Biology subjects

Nair, N. U.

Publications and source records attributed to Nair, N. U..

At least 19 recordsLinked to original sources

bioRxiv2026

An engineered disulfide staple restricts lid loop dynamics and alters substrate specificity of phenylalanine ammonia-lyase

In Anabaena variabilis (Trichormus variabilis) phenylalanine ammonia-lyase (AvPAL), a conserved lid-like loop sits over the active site and has been studied both for its role in positioning a catalytic tyrosine and for its contribution to phenylalanine aminomutase (PAM) activity. While the active site architecture and substrate specificity of AvPAL have been extensively characterized, the dynamic behavior of this unstructured loop beyond its role in catalysis remains poorly understood. Here, we investigate the functional role of this loop by restricting its mobility through targeted interchain disulfide bond engineering. Three in-house approaches were designed to predict ideal cysteine residue pairs: (i) quantifying pair interaction energies via electrostatic and van der Waals forces, (ii) generating a contact map of residues within 5 [A] proximity, and (iii) implementing a machine-learning model trained on datasets from PDBCYS, SPX, and an internal database to rank cysteine pair likelihood within disulfide bond geometric constraints. Our machine-learning-guided strategy yielded a successful variant with complete oxidation efficiency in E. coli. Rigidification of this loop reveals that it also functions as a regulator of substrate specificity. Multi-scale molecular simulation analyses (molecular dynamics, metadynamics, quantum/molecular mechanics) reveal that this modification alters the active-site pocket by reducing the conformational dynamics of substrate binding. Our findings underscore the delicate balance between enzyme flexibility and catalytic efficiency, providing novel insights into the role of this understudied dynamic loop region in AvPAL.

bioengineering↗

bioRxiv2026

Enhanced Bacillus subtilis natural competence enables multiplexed genome and spore engineering

Bacillus subtilis is an important chassis for biotechnology, but its use in multiplex genome engineering is limited by low natural transformation efficiency. Here, we compared inducible promoter systems for synthetic activation of the competence regulator ComK and evaluated their effects on the comG operon competence reporter and transformation efficiency. Xylose- and mannitol-inducible systems outperformed IPTG-based constructs and shifted 96-99% of cells into a reporter-positive competent state. However, reporter activation alone did not predict transformation potential. Optimization of culture density and induction timing increased transformant yield 45-fold relative to the initial protocol and 2800-fold relative to the conventional Spizizen method. Disruption of native competence regulatory genes did not improve performance and often reduced transformation output, highlighting the importance of endogenous regulatory circuitry. Using the optimized strain and protocol, we achieved co-transformation frequencies of 11-18% and constructed multiplex spore-display libraries containing fluorescent protein fusions integrated at multiple loci. Screening identified strong dual-display combinations and showed that cargo loading depends on anchor protein, integration locus, and genetic background. SscA fusions supported the highest display capacity and promoted synergistic co-display. Together, these results show improvements in natural transformation-based genome engineering in B. subtilis and provide insight into the construction of multifunctional engineered spores.

synthetic biology↗

bioRxiv2026

Engineered Vibrio natriegens lysate can replace multiple components of cell culture media

Reducing the cost and environmental impact of cell culture media is an important goal for cultivated meat, the process of generating meat in vitro using proliferating animal cells. While prior approaches have demonstrated the use of microbial lysates to replace expensive animal-based fetal bovine serum (FBS) in media, these formulations still rely on large quantities of growth factors such as fibroblast-like growth factor 2 (FGF2). Here, we demonstrate the use of FGF2-expressing Vibrio natriegens to create whole-cell lysates that replace both FBS and FGF2 in cell culture media for cultivated meat applications. This medium, named "VN40FGF", supports rapid proliferation of immortalized bovine muscle satellite cells (iBSCs) in the absence of supplemented FGF2. Cells grown in VN40FGF maintain phenotype and differentiation capacity. We also demonstrate that engineered V. natriegens can grow in spent cell culture media, further improving sustainability and economics, and reducing potential eutrophication concerns associated with waste disposal. Our approach combines multiple strategies for reducing the total number of media inputs, demonstrating opportunities for more economical and sustainable cell culture, especially for cultivated meats.

bioengineering↗

bioRxiv2026

Substrate transport limits phenylalanine ammonia-lyase activity in engineered Lacticaseibacillus rhamnosus GG

Probiotic-based encapsulation offers unique advantages over purified enzymes, such as increased protection from thermal-, pH-, and protease-mediated degradation, for oral therapeutic delivery applications. However, one of the major disadvantages of whole-cell systems is lower reaction rate due to substrate-product transport limitations imposed by the cell membrane and/or wall. In this work, we explore the potential of different lactic acid bacteria (LAB) - Lacticaseibacillus rhamnosus GG (LGG), Lactococcus lactis (Ll), and Lactiplantibacillus plantarum (Lp) - as expression hosts for recombinant Anabaena variabilis phenylalanine ammonia-lyase (AvPAL*). AvPAL* is used as a therapeutic to treat Phenylketonuria (PKU), a rare autosomal recessive metabolic disorder. Among the three species tested, LGG showed the highest PAL activity followed by L. lactis. Next, we attempted to overcome mass transfer limitation in whole-cell biocatalysts in two ways - expression of heterologous transporters and treatment with different chemical surfactants. Engineered strains expressing heterologous transporters exhibited approximately 3-4-fold increased PAL activity, while chemical treatment did not improve reaction rates. This work highlights the challenges and advances in realizing the potential of LAB as biotherapeutics. Impact StatementOral delivery of phenylalanine ammonia-lyase (PAL) using engineered probiotics is a promising therapeutic strategy to treat Phenylketonuria (PKU). Although PAL expression has been reported in probiotic strains of Limosilactobacillus reuteri, Lactococcus lactis, and E. coli, a systematic comparison of lactic acid bacteria (LAB) is underexplored. This study explores the potential of multiple LAB as hosts for PAL expression and investigates strategies to improve whole cell enzymatic activity. The findings from this study provide a foundation for implementing LAB-based delivery of PAL and indicate an important step towards development of probiotic platform for PKU management.

synthetic biology↗

bioRxiv2025

Pharmacophore-driven antibody discovery on the yeast surface

Protein-small molecule hybrids are structures capable of combining the inhibitory properties of small molecules and the specificities of binding proteins. However, discovery of such synergistic conjugates is a substantial engineering challenge. Here, we describe pharmacophore-driven antibody discovery as a high throughput approach to hybrid discovery. In this approach, we use a yeast display antibody library containing reactive noncanonical amino acids (ncAAs) and further diversify it by conjugating the library to four sulfonamide pharmacophores. Yeast display binding screens with each of the resulting billion-member hybrid collections against bovine carbonic anhydrase (bCA) yielded diverse collections of hybrids. Individual hybrids exhibited double digit nanomolar binding affinities, and frequently exhibited inhibitory properties in solution, despite the fact that the screens were based solely on binding phenotypes. Deep sequencing of sorted populations revealed that enrichments were strongly pharmacophore-dependent. In particular, screens with a potent pharmacophore led to collections of hybrids varying substantially in pharmacophore attachment point and antibody sequence features, while screens with moderate or weak pharmacophores led to collections with much narrower sets of enriched attachment points and antibody sequence features. Identification of the most frequently isolated CDR-H3 sequences and clustering CDR-H3 sequences by similarity within enriched populations provided further evidence for pharmacophore-dependent sorting outcomes. Experimental binding assays in which the pharmacophore warhead used during screening was replaced by another warhead indicated that isolated clones can tolerate alternative pharmacophores, but tend to prefer the warhead used during screening. Overall, these efforts demonstrate the utility of introducing pharmacophores into antibody libraries along with several lines of evidence that screening outcomes are pharmacophore-driven. These findings advance our understanding of hybrid discovery and highlight opportunities to pursue hybrids as research tools and potential therapeutic leads. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=68 SRC="FIGDIR/small/682880v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@11c2a65org.highwire.dtl.DTLVardef@237055org.highwire.dtl.DTLVardef@a3fb4borg.highwire.dtl.DTLVardef@1c71700_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2025

Engineered antimicrobial-derived peptides to manipulate mixed microbial systems

Due to complexity of microbial communities and coarseness of currently available manipulation techniques (e.g. transplantation, antibiotic-treatment), it is often difficult to fully elucidate the interactions between members that define community structure and function from the top-down. Thus, it is imperative to be able to observe and manipulate subpopulations within microbial communities to enable a fine-detail understanding of the full-spectrum and mechanism of community functions. However, there is a technological gap that prevents targeted manipulation of subpopulations within intact microbial mixtures and communities. In this work, we develop molecular probes to manipulate specific subpopulations within multispecies microbial populations and validate these methods using model synthetic populations in vitro. We leverage the narrow-spectrum of class II peptide bacteriocin (a bacterially-synthesized antimicrobial peptide), pediocin PA-1, as a model to develop molecular probes. We first demonstrate the narrow-spectrum activity of pediocin and quantify its potency against a panel of bacteria. Next, we conjugate chemical handles on the bacteriocin and show that the binding spectrum is largely unchanged. Finally, using truncated variants, also conjugated to chemical handles, we show functional non-bactericidal binders that largely maintain their specificity. Finally, with the unmodified and modified bacteriocins, we show that specific bacteria can be depleted through killing or cell sorting within a mixture of highly similar bacteria. While we developed the system with a single bacteriocin, we expect that the elucidated design rules may be applicable to a variety of natural bacteriocins to develop a generalized approach for manipulating specific bacterial members within a community. Development of such molecular probes would be transformative to advancing mechanistic underpinnings of microbial community and microbiota structure-function relationships.

synthetic biology↗

bioRxiv2025

A Novel Phosphatase Reverses the Leloir Pathway to Promote Tagatose Synthesis from Glucose

D-Tagatose is a natural, low-calorie, rare monosaccharide that has gained substantial interest as an alternative sweetener. It offers numerous benefits, including a low glycemic index, prebiotic properties, and the ability to lower blood sugar levels. Currently, tagatose is primarily produced industrially through the isomerization of galactose, utilizing both chemical and enzymatic catalysis. While these established processes can produce tagatose, they are inefficient and expensive. Recent works have demonstrated alternative biosynthetic routes to produce D-tagatose but suffer from low theoretical yield and/or reliance on expensive feedstocks. This study demonstrates a novel biochemical pathway to produce D-tagatose directly from glucose using a whole-cell process with Escherichia coli. This process is distinct from other biosynthetic schemes and utilizes a newly discovered galactose-1-phosphate-selective phosphatase to drive the native Leloir pathway in reverse and synthesize the substrate D-galactose directly from D-glucose. Our analysis of the phosphatase reveals how an ensemble of intermolecular hydrogen bonds governs substrate specificity. By co-expressing this phosphatase and an L-arabinose isomerase in a modified strain background, we demonstrate production of tagatose directly from glucose. In initial studies, we generated [~]10.5 g/L galactose from 30 g/L glucose (35 % yield) while also producing > 1 g/L tagatose. This demonstrates the feasibility of a novel approach to tagatose production in vivo with a theoretical pathway yield of 94.9 %, which is substantially higher than previously proposed tagatose biosynthetic schemes.

bioengineering↗

bioRxiv2025

Path2Omics: Enhanced transcriptomic and methylation prediction accuracy from tumor histopathology

Precision oncology is becoming increasingly integral to clinical practice, demonstrating notable improvements in treatment outcomes. While molecular data provide comprehensive insights, obtaining such data remains costly and time-consuming. To address this challenge, we developed Path2Omics, a deep learning model that predicts gene expression and methylation from histopathology for 23 cancer types. Path2Omics was trained on 20,497 slides (9,456 formalin-fixed and paraffin-embedded (FFPE) and 11,041 fresh frozen (FF)) from 8,007 patients across 23 The Cancer Genome Atlas cohorts. When tested on FFPE slides, the most readily available format in clinical pathology practice, the integrated model outperformed its individual FF and FFPE components, robustly predicting nearly 5,000 genes on average, approximately five times more than our recently published DeepPT model. Externally evaluated on seven independent cohorts, Path2Omics robustly predicted the expression of approximately 4,400 genes, yielding a 30% increase over the FFPE model alone. Finally, we demonstrate that the inferred gene expression is nearly as effective as the actual values in predicting patient survival and treatment response. These results lay the basis for using Path2Omics to advance precision oncology from histopathology slides in a speedy and cost-effective manner. Statement of significancePath2Omics is a deep learning model that accurately predicts gene expression and methylation from histopathology slides across 23 cancer types. Unlike existing approaches that rely solely on FFPE slides for training, Path2Omics leverages both FFPE and FF slides by constructing two separate models and integrating them. Downstream analyses show that the inferred values from Path2Omics are nearly as effective as actual values in predicting patient survival and treatment response.

bioinformatics↗

bioRxiv2024

Advancing protein display on bacterial spores through an extensive survey of coat components

The profound stability of bacterial spores makes them a promising platform for biotechnological applications like biocatalysis, bioremediation, drug delivery, etc. However, though the Bacillus subtilis spore is composed of >40 proteins, only [~]12 have been explored as fusion carriers for protein display. Here, we assessed the suitability of 33 spore proteins (SPs) as enzyme display carriers by direct allele tagging at native genomic loci. Of the 33 SP investigated, 26 formed functional fusions with {beta}-glucuronidase (GUS) - a [~]272 kDa homotetramer. This almost triples the number of SPs assessed for enzyme display and doubles the number of functional fusions documented in the literature. We quantitatively assessed the 1) SP promoter activation dynamics during growth, 2) supported GUS activity on spores, 3) surface availability, 4) protection from thermal and proteolytic degradation, and 5) compatibility of co-expression of many of these fusions. Multi-copy expression and pairwise co-expression of the most promising SP-GUS fusions highlighted the complexity of spore structure/assembly and difficulty in predicting compatibility between different SPs fusions. We also assessed the suitability of engineered spores to degrade PET (polyethylene terephthalate) films and found that surface exposed SPs were most effective. Beyond the broad survey, a key outcome of our work was the identification of SscA (small spore coat assembly protein A) as an effective spore display carrier. SscA supported enzyme activity at least fourfold higher than any other SP, including the well-established and popular anchor, CotY. We attribute this to the biochemical and genetic features of SscA; its promoter demonstrated early and sustained activation relative to other SPs and its small size ([~]3 KDa) likely minimally interferes with enzyme folding, oligomerization, and activity. Although the specific localization of SscA within the spore coat has not been established, its hydrophobic nature and low surface availability suggests that it assembles internally within the spore coat, which makes it highly stabilizing and suitable for many biocatalytic applications. Overall, this work serves as a knowledgebase to advance the biotechnological utility of B. subtilis spores.

synthetic biology↗

bioRxiv2024

Microbial lysates as low-cost serum replacements in cellular agriculture media formulation

Cultivated meat, the process of generating meat in vitro without sacrificing animals, is a promising alternative to the traditional practice of livestock agriculture. However, the success of this field depends on finding sustainable and economical replacements for animal-derived and expensive fetal bovine serum (FBS) that is typically used in cell culture processes. Here, we outline an effective screening process to vet the suitability of microbial lysates to support the growth of immortalized bovine satellite cells (iBSCs) and mackerel (Mack1) cells. We show that easily producible, low-cost whole-cell lysates from Vibrio natriegens can be used to create serum-free media for the long-term growth of iBSCs. The optimized medium, named "VN40" (basal B8 media containing Vibrio natriegens lysate proteins at 40 {micro}g/mL), outperforms previously established serum-free media while maintaining cell phenotype and myogenicity. Overall, this study shows a novel approach to producing serum-free media for cultivated meat production using microbially-derived lysates.

bioengineering↗

bioRxiv2024

Chromosome 7 to the rescue: overcoming chromosome 10 loss in gliomas

The co-occurrence of chromosome 10 loss and chromosome 7 gain in gliomas is the most frequent loss-gain co-aneuploidy pair in human cancers, a phenomenon that has been investigated without resolution since the late 1980s. Expanding beyond previous gene-centric studies, we investigate the co-occurrence in a genome-wide manner taking an evolutionary perspective. First, by mining large tumor aneuploidy data, we predict that the more likely order is 10 loss followed by 7 gain. Second, by analyzing extensive genomic and transcriptomic data from both patients and cell lines, we find that this co-occurrence can be explained by functional rescue interactions that are highly enriched on 7, which can possibly compensate for any detrimental consequences arising from the loss of 10. Finally, by analyzing transcriptomic data from normal, non-cancerous, human brain tissues, we provide a plausible reason why this co-occurrence happens preferentially in cancers originating in certain regions of the brain.

cancer biology↗

bioRxiv2023

Rapid spectrophotometric detection for optimized production of landomycins and characterization of their therapeutic potential

Microbial derived natural products remain a major source of structurally diverse bioactive compounds and chemical scaffolds that have potential as new therapeutics to target drug resistant pathogens and cancers. In particular, genome mining has revealed the vast number of cryptic or low yield biosynthetic gene clusters in the genus Streptomyces. Here, we describe our efforts to improve yields of landomycins - angucycline family polyketides under investigation as cancer therapeutics - by a genetically modified Streptomyces cyanogenus 136. After simplifying the extraction process from S. cyanogenus cultures, we identified a wavelength at which the major landomycin products absorb in culture extracts, which we used to systematically explore culture medium compositions to improve total landomycin titers. Through correlational analysis, we simplified the culture optimization process by identifying an alternative wavelength at which culture supernatants absorb yet is representative of total landomycin titers. Using the subsequently improved sample throughput, we explored landomycin production during the culturing process to further increase landomycin yield and reduce culture time. Testing the antimicrobial activity of the isolated landomycins, we report broad inhibition of Gram-positive bacteria, inhibition of fungi by landomycinone, and broad landomycin resistance by Gram-negative bacteria that is likely mediated by exclusion of landomycins by the bacterial membrane. Finally, the anticancer activity of the isolated landomycins against A549 lung carcinoma cells agrees with previous reports on other cell lines that glycan chain length correlates with activity. Given the prevalence of natural products produced by Streptomyces, as well as the light-absorbing moieties common to bioactive natural products and their metabolic precursors, our method is relevant to improving the yields of other natural products of interest.

bioengineering↗

bioRxiv2022

Towards universal synthetic heterotrophy using a metabolic coordinator

Engineering the utilization of non-native substrates, or synthetic heterotrophy, in proven industrial microbes such as Saccharomyces cerevisiae represents an opportunity to valorize plentiful and renewable sources of carbon and energy as potential inputs to biotechnological processes. We previously demonstrated that activation of the galactose (GAL) regulon, a regulatory structure used by this yeast to coordinate substrate utilization with biomass formation during growth on galactose, during growth on the non-native substrate xylose results in a vastly altered gene expression profile and faster growth compared with constitutive overexpression of the same heterologous catabolic pathway. However, this effort involved the creation of a xylose-inducible variant of Gal3p (Gal3pS25144.1), the sensor protein of the GAL regulon, preventing this semi-synthetic regulon approach from being easily adapted to additional non-native substrates. Here, we report the construction of a variant Gal3pMC (metabolic coordinator) that exhibits robust GAL regulon activation in the presence of structurally diverse substrates and recapitulates the dynamics of the native system. Multiple molecular modeling studies confirm that Gal3pMC occupies conformational states corresponding to galactose-bound Gal3p in an inducer-independent manner. Using Gal3pMC to test a regulon approach to the assimilation of the non-native lignocellulosic sugars xylose, arabinose, and cellobiose yields higher growth rates and final cell densities when compared with a constitutive overexpression of the same set of catabolic genes. The subsequent demonstration of rapid and complete co-utilization of all three non-native substrates suggests that Gal3pMC-mediated dynamic global gene expression changes by GAL regulon activation may be universally beneficial for engineering synthetic heterotrophy.

synthetic biology↗

bioRxiv2022

Specific Codons Control Cellular Resources and Fitness

As cellular engineering progresses from simply overexpressing proteins to imparting complex metabolic and regulatory phenotypes through multigene expression, judicious appropriation of cellular resources is essential. Since there is degeneracy in codons and their use is biased, codons may control cellular resources at a translational level. We investigate how partitioning tRNA resources by incorporating dissimilar codon usage can drastically alter interdependence of expression level and burden on the host. By isolating the effect of individual codons use during elongation, while eliminating confounding factors like mRNA structure, GC content, transcript level, and translation initiation rates, we show that codon choice can trans-regulate fitness of the host and expression of other heterologous genes. We correlate specific codon usage patterns with host fitness, and derive a coding scheme for multi-gene expression called the Codon Health Index (CHI, {chi}). This empirically derived coding scheme ({chi}) enables the design of multi-gene expression systems that avoid catastrophic cellular burden and is robust across multiple growth conditions.

synthetic biology↗

bioRxiv2022

Integration of metabolism and regulation reveals rapid adaptability to growth on non-native substrates.

Engineering synthetic heterotrophy (i.e., growth on non-native substrates) is key to the efficient bio-based valorization of renewable and waste substrates. Among these, engineering hemicellulosic pentose utilization has been well-explored in Saccharomyces cerevisiae (yeast) over several decades - yet the answer to what makes their utilization inherently recalcitrant remains elusive. Through implementation of a semi-synthetic regulon, we find that harmonizing cellular and engineering objectives are key to obtaining highest growth rates and yields with minimal metabolic engineering effort. Concurrently, results indicate that "extrinsic" factors - specifically, upstream genes that direct flux of pentoses into central carbon metabolism - are rate-limiting. We also reveal that yeast metabolism is innately highly adaptable to rapid growth on non-native substrates and that systems metabolic engineering (i.e., flux balancing, directed evolution, functional genomics, and network modeling) is largely unnecessary. We posit that the need for extensive engineering espoused by prior works is a consequence of unfortunate (albeit avoidable) antagonism between engineering and cellular objectives. We also found that deletion of endogenous genes to promote growth demonstrate inconsistent outcomes that are genetic-context- and condition-dependent. For the most part, these knockouts also lead to deleterious pleiotropic effects that decrease the robustness of strains against inhibitors and stressors associated with bioprocessing. Thus, at best, perturbation of "intrinsic" factors (e.g., native metabolic, regulatory genes) results in incremental and inconsistent benefits. At worst, they are detrimental. Overall, this work provides insight into the limitations and pitfalls to realizing efficient synthetic heterotrophy using traditional/systems metabolic engineering approaches, demonstrates the innate adaptability of yeast for metabolism of non-native substrates, and provides an alternate, novel, holistic (and yet minimalistic) approach based on integrating non-native metabolic genes with a native regulon system.

synthetic biology↗

bioRxiv2022

Transcriptomics based prediction of survival and response to therapy in malignant mesothelioma

Malignant mesothelioma is an aggressive cancer with limited treatment options and poor prognosis. Better understanding of mesothelioma genomics and transcriptomics could advance novel therapies. We performed whole-exome and RNA-sequencing of germline and tumors of 122 patients with pleural, peritoneal, and tunica-vaginalis mesothelioma. We identify a 48 gene prognostic signature that is highly predictive of mesothelioma patient survival including CCNB1, whose expression is highly predictive of patient survival on its own. Using a synthetic-lethality (SL) based pipeline for analyzing the patients transcriptomic data, we identified SL-based signatures predictive of response to an anti-PD1 immune checkpoint inhibitor and combination therapies with pemetrexed. These SL-profiles successfully predict the overall patient-response observed across targeted, immuno- and chemotherapies in 11 independent mesothelioma clinical trials spanning 7 different treatments. These findings lay a basis for future studies aimed specifically at testing the ability of these SL profiles to serve as treatment biomarkers in mesothelioma.

cancer biology↗

bioRxiv2022

A silk-based platform to stabilize phenylalanine ammonia-lyase (PAL) for orally administered enzyme replacement therapy

Phenylalanine ammonia-lyase (PAL) has gained attention in recent years for the treatment of phenylketonuria (PKU), a genetic disorder that affects [~]1 in 15,000 individuals globally. However, the enzyme is easily degraded by proteases, unstable at room temperature, and is currently administered in PKU patients as daily subcutaneous injections. We report here the stabilization of the PAL from Anabaena variabilis, which is currently used to formulate pegvaliase, through incorporation in a silk fibroin matrix. The combination with silk stabilizes PAL at 37 {degrees}C. In addition, in vitro studies showed that inclusion in a silk matrix preserves the biological activity of the enzyme in simulated intestinal fluid, enabling the oral administration of pegvaliase for the treatment of PKU.

bioengineering↗

bioRxiv2022

Clinically oriented prediction of patient response to targeted and immunotherapies from the tumor transcriptome

BackgroundPrecision oncology is gradually advancing into mainstream clinical practice, demonstrating significant survival benefits. However, eligibility and response rates remain limited in many cases, calling for better predictive biomarkers. MethodsWe present ENLIGHT, a transcriptomics-based computational approach that identifies clinically relevant genetic interactions and uses them to predict a patients response to a variety of therapies in multiple cancer types, without training on previous treatment response data. We study ENLIGHT in two translationally oriented scenarios: Personalized Oncology (PO), aimed at prioritizing treatments for a single patient, and Clinical Trial Design (CTD), selecting the most likely responders in a patient cohort. FindingsEvaluating ENLIGHTs performance on 21 blinded clinical trial datasets in the PO setting, we show that it can effectively predict a patients treatment response across multiple therapies and cancer types. Its prediction accuracy is better than previously published transcriptomics-based signatures and is comparable to that of supervised predictors developed for specific indications and drugs. In combination with the IFN-{gamma}signature, ENLIGHT achieves an odds ratio larger than 4 in predicting response to immune checkpoint therapy. In the CTD scenario, ENLIGHT can potentially enhance clinical trial success for immunotherapies and other monoclonal antibodies by excluding non-responders, while overall achieving more than 90% of the response rate attainable under an optimal exclusion strategy. ConclusionENLIGHT demonstrably enhances the ability to predict therapeutic response across multiple cancer types from the bulk tumor transcriptome. FundingThis research was supported in part by the Intramural Research Program, NIH and by the Israeli Innovation Authority.

bioinformatics↗