Biology subjects

Basile, C.

Publications and source records attributed to Basile, C..

3 recordsLinked to original sources

bioRxiv2025

Mapping the diverse topologies of protein-protein interaction fitness landscapes

De novo binder discovery is unpredictable and inefficient due to a lack of quantitative understanding of protein-protein interaction (PPI) sequence-function landscapes. Here, we use our PANCS-Binder technology to perform >1,300 independent selections of various library sizes and compositions of a randomized small protein to identify binders to a panel of 96 distinct target proteins. For successful selections, we discovered reproducible fitness landscapes that group into a few, target-specific, clusters. Each cluster defines a minimal binding motif whose frequency is inversely proportional to the number of specified amino acids ([~]2-8) and determines selection success, which is quantifiable by the density of binders to the target within a theoretical sequence space. We leverage these data to develop a supervised contrastive learning approach that discriminates binders from non-binders and demonstrates generalization beyond a threshold amount of data. Together, this framework renders PPI landscapes measurable and predictive, accelerating de novo binder discovery and optimization.

synthetic biology↗

bioRxiv2025

Encoding of visual stimuli and behavioral goals in distinct anatomical areas of monkey ventrolateral prefrontal cortex

The lateral prefrontal cortex has been classically defined as an associative region involved in the so-called executive functions, such as guiding behavior based on abstract rules and mnemonic information. However, most neurophysiological studies on monkeys did not address the issue of whether distinct anatomical sectors of lateral prefrontal cortex play different functional roles. The main aim of this work is to study functional properties of neurons recorded from a large part of ventrolateral prefrontal cortex (VLPF) of two monkeys performing passive visual tasks and a visuo-motor task, and to map them on the anatomical areas defined on the basis of our recent parcellations. Our results show that distinct VLPF areas differently contribute to visual processing and action organization along the caudo-rostral axis. In particular, the processing of visual stimuli, independent of whether passively presented or exploited for guiding behavior, primarily involves posterior VLPF areas (especially caudal area 12r), while the elaboration of visual and contextual information for action organization mainly involves intermediate VLPF areas (especially middle 46v). In this latter sector, visual stimuli/instructions appear to be encoded in a pragmatic format, that is in terms of the associated behavioral outcome. Finally, more anterior areas are characterized by a low responsiveness to the employed tasks. Altogether, our findings indicate that posterior VLPF areas represent the first processing stage of visual input, intermediate areas primarily contribute to the selection and planning of contextually appropriate behaviors, while rostral areas could be involved in more complex abstract processes.

neuroscience↗

bioRxiv2025

High-throughput protein binder discovery by rapid in vivo selection

Proteins that selectively bind to a target of interest are foundational components of research pipelines1,2, diagnostics3, and therapeutics4. Current immunization-based5,6, display-based7-14, and computational approaches15-17,18 for discovering binders are laborious and time-consuming - taking months or more, suffer from high false positives - necessitating extensive secondary screening, and have a high failure rate, especially for disordered proteins and other challenging target classes. Here we establish Phage-Assisted Non-Continuous Selection of Protein Binders (PANCS-binders), an in vivo selection platform that links the life cycle of M13 phage to target protein binding though customized proximity-dependent split RNA polymerase biosensors, allowing for complete and comprehensive high-throughput screening of billion-plus member protein variant libraries with high signal-to-noise. We showcase the utility of PANCS-Binders by screening multiple protein libraries each against a panel of 95 separate therapeutically relevant targets, thereby individually assessing over 1011 protein-protein interaction pairs, completed in two days. These selections yielded large, high-quality datasets and hundreds of novel binders, which we showed can be affinity matured or directly used in mammalian cells to inhibit or degrade targets. PANCS-Binders dramatically accelerates and simplifies the binder discovery process, the democratization of which will help unlock new creative potential in proteome-targeting with engineered binder-based biotechnologies.

synthetic biology↗