22 September 2025

Predicting the prognosis of hepatocellular carcinoma based on genes related to polyamine metabolism

"This manuscript presents a comprehensive analysis of polyamine metabolism-related genes (PMRGs) in hepatocellular carcinoma (HCC), utilizing both bulk and single-cell RNA sequencing datasets. The study identifies distinct molecular subtypes and constructs a prognostic risk model, integrating bioinformatics analyses with experimental validation. The identification of key genes such as G6PD, ADH4, S100A9, and AKR1B15, as well as the development of a nomogram for survival prediction, demonstrate a methodical approach that combines computational and laboratory techniques. The findings offer additional understanding of the heterogeneity of HCC and provide potential biomarkers that may inform future research on molecular subtyping and personalized treatment strategies. While the study addresses an area of ongoing interest and incorporates several well-established analytical methods, the novelty and translational potential remain to be further substantiated by larger-scale clinical validation. The work contributes to the growing body of knowledge regarding the molecular landscape of HCC and supports further investigation into polyamine metabolism as a potentially relevant pathway in the prognosis and treatment of this malignancy."

Fanglin Guan, Handling Editor

18 September 2025

Expression characterization of the guanylate-binding protein gene family in breast cancer and its association with the immune microenvironment

"This article addresses an important aspect of breast cancer prognostic assessment by focusing on the involvement of guanylate-binding protein (GBP) genes and their association with the tumor immune microenvironment. The study employs a combination of bioinformatics approaches, including ssGSEA, WGCNA, and regression analyses, to construct a risk model based on GBP-related genes. The integration of immune infiltration analysis and experimental validation of DACT2 function in breast cancer cell lines provides additional biological context to the findings. While the methodology is comprehensive and the risk model appears to offer prognostic value, the novelty and clinical applicability of the results would benefit from further validation in independent cohorts and real-world clinical settings. The study presents a methodologically sound framework for exploring immune-related prognostic markers in breast cancer, which could contribute to improved risk stratification and potentially inform individualized treatment strategies, though its immediate translational impact may be limited at this stage."

Fanglin Guan, Handling Editor

3 September 2025

BMP2 alterations in mucinous cystadenocarcinoma of the breast: insights from whole-exome sequencing

"The article presents a rare and understudied breast cancer subtype, and the integrative approach using whole exome sequencing (WES) and immunohistochemistry (IHC) provides valuable initial insights into its possible molecular pathogenesis. However, limited sample size (n=3) and lack of downstream functional analyses are limiting factors."

Mehmet Burak Ateş, Handling Editor

28 August 2025

Uncovering tissue-specific endophytic microbiota composition and activity in Rhizophora mangle L.: a metagenomic and metatranscriptomic approach

"Understanding the structure and functional activity of mangrove tree-associated microbiomes paves the way for mangrove ecosystem conservation and future biotechnological applications"

Paripok Phitsuwan, Handling Editor

27 August 2025

Exploration of prognostic genes associated with lymphangiogenesis in breast cancer based on transcriptomics and experimental verification

"This research contributes to precision medicine in BC by identifying actionable biomarkers, elucidating their biological roles, and suggesting potential treatments, all of which could enhance diagnosis, prognosis, and therapy for patients with breast cancer."

Rodolfo García-Contreras, Handling Editor

18 August 2025

Genomewide analysis of the Class III peroxidase gene family in apple (Malus domestica)

"The manuscript presents a robust genome-wide analysis of Class III peroxidases in Malus domestica, uncovering their structural diversity, evolution, and expression patterns. It highlights antagonistic roles of PRX subgroups in rootstock vigor and bud differentiation, offering valuable insights into ROS-mediated regulation and apple breeding strategies."

Ganesh Nikalje, Handling Editor

11 July 2025

An R package for survival-based gene set enrichment analysis

"This article presents SGSEA, a novel adaptation of traditional GSEA that incorporates survival data into pathway enrichment analysis. The development of both an R package and Shiny App makes this method accessible to researchers across disciplines. While standard GSEA has been effective for comparing differential expression between experimental conditions, SGSEA addresses the need to link transcriptomic variations with clinical outcomes like patient survival. The authors demonstrate the method's utility through a case study of kidney renal clear cell carcinoma, where pathways identified by SGSEA align with previously documented survival associations. This alignment with existing knowledge helps validate the approach. The method enables researchers to identify pathways relevant to disease progression and mortality risk in a systematic way, complementing insights from traditional GSEA. The provision of standardized tools addresses a gap in the current analytical landscape. While the approach shows promise, further validation across different cancer types and diseases would help establish its broader applicability. The development of SGSEA represents a practical contribution to the field of functional genomics and survival analysis, potentially aiding in the identification of clinically relevant pathways."

Fanglin Guan, Section Editor

10 July 2025

Expression of the IL-18-related gene PTX3 correlates with clinicopathological features and prognosis in glioma patients

"This study provides a comprehensive analysis of PTX3's role in glioma progression through multi-dimensional research approaches. The investigation combines bioinformatics analysis of TCGA data with experimental validation, offering insights into both molecular mechanisms and clinical implications. The study's methodology is systematic, employing various analytical tools including LASSO Cox regression, functional enrichment analysis, and immune infiltration assessment. The identification of a nine-gene prognostic signature and the correlation between PTX3 expression and immune cell infiltration advances our understanding of glioma's molecular landscape. The research presents evidence linking PTX3 expression to clinical features and survival outcomes, supported by immunohistochemistry validation in patient specimens. While the findings are consistent with existing literature on tumor-associated molecular markers, this work adds specific insights about PTX3's potential as a prognostic indicator in glioma. The study's results may contribute to the development of targeted therapies, though additional validation studies would be beneficial. This research provides a foundation for future investigations into PTX3-based therapeutic strategies, while maintaining appropriate consideration of the complexities involved in translating molecular findings to clinical applications."

Fanglin Guan, Section Editor

26 June 2025

Genome-wide identification and characterization of the NF-Y proteins in Zanthoxylum armatum

"This research addresses a relevant knowledge gap by conducting a systematic analysis of NF-Y transcription factors in Zanthoxylum armatum, focusing on their potential role in nucellar embryogenesis. The identification of 67 ZaNF-Y transcription factors and their classification into three subfamilies provides a foundation for understanding their functional evolution. The study's examination of gene duplication, conserved domains, and motif patterns offers insights into the structural characteristics of these transcription factors. The analysis of tissue-specific expression patterns, particularly the differential expression of ZaNF-YB5 and ZaNF-YC1 in female flowers and young fruit, suggests potential regulatory mechanisms in nucellar embryo formation. The protein association network analysis contributes to understanding the complexity of ZaNF-Y complexes. While the findings are primarily descriptive and require further functional validation, this work provides baseline information that could be useful for future research on apomixis manipulation in crop breeding. The study represents a step toward understanding the molecular mechanisms of nucellar embryogenesis, though additional research would be needed to establish direct functional relationships and practical applications."

Fanglin Guan, Section Editor

28 May 2025

Gene expression profiling of extraocular muscles in primary inferior oblique overaction

"This study addresses an knowledge gap in understanding the molecular mechanisms underlying primary and secondary inferior oblique overaction (IOOA), a common form of strabismus. Through transcriptome sequencing and comprehensive bioinformatic analyses, the research identifies distinct gene expression patterns between primary and secondary IOOA, particularly in pathways related to myelination, ion channels, M-bands, and collagen fibril organization. The identification of 258 differentially expressed genes and their associated pathways provides a foundation for understanding the neuromuscular characteristics that distinguish these two conditions. The findings suggest potential mechanisms for the increased presence of multiply innervated muscle fibers in primary IOOA and elevated collagen fibrils in secondary IOOA, which may explain observed differences in muscle tension and elasticity. While the study is preliminary and requires further validation, it contributes to the field by offering molecular insights that could inform future therapeutic strategies. The methodological approach combining transcriptome sequencing with multiple bioinformatic analyses strengthens the reliability of the findings, though larger sample sizes and functional studies would be beneficial for confirming these results."

Fanglin Guan, Section Editor