Pub Date : 2024-09-11DOI: 10.1101/2024.09.05.611421
Giovanni Talei Franzesi, Ishan Gupta, Ming Hu, Kiryl Piatkveich, Murat Yildirim, Jian-Ping Zhao, Minho Eom, Seungjae Han, Demian Park, Himashi Andaraarachchi, Zhaohan Li, Jesse Greenhagen, Amirul Muhammad Islam, Parth Vashishtha, Zahid Yaqoob, Nikita Pak, Alexander D. Wissner-Gross, Daniel Martin-Alarcon, Jonathan Veinot, Peter T. So, Uwe Kortshagen, Young-Gyu Yoon, Mriganka Sur, Edward S. Boyden
Established methods for imaging the living mammalian brain have, to date, taken optical properties of the tissue as fixed; we here demonstrate that it is possible to modify the optical properties of the brain itself to significantly enhance at-depth imaging while preserving native physiology. Using a small amount of any of several biocompatible materials to raise the refractive index of solutions superfusing the brain prior to imaging, we could increase several-fold the signals from the deepest cells normally visible and, under both one-photon and two-photon imaging, visualize cells previously too dim to see. The enhancement was observed for both anatomical and functional fluorescent reporters across a broad range of emission wavelengths. Importantly, visual tuning properties of cortical neurons in awake mice, and electrophysiological properties of neurons assessed ex vivo, were not altered by this procedure.
{"title":"In Vivo Optical Clearing of Mammalian Brain","authors":"Giovanni Talei Franzesi, Ishan Gupta, Ming Hu, Kiryl Piatkveich, Murat Yildirim, Jian-Ping Zhao, Minho Eom, Seungjae Han, Demian Park, Himashi Andaraarachchi, Zhaohan Li, Jesse Greenhagen, Amirul Muhammad Islam, Parth Vashishtha, Zahid Yaqoob, Nikita Pak, Alexander D. Wissner-Gross, Daniel Martin-Alarcon, Jonathan Veinot, Peter T. So, Uwe Kortshagen, Young-Gyu Yoon, Mriganka Sur, Edward S. Boyden","doi":"10.1101/2024.09.05.611421","DOIUrl":"https://doi.org/10.1101/2024.09.05.611421","url":null,"abstract":"Established methods for imaging the living mammalian brain have, to date, taken optical properties of the tissue as fixed; we here demonstrate that it is possible to modify the optical properties of the brain itself to significantly enhance at-depth imaging while preserving native physiology. Using a small amount of any of several biocompatible materials to raise the refractive index of solutions superfusing the brain prior to imaging, we could increase several-fold the signals from the deepest cells normally visible and, under both one-photon and two-photon imaging, visualize cells previously too dim to see. The enhancement was observed for both anatomical and functional fluorescent reporters across a broad range of emission wavelengths. Importantly, visual tuning properties of cortical neurons in awake mice, and electrophysiological properties of neurons assessed ex vivo, were not altered by this procedure.","PeriodicalId":501308,"journal":{"name":"bioRxiv - Bioengineering","volume":"72 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142216589","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-10DOI: 10.1101/2024.08.29.610300
Jason Zhaoxing Zhang, Xinting Li, Caixuan Liu, Hanlun Jiang, Kejia Wu, David Baker
The proto-oncogene Ras which governs diverse intracellular pathways has four major isoforms (KRAS4A, KRAS4B, HRAS, and NRAS) with substantial sequence homology and similar in vitro biochemistry. There is considerable interest in investigating the roles of these independently as their association with different cancers vary, but there are few Ras isoform-specific binding reagents as the only significant sequence differences are in their disordered and highly charged C-termini which have been difficult to elicit antibodies against. To overcome this limitation, we use deep learning-based methods to de novo design Ras isoform-specific binders (RIBs) for KRAS4A, KRAS4B, and NRAS that specifically target the Ras C-terminus. The RIBs bind to their target Ras isoforms both in vitro and in cells with remarkable specificity, disrupted their membrane localization, and inhibited Ras activity. Therefore, these tools can contribute to dissecting the distinct roles of Ras isoforms in biology and disease.
{"title":"De novo design of Ras isoform selective binders","authors":"Jason Zhaoxing Zhang, Xinting Li, Caixuan Liu, Hanlun Jiang, Kejia Wu, David Baker","doi":"10.1101/2024.08.29.610300","DOIUrl":"https://doi.org/10.1101/2024.08.29.610300","url":null,"abstract":"The proto-oncogene Ras which governs diverse intracellular pathways has four major isoforms (KRAS4A, KRAS4B, HRAS, and NRAS) with substantial sequence homology and similar in vitro biochemistry. There is considerable interest in investigating the roles of these independently as their association with different cancers vary, but there are few Ras isoform-specific binding reagents as the only significant sequence differences are in their disordered and highly charged C-termini which have been difficult to elicit antibodies against. To overcome this limitation, we use deep learning-based methods to de novo design Ras isoform-specific binders (RIBs) for KRAS4A, KRAS4B, and NRAS that specifically target the Ras C-terminus. The RIBs bind to their target Ras isoforms both in vitro and in cells with remarkable specificity, disrupted their membrane localization, and inhibited Ras activity. Therefore, these tools can contribute to dissecting the distinct roles of Ras isoforms in biology and disease.","PeriodicalId":501308,"journal":{"name":"bioRxiv - Bioengineering","volume":"34 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142216611","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-10DOI: 10.1101/2024.09.05.611434
Ana P Spencer, Adriana Vilaca, Miguel Xavier, Rafael Santos, Ariel Ionescu, Maria Lazaro, Victoria Leiro, Eran Perlson, Sofia C Guimaraes, Ben M Maoz, Ana P Pego
Gene therapy using small interfering RNA (siRNA) holds promise for treating neurological disorders by silencing specific genes, such as the phosphatase and tensin homolog (PTEN) gene, which restricts axonal growth. Yet, delivering siRNA to neurons efficiently is challenging due to premature degradation and unspecific delivery. Chitosan-based delivery systems have shown great potential due to their well-established biocompatibility. However, their limited transfection efficiency and lack of neuronal tropism require further modification. Building on our previous successes with neuron-targeted DNA delivery using chitosan, a novel approach for siRNA delivery aimed at PTEN downregulation is proposed. This involves using thiolated trimethyl chitosan (TMCSH)-based siRNA nanoparticles functionalized with the neurotropic C-terminal fragment of the tetanus neurotoxin heavy chain (HC) for efficient delivery to both peripheral and central neurons. These polyplexes demonstrated suitable physicochemical properties, biocompatibility, and no adverse effects on neuronal electrophysiology. Diverse neuronal models, including 3D ex vivo cultures and microfluidics, confirmed polyplexes efficiency and neurospecificity. HC targeting significantly enhanced nanoparticle neuronal binding, and live cell imaging revealed five times faster retrograde transport along axons. Furthermore, siRNA delivery targeting PTEN promoted axonal outgrowth in embryonic cortical neurons. Thus, these polyplexes represent a promising platform for siRNA delivery, offering potential for clinical translation and therapeutic applications.
{"title":"Engineered chitosan-derived nanocarrier for efficient siRNA delivery to peripheral and central neurons","authors":"Ana P Spencer, Adriana Vilaca, Miguel Xavier, Rafael Santos, Ariel Ionescu, Maria Lazaro, Victoria Leiro, Eran Perlson, Sofia C Guimaraes, Ben M Maoz, Ana P Pego","doi":"10.1101/2024.09.05.611434","DOIUrl":"https://doi.org/10.1101/2024.09.05.611434","url":null,"abstract":"Gene therapy using small interfering RNA (siRNA) holds promise for treating neurological disorders by silencing specific genes, such as the phosphatase and tensin homolog (PTEN) gene, which restricts axonal growth. Yet, delivering siRNA to neurons efficiently is challenging due to premature degradation and unspecific delivery. Chitosan-based delivery systems have shown great potential due to their well-established biocompatibility. However, their limited transfection efficiency and lack of neuronal tropism require further modification. Building on our previous successes with neuron-targeted DNA delivery using chitosan, a novel approach for siRNA delivery aimed at PTEN downregulation is proposed. This involves using thiolated trimethyl chitosan (TMCSH)-based siRNA nanoparticles functionalized with the neurotropic C-terminal fragment of the tetanus neurotoxin heavy chain (HC) for efficient delivery to both peripheral and central neurons. These polyplexes demonstrated suitable physicochemical properties, biocompatibility, and no adverse effects on neuronal electrophysiology. Diverse neuronal models, including 3D ex vivo cultures and microfluidics, confirmed polyplexes efficiency and neurospecificity. HC targeting significantly enhanced nanoparticle neuronal binding, and live cell imaging revealed five times faster retrograde transport along axons. Furthermore, siRNA delivery targeting PTEN promoted axonal outgrowth in embryonic cortical neurons. Thus, these polyplexes represent a promising platform for siRNA delivery, offering potential for clinical translation and therapeutic applications.","PeriodicalId":501308,"journal":{"name":"bioRxiv - Bioengineering","volume":"23 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142216612","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Aortic stenosis (AS) leads to alterations of supra-valvular flow patterns. These patterns might lead to, inter alia, increased damage of red blood cell (RBC) membranes. We investigated these patient specific patterns of a severe AS patient and their reversal in healthy flow through a 4D Flow MRI-based CFD methodology. Computational models of subject-specific aortic geometries were created using in-vivo medical imaging data. Temporally and spatially resolved boundary conditions derived from 4D Flow MRI were implemented for an AS patient and a healthy subject. After validation of the in-silico results with in-vivo data, a healthy inflow profile was set for the AS patient in the CFD model. Pathological versus healthy flow fields were compared regarding their blood flow characteristics, i.e. shear stresses on RBCs and helicity. The accuracy of the 4D Flow MRI-based CFD model was proven with excellent agreement between in-vivo and in-silico velocity fields and R² = 0.9. A pathological high shear stress region in the bulk flow was present during late systole with an increase of 125 % compared to both healthy flow. The physiological bihelical structure with predominantly right-handed helices vanished for the pathological state. Instead, a left-handed helix appeared, accompanied by an overall increase in turbulent kinetic energy in areas of accumulated left-handed helicity. The validated 4D Flow MRI-based CFD model identified marked differences between AS and healthy flow. It suggests that altered turbulent and helical structures in the bulk flow are the cause for increased, potentially damaging forces acting upon RBCs in AS.
{"title":"Investigation of hemodynamic bulk flow patterns caused by aortic stenosis using a combined 4D Flow MRI-CFD framework","authors":"Tianai Wang, Christine Quast, Florian Bönner, Malte Kelm, Tobias Zeus, Teresa Lemainque, Ulrich Steinseifer, Michael Neidlin","doi":"10.1101/2024.09.09.611958","DOIUrl":"https://doi.org/10.1101/2024.09.09.611958","url":null,"abstract":"Aortic stenosis (AS) leads to alterations of supra-valvular flow patterns. These patterns might lead to, inter alia, increased damage of red blood cell (RBC) membranes. We investigated these patient specific patterns of a severe AS patient and their reversal in healthy flow through a 4D Flow MRI-based CFD methodology. Computational models of subject-specific aortic geometries were created using in-vivo medical imaging data. Temporally and spatially resolved boundary conditions derived from 4D Flow MRI were implemented for an AS patient and a healthy subject. After validation of the in-silico results with in-vivo data, a healthy inflow profile was set for the AS patient in the CFD model. Pathological versus healthy flow fields were compared regarding their blood flow characteristics, i.e. shear stresses on RBCs and helicity. The accuracy of the 4D Flow MRI-based CFD model was proven with excellent agreement between in-vivo and in-silico velocity fields and R² = 0.9. A pathological high shear stress region in the bulk flow was present during late systole with an increase of 125 % compared to both healthy flow. The physiological bihelical structure with predominantly right-handed helices vanished for the pathological state. Instead, a left-handed helix appeared, accompanied by an overall increase in turbulent kinetic energy in areas of accumulated left-handed helicity. The validated 4D Flow MRI-based CFD model identified marked differences between AS and healthy flow. It suggests that altered turbulent and helical structures in the bulk flow are the cause for increased, potentially damaging forces acting upon RBCs in AS.","PeriodicalId":501308,"journal":{"name":"bioRxiv - Bioengineering","volume":"59 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142216568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-10DOI: 10.1101/2024.09.05.611489
Zhen Zhou, Bruce Fischl, Iman Aganj
The increasing prevalence of multi-site diffusion-weighted magnetic resonance imaging (dMRI) studies potentially offers enhanced statistical power for investigating brain structure. However, these studies face challenges due to variations in scanner hardware and acquisition protocols. While several methods exist for dMRI data harmonization, few specifically address structural brain connectivity. We introduce a new distribution-matching approach to harmonizing structural brain connectivity across different sites and scanners. We evaluate our method using structural brain connectivity data from two distinct datasets of OASIS-3 and ADNI-2, comparing its performance to the widely used ComBat method. Our approach is meant to align the statistical properties of connectivity data from these two datasets. We examine the impact of harmonization on the correlation of brain connectivity with the Mini-Mental State Examination score and age. Our results demonstrate that our distribution-matching technique more effectively harmonizes structural brain connectivity, often producing stronger and more significant correlations compared to ComBat. Qualitative assessments illustrate the desired distributional alignment of ADNI-2 with OASIS-3, while quantitative evaluations confirm robust performance. This work contributes to the growing field of dMRI harmonization, potentially improving the reliability and comparability of structural connectivity studies that combine data from different sources in neuroscientific and clinical research.
{"title":"Harmonization of Structural Brain Connectivity through Distribution Matching","authors":"Zhen Zhou, Bruce Fischl, Iman Aganj","doi":"10.1101/2024.09.05.611489","DOIUrl":"https://doi.org/10.1101/2024.09.05.611489","url":null,"abstract":"The increasing prevalence of multi-site diffusion-weighted magnetic resonance imaging (dMRI) studies potentially offers enhanced statistical power for investigating brain structure. However, these studies face challenges due to variations in scanner hardware and acquisition protocols. While several methods exist for dMRI data harmonization, few specifically address structural brain connectivity. We introduce a new distribution-matching approach to harmonizing structural brain connectivity across different sites and scanners. We evaluate our method using structural brain connectivity data from two distinct datasets of OASIS-3 and ADNI-2, comparing its performance to the widely used ComBat method. Our approach is meant to align the statistical properties of connectivity data from these two datasets. We examine the impact of harmonization on the correlation of brain connectivity with the Mini-Mental State Examination score and age. Our results demonstrate that our distribution-matching technique more effectively harmonizes structural brain connectivity, often producing stronger and more significant correlations compared to ComBat. Qualitative assessments illustrate the desired distributional alignment of ADNI-2 with OASIS-3, while quantitative evaluations confirm robust performance. This work contributes to the growing field of dMRI harmonization, potentially improving the reliability and comparability of structural connectivity studies that combine data from different sources in neuroscientific and clinical research.","PeriodicalId":501308,"journal":{"name":"bioRxiv - Bioengineering","volume":"283 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142216609","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-10DOI: 10.1101/2024.09.07.610493
Susannah Waxman, Hannah Schilpp, Ashley Linton, Tatjana C. Jakobs, Ian A Sigal
Purpose: Although the mechanisms underlying glaucomatous neurodegeneration are not yet well understood, cellular and small animal models suggest that LC astrocytes undergo early morphologic and functional changes, indicating their role as early responders to glaucomatous stress. These models, however, lack the LC found in larger animals and humans, leaving the in situ morphology of LC astrocytes and their role in glaucoma initiation underexplored. In this work, we aimed to characterize the morphology of LC astrocytes in situ and determine differences and similarities with astrocytes in the mouse glial lamina (GL), the analogous structure in a prominent glaucoma model. Methods: Astrocytes in the LCs of twenty-two eyes from goats, sheep, and pigs were stochastically labeled via Multicolor DiOlistics and imaged in situ using confocal microscopy. 3D models of DiOlistically-labeled LC astrocytes and hGFAPpr-GFP mouse GL astrocytes were constructed to quantify morphological features related to astrocyte functions. LC and GL astrocyte cross-pore contacts, branching complexity, branch tortuosity, and cell and branch span were compared. Results: LC astrocytes displayed distinct spatial relationships with collagen, greater branching complexity, and higher branch tortuosity compared to GL astrocytes. Despite substantial differences in their anatomical environments, LC and GL astrocytes had similar cell and branch spans. Conclusions: Astrocyte morphology in the LC was characterized through Multicolor DiOlistic labeling. LC and GL astrocytes have both distinct and shared morphological features. Further research is needed to understand the potentially unique roles of LC astrocytes in glaucoma initiation and progression.
{"title":"Morphological comparison of astrocytes in the lamina cribrosa and glial lamina","authors":"Susannah Waxman, Hannah Schilpp, Ashley Linton, Tatjana C. Jakobs, Ian A Sigal","doi":"10.1101/2024.09.07.610493","DOIUrl":"https://doi.org/10.1101/2024.09.07.610493","url":null,"abstract":"Purpose: Although the mechanisms underlying glaucomatous neurodegeneration are not yet well understood, cellular and small animal models suggest that LC astrocytes undergo early morphologic and functional changes, indicating their role as early responders to glaucomatous stress. These models, however, lack the LC found in larger animals and humans, leaving the in situ morphology of LC astrocytes and their role in glaucoma initiation underexplored. In this work, we aimed to characterize the morphology of LC astrocytes in situ and determine differences and similarities with astrocytes in the mouse glial lamina (GL), the analogous structure in a prominent glaucoma model. Methods:\u0000Astrocytes in the LCs of twenty-two eyes from goats, sheep, and pigs were stochastically labeled via Multicolor DiOlistics and imaged in situ using confocal microscopy. 3D models of DiOlistically-labeled LC astrocytes and hGFAPpr-GFP mouse GL astrocytes were constructed to quantify morphological features related to astrocyte functions. LC and GL astrocyte cross-pore contacts, branching complexity, branch tortuosity, and cell and branch span were compared. Results: LC astrocytes displayed distinct spatial relationships with collagen, greater branching complexity, and higher branch tortuosity compared to GL astrocytes. Despite substantial differences in their anatomical environments, LC and GL astrocytes had similar cell and branch spans. Conclusions:\u0000Astrocyte morphology in the LC was characterized through Multicolor DiOlistic labeling. LC and GL astrocytes have both distinct and shared morphological features. Further research is needed to understand the potentially unique roles of LC astrocytes in glaucoma initiation and progression.","PeriodicalId":501308,"journal":{"name":"bioRxiv - Bioengineering","volume":"283 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142216569","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-10DOI: 10.1101/2024.09.05.610277
Xuehuan He, Mohammad R. Islam, Fengting Ji, Bingrui Wang, Ian A Sigal
Collagen fibers are the main load-bearing component of soft tissues but difficult to incorporate into models. Whilst simplified homogenization models suffice for some applications, a thorough mechanistic understanding requires accurate prediction of fiber behavior, including both detailed fiber-level strains and long-distance transmission. Our goal was to compare the performance of a continuum model of the optic nerve head (ONH) built using conventional techniques with a fiber model we recently introduced which explicitly incorporates the complex 3D organization and interaction of collagen fiber bundles [1]. To ensure a fair comparison, we constructed the continuum model with identical geometrical, structural, and boundary specifications as for the fiber model. We found that: 1) although both models accurately matched the intraocular pressure (IOP)-induced globally averaged displacement responses observed in experiments, they diverged significantly in their ability to replicate specific 3D tissue-level strain patterns. Notably, the fiber model faithfully replicated the experimentally observed depth-dependent variability of radial strain, the ring-like pattern of meridional strain, and the radial pattern of circumferential strain, whereas the continuum model failed to do so; 2) the continuum model disrupted the strain transmission along each fiber, a feature captured well by the fiber model. These results demonstrate limitations of the conventional continuum models that rely on homogenization and affine deformation assumptions, which render them incapable of capturing some complex tissue-level and fiber-level deformations. Our results show that the strengths of explicit fiber modeling help capture intricate ONH biomechanics. They potentially also help modeling other fibrous tissues.
{"title":"Comparing continuum and direct fiber models of soft tissues. An ocular biomechanics example reveals that continuum models may artificially disrupt the strains at both the tissue and fiber levels","authors":"Xuehuan He, Mohammad R. Islam, Fengting Ji, Bingrui Wang, Ian A Sigal","doi":"10.1101/2024.09.05.610277","DOIUrl":"https://doi.org/10.1101/2024.09.05.610277","url":null,"abstract":"Collagen fibers are the main load-bearing component of soft tissues but difficult to incorporate into models. Whilst simplified homogenization models suffice for some applications, a thorough mechanistic understanding requires accurate prediction of fiber behavior, including both detailed fiber-level strains and long-distance transmission. Our goal was to compare the performance of a continuum model of the optic nerve head (ONH) built using conventional techniques with a fiber model we recently introduced which explicitly incorporates the complex 3D organization and interaction of collagen fiber bundles [1]. To ensure a fair comparison, we constructed the continuum model with identical geometrical, structural, and boundary specifications as for the fiber model. We found that: 1) although both models accurately matched the intraocular pressure (IOP)-induced globally averaged displacement responses observed in experiments, they diverged significantly in their ability to replicate specific 3D tissue-level strain patterns. Notably, the fiber model faithfully replicated the experimentally observed depth-dependent variability of radial strain, the ring-like pattern of meridional strain, and the radial pattern of circumferential strain, whereas the continuum model failed to do so; 2) the continuum model disrupted the strain transmission along each fiber, a feature captured well by the fiber model. These results demonstrate limitations of the conventional continuum models that rely on homogenization and affine deformation assumptions, which render them incapable of capturing some complex tissue-level and fiber-level deformations. Our results show that the strengths of explicit fiber modeling help capture intricate ONH biomechanics. They potentially also help modeling other fibrous tissues.","PeriodicalId":501308,"journal":{"name":"bioRxiv - Bioengineering","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142216595","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-10DOI: 10.1101/2024.09.05.611548
Adnan A Hirad, Faisal S. Fakhouri, Brian Raterman, Ronald Lakony, Maxwell Wang, Dakota Gonring, Baqir Kedwai, Arunark Kolipaka, Doran A Mix
Type-B aortic dissection (TBAD) represents a serious medical emergency with up to a 50% associated 5-year mortality caused by thoracic aorta, dissection-associated aneurysmal (DAA) degeneration, and rupture. Unfortunately, conventional size related diagnostic methods cannot distinguish high-risk DAAs that benefit from surgical intervention from stable DAAs. Our goal is to use DAA stiffness measured with magnetic resonance elastography (MRE) as a biomarker to distinguish high-risk DAAs from stable DAAs. This is a feasibility study using MRE to 1) fabricate human-like geometries TBAD phantoms with different stiffnesses. 2) measure stiffness in TBAD phantoms with rheometry and 3) demonstrate the first successful application of MRE to the thoracic aorta of a human volunteer. Aortic dissection phantoms with heterogenous wall stiffness demonstrated the correlation between MRE-derived stiffness and rheometric measured stiffness. A pilot scan was performed in a healthy volunteer to test the technique's feasibility in the thoracic aorta.
{"title":"Feasibility of Measuring Magnetic Resonance Elastography-derived Stiffness in Human Thoracic Aorta and Aortic Dissection Phantoms","authors":"Adnan A Hirad, Faisal S. Fakhouri, Brian Raterman, Ronald Lakony, Maxwell Wang, Dakota Gonring, Baqir Kedwai, Arunark Kolipaka, Doran A Mix","doi":"10.1101/2024.09.05.611548","DOIUrl":"https://doi.org/10.1101/2024.09.05.611548","url":null,"abstract":"Type-B aortic dissection (TBAD) represents a serious medical emergency with up to a 50% associated 5-year mortality caused by thoracic aorta, dissection-associated aneurysmal (DAA) degeneration, and rupture. Unfortunately, conventional size related diagnostic methods cannot distinguish high-risk DAAs that benefit from surgical intervention from stable DAAs. Our goal is to use DAA stiffness measured with magnetic resonance elastography (MRE) as a biomarker to distinguish high-risk DAAs from stable DAAs. This is a feasibility study using MRE to 1) fabricate human-like geometries TBAD phantoms with different stiffnesses. 2) measure stiffness in TBAD phantoms with rheometry and 3) demonstrate the first successful application of MRE to the thoracic aorta of a human volunteer. Aortic dissection phantoms with heterogenous wall stiffness demonstrated the correlation between MRE-derived stiffness and rheometric measured stiffness. A pilot scan was performed in a healthy volunteer to test the technique's feasibility in the thoracic aorta.","PeriodicalId":501308,"journal":{"name":"bioRxiv - Bioengineering","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142216592","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-10DOI: 10.1101/2024.09.04.611223
David Saeb, Emma E Lietzke, Daisy I Fuchs, Emma C Aldrich, Kimberley D Bruce, Kayla G Sprenger
The microglial surface protein Triggering Receptor Expressed on Myeloid Cells 2 (TREM2) plays a critical role in mediating brain homeostasis and inflammatory responses in Alzheimer's disease (AD). The soluble form of TREM2 (sTREM2) exhibits neuroprotective effects in AD, though the underlying mechanisms remain elusive. Moreover, differences in ligand binding between TREM2 and sTREM2, which have major implications for their roles in AD pathology, remain unexplained. To address these knowledge gaps, we conducted the most computationally intensive molecular dynamics simulations to date of (s)TREM2, exploring their interactions with key damage- and lipoprotein-associated phospholipids and the impact of the AD-risk mutation R47H. Our results demonstrate that the flexible stalk domain of sTREM2 serves as the molecular basis for differential ligand binding between sTREM2 and TREM2, facilitated by its role in stabilizing the Ig-like domain and altering the accessibility of canonical ligand binding sites. We identified a novel ligand binding site on sTREM2, termed the 'Expanded Surface 2', which emerges due to competitive binding of the stalk with the Ig-like domain. Additionally, we observed that the stalk domain itself functions as a site for ligand binding, with increased binding in the presence of R47H. This suggests that sTREM2's neuroprotective role in AD may, at least in part, arise from the stalk domain's ability to rescue dysfunctional ligand binding caused by AD-risk mutations. Lastly, our findings indicate that R47H-induced dysfunction in membrane-bound TREM2 may result from both diminished ligand binding due to restricted complementarity-determining region 2 loop motions and an impaired ability to differentiate between ligands, proposing a novel mechanism for loss-of-function. In summary, these results provide valuable insights into the role of sTREM2 in AD pathology, laying the groundwork for the design of new therapeutic approaches targeting (s)TREM2 in AD.
小胶质细胞表面蛋白髓系细胞上表达的触发受体 2（TREM2）在阿尔茨海默病（AD）中介导大脑稳态和炎症反应方面起着关键作用。TREM2 的可溶性形式（sTREM2）在阿尔茨海默病中具有神经保护作用，但其潜在机制仍难以捉摸。此外，TREM2 和 sTREM2 之间配体结合的差异对它们在 AD 病理学中的作用具有重要影响，但这些差异仍未得到解释。为了填补这些知识空白，我们对（s）TREM2 进行了迄今为止计算强度最高的分子动力学模拟，探索了它们与关键损伤和脂蛋白相关磷脂的相互作用以及 AD 风险突变 R47H 的影响。我们的研究结果表明，sTREM2 的柔性柄结构域是 sTREM2 和 TREM2 之间不同配体结合的分子基础，它在稳定 Ig 样结构域和改变经典配体结合位点的可及性方面起着促进作用。我们在 sTREM2 上发现了一个新的配体结合位点，称为 "扩展表面 2"，它的出现是由于柄与 Ig 样结构域的竞争性结合。此外，我们还观察到，柄结构域本身也是一个配体结合位点，在 R47H 存在的情况下，其结合率会增加。这表明，sTREM2在AD中的神经保护作用可能至少部分源于柄结构域挽救由AD风险突变引起的配体结合功能障碍的能力。最后，我们的研究结果表明，R47H诱导的膜结合TREM2功能障碍可能是由于互补决定区2环运动受限导致配体结合减弱，以及配体之间的分辨能力受损，从而提出了一种新的功能缺失机制。总之，这些结果为了解 sTREM2 在 AD 病理学中的作用提供了宝贵的见解，为设计针对 (s)TREM2 的 AD 新疗法奠定了基础。
{"title":"The flexible stalk domain of sTREM2 modulates its interactions with phospholipids in the brain","authors":"David Saeb, Emma E Lietzke, Daisy I Fuchs, Emma C Aldrich, Kimberley D Bruce, Kayla G Sprenger","doi":"10.1101/2024.09.04.611223","DOIUrl":"https://doi.org/10.1101/2024.09.04.611223","url":null,"abstract":"The microglial surface protein Triggering Receptor Expressed on Myeloid Cells 2 (TREM2) plays a critical role in mediating brain homeostasis and inflammatory responses in Alzheimer's disease (AD). The soluble form of TREM2 (sTREM2) exhibits neuroprotective effects in AD, though the underlying mechanisms remain elusive. Moreover, differences in ligand binding between TREM2 and sTREM2, which have major implications for their roles in AD pathology, remain unexplained. To address these knowledge gaps, we conducted the most computationally intensive molecular dynamics simulations to date of (s)TREM2, exploring their interactions with key damage- and lipoprotein-associated phospholipids and the impact of the AD-risk mutation R47H. Our results demonstrate that the flexible stalk domain of sTREM2 serves as the molecular basis for differential ligand binding between sTREM2 and TREM2, facilitated by its role in stabilizing the Ig-like domain and altering the accessibility of canonical ligand binding sites. We identified a novel ligand binding site on sTREM2, termed the 'Expanded Surface 2', which emerges due to competitive binding of the stalk with the Ig-like domain. Additionally, we observed that the stalk domain itself functions as a site for ligand binding, with increased binding in the presence of R47H. This suggests that sTREM2's neuroprotective role in AD may, at least in part, arise from the stalk domain's ability to rescue dysfunctional ligand binding caused by AD-risk mutations. Lastly, our findings indicate that R47H-induced dysfunction in membrane-bound TREM2 may result from both diminished ligand binding due to restricted complementarity-determining region 2 loop motions and an impaired ability to differentiate between ligands, proposing a novel mechanism for loss-of-function. In summary, these results provide valuable insights into the role of sTREM2 in AD pathology, laying the groundwork for the design of new therapeutic approaches targeting (s)TREM2 in AD.","PeriodicalId":501308,"journal":{"name":"bioRxiv - Bioengineering","volume":"17 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142216596","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The gold standard therapy for peripheral nerve injuries involves surgical repair, which is invasive and leads to major variations in therapeutic outcomes. Because of this, smaller injuries often go untreated. However, alternative, non-invasive routes of administration are currently unviable due to the presence of the blood-nerve barrier (BNB), which prevents passage of small molecules from the blood into the endoneurium and the nerve. This paper demonstrates that ligands on the surface of nanoparticles, called polymersomes, can enable delivery to the nerve through non-invasive intramuscular injections. Polymersomes made from polyethylene glycol (PEG)-b-polylactic acid (PLA) were conjugated with either apolipoprotein E (ApoE) or rabies virus glycoprotein-based peptide, RVG29 (RVG) and loaded with near infrared dye, AlexaFluor647. ApoE was used to target receptors upregulated in post-injury inflammation, while RVG targets neural specific receptors. Untagged, ApoE-tagged, and RVG-tagged polymersomes were injected at 100 mM either intranerve (IN) or intramuscular (IM) into Sprague Dawley rats post sciatic nerve injury. The addition of the ApoE and RVG tags enabled increased AlexaFluor647 fluorescence in the injury site at 1 hour post IN injection compared to the untagged polymersome control. However, only the RVG-tagged polymersomes increased AlexaFluor647 fluorescence after intramuscular injection. Ex vivo analysis of sciatic nerves demonstrated that ApoE-tagged polymersomes enabled the greatest retention of AlexaFluor647 regardless of the injection route. This led us to conclude that using ApoE to target inflammation enabled the greatest retention of polymersome-delivered payloads while RVG to target neural cells more specifically enabled the penetration of polymersome-delivered payloads. Observations were confirmed by calculating area under the curve pharmacokinetic parameters and the use of a two-compartment pharmacokinetic model.
{"title":"Targeted Polymersomes Enable Enhanced Delivery to Peripheral Nerves Post-Injury","authors":"Kayleigh Trumbull, Sophia Fetten, Dru Montgomery, Vanessa Marahrens, Olivia Myers, Noah Arnold, Jeffery L Twiss, Jessica Larsen","doi":"10.1101/2024.09.05.611478","DOIUrl":"https://doi.org/10.1101/2024.09.05.611478","url":null,"abstract":"The gold standard therapy for peripheral nerve injuries involves surgical repair, which is invasive and leads to major variations in therapeutic outcomes. Because of this, smaller injuries often go untreated. However, alternative, non-invasive routes of administration are currently unviable due to the presence of the blood-nerve barrier (BNB), which prevents passage of small molecules from the blood into the endoneurium and the nerve. This paper demonstrates that ligands on the surface of nanoparticles, called polymersomes, can enable delivery to the nerve through non-invasive intramuscular injections. Polymersomes made from polyethylene glycol (PEG)-b-polylactic acid (PLA) were conjugated with either apolipoprotein E (ApoE) or rabies virus glycoprotein-based peptide, RVG29 (RVG) and loaded with near infrared dye, AlexaFluor647. ApoE was used to target receptors upregulated in post-injury inflammation, while RVG targets neural specific receptors. Untagged, ApoE-tagged, and RVG-tagged polymersomes were injected at 100 mM either intranerve (IN) or intramuscular (IM) into Sprague Dawley rats post sciatic nerve injury. The addition of the ApoE and RVG tags enabled increased AlexaFluor647 fluorescence in the injury site at 1 hour post IN injection compared to the untagged polymersome control. However, only the RVG-tagged polymersomes increased AlexaFluor647 fluorescence after intramuscular injection. Ex vivo analysis of sciatic nerves demonstrated that ApoE-tagged polymersomes enabled the greatest retention of AlexaFluor647 regardless of the injection route. This led us to conclude that using ApoE to target inflammation enabled the greatest retention of polymersome-delivered payloads while RVG to target neural cells more specifically enabled the penetration of polymersome-delivered payloads. Observations were confirmed by calculating area under the curve pharmacokinetic parameters and the use of a two-compartment pharmacokinetic model.","PeriodicalId":501308,"journal":{"name":"bioRxiv - Bioengineering","volume":"42 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142216610","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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