Biology subjects

Caplen, N.

Publications and source records attributed to Caplen, N..

5 recordsLinked to original sources

bioRxiv2026

Oncolytic virus-antibody combinations enhance immune-mediated killing of osteosarcoma

A major barrier to effective immunotherapy in osteosarcoma (OS) is the highly immunosuppressive tumour microenvironment (TME), which limits immune recognition and elimination of tumour cells. We evaluated a panel of oncolytic herpes simplex viruses (oHSVs) for their direct oncolytic activity, immune-modulatory properties and capacity to counteract OS-associated immunosuppression using immunologically relevant in vitro models. We demonstrate that established OS cell lines, primary cell cultures and dissociated OS cells from freshly resected tumour samples are susceptible to direct oncolysis by three oHSVs; HSV1716, HSV1716-GMCSF, and HSV47{Delta}, although susceptibility levels varied. Treatment of peripheral blood mononuclear cells from healthy donors and OS patients with oHSVs enhanced natural killer (NK) cell activation and promoted immune-mediated killing of OS cell lines and primary OS cell cultures. Among the three viruses, HSV1716-GMCSF exhibited the strongest immune-stimulatory effects and was uniquely capable of reducing the abundance of CD163+CD206+ immunosuppressive TAMs; use of this oHSV was therefore prioritised. We developed a multicellular spheroid model of OS, incorporating OS cells, mesenchymal stem cells and TAMs, which exhibits resistance to immune-mediated killing, better reflecting the immunosuppressive TME in patients. In this model, pairing HSV1716-GMCSF treatment with either anti-GD2 or anti-EGFR monoclonal antibodies (mAbs), selected according to OS tumour antigen expression, significantly increased immune-mediated tumour cell killing. These findings suggest that personalised combination strategies pairing oHSVs with appropriate mAbs provide a promising therapeutic approach for OS by integrating direct oncolysis, remodelling of the immunosuppressive TME and enhanced immune-mediated tumour destruction.

cancer biology↗

bioRxiv2026

FUS and TAF15 safeguard the critical functions of the ribonucleoprotein network formed by EWSR1 and newly synthesized RNA

The FET family of RNA-binding proteins, FUS, EWSR1, and TAF15, contribute to transcriptional regulation and RNA maturation, but their core functions remain unclear. Chromosomal rearrangements involving FUS, EWSR1, or TAF15 drive multiple cancers, and mutations in the genes encoding the FET proteins are associated with neurodegenerative disease. Here, using nanoscale imaging, we show that endogenous EWSR1 and newly synthesized RNA exhibit a network-like organization with EWSR1 foci forming the nodes of this ribonucleoprotein network. Acute depletion of EWSR1 causes a rapid but transient reduction in nascent RNA levels and cellular metabolic activity without affecting active transcription. Notably, loss of EWSR1 induces a compensatory mechanism involving the reorganization of FUS and TAF15 to closely resemble that of EWSR1, including enhanced clustering with newly synthesized RNA. Together, our findings reveal functional redundancy within the FET protein family that is critical for the homeostatic regulation of nascent RNA levels. In briefSundara Rajan et al. show that endogenous EWSR1 and nascent RNA form a ribonucleoprotein network. EWSR1 depletion transiently reduces nascent RNA and metabolic activity without impairment of transcriptional elongation. Loss of EWSR1 induces compensatory reorganization of FUS and TAF15, revealing a protein family mechanism required for the homeostatic regulation of nascent RNA levels. HighlightsO_LIEWSR1 and nascent RNA form a ribonucleoprotein network C_LIO_LIEWSR1 loss transiently reduces nascent RNA and metabolic activity C_LIO_LIFUS and TAF15 undergo compensatory nuclear reorganization upon EWSR1 loss C_LIO_LIFUS and TAF15 functionally replace EWSR1 C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/713985v1_ufig1.gif" ALT="Figure 1"> View larger version (59K): org.highwire.dtl.DTLVardef@b66671org.highwire.dtl.DTLVardef@ff8d49org.highwire.dtl.DTLVardef@194cfd4org.highwire.dtl.DTLVardef@d889f5_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2026

Non-canonical function of the splicing activator U2AF2 in promoting intron retention in the lncRNAs PURPL and MALAT1

Intron retention (IR) is increasingly recognized as a feature of long noncoding RNAs (lncRNAs), yet the mechanisms that shape IR in lncRNAs and the functional consequences of this process remain largely unexplored. To investigate how IR contributes to lncRNA regulation, we performed a genome-wide screen to identify factors controlling IR in the lncRNA PURPL. This approach uncovered a prominent role for U2AF2, which promotes retention of a specific intron in PURPL through a weak polypyrimidine tract. IR of this intron drives nuclear enrichment of PURPL and enhances cell proliferation, revealing biological relevance. Transcriptome-wide analyses showed that although U2AF2 broadly supports canonical splicing consistent with its well-established function in promoting splicing, it also facilitates IR within a distinct subset of RNAs, including the nuclear speckle-associated lncRNA MALAT1. Loss of U2AF2 disrupts MALAT1 speckle localization and using MALAT1 knockout cells reconstituted with wild-type or intron deleted variants, we identified a single intron critical for MALAT1s speckle localization. Deletion of this intron from endogenous MALAT1 impaired speckle localization and reduced cell migration, phenocopying the loss of MALAT1. Together, these findings reveal IR as a key regulatory mechanism governing lncRNA localization and function and uncover an unexpected role for U2AF2 in promoting IR within specific lncRNA contexts.

cell biology↗

bioRxiv2025

HNRNPH1-mediated splicing events regulate EIF4G1 transcript variant composition and the organization of the AURKA 5' UTR

HNRNPH1 is a regulator of alternative splicing, but few studies have defined the splicing events it mediates. Here, we used short- and long-read RNA sequencing to interrogate the transcriptome-wide effects of HNRNPH1 depletion and its regulation of specific splicing events. Differential alternative splicing analysis revealed effects on the transcriptome that involved all splice event categories. We confirmed HNRNPH1s regulation of a splicing event involving TCF3-exons 18a and 18b that encode distinct TCF3 transcription factor isoforms. Extending this finding, we present evidence that in neuroblastoma, HNRNPH1 is a MYCN target, potentially explaining the higher levels of HNRNPH1 and TCF3-exon 18a transcript variants in this tumor type. Analysis of two skipped exon events determined that HNRNPH1 regulates the splicing of exons encoding part of the EIF4G1 translation initiation factors N-terminus and an exon included in the 5UTR of specific transcript variants encoding the mitotic kinase AURKA. Using reporter constructs, we show this AURKA 5UTR exon enhances expression, suggesting HNRNPH1 could contribute to regulating AURKA protein levels. Our findings highlight HNRNPH1s roles in regulating the expression of proteins with diverse cellular functions. Key pointsO_LIHNRNPH1 regulates the expression of proteins with diverse cellular functions, including proteins involved in the regulation of gene expression and essential cellular mechanisms. C_LIO_LIDepletion of HNRNPH1 alters the expression of specific protein-coding EIF4G1 transcript variants. C_LIO_LIHNRNPH1 mediates the inclusion of an AURKA 5UTR exon that enhances protein expression. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/667222v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@13780f1org.highwire.dtl.DTLVardef@f276d8org.highwire.dtl.DTLVardef@588245org.highwire.dtl.DTLVardef@d08551_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2023

ETS1, a target gene of the EWSR1::FLI1 fusion oncoprotein, regulates the expression of the focal adhesion protein TENSIN3

The mechanistic basis for the metastasis of Ewing sarcomas remains poorly understood, as these tumors harbor few mutations beyond the chromosomal translocation that initiates the disease. Instead, the epigenome of Ewing sarcoma (EWS) cells reflects the regulatory state of genes associated with the DNA binding activity of the fusion oncoproteins EWSR1::FLI1 or EWSR1::ERG. In this study, we examined the EWSR1::FLI1/ERGs repression of transcription factor genes, concentrating on those that exhibit a broader range of expression in tumors than in EWS cell lines. Focusing on one of these target genes, ETS1, we detected EWSR1::FLI1 binding and an H3K27me3 repressive mark at this locus. Depletion of EWSR1::FLI1 results in ETS1s binding of promoter regions, substantially altering the transcriptome of EWS cells, including the upregulation of the gene encoding TENSIN3 (TNS3), a focal adhesion protein. EWS cell lines expressing ETS1 (CRISPRa) exhibited increased TNS3 expression and enhanced movement compared to control cells. The cytoskeleton of control cells and ETS1-activated EWS cell lines also differed. Specifically, control cells exhibited a distributed vinculin signal and a network-like organization of F-actin. In contrast, ETS1-activated EWS cells showed an accumulation of vinculin and F-actin towards the plasma membrane. Interestingly, the phenotype of ETS1-activated EWS cell lines depleted of TNS3 resembled the phenotype of the control cells. Critically, these findings have clinical relevance as TNS3 expression in EWS tumors positively correlates with that of ETS1. SignificanceETS1s transcriptional regulation of the gene encoding the focal adhesion protein TENSIN3 in Ewing sarcoma cells promotes cell movement, a critical step in the evolution of metastasis. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/572864v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@98d35aorg.highwire.dtl.DTLVardef@15bf897org.highwire.dtl.DTLVardef@11da61aorg.highwire.dtl.DTLVardef@18429d9_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗