Biology subjects

Nguyen, N.

Publications and source records attributed to Nguyen, N..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Integrated single cell spatial multi-omics landscape of WHO grades 2-4 diffuse gliomas identifies locoregional metabolomic regulators of glioma growth

Diffuse infiltrating gliomas are aggressive tumors of the central nervous system driven by intra-tumoral heterogeneity and aberrant normal-tumor cell-cell interactions. Grade specific and locoregional metabolic dependencies driving aberrant cell-states linked to treatment resistance, seizures and infiltration of gliomas remain elusive. Here, we applied spatial transcriptomics (stRNAseq), imaging mass cytometry (IMC) and mass spectrometry imaging (MSI; metabolites, peptides and glycans) to the core and edge tumor tissue from patients with World Health Organization (WHO) grades 2-4 diffuse infiltrating gliomas including isocitrate dehydrogenase (IDH) mutant oligodendrogliomas (WHO Grades 2 and 3) and IDH wildtype astrocytomas including anaplastic astrocytoma (prior 2016 WHO histological grade 3) and glioblastoma (GBM, WHO grade 4) stRNAseq identified regions-specific differentially expressed genes with significant overall survival implications particularly in IDH wildtype GBM. Integration of stRNA seq and MSI-derived metabolite expression demonstrated enrichment of L-glutamine in SOX4+ Neural progenitor-like (NPC-like) cells and DL-dopamine in GPNMB+ Mesenchymal-like (MES-like) GBM cells at the tumor edge relative to the core. Our results uncover clinically relevant and locoregional cell state-specific metabolites that may contribute to GBM proliferation, infiltration and seizures. This comprehensive pan-diffuse infiltrating glioma multi-omics study could serve as a resource for uncovering region-specific metabolic vulnerabilities encompassing metabolites, glycans and peptides within transcriptionally defined cell states across WHO 2-4 diffuse glioma.

cancer biology↗

bioRxiv2025

Predicting Mycobacterium abscessus proteins with atypical amino acid composition essential for human infections

Mycobacterium abscessus is an emerging opportunistic pathogen that causes chronic, difficult-to-treat lung infections, particularly in individuals with underlying lung disease or immune suppression. Despite its clinical significance, the fundamental biological systems of M. abscessus remain poorly understood due to limited research on this organism. Proteins that are unique to an organism are likely to contribute to the organisms distinctive phenotypic traits. Therefore, we initiated this study by identifying proteins with unique features, hypothesizing that such proteins could be critical for M. abscessus pathogenesis. To identify these proteins, we analyzed the genome sequence of the laboratory reference strain using bioinformatics tools to detect proteins with unusual amino acid compositions. We then examined the genomes of a large collection of patient-derived M. abscessus isolates to predict proteins essential for the pathogens ability to cause disease in humans. Our analysis identified 10 proteins--MAB_0010, MAB_0039, MAB_1134, MAB_1602, MAB_1657, MAB_3052, MAB_3131, MAB_3413, MAB_4263, and MAB_4537--that exhibit restricted evolutionary variation in human infections, similar to five known essential proteins DnaA, DnaN, RpoA, RpoB and RpoC which comprise proteins involved in DNA and RNA synthesis. A majority of these proteins lack sequence homology with proteins of known function and are currently annotated as proteins of unknown function. The unique amino acid compositions of these proteins, their limited capacity to tolerate mutations, and their apparent exclusivity to M. abscessus suggest that they play essential roles in the pathogens ability to establish and maintain infection in humans. These findings highlight potentially promising targets for future drug development aimed at combating M. abscessus infections.

microbiology↗

bioRxiv2025

Genome modeling and design across all domains of life with Evo 2

All of life encodes information with DNA. While tools for sequencing, synthesis, and editing of genomic code have transformed biological research, intelligently composing new biological systems would also require a deep understanding of the immense complexity encoded by genomes. We introduce Evo 2, a biological foundation model trained on 9.3 trillion DNA base pairs from a highly curated genomic atlas spanning all domains of life. We train Evo 2 with 7B and 40B parameters to have an unprecedented 1 million token context window with single-nucleotide resolution. Evo 2 learns from DNA sequence alone to accurately predict the functional impacts of genetic variation--from noncoding pathogenic mutations to clinically significant BRCA1 variants--without task-specific finetuning. Applying mechanistic interpretability analyses, we reveal that Evo 2 autonomously learns a breadth of biological features, including exon-intron boundaries, transcription factor binding sites, protein structural elements, and prophage genomic regions. Beyond its predictive capabilities, Evo 2 generates mitochondrial, prokaryotic, and eukaryotic sequences at genome scale with greater naturalness and coherence than previous methods. Guiding Evo 2 via inference-time search enables controllable generation of epigenomic structure, for which we demonstrate the first inference-time scaling results in biology. We make Evo 2 fully open, including model parameters, training code, inference code, and the OpenGenome2 dataset, to accelerate the exploration and design of biological complexity.

genomics↗

bioRxiv2024

A genetic safeguard for eliminating target genes in synthetic probiotics in a gut environment

Following the development of therapeutic probiotics, there is an emerging demand for constraining engineered microbial activities to ensure biosafety. Many biocontainment studies developed genetic devices that involve cell death and growth inhibition on the engineered microbes, which often create basal levels of cytotoxicity that hamper cell fitness and performance on therapeutic functions; furthermore, these toxic pathways may promote genetic instability that leads to mutations and breakdown of biocontainment circuit. To address this issue, here we explore a circuit design that destroys the engineered genetic materials in a probiotic strain, instead of killing these cells, under non-permissive conditions. Our safeguard circuit involves a two-layered transcriptional regulatory circuit to control the expression of a CRISPR system that targets the engineered genes for degradation. In Escherichia coli Nissle 1917 (EcN), the biocontainment system continuously scavenged and destroyed the target until no engineered cellular function could be detected, suggesting this strategy has the potential to avoid escapee formation. Additionally, this safeguard circuit did not affect EcN cell fitness. We further demonstrated that the engineered probiotics inhabited in mouse guts and continued the engineered activities for at least 7 days when the permissive signal was supplied constantly; when the permissive signal was not provided, the engineered activities became undetectable within two days. Together, these studies support that our safeguard design is feasible for synthetic probiotic applications. HIGHLIGHTSO_LIOur safeguard system only destroys target genes and does not kill the host microbes C_LIO_LIIt terminated engineered activities in guts in response to a loss of a signal C_LIO_LIThis safeguard allowed synthetic probiotics to inhabit in guts for at least a week C_LIO_LICellobiose has great potential to serve as a continuous genetic signal in guts C_LI

synthetic biology↗

bioRxiv2024

Limitations of the radiotheranostic concept in neuroendocrine tumors due to lineage-dependent somatostatin receptor expression on hematopoietic stem and progenitor cells

Radiopharmaceutical therapy (RPT) has become an effective treatment option for neuroendocrine tumors (NETs) and castration-resistant prostate cancer and is in clinical development for a growing number of indications. One of the major advantages of theranostic RPT is that the distribution of radiopharmaceuticals in the human body can be imaged, and radiation doses to the patients organs can be calculated. However, accurate dosimetry may be fundamentally limited by microscopic heterogeneity of radiopharmaceutical distribution. We developed fluorescent analogs of somatostatin-receptor-subtype 2 (SSTR2) targeting Lutetium-177 labelled radiopharmaceuticals that are clinically used in patients with neuroendocrine tumors (NETs) and studied their uptake by hematopoietic stem and progenitor cells (HSPC). Hematopoietic stem cells (HSCs) and multipotent progenitor cells (MPPs) showed high and specific SSTR2-ligand uptake, which was at similar levels as neuroendocrine tumor cells. Furthermore, they displayed a several-fold higher uptake of SSTR2-antagonists than of SSTR2-agonists. HSPC treatment with a 177Lu-labelled antagonist and agonist showed a stronger reduction of HSC proliferation by the antagonist. Due to the scarcity of HSCs and MPPs, their contribution to total bone marrow uptake of SSTR2-ligands is not detectable in imaging-based dosimetry studies. This likely explains why SSTR2-antagonists caused pancytopenia in clinical trials despite safe dosimetry estimates. In conclusion, target expression heterogeneity can lead to underestimation of radiopharmaceutical toxicity and should be considered when designing clinical trials for new radiopharmaceuticals. The implications of our findings go beyond somatostatin receptor-targeted radiopharmaceuticals and suggest more generally that first-in-human studies should not only be guided by radiation dosimetry from imaging studies but should also include careful escalation of the administered therapeutic activity. The MMC technology is modular and can be applied to other peptide or protein-based radiopharmaceuticals to study cellular distribution and potential bone marrow uptake prior to clinical testing.

cancer biology↗

bioRxiv2024

Early brain neuroinflammatory and metabolic changes identified by dual tracer microPET imaging in mice with acute liver injury

BackgroundAcute liver injury (ALI) that progresses into acute liver failure (ALF) is a life-threatening condition with an increasing incidence and associated costs. Acetaminophen (N-acetyl-p-aminophenol, APAP) overdosing is among the leading causes of ALI and ALF in the Northern Hemisphere. Brain dysfunction defined as hepatic encephalopathy is one of the main diagnostic criteria for ALF. While neuroinflammation and brain metabolic alterations significantly contribute to hepatic encephalopathy, their evaluation at early stages of ALI remained challenging. To provide insights, we utilized post-mortem analysis and non-invasive brain micro positron emission tomography (microPET) imaging of mice with APAP-induced ALI. MethodsMale C57BL/6 mice were treated with vehicle or APAP (600 mg/kg, i.p.). Serum alanine aminotransferase (ALT), aspartate aminotransferase (AST), liver damage (using H&E staining), hepatic and serum IL-6 levels, and hippocampal IBA1 (using immunolabeling) were evaluated at 24h and 48h. Vehicle and APAP treated animals also underwent microPET imaging utilizing a dual tracer approach, including [11C]-peripheral benzodiazepine receptor ([11C]PBR28) to assess microglia/astrocyte activation and [18F]-fluoro-2-deoxy-2-D-glucose ([18F]FDG) to assess energy metabolism. Brain images were pre-processed and evaluated using conjunction and individual tracer uptake analysis. ResultsAPAP-induced ALI and hepatic and systemic inflammation were detected at 24h and 48h by significantly elevated serum ALT and AST levels, hepatocellular damage, and increased hepatic and serum IL-6 levels. In parallel, increased microglial numbers, indicative for neuroinflammation were observed in the hippocampus of APAP-treated mice. MicroPET imaging revealed overlapping increases in [11C]PBR28 and [18F]FDG uptake in the hippocampus, thalamus, and habenular nucleus indicating microglial/astroglial activation and increased energy metabolism in APAP-treated mice (vs. vehicle-treated mice) at 24h. Similar significant increases were also found in the hypothalamus, thalamus, and cerebellum at 48h. The individual tracer uptake analyses (APAP vs vehicle) at 24h and 48h confirmed increases in these brain areas and indicated additional tracer- and region-specific effects including hippocampal alterations. ConclusionPeripheral manifestations of APAP-induced ALI in mice are associated with brain neuroinflammatory and metabolic alterations at relatively early stages of disease progression, which can be non-invasively evaluated using microPET imaging and conjunction analysis. These findings support further PET-based investigations of brain function in ALI/ALF that may inform timely therapeutic interventions.

physiology↗

bioRxiv2024

Airway basal stem cells are necessary for the maintenance of functional intraepithelial airway macrophages.

Adult stem cells play a crucial role in tissue homeostasis and repair through multiple mechanisms. In addition to being able to replace aged or damaged cells, stem cells provide signals that contribute to the maintenance and function of neighboring cells. In the lung, airway basal stem cells also produce cytokines and chemokines in response to inhaled irritants, allergens, and pathogens, which affect specific immune cell populations and shape the nature of the immune response. However, direct cell-to-cell signaling through contact between airway basal stem cells and immune cells has not been demonstrated. Recently, a unique population of intraepithelial airway macrophages (IAMs) has been identified in the murine trachea. Here, we demonstrate that IAMs require Notch signaling from airway basal stem cells for maintenance of their differentiated state and function. Furthermore, we demonstrate that Notch signaling between airway basal stem cells and IAMs is required for antigen-induced allergic inflammation only in the trachea where the basal stem cells are located whereas allergic responses in distal lung tissues are preserved consistent with a local circuit linking stem cells to proximate immune cells. Finally, we demonstrate that IAM-like cells are present in human conducting airways and that these cells display Notch activation, mirroring their murine counterparts. Since diverse lung stem cells have recently been identified and localized to specific anatomic niches along the proximodistal axis of the respiratory tree, we hypothesize that the direct functional coupling of local stem cell-mediated regeneration and immune responses permits a compartmentalized inflammatory response.

cell biology↗

bioRxiv2024

Modulation of ribosomal subunit associations by eIF6 is critical for mitotic exit and cancer progression.

Moderating the pool of active ribosomal subunits is critical for maintaining global translation rates. A factor crucial for modulating the 60S ribosomal subunits is eukaryotic translation initiation factor 6. Release of eIF6 from 60S is essential to permit 60S interactions with 40S. Here, using the N106S mutant of eIF6, we show that disrupting eIF6 interaction with 60S leads to an increase in vacant 80S. It further highlights a dichotomy in the anti-association activity of eIF6 that is distinct from its role in 60S biogenesis and shows that the nucleolar localization of eIF6 is not dependent on uL14-BCCIP interactions. Limiting active ribosomal pools markedly deregulates translation especially in mitosis and leads to chromosome segregation defects, mitotic exit delays and mitotic catastrophe. Ribo-Seq analysis of the eIF6-N106S mutant shows a significant downregulation in the translation efficiencies of mitotic factors and specifically transcripts with long 3'UTRs. eIF6-N106S mutation also limits cancer invasion, and this role is correlated with the overexpression of eIF6 only in high-grade invasive cancers suggesting that deregulation of eIF6 is probably not an early event in cancers. Thus, this study highlights the segregation of eIF6 functions and its role in moderating 80S availability for mitotic translation and cancer progression.

molecular biology↗

bioRxiv2024

A Patient-Specific Morphoelastic Growth Model of Aortic Dissection Evolution

The human aorta undergoes complex morphologic changes that indicate the evolution of disease. Finite element analysis enables the prediction of aortic pathologic states, but the absence of a biomechanical understanding hinders the applicability of this computational tool. We incorporate geometric information from computed tomography angiography (CTA) imaging scans into finite element analysis (FEA) to predict a trajectory of future geometries for four aortic disease patients. Through defining a geometric correspondence between two patient scans separated in time, a patient-specific FEA model can recreate the deformation of the aorta between the two time points, showing pathologic growth drives morphologic heterogeneity. A shape-size geometric feature space plotting the variance of the shape index versus the inverse square root of aortic surface area ({delta}[S] vs. [Formula]) quantitatively demonstrates the simulated breakdown in aortic shape. An increase in {delta}[S] closely parallels the true geometric progression of aortic disease patients.

bioengineering↗

bioRxiv2024

Systematic Development of Reprogrammed Modular Integrases Enables Precise Genomic Integration of Large DNA Sequences

Despite recent progress in the ability to manipulate the genomes of eukaryotic cells1-3, there is still no effective and practical method to precisely integrate large synthetic DNA constructs into desired chromosomal sites using a programmable integrase. Serine integrases can perform the necessary molecular steps4, but only if their natural target site is first installed into the recipient genome by other methods. A more elegant approach would be to directly reprogram the serine integrase itself to target a desired genomic site that is different from the natural recognition site of the integrase5. Here, we describe the development of a Modular Integrase (MINT) platform, a versatile protein-guided genome editing tool that can facilitate site-directed targeted integration (TI) of synthetic DNA into chromosomal sites. Through a combination of structural modeling, directed evolution, and screening in human cells we have reprogrammed the specificity of the serine integrase Bxb1. We demonstrate the therapeutic potential of the MINT platform by retargeting Bxb1 to the human AAVS1 and TRAC loci where wild-type Bxb1 has no detectable activity. By combining the MINT platform with known activity-increasing Bxb1 mutants, we achieved 14% TI at the AAVS1 locus, and by additionally fusing zinc finger DNA binding domains to engineered Bxb1 variants, we achieved 35% TI at the TRAC locus in human K562 cells. To further demonstrate clinical potential, we achieved stable 15% TI of a functional donor construct in human T cells.

synthetic biology↗

bioRxiv2024

Complex-based Ligand-Binding Proteins Redesign by Equivariant Diffusion-based Generative Models

Proteins, serving as the fundamental architects of biological processes, interact with ligands to perform a myriad of functions essential for life. Designing functional ligand-binding proteins is pivotal for advancing drug development and enhancing therapeutic efficacy. In this study, we introduce ProteinReDiff, an efficient computational framework targeting the redesign of ligand-binding proteins. Using equivariant diffusion-based generative models, ProteinReDiff enables the creation of high-affinity ligand-binding proteins without the need for detailed structural information, leveraging instead the potential of initial protein sequences and ligand SMILES strings. Our evaluations across sequence diversity, structural preservation, and ligand binding affinity underscore ProteinReDiffs potential to advance computational drug discovery and protein engineering. Our source code is publicly available at https://github.com/HySonLab/Protein_Redesign.

bioinformatics↗

bioRxiv2024

Treponema pallidum periplasmic and membrane proteins are recognized by circulating and skin CD4+ T cells

BackgroundHistologic and serologic studies suggest the induction of local and systemic Treponema pallidum (Tp)-specific CD4+ T cell responses to Tp infection. We hypothesized that Tp-specific CD4+ T cells are detectable in blood and in the skin rash of secondary syphilis and persist in both compartments after treatment. MethodsPBMC collected from 67 participants were screened by IFN{gamma} ELISPOT response to Tp sonicate. Tp-reactive T cell lines from blood and skin were probed for responses to 88 recombinant Tp antigens. Peptide epitopes and HLA class II restriction were defined for selected antigens. ResultsWe detected CD4+ T cell responses to Tp sonicate ex vivo. Using Tp-reactive T cell lines we observed recognition of 14 discrete proteins, 13 of which localize to bacterial membranes or the periplasmic space. After therapy, Tp-specific T cells persisted for at least 6 months in skin and 10 years in blood. ConclusionsTp infection elicits an antigen-specific CD4+ T cell response in blood and skin. Tp-specific CD4+ T cells persist as memory in both compartments long after curative therapy. The Tp antigenic targets we identified may be high priority vaccine candidates.

immunology↗

bioRxiv2024

Disrupting CD38-driven T cell dysfunction restores sensitivity to cancer immunotherapy

A central problem in cancer immunotherapy with immune checkpoint blockade (ICB) is the development of resistance, which affects 50% of patients with metastatic melanoma1,2. T cell exhaustion, resulting from chronic antigen exposure in the tumour microenvironment, is a major driver of ICB resistance3. Here, we show that CD38, an ecto-enzyme involved in nicotinamide adenine dinucleotide (NAD+) catabolism, is highly expressed in exhausted CD8+ T cells in melanoma and is associated with ICB resistance. Tumour-derived CD38hiCD8+ T cells are dysfunctional, characterised by impaired proliferative capacity, effector function, and dysregulated mitochondrial bioenergetics. Genetic and pharmacological blockade of CD38 in murine and patient-derived organotypic tumour models (MDOTS/PDOTS) enhanced tumour immunity and overcame ICB resistance. Mechanistically, disrupting CD38 activity in T cells restored cellular NAD+ pools, improved mitochondrial function, increased proliferation, augmented effector function, and restored ICB sensitivity. Taken together, these data demonstrate a role for the CD38-NAD+ axis in promoting T cell exhaustion and ICB resistance, and establish the efficacy of CD38 directed therapeutic strategies to overcome ICB resistance using clinically relevant, patient-derived 3D tumour models.

cancer biology↗

bioRxiv2023

Engineered Protein Nanosheets for the Scale up of Mesenchymal Stem Cell Culture on Bioemulsions

The rapid progress in cell therapies and stem cell technologies requires the development of novel bioprocessing and biomanufacturing pipelines able to cope with the scale up of cell manufacturing. In this respect, microdroplet technologies have already revolutionised the field of biotechnologies, but remain ill-suited to the culture of adherent cells. In this report, we describe the engineering of albumins with cell adhesive peptides for the stabilisation of microdroplets enabling the scale up of mesenchymal stem cell (MSC) expansion. We characterise the modified albumins prior to study their self-assembly at liquid-liquid interfaces via interfacial shear rheology, and mechanical strengthening through the formation of crosslinked nanosheets. The biofunctionalisation of these protein nanosheets is then characterised by fluorescence microscopy. In turn, the ability of the resulting bioactive microdroplets to promote rapid cell adhesion and expansion is examined and the extensive deposition of matrix associated with such cultures is characterised. The culture of MSCs is then scaled up 100 fold, first at the surface of fluorinated oil emulsions, then on plant-based emulsions stabilised by engineered protein nanosheets and the phenotype of resulting cells is characterised. The microdroplet culture system presented displays attractive advantages over existing technologies, in terms of simplicity of processing, compatibility with regulatory expectations and costs of production, and offers exciting opportunities for translation to cell manufacturing, for cell therapies and cultivated meat applications.

bioengineering↗

bioRxiv2023

Benchmarking AlphaSC: A Leap in Single-Cell Data Processing

AO_SCPLOWBSTRACTC_SCPLOWWe benchmarked AlphaSC, BioTurings GPU-accelerated single-cell analytics package, against other popular tools including Scanpy, Seurat, and RAPIDS. The results demonstrate that AlphaSC operates thousands of times faster than Seurat and Scanpy. Additionally, it surpasses RAPIDS, another GPU-accelerated package from NVIDIA, by an order of magnitude in terms of speed while also consuming considerably less RAM and GPU memory. Importantly, this significant increase in AlphaSCs performance does not compromise its quality. 1

bioinformatics↗

bioRxiv2022

e-cone and d-cone singularities drive submucosal collagen fiber remodeling in intestinal anastomotic surgery

Following resection of a diseased segment of intestine, a reconnection (anastomotic) geometry is chosen to reduce postoperative stress and optimize outcomes. As proper healing of an intestinal anastomosis is strongly affected by its mechanobiology, much attention has been devoted to the conical structures formed along the suture lines, where stress-focusing is expected. However, geometric considerations reveal that in addition to the obvious loci of stress-focusing, additional remote locations of stress-focusing may form. We identify conical structures that inevitably form within regions of otherwise uninterrupted tissue. In this work we use geometric analysis, finite element modeling (FEM), and in-vivo experiments to investigate these emergent stress-focusing structures, their mechanical stresses, and the resulting submucosal collagen fiber re-orientation, as these naturally arise in the side-to-side small bowel anastomosis (SBA), the most common configuration performed in patients. FEM predicts the appearance of remote high-stress regions. Allowing for tissue remodeling, our simulations also predict an increased dispersion of submucosal collagen fibers in these regions. In-vivo experiments performed on ten-week-old male C57BL/6 mice assigned the creation of side-to-side SBA or sham-laparotomy corroborate this result. Anastomoses were analyzed at sacrifice on post-operative day (POD) 14 and 88 with histologic-sectioning, staining, high magnification imaging, and submucosal collagen fiber orientation ({kappa}) mapping. The mean and variance of{kappa} , a measure of collagen fiber dispersion, at POD-14 far from the anastomosis show similar values to those obtained for sham-operated mice, while the FEM-predicted loci of stress-focusing display statistically significant higher values. The values at POD-88 at all loci show no statistically-significant difference, and agree with those of the sham-operated mice at POD-14.

bioengineering↗

bioRxiv2022

EGFR-initiated endocytosis of Wnt9a and Fzd9b is required for β-catenin signaling

Cell to cell communication through secreted ligands like those encoded by the Wnt gene family is critical for development and homeostasis during organismal life. One of the bottlenecks in the Wnt field has been identifying specific ligand/receptor pairings and decoding the mechanisms for their downstream signals. We previously discovered that the Wnt9a ligand signals through the cell surface receptors Fzd9b, LRP5/6 and EGFR to promote early proliferation of hematopoietic stem cells during development. We used this exquisitely specific ligand/receptor complex as a platform to determine if Wnt9a requires endocytosis for signaling. Using fluorescently labeled, biologically active Wnt9a and Fzd9b fusion proteins, we demonstrate here that the Wnt9a receptor complex is rapidly endocytosed within one minute of contact with Fzd9b. Following this, the Wnt9a/Fzd9b complex is trafficked through the cell to early and late endosomes, lysosomes, and the endoplasmic reticulum; it is also recycled back to the membrane. Using small molecule inhibitors, genetic and siRNA approaches, we identified that mechanistically this endocytosis requires EGFR-mediated phosphorylation of the Fzd9b tail, followed by endocytosis through a caveolin and EPS15 dependent pathway. Specific modes of endocytosis and trafficking may represent one of the ways in which Wnt/Fzd specificity is established, since other Wnt ligands do not require endocytosis for activity.

cell biology↗

bioRxiv2022

Aortic Shape Space Topology

Clinical imaging modalities are a mainstay of modern disease management, but the full utilization of imaging-based data remains elusive. Aortic disease is defined by anatomic scalars quantifying aortic size, even though aortic disease progression initiates complex shape changes. We present an imaging-based geometric descriptor, inspired by fundamental ideas from topology and soft-matter physics that captures dynamic shape evolution. The aorta is reduced to a two-dimensional mathematical surface in space whose geometry is fully characterized by the local principal curvatures. Disease causes deviation from the smooth bent cylindrical shape of normal aortas, leading to a family of highly heterogeneous surfaces of varying shapes and sizes. To deconvolute changes in shape from size, the shape is characterized using integrated Gaussian curvature or total curvature. The fluctuation in total curvature ({delta}K) across aortic surfaces captures heterogeneous morphologic evolution by characterizing local shape changes. We discover that aortic morphology evolves with a power-law defined behavior with rapidly increasing{delta} K forming the hallmark of aortic disease. Divergent{delta} K is seen for highly diseased aortas indicative of impending topologic catastrophe or aortic rupture. We also show that aortic size (surface area or enclosed aortic volume) scales as a generalized cylinder for all shapes. Classification accuracy for predicting aortic disease state (normal, diseased with successful surgery, and diseased with failed surgical outcomes) is 92.8 {+/-}1.7%. The analysis of{delta} K can be applied on any three-dimensional geometric structure and thus may be extended to other clinical problems of characterizing disease through captured anatomic changes.

bioengineering↗