Journal of Molecular Pathology

Background: Variants of uncertain significance (VUSs) in TP53 and CDKN2A are reported often in oral squamous cell carcinoma (OSCC), yet variant-level evidence tends to lag behind established gene-level associations. Candidate variant lists compiled by automated literature synthesis, registry mining, or AI-assisted extraction carry a risk of gene-level or transcript-level mis-annotation that is not widely recognized. Methods: Ten candidate VUSs (one TP53 and nine CDKN2A), drawn from a candidate list generated by an AI-assisted literature and registry search (SciSpace, PubMed, Google Scholar, and ClinicalTrials.gov), were curated using ClinVar, dbSNP/NCBI Gene, gnomAD (via VarSome), and UCSC phyloP conservation tracks. To address regional population representation, two Indian genomic resources (dbGENVOC and TMC-SNPdb 2.0) and one OSCC-specific catalogue (dbGVOSCC) were also queried. Gene and transcript assignment was verified independently for every variant before evaluation against American College of Medical Genetics and Genomics and Association for Molecular Pathology (ACMG/AMP) criteria. Results: The candidate TP53 variant (rs2543751607) is a coding variant of the adjacent gene WRAP53 and is non-coding relative to TP53; it was excluded. All CDKN2A variants mapped only to the p14(ARF) transcript (NM_058195.4) and not to the p16(INK4a) transcript (NM_000077.5) that underlies the CDK4/6-inhibitor predictive-biomarker role of CDKN2A. One rsID (rs2489327173) resolved to two distinct missense variants, giving ten evaluated CDKN2A variants: two Likely Pathogenic (provisional, isoform-qualified), seven Uncertain Significance, and one Uncertain Significance and leaning benign. None of the ten was recorded in dbGENVOC, TMC-SNPdb 2.0, or dbGVOSCC. In dbGENVOC the only CDKN2A coding variants in Indian OSCC patients fell in the shared exon 2, and in dbGVOSCC the curated OSCC CDKN2A events were mainly deletions and p16 methylation. Curation also corrected an allele-matching error at a multiallelic position and resolved two conservation-score discordances by independent phyloP querying. Conclusions: Public-database curation of a small candidate VUS set exposed structural annotation problems, namely gene misassignment and isoform misassignment, that change the clinical interpretation of the source synthesis. Variant lists derived automatically or from the literature warrant independent gene-level and transcript-level verification, and CDKN2A isoform specificity should be stated explicitly whenever it is discussed as a biomarker in OSCC or HNSCC.

Age-related macular degeneration (AMD) remains the leading cause of irreversible, severe visual loss among elderly populations in industrialized nations. The clinical spectrum ranges from early forms, characterized by the accumulation of extracellular deposits known as drusen, to advanced, vision-threatening late stages. While anti-vascular endothelial growth factor (anti-VEGF) therapy for neovascular AMD is the standard of care, geographic atrophy has remained a progressive condition. Geographic atrophy is a chronic neurodegenerative disease defined pathologically by the concurrent, progressive loss of the retinal pigment epithelium (RPE), the overlying photoreceptors, and the underlying choriocapillaris. Historically, the diagnosis and monitoring of GA relied on color fundus photography, which identified the lesions as sharply demarcated, well-circumscribed round or oval areas of depigmentation through which underlying choroidal vessels became clinically visible. However, the advent of high-resolution multimodal imaging—particularly fundus autofluorescence (FAF) and optical coherence tomography (OCT)—has necessitated a modernization of this terminology. Despite the imaging consensus, the fundamental pathophysiology of GA remains the subject of intense academic and clinical debate. The controversy focuses on identifying the primary cellular culprit responsible for initiating the cascade of degeneration. The “top-down” hypothesis suggests that intracellular metabolic failure, oxidative stress, and senescence within the RPE trigger the secondary dysfunction and death of the adjacent photoreceptors and choriocapillaris. Conversely, the “bottom-up” vascular hypothesis argues that age-related and complement activation–driven hemodynamic insufficiency, ischemic dropout, and structural involution of the choriocapillaris precede RPE dysfunction, creating a hypoxic microenvironment that drives the subsequent epithelial collapse. This narrative review scrutinizes the exact molecular, genetic, and structural mechanisms governing the expansion of geographic atrophy. By dissecting the evidence supporting both the RPE and the choriocapillaris as primary instigators, this analysis explores the paradigm that GA represents a synergistic failure of the outer blood–retinal barrier—a symbiotic trophic unit highly dependent on precise vascular and epithelial crosstalk, tightly regulated complement cascades, and extracellular matrix integrity.

Background: Recent pan-cancer transcriptome analyses have identified ENST00000453316 as a cancer biomarker candidate, showing consistent and significant deregulation across multiple cancer types. Methods: This study investigated the transcript as a regulatory RNA in cancer-associated processes and its potential as a biomarker using a bioinformatics approach. Results: In silico characterization classified ENST00000453316 as a non-coding transcript with regulatory features and stable structure. Curated annotations documented the binding of 21 RNA-binding proteins across the transcript region, with core spliceosomal factors at the unique splice junction and cytoplasmic 3′-end factors at the terminal exon, in agreement with the sequence-based predictions. Promoter analysis revealed a TATA-less, CpG-poor region with multiple putative transcriptional regulator binding sites. Its expression was higher in most solid tumor types analyzed, with minimal expression in non-tumor tissues, indicating a tumor-associated pattern. Discrimination between tumor and adjacent non-tumor tissue within TCGA was good in five of the ten tissue types with sufficient adjacent-normal samples, with the area under the ROC curve reaching 0.82 in the lung, 0.78 in the bladder and 0.71–0.75 in the colon, breast and stomach, but close to chance in the kidney, thyroid and prostate. Conclusions: These results suggest that ENST00000453316 is a cancer-associated, promoter-driven non-coding transcript with potential regulatory relevance. Despite its revised annotation, it exemplifies how alternative promoter usage generates biologically and clinically meaningful transcripts contributing to tumor-specific gene regulation. Future experimental validation is needed to confirm the role of ENST00000453316 as a functional regulatory RNA and assess its clinical potential as a cancer biomarker.