Biochemistry and Biophysics Reports最新文献

{"title":"Benchmarking AlphaMissense pathogenicity predictions against APP, PSEN1, and PSEN2 variants of unknown significance","authors":"Joshua Pillai ,&nbsp;Sophia Liu ,&nbsp;Kijung Sung ,&nbsp;Linda Shi ,&nbsp;Chengbiao Wu","doi":"10.1016/j.bbrep.2025.102049","DOIUrl":"10.1016/j.bbrep.2025.102049","url":null,"abstract":"<div><div>Alzheimer's disease (AD) is a progressive neurodegenerative disease characterized by progressive cognitive decline. Over 200 pathogenic mutations in <em>amyloid-β precursor protein (APP)</em>, <em>presenilin-1</em> (<em>PSEN1</em>), and <em>presenilin-2</em> (<em>PSEN2</em>), have been implicated in AD. Yet, many rare and common variants have not been completely classified as protective or benign, risk-modifiers, or pathogenic, which is important for research on the disease mechanisms and discovery of treatment methods. The majority of these variants are missense mutations, and there is an active need for computational approaches to accurately predict their molecular consequences. AlphaMissense (AM) is a novel technology that uses population frequency data along with structural and sequential contexts from AlphaFold to predict the pathogenicity of missense mutations. Herein, we sought to evaluate the capabilities of AM on 114 variants of unknown significance (VUS), including 56 missense variants of <em>PSEN1</em>, 25 of <em>APP</em>, and 33 of <em>PSEN2</em> by benchmarking its prediction against their respective Aβ isoform levels <em>in vitro</em>, respectively. We found that the AM scores correlated moderately well with the critical Aβ42/Aβ40 biomarker and Aβ40 levels in the transmembrane proteins compared to weaker correlations in traditional approaches, including Combined Annotation Dependent Depletion (CADD) v1.7, evolutionary model of variant effect (EVE), and Evolutionary Scale Modeling-1b (ESM-1B). Yet, there were non-significant correlations identified with Aβ42 levels in all models. Furthermore, we found that AM does not rely completely on structural contexts from AlphaFold2, as it accurately predicted the effects of known variants on residues with a low predicted local distance difference test (pLDDT) score. Additionally, based on the receiver operating characteristic-area under the curve analysis (ROC-AUC), we found that AM retained a high performance on 263 validated variants of these amyloidogenic genes, and performed the greatest compared to other models for the 114 VUS. We believe this is the first study to provide comprehensive characterization and validation of AM in comparison to the widely utilized pathogenicity scoring models for VUS involved in proteins implicated in AD.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"42 ","pages":"Article 102049"},"PeriodicalIF":2.3,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144069322","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A novel small molecule that enhances lysyl hydroxylase 2 activity and matrix mineralization","authors":"Saori Tomiku ,&nbsp;Atsushi Kasamatsu ,&nbsp;Reo Fukushima ,&nbsp;Tomoaki Saito ,&nbsp;Ryunosuke Nozaki ,&nbsp;Akiko Suganami ,&nbsp;Yutaka Tamura ,&nbsp;Mitsuo Yamauchi ,&nbsp;Katsuhiro Uzawa","doi":"10.1016/j.bbrep.2025.102053","DOIUrl":"10.1016/j.bbrep.2025.102053","url":null,"abstract":"<div><div>Lysyl hydroxylase 2 (LH2), encoded by the <em>procollagen lysine 2-oxoglutarate 5-dioxygenase 2</em> (<em>Plod2</em>) gene, catalyzes the hydroxylation of lysine residues in the fibrillar collagen telopeptides. This post-translational modification is essential for forming the stable hydroxylysine-aldehyde derived collagen cross-links that play a critical role in collagen stability, mechanical strength, and bone formation. Defective LH2 activities have been implicated in bone disorders including Bruck syndrome, however, effective agents that control LH2 activity have not been developed until now. In this study, using <em>in silico</em> docking simulations, we identified a small molecule (KS122-0485428) that specifically binds LH2, and assessed the effects of this compound on collagen cross-linking, cell proliferation, and mineralization using the murine osteoblastic cell line MC3T3-E1. While KS122-0485428 did not affect cell proliferation and LH2 expression, it significantly accelerated mineralization. The hydroxylysine-aldehyde derived collagen cross-links were also significantly increased at the expense of the lysine-aldehyde derived cross-link. These results demonstrate that KS122-0485428 enhances LH2 activity leading to accelerated mineralization. Thus, this novel LH2 activator has the potential as a therapeutic agent for bone repair and regeneration.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"42 ","pages":"Article 102053"},"PeriodicalIF":2.3,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144069255","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optimizing PCR amplification of GC-rich nicotinic acetylcholine receptor subunits from invertebrates","authors":"Muhammad Tanveer Khan ,&nbsp;Coralie Belgrano ,&nbsp;Lucien Rufener ,&nbsp;Tor Einar Horsberg ,&nbsp;Marit Jorgensen Bakke","doi":"10.1016/j.bbrep.2025.102052","DOIUrl":"10.1016/j.bbrep.2025.102052","url":null,"abstract":"<div><div>Polymerase chain reaction (PCR) is a widely used molecular biology technique for amplifying specific DNA sequences. However, amplifying templates with a high GC content (&gt;60 %) poses challenges owing to strong hydrogen bonds and secondary structure formation, hindering DNA polymerase activity and primer annealing. Given these challenges, our study focuses on refining PCR protocols for the nicotinic acetylcholine receptor subunits, pivotal for understanding signal transduction in various organisms and potential important drug targets. We optimized the PCR protocol to efficiently amplify the beta1 and alpha1 subunits of the nicotinic acetylcholine receptor from <em>Ixodes ricinus</em> (<em>Ir-nAChRb1</em>) and <em>Apis mellifera</em> (<em>Ame-nAChRa1</em>). <em>Ir-nAChRb1</em> and <em>Ame-nAChRa1</em> have open reading frames of 1743 and 1884 bp, respectively, with overall GC contents of 65 % and 58 %. Various DNA polymerases and organic additives have been evaluated at different annealing temperatures. The tailored protocol incorporated organic additives, such as DMSO and betaine, increased enzyme concentration, and adjusted annealing temperatures. This study demonstrates the importance of a multipronged approach involving various organic molecules, DNA polymerases, PCR conditions, and primer adjustments to overcome the challenges of amplifying GC-rich sequences.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"42 ","pages":"Article 102052"},"PeriodicalIF":2.3,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144069253","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Therapeutic mechanisms of icariin in intervertebral disc degeneration: A critical narrative review","authors":"LiLun Zhong ,&nbsp;ZhenWen Xu ,&nbsp;YingJun Peng ,&nbsp;SongPeng Li ,&nbsp;An Liu ,&nbsp;ZhiDong Lin","doi":"10.1016/j.bbrep.2025.102047","DOIUrl":"10.1016/j.bbrep.2025.102047","url":null,"abstract":"<div><div>Intervertebral disc degeneration (IDD), a primary cause of low back pain, involves complex pathological mechanisms. Current research emphasizes identifying strategies to mitigate degenerative processes and enhance intrinsic disc repair. Emerging evidence highlights the therapeutic potential of icariin (ICA) in promoting disc repair and delaying IDD progression. ICA exerts its effects through multiple mechanisms, including anti-inflammatory actions, oxidative stress mitigation, modulation of bone and collagen metabolism, and inhibition of ferroptosis and pyroptosis. This review synthesizes current research on ICA's therapeutic applications in IDD management.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"42 ","pages":"Article 102047"},"PeriodicalIF":2.3,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143947208","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fibroblast activation protein-α is a potential prognostic biomarker related to ferroptosis in head and neck squamous cell carcinoma","authors":"Kun Cui ,&nbsp;Shifu Tang ,&nbsp;Jing Wei ,&nbsp;Wanping Wang ,&nbsp;Yaoming Deng","doi":"10.1016/j.bbrep.2025.102046","DOIUrl":"10.1016/j.bbrep.2025.102046","url":null,"abstract":"<div><div>Head and neck squamous cell carcinoma (HNSC) is the sixth most prevalent cancer worldwide, with approximately 700,000 new cases each year. Due to its heterogeneity, reliable biomarkers are crucial for guiding treatment. Fibroblast activation protein (FAP) has been implicated in HNSC progression, but its specific involvement in ferroptosis and the ceRNA network is still not well understood.</div><div>In this study, data from The Cancer Genome Atlas (TCGA) HNSC dataset were analyzed to examine the relationship between FAP expression and drug sensitivity, clinical features, methylation status, ferroptosis, immune infiltration, prognosis, and ceRNA networks. The results showed that FAP expression was significantly higher in HNSC tissues compared to normal tissues and was linked to increased sensitivity to 25 antitumor drugs, as well as poorer prognosis and unfavorable clinicopathological features. Lower methylation levels of FAP were also associated with higher mRNA expression and worse outcomes.</div><div>Thirteen ferroptosis-related genes (FRGs) were identified, and four distinct ferroptosis clusters were characterized, with one cluster (C3) showing better survival rates. FAP was further linked to multiple immune cell types, immune markers, and key pathways such as PI3K-Akt and TGF-β. Additionally, a ceRNA network (NOP14-AS1/hsa-miRNA-30e-5p/FAP) was established, which correlated with overall survival in HNSC patients. These findings suggest that FAP may serve as a promising prognostic biomarker in HNSC, influencing both ferroptosis and the tumor microenvironment, providing potential targets for future therapies.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"42 ","pages":"Article 102046"},"PeriodicalIF":2.3,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144069254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Intrinsic clustering of flagellar basal body proteins in E. coli: A self-organization mechanism for assembly and regulation","authors":"Yun-Sing Sung,&nbsp;De-Fa Hong,&nbsp;Yi-Ren Chang","doi":"10.1016/j.bbrep.2025.102051","DOIUrl":"10.1016/j.bbrep.2025.102051","url":null,"abstract":"<div><div>The assembly and spatial organization of flagellar basal bodies in <em>Escherichia coli</em> are crucial for motility and chemotaxis. Using fluorescence and single-molecule microscopy, we demonstrate that key basal body proteins, FliF and FlhA, self-organize into clusters from low to high expression conditions. Rather than forming new basal bodies, excess proteins accumulate around pre-existing structures, suggesting an autocatalytic mechanism. It is confirmed that clustering occurs even at low protein levels, indicating an intrinsic organizational principle rather than an artifact of overexpression. Fluorescence recovery after photobleaching (FRAP) revealed dynamic protein exchange within clusters, supporting a diffusion-capture model. Single-molecule analysis showed that FlhA actively remodels clusters, while FliF stabilizes them. 3D imaging suggested that basal body positioning optimizes flagellar distribution for efficient motility. These findings highlight a robust mechanism that regulates basal body positioning and flagellar assembly, ensuring adaptability to varying cellular conditions.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"42 ","pages":"Article 102051"},"PeriodicalIF":2.3,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143942952","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"β-suppressor protein 1 (ARRB1)-△exon13 modulates the progression of glioblastoma via combination with glycolysis-related proteins","authors":"Zi-Long Wei ,&nbsp;Shuo Han ,&nbsp;Dong-Hua Han ,&nbsp;Xue-Tao Li ,&nbsp;Yu-Lun Huang ,&nbsp;Zhi-Min Wang","doi":"10.1016/j.bbrep.2025.102048","DOIUrl":"10.1016/j.bbrep.2025.102048","url":null,"abstract":"<div><div>Glioblastoma multiform (GBM) constitutes approximately 14.7 % of all central nervous system tumors (CNSTs) and 45.2 % of primary malignant CNSTs. Extensive research has indicated that β-arrestin 1 (ARRB1) plays a significant role in tumor malignancy. In this investigation, we established GBM cell lines representing normal control (NC), overexpression (OE) and Δexon13 GBM variants (△exon13) of ARRB1. Our findings indicate that the ARRB1-OE isoform facilitated GBM cell proliferation and migration, with the ARRB1-△exon13 isoform further augmenting this effect. Notably, the isoform ARRB1-△exon13 binds to glycolytic proteins including ENO1 and ALDOA and regulates glycolysis. In vivo studies corroborate the tumor-promoting effects of ARRB1-Δexon13. Furthermore, we demonstrate that 2-DG effectively inhibits the malignancy-promoting capabilities of ARRB1-Δexon13 by reducing pyruvate levels. Our identification of alternative RNA splicing events of ARRB1 reveals a mechanism by which GBM cell malignancy is augmented through ARRB1-Δexon13, which mediates glycolysis-related pathways.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"42 ","pages":"Article 102048"},"PeriodicalIF":2.3,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143936082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gene network changes after exposure to nanoliposomes containing antisense miR-21 and miR-373 in bladder cancer Cells: An in vitro model study","authors":"Omid Nikkhah ,&nbsp;Behzad Einollahi ,&nbsp;Mosa Asadi ,&nbsp;Mohammad Heiat ,&nbsp;Kiavash Hushmandi","doi":"10.1016/j.bbrep.2025.102041","DOIUrl":"10.1016/j.bbrep.2025.102041","url":null,"abstract":"<div><h3>Aims</h3><div>This study aimed to examine the changes in gene expression profiles of the bladder cancer cell line (HTB-9) after exposure with nanoliposomes (NLs) containing antisense miR-21, antisense miR-373, or a combination of both antisense miR-21 and antisense miR-373 oligonucleotides.</div></div><div><h3>Methods</h3><div>The sequence of miR-21 and miR-373 was obtained from the NCBI, and the optimal corresponding antisense oligonucleotides (ASOs) were selected and synthesized using the Oligowalk online server. After encapsulating the ASOs in liposomes and characterizing them, the liposomal ASOs were incubated with the target cells for 24 h at 37 °C. Following incubation, total RNA was extracted, and cDNA was synthesized. The expression levels of miR-21, miR-373, and eight additional core genes (<em>STK38L</em>: Serine/threonine-protein kinase 38-like; <em>PCDH19</em>: Protocadherin-19; <em>YOD1:</em> Ubiquitin thioesterase OTU1; <em>PRDM11:</em> PR domain-containing protein 11; <em>CROT:</em> Peroxisomal carnitine <em>O</em>-octanoyltransferase; <em>LATS2:</em> Serine/threonine-protein kinase; <em>ZNF845:</em> Zinc finger protein 845; <em>ZC3H6:</em> Zinc finger CCCH domain-containing protein 6) were then analyzed using quantitative Reverse Transcriptase - PCR (qRT-PCR).</div></div><div><h3>Results</h3><div>ASOmiR-21 (AUCUCAUGGCAACACCAGU) and ASOmiR-373 (AAGUGCUUCGAUUUUGGGG) nucleotides were used in this study, respectively. Data analysis revealed that the expression levels of miR-21 and miR-373 were significantly reduced in HTB-9 cells exposed to nanoliposomal ASOs (NL-ASOs) with sizes ranging from 100 ± 5 to 260 ± 10 nm, compared to the control groups. Furthermore, HTB-9 cells exposed simultaneously to both liposomal ASOs (NL-ASOmiR-21+ASOmiR-373) exhibited a greater reduction in miR-21 and miR-373 expression. Additionally, all studied genes (<em>STK38L</em>, <em>PCDH19</em>, <em>YOD1</em>, <em>PRDM11</em>, <em>CROT</em>, <em>LATS2</em>, <em>ZNF845</em>, <em>ZC3H6</em>) showed significant decreases in expression in HTB-9 cells exposed to NL-ASOs across all experimental designs.</div></div><div><h3>Conclusions</h3><div>The results demonstrated that miR-21 and miR-373 play crucial roles in gene expression and that their inhibition can significantly impact the expression profile of a gene network in bladder cancer. Therefore, to regulate the expression of a gene network in bladder cancer, we can use antimir technology as an effective strategy.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"42 ","pages":"Article 102041"},"PeriodicalIF":2.3,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143936081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of ibrutinib and venetoclax on the expression of immune checkpoint molecules in leukemic blasts of patients with acute lymphoblastic leukemia","authors":"Armin Dozandeh-Jouybari ,&nbsp;Fatemeh Mousavi-Mirkalaei ,&nbsp;Saeid Taghiloo ,&nbsp;Hossein Karami ,&nbsp;Mohammad Naderisorki ,&nbsp;Ehsan Zaboli ,&nbsp;Mohammad Eslami-Jouybari ,&nbsp;Tohid Kazemi ,&nbsp;Hossein Asgarian-Omran","doi":"10.1016/j.bbrep.2025.102045","DOIUrl":"10.1016/j.bbrep.2025.102045","url":null,"abstract":"<div><h3>Background</h3><div>In recent decades, targeted therapy using small molecule inhibitors (SMI) have been shown very promising results in the treatment of a variety of solid and hematopoietic malignancies. However, their exact mechanisms, especiallay on the evasion strategies of tumor cells from the host immune system are not fully understood. The current study investigates the effects of two SMIs, ibrutinib and venetoclax, on the expression of inhibitory immune checkpoint molecules in patients with acute lymphoblastic leukemia (ALL).</div></div><div><h3>Methods</h3><div>Leukemic cells were isolated from 20 patients with ALL by magnetic activated cell sorting (MACS) technique. Isolated leukemic cells were cultured and treated by ibrutinib and venetoclax for 48 h. Cell viability and apoptosis were monitored through MTT and flow cytometry assays, respectively. The mRNA expression levels of checkpoint molecules PD-L1, galectin-9, CD200, CD155, CD47, and anti-inflammatory cytokine TGF-β were determined by Real-Time PCR method.</div></div><div><h3>Results</h3><div>The purity of MACS-isolated ALL leukemic cells was &gt;98% as determined by flow cytometry. Following treatment, the proliferation of leukemic cells was significantly decreased and the apoptosis rate was significantly increased, which was more remarkable for venetoclax. Moreover, treatment of leukemic cells with ibrutinib and venetoclax showed alterations in the mRNA expression of immune checkpoint inhibitory ligands and TGF-β.</div></div><div><h3>Conclusion</h3><div>Our results indicated that small molecule inhibitors not only hinder proliferation and enhance apoptosis, but also affect the expression of inhibitory immune checkpoint ligands. By elucidating the precise underlying mechanisms, these drugs could emerge as promising therapeutic options, particularly in the context of combination therapy for ALL.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"42 ","pages":"Article 102045"},"PeriodicalIF":2.3,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143936080","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-cell RNA-seq analysis reveals the multi-step process of cellular senescence","authors":"Minseo Ahn ,&nbsp;Junil Kim ,&nbsp;Jae Ho Seo","doi":"10.1016/j.bbrep.2025.102042","DOIUrl":"10.1016/j.bbrep.2025.102042","url":null,"abstract":"<div><div>Cellular senescence is a phenomenon marked by an irreversible growth arrest with altered physiological properties. Many studies have focused on the characteristics of cells that have already entered a senescent state. However, to elucidate the mechanisms of cellular aging, it is essential to investigate the gradual transition of proliferative cells into senescent cells. We hypothesized that cellular senescence is a complex, multi-step process in which each stage is characterized by distinct cellular features and transcription factor expression patterns. To test this hypothesis, we utilized publicly available single-cell RNA-Seq (scRNA-Seq) data from human umbilical vein endothelial cells (HUVECs) undergoing replicative senescence. We employed Seurat and Monocle 3 to capture the transition from proliferating to senescent states in HUVECs. Four clusters were identified, and each cluster displayed distinct expression patterns of cellular senescence markers and the senescence-associated secretory phenotypes (SASPs). We also employed SCENIC to identify the expression patterns of core transcription factors (TFs) during replicative senescence. While the majority of TFs exhibited a linear trend, HMGB1, FOSL1, SMC3, RAD21, SOX4, and XBP1 showed fluctuating expression patterns during replicative senescence. Furthermore, the expression of these TFs exhibited different patterns in the ionizing radiation (IR) model of senescence. Overall, our study unveils the distinct characteristics of each phase during replicative senescence and identifies expression trends in SASPs and TFs that may play pivotal roles in this process. Unlike previous bulk RNA-seq studies, this work uniquely integrates single-cell trajectory and transcription factor dynamics to decode phase-specific molecular signatures during replicative senescence. Here, we identify key transcription factors potentially involved in senescence induction and provide novel insights into the regulatory complexity of cellular aging.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"42 ","pages":"Article 102042"},"PeriodicalIF":2.3,"publicationDate":"2025-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143931832","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}