Light-Seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing.

We present Light-Seq, an approach for multiplexed spatial indexing of intact biological samples using light-directed DNA barcoding in fixed cells and tissues followed by ex situ sequencing. Light-Seq combines spatially targeted, rapid photocrosslinking of DNA barcodes onto complementary DNAs in situ with a one-step DNA stitching reaction to create pooled, spatially indexed sequencing libraries. This light-directed barcoding enables in situ selection of multiple cell populations in intact fixed tissue samples for full-transcriptome sequencing based on location, morphology or protein stains, without cellular dissociation. Applying Light-Seq to mouse retinal sections, we recovered thousands of differentially enriched transcripts from three cellular layers and discovered biomarkers for a very rare neuronal subtype, dopaminergic amacrine cells, from only four to eight individual cells per section. Light-Seq provides an accessible workflow to combine in situ imaging and protein staining with next generation sequencing of the same cells, leaving the sample intact for further analysis post-sequencing.

Concurrent inhibition of CDK2 adds to the anti-tumour activity of CDK4/6 inhibition in GIST.

BACKGROUND: Advanced gastrointestinal stromal tumour (GIST) is characterised by genomic perturbations of key cell cycle regulators. Oncogenic activation of CDK4/6 results in RB1 inactivation and cell cycle progression. Given that single-agent CDK4/6 inhibitor therapy failed to show clinical activity in advanced GIST, we evaluated strategies for maximising response to therapeutic CDK4/6 inhibition. METHODS: Targeted next-generation sequencing and multiplexed protein imaging were used to detect cell cycle regulator aberrations in GIST clinical samples. The impact of inhibitors of CDK2, CDK4 and CDK2/4/6 was determined through cell proliferation and protein detection assays. CDK-inhibitor resistance mechanisms were characterised in GIST cell lines after long-term exposure. RESULTS: We identify recurrent genomic aberrations in cell cycle regulators causing co-activation of the CDK2 and CDK4/6 pathways in clinical GIST samples. Therapeutic co-targeting of CDK2 and CDK4/6 is synergistic in GIST cell lines with intact RB1, through inhibition of RB1 hyperphosphorylation and cell proliferation. Moreover, RB1 inactivation and a novel oncogenic cyclin D1 resulting from an intragenic rearrangement (CCND1::chr11.g:70025223) are mechanisms of acquired CDK-inhibitor resistance in GIST. CONCLUSIONS: These studies establish the biological rationale for CDK2 and CDK4/6 co-inhibition as a therapeutic strategy in patients with advanced GIST, including metastatic GIST progressing on tyrosine kinase inhibitors.

Cationic zinc is required for factor XII recruitment and activation by stimulated platelets and for thrombus formation in vivo.

BACKGROUND: Although divalent zinc (Zn2+ ) is known to bind factor (F)XII and affect its sensitivity to autoactivation, little is known about the role of Zn2+ in the binding of FXII to platelets, where FXII activation is thought to occur in vivo, and the function of Zn2+ during thrombus formation following vascular injury remains poorly understood. OBJECTIVES: To evaluate the role of Zn2+ in platelet-dependent FXIIa generation. METHODS: FXII binding to platelets and FXII activation by stimulated platelets were assessed using flow cytometry and a platelet-dependent thrombin generation assay. The mouse cremaster laser injury model was used to evaluate the impact of Zn2+ chelation on thrombus formation in vivo. RESULTS: Our data demonstrate that stimulated platelets support FXII-dependent thrombin generation and that FXII activation by platelets requires the presence of Zn2+ . By contrast, thrombin generation by stimulated endothelial cells occurred independently of FXII and Zn2+ . Using flow cytometry, we found that FXII-fluorescein-5-isothiocyanate binds to the surfaces of stimulated platelets in a specific and Zn2+ -dependent manner, whereas resting platelets demonstrated minimal binding. Other physiologically-relevant divalent cations are unable to support this interaction. Consistent with these findings, the Zn2+ -specific chelator ethylenediaminetetraacetic acid calcium disodium salt confers thromboprotection in the mouse cremaster laser injury model without causing increased bleeding. We observed an identical phenotype in FXII null mice tested in the same system. CONCLUSIONS: Our results suggest a novel role for Zn2+ in the binding and activation of FXII at the platelet surface, an interaction that appears crucial to FXII-dependent thrombin generation but dispensable for hemostasis.