bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/325092

S-MiRAGE: A quantitative, secreted RNA-based reporter of gene expression and cell persistence

Mitra, K.·Feist, W. N.·Alfossi, S.·Fuentes-Mattei, E.·Almeida, M. I.·Kim, J. J.·Calin, G. A.·Warmflash, A.
View original source ↗Export metadata ↓

Abstract

Non-destructive measurements of cell persistence and gene expression are crucial for longitudinal research studies and for prognostic assessment of cell therapies. Here we describe S-MiRAGE, a platform that utilizes small secreted RNA molecules as sensitive and quantitatively accurate reporters of cellular processes. We demonstrate the utility of S-MiRAGE by monitoring the differentiation status of human embryonic stem cells in vitro, and tumor growth in a mouse model in vivo.

Source connections

Explore related subjects

bioengineeringPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Mitra, K., Feist, W. N., Alfossi, S., Fuentes-Mattei, E., Almeida, M. I., Kim, J. J., Calin, G. A., Warmflash, A.. 2018-05-17. S-MiRAGE: A quantitative, secreted RNA-based reporter of gene expression and cell persistence. https://doi.org/10.1101/325092

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Engineering and characterisation of AAVS1 FRT cell lines for inducible and dose-dependent gene expression

Investigating biological function with high reproducibility requires the generation of stable cell lines that offer precise and inducible transgene expression. However, traditional methods often suffer from the limitations of random genomic integration, including unpredictable expression levels, leaky basal activity, and disruption of endogenous loci. To address these challenges, we engineered a versatile RPE1 cell line by integrating a TetOn3G-FRT cassette into the AAVS1 safe-harbour locus using CRISPR/Cas9(D10A) nickase. This platform utilises the Flp-FRT recombination system to facilitate rapid, site-specific "plug-and-play" insertion of transgenes, combined with the Tet-On 3G system for tight, dose-dependent expression control. The resulting RPE1 AAVS1 FRT8 line enables highly consistent transgene induction across independent clones, behaving as a monoclonal population. We highlight the importance of rigorous cell line characterisation through a multi-omics approach. Whole genome sequencing identified precise heterozygous integration at the target locus and de novo genomic duplications on other chromosomes. By integrating WGS with high-resolution proteomics and cell cycle analysis, we confirmed that these alterations did not significantly perturb cellular homeostasis or phenotypic fitness. This work establishes a robust and reliable platform for the efficient generation of inducible AAVS1 FRT stable cell lines, facilitating reproducible research in modern molecular biology.

bioengineering↗
bioRxiv2026

Raman-probe-derived biomarkers account for cartilage composition, structure, and viscoelastic properties

Raman spectroscopy is an inelastic light scattering technique that reflects the vibrational modes of the biochemical building blocks of the major constituents that comprise the cartilage extracellular matrix (ECM): glycosaminoglycans (GAG), type-II collagen (COL), and water. We investigated whether ECM-specific biomarkers measured with our recently developed arthroscopy-compatible Raman needle probe characterize the functional viscoelastic properties of articular cartilage explants. Equine osteochondral explants were harvested from high-load (femoral condyle) and low-load (intertrochlear groove) sites to evaluate Raman-derived biomarkers of cartilage structure and function. Viscoelastic material properties (equilibrium/dynamic modulus, phase shift) were determined by mechanical indentation. A computational fibril-reinforced biphasic material model was used to estimate the glycosaminoglycan-associated non-fibrillar-matrix modulus, the collagen-associated fibril-network modulus, and hydraulic permeability. Raman-derived biomarkers enabled evaluation of cartilage tissue composition and structure, accounting for 81% of the variation in GAG content, 53% of the variation in COL content, and 58% of the variation in COL anisotropy. Biomarkers also accounted for 81% of the variation in equilibrium modulus, 58% in dynamic modulus, and 51% in phase shift. For poroelastic properties, biomarkers accounted for 83% of the variation in non-fibrillar-matrix modulus, 25% of the variation in fibril-network modulus, and 34% of the variation in hydraulic permeability. Clinical Significance: Raman spectroscopy provides objective compositional biomarkers that account for viscoelastic material properties underlying articular cartilage function. These findings support its future use as an arthroscopic platform for objective assessment of cartilage injury, monitoring of disease progression, and evaluation of therapeutic interventions.

bioengineering↗
bioRxiv2026

An adjuvant for in vivo CAR-T therapy potentiation against solid tumors

In vivo CAR-T therapy offers rapid and controllable T-cell engineering but has yet to achieve durable efficacy against solid tumors. Rather than focusing solely on CAR-T cells, we harness the intact immune system via an in vivo CAR-T adjuvant (iCTA). Composed of aluminum-manganese hydrogel, iCTA can form a spatially confined antigenic and immunostimulatory niche in-situ. By coupling controlled antigen exposure with STING-type I interferon signaling, iCTA not only recruited and reactivated CAR-T cells, but engage the CAR-negative immunocytes with enhanced dendritic-cell antigen presentation and mobilized endogenous antigen-specific T-cell responses. Combined with mRNA-LNP-mediated in vivo CAR-T generation, a single administration of iCTA increased CAR+ T-cell abundance in draining lymph nodes and blood by 2-fold. It also increased T and NK cell infiltration, established an IFNgamma-enriched tumor microenvironment, and reduced exhaustion-associated T-cell states. iCTA improved tumor regression and survival, establishing an adjuvant strategy to enhance in vivo CAR-T therapy.

bioengineering↗