Biology subjects

Mnatsakanyan, H.

Publications and source records attributed to Mnatsakanyan, H..

6 recordsLinked to original sources

bioRxiv2026

Integrated single-cell profiling of RNA and DNA interactomes reveals targetable chromatin architectures in cancer

The human genome is pervasively transcribed into protein-coding and regulatory non-coding RNAs whose functions are coordinated within higher-order nuclear architectures. However, direct mapping of RNA-RNA and DNA-DNA interaction networks in complex human tissues at single-cell resolution has remained a major challenge. Here, we present SCIENCE-seq, a multimodal single-cell interactomics platform enabling simultaneous detection of RNA-RNA interactions and chromatin DNA-DNA contacts within individual cells. Applied to primary glioma specimens, SCIENCE-seq reveals cancer-specific interactions organized by lncRNAs and centered on key oncogenic drivers, including EGFR, hTERT, SOX2, CDK6, CDC42, CD47, and HOX loci. These datasets uncover previously unrecognized molecular relationships between premature lncRNAs and pre-mRNAs that regulate transcription, alternative splicing, and polyadenylation. Notably, we identify a glioma-specific trans-chromosomal HOX hub driven by five interacting lncRNAs. Targeting specific RNA and DNA interactions using steric antisense oligonucleotides (ASOs) or CRISPRi selectively suppresses oncogenic programs in malignant cells while sparing normal tissue, establishing chromatin interactomes as actionable therapeutic targets.

cancer biology↗

bioRxiv2026

Overcoming the accuracy-generalization tradeoff in docking and scoring for prospective virtual screening

Virtual screening promises access to tens of billions of synthetically accessible, diverse compounds, yet it is rarely used as a primary hit-discovery strategy in contemporary drug-discovery campaigns. We argue that this gap reflects the real-world underperformance of the underlying docking and scoring methods: classical docking is generalizable but limited in accuracy by simple functional forms and parsimonious parameterization, whereas recent machine-learning approaches are highly expressive but do not generalize well to novel molecules and pockets, their reported accuracy often inflated by train-test leakage. To address these challenges, we introduce DODock and DOScore, docking and scoring ML/physics hybrid frameworks that are also highly expressive, yet generalize much better out of distribution compared with the prior ML approaches. This generalization has been prospectively tested in several ways. First, DODocks blind prediction of a drug candidate binding to PCSK9 was compared to the crystal structure that was subsequently solved, recovering the binding pose to 1.2 [A] RMSD. We also used DODock and DOScore in prospective virtual screening campaigns against four therapeutic targets, spanning an ectoenzyme (CD73), a kinase (IRAK4), an extended-substrate protease (FXI), and an allosteric inhibition of protein-protein interface (IL17). These screens yielded many chemically novel, biochemically and cellularly active inhibitors. In the case of CD73, which is a historically challenging target for virtual screening, our screen resulted in a roughly hundredfold improvement in hit rate over a recent machine-learning screen. Our results indicate that the apparent ceiling in the accuracy of virtual screening that seemed to have somewhat plateaued in the last two decades is not fundamental, and that structure-based interrogation of ultralarge chemical space may eventually become a credible primary route to novel chemical matter.

biophysics↗

bioRxiv2025

NaBC1 Acts as a Mechanosensitive Co-regulator of Fibronectin-binding Integrins Adhesion and Myoblast Polarization

Cell-matrix interactions are central to the regulation of cell mechanics, polarity, and signal transduction. In this study, we investigate the contribution of the borate transporter NaBC1 to myoblast adhesion dynamics and mechanotransductive responses. Using C2C12 myoblasts cultured on fibronectin-coated substrates, we show that NaBC1 activation rapidly reinforces cell-substrate attachment, leading to accelerated spreading and the establishment of polarized cell morphologies. These changes are associated with the assembly of enlarged focal adhesions and a marked slowdown of actin retrograde flow, consistent with increased force transmission across adhesion sites. NaBC1 stimulation also induces a coordinated increase in the expression of fibronectin-binding integrins, including 5{beta}1 and v{beta}3, at both transcriptional and protein levels. Proximity ligation assays reveal an enhanced spatial association between NaBC1 and these integrins at the cell membrane, supporting the formation of cooperative adhesion complexes. In parallel, fluorescently labelled boron accumulates at focal adhesions and within intracellular compartments such as mitochondria, lysosomes, and the endoplasmic reticulum, suggesting a link between NaBC1-dependent adhesion signaling and subcellular organization. Importantly, the adhesive and mechanotransductive effects driven by NaBC1 are strictly dependent on fibronectin integrity and are lost on mutant fibronectins lacking RGD or synergy motifs, as well as on laminin-111 substrates that do not support molecular clutch engagement. Together, these findings identify NaBC1 as an integral component of fibronectin-integrin adhesion systems, contributing to the regulation of myoblast mechanics and polarity through cooperative interactions with fibronectin-binding integrins.

bioengineering↗

bioRxiv2025

SCD1 and SCD5 Modulate PARP-Dependent DNA Repair via Fatty Acid Desaturation in Glioblastoma

Glioblastoma (GBM) relies on fatty acid metabolism to sustain its aggressive growth. While the role of stearoyl-CoA desaturase-1 (SCD1) in GBM is established, the function of its brain-enriched isoform, SCD5, remains unexplored. Here, we demonstrate that SCD5 is essential for glioblastoma stem cell (GSC) maintenance and genomic stability, with elevated expression in GSCs that declines upon differentiation, underscoring its role in tumor initiation. Through shotgun lipidomics, 13C metabolic flux analysis, and functional genomics, we reveal that SCD1 and SCD5 play non-redundant roles in fatty acid desaturation, with SCD5 preferentially desaturating C18:0 and uniquely contributing to sphingolipid remodeling. Genetic silencing of either isoform disrupts cell cycle progression, impairs DNA damage repair, and reduces GSC viability, while SCD5 knockdown significantly extends survival in orthotopic GBM models. Mechanistically, loss of SCD activity or saturated fatty acid accumulation triggers PARP1 hyperactivation and subsequent degradation, depleting RAD51 to compromise homologous recombination and induce parthanatos. These findings uncover a lipid-mediated vulnerability in GBM, linking fatty acid desaturation to PARP1-dependent genome integrity. Targeting SCD5 may offer a novel therapeutic strategy to eliminate therapy-resistant GSCs and enhance the efficacy of genotoxic or immunotherapeutic interventions.

cancer biology↗

bioRxiv2025

Multi-Region Brain Organoid: Fusion Organoid with Cerebral, Endothelial and Mid-Hindbrain Components

Brain organoid technology has revolutionized our ability to model human neurodevelopment in vitro. However, current techniques remain limited by their reliance on simplified endothelial cell populations rather than a complete endothelial system. We engineered Multi-Region Brain Organoids (MRBOs) that integrate cerebral, mid/hindbrain, and complex endothelial organoids into one structure. Different from the earlier approaches based on isolated HUVECs, our endothelial organoids contain diverse vascular cell types, including vascular progenitors, mature endothelial cells, pericytes, proliferating angiogenic cells and stromal cells. Our strategy employs a sequential modulation of key developmental pathways to generate individual organoids, followed by optimized fusion conditions that maintain regional identities while supporting cellular integration. Single-nucleus RNA sequencing shows that MRBOs develop discrete neural populations specific to each brain region alongside specialized endothelial populations that establish paracrine signalling networks. Integration analysis with human fetal brain data shows that MRBOs contribute to 80% of cellular clusters found in human fetal brain tissue (Carnegie stages 12-16), whereas CellChat analysis identifies 13 previously uncharacterized endothelial-neural signalling interactions. Notably, we uncover endothelial-derived factors that support the persistence of intermediate progenitor populations during hindbrain development, but not during the cerebral one thereby revealing a new role for complex endothelial populations in regional brain patterning. This platform enables matching multiple developmental regions, fully incorporating the endothelial nature at the same time providing opportunities for studying neurodevelopmental disorders in which neural-endothelial interactions are disrupted. Our engineered MRBO system establishes a foundation for investigating complex neurodevelopmental processes, providing an enabling context closer to physiological relevance.

bioengineering↗

bioRxiv2020

Lithium directs embryonic stem cell differentiation versus hemogenic endothelium

The discovery that the definitive hematopoietic stem cells (HSCs) derive from specialized regions of the endothelium, known as the hemogenic endothelium (HE), shed a good deal of light on HSC embryonic developmental processes. This knowledge opened up new possibilities for the design of new strategies to obtain HSCs in vitro from pluripotent stem cells (PSCs). Previous advances in this field have shown that the Wnt/{beta}-catenin signaling pathway plays a key role in PSC-derived HSC formation. In this work, we identified lithium, a GSK3 inhibitor, as an element capable of stabilizing {beta}-catenin and inducing ESC differentiation in the mesoderm lineage and subsequently in the HE, highly consistent with the role of Wnt agonists on ESC differentiation. ESCs treated with 10 mM lithium express CD31+, Sca-1+, Nkx2-5+ and Runx1+ cells characteristic of HE cells. The ability of lithium-treated ESCs to further derive into HSCs was confirmed after defined maturation, resulting in rounded cell aggregates positive for fetal and mature HSCs markers, confirming the endothelial to hematopoietic transition. Our results represent a novel strategy for generating HSC in vitro as a multipotent source of stem cells for blood and muscle disease therapies.

cell biology↗