Critical role of tripartite fusion and LBD truncation in certain RARA- and all RARG-related atypical APL.

ABSTRACT: Atypical acute promyelocytic leukemia (aAPL) presents a complex landscape of retinoic acid receptor (RAR) fusion genes beyond the well-known PML::RARA fusion. Among these, 31 individually rare RARA and RARG fusion genes have been documented, often reported in the canonical X::RAR bipartite fusion form. Intriguingly, some artificially mimicked bipartite X::RAR fusions respond well to all-trans retinoic acid (ATRA) in vitro, contrasting with the ATRA resistance observed in patients. To unravel the underlying mechanisms, we conducted a comprehensive molecular investigation into the fusion transcripts in 27 RARA fusion gene-positive aAPL (RARA-aAPL) and 21 RARG-aAPL cases. Our analysis revealed an unexpected novel form of X::RAR::X- or X::RAR::Y-type tripartite fusions in certain RARA-aAPL and all RARG-aAPL cases, with shared features and notable differences between these 2 disease subgroups. In RARA-aAPL cases, the occurrence of RARA 3' splices was associated with their 5' fusion partner genes, mapping across the coding region of helix 11_12 (H11_12) within the ligand-binding domain (LBD), resulting in LBD-H12 or H11_12 truncation. In RARG-aAPL cases, RARG 3' splices were consistently localized to the terminus of exon 9, leading to LBD-H11_12 truncation. Significant differences were also observed between RARA and RARG 5' splice patterns. Our analysis also revealed extensive involvement of transposable elements in constructing RARA and RARG 3' fusions, suggesting transposition mechanisms for fusion gene ontogeny. Both protein structural analysis and experimental results highlighted the pivotal role of LBD-H11_12/H12 truncation in driving ATRA unresponsiveness and leukemogenesis in tripartite fusion-positive aAPL, through a protein allosteric dysfunction mechanism.

Assessing the comparability of cycle threshold values derived from five external quality assessment rounds for omicron nucleic acid testing.

BACKGROUND: A variety of open-system real-time reverse transcriptase polymerase chain reaction (RT-PCR) assays for several acute respiratory syndrome coronavirus 2 are currently in use. This study aimed to ensure the quality of omicron nucleic acid testing and to assess the comparability of cycle threshold (Ct) values derived from RT-PCR. METHODS: Five external quality assessment (EQA) rounds using the omicron virus-like particles were organized between February 2022 and June 2022. RESULTS: A total of 1401 qualitative EQA reports have been collected. The overall positive percentage agreement was 99.72%, the negative percentage agreement was 99.75%, and the percent agreement was 99.73%. This study observed a significant variance in Ct values derived from different test systems. There was a wide heterogeneity in PCR efficiency among different RT-PCR kits and inter-laboratories. CONCLUSION: There was strong concordance among laboratories performing qualitative omicron nucleic acid testing. Ct values from qualitative RT-PCR tests should not be used for clinical or epidemiological decision-making to avoid the potential for misinterpretation of the results.

Development of a matrix-based candidate reference material for human glycated albumin using isotope-dilution liquid chromatography/tandem mass spectrometry.

Glycated albumin (GA) in human serum is tested clinically as a short-term indicator for glucose monitoring. Here, we evaluated a candidate serum reference material (RM) at three different GA concentrations to help standardize serum GA measurements. Both albumin and GA were quantitatively determined using isotope-dilution liquid chromatography/tandem mass spectrometry with lysine-4,4,5,5-D4·2HCl (D4-lysine) and Nε-l3C6-(l-deoxy-d-fructose-1-yl)-l-lysine (13C6-DOF-lysine) as internal standards and lysine and synthetic DOF-lysine as calibration standards. The method was evaluated with the RM, JCCRM611-1, from the Reference Material Institute for Clinical Chemistry Standards. The homogeneity and stability of the candidate RMs were examined using a commercial biochemical analyzer. Fifteen units were randomly selected, and statistical analysis showed no inhomogeneity. The candidate RMs were stable for at least 6 months at -80 °C. The coefficients of variation (CVs) for the JCCRM611-1 RM ranged from 3.2% to 2.3%, and the biases ranged from 4.12% to -1.84%. GA was tested at low, medium, and high concentrations, which were quantified as 249.53 ± 13.29, 408.02 ± 11.70, and 637.22 ± 17.03 mmol/mol, respectively. The overall CVs ranged from 0.99% to 2.51%. The candidate RMs can potentially be used to develop a traceability chain to improve the accuracy of GA measurements.

A machine learning-based approach for low-density lipoprotein cholesterol calculation using age, and lipid parameters.

BACKGROUND: Low-density lipoprotein cholesterol (LDL-C) is a critical biomarker for cardiovascular disease. However, no consensus exists on the best method for estimating LDL-C in Chinese laboratories. This study aimed to develop a machine learning (ML) method for LDL-C estimation. METHODS: An extensive data set of 111,448 samples were randomized into five equal subsets. ML-based equations were developed using age, sex, and lipid parameters based on five-fold cross-validation. The trained ML equations were externally validated in three different data sets. The performance of the ML equations was compared with the Friedewald, Martin/Hopkins, and Sampson equations. RESULTS: The selected ML equations showed less bias with direct LDL-C than other LDL-C equations in the Chinese population, including those with triglycerides (TG) ≥ 400 mg / dL and LDL-C < 40 mg / dL. The performance of the ML equations was less susceptible to age. External validation showed the generalization of the ML equations. CONCLUSIONS: This study highlights the potential of integrating sex, age, and lipid parameters into the ML equations to obtain a more robust and reliable LDL-C calculation.

Routine blood biomarkers for the detection of multiple myeloma using machine learning.

INTRODUCTION: Primary laboratory tests performed in the diagnosis of multiple myeloma (MM) include bone marrow examination and free light chain assay; however, these may only be ordered after clinical suspicion of disease. In contrast, routine blood test results are readily available. METHODS: Machine learning algorithms (ML) combined with routine blood tests were used to detect MM. Feature selection was performed to achieve improved classification performance. The robustness of the classification models was assessed in an internal and external validation data set. To minimize the divergence, the training and validation data sets were combined and used to assess the performance of the ML algorithms. RESULTS: The AdaBoost-DecisionTable produced the best performance (accuracy =94.75%, sensitivity =87.70%, positive predictive value (PPV) =92.50%, F-measure =90.00%, and areas under the receiver operating characteristic curves (AUC) =97.50%) in the training data set using a 10-fold cross-validation. Performance in the validation data sets was affected by the divergence of the data sets, with accuracy greater than 85% and AUC greater than 90% in the validation data sets. The ML algorithm achieved a high accuracy of 92.61%, high AUC (96.80%), a sensitivity value of 85.20%, a PPV value of 88.50%, and an F-measure of 86.80% in a test set that was randomly selected from the combined data set. CONCLUSIONS: Combining ML and routine serum biomarkers hold a potential benefit in MM diagnosis.

Prognostic value of EGFR and KRAS in circulating tumor DNA in patients with advanced non-small cell lung cancer: a systematic review and meta-analysis.

EGFR (exon 19 and exon 21) mutations in patients with advanced non-small cell lung cancer (NSCLC) treated by EGFR-TKIs are associated with a better survival; while KRAS mutations predict a worse prognosis. However, there are divergent findings regarding the prognostic value of EGFR and KRAS mutations in circulating tumor DNA (ctDNA). We aimed to summarize the evidence for the use of circulating EGFR and KRAS mutations as prognostic factors in advanced NSCLC patients.We searched the network databases for studies reporting progression-free survival (PFS) and overall survival (OS) stratified by EGFR or KRAS mutations in ctDNA in advanced NSCLC patients. Thirteen studies enrolling 2,293 patients were reviewed. Correlation of circulating EGFR or KRAS mutations with patients' prognosis was assessed by meta-analysis.The pooled analyses showed that EGFR mutations in ctDNA significantly prolong PFS (HR=0.64,95% CI 0.51-0.81, I2=0%, p=0.0002), namely, in patients treated by EGFR-TKIs. There is a trend to have a prolonged OS for advanced NSCLC patients with circulating EGFR mutations who were treated by EGFR-TKIs (HR=0.79, 95% CI 0.52-1.21, I2=0, p=0.28). KRAS mutations detected in ctDNA predict a worse PFS (HR=1.83, 95% CI 1.40-2.40, p<0.0001) and OS (HR=2.07, 95% CI 1.54-2.78, p<0.00001) in advanced NSCLC patients treated by chemotherapy. Sensitivity analyses and subgroup analyses demonstrated the stability of our conclusion.Our analysis showed that EGFR mutations in ctDNA predicted a better PFS, in particular in advanced NSCLC patients treated by EGFR-TKIs. KRAS mutations in ctDNA indicated a worse PFS and OS in patients treated by chemotherapy.

Prognostic value of circulating tumor DNA in patients with colon cancer: Systematic review.

The application of circulating tumor DNA(ctDNA) represents a non-invasive method for tumor detection. Its prognostic significance in patients with colorectal cancer is controversial. We performed a systematic review of data from published studies to assess the prognostic values of ctDNA in patients with colorectal cancer. We searched Medline, Embase, Web of Science, the Cochrane Library, and Scopus databases to identify eligible studies reporting disease-free survival (DFS) and overall survival (OS) stratified by ctDNA prior to December 6, 2016. We evaluated the quality and design of these studies. A total of 22 studies were eligible for systematic review. Among them, 11 studies investigated the prognostic value of ctDNA on disease-free survival (DFS). Seven of 11 studies showed that ctDNA was an independent variable to estimate the probability of DFS by multivariate analyses. Thirteen studies assessed the relationship between ctDNA and overall survival (OS). Eight of 13 studies showed that ctDNA was an independent predictor of worse OS through the use of multivariate analyses. This analysis provides evidence that ctDNA may be a prognostic biomarker, negatively correlated with the survival of patients with colorectal cancer.

Engineering Antibodies for the Treatment of Infectious Diseases.

Historically, serum therapy was previously used to combat infectious pathogens. However, serum sickness and anaphylaxis limited its broad application. The advancement of antibody engineering technologies has made it feasible to generate monoclonal antibodies. There are divergent methods for antibody engineering and optimization. In this chapter, we summarized the latest developments in engineering antibodies for infectious diseases.

The reliable assurance of detecting somatic mutations in cancer-related genes by next-generation sequencing: the results of external quality assessment in China.

To evaluate the proficiencies of laboratories utilizing next-generation sequencing (NGS) to detect somatic mutations in cancer-related genes, an external quality assessment (EQA) was implemented by the National Center for Clinical Laboratories of China in 2015. We prepared a panel of samples that comprised eight samples made by mixing synthetic mutated DNA fragments with normal human genomic DNA and one reference sample containing only genomic DNA. We validated our sample panel, and then distributed it to laboratories across China. We received complete results from 64 laboratories. The performances of 51.6 % (33/64) respondent labs were acceptable and 26.6 % (17/64) of the labs returned perfect results. In total, 449 mistakes were reported, including 201 false-negatives (201/449, 44.8 %) and 222 false-positives (222/449, 49.4 %) and 26 slightly discordant results (26/449, 5.8 %). We believe these unsatisfactory results and varied performances are mainly due to the enrichment methods used, the diverse sequencing chemistries of the different NGS platforms, and other errors within the sequencing process. The results indicate that our sample panel is suitable for use in EQA studies, and that further laboratory training in targeted NGS testing is urgently required. To address this, we propose a targeted NGS workflow with details on quality assurance procedures according to the current guidelines.

Hybrid kappa\lambda antibody is a new serological marker to diagnose autoimmune pancreatitis and differentiate it from pancreatic cancer.

The only generally accepted serological marker currently used for the diagnosis of autoimmune pancreatitis (AIP) is IgG4. Our aim was mainly to determine whether hybrid κ\λ antibody can help to diagnose AIP and to differentiate it from pancreatic cancer. We established an enzyme-linked immunosorbent assay (ELISA) system to measure the levels of hybrid κ\λ antibodies in human sera. Sera were obtained from 338 patients, including 61 with AIP, 74 with pancreatic cancer, 50 with acute pancreatitis, 40 with ordinary chronic pancreatitis, 15 with miscellaneous pancreatic diseases, and 98 with normal pancreas. Our study showed levels of hybrid κ\λ antibodies in the AIP group were significantly higher than in the non-AIP group (P < 0.001). The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) for the diagnosis of AIP were 80.3%, 91%, 66.2% and 95.5% respectively. Furthermore, the combined measurement of serum hybrid κ\λ antibody and IgG4 tended to increase the sensitivity although the difference was not statistically significant (90.2% vs. 78.7%, P = 0.08), compared to measurement of IgG4 alone. Our findings suggest that hybrid κ\λ antibody could be a new serological marker to diagnose AIP and differentiate it from pancreatic cancer.

Increased Kappa/Lambda Hybrid Antibody in Serum Is a Novel Biomarker Related to Disease Activity and Inflammation in Rheumatoid Arthritis.

The κ/λ hybrid antibodies in normal human serum were reported recently, but their clinical relevance has not yet been explored. Rheumatoid arthritis (RA) is one of the major joint diseases, and the early diagnosis and treatment of RA remain a challenge. Here, we developed a double-sandwich enzyme-linked immunosorbent assay system to quantify relative serum κ/λ hybrid antibody levels in RA patients, osteoarthritis (OA) patients, and healthy controls (HC) in order to assess their potential use as a serological biomarker of early disease and clinical activity and to preliminarily investigate their immunomodulatory roles in RA. Surprisingly, we found that κ/λ hybrid antibody was markedly increased in both early and established RA. Serum κ/λ hybrid antibody levels were significantly correlated with clinical indexes and inflammatory markers in RA. Further analysis showed a positive correlation between κ/λ hybrid antibody levels and the 28-joint disease activity score (DAS28). In conclusion, serum κ/λ hybrid antibodies in RA were identified for the first time. High levels of κ/λ hybrid antibody may be a useful tool in distinguishing early RA from OA and HC. We suggest κ/λ hybrid antibody as a marker for disease activity. The increased κ/λ hybrid antibodies were associated with inflammatory conditions in RA.

Diagnostic Value of Serum IgG4 for IgG4-Related Disease: A PRISMA-compliant Systematic Review and Meta-analysis.

Many studies about serum IgG4 for the diagnosis of IgG4-related disease (IgG4-RD) have been reported. However, these studies had relatively small sample sizes and the diagnostic accuracy values varied much between them.The aim of this study was to perform a meta-analysis to evaluate the diagnostic value of serum IgG4 for IgG4-RD.We conducted a search of relevant articles using MEDLINE, EMBASE, Web of Science, SCOPUS, and Cochrane Library databases published before December 2015.Studies those assessed the diagnostic accuracy of serum IgG4 for IgG4-RD and those provided the cut-off value for serum IgG4 were included.Data were synthesized using the random-effect model. Statistical analysis was performed using STATA with the MIDAS module and Meta-DiSc 1.4 software.A total of 9 case-control studies were analyzed, which included 1235 patients with IgG4-RD and 5696 overall controls. The pooled estimate, for a cut-off value ranged from 135 to 144 mg/dL, produced a sensitivity of 87.2% (95% CI, 85.2-89.0%) and a specificity of 82.6% (95% CI, 81.6-83.6%). The positive likelihood ratio (PLR), negative likelihood ratio (NLR), and diagnostic odds ratio (DOR) were 6.48 (95% CI, 3.98-10.57), 0.14 (95% CI, 0.09-0.21), and 45.15 (95% CI, 23.41-87.06), respectively. The area under the curve (AUC) of the summary receiver operating characteristic curve (SROC) was 0.94 (0.92-0.96). When a cut-off value of 2-fold the upper limit of normal was used (ranged from 270 to 280 mg/dL), the pooled sensitivity was 63% (95% CI, 60.0-66.0%), and the specificity was 94.8% (95% CI, 94.1-95.4%). The PLR, NLR, and DOR were 13.3 (95% CI, 7.39-24.0), 0.41 (95% CI, 0.29-0.58) and 33.42 (95% CI, 13.88-80.43), respectively. The AUC of the SROC was 0.92 (0.90-0.94).Only a relatively small number of studies were included, and significant heterogeneity was observed in this meta-analysis.Serum IgG4 is a modestly effective marker to diagnose IgG4-RD. Doubling the cut-off value for IgG4 could not improve the overall test characteristics. A high specificity inevitably accompanies with a significant sacrifice in sensitivity.

Diagnostic value of Der p 1 and Der p 2 specific IgE in Dermatophagoides pteronyssinus IgE sensitization.

OBJECTIVE: To assess the diagnostic performance of Der p 1 and Der p 2 specific IgE (sIgE). DATA SOURCES: Studies were systematic computerized searches of the PubMed, EMBASE, and Cochrane libraries (published 1966 to September 5, 2015). STUDY SELECTION: Records were screened by title and abstract and then by full-text articles of relevant studies. Eligible studies were selected according to inclusion criteria: (1) all house dust mite allergy diagnosed on the basis of clinical symptoms in combination with a dust mite extract skin prick test result; (2) the inclusion of controls in the study; and (3) enough data to construct the diagnostic 2 × 2 table. True-positive, false-positive, false-negative, and true-negative values were extracted from or calculated for each study. Then the pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, and diagnostic odds ratio were calculated. A summary receiver operating characteristic curve and area under the curve were used to evaluate the overall diagnostic performance. RESULTS: Seven eligible studies that involved 1040 cases were included in this meta-analysis. The meta-analysis found that detection of Der p 1 or Der p 2 sIgE is of sufficient diagnostic accuracy for use in the diagnosis of Dermatophagoides pteronyssinus IgE sensitization. CONCLUSION: Detection of Der p 1 or Der p 2 sIgE is a promising diagnostic tool in the diagnosis of D pteronyssinus IgE sensitization.

Bispecific antibodies and their applications.

Bispecific antibodies (BsAbs) recognize two different epitopes. This dual specificity opens up a wide range of applications, including redirecting T cells to tumor cells, blocking two different signaling pathways simultaneously, dual targeting of different disease mediators, and delivering payloads to targeted sites. The approval of catumaxomab (anti-EpCAM and anti-CD3) and blinatumomab (anti-CD19 and anti-CD3) has become a major milestone in the development of bsAbs. Currently, more than 60 different bsAb formats exist, some of them making their way into the clinical pipeline. This review summarizes diverse formats of bsAbs and their clinical applications and sheds light on strategies to optimize the design of bsAbs.

A new type of natural bispecific antibody with potential protective effect in Hashimoto thyroiditis.

CONTEXT: As a new antibody concept, natural bispecific antibodies (nBsAbs) have been detected in long-term passive immunization and some diseases, but their potential immunomodulatory role remains unclear. Hashimoto thyroiditis (HT) appears to fulfill the condition for nBsAb production but has not yet been characterized. OBJECTIVE: The objective of the study was to identify a new nBsAb against thyroid peroxidase (TPO) and thyroglobulin (Tg) in HT patients and to preliminarily explore its immunomodulatory role. DESIGN, SETTING, AND PATIENTS: Serum samples were obtained from 136 HT patients, 92 diseased controls, and 99 healthy controls for anti-TPO/Tg nBsAb detection. The relationship between anti-TPO/Tg nBsAb and other clinical parameters was also analyzed. MAIN OUTCOME MEASURES: The anti-TPO/Tg nBsAb was detected using a double-antigen sandwich ELISA. Higher nBsAb levels were found to be associated with decreased inflammation in HT patients. RESULTS: The prevalence of anti-TPO/Tg nBsAb in HT was 44.9% (61 of 136), significantly higher than that of diseased controls (2.2%, 2 of 92) (P < .0001) and healthy controls (0%, 0 of 99) (P < .0001). HT patients who were nBsAb positive were prone to have significantly lower levels of serum C-reactive protein and TNF-α compared with the nBsAb-negative individuals (P < .05). The serum amyloid A and interferon-γ levels also showed a similar trend in the two groups. The IgG subclass of anti-TPO/Tg nBsAb was IgG4. Further analysis showed a negative correlation between anti-TPO/Tg nBsAb and serum total IgG4 (r = -0.697, P = .025) in IgG4 thyroiditis patients. CONCLUSIONS: A new type of nBsAb against TPO and Tg in HT patients is identified. Our data also indicate a protective effect of anti-TPO/Tg nBsAb in the pathogenesis of HT and extend prior knowledge about nBsAb in diseases.

Identification of circulating microRNAs as biomarkers in cancers: what have we got?

During the past few years there has been great interest in the development of circulating microRNAs (miRNAs) as stable blood-based biomarkers for cancer detection. Deregulation of miRNAs in blood samples has shown considerable clinical utilities in cancers. Due to poorly characterized preanalytical and analytical variables and the lack of a standardized measurement protocol, the application of these miRNA fingerprints is hindered by conflicting results. In this review,we outline our current understanding of preanalytically and analytically confounding factors. We believe that great consideration should be taken in the development of circulating miRNA as tumor biomarkers.

Regions identity between the genome of vertebrates and non-retroviral families of insect viruses.

BACKGROUND: The scope of our understanding of the evolutionary history between viruses and animals is limited. The fact that the recent availability of many complete insect virus genomes and vertebrate genomes as well as the ability to screen these sequences makes it possible to gain a new perspective insight into the evolutionary interaction between insect viruses and vertebrates. This study is to determine the possibility of existence of sequence identity between the genomes of insect viruses and vertebrates, attempt to explain this phenomenon in term of genetic mobile element, and try to investigate the evolutionary relationship between these short regions of identity among these species. RESULTS: Some of studied insect viruses contain variable numbers of short regions of sequence identity to the genomes of vertebrate with nucleotide sequence length from 28 bp to 124 bp. They are found to locate in multiple sites of the vertebrate genomes. The ontology of animal genes with identical regions involves in several processes including chromatin remodeling, regulation of apoptosis, signaling pathway, nerve system development and some enzyme-like catalysis. Phylogenetic analysis reveals that at least some short regions of sequence identity in the genomes of vertebrate are derived the ancestral of insect viruses. CONCLUSION: Short regions of sequence identity were found in the vertebrates and insect viruses. These sequences played an important role not only in the long-term evolution of vertebrates, but also in promotion of insect virus. This typical win-win strategy may come from natural selection.