In this paper, we report a study on the clinical relevance of prothymosin-α expression and its correlation with intratumoral Foxp3(+) and CD8(+) lymphocytes (Foxp3(+)TIL and CD8(+)TIL) in bladder cancer patients. We used immunohistochemical staining for prothymosin-α, Foxp3, and CD8 on 101 tumor specimens harvested by endoscopic resection. The results were correlated with clinicopathological variables and clinical outcome in bladder cancer patients, particularly in 73 patients with superficial disease, using the log-rank test and Cox proportional hazard model. Overall, of the tumors, 30 % were negative, 34 % showed nuclear, and 37 % showed cytoplasmic prothymosin-α expression. Foxp3(+)TILs were detected in 11 % of patients (nonnuclear vs. nuclear, p = 0.096). Patients with a history of urothelial carcinoma have a higher frequency of nonnuclear prothymosin-α expression than those without (p = 0.016, chi-square test). By univariate and multivariate analyses of cases with superficial disease, grade and stage were identified as independent predictors for recurrence-free survival (p = 0.016 and 0.016, respectively). Higher stage and nonnuclear prothymosin-α expression independently predict shorter progression-free survival (p = 0.006 and 0.043, respectively). The presence of Foxp3(+)TILs was significantly associated with disease progression by univariate analysis (p = 0.022), but not by multivariate analysis (p = 0.147). In vitro assays showed that J82 cells which express ectopically nuclear prothymosin-α exhibit higher growth rate and secrete less TGF-β1 than those with cytoplasmic expression or control cells. Altogether, prothymosin-α expression is a determinant of disease progression in superficial bladder cancer. Foxp3(+)TILs tend to be found more often in bladder cancer with nonnuclear prothymosin-α expression. Future study is required to unravel their interaction.
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Brief Bioinform
November 2024
School of Engineering, Westlake University, No. 600 Dunyu Road, 310030 Zhejiang, P.R. China.
Single-cell RNA sequencing (scRNA-seq) offers remarkable insights into cellular development and differentiation by capturing the gene expression profiles of individual cells. The role of dimensionality reduction and visualization in the interpretation of scRNA-seq data has gained widely acceptance. However, current methods face several challenges, including incomplete structure-preserving strategies and high distortion in embeddings, which fail to effectively model complex cell trajectories with multiple branches.
View Article and Find Full Text PDFBrief Bioinform
November 2024
Biotherapeutics Molecule Discovery, Boehringer Ingelheim Pharmaceutical Inc., 900 Ridgebury Road, Ridgefield, CT 06877, United States.
Antibody generation requires the use of one or more time-consuming methods, namely animal immunization, and in vitro display technologies. However, the recent availability of large amounts of antibody sequence and structural data in the public domain along with the advent of generative deep learning algorithms raises the possibility of computationally generating novel antibody sequences with desirable developability attributes. Here, we describe a deep learning model for computationally generating libraries of highly human antibody variable regions whose intrinsic physicochemical properties resemble those of the variable regions of the marketed antibody-based biotherapeutics (medicine-likeness).
View Article and Find Full Text PDFBrief Bioinform
November 2024
Guangdong Provincial Key Laboratory of Mathematical and Neural Dynamical Systems, Great Bay University, No. 16 Daxue Rd, Songshanhu District, Dongguan, Guangdong, 523000, China.
Multimodal omics provide deeper insight into the biological processes and cellular functions, especially transcriptomics and proteomics. Computational methods have been proposed for the integration of single-cell multimodal omics of transcriptomics and proteomics. However, existing methods primarily concentrate on the alignment of different omics, overlooking the unique information inherent in each omics type.
View Article and Find Full Text PDFTIGIT and PVRIG are immune checkpoints co-expressed on activated T and NK cells, contributing to tumor immune evasion. Simultaneous blockade of these pathways may enhance therapeutic efficacy, positioning them as promising dual targets for cancer immunotherapy. This study aimed to develop a bispecific antibody (BsAb) to co-target TIGIT and PVRIG.
View Article and Find Full Text PDFEmerg Microbes Infect
January 2025
Key Laboratory of Jiangxi Province for Transfusion Medicine, Department of Blood Transfusion, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, China.
The tRNA-derived small RNAs (tsRNAs) are a new class of non coding RNAs, which are stable in body fluids and can be used as potential biomarkers for disease diagnosis. However, the exact value of tsRNAs in the diagnosis of tuberculosis (TB) is still unclear. The objective of the present study was to evaluate the performance of the serum tsRNAs biosignature to distinguish between active TB, healthy controls, latent TB infection, and other respiratory diseases.
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