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Biology subjects

Levy, R.

Publications and source records attributed to Levy, R..

At least 19 recordsLinked to original sources

Behavioral and brain responses to language reflect different levels of linguistic representation

Human language processing can be studied through both behavior and brain activity, yet it remains unclear whether these two data types reflect sensitivity to the same information. One influential view holds that both behavioral and neural responses are largely determined by processing effort, often estimated by word surprisal together with the context-independent properties of word frequency and length. At the same time, neural responses have been shown to encode richer aspects of linguistic content, including meaning. Here, we use neural network language models to operationalize these alternatives and systematically compare, within the same analytic computational framework, the predictive power of low-dimensional effort-based predictors and high-dimensional embedding representations that encode contextualized linguistic content, including meaning. Across 8 behavioral datasets and 5 neural datasets (4 fMRI and 1 ERP), we find that processing effort captures substantial variance in both behavioral and neural measures of language processing, in line with much previous work. However, for brain responses---but not for behavioral measures---embedding representations carry substantial predictive power beyond the estimates of processing effort. These results therefore suggest that neural data provide access to rich, high-dimensional dynamics of language comprehension, whereas behavioral data reflect a bottlenecking of these dynamics into a small set of theoretically motivated properties of contextualized linguistic input.

neuroscience↗

Personalized Neoantigen Vaccines Synergize with Immune Checkpoint Therapy and CD8-Targeted Cytokines to Control B-Cell Lymphoma

Personalized neoantigen (neoAg) vaccines have shown clinical promise in solid tumors1-8, yet their efficacy and mechanism of action in hematopoietic malignancies remain poorly defined9-11. Herein, we establish an immunocompetent syngeneic A20 B-cell lymphoma platform to test the efficacy of neoAg vaccines used either as mono- or combinatorial therapies with other immunotherapies12-17. Whereas subcutaneous A20 tumors were refractory to single-agent PD-1 or CTLA4 therapy, they were eradicated in a T cell-dependent manner in 90% of syngeneic hosts treated with dual immune checkpoint therapy (dual ICT, i.e., PD-1 + CTLA4). By mapping antigen specificity of dual-ICT-elicited T cells, we identified and validated dominant endogenous A20 MHC-I and MHC-II neoantigens and designed therapeutic synthetic long peptide (SLP) vaccines containing these neoepitopes. This vaccine (A20 neoVAX) promoted robust neoAg-specific CD4{square} and CD8{square} T cell responses in naive syngeneic BALB/c mice and induced tumor rejection in [~]70% of subcutaneous tumor-bearing mice. In addition, nearly all mice rejected their subcutaneous A20 tumors when A20 neoVAX was combined with PD-1. To render the results of this study more physiologic, we developed a systemic A20 lymphoma model and found that dual ICT failed to control tumor progression and A20 neoVAX delayed tumor progression and prolonged animal survival but did not induce tumor rejection. In contrast, A20 neoVAX plus dual ICT achieved durable systemic tumor elimination. Mechanistically, the combination of A20 neoVAX plus dual ICT amplified priming of A20 neoAg-specific T cells, prevented T cell dysfunction, sustained the cytotoxic capacity of tumor-specific CD8+ T cells, and induced Th1-skewing of CD4+ T cells in tumor and peripheral compartments. To increase the clinical relevance of these findings and to minimize potential adverse events in tumor-bearing, therapeutically treated individuals, we substituted CD8-targeted cytokine muteins (CD8-IL2 or CD8-IL21) for CTLA4. These agents represent genetically modified forms of IL-2 or IL-21 that selectively stimulate CD8+ T cells but have significantly reduced capacity to activate chronic inflammation and immunosuppressive functions of other immune cells. Whereas mice bearing systemic A20 lymphoma treated with either nothing, A20 neoVAX, or A20 neoVAX + CD8-IL2 failed to control tumor outgrowth, 66.7% of tumor-bearing mice treated with A20 neoVAX + CD8-IL2 + PD-1 rejected their tumors. In similar experiments in which CD8-IL21 was substituted for CD8-IL2, tumor clearance was also observed in two-thirds of A20-bearing mice but now rejection occurred in the absence of PD1. Together, these data define a framework for optimal personalized neoAg vaccination in B-lymphoma and demonstrate that neoAg vaccines can safely synergize with CD8+ T cell-selective immunotherapies to prevent T-cell dysfunction and generate durable systemic anti-tumor immunity.

immunology↗

Dynamin 2–dependent endocytosis differentially regulates ligand and receptor contributions to Notch signaling during neural precursor cell fate determination

A critical event in the development of the highly structured cerebral cortex is the appropriate generation of differentiated daughter cell populations from asymmetric precursor cell divisions. Internalization of extracellular receptors and ligands in the process of endocytosis is key to the establishment of asymmetry. However, the detailed mechanisms mediating this exchange are incompletely understood. The dynamin family of membrane remodeling GTPases is considered critical for many forms of clathrin-mediated endocytosis (CME) but its role in brain development is unexplored. Here we found that dynamin 2 (Dnm2), a protein involved in CME through vesicle release from the plasma membrane, is essential for the maintenance of neural stem cells. Conditional deletion of Dnm2 leads to early exhaustion of neural precursor cells and premature neurogenesis, resulting in gross structural abnormalities, periventricular hemorrhaging and increased perinatal mortality. Notably, Notch ligands accumulate at the cell surface and cleaved NICD is reduced in neural stem cells, consistent with impaired ligand-mediated activation. In contrast, inhibition of CME in receptor-expressing cells increases cell autonomous Notch signaling, likely by promoting receptor accumulation at the plasma membrane. Further, dynamin 1, 2, and 3 can rescue loss of Dnm2 to different extents. Taken together, these findings reveal that Dnm2 is the essential isoform for physiological non-cell autonomous Notch-mediated neural stem cell maintenance, and that CME exerts fundamentally distinct roles in Notch signaling, promoting ligand activity while restricting receptor signaling through control of surface receptor abundance.

Developmental Biology↗

Evolutionary Sequence and Structural Basis for the Epistatic Origins of Drug Resistance in HIV

The emergence of drug resistance in the human immunodeficiency virus (HIV) remains a formidable challenge to the long-term efficacy of antiretroviral therapy (ART). A growing body of evidence highlights the critical role of epistasis, the dependence of mutational effects on the sequence context, in shaping the fitness landscape of HIV under ART-induced selection pressure. However, the biophysical origins of the epistatic interactions involved in engendering drug-resistance mutations (DRMs) remain unclear. Are the mutational correlations "intrinsic" to the properties of the protein, or do they arise because of drug binding? We use a Potts sequence-covariation statistical energy model built on patient-derived HIV-1 protein sequences to construct computational double mutant cycles that probe pairwise epistasis for all observed mutations across the three major HIV drug-target enzymes. We find that the strongest epistatic effects occur between mutations at residue positions that frequently mutate during the course of ART, termed resistance-associated positions. To investigate the structural origins of the strongest epistatic interactions, we perform [~]100 free energy perturbation molecular dynamics simulations, revealing that the primary contribution to the pairwise epistasis between DRMs arises from cooperative effects on protein stability and folding as an intrinsic consequence of the protein mutational landscape. The results collectively reinforce a mechanism of resistance evolution whereby viruses escape drug pressure by selectively engendering mutations at "intrinsically" coupled sites, allowing them to cooperatively ameliorate fitness detriments incurred by individual DRMs. SignificanceEpistasis refers to the phenomenon where the effect of a mutation on protein structure and function is dependent on the genetic sequence background of the mutation, resulting in the combined effect of mutations being non-additive. Epistasis plays a significant role in the evolution of drug resistance in viruses such as HIV under therapeutic selection pressure. We combine a protein sequence coevolutionary model and molecular dynamics free energy simulations to identify and probe the mechanistic origins of the strongest epistatic interactions connecting HIV drug-resistance mutations. The work establishes a foundation to probe the molecular bases of epistasis and predict the evolution of resistance predicated on the knowledge of epistatic interaction networks.

biophysics↗

In vivo mRNA delivery to the lung vascular endothelium by dicationic Charge-Altering Releasable Transporters

Endothelial cells (EC) comprise the pulmonary vascular bed and play a significant role in health and disease. Consequently, the EC niche represents an attractive therapeutic target for treating a wide range of pulmonary vascular diseases. We have identified a new class of dicationic Charge-Altering Releasable Transporters. These single-component transporters selectively deliver mRNA to the lung upon intravenous administration without the use of a targeting ligand. Significantly, the number and spatial array of cationic charges within the repeating units of the CART polymer are found to control both mRNA delivery efficacy and tissue tropism. High-resolution imaging revealed efficient mRNA delivery to endothelial cells in pulmonary arteries, veins and capillaries. The selective lung tropism of these new CARTs, coupled with the efficient and tunable synthesis of this new family of CART amphiphiles, represents an enabling platform for research and clinical applications.

bioengineering↗

Enhanced Brain-Heart Connectivity as a Precursor of Reduced State Anxiety After Therapeutic Virtual Reality Immersion

State anxiety involves transient feelings of tension and nervousness in response to threats, which can escalate into anxiety disorders if persistent. Despite treatments, 30%-50% of individuals show limited improvement, and neurophysiological mechanisms of treatment responsiveness remain unclear, requiring the development of objective biomarkers. In this study, we monitored multimodal electrophysiological parameters: heart rate variability (high-frequency, low-frequency, LF/HF ratio), EEG beta and alpha relative power, and brain-to-heart connectivity in participants with real-life state anxiety. Participants underwent a therapeutic intervention combining virtual-reality immersion, hypnotic script, and a breath control exercise. Real-life state anxiety was captured using the STAI-Y1 scale before and after the intervention. We observed reduced anxiety immediately after the intervention in 16 out of 27 participants. While all participants, independently of their STAI-Y1 score, showed increased HRV low frequency power, only treatment-responders displayed increased overall autonomic tone (high and low frequency HRV), increased midline beta power and brain-to-heart connectivity. Notably, the LF/HF ratio showed a significant linear relationship with anxiety reduction, with higher ratios linked to greater therapeutic response. These findings suggest that increased cognitive regulation of brain-to-heart connectivity could serve as a biomarker for therapeutic efficacy, with elevated midline beta power facilitating improved cardiac tone in responders. Significance StatementElevated state anxiety can escalate into debilitating disorders, such as generalized anxiety disorder, yet treatment efficacy remains inconsistent, and reliable biomarkers predicting therapeutic outcomes are lacking. This study identifies key neural and physiological markers linked to effective anxiety reduction following a virtual reality-based non-pharmacological intervention in healthy participants with increased state anxiety. Anxiety reduction is associated with increased midline beta power, heightened heart rate variability (LF/HF ratio), and enhanced brain-to-heart connectivity. These findings highlight the role of brain-to-heart modulation and autonomic nervous system functioning in therapeutic response. By highlighting these biomarkers, this research aims at advancing our understanding of anxiety treatment mechanisms and offering insights into the development of biomarker-driven, scalable interventions.

neuroscience↗

A structural MRI marker predicts individual differences in impulsivity and classifies patients with behavioral-variant frontotemporal dementia from matched controls

Impulsive decision-making is a symptom across many neuropsychiatric and neurological disorders. Yet, it is still unknown whether impulsivity can be predicted based on individual differences in brain structure. Here, we used machine-learning to develop a structural MRI signature of impulsivity, tested its validity in several independent samples, and assessed its diagnostic value in patients with behavioral variant frontotemporal dementia (bvFTD)--a neurodegenerative disease characterized by high impulsivity. The resulting whole-brain grey matter density pattern--the Structural Impulsivity Signature (SIS)--showed a good prediction-outcome correlation of r=0.35 (out-of-sample, p=0.0028) in the training sample of healthy adults (N=117) and significantly predicted individual differences in impulsivity in four other, independent studies (total N=626), including healthy and clinical participants with neuropsychiatric and neurological conditions. Further, the SIS separated bvFTD patients from controls with high accuracy (81% correct, p=0.002) and predicted impulsivity-related symptom severity among patients. The spatial distribution of weights in the SIS brain pattern highlights the key role of brain regions associated with affective processing in impulsivity. Together, these results provide evidence for a new structural neuromarker of individual differences in impulsivity that can be easily applied to new samples. Future studies can further assess its predictive value towards better prevention, diagnosis and treatment of mental disorders associated with impulsivity symptoms.

neuroscience↗

On the same side: The immune regulatory protein Vista and its ligands interact in cis

VISTA, an essential immune checkpoint regulatory protein, regulates peripheral T-cell quiescence and tolerance. Despite its potential as a target for anti-tumor and autoimmune disease therapies, uncertainty regarding VISTAs binding mode and membrane orientation has hindered these developments. Contrary to the prevailing paradigm, we found using cell aggregation assays that VISTA cannot interact with its ligands in trans (between cells). Using MST and flow cytometry, we showed that soluble VISTA binds to its ligands, suggesting that VISTAs membrane orientation restricts trans interactions. In contrast, split luciferase complementation assays showed that VISTA interacts with its ligands in cis. We propose that a disulfide bond bends VISTAs Ig domain towards the membrane in an orientation that prevents trans while enabling cis interactions. Co-expression data analysis from the cancer genome atlas showed a strong correlation between VISTA and its ligand, PSGL-1, consistent with our in-vitro cis interaction data. Our findings reveal VISTAs binding mechanism and suggest an intrinsic inhibition signaling pathway independent of additional cells. Importantly, our experimental framework provides a platform for identifying novel VISTA-targeted therapeutics.

immunology↗

High delay discounting relates to core symptoms and to pulvinar atrophy in frontotemporal dementia

Behavioural variant frontotemporal dementia (bvFTD) is a neurodegenerative disorder characterized by behavioural changes and atrophy in brain regions important for decision-making. Computations such as trading off between larger later (LL) and smaller sooner (SS) rewards -- called delay discounting in behavioural economics -- might be heavily impaired by bvFTD. In this cross-sectional study, our objectives were to investigate (1) whether bvFTD patients show higher delay discounting than healthy controls, (2) whether this maladaptive discounting correlates with impulsivity-related bvFTD symptoms, and (3) in which brain regions atrophy is related to bvFTDs steeper discounting. BvFTD patients (N=24) and matched controls (N=18) performed two delay discounting tasks: one with monetary rewards and one with food rewards. We compared discount rates (log(k)) in bvFTD patients and controls and tested their correlations with symptoms. We used participants structural MRI data and applied whole-brain mediation analyses to investigate brain structures mediating the effect of bvFTD on delay discounting. For both monetary and food rewards, delay discounting was significantly higher in bvFTD patients than in healthy controls. BvFTD patients higher discounting of both money and food was associated with their greater disinhibition and eating behaviour changes. Whole-brain mediation analyses revealed that (1) several brain regions (left thalamic pulvinar, left parahippocampal cortex, right temporal lobe) were predictive of steeper discounting of both money and food and (2) grey matter density in these brain regions, including most prominently the medial pulvinar, mediated the effect of bvFTD on discounting. The impulsive preference for sooner rewards captured by delay discounting might constitute a common mechanism of the behavioural symptoms of inhibition deficit and eating behaviour changes in bvFTD. Future studies could further investigate the potential role of medial pulvinar structural modifications as a transdiagnostic marker and a therapeutic target of impulsivity troubles.

neuroscience↗

Evolutionary sequence and structural basis for the distinct conformational landscapes of Tyr and Ser/Thr kinases

Protein kinases are molecular machines with rich sequence variation that distinguishes the two main evolutionary branches - tyrosine kinases (TKs) from serine/threonine kinases (STKs). Using a sequence co-variation Potts statistical energy model we previously concluded that TK catalytic domains are more likely than STKs to adopt an inactive conformation with the activation loop in an autoinhibitory "folded" conformation, due to intrinsic sequence effects. Here we investigated the structural basis for this phenomenon by integrating the sequence-based model with structure-based molecular dynamics (MD) to determine the effects of mutations on the free energy difference between active and inactive conformations, using a novel thermodynamic cycle involving many (n=108) protein-mutation free energy perturbation (FEP) simulations in the active and inactive conformations. The sequence and structure-based results are consistent and support the hypothesis that the inactive conformation "DFG-out Activation Loop Folded", is a functional regulatory state that has been stabilized in TKs relative to STKs over the course of their evolution via the accumulation of residue substitutions in the activation loop and catalytic loop that facilitate distinct substrate binding modes in trans and additional modes of regulation in cis for TKs.

biophysics↗

A new archaeal virus that suppresses the transcription of host immunity genes

In some extreme environments, archaeal cells have been shown to have chronic viral infections, and such infections are well-tolerated by the hosts and may potentially protect against more lethal infections by lytic viruses. We have discovered that a natural Haloferax strain (48N), which is closely related to the model organism Haloferax volcanii, is chronically-infected by a lemon-shaped virus, which we could purify from the medium. The chronic infection by this virus, which we named LSV-48N, is never cleared, despite the multiple defense systems of the host that include CRISPR-Cas, and two CBASS systems. Curing 48N of its virus by genetic engineering, led to radical changes in the gene expression profile of 48N and a dramatic improvement in its growth rate. Remarkably, the cured 48N is the fastest-growing haloarchaeon reported to date, with a generation time of approximately 1 hour at 45{degrees}C compared to the typical 2.5 hours of H. volcanii or its infected isogen, and faster than any known haloarchaeon. The virus subverts host defenses by reducing their transcription and interfering with the CRISPR spacer acquisition machinery. Our results suggest that the slow growth of many halophilic archaea could be due to the effects of proviruses within their genomes that consume resources and alter the gene expression of their hosts.

microbiology↗

Mouse Auditory Cortex Undergoes Asynchronous Maturation in the Right and Left Hemispheres

Despite the significance of lateralized auditory processing in human cognition, there are limited studies in animal models exploring the developmental mechanisms of this cortical specialization. Here, we find that cellular and network signs of maturity in the Auditory Cortex (ACx) appear earlier in the right hemisphere in male mice. We further demonstrate that persistent, experience dependent map reorganization is confined to the hemisphere that is actively maturing and can be differentially engaged by temporally limited manipulations of the sensory environment. Our data suggests that differential timing in hemisphere development could lead to lateralized auditory functioning.

neuroscience↗

Elucidating the molecular determinants for binding modes of a third-generation HIV-1 integrase strand transfer inhibitor: Importance of side chain and solvent reorganization

The first and second-generation clinically used HIV-1 integrase (IN) strand transfer inhibitors (INSTIs) are key components of antiretroviral therapy (ART), which work by blocking the integration step in the HIV-1 replication cycle that is catalyzed by a nucleoprotein assembly called an intasome. However, resistance to even the latest clinically used INSTIs is beginning to emerge. Developmental third-generation INSTIs, based on naphthyridine scaffold, are promising candidates to combat drug-resistant viral variants. Among these novel INSTIs, compound 4f exhibits two distinct conformations when binding to intasomes from HIV-1 and the closely related prototype foamy virus (PFV), despite the high structural similarity of their INSTI binding pockets. The molecular mechanism and the key active site residues responsible for these differing binding modes in closely related intasomes remain elusive. To unravel the molecular determinants governing the two distinct binding modes, we employ a novel molecular dynamics-based free energy approach that utilizes alchemical pathways to overcome the sampling challenges associated with transitioning between two ligand conformations within crowded environments along physical pathways. The calculated conformational free energies successfully recapitulate the experimentally observed binding mode preferences in the two viral intasomes. Analysis of the simulated structures suggests that the observed binding mode preferences are caused by amino acid residue differences in both the front and the central catalytic sub-pocket of the INSTI binding site in HIV-1 and PFV. Additional free energy calculations on mutants of HIV-1 and PFV revealed that while both sub-pockets contribute to the binding mode selection, the central sub-pocket plays a more important role. These results highlight the importance of both side chain and solvent reorganization, as well as the conformational entropy in determining the ligand binding mode and will help inform the development of more effective INSTIs for combatting drug-resistant viral variants.

biophysics↗

Temporal genomic analysis of melanoma rejection identifies regulators of tumor immune evasion

Decreased intra-tumor heterogeneity (ITH) correlates with increased patient survival and immunotherapy response. However, even highly homogenous tumors may display variability in their aggressiveness, and how immunologic-factors impinge on their aggressiveness remains understudied. Here we studied the mechanisms responsible for the immune-escape of murine tumors with low ITH. We compared the temporal growth of homogeneous, genetically-similar single-cell clones that are rejected vs. those that are not- rejected after transplantation in-vivo using single-cell RNA sequencing and immunophenotyping. Non- rejected clones showed high infiltration of tumor-associated-macrophages (TAMs), lower T-cell infiltration, and increased T-cell exhaustion compared to rejected clones. Comparative analysis of rejection- associated gene expression programs, combined with in-vivo CRISPR knockout screens of candidate mediators, identified Mif (macrophage migration inhibitory factor) as a regulator of immune rejection. Mif knockout led to smaller tumors and reversed non-rejection-associated immune composition, particularly, leading to the reduction of immunosuppressive macrophage infiltration. Finally, we validated these results in melanoma patient data. Statement of significanceHere, we uncover the association of Mif expression with tumor growth and aggressiveness, specifically in low ITH tumors. These findings could facilitate the development of new strategies to treat patients with homogeneous, high-MIF expressing tumors that are unresponsive to immune checkpoint therapy.

cancer biology↗

A bistable inhibitory OptoGPCR for multiplexed optogenetic control of neural circuits

Information is transmitted between brain regions through the release of neurotransmitters from long-range projecting axons. Understanding how the activity of such long-range connections contributes to behavior requires efficient methods for reversibly manipulating their function. Chemogenetic and optogenetic tools, acting through endogenous G-protein coupled receptor (GPCRs) pathways, can be used to modulate synaptic transmission, but existing tools are limited in sensitivity, spatiotemporal precision, or spectral multiplexing capabilities. Here we systematically evaluated multiple bistable opsins for optogenetic applications and found that the Platynereis dumerilii ciliary opsin (PdCO) is an efficient, versatile, light-activated bistable GPCR that can suppress synaptic transmission in mammalian neurons with high temporal precision in-vivo. PdCO has superior biophysical properties that enable spectral multiplexing with other optogenetic actuators and reporters. We demonstrate that PdCO can be used to conduct reversible loss-of-function experiments in long-range projections of behaving animals, thereby enabling detailed synapse-specific functional circuit mapping.

neuroscience↗

Lexical semantic content, not syntactic structure, is the main contributor to ANN-brain similarity of fMRI responses in the language network

Representations from artificial neural network (ANN) language models have been shown to predict human brain activity in the language network. To understand what aspects of linguistic stimuli contribute to ANN-to-brain similarity, we used an fMRI dataset of responses to n=627 naturalistic English sentences (Pereira et al., 2018) and systematically manipulated the stimuli for which ANN representations were extracted. In particular, we i) perturbed sentences word order, ii) removed different subsets of words, or iii) replaced sentences with other sentences of varying semantic similarity. We found that the lexical semantic content of the sentence (largely carried by content words) rather than the sentences syntactic form (conveyed via word order or function words) is primarily responsible for the ANN-to-brain similarity. In follow-up analyses, we found that perturbation manipulations that adversely affect brain predictivity also lead to more divergent representations in the ANNs embedding space and decrease the ANNs ability to predict upcoming tokens in those stimuli. Further, results are robust to whether the mapping model is trained on intact or perturbed stimuli, and whether the ANN sentence representations are conditioned on the same linguistic context that humans saw. The critical result--that lexical- semantic content is the main contributor to the similarity between ANN representations and neural ones--aligns with the idea that the goal of the human language system is to extract meaning from linguistic strings. Finally, this work highlights the strength of systematic experimental manipulations for evaluating how close we are to accurate and generalizable models of the human language network.

neuroscience↗

Temporal Evolution of the HIV Viral Population under Drug Selection Pressure

Drug resistance in human immunodeficiency virus (HIV) is a pervasive problem that affects the lives of millions of people worldwide. Although records of drug-resistant mutations (DRMs) have been extensively tabulated within public repositories, our understanding of the evolutionary kinetics of DRMs and how they evolve together remains limited. Epistasis, the interactions between a DRM and other residues in HIV protein sequences, is found to be key to the temporal evolution of drug resistance. We use a Potts sequence-covariation statistical-energy model of HIV protein fitness under drug selection pressure, which captures epistatic interactions between all positions, combined with kinetic Monte-Carlo simulations of sequence evolutionary trajectories, to explore the acquisition of DRMs as they arise in an ensemble of drug-naive patient protein sequences. We follow the time course of 52 DRMs in the enzymes protease, reverse transcriptase, and integrase, the primary targets of antiretroviral therapy (ART). The rates at which DRMs emerge are highly correlated with their observed acquisition rates reported in the literature when drug pressure is applied. This result highlights the central role of epistasis in determining the kinetics governing DRM emergence. Whereas rapidly acquired DRMs begin to accumulate as soon as drug pressure is applied, slowly acquired DRMs are contingent on accessory mutations that appear only after prolonged drug pressure. We provide a foundation for using computational methods to determine the temporal evolution of drug resistance using Potts statistical potentials, which can be used to gain mechanistic insights into drug resistance pathways in HIV and other infectious agents. SignificanceHIV affects the lives of millions of patients worldwide; cases of pan-resistant HIV are emerging. We use kinetic Monte-Carlo methods to simulate the evolution of drug resistance based on HIV patient-derived sequence data available on public databases. Our simulations capture the timeline for the evolution of DRMs reported in the literature across the major drug-target enzymes - PR, RT, and IN. The network of epistatic interactions with the primary DRMs determines the rate at which DRMs are acquired. The timeline is not explained by the overall fitness of the DRMs or features of the genetic code. This work provides a framework for the development of computational methods that forecast the time course over which drug resistance to antivirals develops in patients.

biophysics↗

Adaptive nanopore sequencing for single cell characterization of cancer mutations and gene rearrangements

In this proof-of-concept study, we developed a single cell method that identifies somatic alterations found in coding regions of mRNAs and integrates these mutation genotypes with their matching cell transcriptomes. We used nanopore adaptive sampling on single cell cDNA libraries, generated long read sequences from target gene transcripts and identified coding variants among individual cells. Short-read single cell transcriptomes characterized the cell types with mutations. We delineated CRISPR edits from a cancer cell line. From primary cancer samples, we targeted hundreds of cancer genes, identified somatic coding mutations and a gene rearrangement among individual tumor cells.

genomics↗