LFQ-Based Peptide and Protein Intensity Differential Expression Analysis.

Testing for significant differences in quantities at the protein level is a common goal of many LFQ-based mass spectrometry proteomics experiments. Starting from a table of protein and/or peptide quantities from a given proteomics quantification software, many tools and R packages exist to perform the final tasks of imputation, summarization, normalization, and statistical testing. To evaluate the effects of packages and settings in their substeps on the final list of significant proteins, we studied several packages on three public data sets with known expected protein fold changes. We found that the results between packages and even across different parameters of the same package can vary significantly. In addition to usability aspects and feature/compatibility lists of different packages, this paper highlights sensitivity and specificity trade-offs that come with specific packages and settings.

Construction of TME and Identification of crosstalk between malignant cells and macrophages by SPP1 in hepatocellular carcinoma.

Liver cancer accounts for 6% of all malignancies causing death worldwide, and hepatocellular carcinoma (HCC) is the most common histological type. HCC is a heterogeneous cancer, but how the tumour microenvironment (TME) of HCC contributes to the progression of HCC remains unclear. In this study, we investigated the immune microenvironment by multiomics analysis. The tumour immune infiltration characteristics of HCC were determined at the genomic, epigenetic, bulk transcriptome and single-cell levels by data from The Cancer Genome Atlas portal and the Gene Expression Omnibus (GEO). An epigenetic immune-related scoring system (EIRS) was developed to stratify patients with poor prognosis. SPP1, one gene in the EIRS system, was identified as an immune-related predictor of poor survival in HCC patients. Through receptor-ligand pair analysis in single-cell RNA-seq, SPP1 was indicated to mediate the crosstalk between HCC cells and macrophages via SPP1-CD44 and SPP1-PTGER4 association. In vitro experiments further validate SPP1 can trigger the polarization of macrophages to M2-phenotype tumour-associated macrophages (TAMs).

Two-atomic-layered optoelectronic device enabled by charge separation on graphene/semiconductor interface.

The Fermi level of graphene on different substrates usually changes significantly due to the interface difference between graphene and two-dimensional semiconductors. This feature opens many possibilities of manipulating optoelectronic devices by constructing graphene heterostructures through interface modification. Herein, we report the fabrication and optoelectronic response of an unconventional heterojunction device based on a graphene-MoSe2 hybrid interface. Different from the traditional three or more layered structure where the semiconductor is sandwiched between two electrodes, this device contains only two atomic layers: the MoSe2 layer serving as the photon absorber and the graphene layer functioning as the charge acceptor and both electrodes. This structure looks like short-circuited but shows an obvious photoelectric response, which is aided by electron transfers from MoSe2 to graphene. The photocurrent generation is explored quantitatively with electronic dynamics of graphene aided with ultrafast measurements. The two-layered architecture simplifies the fabrication of atomic-thick optoelectronic devices, allowing the as-grown semiconductors to be directly used and eliminating the damage-prone transfer process.

Second-harmonic generation divergence-a method for domain size evaluation of 2D materials.

Single-atomic-layered materials are important for future electronics. They allow optoelectronic devices to be fabricated at the single-atomic layer level. A single-atomic-layered two-dimensional (2D) transition metal dichalcogenide (TMD) film is usually composed of randomly orientated single-crystalline domains, and the size distribution of the domains on a large-area film has a significant impact on the applications of the film, but the impact is difficult to characterize. We report an approach to evaluate the size of the single-crystalline domains by measuring the second-harmonic generation divergence caused by the domains of different orientations. Using this method, domain size mapping on an 8×8mm2 region of a continuous MoS2 film is achieved. This method provides a fast and efficient way of domain size characterization across a large area in a non-destructive and transfer-free manner for single-atomic-layered TMD films.

Prognostic biomarker SMARCC1 and its association with immune infiltrates in hepatocellular carcinoma.

BACKGROUND: Epigenetic alterations contribute greatly to metastasis and dissemination in hepatocellular carcinoma (HCC). SMARCC1, as a SWI/SNF chromatin remodeling factor, has been reported to play important roles in many cancers. For the first time, with the bioinformatics analysis and wet-bench experiments, we explored the biological significance of SMARCC1 and its potential as putative therapeutic target in HCC. METHODS: The mRNA expression profiles and prognostic value of SMARCC1 were analyzed in the Oncomine, UALCAN and Kaplan-Meier Plotter databases. The expression of SMARCC1 and associated clinicopathological factors were further evaluated using a tissue microarray. Differentially expressed genes associated with SMARCC1 in HCC were obtained and analyzed via the LinkedOmics and GEPIA databases and Cytoscape software. To verify the important role of SMARCC1 in HCC, we knocked down and overexpressed SMARCC1 in different hepatic cell lines and conducted several functional experiments. Then, we evaluated the mutation profiles and transcriptional regulators of SMARCC1 using the cBioPortal, COSMIC, CistromeDB and TCGA databases. Finally, we addressed the relationship of SMARCC1 expression with immune cell infiltration via TIMER database analysis. RESULTS: Through data mining and tissue microarray verification, we found that the protein and mRNA levels of SMARCC1 are high in tumor tissues, which has remarkable diagnostic value in HCC patients. SMARCC1 and its hub genes showed prognostic value in HCC. Furthermore, we confirmed that SMARCC1 influenced the proliferation, migration, and invasion of HCC cells. Moreover, correlation analyses revealed that SMARCC1 expression was positively correlated with ZBTB40 transcription factors and negatively correlated with the DNA methylation level. Overall, we found that SMARCC1 affects immune infiltration and plays a tumor-promoting role in HCC. CONCLUSIONS: SMARCC1 is overexpressed and is a putative prognostic predictor in HCC. Due to the tumor-promoting role of SMARCC1, treatments inhibiting DNA methyltransferases and transcription factors or weakening the role of SMARCC1 in immune infiltration might improve the survival of HCC patients.

Cyclin-dependent kinase 19 upregulation correlates with an unfavorable prognosis in hepatocellular carcinoma.

OBJECTIVES: Cyclin-dependent kinase 19 (CDK19) is a component of the mediator coactivator complex, which is required for transcriptional activation. In this study, we utilized public databases and wet-bench hepatic cell line experiments to elucidate the potential roles of CDK19 in hepatocellular cancer (HCC). MATERIALS AND METHODS: We studied the relationships between CDK19 expression and several clinical features related to HCC via the Oncomine and UALCAN databases. The prognostic value of CDK19 was tested using the Kaplan-Meier Plotter database. We presented the mutations of CDK19 and addressed the relation of CDK19 expression with immune cell infiltration by means of the cBioPortal, Catalogue of Somatic Mutations in Cancer (COSMIC) and Tumor IMmune Estimation Resource (TIMER) databases. Hub genes were obtained and further analyzed using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database. To test the in silico findings, we knocked down CDK19 with short hairpin RNA (shRNA) technology in two hepatic cell lines and conducted several functional characterization experiments. RESULTS: Marked CDK19 upregulation was found in HCC tissues versus normal liver tissues, and CDK19 mRNA expression had high diagnostic value in HCC patients. Subgroup analysis showed that CDK19 overexpression was associated with sex, tumor stage and TP53 mutation status. The prognostic value of CDK19 upregulation for overall survival (OS) was significant in patients with stage 2-3, stage 3-4, and grade 2 disease. One percent of the patients had CDK19 mutations, but no relationship between CDK19 mutation and prognosis was observed. CDK19 was positively correlated with the abundances of CD4 + T cells, macrophages and dendritic cells. We identified 10 genes correlated with CDK19, 8 of which presented excellent prognostic value in HCC. These hub genes were directly involved in cell division and regulation of the G2/M cell cycle transition. Protein-protein interaction (PPI) and pathway predictions indicated that CDK19 is highly likely to be involved in several cellular functions, such as proliferation, migration, and invasion. These functions were strongly interfered from two independent hepatic cell lines after CDK19 knockdown. CONCLUSIONS: CDK19 could be a prognostic marker in HCC, and its therapeutic potential in HCC needs further study.

Photoluminescence of monolayer MoS2 modulated by water/O2/laser irradiation.

The low photoluminescence (PL) quantum yields of transition metal dichalcogenide monolayers have been a limiting factor for their optoelectronic applications. Various and even inconsistent mechanisms have been proposed to modulate their PL efficiencies. Herein, we use PL/Raman microspectroscopy and the corresponding in situ mapping, atomic force microscopy, and field-effect transistor (FET) characterization to investigate the changes in the structural and optical properties of monolayer MoS2. Relatively low power density (<4.08 × 105 W cm-2) of laser irradiation in ambient air can cause a slight PL suppression effect on monolayer MoS2, whereas relatively high power density (∼1.02 × 106 W cm-2) of laser irradiation brings significant PL enhancement. Experiments under different atmospheres reveal that the laser-irradiation-induced enhancement only occurs in the atmosphere containing O2 and is more remarkable in pure O2. In addition, physically adsorbed water can also induce PL enhancement of monolayer MoS2. FET devices suggest that the adsorbed water produces a p-doping effect on MoS2, and the laser irradiation in ambient air generates an n-doping effect, and both types of doping can enhance the PL intensity. The island-shaped defects caused by laser irradiation can be stabilized by oxygen atoms and act as trapping centers for excited trions or electrons, thus reducing the non-radiative recombination ratio and enhancing the PL intensity. The physically adsorbed water works in a similar way. A low power density of laser irradiation can sweep away the originally adsorbed H2O on the surface, thus reducing the PL.

miRNA miR-17-92 cluster is differentially regulated in the imiqumod-treated skin but is not required for imiqumod-induced psoriasis-like dermatitis in mice.

MicroRNAs (miRNAs) play very important roles in the control of immune cell and keratinocyte development and function and are implicated in skin inflammatory diseases, including psoriasis. miRNA miR-17-92 was reported to promote the differentiation of Th1 and Th1 cells and to regulate cell proliferation and apoptosis. Here we showed that imiquimod (IMQ) differentially regulates the expression of miR-17-92 cluster in the mouse skin, upregulating miR-17 and miR-19 families and downregulating miR-92. To investigate whether miR-17-92 cluster is functionally involved in the psoriasis, we have generated three mutant mice with specific deletion or overexpression of miR-17-92 cluster in keratinocytes, or with deletion of miR-17-92 cluster in T cells. Interestingly, deletion or overexpression of miR-17-92 cluster in keratinocytes, or deletion of miR-17-92 in T cells did not significantly affect IMQ-induced psoriasis-like dermatitis development in the mutant mice compared with wild-type littermates. Thus, miRNA miR-17-92 cluster may not be a key factor regulating imiqumod-induced psoriasis-like dermatitis.

Roles of microRNAs in psoriasis: Immunological functions and potential biomarkers.

MicroRNAs (miRNAs) are small non-coding RNA molecules, which function in RNA silencing and post-transcriptional regulation of gene expression. Psoriasis is an inflammatory skin disease characterized by the dysfunction of keratinocytes, with the immune dysregulation. We reviewed the recent studies on the roles of miRNAs in psoriasis and showed that miRNAs play key roles in psoriasis, including the regulation of hyperproliferation, cytokine and chemokine production in keratinocyte, as well as mediating immune dysfunction in psoriasis. Furthermore, miRNAs, particularly, circulating miRNAs may serve as novel biomarkers for diagnosis, monitoring therapy response and reflecting the disease severity. Thus, targeting specific miRNAs may be used to develop new therapeutic methods for psoriasis.

Application of metabolomics on diagnosis and treatment of patients with psoriasis in traditional Chinese medicine.

Traditional Chinese medicine (TCM) is one of the oldest forms of medical system. With syndrome as the core of diagnosis and therapy in TCM, it has the advantage of collecting macroscopic information of patients for diagnosis. To understand the in vivo mechanism of TCM, a metabolomics approach was used to investigate the global biological characterization of the urine of psoriasis patients with Blood Stasis Syndrome and the therapeutic metabolomics mechanism of the Optimized Yinxieling formula. A total of 41 cases of psoriasis patients with Blood Stasis Syndrome and 19 healthy volunteers were enrolled in this study. Fasting urine samples from patients with consecutive Optimized Yinxieling intake after 0, 4, 8 and 12 weeks and from healthy volunteers were analyzed by Orthogonal Projection on Latent Structures Discriminant Analysis (OPLS-DA), which was utilized for High Performance Liquid Chromatography (HPLC) analysis and temporal metabolic changes identification. For psoriasis group, the scores of PASI of patients decreased after 12 weeks of Optimized Yinxieling treating. The metabolic variations visualized not only in the healthy group and psoriasis group, but also in the psoriasis group before and after Optimized Yinxieling treatment, demonstrated that the metabolic characteristics of the two groups were significantly different. The optimized complex structure of the target proteins from Protein Data Bank was analyzed by software package Discovery Studio. With docking score of original inhibitor and the receptor as the threshold values, two compounds from Chinese medicinal chemical database were predicted to have good interactions with the target proteins. The Metabolomics technique combining molecular docking analysis enhanced our current understanding of the metabolic response to Blood Stasis Syndrome of Psoriasis and the action mechanism of Optimized Yinxieling. This article is part of a Special Issue entitled: Computational Proteomics, Systems Biology & Clinical Implications. Guest Editor: Yudong Cai.

Prognostic Value of IGFBP6 in Breast Cancer: Focus on Glucometabolism.

IGFBP6, a member of the IGF binding protein (IGFBP) family, is a specific inhibitor of insulin-like growth factor II (IGF-II) and can inhibit the growth of malignant tumors overexpressing IGF-II. Type 2 diabetes (T2D) is a basic disorder of glucose metabolism that can be regulated by IGF-related pathways. We performed bioinformatics analysis of the TCGA database to explore the possible mechanism of IGFBP6 in breast cancer (BC) metabolism and prognosis and collected clinical samples from BC patients with and without T2D to compare and verify the prognostic effect of IGFBP6. In our study, the levels of IGFBP1-6 were positively correlated with overall survival (OS) in patients with breast cancer. IGFBP6 was upregulated in estrogen receptor (ER)-positive BC, and ER-positive and progesterone receptor (PR) positive patients had a higher expression level of IGFBP6 than ER-negative and PR-negative patients. IGFBP6 could be used as an independent prognostic factor in BC. The expression of IGFBP6 was decreased in BC tissue, and BC tissue from patients with T2D had lower IGFBP6 expression levels than BC tissue from patients without T2D. IGFBP6 is mainly involved in the PI3K-Akt and TGF-ß signaling pathways and tumor microenvironment regulation. In terms of metabolism, the expression of IGFBP6 was negatively correlated with that of most glucose metabolism-related genes. IGFBP6 expression was mainly correlated with mutations in TP53, PIK3CA, CDH1, and MAP3K1. In addition, the upregulation of IGFBP6 in BC increased the drug sensitivity to docetaxel, paclitaxel and gemcitabine. Overall, these results indicated that high expression of IGFBP6 is associated with a good prognosis in BC patients, especially in those without T2D. It is not only involved in the maintenance of the tumor microenvironment in BC but also inhibits the energy metabolism of cancer cells through glucose metabolism-related pathways. These findings may provide a new perspective on IGFBP6 as a potential prognostic marker for BC.

Thermal-Responsive Antibacterial Hydrogel with Photothermal Therapy and Improving Wound Microenvironment for Promote Healing.

Skin damage is one of the most prevalent human injuries, which affects the health of human beings. However, skin damage is often accompanied by bacterial infection and wound microenvironment changes, causing damage to normal cells and inhibiting wound healing. Herein, we designed a thermal-responsive antibacterial hydrogel (GAG hydrogel) loaded with catalase (CAT)-like Au@Pt@MgSiO3 nanoparticles (APM NPs) and gentamicin (GM) to promote wound healing. The GAG hydrogel was used in a photothermal therapy (PTT)/antibiotic combination to kill bacteria, reduce the use of antibiotics, improve the wound microenvironment, promote cell proliferation, and accelerate wound healing. Under near-infrared laser irradiation, APM NPs in the hydrogel generated local hyperthermia to kill bacteria. Meanwhile, the generated heat led to a change in the hydrogel's morphology, enabling it to release GM and APM NPs to prevent the overuse of antibiotics. Subsequently, the CAT-like ability of the APM NPs decreased the oxidative stress caused by hydrogen peroxide (H2O2), thus remodeling the wound microenvironment. Then, the weakly acidic microenvironment of the wound caused the decomposition of the APM NPs and the release of magnesium ions (Mg2+), promoting the growth and migration of cells for wound healing. Therefore, the studied thermal-responsive antibacterial (GAG) hydrogel has potential in the field of wound healing.

AFDN Deficiency Promotes Liver Tropism of Metastatic Colorectal Cancer.

Liver metastasis is a major cause of morbidity and mortality in patients with colorectal cancer. A better understanding of the biological mechanisms underlying liver tropism and metastasis in colorectal cancer could help to identify improved prevention and treatment strategies. In this study, we performed genome-wide CRISPR loss-of-function screening in a mouse colorectal cancer model and identified deficiency of AFDN, a protein involved in establishing and maintaining cell-cell contacts, as a driver of liver metastasis. Elevated AFDN expression was correlated with prolonged survival in patients with colorectal cancer. AFDN-deficient colorectal cancer cells preferentially metastasized to the liver but not in the lungs. AFDN loss in colorectal cancer cells at the primary site promoted cancer cell migration and invasion by disrupting tight intercellular junctions. Additionally, CXCR4 expression was increased in AFDN-deficient colorectal cancer cells via the JAK-STAT signaling pathway, which reduced the motility of AFDN-deficient colorectal cancer cells and facilitated their colonization of the liver. Collectively, these data shed light on the mechanism by which AFDN deficiency promotes liver tropism in metastatic colorectal cancer. Significance: A CRISPR screen reveals AFDN loss as a mediator of liver tropism in colorectal cancer metastasis by decreasing tight junctions in the primary tumor and increasing interactions between cancer cells and hepatocytes.

Characterization of MKK family genes and their responses to temperature stress and Vibrio parahaemolyticus infection in noble scallop Chlamys nobilis.

Mitogen-activated protein kinase kinase (MKK), the key element of the Mitogen-activated protein kinase (MAPK) signaling pathway, is crucial for the immune response to adverse environments in aquatic animals. Nevertheless, there is limited information regarding the role of the MKK gene family in mollusks. In our study, genome data and transcriptome were used to identify four MKK genes (CnMKK4, CnMKK5, CnMKK6, and CnMKK7) in the noble scallop. The result of the gene structure, motif analysis, and phylogenetic tree revealed that MKK genes are relatively conserved in bivalves. Moreover, four CnMKK genes were significantly highly expressed in immune-related tissues, suggesting that CnMKKs may related to bivalve immunity. Furthermore, CnMKK6 and CgMKK4 were significantly differentially expressed (P < 0.05) under 24 h of temperature stress, and all CnMKKs were significantly differentially expressed (P < 0.05) under 24 h of Vibrio parahaemolyticus infection. These results showed that the CnMKKs may have a significant impact under biotic and abiotic stresses. In conclusion, the result of the CnMKKs provides valuable insights into comprehending the function of MKK genes in mollusks.

Age­integrated breast imaging reporting and data system assessment model to improve the accuracy of breast cancer diagnosis.

Early diagnosis is an effective strategy for decreasing breast cancer mortality. Ultrasonography is one of the most predominant imaging modalities for breast cancer owing to its convenience and non-invasiveness. The present study aimed to develop a model that integrates age with Breast Imaging Reporting and Data System (BI-RADS) lexicon to improve diagnostic accuracy of ultrasonography in breast cancer. This retrospective study comprised two cohorts: A training cohort with 975 female patients from Renmin Hospital of Wuhan University (Wuhan, China) and a validation cohort with 500 female patients from Maternal and Child Health Hospital of Hubei Province (Wuhan, China). Logistic regression was used to construct a model combining BI-RADS score with age and to determine the age-based prevalence of breast cancer to predict a cut-off age. The model that integrated age with BI-RADS scores demonstrated the best performance compared with models based solely on age or BI-RADS scores, with an area under the curve (AUC) of 0.872 (95% CI: 0.850-0.894, P<0.001). Furthermore, among participants aged <30 years, the prevalence of breast cancer was lower than the lower limit of the reference range (2%) for BI-RADS subcategory 4A lesions but within the reference range for BI-RADS category 3 lesions, as indicated by linear regression analysis. Therefore, it is recommended that management for this subset of participants are categorized as BI-RADS category 3, meaning that biopsies typically indicated could be replaced with short-term follow-up. In conclusion, the integrated assessment model based on age and BI-RADS may enhance accuracy of ultrasonography in diagnosing breast lesions and young patients with BI-RADS subcategory 4A lesions may be exempted from biopsy.

Genome-wide identification of gap junction gene family and their expression profiles under low temperature stress in noble scallop Chlamys nobilis.

Gap junctions, formed by gap junction proteins (GJ), play crucial roles in cell signaling and immune responses. The structure and function of the GJ from vertebrates (called connexins) have been extensively studied. However, little is known about the proteins forming gap junctions in invertebrates (called innexins). In this study, 14 GJ genes of Chlamys nobilis were identified. GJ proteins are mainly distributed on the plasma membrane, and all proteins are hydrophilic Phylogenetic tree analysis showed that the GJ proteins in C. nobilis were distantly related to those in vertebrates but closely related to those in invertebrates. Conserved motifs analysis of these GJ proteins in C. nobilis identified to have 10 conserved motifs, similar to gap junction proteins in other bivalves. Moreover, expression profiles of CnGJ genes under chronic and acute low temperature stress were also investigated. Results showed that chronic low temperature stress had a significant effect on the expression levels of CnGJ genes, and the expression profiles of CnGJ genes showed significantly variation under acute low temperature stress. All these results indicated that CnGJ genes play important roles in environmental adaptation in scallops. The present study initially elucidated the function of gap junction genes in noble scallop C. nobilis, which provides new insights into the GJ genes in mollusks and will help us better understand their roles in environmental stress in scallops.

Monitoring response to neoadjuvant therapy for breast cancer in all treatment phases using an ultrasound deep learning model.

Purpose: The aim of this study was to investigate the value of a deep learning model (DLM) based on breast tumor ultrasound image segmentation in predicting pathological response to neoadjuvant chemotherapy (NAC) in breast cancer. Methods: The dataset contains a total of 1393 ultrasound images of 913 patients from Renmin Hospital of Wuhan University, of which 956 ultrasound images of 856 patients were used as the training set, and 437 ultrasound images of 57 patients underwent NAC were used as the test set. A U-Net-based end-to-end DLM was developed for automatically tumor segmentation and area calculation. The predictive abilities of the DLM, manual segmentation model (MSM), and two traditional ultrasound measurement methods (longest axis model [LAM] and dual-axis model [DAM]) for pathological complete response (pCR) were compared using changes in tumor size ratios to develop receiver operating characteristic curves. Results: The average intersection over union value of the DLM was 0.856. The early-stage ultrasound-predicted area under curve (AUC) values of pCR were not significantly different from those of the intermediate and late stages (p< 0.05). The AUCs for MSM, DLM, LAM and DAM were 0.840, 0.756, 0.778 and 0.796, respectively. There was no significant difference in AUC values of the predictive ability of the four models. Conclusion: Ultrasonography was predictive of pCR in the early stages of NAC. DLM have a similar predictive value to conventional ultrasound for pCR, with an add benefit in effectively improving workflow.

Systematic analysis of serum peptidase inhibitor 3 in psoriasis diagnosis and treatment.

BACKGROUND: Psoriasis is a chronic inflammatory skin disease. To date, there are no serum biomarkers for psoriasis that have been validated to diagnose or treat psoriasis. METHODS: Peptidase inhibitor 3 (PI3) levels in serum were measured using chemiluminescence immunoassay (CLIA) in two independent cohorts including healthy controls (HC) and patients diagnosed with chronic urticaria (CU), chronic eczema (CE), systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), psoriatic arthritis (PsA), or psoriasis vulgaris (PV). Receiver operating characteristic (ROC) curve analysis determined the diagnostic performance of PI3 in patients with psoriasis. The correlation between PI3 levels and the Psoriasis Area Severity Index (PASI) score was analyzed using the Spearman correlation method. Additionally, the study evaluated PI3 expression and treatment response of PV patients 12 weeks before and after topical treatment with calcipotriol betamethasone and calcipotriol ointment (T#1) or topical therapy plus PSORI-CM01 granules (T#2). RESULTS: In cohort #1, PI3 levels effectively discriminate PV patients from HC and CU patients, with AUCs of 0.909 and 0.840, respectively. In cohort #2, AUCs for detecting PV patients among HC, CU, CE, SLE, and RA patients were 0.940, 0.926, 0.802, 0.989, and 0.951, respectively. For PsA patients, AUCs were 0.989, 0.986, 0.910, 1.000, and 0.984 compared to HC, CU, CE, SLE, and RA patients, respectively. In both cohorts, PI3 levels correlated significantly with PASI scores in PV patients (cohort #1, r = 0.433; cohort #2, r = 0.634) and PsA patients (cohort #2, r = 0.718). Moreover, univariate logistic regression analyses revealed that PV patients with higher PI3 expression had a significantly higher risk of treatment resistance, with an odds ratio of 3.45 [95% confidence interval (CI) 1.54, 7.74, p = 0.003]. Finally, PI3 levels decreased nearly 35-fold more in the responder than in the non-responder group before and after treatment. CONCLUSIONS: Serological PI3 is a reliable biomarker for PV diagnosis and may have the potential to predict and monitor the progression of PV before and after treatment. Key Points • This study validated PI3's diagnostic performance in two independent psoriasis cohorts using CLIA. • PI3 expression is significantly correlated with the psoriasis severity and with patients who benefited from the treatments. • Serological PI3 is a reliable biomarker for psoriasis diagnosis and may have the potential to monitor the psoriasis progression with and without treatments.

Comprehensive analysis of cuproptosis-related genes involved in immune infiltration and their use in the diagnosis of hepatic ischemia‒reperfusion injury: an experimental Study.

BACKGROUND: Hepatic ischemia reperfusion injury (HIRI) is a common injury not only during liver transplantation but also during major hepatic surgery. HIRI causes severe complications and affects the prognosis and survival of patients. Cuproptosis, a newly identified form of cell death, plays an important role in a variety of illnesses. However, its role in HIRI remains unknown. MATERIALS AND METHODS: The GSE151648 dataset was mined from the Gene Expression Omnibus (GEO) database, and differences were analyzed for intersections. Based on the differentially expressed genes (DEGs), functional annotation, differentially expressed cuproptosis-related genes (DE-CRGs) identification and lasso logistic regression were conducted. Correlation analysis of DE-CRGs and immune infiltration was further conducted, and DE-CRGs were applied to construct an HIRI diagnostic model. The hierarchical clustering method was used to classify the specimens of HIRI, and functional annotation was conducted to verify the accuracy of these DE-CRGs in predicting HIRI progression. The GSE14951 microarray dataset and GSE171539 single-cell sequencing dataset were chosen as validation datasets. At the same time, the significance of DE-CRGs was verified using a mouse model of HIRI with cuproptosis inhibitors and inducers. Finally, a network of transcription-factor-DE-CRGs and miRNA-DE-CRGs was constructed to reveal the regulation mechanisms. And potential drugs for DE-CRGs were predicted using Drug Gene Interaction Database (DGIdb). RESULTS: Overall, 2390 DEGs and 19 DE-CRGs were identified. Through machine learning algorithms, 8 featured DE-CRGs (GNL3, ALAS1, TSC22D2, KLF5, GTF2B, DNTTIP2, SLFN11 and HNRNPU) were screened, and 2 cuproptosis-related subclusters were defined. Based on the 8 DE-CRGs obtained from the HIRI model (AUC=0.97), the nomogram model demonstrated accuracy in predicting HIRI. Eight DE-CRGs were highly expressed in HIRI samples and were negatively related to immune cell infiltration. A higher level of immune infiltration and expression of CRG group B was found in the HIRI population. Differences in cell death and immune regulation were found between the 2 groups. The diagnostic value of the 8 DE-CRGs was confirmed in the validation of two datasets. The identification of 7 DE-CRGs (SLFN11 excluded) by HIRI animal model experiments was also confirmed. Using hTFtarget, miRWalk and DGIDB database, we predicted that 17 transcription factors, 192 miRNAs and 10 drugs might interact with the DE-CRGs. CONCLUSION: This study shows that cuproptosis may occur in HIRI and is correlated with immune infiltration. Additionally, a cuproptosis-related predictive model was constructed for studying the causes of HIRI and developing targeted treatment options for HIRI.

Predicting life span of type 2 diabetes patients through alkaline phosphatase and vitamin D: Results from NHANES 1999-2018.

BACKGROUND AND AIMS: Disparities in serum biomarker levels related to mortality persist within the US diabetic population. We conducted a study to explore the impact of alkaline phosphatase (ALP) on all-cause mortality and cardiovascular disease (CVD) mortality in type 2 diabetes patients. METHODS: We analyzed a nationally representative sample of individuals aged 20 years and above from the National Health and Nutrition Examination Survey (NHANES) conducted in the United States between 1999 and 2018. Baseline demographic information and biochemical markers, including blood glucose, γ-glutamyltranspeptidase, vitamin D and albumin, were collected. Participants were divided into four groups based on ALP levels and linked to the National Death Index to assess mortality. Follow-up continued until December 2019, and multiple mediation analyses were performed to assess the combined impact of different indicators on ALP differences in all-cause mortality and cardiovascular mortality risk. RESULTS: Our analysis included 6481 NHANES participants, categorized as follows: 1626 (21.9%) had ALP levels below 58 U/L, 1674 in the second quartile (58-72 U/L), 1569 in the third quartile (72-88.3 U/L), and 1612 in the fourth quartile (above 88.3U/L). Significantly higher all-cause mortality and cardiovascular mortality rates were observed among participants in the 4th ALP quartile compared to other levels. The all-cause mortality rate was 38.06 per 1000 person-years (95% CI 34.89-41.51), and the cardiovascular mortality rate was 10.67 (9.06-12.57). Mediation analysis indicated that Vitamin D and albumin played a mediating role in the association between all-cause mortality, cardiovascular mortality, and ALP levels, with mediation proportions ranging from 10.33% to 27.64%. CONCLUSIONS: Our study suggests that ALP levels have clinical value in predicting all-cause and CVD mortality risk in T2DM patients. The upregulation of Vitamin D and albumin might play a significant role in improving risk prediction and enable targeted interventions for reducing mortality risk in this population.