Biology subjects

Dama, P.

Publications and source records attributed to Dama, P..

3 recordsLinked to original sources

bioRxiv2026

Quantifying Assay Confidence in Barrier Organ-on-Chip Systems: A Monte Carlo Assay-Readiness Framework for Detecting Modest Permeability Shifts

Organ-on-chip (OoC) systems are increasingly used to generate human-relevant evidence in drug discovery and preclinical development, yet interpretation can be limited by the interaction of biological variability, device-to-device variability, and technical assay noise. Here, we describe the UstarFlowAI barrier-confidence framework, an in silico assay-readiness approach that quantifies whether a predefined permeability-related effect is resolvable under specified uncertainty. The proposed context of use is decision support for laminar, low-Reynolds-number airway epithelial monolayer barrier OoC assays in which device fabrication, pump performance, flow, wall shear stress, and biological fluctuation may affect permeability-related readouts. Monte Carlo simulations propagate defined manufacturing, biological, systemic, and well-level uncertainty and estimate the minimum detectable shift (MDS) under a prespecified decision rule. In the present proof-of-concept design, the reference workflow was parameterized at 9.4% technical coefficient of variation (CV), whereas the standardized workflow was parameterized at 5.0% CV, corresponding to an approximately 46.8% reduction in the modeled technical-noise component. At n = 48 replicate wells per group and a nominal total assay-noise operating point of 17% CV, a predefined 10% permeability shift exceeded the upper MDS uncertainty bound for the standardized workflow in both best- and worst-case scenarios, whereas it overlapped the 95% MDS interval for the reference workflow and therefore did not meet the prespecified PASS criterion. These findings demonstrate the behavior of the computational framework under the stated assumptions; they do not constitute experimental validation, regulatory qualification, or evidence that a 10% shift is universally meaningful across barrier OoC systems. We therefore propose a prospective wet-lab validation strategy in which model predictions are tested against airway barrier measurements generated under controlled sources of technical and biological variability. The framework is intended to complement, rather than replace, the underlying biological model by making assay uncertainty and decision thresholds explicit and auditable.

bioengineering↗

bioRxiv2026

Mature tumoroids recapitulate clinically relevant drug response through extended 3D culture in PDAC

BackgroundDrug responses in pancreatic ductal adenocarcinoma (PDAC) vary sharply across in vitro culture formats, but most 2D-3D comparisons conflate microenvironmental cues with time-dependent cellular adaptation. As a result, conventional assays frequently overestimate drug efficacy and poorly reflect clinical pharmacology. Main findingsWe profiled MiaPaCa-2, PANC-1, and CFPAC-1 grown in an extracellular-matrix (ECM) hydrogel for 1-12 days, defining extended 3D cultures ([≥]10 days) as mature tumoroids, and quantified 72 h drug responses to a multi-class oncology panel using growth-rate (GR) metrics to normalize for proliferation across formats and durations. Prolonged 3D pre-culture induced broad tolerance, with typical 10-100x reductions in sensitivity to standards of care (5-fluorouracil, SN38, oxaliplatin, gemcitabine, paclitaxel), following a reproducible susceptibility hierarchy (MiaPaCa-2 > PANC-1 > CFPAC-1) after GR correction. In mature tumoroids, GR values closely approximated clinically observed plasma exposures (e.g., within <4x for 5-FU and <0.5x for gemcitabine), whereas 2D and short-term organoid assays markedly underestimated resistance, often by >100x, thereby overstating drug activity. Notably, CFPAC-1 exhibited increased sensitivity to SN38 and trametinib under mature-organoid conditions, demonstrating that microenvironmental conditioning can invert responses for selected mechanisms. Transcriptomic profiling revealed coordinated up-regulation of multiple ABC transporters with extended 3D residence, tracking resistance phenotypes across lines and implicating transporter-linked tolerance programs. SignificanceTogether, these data identify time-in-3D and the emergence of mature tumoroids as dominant, previously under-controlled determinants of PDAC pharmacology that both induce tolerance and unmask context-dependent vulnerabilities. We propose incorporating both short-term and mature-tumoroid screening arms into preclinical workflows, reporting pre-culture duration alongside GR-normalized effect sizes, and leveraging transporter-informed biomarkers to guide regimen prioritization and sequencing. This framework enhances physiological relevance, reproducibility, and translational fidelity in PDAC drug discovery.

cancer biology↗

bioRxiv2023

CRISPR screens in 3D tumourspheres identified miR-4787-3p as a transcriptional start site miRNA essential for breast tumour-initiating cell growth

Breast cancer (BC) is a heterogeneous malignancy with distinct molecular subtypes and clinical characteristics. Tumour-initiating cells (TICs) are a small subset of cancer cells that are responsible for tumour initiation and progression. Our study employed pooled CRISPR screens, integrating 2D and 3D culture models, to identify miRNAs critical in BC tumorsphere formation. These screens combined with RNA-seq experiments allowed us to identify the miRNA signature and their targets that are essential for tumoursphere growth. Amongst them, miR-4787-3p exhibited significant up-regulation in BC, particularly in basal-like BCs, suggesting its association with aggressive disease phenotypes. Surprisingly, despite its location within the 5UTR of a protein coding gene, which define DROSHA-independent transcription start site (TSS)-miRNAs, our findings revealed its dependence on both DROSHA and DICER1 for maturation. Inhibition of miR-4787-3p hindered tumorsphere formation, highlighting its potential as a therapeutic target in BC. Moreover, our study proposes elevated miR-4787-3p expression as a potential prognostic biomarker for adverse outcomes in BC patients. We found that protein-coding genes positively selected in the CRISPR screens were enriched of miR-4787-3p putative targets. Amongst these identified key targets, we selected ARHGAP17, FOXO3A, and PDCD4 because are known tumour suppressors in cancer and experimentally validated the interaction of miR-4787-3p with their 3UTRs. Our work illuminates the molecular mechanisms underpinning miR-4787-3ps oncogenic role in BC. These findings advocate for further clinical investigations targeting miR-4787-3p and underscore its prognostic significance, offering promising avenues for tailored therapeutic interventions and prognostic assessments in BC.

cell biology↗