Biology subjects

Figueroa, B.

Publications and source records attributed to Figueroa, B..

4 recordsLinked to original sources

bioRxiv2026

Engineering the mechanosensitivity of single DNA molecules via high-throughput microfluidic force spectroscopy

Single-molecule force spectroscopy (SMFS) is a powerful tool to measure how biomolecules respond to mechanical force, but limited sequence throughput constrains its potential. Here, we present a single-molecule, multiplexed, microfluidic force spectroscopy (SM3FS) assay that uses parallelized microfluidics to measure up to 80 sequence variants per experiment. Using SM3FS, we stretched, overstretched, or unzipped 241 different DNA structures and generated 131,847 single-molecule traces from a quarter-million observations. High sequence throughput allowed us to identify DNA structures that are kinetically stable yet mechanically fragile (Frupture < 3 pN at 0.5 pN s-1), revealing how mechanosensitivity can arise as an intrinsic property of multivalent systems. By enabling systematic sequence-function mapping under force, SM3FS opens a path to high-throughput nonequilibrium studies of biomolecules.

biophysics↗

bioRxiv2025

Development of a Serum-Free Producer Cell Line Generation Process for Scalable and Efficient rAAV Production for gene therapy applications

1.The growing field of recombinant Adeno-Associated Virus (rAAV) gene therapy demands scalable and efficient production platforms. Manufacturing platforms based on producer cell lines (PCL) hold substantial promise due to their capacity for high productivity and scalability. However, the generation of stable cell lines for rAAV production is typically performed using serum-containing processes, which pose a risk due to safety and regulatory concerns related to animal-derived components. In this study, we established a fully serum-free process for PCL generation for rAAV production, optimizing critical stages of this process, including transfection methodologies for stable plasmid integration, isolation of highly productive cell pools, and media supplementation to support single-cell cloning. The developed serum-free process generated clonally derived PCLs with productivity and product quality on par with traditional serum-based methods. This approach significantly reduced the cell line generation timeline and eliminated the challenge related to serum supplementation, adapting it to industry requirements. The reported advances overcome a critical step in cell line development for rAAV production, facilitating the implementation of scalable and efficient production platforms to support the development of rAAV-based gene therapies.

bioengineering↗

bioRxiv2025

Single-cell neural network classifiers reveal that PM21 NK cell expansion is dependent on B cell signaling

In the field drug development ML/AI methods are being applied to improve drug production speed, costs, and reliability. In allogenic NK cell therapy production, one of the biggest challenges is the inherent variability in the donors that provide the starting material for NK cell expansion. In this study we performed PM21-mediated NK cell expansion on 26 donors, and in parallel performed single-cell transcriptomics on the same donor sample prior to expansion. Canonical differential expression analysis and cell state abundance did not highlight any significant difference between donors with high and low NK cell expansion yield. Instead, training neural networks classifiers for high-yield donors enabled identifying several highly predictive models with perfect cross-validation recall. Further investigation of the most predictive models unveiled a previously unknown role for B cell in supportive NK cell expansion. Overall, this study represents a blueprint for combining deep phenotyping and machine learning methods to unveil novel biology and improve the quality and speed of delivery of cell therapeutics to patients.

systems biology↗

bioRxiv2021

Quantitative imaging of intracellular density with ratiometric stimulated Raman scattering microscopy

Cell size and density impact a wide range of physiological functions, including tissue homeostasis, growth regulation, and osmoregulation. Both are tightly regulated in mammalian cells. In comparison, density variation of a given cell type is much smaller than cell size, indicating that maintenance of cell type-specific density is important for cell function. Despite this importance, little is known about how cell density affects cell function and how it is controlled. Current tools for intracellular cell density measurements are limited either to suspended cells or cells growing on 2D substrates, neither of which recapitulate the physiology of single cells in intact tissue. While optical measurements have the potential to measure cell density in situ and noninvasively, light scattering in multicellular systems prevents direct quantification. Here, we introduce an intracellular density imaging technique based on ratiometric stimulated Raman scattering microscopy (rSRS). It quantifies intracellular drymass density through vibrational imaging of macromolecules. Moreover, water is used as an internal standard to correct for aberration and light scattering. We demonstrate real-time measurement of intracellular density quantification and show that density is tightly regulated across different cell types and can be used to differentiate cell types as well as cell states. We further demonstrate dynamic imaging of density change in response to osmotic challenge as well as intracellular density imaging of a 3D tumor spheroid. Our technique has the potential for imaging intracellular density in intact tissue and understanding density regulation and its role in tissue homeostasis.

biophysics↗