Biology subjects

Snyder, A.

Publications and source records attributed to Snyder, A..

14 recordsLinked to original sources

bioRxiv2026

A high throughput platform for measuring and predicting vitrification behavior in multicomponent aqueous solutions

Cryopreservation depends critically on suppression of ice formation by cryoprotective agents (CPAs), but limited data is available on the CPA concentration required for vitrification (Cv). Here, we introduce a high-throughput 384-well platform that integrates automated liquid handling, randomized plate layouts, and a binary-search strategy to rapidly determine Cv across hundreds of formulations. Relative to conventional methods, this approach increases throughput by [~]50-fold, compressing a year of measurements into one week, while markedly reducing manual labor. Across [~]200 CPA compositions, we demonstrate that environmental boundary conditions strongly influence vitrification behavior: plates sealed with silicone mats exhibited lower Cv than open plates, indicating that sealed configurations promote vitrification. Further, the data reveal a decrease in Cv with increasing CPA molecular weight, consistent with enhanced ice suppression by larger molecules. We also present a simple mixture model that accurately predicts Cv for a broad range of CPA formulations, including mixtures containing up to seven CPAs (R{superscript 2} [≥] 0.93), and use this model to evaluate published CPA toxicity data to identify formulations that operate near their vitrification threshold while maintaining relatively low toxicity. Together, these results establish a framework for rapid Cv determination, predictive modeling of vitrification behavior, and rational design of CPA formulations.

bioengineering↗

bioRxiv2024

Sex differences in the clinical manifestation of autosomal dominant frontotemporal dementia

INTRODUCTIONSex differences are apparent in neurodegenerative diseases, but have not been comprehensively characterized in frontotemporal dementia (FTD). METHODSParticipants included 337 adults with autosomal dominant FTD enrolled in the ALLFTD Consortium. Clinical assessments and plasma were collected annually for up to six years. Linear mixed-effects models investigated how sex and disease stage associated with longitudinal trajectories of cognition, function, and neurofilament light chain (NfL). RESULTSWhile sex differences were not apparent at asymptomatic stages, females showed more rapid declines across all outcomes in symptomatic stages compared to males. In asymptomatic participants, the association between baseline NfL and clinical trajectories was weaker in females versus males, a difference that attenuated in symptomatic participants. DISCUSSIONIn genetic FTD, females show cognitive resilience in early disease stages followed by steeper clinical declines later in disease. Baseline NfL may be a less sensitive prognostic tool for clinical progression in females with FTD-causing mutations.

neuroscience↗

bioRxiv2024

Neural Dynamics Underlying False Alarms in Extrastriate Cortex

The unfolding of neural population activity can be approximated as a dynamical system. Stability in the latent dynamics that characterize neural population activity has been linked with consistency in animal behavior, such as motor control or value-based decision-making. However, whether similar dynamics characterize perceptual activity and decision-making in the visual cortex is not well understood. To test this, we recorded V4 populations in monkeys engaged in a non-match-to-sample visual change-detection task that required sustained engagement. We measured how the stability in the latent dynamics in V4 might affect monkeys perceptual behavior. Specifically, we reasoned that unstable sensory neural activity around dynamic attractor boundaries may make animals susceptible to taking incorrect actions when withholding action would have been correct ("false alarms"). We made three key discoveries: 1) greater stability was associated with longer trial sequences; 2) false alarm rate decreased (and reaction times slowed) when neural dynamics were more stable; and, 3) low stability predicted false alarms on a single-trial level, and this relationship depended on the elapsed time during the trial, consistent with the latent neural state approaching an attractor boundary. Our results suggest the same outward false alarm behavior can be attributed to two different potential strategies that can be disambiguated by examining neural stability: 1) premeditated false alarms that might lead to greater stability in population dynamics and faster reaction time and 2) false alarms due to unstable sensory activity consistent with misperception.

neuroscience↗

bioRxiv2024

TDP43 autoregulation gives rise to shortened isoforms that are tightly controlled by both transcriptional and post-translational mechanisms

The nuclear RNA-binding protein TDP43 is integrally involved in the pathogenesis of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Previous studies uncovered N-terminal TDP43 isoforms that are predominantly cytosolic in localization, highly prone to aggregation, and enriched in susceptible spinal motor neurons. In healthy cells, however, these shortened (s)TDP43 isoforms are difficult to detect in comparison to full-length (fl)TDP43, raising questions regarding their origin and selective regulation. Here, we show that sTDP43 is created as a byproduct of TDP43 autoregulation and cleared by nonsense mediated RNA decay (NMD). The sTDP43-encoding transcripts that escape NMD can lead to toxicity but are rapidly degraded post-translationally. Circumventing these regulatory mechanisms by overexpressing sTDP43 results in neurodegeneration in vitro and in vivo via N-terminal oligomerization and impairment of flTDP43 splicing activity, in addition to RNA binding-dependent gain-of-function toxicity. Collectively, these studies highlight endogenous mechanisms that tightly regulate sTDP43 expression and provide insight into the consequences of aberrant sTDP43 accumulation in disease.

neuroscience↗

bioRxiv2023

Automated customization of large-scale spiking network models to neuronal population activity

Understanding brain function is facilitated by constructing computational models that accurately reproduce aspects of brain activity. Networks of spiking neurons capture the underlying biophysics of neuronal circuits, yet the dependence of their activity on model parameters is notoriously complex. As a result, heuristic methods have been used to configure spiking network models, which can lead to an inability to discover activity regimes complex enough to match large-scale neuronal recordings. Here we propose an automatic procedure, Spiking Network Optimization using Population Statistics (SNOPS), to customize spiking network models that reproduce the population-wide covariability of large-scale neuronal recordings. We first confirmed that SNOPS accurately recovers simulated neural activity statistics. Then, we applied SNOPS to recordings in macaque visual and prefrontal cortices and discovered previously unknown limitations of spiking network models. Taken together, SNOPS can guide the development of network models and thereby enable deeper insight into how networks of neurons give rise to brain function.

neuroscience↗

bioRxiv2023

HIV-1 resistance to islatravir/tenofovir combination therapy in wild-type or NRTI resistant strains of diverse HIV-1 subtypes

Tenofovir disoproxil fumarate (TDF) and islatravir (ISL, 4-ethynyl-2-fluoro-2-deoxyadensine, or MK-8591) are highly potent nucleoside reverse transcriptase inhibitors. Resistance to TDF and ISL is conferred by K65R and M184V, respectively. Furthermore, K65R and M184V increase sensitivity to ISL and TDF, respectively. Therefore, these two nucleoside analogs have opposing resistance profiles and could present a high genetic barrier to resistance. To explore resistance to TDF and ISL in combination, we performed passaging experiments with HIV-1 WT, K65R, or M184V in the presence of ISL and TDF. We identified K65R, M184V, and S68G/N mutations. The mutant most resistant to ISL was S68N/M184V, yet it remained susceptible to TDF. To further confirm our cellular findings, we implemented an endogenous reverse transcriptase assay to verify in vitro potency. To better understand the impact of these resistance mutations in the context of global infection, we determined potency of ISL and TDF against HIV subtypes A, B, C, D, and circulating recombinant forms (CRF) 01_AE and 02_AG with and without resistance mutations. In all isolates studied, we found K65R imparted hypersensitivity to ISL whereas M184V conferred resistance. We demonstrated that the S68G polymorphism can enhance fitness of drug-resistant mutants in some genetic backgrounds. Collectively, the data suggest that the opposing resistance profiles of ISL and TDF suggest that a combination of the two drugs could be a promising drug regimen for the treatment of patients infected with any HIV-1 subtype, including those who have failed 3TC/FTC-based therapies.

microbiology↗

bioRxiv2022

Real-time imaging of mitochondrial redox reveals increased mitochondrial oxidative stress associated with amyloid beta aggregates in vivo in a mouse model of Alzheimer's disease

BackgroundReactive oxidative stress is a critical player in the amyloid beta (A{beta}) toxicity that contributes to neurodegeneration in Alzheimers disease (AD). Mitochondrial damage, observed in AD, is one of the main sources of reactive oxygen species. Although A{beta} causes neuronal mitochondria-associated reactive oxidative stress in vitro, this has never been directly observed in the in vivo living brain. Here, we tested whether A{beta} plaques and soluble oligomers induce mitochondrial oxidative stress in surrounding neurons in vivo, and whether the neurotoxic effect can be abrogated using mitochondrial-targeted antioxidants. MethodsWe expressed a genetically encoded fluorescent ratiometric mitochondria-targeted reporter of oxidative stress in mouse models of the disease, and performed intravital multiphoton microscopy of neuronal mitochondria and A{beta} plaques. ResultsFor the first time, we demonstrated by direct observation exacerbated mitochondrial oxidative stress in neurons after both A{beta} plaque deposition and direct application of soluble oligomeric A{beta} onto the brain, and determined the most likely pathological sequence of events leading to oxidative stress in vivo. Oxidative stress could be inhibited by both blocking calcium influx into mitochondria and treating with the mitochondria-targeted antioxidant SS31. ConclusionsConsidering these results, mitochondria-targeted compounds hold promise as neuroprotective drugs for the prevention and/or treatment of AD.

neuroscience↗

bioRxiv2021

Task Demands Change Motion Information Coding in Area MT of the Macaque

Neurons in the primate Middle Temporal (MT) area signal information about visual motion and work together with the lateral prefrontal cortex (LPFC) to support memory-guided comparisons of visual motion direction. These areas are reciprocally connected, and both contain neurons that signal visual motion direction in the strength of their responses. Previously, LPFC was shown to display marked changes in stimulus coding with altered task demands, including changes in selectivity for motion direction, trial-to-trial variability in responses, and comparison effects. Since MT and LPFC are directly interconnected, we sought to determine if MT neurons display similar dependence on task demands. We found that active participation in a motion direction comparison task affected both sensory and non-sensory activity in MT neurons. In fact, neurons that became less-selective for motion direction during the active task showed increased signalling for cognitive aspects of the task. This heterogeneity in neural modification with heightened task demands suggests a division of labor in MT, whereby sensory and cognitive signals are both heightened in different subpopulations of neurons.

neuroscience↗

bioRxiv2019

Computed Tomography Measures of Inter-site tumor Heterogeneity for Classifying Outcomes in High-Grade Serous Ovarian Carcinoma: a Retrospective Study

AbstractO_ST_ABSBackgroundC_ST_ABSHigh grade serous ovarian carcinoma shows marked intra-tumoral heterogeneity which is associated with decreased survival and resistance to platinum-based chemotherapy. Pre-treatment quantification of spatial tumor heterogeneity by multiple tissue sampling is not clinically feasible. Using standard-of-care CT imaging to non-invasively quantify heterogeneity could have high clinical utility and would be highly cost-effective. Texture analysis measures local variations in computed tomography (CT) image intensity. Haralick texture methods are typically used to capture the heterogeneity of entire lesions; however, this neglects the possible presence of texture habitats within the lesion, and the differences between metastatic sites. The primary aim of this study was to develop texture analysis of intra-site and inter-site spatial heterogeneity from standard-of-care CT images and to correlate these measures with clinical and genomic features in patients with HGSOC. Methods and findingsWe analyzed the data from a retrospective cohort of 84 patients with HGSOC consisting of 46 patients from Memorial Sloan Kettering Cancer Center (MSKCC) and 38 non-MSKCC cases selected from The Cancer Imaging Archive (TCIA). Inclusion criteria consisted of FIGO stage II-IV HGSOC, attempted primary cytoreductive surgery, intravenous contrast-enhanced CT of abdomen and pelvis performed prior to surgery and availability of molecular tumor data analysed as per the Cancer Genome Atlas (TCGA) Research Network ovarian cancer project. Manual segmentation and image analysis was performed on 463 metastatic tumor sites from 84 patients. In the MSKCC cohort the median number of tumor sites was 7 (interquartile range 5-9) and 4 (interquartile range 3-4) in the TCIA patients. Sub-regions were produced within each tumor site by grouping voxels with similar Haralick texture using the Kernel K-means method. We derived statistical measures of intra- and inter-site tumor heterogeneity (IISTH) including cluster sites entropy (cSE), cluster sites standard deviation (cluDev) and cluster sites dissimilarity (cluDiss) from sub-regions identified within and between individual tumor sites. Unsupervised clustering was used to group patient IISTH measures into low, medium, high, and ultra-high heterogeneity clusters from each cohort. The IISTH measure cluDiss was an independent predictor of progression-free survival (PFS) in multivariable analysis in both datasets (MSKCC hazard ratio [HR] 1.04, 95% CI 1.01-1.06, P = 0.002; TCIA HR 1.05, 95% CI 1.00-1.10, P = 0.049). Low and medium IISTH clusters were associated with longer PFS in multivariable analysis (MSKCC HR 2.94, 90% CI 1.29-6.70, P = 0.009, TCIA HR 5.94, 95% CI 1.05-33.6, P = 0.044). IISTH measures were robust to differences in the CT imaging systems. Average Haralick textures contrast (TCIA HR 1.08, 95% CI 1.01-1.10, P = 0.019) and homogeneity (TCIA HR 1.09, 95% CI 1.02-1.16, P = 0.008) were associated with PFS in mutivariate analysis only in the TCIA dataset. All other average Haralick textures and total tumor volume were not associated with PFS in either dataset. ConclusionsTexture measures of intra- and inter-site tumor heterogeneity from standard of care CT images are correlated with shorter PFS in HGSOC patients. These quantitative methods are independent of the CT imaging system and can thus be applied in clinical practice. The methodology proposed here enables the non-invasive quantification of intra-tumoral heterogeneity and disease stratification for future experimental medicine studies and clinical trials, particularly in cases where total tumour volume and averaged textures have low predictive power. Author summaryO_ST_ABSWhy was this study done?C_ST_ABSO_LITumor heterogeneity is a feature of many solid malignancies including ovarian cancer. C_LIO_LIRecent genomic research suggests that intra-site tumor heterogeneity (heterogeneity within a single tumor site) and inter-site tumor heterogeneity (heterogeneity between different metastatic sites in the same patient) correlate with clinical outcome in HGSOC. C_LI What did the researchers do and find?O_LIWe developed quantitative and non-invasive image-analysis based measures for predicting outcome in HGSOC patients by combining image-based information from within and between multiple tumor sites. C_LIO_LIUsing datasets from two sources, we demonstrate that these image-based tumor heterogeneity measures predict progression free survival in patients with HGSOC. C_LI What do these findings mean?O_LINon-invasive measures of CT image heterogeneity may predict outcomes in HGSOC patients. C_LIO_LIWider application of these CT image heterogeneity measures could prove useful for stratifying patients to different therapies given that total tumour volume and averaged textures have low predictive power. C_LI

bioinformatics↗

bioRxiv2018

Unraveling Tumor-Immune Heterogeneity in Advanced Ovarian Cancer Uncovers Immunogenic Effect of Chemotherapy

In metastatic cancer, the role of heterogeneity at the tumor-immune microenvironment, its molecular underpinnings and clinical relevance remain largely unexplored. To understand tumor-immune dynamics at baseline and upon chemotherapy treatment, we performed unbiased pathway and cell type-specific immunogenomics analysis of treatment-naive (38 samples from 8 patients) and paired chemotherapy treated (80 paired samples from 40 patients) high-grade serous ovarian cancer (HGSOC) samples. Whole transcriptome analysis and image-based quantification of T cells from treatment-naive tumors revealed ubiquitous variability in immune signaling and distinct immune microenvironments co-existing within the same individuals and within tumor deposits at diagnosis. To systematically explore cell type composition of the tumor microenvironment using bulk mRNA, we derived consensus immune and stromal cell gene signatures by intersecting state-of-the-art deconvolution methods, providing improved accuracy and sensitivity when compared to HGSOC immunostaining and leukocyte methylation data sets. Cell-type deconvolution and pathway analyses revealed that Myc and Wnt signaling associate with immune cell exclusion in untreated HGSOC. To evaluate the effect of chemotherapy on the intrinsic tumor-immune heterogeneity, we compared site-matched and site-unmatched tumors before and after neoadjuvant chemotherapy. Transcriptomic and T-cell receptor sequencing analyses showed that site-matched samples had increased cytotoxic immune activation and oligoclonal expansion of T cells after chemotherapy, which was not seen in site-unmatched samples where heterogeneity could not be accounted for. These results demonstrate that the tumor-immune interface in advanced HGSOC is intrinsically heterogeneous, and thus requires site-specific analysis to reliably unmask the impact of therapy on the tumor-immune microenvironment.

cancer biology↗

bioRxiv2017

A Multifactorial Model of T Cell Expansion and Durable Clinical Benefit in Response to a PD-L1 Inhibitor

Checkpoint inhibitor immunotherapies have had major success in treating patients with late-stage cancers, yet the minority of patients benefit [1]. Mutation load and PD-L1 staining are leading biomarkers associated with response, but each is an imperfect predictor. A key challenge to predicting response is modeling the interaction between the tumor and immune system. We begin to address this challenge with a multifactorial model for response to anti-PD-L1 therapy. We train a model to predict immune response in patients after treatment based on 36 clinical, tumor, and circulating features collected prior to treatment. We analyze data from 21 bladder cancer patients [2] using the elastic net high-dimensional regression procedure [3] and, as training set error is a biased and overly optimistic measure of prediction error, we use leave-one-out cross-validation to obtain unbiased estimates of accuracy on held-out patients. In held-out patients, the model explains 79% of the variance in T cell clonal expansion. This predicted immune response is multifactorial, as the variance explained is at most 23% if clinical, tumor, or circulating features are excluded. Moreover, if patients are triaged according to predicted expansion, only 38% of non-durable clinical benefit (DCB) patients need be treated to ensure that 100% of DCB patients are treated. In contrast, using mutation load or PD-L1 staining alone, one must treat at least 77% of non-DCB patients to ensure that all DCB patients receive treatment. Thus, integrative models of immune response may improve our ability to anticipate clinical benefit of immunotherapy.

cancer biology↗

bioRxiv2017

Global Cancer Transcriptome Quantifies Repeat Element Polarization Between Immunotherapy Responsive and T cell Suppressive Classes

Growing evidence indicates that innate immune pathway activation is critical for responses to immunotherapy and overall cancer prognosis. It has been posited that innate immunity in the tumor microenvironment can be driven by derepression of endogenous repetitive element RNA. The ability to characterize these species can potentially provide novel predictive biomarkers for tumor immune responses and a mechanistic basis for elements of innate activation by tumors. We first compared total RNA and poly(A)-capture protocols applied to tumor RNA-sequencing to detect non-RNA coding transcriptomes in the TCGA. While the poly(A) protocol efficiently detects coding, most non-coding genes, and much of the LINE/SINE/ERV repeat repertoire, we found that it fails to capture overall repeat expression and co-expression. The probing of total RNA expression reveals distinct repetitive co-expression subgroups. Secondly, we found that total repeat element expression delivers the most dynamic changes in samples, which may serve as more robust biomarkers of clinical outcomes. Finally, we show that while expression of ERVs, but not other immunostimulatory repeats such as HSATII, is associated with response to immunotherapy in a cohort of patients with urothelial cancer treated with anti-PD-L1 therapy, global repeat derepression strongly correlates with an immunosuppressive phenotype in the microenvironment of colorectal and pancreatic tumors. We validate in situ in human primary tumors, associating the immunosuppressive phenotype with HSATII expression. In conclusion, we demonstrate the importance of analyzing repetitive element RNAs as potential biomarkers of response to immunotherapy and the need to better characterize these features in next generation sequencing protocols.

cancer biology↗

bioRxiv2016

Somatic Mutations and Neoepitope Homology in Melanomas Treated with CTLA-4 Blockade

Immune checkpoint inhibitors are promising treatments for patients with a variety of malignancies. Toward understanding the determinants of response to immune checkpoint inhibitors, it was previously demonstrated that somatic mutation burden is associated with benefit and a hypothesis was posited that neoantigen homology to pathogens may in part explain the link between somatic mutations and response. To further examine this hypothesis, we reanalyzed cancer exome data obtained from a previously published study of 64 melanoma patients treated with CTLA-4 blockade and a new dataset of RNA-Seq data from 24 of those patients. We found that the predictive accuracy does not increase as analysis narrows from somatic mutation burden to predicted MHC Class I neoantigens, expressed neoantigens, or homology to pathogens. Further, the association between somatic mutation burden and response is only found when examining samples obtained prior to treatment. Neoantigen and expressed neoantigen burden are also associated with response, but neither is more predictive than somatic mutation burden. Neither the previously-described tetrapeptide signature nor an updated method to evaluate neoepitope homology to pathogens were more predictive than mutation burden.

cancer biology↗

bioRxiv2016

Multi-omic analysis of urothelial cancer patients treated with PD-L1 blockade demonstrates the contribution of both systemic and somatic factors to the biology of response and resistance

BackgroundInhibition of programmed death-ligand one (PD-L1) with atezolizumab can induce durable clinical benefit (DCB) in patients with metastatic urothelial cancers, including complete remissions in patients with chemotherapy refractory disease. Although mutation load and PD-L1 immune cell (IC) staining have been associated with response, they lack sufficient sensitivity and specificity for clinical use. Thus, there is a need to evaluate the peripheral blood immune environment and to conduct detailed analyses of mutation load, predicted neoantigens and immune cellular infiltration in tumors to enhance our understanding of the biologic underpinnings of response and resistance.\n\nMethods and FindingsThe goals of this study were to (1) evaluate the association of mutation load and predicted neoantigen load with therapeutic benefit, and (2) determine whether intratumoral and peripheral blood T cell receptor (TCR) clonality inform clinical outcomes in urothelial carcinoma treated with atezolizumab. We hypothesized that an elevated mutation load in combination with T cell clonal dominance among intratumoral lymphocytes prior to treatment or among peripheral T cells after treatment would be associated with effective tumor control upon treatment with anti-PD-L1 therapy. We performed whole exome sequencing (WES), RNA sequencing (RNA-seq), and T cell receptor sequencing (TCR-seq) of pre-treatment tumor samples as well as TCR sequencing of matched, serially collected peripheral blood collected before and after treatment with atezolizumab. These parameters were assessed for correlation with DCB (defined as progression free survival (PFS) > 6 months), PFS, and overall survival (OS), both alone and in the context of clinical and intratumoral parameters known to be predictive of survival in this disease state.\n\nPatients with DCB displayed a higher proportion of tumor infiltrating T lymphocytes (TIL) (n=24, Mann-Whitney p=0.047). Pre-treatment peripheral blood TCR clonality below the median was associated with improved PFS (n=29, log-rank p=0.048) and OS (n=29, log-rank p=0.011). Patients with DCB also demonstrated more substantial expansion of tumor-associated TCR clones in the peripheral blood 3 weeks after starting treatment (n=22, Mann-Whitney p=0.022). The combination of high pre-treatment peripheral blood TCR clonality with elevated PD-L1 IC staining in tumor tissue was strongly associated with poor clinical outcomes (n=10, HR (mean)=89.88, HR (median)=23.41, 95% CI (2.43, 506.94), p(HR>1)=0.0014). Marked variations in mutation loads were seen with different somatic variant calling methodologies, which in turn impacted associations with clinical outcomes. Missense mutation load, predicted neoantigen load and expressed neoantigen load did not demonstrate significant association with DCB (n=25, Mann-Whitney p=0.22, n=25, Mann-Whitney p=0.55, and n=25, Mann-Whitney p=0.29 respectively). Instead, we found evidence of time-varying effects of somatic mutation load on progression-free survival in this cohort (n=25, p=0.044). A limitation of our study is its small sample size (n=29), a subset of the patients treated on IMvigor 210 (NCT02108652). Given the number of exploratory analyses performed, we intend for these results to be hypothesis-generating.\n\nConclusionsThese results demonstrate the complex nature of immune response to checkpoint blockade and the compelling need for greater interrogation and data integration of both host and tumor factors. Incorporating these variables in prospective studies will facilitate identification and treatment of resistant patients.

cancer biology↗