Biology subjects

Agarwal, M.

Publications and source records attributed to Agarwal, M..

At least 19 recordsLinked to original sources

bioRxiv2026

VascFlexMap: Microvascular Ultrasound Imaging at Low Frame Rates Using Sparse Data and a Transformer-Decoder Network

ObjectiveSuper-resolution ultrasound (SR-US) reveals microvascular structures with exquisite resolution, but clinical translation remains limited by the need for ultrafast frame rates, massive data volumes, and long reconstruction times. This work proposes a deep learning framework that reconstructs microvascular maps from low-frame-rate enhanced ultrasound sequences, bypassing explicit microbubble localization and tracking. MethodsA transformer-decoder network with learned linear projections was designed to model spatiotemporal dependencies across sparse contrast-enhanced ultrasound sequences and reconstruct vessel probability maps, refined via a post-processing enhancement stage. Single-head self-attention captures temporal correlations under challenging conditions including overlapping microbubbles and low signal-to-noise ratios. Binary cross-entropy loss guided training to preserve vascular topology across synthetic and in vivo datasets. In vivo rat brain bolus data from the PALA challenge was used to evaluate this approach under up to 500 - fold data reduction (341 frames at 2 FPS vs. 170400 frames at 1000 FPS in standard ULM). ResultsDespite aggressive undersampling, the proposed pipeline recovered coherent microvascular architecture where conventional ULM pipelines applied to the same sparse data failed to produce continuous vascular networks. Major branches and higher-order microvessels remained visible with apparent vessel widths broadened by approximately three-fold relative to reference SR-US. End-to-end reconstruction completed in 28-133 seconds on an NVIDIA H100 GPU depending on the number of frames employed. ConclusionThe reported approach preserved vascular topology with fast reconstruction and low data overhead, albeit at lower resolution. The substantial reduction in frames and computation time highlights the translational potential of this SR-US-inspired microvascular imaging approach.

bioengineering↗

bioRxiv2026

The ER membrane protein complex acts as a chaperone to promote the biogenesis of multi-bundle membrane proteins

Nearly half of the [~]5,000 human membrane proteins need to assemble into stoichiometric complexes as part of their biogenesis at the endoplasmic reticulum (ER) membrane. How ER resident biogenesis factors coordinate membrane insertion, folding and assembly is not well understood. Here, we demonstrate that the ER membrane protein complex (EMC) insertase additionally acts as a chaperone to facilitate the assembly of heterotrimeric voltage-gated calcium channels (Cav). Using function-separating mutations and inhibitory nanobodies we show that nascent Cav channels are degraded prematurely when EMCs chaperone function is selectively perturbed. Blocking EMCs chaperone function strongly impaired Cav-dependent cardiomyocyte contraction. EMC engagement of the pore-forming Cav-subunit occurred co-translationally and required Cavs first transmembrane domain bundle to protrude from the nascent ribosome*Sec61*multipass translocon complex. Our findings establish a chaperone function for the EMC and reveal that biogenesis of multi-bundle membrane proteins requires a highly orchestrated, co-translational interplay between ER biogenesis factors.

cell biology↗

bioRxiv2025

Deep learning the dynamic regulatory sequence code of cardiac organoid differentiation

Defining temporal gene regulatory programs driving human organogenesis is essential for understanding congenital defects. We combined a time-resolved, single-cell multi-omic atlas of human induced pluripotent stem cell-derived cardiac organoids with deep learning models of chromatin accessibility, enabling systematic discovery of cis-regulatory syntax underlying heart development and disease. This framework identified cell-state-specific motif syntax, linked motif instances to candidate target genes, and resolved programs governing lineage divergence. Integrating cell-state-resolved molecular profiles with computationally predicted variant effects from congenital heart disease (CHD) cases enabled the prioritization of noncoding variants predicted to disrupt developmental transitions, supporting the paradigm that disease etiology derives from perturbations to regulatory networks governing cardiogenesis. Experimental validation demonstrated that an intronic ANGPTL2 variant altered differentiation outcomes, implicating ANGPTL2 in CHD. This study bridges developmental regulation with disease genetics, establishing a framework for discovering the genetic and molecular basis of congenital disorders.

genetics↗

bioRxiv2025

Lysyl oxidase-dependent bone marrow stiffening promotes neutrophil activation in diabetes

Persistent neutrophil activation contributes to the development of diabetic vascular complications in many organs including the retina. Past studies have implicated abnormal molecular or biochemical cues in neutrophil activation. Here we show that neutrophils can also be mechanically activated through an increase in bone marrow (BM) stiffness that results from diabetes-induced overexpression of matrix collagens and their crosslinker lysyl oxidase (LOX). Administration of LOX inhibitor {beta}-aminopropionitrile (BAPN) in diabetic mice concomitantly blocked BM matrix stiffening and neutrophil activation (superoxide generation and gp91phox upregulation), which predictably inhibited neutrophil cytotoxicity towards co-cultured retinal endothelial cells. Further, culturing neutrophils within BM-mimicking hydrogels of tunable stiffness indicate that matrix-localized and soluble LOX act synergistically to mechanochemically activate neutrophils in the BM. Thus, LOX-dependent changes in the BM physical environment offer a new mechanistic basis and therapeutic target for diabetic complications marked by neutrophil activation.

pathology↗

bioRxiv2025

Yeast two-hybrid screening identifies Dad1 as a candidate substrate of Hrr25 kinase in Saccharomyces cerevisiae

In Saccharomyces cerevisiae, sister kinetochores are mono-oriented during meiosis I, ensuring that homologous chromosomes segregate to opposite poles, a process critically dependent on the kinase activity of Hrr25, a casein kinase. However, the direct substrates of Hrr25 involved in this mechanism remain poorly defined. In this study, we used a yeast two-hybrid (Y2H) approach to screen for and identify physical interactors of Hrr25. The HRR25 gene was cloned into a Y2H bait vector, and its functional expression was confirmed by complementation of a temperature-sensitive hrr25-ts mutant. Screening independent Y2H libraries in three reading frames, followed by validation via reporter assays, restriction analysis, and sequencing, we identified six putative interactors: HED1, DAD1, YDR015C (from clone C1-5), REP1 (C2-15), and CYR1 and SYS1 (C3-7). Phosphorylation site prediction and AlphaFold 3.0 structural modeling identified high-confidence Hrr25 target residues, including S70/T73 on Hed1 and S63 on Dad1, S323 on Rep1, and S198/S527 on Cyr1, each located in structurally accessible and potentially functional regions. Plasmid-dependent assays confirmed that reporter activation in C1-5 depended on the presence of the prey plasmid, and restriction mapping demonstrated that C1-5 contained a full-length DAD1 ORF. Given Dad1s known role in DASH/Dam1 kinetochore complex and its function in kinetochore-microtubule attachment, along with previous findings that DAD1 mutations cause meiosis I defects, our data suggest that Dad1 may be a substrate of Hrr25. We propose that Hrr25-mediated phosphorylation of Dad1 could facilitate sister kinetochore co-orientation during meiosis I. These results provide new insights into the molecular mechanisms of chromosome segregation and identify Dad1 as a potential candidate substrate for Hrr25 in meiotic regulation.

cell biology↗

bioRxiv2025

Restriction of HIV-1 infectivity by interferon and IFITM3 is counteracted by Nef

The viral accessory protein Nef is a major determinant of HIV-1 pathogenicity in vivo. Nef is a multifunctional, immunomodulatory protein that downmodulates cell surface proteins, including CD4 and MHC class I (MHC-I) important for T-cell-mediated immunity. In addition, Nef also regulates cell-intrinsic immunity--Nef boosts the infectivity of virions produced and released from HIV-infected cells, at least in part, by counteracting the antiviral activity of transmembrane proteins SERINC3 and SERINC5. However, it has been reported that the enhancement of HIV-1 infectivity by Nef persists in certain cell lines deficient for SERINC3/5, revealing the existence of other Nef-sensitive host factors that impact HIV-1 infectivity. Here, we show that Nef proteins, especially those derived from many primary isolates of HIV-1, restore infectivity in interferon-treated cells and confer resistance to interferon-induced transmembrane protein 3 (IFITM3). IFITM3 is a restriction factor that reduces retroviral infectivity by incorporating into virions, inhibiting Envelope glycoprotein function, and reducing entry into cells. Using a primary isolate of Nef derived from HIV-1 clade C, we found that Nef interacts with IFITM3 in membranes and uses the endocytic adaptor protein AP-2 to counteract it. Furthermore, Nef reduced IFITM3 cell surface levels, increased IFITM3 levels in early endosomes, and reduced IFITM3 incorporation into HIV-1 virions. Nef also impaired IFITM3 oligomerization and restored membrane fluidity in IFITM3-expressing cells. The antiviral activity of IFITM3 and its inhibition by Nef were unaffected by SERINC5 knockdown, suggesting that the counteraction of IFITM3 represents a unique function of Nef. Our findings reveal a previously unrecognized immunomodulatory role for Nef in the setting of the interferon-induced antiviral state during HIV-1 infection.

microbiology↗

bioRxiv2025

Lysyl oxidase promotes actin-dependent neutrophil activation and cytotoxicity in diabetes: Implications for diabetic retinopathy

Activated neutrophils contribute to retinal endothelial cell (EC) death and capillary degeneration associated with early diabetic retinopathy (DR). However, the factors and mechanisms driving neutrophil activation and cytotoxicity in diabetes remain insufficiently understood. Here we show that lysyl oxidase (LOX), a collagen crosslinking and matrix stiffening enzyme that increases retinal EC susceptibility to activated neutrophils, simultaneously activates neutrophils in its alternate soluble form. Specifically, treatment of diabetic mice with LOX inhibitor {beta}-aminopropionitrile (BAPN) prevented the diabetes-induced increase in neutrophil activation (extracellular release of neutrophil elastase and superoxide) and cytotoxicity towards co-cultured mouse retinal ECs. Mouse neutrophils and differentiated (neutrophil-like) human HL-60 cells treated with recombinant LOX alone exhibited similar activation and cytotoxicity. Mechanistically, this LOX-induced neutrophil activation was associated with biphasic F-actin remodeling, with the initial and rapid (<15 min) F-actin depolymerization followed by a significant increase in F-actin polymerization and polarization. Preventing the initial F-actin depolymerization blocked LOX-induced neutrophil activation and cytotoxicity towards co-cultured retinal ECs. Finally, we show that this biphasic F-actin remodeling is essential for LOX-induced membrane clustering of azurophilic granule marker CD63 and NADPH organizer p47 that are associated with extracellular release of neutrophil elastase and superoxide, respectively. By revealing a causal and previously unrecognized link between LOX and actin-dependent neutrophil activation in diabetes, these findings provide fresh mechanistic insights into the proinflammatory role of LOX in early DR that goes beyond its canonical matrix-stiffening effects.

pathology↗

bioRxiv2024

Leveraging machine learning and accelerometry to classify animal behaviours with uncertainty

O_LIAnimal-worn sensors have revolutionised the study of animal behaviour and ecology. Accelerometers, which measure changes in acceleration across planes of movement, are increasingly being used in conjunction with machine learning models to classify animal behaviours across taxa and research questions. However, the widespread adoption of these methods faces challenges from imbalanced training data, unquantified uncertainties in model outputs, shifts in model performance across contexts, and noisy classifications in continuous data streams, where predicted behaviours change abruptly within a sequence. C_LIO_LITo address these challenges, we introduce an open-source approach for classifying animal behaviour from raw acceleration data. Our approach integrates machine learning and statistical inference techniques to evaluate and mitigate class imbalances, changes in model performance across ecological settings, and noisy classifications. Importantly, we extend predictions from single behaviour classifications to prediction sets: sets of behaviour labels guaranteed to contain the true behaviour with a pre-specified probability, in a framework analogous to the use of prediction intervals in statistical analyses. C_LIO_LIWe evaluate our approach via simulation and highlight its utility using data collected from a free-ranging large carnivore, African wild dogs (Lycaon pictus), in the Okavango Delta, Botswana. We demonstrate significantly improved predictions along with associated uncertainty metrics in African wild dog behaviour classification, particularly for rare and ecologically important behaviours such as feeding, where correct classifications more than doubled following quality checks and data rebalancing introduced in our pipeline. C_LIO_LIOur approach is applicable across taxa and represents a key step towards advancing the burgeoning use of machine learning to remotely observe around-the-clock behaviours of free-ranging animals. Future work could include the integration of multiple data streams, such as accelerometer, audio, and GPS data, for model training and could be incorporated directly into our pipeline. C_LI

ecology↗

bioRxiv2024

Stiffness Measurement of Retinal Capillaries and Subendothelial Matrix using Atomic Force Microscopy

Retinal capillary degeneration is a clinical hallmark of the early stages of diabetic retinopathy (DR). Our recent studies have revealed that diabetes-induced increase in retinal capillary stiffness plays a crucial and previously unrecognized causal role in inflammation-mediated degeneration of retinal capillaries. Retinal capillary stiffening results from overexpression of lysyl oxidase, an enzyme that crosslinks and stiffens the subendothelial matrix. Since tackling DR at the early stage is expected to prevent or slow down DR progression and associated vision loss, subendothelial matrix and capillary stiffness represent relevant and novel therapeutic targets for early DR management. Further, direct measurement of retinal capillary stiffness can serve as a crucial preclinical validation step for the development of new imaging techniques for non-invasive assessment of retinal capillary stiffness in animal and human subjects. With this view in mind, we here provide a detailed protocol for the isolation and stiffness measurement of mouse retinal capillaries and retinal subendothelial matrix using atomic force microscopy.

pathology↗

bioRxiv2023

CD8 T-cell dysfunction is linked with CAR T-cell failure and can be mitigated by a non-alpha IL-2 agonist, pegenzileukin

Chimeric antigen receptor (CAR) T-cell therapy has been a breakthrough for relapsed or refractory large B-cell lymphoma (rrLBCL). However, suboptimal CAR T-cell activity can lead to therapeutic failure and dismal outcome. Using single cell RNA-sequencing of rrLBCL tumors, we identify a prominent population of clonally expanded dysfunctional CAR+ CD8 T-cells indicative of ongoing tumor cell engagement, proliferation, and dysfunction at the time of progression from CAR T-cell therapy. Furthermore, we show that rrLBCL patient-derived CAR T-cells are more prone to dysfunction and loss of cytotoxicity compared to healthy donor-derived CAR T-cells. Using both antigen-driven and CAR-driven models of T-cell dysfunction, we show that pegenzileukin, a non-alpha IL2 agonist, can prevent T-cell dysfunction. In both in vitro and in vivo CAR T-cell models, pegenzileukin improved T-cell expansion and tumor control. This provides pre-clinical rational for use of pegenzileukin in combatting T-cell dysfunction, a central mechanism of CAR T-cell failure. HIGHLIGHTSO_LITumor-infiltrating CD8 CAR T-cells show clonal expansion and dysfunction at the time of progression. C_LIO_LIrrLBCL patient-derived CAR T-cells are more prone to dysfunction compared to healthy-donor-derived CAR T-cells. C_LIO_LIPegenzileukin, a non-alpha IL2 agonist, rescues antigen- and CAR-driven CD8 T-cell dysfunction and improves CAR T-cell responses in vivo. C_LI

immunology↗

bioRxiv2023

Comparative Genomic and Transcriptomic Analysis of Avirulent and Virulent Strains of Fusarium oxysporum f. sp. carthami: Insights into Pathogenesis and Virulence Determinants in Safflower Infections

Vascular wilt disease incited by Fusarium oxysporum f. sp. carthami (Foc) in Safflower poses a significant threat to its production in India. A comprehensive understanding of the molecular underpinning of compatible and incompatible interaction is of extreme economic importance. In the present study, the genome of a virulent (IARI-5175) and a avirulent (F-00845) Foc strain were sequenced and assembled using data generated from Illumina in combination with Nanopore technologies and HiC. Foc genomes were assembled into 88 and 23 scaffolds with an estimated total size of 46 Mb and 42 Mb respectively for IARI-5175 and F-00845 strains. Reference based mapping of Foc genome with F. oxysporum f. sp. lycopersici (Fol) resulted in chromosomal level ordering of genome and simultaneous identification of accessory genome. Additionally, two lineage specific chromosomes were also identified for virulent Foc strain IARI-5175. Genomic comparisons were made on the basis of effectors, CAZymes, secondary metabolites and mycotoxins to understand the global view pathogenicity in Foc. Moreover, the transcriptome of Foc during compatible and incompatible interaction was sequenced and analyzed leading to the identification of differentially regulated genes. Taken together our study laid a solid foundation to explore novel effector genes that play a crucial role in the establishment of disease and can further be used as targets to devise new strategies to curb wilt disease in safflower.

genomics↗

bioRxiv2022

Mechanical regulation of retinal vascular inflammation and degeneration in diabetic retinopathy

Vascular inflammation is known to cause degeneration of retinal vessels in early diabetic retinopathy (DR). Past studies investigating these diabetes-induced vascular abnormalities have focused primarily on the role of molecular or biochemical cues. Here we show that retinal vascular inflammation and degeneration in DR are also mechanically regulated by retinal vascular stiffening that is caused by overexpression of collagen-crosslinking enzyme lysyl oxidase (LOX) in retinal vessels. Treatment of diabetic mice with LOX inhibitor BAPN prevented the increase in retinal vascular stiffness, vascular ICAM-1 overexpression, and leukostasis. Consistent with these anti-inflammatory effects, BAPN treatment of diabetic mice blocked the upregulation of proapoptotic caspase-3 in retinal vessels, which concomitantly reduced retinal vascular degeneration and the diabetes-induced loss of contrast sensitivity in these mice. Finally, we show that increasing substrate stiffness alone increases the adhesiveness and neutrophil elastase-induced death of cultured retinal endothelial cells. By uncovering a link between LOX-dependent vascular stiffening and the development of retinal vascular and functional defects in diabetes, these findings offer unique insights into DR pathogenesis that has important translational potential.

pathology↗

bioRxiv2022

Lysyl oxidase-dependent subendothelial matrix stiffening promotes RAGE-mediated retinal endothelial activation in diabetes

Endothelial cell (EC) activation is a crucial determinant of retinal vascular inflammation associated with diabetic retinopathy (DR), a major microvascular complication of diabetes. We previously showed that, similar to abnormal biochemical factors, aberrant mechanical cues in the form of lysyl oxidase (LOX)-dependent subendothelial matrix stiffening also contribute significantly to retinal EC activation in diabetes. Yet, how LOX is itself regulated and precisely how it mechanically controls retinal EC activation in diabetes is poorly understood. Here we show that high glucose-induced LOX upregulation in human retinal ECs (HRECs) is mediated by proinflammatory RAGE (receptor for advanced glycation end products/AGEs). HRECs treated with methylglyoxal (MGO), an active precursor to the AGE MG-H1, exhibited LOX upregulation that was blocked by a RAGE inhibitor, thus confirming the ability of RAGE to promote LOX expression. Crucially, as a downstream effector of RAGE, LOX was found to mediate both the proinflammatory and matrix remodeling effects of MGO/RAGE, primarily through its ability to crosslink/stiffen matrix. Finally, using decellularized HREC-derived matrices and a mouse model of diabetes, we demonstrate that LOX-dependent matrix stiffening feeds back to enhance RAGE, thereby achieving its autoregulation and proinflammatory effects. These fresh insights into the regulation and proinflammatory role of LOX-dependent mechanical cues may help identify new therapeutic targets to block AGE/RAGE signaling in DR.

pathology↗

bioRxiv2021

Transcriptional and post-transcriptional regulation of young genes in plants

New genes continuously emerge from non-coding DNA or by diverging from existing genes, but most of them are rapidly lost and only a few become fixed within the population. We hypothesized that young genes are subject to transcriptional and post-transcriptional regulation to limit their expression and minimize their exposure to purifying selection. We found that young genes in rice have relatively low expression levels, which can be attributed to distal enhancers, and closed chromatin conformation at their transcription start sites (TSS). The chromatin in TSS regions can be re-modeled in response to abiotic stress, indicating conditional expression of young genes. Furthermore, transcripts of young genes in Arabidopsis tend to be targeted by nonsense-mediated RNA decay, presenting another layer of regulation limiting their expression. Together, these data suggest that transcriptional and post-transcriptional mechanisms contribute to the conditional expression of young genes, which may alleviate purging selection while providing an opportunity for phenotypic exposure and functionalization.

evolutionary biology↗

bioRxiv2021

WebSeq: A Genomic Data Analytics Platform for Monogenic Disease Discovery

Whole exome sequencing (WES) is commonly used to study monogenic diseases. The application of this sequencing technology has gained in popularity amongst clinicians and researchers as WES pricing has declined. The accumulation of WES data creates a need for a robust, flexible, scalable and easy-to-use analytics platform to allow researchers to gain biological insight from this genomic data. We present WebSeq, a self-contained server and web interface to facilitate intuitive analysis of WES data. WebSeq provides access to sophisticated tools and pipelines through a user-friendly and modern web interface. WebSeq has modules that support i) FASTQ to VCF conversion, ii) VCF to ANNOVAR1 CSV conversion, iii) family-based analyses for Mendelian disease gene discovery, iv) cohort-wide gene enrichment analyses, (v) an automated IGV2 browser, and (vi) a virtual gene panel analysis module. WebSeq Pro, our expanded pipeline, also supports SNP genotype analyses such as ancestry inference and kinship testing. WebSeq Lite, our minimal pipeline, supports family-based analyses, cohort-wide gene enrichment analyses, and a virtual gene panel along with the IGV2 browser module. We anticipate that the rigorous use of our web application will allow researchers to expedite discoveries from human genomic data3. WebSeq Lite, WebSeq, and WebSeq Pro are fully containerized using Docker4, run on all major operating systems, and are freely available for personal, academic, and non-profit use at http://bitly.ws/g6cn

bioinformatics↗

bioRxiv2021

Cell Stiffening Contributes to Complement-mediated Injury of Choroidal Endothelial Cells in Early AMD

Age-related macular degeneration (AMD) is the leading cause of blindness in the aging population. Yet, no therapies exist for [~]85% of all AMD patients who have the dry form that is marked by degeneration of the retinal pigment epithelium (RPE) and underlying choroidal vasculature. As the choroidal vessels are crucial for RPE development and maintenance, understanding how they degenerate may lead to effective therapies for dry AMD. One likely causative factor for choroidal vascular loss is the cytolytic membrane attack complex (MAC) of the complement pathway that is abundant on choroidal vessels of humans with early dry AMD. To examine this possibility, we studied the effect of complement activation on choroidal endothelial cells (ECs) isolated from a rhesus monkey model of early AMD that, we report, exhibits MAC deposition and choriocapillaris endothelial loss similar to that seen in human early AMD. Treatment of choroidal ECs from AMD eyes with complement-competent normal human serum caused extensive actin cytoskeletal injury that was significantly less pronounced in choroidal ECs from young normal monkey eyes. We further show that ECs from AMD eyes are significantly stiffer than their younger counterparts and exhibit peripheral actin organization that is distinct from the longitudinal stress fibers in young ECs. Finally, these differences in complement susceptibility and mechanostructural properties were found to be regulated by the differential activity of small GTPases Rac and Rho because Rac inhibition in AMD cells led to simultaneous reduction in stiffness and complement susceptibility while Rho inhibition in young cells exacerbated complement injury. Thus, by identifying cell stiffness and cytoskeletal regulators Rac and Rho as important determinants of complement susceptibility, the current findings offer a new mechanistic insight into choroidal vascular loss in early AMD that warrants further investigation for assessment of translational potential.

pathology↗

bioRxiv2021

Control of SARS-CoV-2 infection after Spike DNA or Spike DNA+Proteinco-immunization in rhesus macaques

The speed of development, versatility and efficacy of mRNA-based vaccines have been amply demonstrated in the case of SARS-CoV-2. DNA vaccines represent an important alternative since they induce both humoral and cellular immune responses in animal models and in human trials. We tested the immunogenicity and protective efficacy of DNA-based vaccine regimens expressing different prefusion-stabilized SARS-CoV-2 Spike antigens upon intramuscular injection followed by electroporation in rhesus macaques. Different Spike DNA vaccine regimens induced antibodies that potently neutralized SARS-CoV-2 in vitro and elicited robust T cell responses. The DNA-only vaccine regimens were compared to a regimen that included co- immunization of Spike DNA and protein in the same anatomical site, the latter of which showed significant higher antibody responses. All vaccine regimens led to control of SARS-CoV-2 intranasal/intratracheal challenge and absence of virus dissemination to the lower respiratory tract. Vaccine-induced binding and neutralizing antibody titers and antibody-dependent cellular phagocytosis inversely correlated with transient virus levels in the nasal mucosa. Importantly, the Spike DNA+Protein co-immunization regimen induced the highest binding and neutralizing antibodies and showed the strongest control against SARS-CoV-2 challenge in rhesus macaques. Author summaryAnti-Spike neutralizing antibodies provide strong protection against SARS-CoV-2 infection in animal models, and correlate with protection in humans, supporting the notion that induction of strong humoral immunity is key to protection. We show induction of robust antibody and T cell responses by different Spike DNA-based vaccine regimens able to effectively mediate protection and to control SARS-CoV-2 infection in the rhesus macaque model. This study provides the opportunity to compare vaccines able to induce different humoral and cellular immune responses in an effort to develop durable immunity against the SARS-CoV-2. A vaccine regimen comprising simultaneous co-immunization of DNA and Protein at the same anatomical site showed best neutralizing abilities and was more effective than DNA alone in inducing protective immune responses and controlling SARS-CoV-2 infection. Thus, an expansion of the DNA vaccine regimen to include co-immunization with Spike protein may be of advantage also for SARS-CoV-2.

immunology↗

bioRxiv2021

Radio-pathomic maps of cell density identify glioma invasion beyond traditional MR imaging defined margins

Current MRI signatures of brain cancer often fail to identify regions of hypercellularity beyond the contrast enhancing region. Therefore, this study used autopsy tissue samples aligned to clinical MRIs in order to quantify the relationship between intensity values and cellularity, as well as to develop a radio-pathomic model to predict cellularity using MRI data. This study used 93 samples collected at autopsy from 44 brain cancer patients. Tissue samples were processed, stained for hematoxylin and eosin (HE) and digitized for nuclei segmentation and cell density calculation. Pre- and post-gadolinium contrast T1-weighted images (T1, T1C), T2 fluid-attenuated inversion recovery (FLAIR) images, and apparent diffusion coefficient (ADC) images calculated from diffusion imaging were collected from each patients final acquisition prior to death. In-house software was used to align tissue samples to the FLAIR image via manually defined control points. Mixed effect models were used to assess the relationship between single image intensity and cellularity for each image. An ensemble learner was trained to predict cellularity using 5 by 5 voxel tiles from each image, employing a 2/3-1/3 train-test split for validation. Single image analyses found subtle associations between image intensity and cellularity, with a less pronounced relationship within GBM patients. The radio-pathomic model was able to accurately predict cellularity in the test set (RMSE = 1015 cells/mm2) and identified regions of hypercellularity beyond the contrast enhancing region. We concluded that a radio-pathomic model for cellularity is able to identify regions of hypercellular tumor beyond traditional imaging signatures.

neuroscience↗