Biology subjects

Taniyama, D.

Publications and source records attributed to Taniyama, D..

6 recordsLinked to original sources

bioRxiv2026

Ubiquitin-dependent recruitment of SLFN11 to chromatin is regulated by deubiquitinase and RNF168

The molecular mechanisms driving SLFN11 chromatin recruitment remain partially elucidated. Using high-throughput imaging of 162 oncology-focused compounds in U2OS cells with inducible SLFN11 expression, we discovered that deubiquitinase (DUB) inhibitors drive massive SLFN11 recruitment to chromatin, preferentially at promoter regions while concurrently suppressing transcription. DUB inhibitors such as VLX-1570 promote ubiquitin-dependent enrichment of SLFN11 without detectable DNA damage, distinct from the camptothecin-induced RPA-associated SLFN11 foci formed at stressed replication forks. Yet, SLFN11 chromatin recruitment both by DUB inhibitors and DNA damage are suppressed by TAK243 demonstrating their ubiquitylation dependency. RNF168 is required for SLFN11 ubiquitylation and its subsequent chromatin association, and ubiquitylation within SLFN11s middle linker domain (lysines 390, 391, and 429) with K27-linked polyubiquitin chains is essential for the chromatin recruitment of SLFN11. These findings suggest the importance of SLFN11 ubiquitylation by RNF168 for SLFN11 chromatin recruitment and SLFN11 transcriptional regulatory role at promoter regions.

cell biology↗

bioRxiv2026

Schlafen 11 (SLFN11) overexpression and nucleolar localization in response to bortezomib in multiple myeloma

Proteins belonging to the Schlafen family are interferon-inducible and participate in the regulation of antiviral responses, immune signaling and proteotoxic stress. SLFN11 also kills cells with replicative damage, serving as a predictive biomarker for chemotherapeutic response. Here we examined SLFN11 expression and significance in multiple myeloma (MM). The TCGA and MMRF CoMMpass datasets were analyzed for SLFN11 expression. Bone marrow and cell lines samples were analyzed for SLFN11 protein. SLFN11-knockout MM cell lines were used to explore how SLFN11 affects bortezomib response. Retrospective analysis of the HOVON-65/GMMG-HD4 phase III trial (n=327) assessed clinical relevance. SLFN11 is consistently highly expressed across MM subtypes (except CD1 and MAF/MAFB) and in normal plasma cells, and its expression strongly correlates with super-enhancer-driven plasma cell transcriptional programs. CD138-positive normal and myeloma plasma cells retain SLFN11 expression even when proliferative activity (MKI67/Ki-67) increases with disease progression. Bortezomib, a first-line MM treatment, induces SLFN11 nucleolar translocation with suppression of ribosomal RNA synthesis. Knocking out SLFN11 in MM cells enhances bortezomib sensitivity and exatecan resistance, supporting SLFN11s protective role in proteotoxic stress and sensitizing role in replication stress. In the HOVON-65/GMMG-HD4 trial, SLFN11-low patients showed selective benefit from bortezomib-based therapy, suggesting that SLFN11 expression may guide therapeutic stratification in MM. SignificanceSLFN11 is highly expressed in normal and malignant plasma cells. Bortezomib induces SLFN11 nucleolar translocation, suppressing ribosomal RNA synthesis and global translation. SLFN11 confers bortezomib resistance while sensitizing to topoisomerase I inhibitors. Clinical analysis supports that low SLFN11 expression predicts bortezomib benefit, providing a mechanistic basis for SLFN11-guided therapeutic stratification.

cancer biology↗

bioRxiv2025

SLFN11 puts the brakes on Alternative lengthening of telomeres

Alternative lengthening of telomeres (ALT) is a homologous recombination-dependent mechanism maintaining telomere length in approximately 10-15% of all cancers that are telomerase (TERT) negative. ALT is most prominent in osteosarcoma. Although many ALT cells feature loss of the ATRX/DAXX chromatin remodeling complex, ATRX/DAXX deficiency alone is insufficient to trigger ALT. Here, we provide evidence that Schlafen 11 (SLFN11) acts as a suppressor of the telomeric ALT pathway. TERT-negative osteosarcoma U2-OS (ALT) cells, that normally lack SLFN11 expression, show SLFN11 localization to telomeres upon doxycycline-induced SLFN11 expression. This re-expression markedly suppresses ALT activity, as evidenced by reduced ALT-associated PML bodies (APBs) and decreased levels of Telomeric Repeat-containing RNA (TERRA). SLFN11 re-expression also attenuates the telomeric DNA damage response (DDR) and induces telomere destabilization in ALT cells. Furthermore, SLFN11 suppresses ALT induction in ATRX-depleted prostate carcinoma DU145 cells. Collectively, our findings identify SLFN11 as a negative telomeric regulator of the ALT pathway, indicating that its loss, together with ATRX/DAXX inactivation, contributes to ALT activation.

cell biology↗

bioRxiv2025

Peroxiredoxin 1 safeguards the nucleolar genome from oxidative damage

Peroxiredoxin 1 (PRDX1) is a highly conserved, thiol-dependent peroxidase that rapidly scavenges reactive oxygen species to modulate redox signaling. PRDX1-null mice exhibited genomic instability, shortened lifespan, and accelerated tumorigenesis, including development of lymphomas, sarcomas, and carcinomas. Despite extensive characterization of these phenotypes, the molecular mechanism by which PRDX1 loss causes genomic instability remains poorly understood. Here we show that PRDX1 deficiency alters nucleolar morphology, impairs RNA Polymerase I (POL-I)-dependent transcription of pre-ribosomal RNAs and triggers nucleolar genomic instability. This oxidative stress-induced nucleolar dysfunction promotes the stability of secondary DNA structures, such as RNA-DNA hybrids and G-quadruplex DNA, contributing to nucleolar genomic instability. We demonstrate that PRDX1 loss reduces nascent rRNA levels and impairs rRNA processing, further affecting ribosome biogenesis. Mechanistically, we established that PRDX1 loss triggers activation of the nucleolar DNA damage response including activation of DNA repair kinase ATM and the nucleolar factor TCOF1 within the nucleolus, and recruitment of the MRE11-RAD50-NBS1 (MRN) complex subunit NBS1 to ribosomal DNA (rDNA) loci. NBS1 accumulation correlates with the repression of rDNA transcription by POL-I, potentially delaying rRNA synthesis, and safeguarding the nucleolar genome from further oxidative damage. Collectively, these findings uncover a previously unrecognized, but critical role, for PRDX1 in maintaining nucleolar integrity and ribosomal biogenesis through redox-dependent regulation of rDNA transcription and processing machinery.

molecular biology↗

bioRxiv2025

SCLC-TumorMiner: A Directly Accessible Genomics Resource for Precision Oncology: Big Data for Small Cells

Small cell lung cancer (SCLC) is among the most aggressive malignancies. Unlike many other cancers, it is not represented in The Cancer Genome Atlas, and available datasets are fragmented across institutions, disease stages, and treatment settings. RNA sequencing provides a powerful and cost-effective approach, but the high dimensionality of transcriptomic data and the heterogeneity of patient cohorts pose significant challenges. To address such challenges, we developed SCLC TumorMiner (https://discover.nci.nih.gov/SclcTumorMinerCDB/), which includes 50 tumor samples from relapse patients at the National Cancer Institute (NCI) and 154 samples from untreated patients at the University of Cologne and Tongji University. SCLC TumorMiner enables molecular classification, genomic pathway analyses, risk stratification, identification of predictive cell-surface biomarkers such as DLL3 or TROP2, and drug-response biomarkers such as SLFN11. SCLC TumorMiner illustrates profound differences between untreated and relapse patient samples. Additionally, "MyPatient", one of SCLC TumorMiners modules, is presented as a medical assistant application prototype.

cancer biology↗

bioRxiv2025

Bimodal genomic approach predicting Semaphorin 7A (SEMA7A) as prognostic biomarker in adrenocortical carcinoma

Adrenocortical carcinoma (ACC) is a rare and aggressive endocrine malignancy with high mortality and poor prognosis. To elucidate the genetic underpinnings of ACCs, we have analyzed the transcriptome data of 112 ACC tumor samples from patients enrolled in the TCGA and NCI. Among 72 bimodally expressed genes stratifying patients into prognostic groups, we focused on SEMA7A, as it encodes a glycosylphosphatidylinositol-anchored membrane glycoprotein (Semaphorin 7a) regulating integrin-mediated signaling, cell migration and immune responses. We find that high SEMA7A gene expression is associated with poor prognosis (hazard ratio = 4.27; p-value < 0.001). In hormone-producing ACCs, SEMA7A expression is elevated and positively correlated with genes driving steroidogenesis, aldosterone and cortisol synthesis, including CYP17A1, CYP11A1, INHA, DLK1, NR5A1 and MC2R. Correlation analyses show that SEMA7A is co-expressed with the integrin-{beta}1, FAK (focal adhesion kinase) and MAPK/ERK (mitogen-activated protein kinase/extracellular signal regulated kinases) signaling pathways. Immunohistochemistry (IHC) staining demonstrates the feasibility of evaluating SEMA7A in ACC tissues and shows significant correlation between gene expression (RNA-Seq) and protein expression (IHC). These findings suggest SEMA7A as a candidate for further research in ACC biology, a candidate for cancer therapy, as well as a potential prognosis biomarker for ACC patients. Translational relevanceAdrenocortical cancer (ACC) remains a challenging disease primarily due to the scarcity of reliable biomarkers for predicting patient outcomes and informing innovative therapeutic strategies, as well as its rarity, which restricts the scope of clinical trials. In our study, we performed RNAseq and IHC analyses of ACC samples sourced from The Cancer Genome Atlas (TCGA), tissue microarray slide, and National Cancer Institute (NCI) cancer patient samples. Our findings indicate that a substantial proportion of ACC tumors exhibit expression of SEMA7A, a glycoprotein involved in Semaphorin cell surface signaling. Notably, elevated levels of SEMA7A were identified as a poor prognostic biomarker and were associated with activation of the integrin-ERK-MAPK kinase signaling pathways. These results suggest that ACC tumors with high SEMA7A expression should be considered at elevated risk, and SEMA7A may serve as a potential target for immunotherapeutic strategies, including antibody-drug conjugates, T-cell engagers, and/or small molecule inhibitors targeting the MAPK pathway.

cancer biology↗