The comprehensive potential of AQP1 as a tumor biomarker: evidence from kidney neoplasm cohorts, cell experiments and pan-cancer analysis.

Aquaporin1 (AQP1) facilitates water transport. Its ability to be a biomarker at the pan-cancer level remains uninvestigated. We performed immunohistochemical staining on tissues from 370 individuals with kidney neoplasms to measure AQP1 expression.

Construction and validation of a regulatory T cells-based classification of renal cell carcinoma: an integrated bioinformatic analysis and clinical cohort study.

Purpose: Renal cell carcinoma (RCC), exhibiting remarkable heterogeneity, can be highly infiltrated by regulatory T cells (Tregs). However, the relationship between Treg and the heterogeneity of RCC remains to be explored.

Methods: We acquired single-cell RNA-seq profiles and 537 bulk RNA-seq profiles of TCGA-KIRC cohort.

Identification of Critical Phosphorylation Sites Enhancing Kinase Activity With a Bimodal Fusion Framework.

Phosphorylation is an indispensable regulatory mechanism in cells, with specific sites on kinases that can significantly enhance their activity. Although several such critical phosphorylation sites (phos-sites) have been experimentally identified, many more remain to be explored. To date, no computational method exists to systematically identify these critical phos-sites on kinases.

A Deep Learning Model for Accurate Maize Disease Detection Based on State-Space Attention and Feature Fusion.

In improving agricultural yields and ensuring food security, precise detection of maize leaf diseases is of great importance. Traditional disease detection methods show limited performance in complex environments, making it challenging to meet the demands for precise detection in modern agriculture. This paper proposes a maize leaf disease detection model based on a state-space attention mechanism, aiming to effectively utilize the spatiotemporal characteristics of maize leaf diseases to achieve efficient and accurate detection.

Unveiling the unique role of TSPAN7 across tumors: a pan-cancer study incorporating retrospective clinical research and bioinformatic analysis.

Background: TSPAN7 is an important factor in tumor progression. However, the precise function of TSPAN7 and its role in pan-cancer are not clear.

Methods: Based on Xinhua cohort incorporating 370 patients with kidney neoplasm, we conducted differential expression analysis by immunohistochemistry between tumor and normal tissues, and explored correlations of TSPAN7 with patients' survival.

Preoperative neoadjuvant targeted therapy remodels intra-tumoral heterogeneity of clear-cell renal cell carcinoma and ferroptosis inhibition induces resistance progression.

Neoadjuvant tyrosine kinase inhibitor (TKI) therapy is an important treatment option for advanced renal cell carcinoma (RCC). Many RCC patients may fail to respond or be resistant to TKI therapy. We aimed to explore the key mechanisms of neoadjuvant therapy résistance.

CRISPR genome-wide screening identifies PAK1 as a critical driver of ARSI cross-resistance in prostate cancer progression.

Next-generation androgen receptor signaling inhibitors (ARSIs), such as enzalutamide (Enza) and darolutamide (Daro), are initially effective for the treatment of advanced prostate cancer (PCa) and castration-resistant prostate cancer (CRPC). However, patients often relapse and develop cross-resistance, which consequently makes drug resistance an inevitable cause of CRPC-related mortality. By conducting a comprehensive analysis of GEO datasets, CRISPR genome-wide screening results, ATAC-seq data, and RNA-seq data, we systemically identified PAK1 as a significant contributor to ARSI cross-resistance due to the activation of the PAK1/RELA/hnRNPA1/AR-V7 axis.

Novel model of pyroptosis-related molecular signatures for prognosis prediction of clear cell renal cell carcinoma patients.

Pyroptosis is a programmed death mode of inflammatory cells, which is closely related to tumor progression and tumor immunity. Clear cell renal cell carcinoma (ccRCC) is the major pathological type of renal cell carcinoma (RCC) with poor prognosis. Many theories have tried to clarify the mechanism in the development of ccRCC, but the role of pyroptosis in ccRCC has not been well described.

Molecular subtyping and characterization of clear cell renal cell carcinoma by tumor differentiation trajectories.

Previous bulk RNA sequencing or whole genome sequencing on clear cell renal cell carcinoma (ccRCC) subtyping mainly focused on ccRCC cell origin or the complex tumor microenvironment (TME). Based on the single-cell RNA sequencing (scRNA-seq) data of 11 primary ccRCC specimens, cancer stem-cell-like subsets could be differentiated into five trajectories, whereby we further classified ccRCC cells into three groups with diverse molecular features. These three ccRCC subgroups showed significantly different outcomes and potential targets to tyrosine kinase inhibitors (TKIs) or immune checkpoint inhibitors (ICIs).

Glycolysis-related biomarker TCIRG1 participates in regulation of renal cell carcinoma progression and tumor immune microenvironment by affecting aerobic glycolysis and AKT/mTOR signaling pathway.

Background: Renal cell carcinoma (RCC) is a hypermetabolic disease. Abnormal up-regulation of glycolytic signaling promotes tumor growth, and glycolytic metabolism is closely related to immunotherapy of renal cancer. The aim of the present study was to determine whether and how the glycolysis-related biomarker TCIRG1 affects aerobic glycolysis, the tumor microenvironment (TME) and malignant progression of clear cell renal cell carcinoma (ccRCC).

Gankyrin-mediated interaction between cancer cells and tumor-associated macrophages facilitates prostate cancer progression and androgen deprivation therapy resistance.

Increasing evidence reveals that the interaction between tumor cells and tumor-associated macrophages (TAMs) facilitates the progression of prostate cancer, but the related mechanisms remained unclear. This study determined how gankyrin, a component of the 19S regulatory complex of the 26S proteasome, regulates the progression and androgen deprivation therapy (ADT) resistance of prostate cancer through tumor cell-TAM interactions. functional experiments and subcutaneous tumor models were used to explore the biological role and molecular mechanisms of gankyrin in prostate cancer cell-TAM interactions.

Single-cell RNA-seq integrated with multi-omics reveals SERPINE2 as a target for metastasis in advanced renal cell carcinoma.

Tumor growth, metastasis and therapeutic response are believed to be regulated by the tumor and its microenvironment (TME) in advanced renal cell carcinoma (RCC). However, the mechanisms underlying genomic, transcriptomic and epigenetic alternations in RCC progression have not been completely defined. In this study, single-cell RNA-sequencing (scRNA-seq) data were obtained from eight tissue samples of RCC patients, including two matched pairs of primary and metastatic sites (lymph nodes), along with Hi-C, transposable accessible chromatin by high-throughput (ATAC-seq) and RNA-sequencing (RNA-seq) between RCC (Caki-1) and human renal tubular epithelial cell line (HK-2).

ENO2 affects the EMT process of renal cell carcinoma and participates in the regulation of the immune microenvironment.

Clear cell renal cell carcinoma (ccRCC) is a frequent malignant tumor of the kidney which has a dismal prognosis. At present, targeted therapies and immunotherapy have achieved significant results; however, the overall survival rate of patients with ccRCC remains unacceptably poor. It is therefore necessary to find novel therapeutic and diagnostic targets for ccRCC.

FCER1G positively relates to macrophage infiltration in clear cell renal cell carcinoma and contributes to unfavorable prognosis by regulating tumor immunity.

Background: Tumor-associated macrophages (TAMs) are closely related to unfavorable prognosis of patients with clear cell renal cell carcinoma (ccRCC). However, the important molecules in the interaction between ccRCC and TAMs are unclear.

Methods: TCGA-KIRC gene expression data of tumor tissues and normal tissues adjacent to tumor were compared to identify differentially expressed genes in ccRCC.

MYL2 as a potential predictive biomarker for rhabdomyosarcoma.

Rhabdomyosarcoma (RMS) is a common malignant soft tissue sarcoma, which is the third most common soft tissue sarcoma after malignant fibrohistoma and liposarcoma. The discovery of potential postbiomarkers could lead to early and more effective treatment measures to reduce the mortality of RMS. The discovery of biomarker is expected to be the direction of targeted therapy, providing a new direction for the precise treatment of RMS.

Integrating HECW1 expression into the clinical indicators exhibits high accuracy in assessing the prognosis of patients with clear cell renal cell carcinoma.

Background: Although many intratumoral biomarkers have been reported to predict clear cell renal cell carcinoma (ccRCC) patient prognosis, combining intratumoral and clinical indicators could predict ccRCC prognosis more accurately than any of these markers alone. This study mainly examined the prognostic value of HECT, C2 and WW domain-containing E3 ubiquitin protein ligase 1 (HECW1) expression in ccRCC patients in combination with established clinical indicators.

Methods: The expression level of HECW1 was screened out by data-independent acquisition mass spectrometry (DIA-MS) and analyzed in ccRCC patients from the The Cancer Genome Atlas (TCGA) database and our cohort.

Bioinformatics analysis and verification of gene targets for renal clear cell carcinoma.

Background: It is estimated that there are 338,000 new renal-cell carcinoma releases every year in the world. Renal cell carcinoma (RCC) is a heterogeneous tumor, of which more than 70% is clear cell renal cell carcinoma (ccRCC). It is estimated that about 30% of new renal-cell carcinoma patients have metastases at the time of diagnosis.

Single-cell analysis reveals transcriptomic remodellings in distinct cell types that contribute to human prostate cancer progression.

Prostate cancer shows remarkable clinical heterogeneity, which manifests in spatial and clonal genomic diversity. By contrast, the transcriptomic heterogeneity of prostate tumours is poorly understood. Here we have profiled the transcriptomes of 36,424 single cells from 13 prostate tumours and identified the epithelial cells underlying disease aggressiveness.

Identification of Autophagy-Related Genes and Small-Molecule Drugs in Esophageal Carcinoma.

BACKGROUND Esophageal carcinoma (ESCA) is associated with a poor prognosis and high mortality rate. Autophagy plays important roles in promoting or suppressing tumor cell survival at different stages of cancer development. However, the roles of autophagy-related genes (ARGs) during ESCA progression and in patient prognosis remain unclear.

Identification of an individualized autophagy prognostic index in clear cell renal cell carcinoma patients.

Clear cell renal cell carcinoma (ccRCC) is the most common subtype of kidney cancer. ccRCC arises from the proximal tubular epithelium and is associated with high mortality. Autophagy may either promote or suppress tumor cell survival at different stages of cancer development.

5-aza-2'-deoxycytidine (DAC) treatment induces the MAGE-A10 expression and improves the cytotoxicity of MAGE-A10-specific CTLs in lung cancer cells.

Background: MAGE-A10 is a subtype of the Melanoma-associated antigen A (MAGE-A), a class of tumor antigens that are extensively expressed in various histological types of tumors and represents an attractive target for tumor immunotherapy. Epigenetic-modifying drugs can enhance the expression of tumor antigens and improve the cytotoxicity of antigen-specific T cells. 5-aza-2'-deoxycytidine (DAC), a DNA methyltransferase inhibitor (DNMTI) considered an epigenetic-modifying drug, could enhance the expression of MAGE-A10 in cancer cells.

Screening and Identification of Key Biomarkers in Pancreatic Cancer: Evidence from Bioinformatic Analysis.

Pancreatic cancer (PC) whose mortality is comparable to morbidity is a highly fatal disease. Early approaches of diagnosis and treatment for PC are quite limited, so it is of great urgency to figure out the exact tumorigenesis and development mechanism of PC. To identify the related molecular markers of pancreatic oncogenesis, we downloaded three microarray datasets (GSE63111, GSE101448, and GSE107610) from Gene Expression Omnibus (GEO) database.