PTPN1 is a prognostic biomarker related to cancer immunity and drug sensitivity: from pan-cancer analysis to validation in breast cancer.

Background: Protein tyrosine phosphatase non-receptor type 1 (PTPN1), a member of the protein tyrosine phosphatase superfamily, has been identified as an oncogene and therapeutic target in various cancers. However, its precise role in determining the prognosis of human cancer and immunological responses remains elusive. This study investigated the relationship between PTPN1 expression and clinical outcomes, immune infiltration, and drug sensitivity in human cancers, which will improve understanding regarding its prognostic value and immunological role in pan-cancer. Methods: The PTPN1 expression profile was obtained from The Cancer Genome Atlas and Cancer Cell Line Encyclopedia databases. Kaplan-Meier, univariate Cox regression, and time-dependent receiver operating characteristic curve analyses were utilized to clarify the relationship between PTPN1 expression and the prognosis of pan-cancer patients. The relationships between PTPN1 expression and the presence of tumor-infiltrated immune cells were analyzed using Estimation of Stromal and Immune cells in Malignant Tumor tissues using Expression data and Tumor Immune Estimation Resource. The cell counting kit-8 (CCK-8) assay was performed to examine the effects of PTPN1 level on the sensitivity of breast cancer cells to paclitaxel. Immunohistochemistry and immunoblotting were used to investigate the relationship between PTPN1 expression, immune cell infiltration, and immune checkpoint gene expression in human breast cancer tissues and a mouse xenograft model. Results: The pan-cancer analysis revealed that PTPN1 was frequently up-regulated in various cancers. High PTPN1 expression was associated with poor prognosis in most cancers. Furthermore, PTPN1 expression correlated highly with the presence of tumor-infiltrating immune cells and the expression of immune checkpoint pathway marker genes in different cancers. Furthermore, PTPN1 significantly predicted the prognosis for patients undergoing immunotherapy. The results of the CCK-8 viability assay revealed that PTPN1 knockdown increased the sensitivity of MDA-MB-231 and MCF-7 cells to paclitaxel. Finally, our results demonstrated that PTPN1 was associated with immune infiltration and immune checkpoint gene expression in breast cancer. Conclusion: PTPN1 was overexpressed in multiple cancer types and correlated with the clinical outcome and tumor immunity, suggesting it could be a valuable potential prognostic and immunological biomarker for pan-cancer.

A Novel Inflammatory Response-Related Gene Signature Predicts Immune Status and Prognosis of Breast Cancer.

Purpose: Breast cancer is the most common type of cancer and the leading cause of cancer-related death in women worldwide. In this study, we aimed to construct an inflammatory response-related gene model for predicting the immune status and prognosis of breast cancer patients. Methods: We obtained the inflammatory response-related genes from the Molecular Signatures Database. Furthermore, we used univariate Cox regression analysis, the least absolute shrinkage and selection operator (LASSO) regression analysis, and multivariate Cox regression to construct an inflammatory response-related gene signature (IRGS) model based on dataset obtained from The Cancer Genome Atlas (TCGA). Patients were consequently categorized into high-risk and low-risk groups. Kaplan-Meier analysis was used to compare the overall survival (OS) of high-risk and low-risk groups. Following that, we validated the model using a dataset (GSE96058) acquired from Gene Expression Omnibus (GEO) database. Univariate and multivariate Cox analyses were used to determine the independent prognostic value of the IRGS in the TCGA and GSE96058 cohorts. A nomogram was constructed to predict the OS in the TCGA cohort. Further, we used Gene Set Enrichment Analysis (GSEA), CIBERSORT, and single-sample Gene Set Enrichment Analysis (ssGSEA) to evaluate the associations of IRGS with immune-associated pathways and immune infiltration. Finally, the relationship between the expression of the signature genes and drug sensitivity was conducted using Pearson correlation analysis. Results: We established an IRGS to stratify breast cancer patients into the low-risk and high-risk groups. In both the training and validation sets, patients in the high-risk group had significantly shorter OS than those in the low-risk group. The risk score was significantly correlated with the clinical characteristics and could be used as a tool to predict the prognosis of breast cancer. Moreover, we found that the IRGS risk score was an independent predictor of OS in breast cancer patients, and a nomogram model based on IRGS risk score and other clinical factors could effectively predict the prognosis of breast cancer patients. Furthermore, the IRGS risk score was correlated with immune characteristics and was inversely associated with the abundance of immune cell infiltration. Patients with a low IRGS risk score had higher expression levels of immune checkpoint genes, suggesting that IRGS can be used as a potential indicator for immunotherapy. Finally, we found that the expression levels of prognostic genes were significantly correlated with tumor cell sensitivity to chemotherapeutic drugs. Conclusion: Overall, these findings suggest that the IRGS can be used to predict the prognosis and immune status of breast cancer patients and provide new therapeutic targets for the treatment of these patients.

PTPRO-related CD8+ T-cell signatures predict prognosis and immunotherapy response in patients with breast cancer.

Background: Poor immunogenicity and extensive immunosuppressive T-cell infiltration in the tumor immune microenvironment (TIME) have been identified as potential barriers to immunotherapy success in "immune-cold" breast cancers. Thus, it is crucial to identify biomarkers that can predict immunotherapy efficacy. Protein tyrosine phosphatase receptor type O (PTPRO) regulates multiple kinases and pathways and has been implied to play a regulatory role in immune cell infiltration in various cancers. Methods: ESTIMATE and single-sample gene set enrichment analysis (ssGSEA) were performed to uncover the TIME landscape. The correlation analysis of PTPRO and immune infiltration was performed to characterize the immune features of PTPRO. Univariate and multivariate Cox analyses were applied to determine the prognostic value of various variables and construct the PTPRO-related CD8+ T-cell signatures (PTSs). The Kaplan-Meier curve and the receiver operating characteristic (ROC) curve were used to estimate the performance of PTS in assessing prognosis and immunotherapy response in multiple validation datasets. Results: High PTPRO expression was related to high infiltration levels of CD8+ T cells, as well as macrophages, activated dendritic cells (aDCs), tumor-infiltrating lymphocytes (TILs), and Th1 cells. Given the critical role of CD8+ T cells in the TIME, we focused on the impact of PTPRO expression on CD8+ T-cell infiltration. The prognostic PTS was then constructed using the TCGA training dataset. Further analysis showed that the PTS exhibited favorable prognostic performance in multiple validation datasets. Of note, the PTS could accurately predict the response to immune checkpoint inhibitors (ICIs). Conclusion: PTPRO significantly impacts CD8+ T-cell infiltration in breast cancer, suggesting a potential role of immunomodulation. PTPRO-based PTS provides a new immune cell paradigm for prognosis, which is valuable for immunotherapy decisions in cancer patients.

Tumor-Derived Exosomal Protein Tyrosine Phosphatase Receptor Type O Polarizes Macrophage to Suppress Breast Tumor Cell Invasion and Migration.

Tumor-derived exosomes, containing multiple nucleic acids and proteins, have been implicated to participate in the interaction between tumor cells and microenvironment. However, the functional involvement of phosphatases in tumor-derived exosomes is not fully understood. We and others previously demonstrated that protein tyrosine phosphatase receptor type O (PTPRO) acts as a tumor suppressor in multiple cancer types. In addition, its role in tumor immune microenvironment remains elusive. Bioinformatical analyses revealed that PTPRO was closely associated with immune infiltration, and positively correlated to M1-like macrophages, but negatively correlated to M2-like macrophages in breast cancer tissues. Co-cultured with PTPRO-overexpressing breast cancer cells increased the proportion of M1-like tumor-associated macrophages (TAMs) while decreased that of M2-like TAMs. Further, we observed that tumor-derived exosomal PTPRO induced M1-like macrophage polarization, and regulated the corresponding functional phenotypes. Moreover, tumor cell-derived exosomal PTPRO inhibited breast cancer cell invasion and migration, and inactivated STAT signaling in macrophages. Our data suggested that exosomal PTPRO inhibited breast cancer invasion and migration by modulating macrophage polarization. Anti-tumoral effect of exosomal PTPRO was mediated by inactivating STAT family in macrophages. These findings highlight a novel mechanism of tumor invasion regulated by tumor-derived exosomal tyrosine phosphatase, which is of translational potential for the therapeutic strategy against breast cancer.

Synthesis and Biological Evaluation of a Novel Glycidyl Metharcylate/Phaytic Acid-Based on Bagasse Xylan Composite Derivative.

The development of natural biomass materials with excellent properties is an attractive way to improve the application range of natural polysaccharides. Bagasse Xylan (BX) is a natural polysaccharide with various biological activities, such as antitumor, antioxidant, etc. Its physic-chemical and biological properties can be improved by functionalization. For this purpose, a novel glycidyl metharcylate/phytic acid based on a BX composite derivative was synthesized by a free radical polymerization technique with glycidyl metharcylate (GMA; GMABX) and further esterification with phytic acid (PA; GMABX-PA) in ionic liquid. The effects of the reaction conditions (i.e., temperature, time, initiator concentration, catalyst concentration, GMA concentration, PA concentration, mass of ionic liquid) on grafting rate(G), conversion rate(C) and degree of substitution(DS) are discussed. The structure of the composite material structure was confirmed by FTIR, 1H NMR and XRD. SEM confirmed the particle morphology of the composite derivative. The thermal stability of GMABX-PA was determined by TG-DTG. Molecular docking was further performed to study the combination mode of the GMABX-PA into the active site of two lung cancer proteins (5XNV, 2EB2) and a blood cancer protein (2M6N). In addition, tumor cell proliferation inhibition assays for BX, GMABX-PA were carried out using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetraz -olium bromide (MTT) method. The results showed that various reaction conditions exhibited favorable gradient curves, and that a maximum G of 56% for the graft copolymerization and a maximum DS of 0.267 can be achieved. The thermal stability was significantly improved, as demonstrated by the fact that there was still 60% residual at 800 °C. The molecular docking software generated satisfactory results with regard to the evaluated binding energy and combining sites. The inhibition ratio of GMABX-PA on NCI-H460 (lung cancer cells) reached 29.68% ± 4.45%, which is five times higher than that of BX. Therefore, the material was shown to be a potential candidate for biomedical applications as well as for use as a heat resistant material.

Preventive Effects of Bacillus licheniformis on Heat Stroke in Rats by Sustaining Intestinal Barrier Function and Modulating Gut Microbiota.

Heat stroke (HS) models in rats are associated with severe intestinal injury, which is often considered as the key event at the onset of HS. Probiotics can regulate the gut microbiota by inhibiting the colonization of harmful bacteria and promoting the proliferation of beneficial bacteria. Here, we investigated the preventive effects of a probiotic Bacillus licheniformis strain (BL, CMCC 63516) on HS rats as well as its effects on intestinal barrier function and gut microbiota. All rats were randomly divided into four groups: control (Con) + PBS (pre-administration with 1 ml PBS twice a day for 7 days, without HS induction), Con + BL group (pre-administration with 1 ml 1 × 108 CFU/ml BL twice a day for 7 days, without HS induction), HS + PBS (PBS, with HS induction), and HS + BL (BL, with HS induction). Before the study, the BL strain was identified by genomic DNA analysis. Experimental HS was induced by placing rats in a hot and humid chamber for 60 min until meeting the diagnostic criterion of HS onset. Body weight, core body temperature, survival rate, biochemical markers, inflammatory cytokines, and histopathology were investigated to evaluate the preventive effects of BL on HS. D-Lactate, I-FABP, endotoxin, and tight-junction proteins were investigated, and the fluorescein isothiocyanate-dextran (FD-4) test administered, to assess the degree of intestinal injury and integrity. Gut microbiota of rats in each group were analyzed by 16S rRNA sequencing. The results showed that pre-administration with BL significantly attenuated hyperthermia, reduced HS-induced death, alleviated multiple-organ injury, and decreased the levels of serum inflammatory cytokines. Furthermore, BL sustained the intestinal barrier integrity of HS rats by alleviating intestinal injury and improving tight junctions. We also found that BL significantly increased the ratios of two probiotic bacteria, Lactobacillus and Lactococcus. In addition, Romboutsia, a candidate biomarker for HS diagnosis, was unexpectedly detected. In summary, BL pre-administration for 7 days has preventative effects on HS that may be mediated by sustaining intestinal barrier function and modulating gut microbiota.

Neuronal Population Reconstruction From Ultra-Scale Optical Microscopy Images via Progressive Learning.

Reconstruction of neuronal populations from ultra-scale optical microscopy (OM) images is essential to investigate neuronal circuits and brain mechanisms. The noises, low contrast, huge memory requirement, and high computational cost pose significant challenges in the neuronal population reconstruction. Recently, many studies have been conducted to extract neuron signals using deep neural networks (DNNs). However, training such DNNs usually relies on a huge amount of voxel-wise annotations in OM images, which are expensive in terms of both finance and labor. In this paper, we propose a novel framework for dense neuronal population reconstruction from ultra-scale images. To solve the problem of high cost in obtaining manual annotations for training DNNs, we propose a progressive learning scheme for neuronal population reconstruction (PLNPR) which does not require any manual annotations. Our PLNPR scheme consists of a traditional neuron tracing module and a deep segmentation network that mutually complement and progressively promote each other. To reconstruct dense neuronal populations from a terabyte-sized ultra-scale image, we introduce an automatic framework which adaptively traces neurons block by block and fuses fragmented neurites in overlapped regions continuously and smoothly. We build a dataset "VISoR-40" which consists of 40 large-scale OM image blocks from cortical regions of a mouse. Extensive experimental results on our VISoR-40 dataset and the public BigNeuron dataset demonstrate the effectiveness and superiority of our method on neuronal population reconstruction and single neuron reconstruction. Furthermore, we successfully apply our method to reconstruct dense neuronal populations from an ultra-scale mouse brain slice. The proposed adaptive block propagation and fusion strategies greatly improve the completeness of neurites in dense neuronal population reconstruction.

Design and synthesis of novel and potent amide linked PPARgamma/delta dual agonists.

A series of potent amide linked PPARgamma/delta dual agonists (1a) has been discovered through rational design. In the ZDF rat model of type 2 diabetes, compound (R)-3-[4-(3-{1-[(5-chloro-1,3-dimethyl-1H-indole-2-carbonyl)-amino]-ethyl}-5-fluoro-phenoxy)-2-ethyl-phenyl]-propionic acid (42) from this series has demonstrated glucose lowering efficacy comparable to the marketed PPARgamma agonist rosiglitazone with less weight gain.

Design and synthesis of dual peroxisome proliferator-activated receptors gamma and delta agonists as novel euglycemic agents with a reduced weight gain profile.

The design and synthesis of the dual peroxisome proliferator-activated receptor (PPAR) gamma/delta agonist (R)-3-{4-[3-(4-chloro-2-phenoxy-phenoxy)-butoxy]-2-ethyl-phenyl}-propionic acid (20) for the treatment of type 2 diabetes and associated dyslipidemia is described. The compound possesses a potent dual hPPAR gamma/delta agonist profile (IC(50) = 19 nM/4 nM; EC(50) = 102 nM/6 nM for hPPARgamma and hPPARdelta, respectively). In preclinical models, the compound improves insulin sensitivity and reverses diabetic hyperglycemia with less weight gain at a given level of glucose control relative to rosiglitazone.

Synthesis and structure-activity relationships of novel dipeptides and reduced dipeptides as ligands for melanocortin subtype-4 receptor.

A series of benzylic piperazines (e.g., 4 and 5) attached to an 'address element', the dipeptide H-D-Tic-D-p-Cl-Phe-OH, 3 has been identified as ligands for the melanocortin subtype-4 receptor (MC4R). We describe herein the structure-activity relationship (SAR) studies on the N-terminal residue of the 'address element'. Several novel dipeptides and reduced dipeptides with high MC4R binding affinities and selectivity emerged from this SAR study.

Synthesis of the C20-C26 building block of halichondrins via a regiospecific and stereoselective S(N)2' reaction.

[reaction: see text] A regiospecific and stereoselective S(N)2' reaction to convert the trisylate into the vinyl iodide is presented. The homoallylic alcohol is used to direct the delivery of LiCu(Me)(2).

In vitro hepatotoxicity of the cyanobacterial alkaloid cylindrospermopsin and related synthetic analogues.

Cylindrospermopsin (CY), a sulfate ester of a tricyclic guanidine substituted with a hydroxymethyluracil, is a cyanobacterial toxin of increasing environmental import as it frequently occurs in drinking water reservoirs. As a toxin, CY mainly targets the liver but also involves other organs. In hepatocytes CY inhibits the synthesis of protein and of glutathione, leading to cell death. The total chemical synthesis of CY has recently been reported (Xie et al., 2000, J. Am. Chem. Soc. 22, 5017-5024). The synthesis has provided analogues of CY to study aspects of the relationship between chemical structure and activity that contribute to toxicity. Protein synthesis inhibition was measured in vitro using a rabbit reticulocyte system. Primary cultures of rat hepatocytes were used to determine the biological activity of CY and analogues in intact cells. Protein synthesis and cell glutathione levels were measured. We could distinguish between CY transport and biological activity by comparing the results in vitro to those in intact cells. The role of the sulfate group in CY toxicity was examined by comparing biological effects of CY with that of CY-DIOL (synthetic CY lacking the sulfate group). The sulfate group was found not to play a role in CY activity or in its uptake into cells, since there was no significant difference in biological activity in vitro or in cells between natural CY and CY-DIOL. The orientation of the hydroxyl group at C7 also had no impact on biological activity or transport of CY, since the C7 epimer of CY (EPI-CY) and the corresponding diol (EPI-DIOL) had activity similar to RAC-CY in vitro and in intact cells. AB-MODEL, the analogue lacking an intact C ring, and the methyl and hydroxyl groups of ring A could inhibit protein synthesis (but at concentrations 500-1000-fold higher than natural CY). Other structurally simpler synthetic analogues lacked biological activity.