Fold Change Research Articles

The diagnostic value of serum lncRNA CATG00000112921.1 as a marker of multiple myeloma

Multiple myeloma (MM) is a malignant plasma cell disease. At present, numerous studies have shown that lncRNA plays a very important role in the occurrence, development and even drug resistance of multiple myeloma. It may become a potential diagnostic and prognostic marker of multiple myeloma and provide new ideas for targeted therapy. Based on the above research background, this study used gene chip technology to screen out the differentially expressed lncRNA in the serum of MM patients and healthy people, and verified more clinical serum samples to screen out the lncRNA with the largest difference as a biomarker for further research. In this research, the data of hospitalized patients diagnosed with MM and healthy people in the Affiliated Hospital of Guangdong Medical University were retrospectively collected. The lncRNA expression profile of serum samples from patients with multiple myeloma and healthy controls was analyzed by lncRNA chip technology. The serum samples were verified by real-time fluorescence quantitative PCR, and the candidate diagnostic markers were screened out. The ROC working curve was drawn to evaluate the diagnostic efficacy of the candidate markers and to determine their stability at different temperatures and time. A total of 44 MM patients and 37 healthy people were involved in this research. Among them, 4 patients with MM and 4 patients with HD were sent for microarray analysis. According to Fold Change ≥ 2 and P < 0.05, a total of 17 differentially expressed lncRNA molecules were screened, of which 9 were up-regulated RNA molecules and 8 were down-regulated RNA molecules. Through real-time fluorescence quantitative PCR verification, it was found that lncRNA CATG00000112921.1 was highly expressed in the healthy control group and diminished in patients with multiple myeloma, P < 0.001. The ROC curve demonstrated that the area under the curve (AUC) was 0.749, the sensitivity was 0.636, the specificity was 0.789, and the 95 % CI was 0.636-0.862 (P < 0.001). In addition, in order to verify the effects of temperature, time and repeated freezing and thawing on lncRNA, it was placed at 25°C, 4°C, -20°C, -80°C for 0h, 24h, 48h, 72h, and placed at-80°C repeated freezing and thawing 0 times, 2 times, 4 times, 8 times, and the expression level was not significantly changed. Serum lncRNA CATG00000112921.1 may be a potential candidate diagnostic marker for multiple myeloma. The ROC curve shows that it has good diagnostic value, and its high stability at different temperatures and different times is a required condition for becoming a diagnostic marker. As far as we know, this is the first study in the world to find differential expression of lncRNA CATG00000112921.1 in peripheral serum of healthy people and newly diagnosed multiple myeloma patients. This study also highlights the application of gene chip technology in screening differentially expressed genes.

Impact of MgtC on the Fitness of Yersinia pseudotuberculosis.

Yersinia pseudotuberculosis is an extracellular foodborne pathogen and usually causes self-limiting diarrhea in healthy humans. MgtC is known as a key subversion factor that contributes to intramacrophage adaptation and intracellular survival in certain important pathogens. Whether MgtC influences the fitness of Y. pseudotuberculosis is unclear. According to in silico analysis, MgtC in Y. pseudotuberculosis might share similar functions with other bacterial pathogens, such as Salmonella. Studies indicated that MgtC was clearly required for Y. pseudotuberculosis growth in vitro and bacterial survival in macrophages under Mg2+ starvation. Transcriptome analysis by RNA-seq indicated that 127 differentially expressed genes (DEGs) (fold change > 2 and p < 0.001) were discovered between wild-type PB1+ and mgtC mutant inside macrophages. However, a lack of MgtC only moderately, albeit significantly, reduced the virulence of Y. pseudotuberculosis in mice. Overall, this study provides additional insights for the role of MgtC in Y. pseudotuberculosis.

Circulating CD8 lymphocytes predict response to atezolizumab-bevacizumab in hepatocellular carcinoma.

Due to the lack of biomarkers predictive of response to atezolizumab-bevacizumab, the standard of care for advanced HCC, we analyzed baseline and early on-treatment variation of peripheral lymphocyte populations of 37 prospective patients treated by atezolizumab-bevacizumab and in 15 prospective patients treated by sorafenib or lenvatinib (TKIs). RNAseq analysis followed by RT-PCR validation on patients-derived PBMC was also performed. At first imaging, re-evaluation 13 patients receiving atezolizumab-bevacizumab, showed an objective response, 17 stable disease, while 7 were nonresponders. Baseline CD8+ and CD8+PD-L1+ peripheral lymphocytes were lower in responders versus nonresponders (T-test, p = 0.012 and 0.004, respectively). At 3 weeks, 28 of 30 responders displayed a rise of CD8+PD1+ lymphocytes with a positive mean fold change of 4.35 (±5.6 SD), whereas 6 of 7 nonresponders displayed a negative fold change of 0.89 (±0.84 SD). These changes were not observed in patients treated by TKIs. TRIM56, TRIM16, TRIM64, and Ki67 mRNAs were validated as upregulated in responders versus nonresponders after 3 weeks after treatment start, providing possible evidence of immune activation. Baseline CD8+ and CD8+PD-L1+ peripheral lymphocytes and early changes in CD8+PD1+ lymphocytes predict response to atezolizumab-bevacizumab providing noninvasive markers to complement clinical practice in the very early phases of treatment of HCC patients.

Proteome Profiling of Brain Vessels in a Mouse Model of Cerebrovascular Pathology.

Cerebrovascular pathology that involves altered protein levels (or signaling) of the transforming growth factor beta (TGFβ) family has been associated with various forms of age-related dementias, including Alzheimer disease (AD) and vascular cognitive impairment and dementia (VCID). Transgenic mice overexpressing TGFβ1 in the brain (TGF mice) recapitulate VCID-associated cerebrovascular pathology and develop cognitive deficits in old age or when submitted to comorbid cardiovascular risk factors for dementia. We characterized the cerebrovascular proteome of TGF mice using mass spectrometry (MS)-based quantitative proteomics. Cerebral arteries were surgically removed from 6-month-old-TGF and wild-type mice, and proteins were extracted and analyzed by gel-free nanoLC-MS/MS. We identified 3602 proteins in brain vessels, with 20 demonstrating significantly altered levels in TGF mice. For total and/or differentially expressed proteins (p ≤ 0.01, ≥ 2-fold change), using multiple databases, we (a) performed protein characterization, (b) demonstrated the presence of their RNA transcripts in both mouse and human cerebrovascular cells, and (c) demonstrated that several of these proteins were present in human extracellular vesicles (EVs) circulating in blood. Finally, using human plasma, we demonstrated the presence of several of these proteins in plasma and plasma EVs. Dysregulated proteins point to perturbed brain vessel vasomotricity, remodeling, and inflammation. Given that blood-isolated EVs are novel, attractive, and a minimally invasive biomarker discovery platform for age-related dementias, several proteins identified in this study can potentially serve as VCID markers in humans.

Exploring testicular miRNA profiles during developmental stages in Dezhou donkeys: A preliminary insight.

Testicular development and spermatogenesis are complex phenomena controlled by various genetic factors, including miRNA-based post-transcriptional gene expression regulation. Exploring the miRNA expression patterns during testicular development in Dezhou donkeys would enhance our understanding of equine fertility and spermatogenesis. In this investigation, we examined the testicular miRNA profiles at various stages of development. The experimental animals were divided into three groups based on their developmental stages: 2 months old (juvenile: n = 3), 12 months old (adolescent; n = 3) and 24 months old (adult; n = 3) donkeys. Total RNA was extracted from dissected testicles for miRNA sequencing and analysis. In total, 586 miRNAs, including 451 known miRNAs and 135 novel miRNAs, were identified. Among identified miRNAs, 315 displayed age-dependent expression differences. The levels of miRNA expression in the juvenile group were significantly higher than in the adolescent or adult groups. The MiR-483 exhibited the maximum fold change between juvenile and adolescent groups. Several screened genes, including SLC45A4 and TFCP2L1, have been linked to male reproductive pathways in donkeys. In addition, miR-744 was predicted to regulate SPIN2B, a gene implicated in spermatocyte cell cycle progression and genomic integrity of spermatozoa. These results contribute to our comprehension of microRNA regulation during testicular development and spermatogenesis in Dezhou donkeys. The identified microRNAs and their target genes have the potential to serve as biomarkers for evaluating the reproductive capacity of stud donkeys.

Is Nontarget Analysis Ready for Regulatory Application? Influence of Peak-Picking Algorithms on Data Analysis.

The use of peak-picking algorithms is an essential step in all nontarget analysis (NTA) workflows. However, algorithm choice may influence reliability and reproducibility of results. Using a real-world data set, the aim of this study was to investigate how different peak-picking algorithms influence NTA results when exploring temporal and/or spatial trends. For this, drinking water catchment monitoring data, using passive samplers collected twice per year across Southeast Queensland, Australia (n = 18 sites) between 2014 and 2019, was investigated. Data were acquired using liquid chromatography coupled to high-resolution mass spectrometry. Peak picking was performed using five different programs/algorithms (SCIEX OS, MSDial, self-adjusting-feature-detection, two algorithms within MarkerView), keeping parameters identical whenever possible. The resulting feature lists revealed low overlap: 7.2% of features were picked by >3 algorithms, while 74% of features were only picked by a single algorithm. Trend evaluation of the data, using principal component analysis, showed significant variability between the approaches, with only one temporal and no spatial trend being identified by all algorithms. Manual evaluation of features of interest (p-value <0.01, log fold change >2) for one sampling site revealed high rates of incorrectly picked peaks (>70%) for three algorithms. Lower rates (<30%) were observed for the other algorithms, but with the caveat of not successfully picking all internal standards used as quality control. The choice is therefore currently between comprehensive and strict peak picking, either resulting in increased noise or missed peaks, respectively. Reproducibility of NTA results remains challenging when applied for regulatory frameworks.

Analysis of expression profile of long non-coding RNA in patients with idiopathic and COVID-19-induced pulmonary fibrosis

Introduction. Idiopathic pulmonary fibrosis (IPF) comprises an interstitial lung disease with unclear pathogenesis, rapid progression, and no effective treatment. Pulmonary fibrosis is reported to be one of the most severe complications induced by a new coronavirus infection COVID-19. The mechanisms triggering pulmonary fibrosis and leading to its rapid progression remain substantially unclear. Evidence suggests that immune and genetic factors contribute to the development of this disease. Among the latter, the role of long non-coding RNAs (dnRNAs) has been actively studied to date. Materials and methods. Considering the role of TP53TG1, LINC00342, H19, MALAT1, DNM3OS, and MEG3 dnRNAs as regulators of signaling pathways associated with fibroblast activation and epithelial-mesenchymal transition, the authors analyzed the expression level of selected dnRNAs in lung tissue and blood mononuclear cells of patients with IPF (N = 12), post-COVID-19 pulmonary fibrosis (N = 14), and in control group (N = 27). Results and discussion. Blood mononuclear cells in patients with IPF and post-COVID-19 PF revealed similar patterns of TP53TG1 and MALAT1 dnRNA expression. The level of relative expression of MALAT1 was significantly higher in patients with IPF (Fold Change=3.207, P = 0.0005) and with post-COVID-19 PF (Fold Change=9.854, P = 0.0003), while the relative expression level of TP53TG1 reduced in patients with IPF (Fold Change=0.4308, P = 0.0313) and with post-COVID-19 PF (Fold Change=0.1888, P = 0.0003 in blood mononuclear cells, Fold Change=0.1791, P = 0.0237 in lung tissue). Increased expression of DNM3OS in blood mononuclear cells (Fold Change=12.899, P = 0.0016) and lung tissue (Fold Change=9.527, P = 0.0001), LINC00342 (Fold Change=2.221, P = 0.0309) in blood mononuclear cells was revealed only in patients with IPF. Conclusion. Evaluation of the dnRNA expression profile of TP53TG1, LINC00342, MALAT1 and DNM3OS in blood mononuclei can be used as an informative and non-invasive biomarker in IPF and post COVID-19 PF.

Plasma-derived exosomal miRNA profiles reveal potential epigenetic pathogenesis of premature ovarian failure.

The role of plasma-derived exosomal miRNA in premature ovarian failure (POF) remains unclear. This study aimed to investigate the epigenetic pathogenesis of POF through exosomal miRNA sequencing. Exosomes were isolated and characterized from six POF patients and four healthy individuals using nanoparticle tracking analysis, transmission electron microscopy and western blot analysis. Exosomal miRNA sequencing was performed to identify differentially expressed miRNAs with |fold change| greater than 1.5 and p value less than 0.05. Bioinformatics analysis in GSE39501 dataset and our sequencing data was conducted to investigate underlying mechanisms of POF. The functional role of hsa-miR-19b-3p was assessed using CCK8, western blot, flow cytometry and fluorescence staining. The regulatory effect of hsa-miR-19b-3p on BMPR2 was investigated through miRNA transfection, qPCR analysis, and luciferase reporter assay. Statistical significance was determined using t-tests and one-way ANOVA (p < 0.05). Exosomal miRNA sequencing revealed 18 dysregulated miRNAs in POF patients compared to healthy controls. Functional enrichment analysis demonstrated their involvement in cell growth, oocyte meiosis and PI3K-Akt signaling pathways. Moreover, the constructed miRNA-mRNA network unveiled potential regulatory mechanisms underlying POF, particularly implicating hsa-miR-19b-3p in the regulation of BMPR2. In vitro assays conducted on KGN cells confirmed that hsa-miR-19b-3p promoted apoptosis, as evidenced by reduced cell viability, decayed mitochondrial membrane potential and increased apoptotic rate, thereby supporting its role in POF. Notably, hsa-miR-19b-3p was found to significantly downregulate BMPR2 expression via targeting its 3'UTR, while co-expression analysis revealed strong associations between BMPR2 and POF-related processes. This study sheds light on the epigenetic pathogenesis of POF by investigating exosomal miRNA profiles. Particularly, hsa-miR-19b-3p emerged as a potential regulator of BMPR2 and demonstrated its functional significance in POF through modulation of apoptosis.

Comparative miRNA-seq analysis revealed molecular mechanisms of red color formation in the early developmental stages of Plectropomus leopardus

MicroRNAs (miRNAs) are endogenous small non-coding RNAs that play important roles in several biological processes, including the regulation of body color. Leopard coral grouper (Plectropomus leopardus) is a valuable marine aquaculture fish; however, at present, there are no published reports on its early body color development. The skin color of P. leopardus undergoes a transition from transparent to red from 26 days post-hatching (dph) to 30 dph. In this study, we performed miRNA sequencing on 26 dph (Transparent, PT) and 30 dph (Red, PR) skin samples of P. leopardus to explore the molecular mechanism underlying red color formation. A total of 44.31 M and 37.55 M clean tags were obtained from PT and PR group, respectively. Among these tags, 981 miRNAs were identified, including 493 known and 488 novel miRNAs. A total of 106 differentially expressed miRNAs (DEMs) were identified in PT vs. PR, with 43 up-regulated and 63 down-regulated miRNAs in the PR group, compared to the PT group (|fold change| &amp;gt; 2 and p-value &amp;lt; 0.05). A miRNA-mRNA network based on 18 candidate miRNAs and 53 target genes related to pigmentation, and KEGG enrichment analysis of the target genes of all DEMs, revealed that miRNAs involved in the formation of red skin color were mainly related to: 1) the inhibition of melanin synthesis (miR-141-z, miR-206-z, miR-206-y, miR-27-z, miR-137-y, miR-204-x, miR-204-y, miR-211-x, miR-211-z); 2) chromatophore development (miR-206-z, miR-206-y, miR-499-y, miR-1-z, miR-2188-x, miR-423-x); and 3) carotenoid metabolism (miR-204-x, miR-204-y, miR-499-y). This study demonstrates the potential role of miRNAs in red color formation and lays the foundation for the molecular mechanism of body color polymorphism in P. leopardus.

Organic acid and sugar components accumulation and flavor associated metabolites dynamic changes in yellow- and white-fleshed seedless loquats (Eriobotrya japonica)

Triploid loquats are divided into yellow- and white-fleshed cultivars. To better understand taste variations in triploid loquat fruits, we used a UPLC-ESI-QTRAP-MS/MS-based widely targeted metabolomic analysis to examine the metabolic composition of two different color fleshed triploid loquats with a sample size of 54 and external validation method within a confidence level of P＜0.05. We identified key flavor-related differentially accumulated metabolites using the variable importance in projection (VIP) value (VIP ≥ 1.0) and fold change ≥ 2 or ≤ 0.5. Furthermore, the results of the HPLC analysis showed that white-fleshed loquats had a low malic acid content. We also performed the UPLC-MS/MS system to investigate the carotenoids contents and lipidome in four triploid cultivars. In the fruits of white-fleshed varieties, the carotenoids contents were significantly downregulated, but the contents of most glycerolphospholipids were increased. Our results reveal the metabolomic changes between the yellow- and white-fleshed cultivars.

MicroRNA-152-3p and MicroRNA-196a-5p Are Downregulated When Müller Cells Are Promoted by Components of the Internal Limiting Membrane: Implications for Macular Hole Healing.

Müller cells play a critical role in the closure of macular holes, and their proliferation and migration are facilitated by the internal limiting membrane (ILM). Despite the importance of this process, the underlying molecular mechanism remains underexplored. This study investigated the effects of ILM components on the microRNA (miRNA) profile of Müller cells. Rat Müller cells (rMC-1) were cultured with a culture insert and varying concentrations of ILM component coatings, namely, collagen IV, laminin, and fibronectin, and cell migration was assessed by measuring cell-free areas in successive photographs following insert removal. MiRNAs were then extracted from these cells and analyzed. Mimics and inhibitors of miRNA candidates were transfected into Müller cells, and a cell migration assay and additional cell viability assays were performed. The results revealed that the ILM components promoted Müller cell migration (p < 0.01). Among the miRNA candidates, miR-194-3p was upregulated, whereas miR-125b-1-3p, miR-132-3p, miR-146b-5p, miR-152-3p, miR-196a-5p, miR-542-5p, miR-871-3p, miR-1839-5p, and miR-3573-3p were significantly downregulated (p < 0.05; fold change > 1.5). Moreover, miR-152-3p and miR-196a-5p reduced cell migration (p < 0.05) and proliferation (p < 0.001), and their suppressive effects were reversed by their respective inhibitors. In conclusion, miRNAs were regulated in ILM component-activated Müller cells, with miR-152-3p and miR-196a-5p regulating Müller cell migration and proliferation. These results serve as a basis for understanding the molecular healing process of macular holes and identifying potential new target genes in future research.

Differences in gene expression profiles in early and late stage rhodesiense HAT individuals in Malawi.

T. b. rhodesiense is the causative agent of Rhodesian human African trypanosomiasis (r-HAT) in Malawi. Clinical presentation of r-HAT in Malawi varies between foci and differs from East African HAT clinical phenotypes. The purpose of this study was to gain more insights into the transcriptomic profiles of patients with early stage 1 and late stage 2 HAT disease in Malawi. Whole blood from individuals infected with T. b. rhodesiense was used for RNA-Seq. Control samples were from healthy trypanosome negative individuals matched on sex, age range, and disease foci. Illumina sequence FASTQ reads were aligned to the GRCh38 release 84 human genome sequence using HiSat2 and differential analysis was done in R Studio using the DESeq2 package. XGR, ExpressAnalyst and InnateDB algorithms were used for functional annotation and gene enrichment analysis of significant differentially expressed genes. RNA-seq was done on 23 r-HAT case samples and 28 healthy controls with 7 controls excluded for downstream analysis as outliers. A total of 4519 genes were significant differentially expressed (p adjusted <0.05) in individuals with early stage 1 r-HAT disease (n = 12) and 1824 genes in individuals with late stage 2 r-HAT disease (n = 11) compared to controls. Enrichment of innate immune response genes through neutrophil activation was identified in individuals with both early and late stages of the disease. Additionally, lipid metabolism genes were enriched in late stage 2 disease. We further identified uniquely upregulated genes (log2 Fold Change 1.4-2.0) in stage 1 (ZNF354C) and stage 2 (TCN1 and MAGI3) blood. Our data add to the current understanding of the human transcriptome profiles during T. b. rhodesiense infection. We further identified biological pathways and transcripts enriched than were enriched during stage 1 and stage 2 r-HAT. Lastly, we have identified transcripts which should be explored in future research whether they have potential of being used in combination with other markers for staging or r-HAT.

Pigment epithelium-derived factor (PEDF) represses the glucose transporter 1 (GLUT1) mRNA expression and may be a potential therapeutic agent in psoriasis: a case–control and experimental study

We investigated the whole blood GLUT1 mRNA expression and serum pigment epithelium-derived factor (PEDF), interleukin-6 (IL-6), fetuin-A, and pentraxin-3 (PTX3) levels in psoriatic patients and tested their correlations with the severity of psoriasis using the psoriasis area and severity index (PASI) score. Also, we tested the GLUT1 mRNA expression after an in vitro treatment of human skin fibroblast (HSF) cell lines with PEDF. The case–control part of the study recruited 74 participants (44 psoriatic patients and 30 healthy volunteers). Whole blood GLUT1 mRNA fold changes were estimated by RT-PCR, and serum PEDF, IL-6, fetuin-A, and PTX3 levels were measured by ELISA kits. In the experimental part, the HSF cell lines were treated with different concentrations of PEDF for different times to test its effect on the GLUT1 mRNA expression. The whole blood GLUT 1 expression significantly increased in psoriatic patients and correlated positively with serum IL-6, fetuin-A, PTX3 levels and with the severity of psoriasis while negatively with serum PEDF levels. The PEDF-treated HSF cell lines showed a time- and dose-dependent decline in the GLUT 1 mRNA expression. The whole blood GLUT 1 mRNA is a non-invasive biomarker that is associated with the severity of psoriasis. PEDF represses GLUT 1 expression and may be a potential therapeutic agent in psoriasis.Trial registration: ClinicalTrials.gov Identifier: NCT04242082.

Improved tolerance capacity and expression of degradation genes drive efficient removal of sulfamethizole by Chlorella pyrenoidosa

In this study, the tolerance capacities and expression of key degradation genes of a microalgal species, Chlorella pyrenoidosa prior exposure to sulfamethizole (SFT) were investigated. The results showed that acclimated microalgae had higher tolerance capacities comparing to the wild type since the half-maximum effective concentrations at 96 h increased from 31.27 mg L−1 to 51.27 mg L−1. Meanwhile, the removal of SFT was enhanced by 45.5% after acclimation, which was mainly induced by biodegradation. Bioaccumulated SFT was 17.65 and 24.61 µg g−1 in wild type and acclimated species. Gradually increased content of reactive oxygen species might act as the secondary massager to monitor the cellular metabolic pathways including synthesis of energy sources and energy metabolism. Key biodegradation genes were identified with upregulated log 2-fold change of > 6. These genes may help to biodegrade SFT in acclimation process. This study tried to unravel the underlying mechanism of acclimation process in microalgal degradation of persistent sulfonamide antibiotics, which might be useful in increasing the engineering feasibility in treatment of antibiotics’ wastewater.

Upregulation of S100A8 in peripheral blood mononuclear cells from patients with depression treated with SSRIs: a pilot study

BackgroundMajor depressive disorder (MDD) affects more than 350 million people worldwide, and there is currently no laboratory test to diagnose it. This pilot study aimed to identify potential biomarkers in peripheral blood mononuclear cells (PBMCs) from MDD patients.MethodsWe used tandem mass tagging coupled to synchronous precursor selection (mass spectrometry) to obtain the differential proteomic profile from a pool of PBMCs from MDD patients and healthy subjects, and quantitative PCR to assess gene expression of differentially expressed proteins (DEPs) of our interest.ResultsWe identified 247 proteins, of which 133 had a fold change ≥ 2.0 compared to healthy volunteers. Using pathway enrichment analysis, we found that some processes, such as platelet degranulation, coagulation, and the inflammatory response, are perturbed in MDD patients. The gene-disease association analysis showed that molecular alterations in PBMCs from MDD patients are associated with cerebral ischemia, vascular disease, thrombosis, acute coronary syndrome, and myocardial ischemia, in addition to other conditions such as inflammation and diabetic retinopathy.ConclusionsWe confirmed by qRT-PCR that S100A8 is upregulated in PBMCs from MDD patients and thus could be an emerging biomarker of this disorder. This report lays the groundwork for future studies in a broader and more diverse population and contributes to a deeper characterization of MDD.

Integrated analyses of transcriptomics and network pharmacology reveal leukocyte characteristics and functional changes in subthreshold depression, elucidating the curative mechanism of Danzhi Xiaoyao powder

ObjectiveTo investigate the molecular mechanism and identify potential drugs for subthreshold depression (SD), and elucidate the detalied mechanism of Danzhi Xiaoyao powder (DZXY) in SD. MethodsUsing RNA-sequencing, we identified differentially expressed genes (DEGs) in leukocytes of SD compared to healthy controls, deciphered their functions and pathways, and identified the hub genes of SD. We also assessed changes in leukocyte transcription factor activity in patients with SD using the TELiS platform. The Connectivity Map database was retrieved to screen candidate drugs for SD. Based on network pharmacology, we elucidated the “multi-component, multi-target, and multi-pathway” mechanism of DZXY in the treatment of SD. ResultsWe identified 1080 DEGs (padj <0.05 and |log2 (fold change)| ≥ 1 & protein coding) in the leukocytes of patients with SD. These DEGs, including hub genes, were primarily involved in immune and inflammatory response-related processes. Transcription factor activity analysis revealed similarities between the leukocyte transcriptome profile in SD and the conserved transcriptional response to adversities in immune cells. Connectivity Map analysis identified 28 potential drugs for SD treatment, particularly SB-202190 and TWS-119. Constructing the “Direct Compounds-Direct Targets-Pathways” network for DZXY and SD revealed the curative mechanisms of DZXY in SD, primarily including inflammatory response, lipid metabolism, immune response, and other processes. ConclusionThese results provide new insights into the characteristics and functional changes of leukocytes in SD, partially illustrate the pathogenesis of SD, and suggest potential drugs for SD. The curative mechanisms of DZXY in SD are also partially elucidated.

Urban wastewater disinfection by iron chelates mediated solar photo-Fenton: Effects on seven pathogens and antibiotic resistance transfer potential

The effects of solar photo-Fenton (SPF) process mediated by the iron chelate Fe3+ imminodisuccinic acid (Fe:IDS) on both the inactivation of seven relevant pathogens and the potential for antibiotic resistance transfer (degradation of antibiotic resistance genes (ARGs) and after treatment regrowth), in real secondary treated urban wastewater, were investigated for the first time. A comparison with results obtained by sunlight/H2O2 process and Fe3+ ethylenediaminedisuccinic acid (Fe:EDDS) SPF was also carried out. ARGs were quantified by polymerase chain reaction (PCR) in samples before and after (3 h) the treatment. The persistence of the selected pathogens and ARGs was also evaluated in regrowth tests (72 h) under environmentally mimicking conditions. Fe:IDS SPF resulted to be more effective (from 1.4 log removal for Staphylococcus spp. to 4.3 log removal for Escherichia coli) than Fe:EDDS SPF (from 0.8 log removal for Pseudomonas aeruginosa to 2.0 log removal for Total coliphages) and sunlight/H2O2 (from 1.2 log removal for Clostridium perfringens to 3.3 log removal for E. coli) processes for the seven pathogens investigated. Potential pathogens regrowth was also severely affected, as no substantial regrowth was observed, both in presence and absence of catalase. A similar trend was observed for ARGs removal too (until 0.001 fold change expression for qnrS after 3 h). However, a poor effect and a slight increase in fold change was observed after treatment especially for gyrA, mefA and intl1. Overall, the effect of the investigated processes on ARGs was found to be ARG dependent. Noteworthy, coliphages can regrow after sunlight/H2O2 treatment unlike SPF processes, increasing the risk of antibiotic resistance transfer by transduction mechanism. In conclusion, Fe:IDS SPF is an attractive solution for tertiary treatment of urban wastewater in small wastewater treatment plants as it can provide effective disinfection and a higher protection against antibiotic resistance transfer than the other investigated processes.

Utilizing geometric morphometrics to investigate gene function during organ growth: Insights through the study of beetle horn shape allometry.

Static allometry is a major component of morphological variation. Much of the literature on the development of allometry investigates how functional perturbations of diverse pathways affect the relationship between trait size and body size. Often, this is done with the explicit objective to identify developmental mechanisms that enable the sensing of organ size and the regulation of relative growth. However, changes in relative trait size can also be brought about by a range of other distinctly different developmental processes, such as changes in patterning or tissue folding, yet standard univariate biometric approaches are usually unable to distinguish among alternative explanations. Here, we utilize geometric morphometrics to investigate the degree to which functional genetic manipulations known to affect the size of dung beetle horns also recapitulate the effect of horn shape allometry. We reasoned that the knockdown phenotypes of pathways governing relative growth should closely resemble shape variation induced by natural allometric variation. In contrast, we predicted that if genes primarily affect alternative developmental processes, knockdown effects should align poorly with shape allometry. We find that the knockdown effects of several genes (e.g., doublesex, Foxo) indeed closely aligned with shape allometry, indicating that their corresponding pathways may indeed function primarily in the regulation of relative trait growth. In contrast, other knockdown effects (e.g., Distal-less, dachs) failed to align with allometry, implicating these pathways in potentially scaling-independent processes. Our findings moderate the interpretation of studies focusing on trait length and highlight the usefulness of multivariate approaches to study allometry and phenotypic plasticity.

Performance of optimized prototype LUMIPULSE G immunoassays for plasma pTau181 and pTau217

AbstractBackgroundThere is a need for automated random access plasma phosphorylated Tau (pTau) methods that reflect AD pathology with consistent performance. LUMIPULSE (LP) assays could offer a solution. Initial prototype pTau181 and pTau217 LP assays showed lower clinical performance versus Quanterix Homebrew assays (Poster #79533 – P4‐06). This new study presents optimized pTau181 and pTau217 LP assays, showing data on their analytical and clinical performance compared to the initial prototype method (Ref) and an in‐house pTau181 Quanterix Homebrew assay.MethodPlasma pTau181 and pTau217 LP assays were developed using recombinant pTau181 mAb RD‐070, resp. pTau217 mAb RD‐085, combined with an ALP‐Fab conjugate from recombinant N‐terminal Tau mAb RD‐073. In the optimized automated protocol, an assay specific diluent (ASD) is added (20%) to the sample to increase signal specificity. Analytical and clinical performance of the reference versus ASD‐treated prototypes to distinguish AD from controls was evaluated using 40 CSF‐confirmed AD‐dementia and 40 age‐matched healthy volunteer plasma samples.ResultAnalytical performance: Both optimized pTau181 and pTau217 LP tests demonstrated high precision comparable to their reference assays (inter‐run %CV on 3 neat plasma samples &lt; 7.4). LLOQ was not affected by ASD‐treatment. Clinical performance: pTau181 LP assays demonstrated comparable AUC and median fold change with (AUC 0.828, fold change 1.9) and without ASD (AUC 0.823, fold change 1.5) while the SIMOA assay demonstrated a higher AUC (0.866) and fold change (2.9). For pTau217, the performance improved from an initial AUC of 0.918 to 0.935, and a fold change of 3.72 instead of initially 2.76. (Figure 1). All assays correlated strongly (p&lt;0.00001) (Table 1); highest correlations among them were observed with the pTau217 ASD‐treated assay.ConclusionUsing an assay specific diluent resulted in improved clinical performance for the pTau217 prototype LUMIPULSE assay, in line with other published pTau217 assays. We did not achieve improved performance of the pTau181 LP assay with the ASD addition. Most important to emphasize, a performant pTau217 assay prototype is under development on an fully automated, scalable platform. Next steps include verification of performance in additional well‐characterized AD cohorts and characterization of lot consistency and robustness of the pTau181 and pTau217 N‐terminal LUMIPULSE assays.

CSF proteomics in autosomal dominant Alzheimer’s disease highlights parallels with sporadic disease

AbstractBackgroundAutosomal dominant Alzheimer’s disease (ADAD) offers a unique opportunity to study pathophysiological changes in a relatively young population with few comorbidities. A comprehensive investigation of proteome changes occurring in ADAD could provide valuable insights into AD‐related biological mechanisms and uncover novel biomarkers and therapeutic targets. Furthermore, ADAD might serve as a model for sporadic AD, but in‐depth proteome comparisons are lacking. We aimed to identify dysregulated CSF proteins in ADAD and determine the degree of overlap with sporadic AD.MethodUsing proximity extension‐based immunoassays (PEA) by Olink, we measured 1472 proteins in CSF of APP or PSEN1 mutation carriers (n = 22) and age‐ and sex‐matched controls (n = 20) from the Amsterdam Dementia Cohort. We compared protein abundance between groups using two‐sided t‐tests and identified enriched biological pathways. Using the same protein panels in paired plasma samples, we investigated correlations between CSF proteins and their plasma counterparts. Finally, we compared our results with recently published PEA data from an international cohort of sporadic AD (n = 230) and non‐AD dementias (n = 301). All analyses were false discovery rate‐corrected.ResultWe detected 66 differentially abundant CSF proteins (65 increased, one decreased) in ADAD compared to controls (q&lt;0.05). The most strongly upregulated proteins (fold change &gt;1.8) were related to immunity (CHIT1, ITGB2, SMOC2), cytoskeletal structure (MAPT, NEFL) and tissue remodeling (TMSB10, MMP‐10). Significant CSF‐plasma correlations were found for the upregulated proteins SMOC2 and LILR1B. 36 of the 66 differentially expressed proteins had been previously measured in the sporadic dementias cohort, 34 of which (94%) were also significantly upregulated in sporadic AD, with a strong correlation between the fold changes of these proteins in both cohorts (rs = 0.730, p&lt;0.001). 29 of these 36 proteins (81%) were also upregulated among non‐AD patients with suspected AD co‐pathology.ConclusionThis CSF proteomics study demonstrates substantial biochemical similarities between ADAD and sporadic AD, suggesting involvement of the same biological processes. Besides known AD‐related proteins, we identified several relatively novel proteins, such as TMSB10, MMP‐10 and SMOC2, which have potential as novel biomarkers. With shared pathophysiological CSF changes, ADAD study findings might be translatable to sporadic AD, which could greatly expedite therapy development.