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

22 May 2025

Sialyltransferase-related genes as predictive factors for therapeutic response and prognosis in cervical cancer

"This study provides a systematic investigation into SiaTs-related genes in cervical cancer, addressing an important aspect of cancer biology related to hypersialylation and metastasis. The research integrates multiple analytical approaches, including TCGA and GEO databases, WGCNA, and immune microenvironment analysis, to develop a risk scoring model for cervical cancer patients. The study demonstrates how this model can predict prognosis and potential responses to both immunotherapy and chemotherapy, offering insights into patient stratification. The findings regarding immune cell scores, checkpoint-correlated genes, and differential pathway activation between risk groups contribute to our understanding of cervical cancer heterogeneity. The validation of key genes through cellular assays, particularly the role of CXCL3 in cell migration and invasion, strengthens the clinical relevance of the findings. While the study primarily focuses on computational analyses, its integration with experimental validation provides a foundation for future research in personalized treatment approaches. The identification of specific molecular markers and their association with treatment responses may assist clinicians in making more informed decisions about therapeutic strategies for cervical cancer patients."

Fanglin Guan, Handling Editor

8 May 2025

Development of an immune-related gene signature applying Ridge method for improving immunotherapy responses and clinical outcomes in lung adenocarcinoma

"This study addresses an important challenge in lung adenocarcinoma (LUAD) treatment by developing an immune prognostic signature (IMMPS) based on tumor-infiltrating lymphocytes. The research methodology is systematic, employing multiple computational approaches and machine learning algorithms to analyze immune-related genes and their association with patient outcomes. The identification of two distinct immune subtypes in LUAD provides insights into patient stratification for immunotherapy. The seven-gene signature developed shows consistent prognostic value across multiple cohorts, with reasonable predictive performance (C-index > 0.69). The study validates its findings through experimental work, demonstrating the relationship between BTNL9 and the signature genes. The comparative analysis with existing gene signatures indicates the potential utility of this new prognostic tool. While the findings contribute to our understanding of LUAD's immunological characteristics, further validation in prospective clinical studies would be beneficial to confirm its practical application. This work provides a foundation for future research in personalizing immunotherapy approaches for LUAD patients, though additional investigation is needed to fully understand the molecular mechanisms underlying these prognostic markers."

Fanglin Guan, Handling Editor