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

Coordinated distributed experiments: an emerging tool for testing global hypotheses in ecology and environmental science

There is a growing realization among scientists and policy makers that an increased understanding of today's environmental issues requires international collaboration and data synthesis. Meta-analyses have served this role in ecology for more than a decade, but the different experimental methodologies researchers use can limit the strength of the meta-analytic approach. Considering the global nature of many environmental issues, a new collaborative approach, which we call coordinated distributed experiments (CDEs), is needed that will control for both spatial and temporal scale, and that encompasses large geographic ranges. Ecological CDEs, involving standardized, controlled protocols, have the potential to advance our understanding of general principles in ecology and environmental science

Single nucleotide polymorphisms at the TRAF1/C5 locus are associated with rheumatoid arthritis in a Han Chinese population

<p>Abstract</p> <p>Background</p> <p>Genetic variants in <it>TRAF1C5 </it>and <it>PTPN22 </it>genes have been shown to be significantly associated with arthritis rheumatoid in Caucasian populations. This study investigated the association between single nucleotide polymorphisms (SNPs) in <it>TRAF1/C5 </it>and <it>PTPN22 </it>genes and rheumatoid arthritis (RA) in a Han Chinese population. We genotyped SNPs rs3761847 and rs7021206 at the <it>TRAF1/C5 </it>locus and rs2476601 SNP in the <it>PTPN22 </it>gene in a Han Chinese cohort composed of 576 patients with RA and 689 controls. The concentrations of anti-cyclic citrullinated peptide antibodies (CCP) and rheumatoid factor (RF) were determined for all affected patients. The difference between the cases and the controls was compared using <it>χ</it>²analysis.</p> <p>Results</p> <p>Significant differences in SNPs rs3761847 and rs7021206 at <it>TRAF1/C5 </it>were observed between the case and control groups in this cohort; the allelic p-value was 0.0018 with an odds ratio of 1.28 for rs3761847 and 0.005 with an odds ratio of 1.27 for rs7021206. This significant association between rs3761847 and RA was independent of the concentrations of anti-CCP and RF. No polymorphism of rs2476601 was observed in this cohort.</p> <p>Conclusions</p> <p>We first demonstrated that genetic variants at the <it>TRAF1/C5 </it>locus are significantly associated with RA in Han Chinese, suggesting that <it>TRAF1/C5 </it>may play a role in the development of RA in this population, which expands the pathogenesis role of <it>TRAF1/C5 </it>in a different ethnicity.</p

Antibody light-chain-restricted recognition of the site of immune pressure in the RV144 HIV-1 vaccine trial is phylogenetically conserved.

CAPRISA, 2014.Abstract available in pdf

Clinic application of tissue engineered bronchus for lung cancer treatment

BACKGROUND Delayed revascularization process and substitute infection remain to be key challenges in tissue engineered (TE) airway reconstruction. We propose an "in-vivo bioreactor" design, defined as an implanted TE substitutes perfused with an intra-scaffold medium flow created by an extracorporeal portable pump system for in situ organ regeneration. The perfusate keeps pre-seeded cells alive before revascularization. Meanwhile the antibiotic inside the perfusate controls topical infection. METHODS A stage IIIA squamous lung cancer patient received a 5-cm TE airway substitute, bridging left basal segment bronchus to carina, with the in-vivo bioreactor design to avoid left pneumonectomy. Continuous intra-scaffold Ringer's-gentamicin perfusion lasted for 1 month, together with orthotopic peripheral total nucleated cells (TNCs) injection twice a week. RESULTS The patient recovered uneventfully. Bronchoscopy follow-up confirmed complete revascularization and reepithelialization four months postoperatively. Perfusate waste test demonstrated various revascularization growth factors secreted by TNCs. The patient received two cycles of chemotherapy and 30 Gy radiotherapy thereafter without complications related to the TE substitute. CONCLUSIONS In-vivo bioreactor design combines the traditionally separated in vitro 3D cell-scaffold culture system and the in vivo regenerative processes associated with TE substitutes, while treating the recipients as bioreactors for their own TE prostheses. This design can be applied clinically. We also proved for the first time that TE airway substitute is able to tolerate chemo-radiotherapy and suitable to be used in cancer treatment

Migration of the distal catheter of a ventriculoperitoneal shunt into the colon: Case report and clinical analysis Migration of the catheter of colon from VPS

AbstractColonic perforation is an extremely rare complication following ventriculoperitoneal (VP) shunting. The common treatment is to remove the perforating catheter and replace it with a new one. Here we report a case of colonic perforation from VP shunting in a 2-year, 8-month-old boy who presented with the distal end of the shunt catheter protruding out of his anus. The distal catheter was removed via the anus and the perforation repaired transanally. The patient's postoperative course was uneventful. This case reminds us that we should not make another rush to perform a new shunt operation unless there are some manifestations of hydrocephalus. Potential mechanisms of migration and its management strategy are discussed

Comparison of whole genome sequences of three Bacillus cereus strains reveals the food safety risks of Apostichopus japonicus in China

Sea cucumber (Apostichopus japonicus) is considered to be an important food and nourishing ingredient in Asian cuisine, but consumers are vulnerable to food safety risks because of eating customs and breeding conditions. Three isolates (CH, HB, and WH) of Bacillus cereus were obtained from sea cucumbers in three coastal aquaculture areas in northeastern China. We performed whole genome sequencing and the complete genome of each isolate was composed of one circular chromosome, which was further analyzed. COG functional categories, pathogenic bacteria virulence factors and evolutionary relationships were investigated. Virulence factor database (VFDB) analysis demonstrated that all three B. cereus isolates possessed multiple potential virulence factors, which indicates the urgent need to improve microbial detection in aquatic products to ensure seafood security in China