalencephaly and megalencephaly, are a spectrum of neurodevelopmental disorders associated with brain overgrowth, cellular and architectural dysplasia, intractable epilepsy, autism and intellectual disability. Importantly, focal cortical dysplasia is the most common cause of focal intractable paediatric epilepsy. Gain and loss of function variants in the PI3K-AKT-MTOR pathway have been identified in this spectrum, with variable levels of mosaicism and tissue distribution. In this study, we performed deep molecular profiling of common PI3K-AKT-MTOR pathway variants in surgically resected tissues using droplet digital polymerase chain reaction (ddPCR), combined with analysis of key phenotype data. A total of 159 samples, including 124 brain tissue samples, were collected from 58 children with focal malformations of cortical development. We designed an ultra-sensitive and highly targeted molecular diagnostic panel using ddPCR for six mutational hotspots in three PI3K-AKT-MTOR pathway genes, namely PIK3CA (p.E542K, p.E545K, p.H1047R), AKT3 (p.E17K) and MTOR (p.S2215F, p.S2215Y). We quantified the level of mosaicism across all samples and correlated genotypes with key clinical, neuroimaging and histopathological data. Pathogenic variants were identified in 17 individuals, with an overall molecular solve rate of 29.31%. Variant allele fractions ranged from 0.14 to 22.67% across all mutation-positive samples. Our data show that pathogenic MTOR variants are mostly associated with focal cortical dysplasia, whereas pathogenic PIK3CA variants are more frequent in hemimegalencephaly. Further, the presence of one of these hotspot mutations correlated with earlier onset of epilepsy. However, levels of mosaicism did not correlate with the severity of the cortical malformation by neuroimaging or histopathology. Importantly, we could not identify these mutational hotspots in other types of surgically resected epileptic lesions (e.g. polymicrogyria or mesial temporal sclerosis) suggesting that PI3K-AKT-MTOR mutations are specifically causal in the focal cortical dysplasia-hemimegalencephaly spectrum. Finally, our data suggest that ultra-sensitive molecular profiling of the most common PI3K-AKT-MTOR mutations by targeted sequencing droplet digital polymerase chain reaction is an effective molecular approach for these disorders with a good diagnostic yield when paired with neuroimaging and histopathology.

Investigation of urinary volatile organic compounds as novel diagnostic and surveillance biomarkers of bladder cancer

BackgroundThe diagnosis and surveillance of urothelial bladder cancer (UBC) require cystoscopy. There is a need for biomarkers to reduce the frequency of cystoscopy in surveillance; urinary volatile organic compound (VOC) analysis could fulfil this role. This cross-sectional study compared the VOC profiles of patients with and without UBC, to investigate metabolomic signatures as biomarkers.MethodsUrine samples were collected from haematuria clinic patients undergoing diagnostic cystoscopy and UBC patients undergoing surveillance. Urinary headspace sampling utilised solid-phase microextraction and VOC analysis applied gas chromatography-mass spectrometry; the output underwent metabolomic analysis.ResultsThe median participant age was 70 years, 66.2% were male. Of the haematuria patients, 21 had a new UBC diagnosis, 125 had no cancer. In the surveillance group, 75 had recurrent UBC, 84 were recurrence-free. A distinctive VOC profile was observed in UBC patients compared with controls. Ten VOCs had statistically significant abundances useful to classify patients (false discovery rate range 1.9 × 10−7–2.8 × 10−2). Two prediction models were evaluated using internal validation. An eight-VOC diagnostic biomarker panel achieved AUROC 0.77 (sensitivity 0.71, specificity 0.72). A six-VOC surveillance biomarker panel obtained AUROC 0.80 (sensitivity 0.71 and specificity 0.80).ConclusionsUrinary VOC analysis could aid the diagnosis and surveillance of UBC.