Biology subjects

Smith, J.

Publications and source records attributed to Smith, J..

At least 127 records · Page 7Linked to original sources

bioRxiv2021

TRIPLE-NEGATIVE BREAST CANCER CELLS RECRUIT NEUTROPHILS BY SECRETING TGF-β AND CXCR2 LIGANDS

Tumor associated neutrophils (TANs) are frequently detected in triple-negative breast cancer (TNBC). Recent studies also reveal the importance of neutrophils in promoting tumor progression and metastasis during breast cancer. However, the mechanisms regulating neutrophil trafficking to breast tumors are less clear. We sought to determine whether neutrophil trafficking to breast tumors is determined directly by the malignant potential of cancer cells. We found that tumor conditioned media (TCM) harvested from highly aggressive, metastatic TNBC cells induced a polarized morphology and robust neutrophil migration, while TCM derived from poorly aggressive estrogen receptor positive (ER+) breast cancer cells had no activity. In a three-dimensional (3D) type-I collagen matrix, neutrophils migrated toward TCM from aggressive breast cancer cells with increased velocity and directionality. Moreover, in a neutrophil-tumor spheroid co-culture system, neutrophils migrated with increased directionality towards spheroids generated from TNBC cells compared to ER+ cells. Based on these findings, we next sought to characterize the active factors secreted by TNBC cell lines. We found that TCM-induced neutrophil migration is dependent on tumor-derived chemokines, and screening TCM elution fractions based on their ability to induce polarized neutrophil morphology revealed the molecular weight of the active factors to be around 12 kDa. TCM from TNBC cell lines contained copious amounts of GRO (CXCL1/2/3) chemokines and TGF-{beta} cytokines compared to ER+ cell-derived TCM. TCM activity was inhibited by simultaneously blocking receptors specific to GRO chemokines and TGF-{beta}, while the activity remained intact in the presence of either single receptor inhibitor. Together, our findings establish a direct link between the malignant potential of breast cancer cells and their ability to induce neutrophil migration. Our study also uncovers a novel coordinated function of TGF-{beta} and GRO chemokines responsible for guiding neutrophil trafficking to the breast tumor.

immunology↗

bioRxiv2021

New SHIVs and Improved Design Strategy for Modeling HIV-1 Transmission, Immunopathogenesis, Prevention and Cure

Simian-human immunodeficiency virus (SHIV) chimeras contain the HIV-1 envelope (env) gene embedded within an SIVmac proviral backbone. Previously, we showed that substitution of Env residue 375-Ser by bulky aromatic residues enhances Env binding to rhesus CD4 and enables primary or transmitted/founder (T/F) HIV-1 Envs to support efficient SHIV replication in rhesus macaques (RMs). Here, we test this design strategy more broadly by constructing and analyzing SHIVs containing ten strategically selected primary or T/F HIV-1 Envs corresponding to subtypes A, B, C, AE and AG, each with six allelic variants at position 375. All ten SHIVs bearing wildtype Env375 residues replicated efficiently in human CD4+ T cells, but only one of these replicated efficiently in rhesus CD4+ T cells. This was a SHIV whose subtype AE Env naturally contained a bulky aromatic His residue at position 375. Replacement of wildtype Env375 residues by Trp, Tyr, Phe or His in the other nine SHIVs uniformly led to efficient replication in rhesus CD4+ T in vitro and in RMs in vivo. Env375-Trp - the residue found most frequently among SIV strains infecting Old World monkeys - was favored for SHIV replication in RMs, although some SHIVs preferred Env375-Tyr, -His or -Phe. Nine SHIVs containing optimized Env375 alleles were grown large scale in primary activated rhesus CD4+ T cells to serve as challenge stocks in preclinical prevention trials. These virus stocks were genetically homogeneous, native-like in Env antigenicity and tier-2 neutralization sensitivity, transmissible by rectal, vaginal, penile, oral or intravenous inoculation routes, and exhibited acute and early replication kinetics that were indistinguishable from HIV-1 infection in humans. Finally, to expedite future SHIV constructions and eliminate short redundant elements in tat1 and env gp41 that were spontaneously deleted in chronically infected monkeys, we engineered a simplified second-generation SHIV design scheme and validated it in RMs. Overall, our findings demonstrate that SHIVs bearing primary or T/F Envs with bulky aromatic amino acid substitutions at position Env375 consistently replicate in RMs, recapitulating many features of HIV-1 infection in humans. We further show that SHIV challenge stocks grown in primary rhesus CD4+ T cells are efficiently transmitted by mucosal routes common to HIV-1 infection and can be used effectively to test for vaccine efficacy in preclinical monkey trials.

microbiology↗

bioRxiv2020

Gastrointestinal ulceration in calves presented to a central Iowa veterinary referral facility: An underappreciated morbidity?

Summary and ImplicationsThe objective of this retrospective investigation is to identify the incidence of gastrointestinal ulceration as a co-morbidity in calves presenting to a referral veterinary hospital. Approximately 24% of calves presented to the hospital that died or were euthanized had evidence of gastrointestinal ulceration. Previous administration of an NSAID was significantly associated with the presence of ulcers, whereas antibiotic administration, age at presentation, gender, or breed were not. Clinicians and producers should consider the risk of ulceration in calves treated with NSAIDs, in light of antiulcer therapies.

pathology↗

bioRxiv2020

The defensive behavior of Indiana mite biting honeybees against Varroa destructor and the structure of mandibles

The honey bee (Apis mellifera) is the most important managed pollinator to sustainable agriculture and our ecosystem. Yet managed honey bee colonies in the United States experience 30-40% losses annually. Among the many biotic stressors, the parasitic mite Varroa destructor is considered one of the main causes of colony losses. Bees mite-biting behavior has been selected as a Varroa-tolerant or Varroa-resistant trait in the state of Indiana for more than a decade. A survey of damaged mites from the bottom of a colony can be used as an extended phenotype to evaluate the mite-biting behavior of a colony. In this study, on average, 37% of mites sampled from the breeding stocks of 59 colonies of mite biters in Indiana were damaged or mutilated, which is significantly higher than the 19% of damaged mites found in commercial colonies in the southern United States. Indiana mite biter colonies had a higher proportion of damaged mites, although among the damaged mites, the number of missing legs was not significantly higher. In addition, the morphology of pollen-forager worker bee mandibles was compared by X-ray microcomputed tomography for six parameters in two populations, and a difference was detected in one parameter. Our results provide scientific evidence that potentially explains the defensive mechanism against Varroa mites: structural changes in the worker bee mandibles.

animal behavior and cognition↗

bioRxiv2020

Predicting potential impacts of ocean acidification on marine calcifiersfrom the Southern Ocean

Understanding the vulnerability of marine calcifiers to ocean acidification is a critical issue, especially in the Southern Ocean (SO), which is likely to be the one of the first, and most severely affected regions. Since the industrial revolution, ~30% of anthropogenic CO2 has been absorbed by the oceans. Seawater pH levels have already decreased by 0.1 and are predicted to decline by ~ 0.3 by the year 2100. This process, known as ocean acidification (OA), is shallowing the saturation horizon, which is the depth below which calcium carbonate (CaCO3) dissolves, likely increasing the vulnerability of many marine calcifiers to dissolution. The negative impact of OA may be seen first in species depositing more soluble CaCO3 mineral phases such as aragonite and high-Mg calcite (HMC). These negative effects may become even exacerbated by increasing sea temperatures. Here we combine a review and a quantitative meta-analysis to provide an overview of the current state of knowledge about skeletal mineralogy of major taxonomic groups of SO marine calcifiers and to make predictions about how OA might affect different taxa. We consider their geographic range, skeletal mineralogy, biological traits and potential strategies to overcome OA. The meta-analysis of studies investigating the effects of the OA on a range of biological responses such as shell state, development and growth rate shows response variation depending on mineralogical composition. Species-specific responses due to mineralogical composition suggest taxa with calcitic, aragonitic and HMC skeletons may be more vulnerable to the expected carbonate chemistry alterations, and low magnesium calcite (LMC) species may be mostly resilient. Environmental and biological control on the calcification process and/or Mg content in calcite, biological traits and physiological processes are also expected to influence species specific responses.

ecology↗

bioRxiv2020

Bilateral enucleation induces homeostatic plasticity in the dorsolateral geniculate nucleus of mice.

Within the nervous system, plasticity mechanisms attempt to stabilize network activity following disruption by injury, disease, or degeneration. Optic nerve injury and age-related diseases can induce homeostatic-like responses in adulthood. We tested this possibility in the thalamocortical (TC) neurons in the dorsolateral geniculate nucleus (dLGN) using patch-clamp electrophysiology, optogenetics, immunostaining, and single-cell dendritic analysis following loss of visual input via bilateral enucleation. We observed progressive loss of vGlut2-positive retinal terminals in the dLGN indicating degeneration post-enucleation that was coincident with changes in microglial morphology indicative of microglial activation. Consistent with the decline of vGlut2 puncta, we also observed loss of retinogeniculate (RG) synaptic function assessed using optogenetic activation of RG axons while performing whole-cell voltage clamp recordings from TC neurons in brain slices. Surprisingly, we did not detect any significant changes in the frequency of miniature post-synaptic currents (mEPSCs) or corticothalamic feedback synapses. Analysis of TC neuron dendritic structure from single-cell dye fills revealed a gradual loss of dendrites proximal to the soma, where TC neurons receive the bulk of RG inputs. Finally, analysis of action potential firing demonstrated that TC neurons have increased excitability following enucleation, firing more action potentials in response to depolarizing current injections. Our findings show that degeneration of the retinal axons/optic nerve and loss of RG synaptic inputs induces structural and functional changes in TC neurons, consistent with neuronal attempts at compensatory plasticity in the dLGN.

neuroscience↗

bioRxiv2020

Parabrachial complex processes dura inputs through a direct trigeminal ganglion-to-parabrachial connection

Migraines cause significant disability and contribute heavily to healthcare costs. Irritation of the meninges outermost layer (the dura mater), and trigeminal ganglion activation contribute to migraine initiation. Maladaptive changes in central pain-processing regions are also important in maintaining pain. The parabrachial complex (PB) is a central region that mediates chronic pain. PB receives diverse sensory information, including a direct input from the trigeminal ganglion. We hypothesized that PB processes inputs from the dura. Using in vivo electrophysiology recordings from single units in anesthetized rats we identified 58 neurons in lateral PB that respond reliably and with short latency to electrical dura stimulation. After injecting tracer into PB, anatomical examination reveals retrogradely labeled cell bodies in the trigeminal ganglion. Neuroanatomical tract-tracing revealed a population of neurons in the trigeminal ganglion that innervate the dura and project directly to PB. These findings indicate that PB is strategically placed to process dura inputs, and suggest that it is directly involved in the pathogenesis of migraine headaches.

neuroscience↗

bioRxiv2020

Neuronal and synaptic plasticity in the visual thalamus in mouse models of glaucoma.

Homeostatic plasticity plays important roles in regulating synaptic and intrinsic neuronal function to stabilize output following perturbations to circuit activity. In glaucoma, a neurodegenerative disease of the visual system commonly associated with elevated intraocular pressure (IOP), early disease is associated with altered synaptic inputs to retinal ganglion cells (RGCs), changes in RGC intrinsic excitability, and deficits in optic nerve transport and energy metabolism. These early functional changes can precede RGC degeneration and are likely to alter RGC outputs to their target structures in the brain and thereby trigger homeostatic changes in synaptic and neuronal properties in those brain regions. In this study, we sought to determine whether and how neuronal and synaptic function is altered in the dorsal lateral geniculate nucleus (dLGN), an important RGC projection target in the thalamus, and how functional changes relate to IOP. We accomplished this using patch-clamp recordings from thalamocortical (TC) relay neurons in the dLGN in two established mouse models of glaucoma - the DBA/2J (D2) genetic mouse model and an inducible glaucoma model with intracameral microbead injections to elevate IOP. We found that the intrinsic excitability of TC neurons was enhanced in D2 mice and these functional changes were mirrored in recordings of TC neurons from microbead-injected mice. Notably, many neuronal properties were correlated with IOP in older D2 mice, but not younger D2 mice or microbead-injected mice. The frequency of miniature excitatory synaptic currents (mEPSCs) was reduced in both ages of D2 mice, and vGlut2 staining of RGC synaptic terminals was reduced in an IOP-dependent manner in older D2 mice. Among D2 mice, functional changes observed in younger mice without elevated IOP were distinct from those observed in older mice with elevated IOP and RGC degeneration, suggesting that glaucoma-associated changes to neurons in the dLGN might represent a combination of stabilizing/homeostatic plasticity at earlier stages and pathological dysfunction at later stages.

neuroscience↗

bioRxiv2020

Could radical pairs play a role in xenon-induced general anesthesia?

Understanding the mechanisms underlying anesthesia would be a key step towards understanding consciousness. The process of xenon-induced general anesthesia has been shown to involve electron transfer, and the potency of xenon as a general anesthetic exhibits isotopic dependence. We propose that these observations can be explained by a mechanism in which the xenon nuclear spin influences the recombination dynamics of a naturally occurring radical pair of electrons. We develop a simple model inspired by the body of work on the radical-pair mechanism in cryptochrome in the context of avian magnetoreception, and we show that our model can reproduce the observed isotopic dependence of the general anesthetic potency of xenon in mice. Our results are consistent with the idea that radical pairs of electrons with entangled spins could be important for consciousness.

biophysics↗

bioRxiv2020

Integrated environmental and genomic analysis reveals the drivers of local adaptation in African indigenous chickens

Elucidating the genetic basis of environmental adaptation in indigenous livestock populations has important implications for sustainable breeding improvement. It requires a detailed untangling of relevant environmental pressures and fine resolution detection of genomic signatures of selection associated with these environmental parameters. Here, we uniquely employed an integrative approach, combining Ecological Niche Modelling (ENM) with (i) genome-wide analyses of positive signatures of selection (SSA) and (ii) genotype-environment association (GEA) analyses to unravel the environmental adaptation of Ethiopian indigenous chickens. We first examined 34 agro-ecological and climatic variables and identified six main environmental selection drivers (one temperature - strongly correlated to elevation, three precipitation, and two soil/land variables). We then performed genomic analyses using high-density SNP data from whole-genome sequencing of 245 Ethiopian chickens from 25 different populations. Environmental genomic association analyses (SSA and GEA) identify a few strongly supported selected genomic regions, often with clusters of candidate genes, related to altitude-induced stresses (hypoxia, thrombosis, and cold temperatures), water scarcity, and the challenges of scavenging feeding behaviour. These analyses support a predominantly oligogenic control of environmental adaptation and possible regulation by one or few genetic elements only. Our study shows that the pre-identification of the key environmental drivers of adaptation, followed by a detailed genomic investigation of the associated genetic mechanisms provides a powerful new approach for elucidating the effect of natural selection in domestic animals. These results represent new landmarks to inform sustainable poultry breeding improvement.

genomics↗

bioRxiv2020

Recapitulation of HIV-1 Env-Antibody Coevolution in Macaques Leading to Neutralization Breadth

Neutralizing antibodies elicited by HIV-1 coevolve with viral Envs in distinctive patterns, in some cases acquiring substantial breadth. Here we show that primary HIV-1 Envs, when expressed by simian-human immunodeficiency viruses in rhesus macaques, elicited patterns of Env-antibody coevolution strikingly similar to those in humans. This included conserved immunogenetic, structural and chemical solutions to epitope recognition and precise Env-amino acid substitutions, insertions and deletions leading to virus persistence. The structure of one rhesus antibody, capable of neutralizing 49% of a 208-strain panel, revealed a V2-apex mode of recognition like that of human bNAbs PGT145/PCT64-35M. Another rhesus antibody bound the CD4-binding site by CD4 mimicry mirroring human bNAbs 8ANC131/CH235/VRC01. Virus-antibody coevolution in macaques can thus recapitulate developmental features of human bNAbs, thereby guiding HIV-1 immunogen design. One sentence summaryVirus-antibody coevolution in rhesus macaques recapitulates developmental features of human antibodies.

immunology↗

bioRxiv2020

Inference of a genome-wide protein-coding gene set of the inshore hagfish Eptatretus burgeri

The group of hagfishes (Myxiniformes) arose from agnathan (jawless vertebrate) lineages and is one of the only two extant cyclostome taxa, together with lampreys (Petromyzontiformes). Even though whole genome sequencing has been achieved for diverse vertebrate taxa, genome-wide sequence information has been highly limited for cyclostomes. Here we sequenced the genome of the inshore hagfish Eptatretus burgeri using DNA extracted from the testis, with a short-read sequencing platform, aiming at reconstructing a high-coverage coding gene catalogue. The obtained genome assembly, scaffolded with mate-pair reads and paired RNA-seq reads, exhibited an N50 scaffold length of 293 Kbp, which allowed the genome-wide prediction of coding genes. This computation resulted in the gene models whose completeness was estimated at the complete coverage of more than 83 % and the partial coverage of more than 93 % by referring to evolutionarily conserved single-copy orthologs. The high contiguity of the assembly and completeness of resulting gene models promises a high utility in various comparative analyses including phylogenomics and phylome exploration.

genomics↗

bioRxiv2020

Mapping QTL associated with resistance to avian oncogenic Mareks Disease Virus (MDV) reveals major candidate genes and variants

Mareks Disease (MD) represents a significant global economic and animal welfare issue. Mareks Disease Virus (MDV) is a highly contagious oncogenic and highly immune-suppressive alpha-herpes virus, which infects chickens, causing neurological effects and tumour formation. Though partially controlled by vaccination, MD continues to have a profound impact on animal health and on the poultry industry. Genetic selection provides an alternative and complementary method to vaccination. However, even after years of study, the genetic mechanisms underlying resistance to MDV remain poorly understood. The MHC is known to play a role in disease resistance, along with a handful of other. In this study, one of the largest to date, we used a multi-facetted approach to identify QTL regions (QTLR) influencing resistance to MDV, including an F6 population from a full-sib advanced intercross line (FSIL) between two elite commercial layer lines differing in resistance to MDV, RNA-seq information from virus challenged chicks, and genome wide association study (GWAS) from multiple commercial lines. Candidate genomic elements residing in the QTLR were further tested for association with offspring mortality in the face of MDV challenge in 8 pure lines of elite egg-layer birds. Thirty-eight QTLR were found on 19 chicken chromosomes. Candidate genes, miRNAs, lncRNAs and potentially functional mutations were identified in these regions. Association tests were carried out in 26 of the QTLR, using 8 pure lines of elite egg-layer birds. Numerous candidate genomic elements were strongly associated with MD resistance. Genomic regions significantly associated with resistance to MDV were mapped, and candidate genes identified. Various QTLR elements were shown to have strong genetic association with resistance. These results provide a large number of significant targets for mitigating the effects of MDV infection on both poultry health and the economy - whether by means of selective breeding, improved vaccine design or gene-editing technologies. Author summaryMareks Disease has a huge impact on the global poultry industry in terms of both animal welfare and economic cost. For many years, researchers have sought to identify the genes underlying resistance to Mareks Disease Virus (MDV). However, this is a complex trait with each genetic locus having a small effect, so identifying causal genes and variants is no easy task. To date, it is known that the MHC confers differing susceptibility/resistance. A few other non-MHC genes have also been implicated in disease resistance, although based on experimental inbred lines and not representing real world commercial poultry. Using an F6 intercross population of birds with differences in MDV survival, we have identified many regions of the genome involved in resistance and highlighted candidate genes, miRNAs and lncRNA. Access to DNA from phenotyped birds spanning 15 generations of 8 elite commercial lines has provided a unique opportunity for us to show genetic association of markers in these transcripts with MDV survival. This genetic study, the largest to date, provides novel targets for mitigation of Mareks Disease within the poultry industry. This could be through selective breeding strategies, improved vaccine design or future gene editing technologies.

genomics↗

bioRxiv2020

Minimal net loss of vegetation via interior pond dynamics in an extensive unditched salt marsh

Ponds in salt marshes are often interpreted as a symptom of degradation, yet ponds can also be part of a cyclical process of pool formation, expansion, tidal breaching and vegetation recovery. Pond dynamics may be altered by accelerated sea level rise, with consequences for the long-term stability of ecosystems. We test the prediction that ponds are in dynamic equilibrium across one the largest expanses of unditched salt marsh in the Northeast USA by (1) examining change in pond and marsh area between 1970 and present and (2) by tracking individual pool dynamics across an 87-year time series. We found that net pond area has remained unchanged since 1970 because the amount of marsh conversion to ponds is equivalent to the amount pond recovery to marsh. The ratio of tidally-connected ponds is increasing relative to non-tidal ponds which suggests that some rates of change may be decoupling, which may be related to a decline in the rate of pond formation. A nuanced understanding of marsh pools needs to be incorporated into marsh condition assessments and establishment of restoration priorities so that ponds are not interpreted as evidence of degradation when they are exhibiting a recovery cycle. Unditched marshes around the world are a rare resource that remains essential for advancing scientific understanding and serving as reference sites for restoration of marshes altered by past management.

ecology↗

bioRxiv2020

Revealing grand-paternal programming of lipid metabolism using a novel computational tool

While the consequences of poor maternal diet on the offspring’s cardio-metabolic health have been studied in detail, the role of the father’s diet on the health of his offspring is poorly understood. We used a known mouse model to establish the impact of an isocaloric paternal low-protein high-carbohydrate diet on the offspring’s lipid metabolism. Detailed lipid profiles were acquired from F1 neonate (3 weeks), F1 adult (16 weeks) and F2 neonate male and female offspring, in serum, liver, brain, heart and abdominal adipose tissues by Mass Spectrometry and Nuclear Magnetic Resonance. Using a purpose-built computational tool for analysing lipid metabolism as a network, we characterised the number, type and abundance of lipid variables in and between tissues (Lipid Traffic Analysis), finding a variety of alterations associated with paternal diet. These elucidate a mechanism for the defective physiological behaviour of systems at risk of cardio-metabolic disease.Competing Interest StatementThe authors have declared no competing interest.View Full Text

developmental biology↗

bioRxiv2020

Reduced horseshoe crab abundance and feeding activity beneath intertidal oyster aquaculture structures in the Delaware Bay

Around the world, tidal flats play a unique ecological role in estuaries and are a primary feeding habitat for shorebirds and other benthic feeding organisms. Development and economic use of tidal flats can exclude species that depend on this habitat and disrupt ecological processes. In this study we examine patterns of abundance and feeding activity of American horseshoe crabs among oyster aquaculture structures on tidal flats that are adjacent to one of the most important horseshoe crab spawning sites in the world. We used custom-designed traps to sample horseshoe crab abundance beneath rack and bag aquaculture structures and adjacent areas without structures. In addition, we developed predictive spatial models representing three hypotheses regarding the movement of horseshoe crabs through aquaculture structures when transiting to and from spawning beaches. We tested the predictive power of each model using data from traps and found the strongest support for an avoidance model, where on average, horseshoe crabs are avoiding arrays of aquaculture structures when moving across inundated tidal flats. The best-supported spatial model also indicates that patterns of structure avoidance by horseshoe crabs can potentially affect abundance on spawning beaches, particularly with larger gear arrays that are closer to shore. We found additional support for aquaculture structure avoidance by examining an independent data set of horseshoe crab feeding pits on the tidal flats. Patterns of feeding pit density mirrored our trapping results, with fewer pits beneath and among aquaculture structures when compared to adjacent control areas. Horseshoe crabs are important constituents of the benthic food web and their displacement by aquaculture may translate to significant disruptions to the ecological function of tidal flats. This impact can be limited through deliberative spatial planning that seeks to balance ecological and economic management objectives.

ecology↗

bioRxiv2020

Disruption of Adaptive Immunity Enhances Disease in SARS-CoV-2 Infected Syrian Hamsters

Animal models recapitulating human COVID-19 disease, especially with severe disease, are urgently needed to understand pathogenesis and evaluate candidate vaccines and therapeutics. Here, we develop novel severe disease animal models for COVID-19 involving disruption of adaptive immunity in Syrian hamsters. Cyclophosphamide (CyP) immunosuppressed or RAG2 knockout (KO) hamsters were exposed to SARS-CoV-2 by the respiratory route. Both the CyP-treated and RAG2 KO hamsters developed clinical signs of disease that were more severe than in immunocompetent hamsters, notably weight loss, viral loads, and fatality (RAG2 KO only). Disease was prolonged in transiently immunosuppressed hamsters and uniformly lethal in RAG2 KO hamsters. We evaluated the protective efficacy of a neutralizing monoclonal antibody and found that pretreatment, even in immunosuppressed animals, limited infection. Our results suggest that functional B and/or T cells are not only important for the clearance of SARS-CoV-2, but also play an early role in protection from acute disease. One Sentence SummaryAn antibody targeting the spike protein of SARS-CoV-2 limits infection in immunosuppressed Syrian hamster models.

microbiology↗

bioRxiv2020

Designing Feature-Controlled Humanoid Antibody Discovery Libraries Using Generative Adversarial Networks

We demonstrate the use of a Generative Adversarial Network (GAN), trained from a set of over 400,000 light and heavy chain human antibody sequences, to learn the rules of human antibody formation. The resulting model surpasses common in silico techniques by capturing residue diversity throughout the variable region, and is capable of generating extremely large, diverse libraries of novel antibodies that mimic somatically hypermutated human repertoire response. This method permits us to rationally design de novo humanoid antibody libraries with explicit control over various properties of our discovery library. Through transfer learning, we are able to bias the GAN to generate molecules with key properties of interest such as improved stability and developability, lower predicted MHC Class II binding, and specific complementarity-determining region (CDR) characteristics. These approaches also provide a mechanism to better study the complex relationships between antibody sequence and molecular behavior, both in vitro and in vivo. We validate our method by successfully expressing a proof-of-concept library of nearly 100,000 GAN-generated antibodies via phage display. We present the sequences and homology-model structures of example generated antibodies expressed in stable CHO pools and evaluated across multiple biophysical properties. The creation of discovery libraries using our in silico approach allows for the control of pharmaceutical properties such that these therapeutic antibodies can provide a more rapid and cost-effective response to biological threats.

immunology↗