Plectin, encoded by PLEC , is a cytoskeletal and scaffold protein with a number of unique isoforms that act on various cellular functions such as cell adhesion, signal transduction, cancer cell invasion, and migration. While plectin has been shown to display high expression and mislocalization in tumor cells, our knowledge of the biological significance of plectin and its isoforms in tumorigenesis remain limited. In this study, we first performed pathway enrichment analysis to identify cancer hallmark proteins associated with plectin. Then, a pan-cancer analysis was performed using RNA-seq data collected from the Cancer Genome Atlas (TCGA) to detect the mRNA expression levels of PLEC and its transcript isoforms, and the prognostic as well as diagnostic significance of the transcript isoforms was evaluated considering cancer stages. We show here that several tissue specific PLEC isoforms are dysregulated in different cancer types and stages but not the expression of PLEC . Among them, PLEC 1d and PLEC 1f are potential biomarker candidates and call for further translational and personalized medicine research. This study makes a contribution as a stride to unravel the molecular mechanisms underpinning plectin isoforms in cancer development and progression by revealing the potent plectin isoforms in different stages of cancer as potential early cancer detection biomarkers. Importantly, uncovering how plectin isoforms guide malignancy and particular cancer types by comprehensive functional studies might open new avenues toward novel cancer therapeutics.

Background: Several studies have demonstrated that the expression status of isoforms is more informative as a biomarker than overall gene expression. This study aimed to determine highly but significantly expressed transcript isoforms and evaluate their prognostic and diagnostic impact in breast invasive carcinoma (BRCA) stage I patients. Methods: The differentially expressed genes and their transcript isoforms in BRCA stage I were determined using the Cancer Differentially Expressed Isoform and gene (Cancer DEIso) platform based on The Cancer Genome Atlas (TCGA) data. The prognostic and diagnostic impact of significantly upregulated top 10 genes and their transcripts were revealed using the Cancer DEIso tool, the Kaplan-Meier (KM) method, and the Receiver Operating Characteristic Curve (ROC) approach, respectively. Isoform-level protein-protein interactions (PPI) were constructed using the Domain Interaction Graph Guided ExploreR (DIGGER) database. ConsensusPathDB was used to perform pathway enrichment analysis based on the constructed interactions. Results: This study revealed that NM_024037, NM_001143782, and NM_021619 transcript isoforms have significant diagnostic ability with AUC values 93.2%, 77.1% and 75.3%, respectively to distinguish stage I BRCA patients from normal. KM-plot analysis showed that these three isoforms have no prognostic significance in stage I patients, but their upregulation was correlated with decreased survival in BRCA patients regardless of stage. Isoform-based pathway enrichment analyses indicated that these three isoforms involved in chromatin organization, senescense, DNA damage and several signalling pathways which promotes cancer when there is misregulation. . Conclusion: NM_024037, NM_001143782, and NM_021619 transcript isoforms are potential biomarkers for detecting early-stage BRCA. Thus, it is essential to find out how these three isoforms contribute to the development of breast carcinogenesis and evolve a new approach for capturing breast tumors at an earlier stage of the clinical landscape.

Lithium (Li) was presented as a protective agent in neuron degeneration which is an important process in neurodegenerative diseases. The aim of this study was to determine the effect of certain amounts of Li on neuroblastoma cells by considering several specific genes which act on neuroprotection. Li solutions were prepared as 1 μM, 15 μM (low dosage), 30 μM and 45 µM (high dosage) concentrations then applied to neuroblastoma cell line. XTT and trypan blue assays were performed to determine the cell proliferation and viability, respectively. mRNA expression levels of NES, BDNF, GRIN2A, LRRK2, PRKN, and SNCA were detected by quantitative real time polymerase chain reaction (qRT-PCR). Cell viability detected as significantly increased in cells treated with low dosage Li however, it was significantly decreased in high dosage applied cells compared to untreated control. In addition, cell proliferation ratios were significantly decreased in high dosage applied cells compared to control. It was demonstrated that mRNA expression levels of several genes (NES, LRRK2, PRKN) were significantly upregulated. Regarding to BDNF, expression of the gene was significantly upregulated in the cells only treated with very low amount of Li. However, no significant data could be obtained for GRIN2A. Furthermore, mRNA expression level of SNCA was determined as significantly downregulated compared to control. Statistically significant expression of NES, LRRK2, PRKN, BDNF and SNCA genes due to the variable Li concentrations applied to cells suggests that Li acts on transcriptional regulation of certain genes associated with neuronal survival. These findings support that dose dependent Li treatment might have a protective effect for neurodegenerative diseases.

Papillary thyroid carcinoma (PTC) typically exhibits a favorable prognosis; however, lymph node and distant metastases continue to present significant clinical challenges. Plectin isoform 1d (PLEC 1d) contributes to myofiber integrity and is implicated in cytoskeletal organization and cancer cell motility, but its role in PTC progression is largely unknown. In this study, PLEC 1d expression was examined by RT-PCR in three PTC cell lines (MDA-T32, MDA-T41, MDA-T120) and normal thyroid cells (Nthy-ori-3-1). CRISPR-Cas9-mediated knockdown (KD) of PLEC 1d was performed in MDA-T41 cells, with KD efficiency confirmed by RT-qPCR. Cell proliferation and migration were assessed using EdU incorporation and wound-healing assays, respectively. RNA sequencing (RNA-seq) combined with RT-qPCR and Western blotting was employed to identify downstream targets. Accordingly, PLEC 1d mRNA and total plectin protein levels were substantially elevated only in MDA-T41 cells. PLEC 1d KD reduced proliferation by 6.6% and migration by 26%. Transcriptomic analysis revealed 170 differentially expressed genes, including significant downregulation of LAMA4, MMP1, and HEY1. HEY1 downregulation was confirmed at both mRNA and protein levels. Although LAMA4 and MMP1 were also downregulated following PLEC 1d KD, LAMA4 mRNA expression varied across PTC cell lines, suggesting cell-line-specific regulation. Notably, MMP1 was consistently upregulated at the mRNA level in all PTC cell lines, while HEY1 showed elevated expression at both the transcript and protein levels. Collectively, these findings indicate that PLEC 1d enhances cell migration and may contribute to cellular processes associated with metastatic behavior in a subset of PTC cells, potentially through a HEY1-dependent mechanism.

İnsan Genom Projesi sonrasında insan proteomunun, alternatif uçbirleştirme, alternatif transkripsiyon başlama bölgesi, alternatif poliadenilasyon ve alternatif translasyon başlama bölgesi seçimi gibi mekanizmalarla 20.000 civarındaki genden çok daha fazla sayıda protein izoformu üreterek geniş bir çeşitlilik kazandığı anlaşılmıştır. Bu protein izoformları hücresel düzeyde farklı işlev, dağılım ve ifadelere sahip olup organizmanın fizyolojik dengesini korumada kritik roller üstlenmektedir. İnsan Proteom Projesi (HPP) de bu karmaşık yapıyı haritalamayı ve hastalıkların moleküler patolojisini aydınlatmayı amaçlamaktadır. Araştırmalar, bu izoform oluşum mekanizmalarında meydana gelen hataların veya düzensizliklerin doğrudan insan sağlığını bozarak birçok ciddi patoloji ile bağlantılı olduğunu göstermiştir. Örneğin alternatif uçbirleştirme kusurları Alzheimer, Konjenital Miyastenik Sendrom, Duchenne Kas Distrofisi ve Miyotonik Distrofide önemli rol oynarken, kritik kontrol noktalarındaki mutasyonlar ve intron tutma olayları çeşitli kanser türlerinin gelişimini tetiklemektedir. Benzer şekilde alternatif transkripsiyon ve poliadenilasyon bölgelerindeki varyasyonlar kalp yetmezliği, Frajil X Sendromu ve hematolojik hastalıklar ile ilişkiliyken, alternatif translasyon başlama hataları ve dokuya özgül plektin izoformlarındaki mutasyonlar kas distrofisi ve deri hastalıklarına yol açmaktadır. Following the comprehensive analysis of the Human Genome Project, it has been realized that the human proteome achieves extensive diversity, producing significantly more protein isoforms than the approximately 20,000 protein-coding genes through mechanisms such as alternative splicing, alternative transcription start site selection, alternative polyadenylation, and alternative translation initiation site selection. These protein isoforms possess distinct functions, cellular distributions, and expressions, playing critical roles in maintaining physiological balance. The Human Proteome Project (HPP) actively aims to map this complex architecture to provide a foundation for understanding the molecular pathology of diseases. Studies demonstrate that errors or dysregulations in these isoform generation factors are heavily linked to various human pathologies. For instance, alternative splicing defects play crucial roles in Alzheimer's disease, Congenital Myasthenic Syndrome, Duchenne Muscular Dystrophy, and Myotonic Dystrophy, while mutations at critical checkpoints and intron retention events trigger cancer development. Similarly, variations in alternative transcription and polyadenylation site selections are associated with heart failure, Fragile X Syndrome, and susceptibility to malignancies, whereas alternative translation initiation errors and mutations in tissue-specific plectin isoforms lead to muscular dystrophies and skin disorders.