Identification of PIK3CA multigene mutation patterns associated with superior prognosis in stomach cancer

Anti-tumor immune modulation and favorable survival outcomes in uterine corpus endometrial carcinoma: insights from PIK3CA/ARID1A co-mutation analysis

BACKGROUND

Uterine corpus endometrial carcinoma (UCEC) is the most prevalent cancer of the female reproductive system, posing significant risks to women's reproductive health and imposing considerable economic burdens on families and society due to high treatment costs.

METHODS

The study population comprised 529 UCEC patients who were selected and retrieved from the cBioPortal public database for a comprehensive integrated analysis. This study aims to explore the prognostic significance of co-mutation in PIK3CA/ARID1A genes in UCEC, utilizing various bioinformatics approaches, including differential expression genes (DEGs) analysis, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, Gene Set Enrichment Analysis (GSEA), immune infiltration analysis, and the establishment of nomogram model.

RESULTS

PIK3CA/ARID1A co-mutation group had a better prognosis than the other three groups. The co-mutation of PIK3CA/ARID1A was associated with a significantly improved overall survival (OS) in patients with UCEC and immunotherapy markers. This result was further corroborated in the MSK cohort, reinforcing the robustness of our observations. Our findings revealed that 222 genes were upregulated and 1,464 genes downregulated in the co-mutation group compared to the non-co-mutation (NCM) group, providing a molecular basis for understanding the biological roles of these gene mutations in UCEC. Additionally, pathway analysis identified significant enrichment in immune-related pathways, emphasizing the potential for co-mutation to influence tumor progression via immune modulation. Notably, patients with co-mutations exhibited improved overall survival (P < 0.05), suggesting their role as vital prognostic markers. The developed Cox proportional hazards model demonstrated high predictive accuracy (C-index = 0.835), supporting personalized management for UCEC patients.

CONCLUSION

In conclusion, this study underscores the importance of PIK3CA and ARID1A co-mutations in UCEC, advocating for their further exploration in clinical applications and therapeutic strategies.

CITMIC: Comprehensive Estimation of Cell Infiltration in Tumor Microenvironment based on Individualized Intercellular Crosstalk

The tumor microenvironment (TME) cells interact with each other and play a pivotal role in tumor progression and treatment response. A comprehensive characterization of cell and intercellular crosstalk in the TME is essential for understanding tumor biology and developing effective therapies. However, current cell infiltration analysis methods only partially describe the TME's cellular landscape and overlook cell-cell crosstalk. Here, this approach, CITMIC, can infer the cell infiltration of TME by simultaneously measuring 86 different cell types, constructing an individualized cell-cell crosstalk network based on functional similarities between cells, and using only gene transcription data. This is a novel approach to estimating the relative cell infiltration levels, which are shown to be superior to the current methods. The TME cell-based features generated by analyzing melanoma data are effective in predicting prognosis and treatment response. Interestingly, these features are found to be particularly effective in assessing the prognosis of high-stage patients, and this method is applied to multiple high-stage adenocarcinomas, where more significant prognostic performance is also observed. In conclusion, CITMIC offers a more comprehensive description of TME cell composition by considering cell-cell crosstalk, providing an important reference for the discovery of predictive biomarkers and the development of new therapeutic strategies.

Targeting PI3K/AKT/mTOR signaling to overcome drug resistance in cancer

This review comprehensively explores the challenge of drug resistance in cancer by focusing on the pivotal PI3K/AKT/mTOR pathway, elucidating its role in oncogenesis and resistance mechanisms across various cancer types. It meticulously examines the diverse mechanisms underlying resistance, including genetic mutations, feedback loops, and microenvironmental factors, while also discussing the associated resistance patterns. Evaluating current therapeutic strategies targeting this pathway, the article highlights the hurdles encountered in drug development and clinical trials. Innovative approaches to overcome resistance, such as combination therapies and precision medicine, are critically analyzed, alongside discussions on emerging therapies like immunotherapy and molecularly targeted agents. Overall, this comprehensive review not only sheds light on the complexities of resistance in cancer but also provides a roadmap for advancing cancer treatment.

Predictive, preventive, and personalized medicine in breast cancer: targeting the PI3K pathway

Breast cancer (BC) is a multifaceted disease characterized by distinct molecular subtypes and varying responses to treatment. In BC, the phosphatidylinositol 3-kinase (PI3K) pathway has emerged as a crucial contributor to the development, advancement, and resistance to treatment. This review article explores the implications of the PI3K pathway in predictive, preventive, and personalized medicine for BC. It emphasizes the identification of predictive biomarkers, such as PIK3CA mutations, and the utility of molecular profiling in guiding treatment decisions. The review also discusses the potential of targeting the PI3K pathway for preventive strategies and the customization of therapy based on tumor stage, molecular subtypes, and genetic alterations. Overcoming resistance to PI3K inhibitors and exploring combination therapies are addressed as important considerations. While this field holds promise in improving patient outcomes, further research and clinical trials are needed to validate these approaches and translate them into clinical practice.

AHNAKs roles in physiology and malignant tumors

The AHNAK family currently consists of two members, namely AHNAK and AHNAK2, both of which have a molecular weight exceeding 600 kDa. Homologous sequences account for approximately 90% of their composition, indicating a certain degree of similarity in terms of molecular structure and biological functions. AHNAK family members are involved in the regulation of various biological functions, such as calcium channel modulation and membrane repair. Furthermore, with advancements in biological and bioinformatics technologies, research on the relationship between the AHNAK family and tumors has rapidly increased in recent years, and its regulatory role in tumor progression has gradually been discovered. This article briefly describes the physiological functions of the AHNAK family, and reviews and analyzes the expression and molecular regulatory mechanisms of the AHNAK family in malignant tumors using Pubmed and TCGA databases. In summary, AHNAK participates in various physiological and pathological processes in the human body. In multiple types of cancers, abnormal expression of AHNAK and AHNAK2 is associated with prognosis, and they play a key regulatory role in tumor progression by activating signaling pathways such as ERK, MAPK, Wnt, and MEK, as well as promoting epithelial-mesenchymal transition.

FDA approved fused-pyrimidines as potential PI3K inhibitors: a computational repurposing approach

Fused pyrimidine scaffold is present in several US FDA-approved drugs for various therapeutic indications. Drug repurposing (or drug repositioning) involves the analysis of existing clinically approved drugs for new therapeutic indications. Phosphoinositide-3-kinase (PI3K), via the regulatory PI3K pathway, is involved in cell growth, proliferation, differentiation, survival, and angiogenesis. It is also considered a target in anticancer drug development as it promotes the growth of cancerous cells and increases resistance to anticancer therapy. The present work employed computational techniques like molecular docking, MMGBSA analysis, and molecular dynamics simulations to explore the PI3K inhibition by FDA-approved drugs with fused pyrimidine scaffold. The work identifies Lapatinib as a pan-class I PI3K inhibitor and Dipyridamole as an γ isoform-specific PI3K inhibitor and is reported here.Communicated by Ramaswamy H. Sarma.

Are genetic drift and stem cell adherence in laboratory culture issues for cultivated meat production?

Mesenchymal stem cell-based cultivated meat is a promising solution to the ecological and ethical problems posed by traditional meat production, since it exhibits a protein content and composition that is more comparable to original meat proteins than any other source of cultivated meat products, including plants, bacteria, and fungi. Nonetheless, the nature and laboratory behavior of mesenchymal stem cells pose two significant challenges for large-scale production: genetic drift and adherent growth in culture. Culture conditions used in the laboratory expose the cells to a selective pressure that causes genetic drift, which may give rise to oncogene activation and the loss of "stemness." This is why genetic and functional analysis of the cells during culture is required to determine the maximum number of passages within the laboratory where no significant mutations or loss of function are detected. Moreover, the adherent growth of mesenchymal stem cells can be an obstacle for their large-scale production since volume to surface ratio is limited for high volume containers. Multi-tray systems, roller bottles, and microcarriers have been proposed as potential solutions to scale-up the production of adherent cells required for cultivated meat. The most promising solutions for the safety problems and large-scale obstacles for cultivated meat production are the determination of a limit number of passages based on a genetic analysis and the use of microcarriers from edible materials to maximize the volume to surface proportion and decrease the downstream operations needed for cultivated meat production.

Multidimensional difference analysis in gastric cancer patients between high and low latitude

Genetic variation has been shown to affect tumor growth and progression, and the temperature at different latitudes may promote the evolution of genetic variation. Geographical data with latitudinal information is of importance to understand the interplay between genetic variants and environmental influence, such as the temperature, in gastric cancer (GC). In this study, we classified the GC samples from The Cancer Genome Atlas database into two groups based on the latitudinal information of patients and found that GC samples with low-latitude had better clinical outcomes. Further analyses revealed significant differences in other clinical factors such as disease stage and grade between high and low latitudes GC samples. Then, we analyzed the genomic and transcriptomic differences between the two groups. Furthermore, we evaluated the activity score of metabolic pathways and infiltrating immune cells in GC samples with different latitudes using the single-sample gene set enrichment analysis algorithm. These results showed that GC samples at low-latitude had lower tumor mutation burden and subclones as well as higher DNA repair activities. Meanwhile, we found that most immune cells were associated with the prognosis of low-latitude GC patients. At last, we constructed and validated an immune-related prognostic model to evaluate the prognosis of GC samples at different latitudes. This study has provided a further understanding of the geographical contribution to GC at the multiomic level and may benefit the individualized treatment of GC patients at different latitudes.

Activation of circ_0072088/miR-1261/PIK3CA pathway accelerates lung adenocarcinoma progression

BACKGROUND

Circular RNAs (circRNAs) are involved in the tumorigenesis and progression of lung adenocarcinoma (LUAD). This study aimed to determine the role of circ_0072088 in LUAD.

METHODS

The existence and expression of circ_0072088 in human LUAD tissues and cell lines were determined through Sanger sequencing, quantitative reverse transcription-polymerase chain reaction, and fluorescence in situ hybridization (FISH). Subsequently, the biological role of circ_0072088 was examined using loss-of-function assays in H1299 cells. Moreover, circ_0072088/miR-1261/PIK3CA pathway-mediated biological effects in H1299 were verified using bioinformatic prediction and experiments, including interaction analysis (FISH, luciferase reporter, and RNA-pulldown assays), and tumor biological function test (CCK8 and colony formation, wound healing, and transwell assays). Finally, miR-1261 and PIK3CA expression and LUAD patient survival were further analyzed using FISH, immunohistochemical staining, and the Kaplan-Meier plotter database, respectively.

RESULTS

First, an increase in circ_0072088 was confirmed in human LUAD tissues. Thereafter, it was mainly localized in the cytoplasm and was found to enhance cell proliferation, migration, and invasion of H1299 cells. Mechanistically, circ_0072088 directly downregulated miR-1261 expression, whereas increased PIK3CA gene expression was associated with poor overall survival of LUAD patients. The activation of the circ_0072088/miR-1261/PIK3CA regulatory pathway may play a significant role in the tumorigenesis and progression of LUAD.

CONCLUSIONS

Circ_0072088-dependent regulation of miR-1261/PIK3CA is important for cell proliferation, migration, and invasion during the tumorigenesis and progression of LUAD, warranting the need to consider the circ_0072088/miR-1261/PIK3CA regulatory pathway as a potential therapeutic target in patients with lung adenocarcinoma.

Prognostic value of microvessel density in esophageal squamous cell carcinoma-a systematic review and meta-analysis

OBJECTIVE

Angiogenesis produced by tumor microenvironment is play an important role in development of esophageal squamous cell carcinoma (ESCC). As a quantitative index of angiogenesis, literature has emerged contradictory results about the prognostic role of microvessel density (MVD) in ESCC. The aim of the study was to explore the impact of the correlation between MVD and the prognosis of ESCC based the published evidence.

METHODS

Pubmed and Web of science database were screened for the relationship of MVD with prognostic feature in ESCC up to March, 2021. 11 relevant articles were used for meta-analysis. The following data were extracted from the literature: author, year, country, the patients number of high/low MVD, tumor-node-metastasis (TNM) classification, clinical stage, lymphoid infiltrates, vessel invasion, invasive depth, differential degree and survival rate. The hazard ratio (HR) and odds ratios (OR) with 95% CI were used to assess the associations between MVD and overall survival (OS). Chi-squared test and I² statistics were completed to evaluate the heterogeneity in our study. A random-effects model was used when significant heterogeneity existed (I²>50% and p < 0.05). Egger test was used to calculate the publication bias. Subgroup analysis was stratified by antibody, region, sample capacity to explore the source of heterogeneity.

RESULTS

11 studies with 1055 patients were analyzed. Our results suggested that high MVD is an important factor to advanced TNM classification and clinical stage, and the high MVD is positive correlation with the lymph node invasion and vascular invasion(p < 0.05) in ESCC, but irrelevant to poor differential and invasive depth(p > 0.05). The result also indicated that low MVD is a benefit factor to prolong the survival rate (p < 0.05). And the source of the heterogeneity maybe is that the antibody used to detect the MVD was not consistent, patient number was not large enough and the count method on MVD.

CONCLUSION

Across multiple studies, high MVD is correlated with clinicopathological criteria of poor prognosis and survival in ESCC. MVD could be the quantitative index to reactive angiogenesis and may play a pivotal role in ESCC development and progression. MVD may represent a valuable addition to current pathologic analysis and help to guide prognosis and treatment.