Biology subjects

Gallant, J.

Publications and source records attributed to Gallant, J..

16 recordsLinked to original sources

bioRxiv2026

Tuning the Structural Properties of a Single-Domain Antibody Scaffold for Improved Fibroblast Activation Protein Targeting

Fibroblast activation protein (FAP) is an attractive target for the development of cancer theranostics due to its selective expression on cancer-associated fibroblasts (CAFs). While a number of small-molecule FAP inhibitors (FAPIs) have been developed, few biologics have been investigated as FAP targeting vectors. Camelid-derived single-domain antibodies, or variable-heavy-heavy domains (VHHs), offer a compelling alternative, combining high affinity with versatile engineering options. In this study, we first identified a novel anti-FAP VHH, F7, from an affinity-matured camelid phage display library. To investigate how valency and molecular weight affected target engagement and in vivo properties, F7 was engineered into three formats: a monomer (F7), a tethered dimer (F7D), and an Fc-fusion protein (F7-Fc). All three were specific for FAP with the two bivalent constructs demonstrating picomolar affinity. Positron emission tomography imaging in FAP-positive xenograft models revealed distinct pharmacokinetic profiles across constructs with notable differences in tumor uptake and clearance. F7 had rapid uptake and clearance resulting in significantly higher tumor uptake than FAPI-46. Low molecular weight bivalent F7D demonstrated similar kinetics but was retained by the tumor resulting in a high tumor-to-blood ratio with secondary uptake limited to clearance organs. The largest construct, F7-Fc, resulted in the highest tumor uptake and allowed for longitudinal imaging. Absorbed dose calculations confirmed that tumors received significantly higher radiation doses compared to normal tissues. These findings demonstrate that tuning VHH scaffold size and valency can improve biodistribution and retention, establishing F7-based constructs as promising targeting vectors for FAP.

cancer biology↗

bioRxiv2026

Visual semantic tuning across the cortex shifts between tasks

Attention is a powerful mechanism that dynamically optimizes brain representations to prioritize behaviorally-relevant information. While previous studies focusing on single tasks have demonstrated that attention shifts tuning towards attended targets, real-world behavior often requires humans to switch between tasks with different demands. How does visual semantic tuning in the human brain shift to support the behavioral demands of different naturalistic tasks? To answer this question, we used voxelwise encoding models to compare visual semantic tuning across the human cerebral cortex between two distinct naturalistic tasks, movie watching and navigation. Results show that visual semantic tuning in the cortex differed substantially between tasks. Principal component analysis reveals that during navigation, tuning shifts increase the representation of vehicles and traffic signs compared to movie watching, and that these shifts were localized to distinct functional networks. These tuning shifts reconfigure the human brains representations of object categories based on their behavioral relevance. These findings demonstrate that visual semantic tuning in the brain dynamically shifts towards task-relevant information across naturalistic tasks, optimizing functional representations to achieve diverse behavioral goals. Significance statementIn real-world situations, we switch between many tasks with behaviorally distinct goals that require us to attend to different targets. Here we show that visual semantic tuning across the human cortex shifts between passive movie-watching and active navigation. These tuning shifts increase the representation of behaviorally-relevant objects, such as cars during navigation. Tuning shifts towards different object categories are distributed across distinct functional networks, suggesting that they engage different cognitive mechanisms. These results show that visual semantic tuning in the human brain is highly task-dependent and is optimized to represent behaviorally-relevant information.

neuroscience↗

bioRxiv2026

Representations of semantic relations in the human cerebral cortex

An essential aspect of human cognition is the ability to explicitly think about semantic relations between concepts. Neuroimaging studies have found that individual concepts are encoded by distributed patterns of cortical activity, but relatively little is known about how semantic relations between concepts are encoded in the brain. Some theoretical models suggest that relation representations are embedded within concept representations, while others suggest that relation representations are independent of any specific concept pair. We designed a study to compare how semantic relations and concepts are encoded across the cerebral cortex. To characterize how relations are encoded across cortex, fMRI was used to record brain activity while six participants each answered over one thousand questions about different semantic relations. We find that relations are encoded independently of the specific concepts that are connected in any particular instance of the relation. Our results further suggest that relations and concepts are represented in the same set of cortical regions, and that, within these regions, each location is preferentially selective for specific relations. Overall, these results suggest that in the human cerebral cortex, relations and concepts may have the same type of functional representation.

neuroscience↗

bioRxiv2026

A MET-Targeted Variable New Antigen Receptor Theranostic for Non-Small Cell Lung Cancer

The MET receptor tyrosine kinase is mutated or amplified in [~]6% of non-small cell lung cancer (NSCLC) and overexpressed in [~]80% of all NSCLC cases. A theranostic agent that can both see and treat MET-altered NSCLC has never been described before in the literature. Here, we report a shark-derived single-domain variable new antigen receptor (VNAR) for MET with theranostic applications. Following the immunization of a juvenile nurse shark (Ginglymostoma cirratum) with the extracellular domain of human MET, we identified a VNAR clone that specifically engaged MET with high affinity. Engineering the lead VNAR into a bivalent human Fc, vMET1-Fc, yielded a construct that selectively targeted and was internalized by MET-positive cells without affecting cell viability or downstream MET signaling. When radiolabeled with the positron emitting isotope Zr-89, [89Zr]Zr-vMET1-Fc enabled longitudinal PET/CT imaging. High tumor uptake with low background was observed in MET-positive NSCLC xenografts administered [89Zr]Zr-vMET1-Fc. As a targeted beta-particle radiotherapy, [{superscript 1}Lu]Lu-vMET1-Fc resulted in marked tumor-growth delay and exhibited a favorable toxicity profile, collectively improving progression-free survival in NSCLC mouse models. Non-human primate PET/CT imaging studies with ([Zr]Zr-vMET1-Fc in healthy rhesus macaques confirmed favorable biodistribution and dosimetry, predictable clearance, and minimal off-target uptake. Additional blood chemistry analysis found no significant immune response or cytotoxicity. Together, these findings establish vMET1-Fc as a theranostic agent for imaging and treating MET-altered NSCLC. Statement of SignificanceA shark-derived antibody selectively targeting MET shows preclinical efficacy as a theranostic agent for MET-altered cancer.

cancer biology↗

bioRxiv2025

A map of the cortical functional network mediating naturalistic navigation

Navigation through the real world requires close coordination of perception, planning, and motor actions. Prior neuroimaging studies that used controlled stimuli and tasks have suggested that navigation-related information is represented broadly across the human cerebral cortex. While three regions in the anterior visual cortex have been well-studied1, the extent and functional properties of regions in the parietal and prefrontal cortices are not as well-characterized 2. To map and characterize the full cortical network that underpins active navigation in the real world, we used functional magnetic resonance imaging to record brain activity from participants performing a naturalistic navigation task. Banded ridge regression was used to fit high-dimensional encoding models for 28,134 features to this data. Results show that naturalistic navigation is supported by a network of 11 functionally distinct cortical regions: five prefrontal and three parietal regions, along with three regions in the visual cortex that had been identified and characterized in previous studies. Analysis of encoding model weights shows that these 11 regions transform perceptual inputs through decision-making processes to produce action outputs, and are organized along distributed cortical functional gradients. These results provide a unified description of the functional properties and organization of the cortical network that mediates naturalistic navigation. We anticipate that these maps will provide rich targets to inform more targeted future studies of human navigation.

neuroscience↗

bioRxiv2025

Disentangling Superpositions: Interpretable Brain Encoding Model with Sparse Concept Atoms

Encoding models using word embeddings or artificial neural network (ANN) features reliably predict brain responses to naturalistic stimuli, yet interpreting these models remains challenging. A central limitation is superposition: distinct semantic features become entangled along correlated directions in dense embeddings when latent features outnumber embedding dimensions. This entanglement renders regression weights non-identifiable--different combinations of semantic directions can produce identical predictions, precluding principled interpretation of voxel selectivity. To address this, we introduce the Sparse Concept Encoding Model, which transforms dense embeddings into a higher-dimensional, sparse, non-negative space of learned concept atoms. This transformation yields an axis-aligned semantic basis where each dimension corresponds to an interpretable concept, enabling direct readout of conceptual selectivity from voxel weights. When applied to fMRI data collected during story listening, our model matches the prediction performance of conventional dense models while substantially enhancing interpretability. It enables novel neuroscientific analyses such as disentangling overlapping cortical representations of time, space, and number, and revealing structured similarity among distributed conceptual maps. This framework offers a scalable and interpretable bridge between ANN-derived features and human conceptual representations in the brain.

neuroscience↗

bioRxiv2025

Individual differences shape conceptual representation in the brain

Each person experiences the world through a unique conceptual lens, shaped by personal experiences, natural variations, or disease. These individual differences have remained largely inaccessible to cognitive neuroscience and clinical neurology, limiting the development of precision medicine approaches to cognitive disorders. To overcome this limitation, here we develop a new statistical framework to measure and interpret individual differences in functional brain representations. We apply this framework to characterize how different individuals represent the same concepts. Twenty-four participants listened to narrative stories while their brain activity was measured with functional MRI (fMRI). Encoding models were used to recover how hundreds of concepts were represented in each persons brain. Despite listening to identical stories, participants showed systematic individual differences in conceptual representations. These differences reveal person-specific biases in how concepts are represented in the brain. Individual variability was highest in regions that represent social information. Because these regions are thought to integrate sensory information with personal beliefs and experiences, the observed individual differences may reflect cognitive traits unique to each person. Our work reveals that individual differences are a systematic, measurable principle of conceptual representations in the human brain. By enabling researchers to measure and interpret differences in person-specific functional brain representations, our work establishes a new paradigm for precision neuroscience. This paradigm provides a rigorous foundation for developing fMRI applications in precision medicine to diagnose and monitor cognitive disorders.

neuroscience↗

bioRxiv2025

A simplified co-culture reveals altered cardiotoxic responses to doxorubicin in hPSC-derived cardiomyocytes in the presence of endothelial cells

Cardiotoxicity is a significant challenge in cancer therapies, particularly with doxorubicin, a widely used anthracycline known for its broad anti-cancer spectrum but life-threatening cardiac side effects. There is a critical need for more predictive in vitro models to understand doxorubicin-induced cardiotoxicity and patient-specific drug responses. In this study, we used human pluripotent stem cell (hPSC)-derived cardiomyocytes (hPSC-CMs), cardiac fibroblasts (hPSC-cFBs) and endothelial cells (hPSC-ECs) to investigate the cardiotoxic effects of doxorubicin in two-dimensional mono-and multi-cell type cultures. By mimicking the cumulative dose effect seen in patients through repeated doxorubicin treatments and using a machine learning-based in silico image analysis tool, we could precisely quantify caspase 3/7 activity as an early toxicity marker and identify hPSC-CMs in multi-cell type cultures. This innovative approach allowed continuous monitoring of apoptosis from phase-contrast images, revealing that hPSC-ECs showed higher sensitivity to doxorubicin than isogenic hPSC-CMs or hPSC-cFBs and significantly enhanced cardiomyocyte toxicity in co-culture. In contrast, dermal fibroblasts differentiated from the same hPSC line showed no toxic response under the same treatment regimen. These results challenge the conventional focus on cardiomyocytes as the target of drug-induced cardiac damage. Our findings not only highlight the complex interplay among different cardiac cell types in mediating the toxic effects of doxorubicin, but also demonstrate the potential of AI-enabled tools to advance personalized drug screening and safety assessments.

pharmacology and toxicology↗

bioRxiv2025

Development of FAP-targeted theranostics discovered by next-generation sequencing-augmented mining of a novel immunized VNAR library

Cancer-associated fibroblasts (CAFs) in the stroma of solid tumors promote an immunosuppressive tumor microenvironment (TME) that drives resistance to therapies. The expression of the protease fibroblast activation protein (FAP) on the surface of CAFs has made FAP a target for development of therapies to dampen immunosuppression. Relatively few biologics have been developed for FAP and none have been developed that exploit the unique engagement properties of Variable New Antigen Receptors (VNARs) from shark antibodies. As the smallest binding domain in nature, VNARs cleverage unique geometries and recognize epitopes conventional antibodies cannot. By directly immunizing a nurse shark with FAP, we created a large anti-FAP VNAR phage display library. This library allowed us to identify a suite of anti-FAP VNARs through traditional biopanning and also by an in silico approach that did not require any prior affinity-based enrichment in vitro. We investigated four VNAR-Fc fusion proteins for theranostic properties and found that all four recognized FAP with high affinity and were rapidly internalized by FAP-positive cells. As a result, the VNAR-Fc constructs were effective antibody-drug conjugates in vitro and were able to localize to FAP-positive xenografts in vivo. Our findings establish VNAR-Fc constructs as a versatile platform for theranostic development that could yield innovative cancer therapies targeting the TME.

synthetic biology↗

bioRxiv2024

Early zygotic engineering promotes targeted large transgene integration and direct production of fully transgenic animals

Genetic engineering has become increasingly feasible with the advent of site-specific nucleases. This technology is highly effective for the generation of small mutations, however targeted insertion of large sequences to generate transgenic animals remains challenging, time consuming, and laborious. Following several failed attempts using the same reagents, we identified a protocol that achieved very high targeted integration of a 3.2 kb transgene into a single locus of a humanized mouse model of Down syndrome. Moreover, we demonstrate in multiple ways that this procedure directly generates numerous non-mosaic founder animals, which bred true to generate all transgenic progeny. In vitro fertilization of oocytes was followed by AAV-mediated delivery of donor sequence and electroporation of Cas9 ribonucleoprotein, all parameters designed to promote early zygotic engineering (EZE). This strategy can obviate the need to breed mosaic animals for germline transmission and can enable engineering of difficult to breed animals. While efforts to improve genome engineering focus on reagents and delivery techniques, findings here suggest a narrow window of time in the early fertilized oocyte, likely before genome replication, is key to achieve both high integration efficiency and one-step generation of non-mosaic, engineered mice.

developmental biology↗

bioRxiv2024

Bilingual language processing relies on shared semantic representations that are modulated by each language

Billions of people throughout the world are bilingual, and they can extract meaning from multiple languages. While some evidence suggests that there is a shared system in the human brain for processing semantic information from native and non-native languages, other evidence suggests that semantic processing is language-specific. We conducted a study to determine how semantic information for different languages is represented in the brains of bilinguals. Functional magnetic resonance imaging (fMRI) was used to record brain responses while participants read several hours of natural narratives in their native (Chinese) and non-native (English) languages. These data were then used to compare semantic representations between the two languages. We find that semantic representations are largely shared between languages, but that there are fine-grained differences in the representation of some semantic categories across languages. These results reconcile current competing theories of bilingual language processing. Significance StatementBilinguals understand the meaning of words in multiple languages. Whether this capacity reflects a shared brain system for processing both native and non-native languages, or whether processing is language-specific is still unclear. Here, we examine whether and how semantic representations in the brain support shared and/or language-specific processing. We recorded brain activity from participants reading narratives in their native (Chinese) and non-native (English) languages, and modeled how their brains represent word meaning in each language. We show that semantic representations are similar between the two language conditions, and that these representations are systematically modulated between native and non-native language comprehension.

neuroscience↗

bioRxiv2023

Novel psilocin prodrugs with altered pharmacological properties as candidate therapies for treatment-resistant anxiety disorders

The psychedelic compound psilocybin has shown therapeutic benefit in the treatment of numerous psychiatric diseases. A recent randomized clinical trial conducted at Johns Hopkins Bayview Medical Center demonstrated the efficacy of psilocybin-assisted therapy in the treatment of Major Depressive Disorder (MDD). Similarly, a phase IIb study evaluating psilocybin-assisted therapy for treatment-resistant depression (TRD) presented statistically meaningful and long-term reduction in depressive symptoms. Also, many studies have reported the successful treatment of severe anxiety after a single oral dose of psilocybin, especially in patients struggling with cancer-related distress (CRD). Despite these compelling clinical results, concerns regarding the duration of the psychedelic experience produced by psilocybin pose a significant barrier to its widespread therapeutic application. Psilocybin, derived from magic mushrooms is the naturally occurring prodrug of the neuroactive compound psilocin. When orally administered, exposure to the acidic gastrointestinal (GI) environment together with enzymatic processing by intestinal and hepatic alkaline phosphatase lead to the dephosphorylation of psilocybin producing elevated levels of systemic psilocin. These plasma levels are detectable up to 24 h and produce a psychoactive episode lasting as long as 6 h post-ingestion. In order to positively modify the kinetics of the acute psychedelic response, we have engineered a library of novel prodrug derivatives (NPDs) of psilocin, introducing a diversity of alternative metabolically cleavable moieties modified at the 4-carbon position of the core indole ring. This library consists of twenty-eight unique compounds represented by nine distinct prodrug classes. Each molecule was screened in vitro for metabolic stability using isolated human serum, and human cellular fractions derived from liver and intestinal tissues. This screen revealed fifteen prodrugs that produced measurable levels of psilocin in vitro, with ester and thiocarbonate-based prodrug derivatives significantly represented. These fifteen NPDs were further evaluated for pharmacokinetic (PK) profiles in mice, assessing plasma levels of both residual prodrug and resultant psilocin. PK results confirmed the efficiency of ester and thiocarbonate-based prodrug metabolism upon oral and intravenous administration, achieving levels reduced, albeit comparable to levels of psilocybin-derived psilocin. Of note, almost all NPDs tested maintained reduced overall exposure of psilocin relative to psilocybin, with no measurable levels detected at 24 h post-dose. Finally, all NPDs were screened for CNS bioavailability in healthy mice using the Head Twitch Response (HTR), a behavioural biomarker of 5-HT2A receptor stimulation and an established proxy for psychoactive potential. Interestingly, five NPDs produced peak HTR that approached or exceeded levels induced by an equivalent dose of psilocybin. Among these bioactive prodrugs, an ester-based and thiocarbonate-based molecule produced long-term anxiolytic benefit in chronically stressed mice evaluated in the marble burying psychiatric model. Overall, this screening campaign identified novel candidate prodrugs of psilocin with altered metabolic profiles and reduced pharmacological exposure, potentially attenuating the duration of the psychedelic response. These molecules still maintained the long-term psychiatric and physiological benefits characteristic of psilocybin therapy. Additionally, these modified parameters also offer the opportunity for altered routes of administration bypassing conventional oral dosing.

pharmacology and toxicology↗

bioRxiv2023

The Cortical Representation of Language Timescales is Shared between Reading and Listening

Language comprehension involves integrating low-level sensory inputs into a hierarchy of increasingly high-level features. Prior work studied brain representations of different levels of the language hierarchy, but has not determined whether these brain representations are shared between written and spoken language. To address this issue, we analyzed fMRI BOLD data recorded while participants read and listened to the same narratives in each modality. Levels of the language hierarchy were operationalized as timescales, where each timescale refers to a set of spectral components of a language stimulus. Voxelwise encoding models were used to determine where different timescales are represented across the cerebral cortex, for each modality separately. These models reveal that between the two modalities timescale representations are organized similarly across the cortical surface. Our results suggest that, after low-level sensory processing, language integration proceeds similarly regardless of stimulus modality.

neuroscience↗

bioRxiv2020

The Development of a Novel Nanobody Therapeutic for SARS-CoV-2

Combating the COVID-19 pandemic requires potent and low-cost therapeutics. We identified a novel series of single-domain antibodies (i.e., nanobody), Nanosota-1, from a camelid nanobody phage display library. Structural data showed that Nanosota-1 bound to the oft-hidden receptor-binding domain (RBD) of SARS-CoV-2 spike protein, blocking out viral receptor ACE2. The lead drug possessing an Fc tag (Nanosota-1C-Fc) bound to SARS-CoV-2 RBD with a Kd of 15.7picomolar ([~]3000 times more tightly than ACE2 did) and inhibited SARS-CoV-2 infection with an ND50 of 0.16microgram/milliliter ([~]6000 times more potently than ACE2 did). Administered at a single dose, Nanosota-1C-Fc demonstrated preventive and therapeutic efficacy in hamsters subjected to SARS-CoV-2 infection. Unlike conventional antibody drugs, Nanosota-1C-Fc was produced at high yields in bacteria and had exceptional thermostability. Pharmacokinetic analysis of Nanosota-1C-Fc documented a greater than 10-day in vivo half-life efficacy and high tissue bioavailability. Nanosota-1C-Fc is a potentially effective and realistic solution to the COVID-19 pandemic. Impact statementPotent and low-cost Nanosota-1 drugs block SARS-CoV-2 infections both in vitro and in vivo and act both preventively and therapeutically.

microbiology↗

bioRxiv2020

Implantation and Gastrulation Abnormalities Characterize Early Embryonic Lethal Mouse Lines

The period of development between the zygote and embryonic day 9.5 in mice includes multiple developmental milestones essential for embryogenesis. The preeminence of this period of development has been illustrated in loss of function studies conducted by the International Mouse Phenotyping Consortium (IMPC) which have shown that close to one third of all mouse genes are essential for survival to weaning age and a significant number of mutations cause embryo lethality before E9.5. Here we report a systematic analysis of 21 pre-E9.5 lethal lines generated by the IMPC. Analysis of pre- and post-implantation embryos revealed that the majority of the lines exhibit mutant phenotypes that fall within a window of development between implantation and gastrulation with few pre-implantation and no post-gastrulation phenotypes. Our study provides multiple genetic inroads into the molecular mechanisms that control early mammalian development and the etiology of human disease, in particular, the genetic bases of infertility and pregnancy loss. We propose a strategy for an efficient assessment of early embryonic lethal mutations that can be used to assign phenotypes to developmental milestones and outline the time of lethality.

developmental biology↗

bioRxiv2017

Electrostatic Tuning of a Potassium Channel in Electric Fish

Molecular and biophysical variation contributes to the evolution of adaptive phenotypes, particularly behavior, though it is often difficult to understand precisely how. The adaptively significant electric organ discharge behavior of weakly electric fish is the direct result of biophysical membrane properties set by ion channels. Here we describe a voltage-gated potassium channel gene in African mormyrid electric fishes, that is under positive selection and highly expressed in the electric organ. The channel produced by this gene shortens electric organ action potentials by activating quickly and at hyperpolarized membrane potentials. Surprisingly, the source of these unique properties is a derived patch of negatively charged amino acids in an extracellular loop near the voltage sensor. Further, we demonstrate that this portion of the channel functions differently in vertebrates than the generally accepted model based on the shaker channel, and suggest a role for this loop in the evolutionary tuning of voltage-dependent channels.

evolutionary biology↗