Biology subjects

Jena, A.

Publications and source records attributed to Jena, A..

6 recordsLinked to original sources

bioRxiv2026

Spatial transcriptomics reveals BMP-dependent stage-specific transcriptional programs underlying migration of cortical neurons

The laminar architecture of the mammalian neocortex depends on precise radial migration of newborn neurons to the appropriate cortical layers. This process is governed by the integration of extracellular signals with cell-intrinsic transcriptional programs. BMP signaling has been previously demonstrated to be essential for radial migration of late-born (E15.5) upper-layer cortical neurons. However, the gene expression programs downstream of BMP signaling that regulate this process remained unknown. To address this, we combined temporally targeted in utero electroporation with GeoMx Digital Spatial Profiling (DSP) to map BMP-responsive transcriptional programs in E15.5-born layer II/III neurons at two defined developmental timepoints: E17.5, when neurons actively migrate through the intermediate zone, and postnatal day 0 (P0), when they have completed migration and have attained their laminar position. BMP inhibition produced largely non-overlapping transcriptional changes at these two stages. At E17.5, chromatin-regulatory programs and ribosomal protein gene expression were collectively upregulated upon BMP inhibition. However, by P0, the same cohort of ribosomal genes exhibited downregulation while membrane lipid biosynthesis and synaptic specialization pathways became dominant, revealing a stage-dependent transcriptional switch. A subset of shared BMP-responsive genes was regulated in opposite directions at these two stages, which lent further support to the hypothesis that there is a temporal reorganization of BMP-dependent transcriptional outputs. We selected four candidates from among the BMP-responsive genes for functional studies, namely Mfap4, Olfm2, Adora1, and Arpp21, which belong to diverse functional categories, including extracellular matrix proteins, G protein-coupled receptors, secreted glycoproteins, and RNA-binding proteins. RNAi-mediated knockdown of all four candidates resulted in radial migration defects that closely phenocopied inhibition of BMP signaling, establishing these genes as functional effectors of the BMP signaling pathway regulating neuronal migration.

developmental biology↗

bioRxiv2026

Mechanism and key RNA determinants of SARS-CoV-2 Nsp1-induced endonucleolytic cleavage of mRNA

SARS-CoV-2 nonstructural protein 1 (Nsp1) binds to 40S ribosomal subunits and induces host protein synthesis shut off by inhibiting translation initiation and triggering endonucleolytic cleavage of cellular mRNAs. Irrespective of the mode of initiation, Nsp1-mediated cleavage is induced by the cooperative action of the N-terminal domain of Nsp1, the RRM domain of eIF3g and 40S subunits. Using in vitro reconstitution, we determined that cleavage occurs by transesterification following intramolecular nucleophilic attack of the 2OH of the ribose on the adjacent phosphodiester bond yielding 5OH and 2,3 -cyclic phosphate termini. Cleavage requires a guanosine [~]10-22 nucleotides from the 5 end of mRNA, occurs within a narrow window upstream of this G, is most efficient between nucleotides at positions -6/-7 and -7/-8 relative to G, and shows a preference for Pu at positions -7 or -8 which provides the 2OH for the nucleophilic attack. Zero-length UV cross-linking of Nsp1 to nucleotides at positions -1 and -2 suggests that the critical guanosine may be recognized by Nsp1. Resistance to Nsp1-mediated cleavage of SARS-CoV-2 mRNA was ensured both by the relatively long distance between its G23G24 and the 5end and by the preceding oligoPy stretch lacking purines at positions -7 or -8 upstream of G23G24.

Preprint↗

bioRxiv2025

Pathogenic mutations in Clathrin Heavy Chain associated with intellectual disability impair synaptic architecture and learning in Drosophila

Clathrin-mediated endocytosis is essential for neural development and function. Recent studies have linked de novo mutations in the clathrin heavy chain (Chc) gene to a range of neurodevelopmental disorders. In this study we have modelled two pathogenic mutations: L1047P and W1108R in Drosophila melanogaster and examined their effects on vesicle dynamics, ligand uptake, neuronal development and memory formation. Our data shows that expression of these mutant forms of Chc result in reduced survival and defective learning when expressed ubiquitously or exclusively in neurons. Our analysis also reveals that these mutations have the ability to disrupt vesicle dynamics and reduce ligand uptake in cells. Although we do not see a defect in neuronal morphology and function at the larval neuro-muscular junction, we see an increase in the number of Dlg-negative boutons, and a significant reduction in Spectrin expression, indicative of disruptions in the process of synapse maturation. Overall, this study provides mechanistic insights into the cellular and molecular basis of Chc-related neurodevelopmental disorders.

cell biology↗

bioRxiv2025

DIFFERENTIAL ROLES OF RAD18 IN REPRESSING CARCINOGEN- AND ONCOGENE-DRIVEN MUTAGENESIS IN VIVO

The DNA repair protein RAD18 activates Y-family Trans-Lesion Synthesis (TLS) DNA polymerases that are DNA damage-tolerant and potentially error-prone. RAD18 is also frequently overexpressed and pathologically activated in cancer cells. However, the extent to which RAD18 shapes cancer genomes and impacts tumorigenesis is unclear. Therefore, we tested the effect of Rad18 status on chemically-induced and oncogene-driven tumorigenesis. In a chemically-induced oral carcinogenesis model, acute (2-16 days) 4NQO-treatment induces expression of Rad18 and TLS polymerase mRNAs in mouse oral epithelial cells prior to emergence of oral squamous cell carcinomas (OSCCs). Chronic (8 week) 4NQO-treatment leads to onset of oral tumors that is accelerated in Rad18-/- mice when compared with Rad18+/+ animals. Analysis of OSCC exomes reveals increased levels of G(C)>T(A) transversions in Rad18-/- tumors when compared with Rad18+/+. Therefore, Rad18 promotes error-free bypass of 4NQO-induced DNA lesions and suppresses 4NQO-induced oral carcinogenesis. In a KrasG12D-induced lung carcinogenesis model, Rad18-deficiency did not affect rates or incidence of oncogene-induced lung tumors or mutations. Taken together, we demonstrate that Rad18 has context-specific tumor-suppressive activity. Given the prevalence of 4NQO-like environmental exposures, RAD18 is highly likely to shape human cancer genomes and perhaps influence other aspects of the tumorigenic process.

cancer biology↗

bioRxiv2024

Age-induced BMP signaling inhibits the ICAT-mediated Wnt pathway to promote osteoarthritis.

Osteoarthritis (OA) is a highly prevalent and debilitating musculoskeletal disorder that affects billions of aging individuals worldwide, causing chronic pain, impaired mobility, and a substantial decline in quality of life, yet effective disease-modifying therapies remain unavailable. Moreover, existing experimental models, however, inadequately capture the complex, age-related factors that contribute to OA pathogenesis, limiting our understanding of underlying molecular mechanisms and hindering therapeutic development. To address this gap, we examined mouse articular cartilage (AC) during natural aging, without surgical or chemical intervention. In young AC, BMP ligand expression is restricted to the bone-cartilage junction, limiting BMP signaling despite widespread BMPR1A receptor expression, while Wnt/{beta}-catenin signaling predominates in the outer layers. With aging, BMP ligand expression expands throughout the cartilage, leading to widespread activation of BMP signaling, which induces ICAT expression, a known inhibitor of Wnt/{beta}-catenin signaling. This elevated BMP signaling triggers chondrocyte hypertrophy while concurrently suppressing Wnt/{beta}-catenin activity. Moreover, genetic or pharmacological activation of BMP signaling in young AC recapitulates the cellular and molecular features of aged cartilage, independent of chronological age. Collectively, our findings demonstrate that an age-dependent shift in BMP-Wnt signaling disrupts AC homeostasis and drives OA progression in mice. Author SummaryDespite the prevalence of osteoarthritis in aging individuals, there are no effective treatments that can stop or reverse disease progression. In this study, we investigated how joint cartilage changes during natural aging in mice. We observed that healthy, young articular cartilage exhibits robust Wnt/{beta}-catenin with minimal BMP siganling. With age, this balance shifts, with BMP signaling becoming dominant, coupled with reduced Wnt/{beta}-catenin activity. This disruption of Wnt-BMP homeostasis induces the pathogenesis of OA. Importantly, local inhibition of BMP signaling significantly alleviates the severity of the disease. Overall, these results show that age-associated changes in key signaling pathways drive OA progression and suggest potential targets for therapeutic intervention. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/616036v2_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@b2be12org.highwire.dtl.DTLVardef@dcb1f3org.highwire.dtl.DTLVardef@126fc40org.highwire.dtl.DTLVardef@7af96c_HPS_FORMAT_FIGEXP M_FIG C_FIG

pathology↗

bioRxiv2022

AGS3 antagonizes LGN to balance oriented cell divisions and cell fate choices in mammalian epidermis

Oriented cell divisions balance self-renewal and differentiation in stratified epithelia such as the skin epidermis. During peak epidermal stratification, the distribution of division angles among basal keratinocyte progenitors is bimodal, with planar and perpendicular divisions driving symmetric and asymmetric daughter cell fates, respectively. An apically-polarized, evolutionarily-conserved spindle orientation complex that includes the scaffolding protein LGN/Pins/Gpsm2 plays a central role in promoting perpendicular divisions and stratification, but little is known about the molecular regulation of planar divisions. Here, we demonstrate that the LGN paralog, AGS3/Gpsm1, is a novel negative regulator of LGN, and inhibits perpendicular divisions. Static and ex vivo live imaging reveal that AGS3 overexpression displaces LGN from the apical cortex and increases planar orientations, while AGS3 loss prolongs cortical LGN localization and leads to a perpendicular orientation bias. Genetic epistasis experiments in double mutants confirm that AGS3 operates through LGN. Finally, clonal lineage tracing shows that LGN and AGS3 promote asymmetric and symmetric fates, respectively, while also influencing differentiation through delamination. Collectively, these studies shed new light into how spindle orientation influences epidermal stratification.

developmental biology↗