Publications by authors named "Sarah Lipp��"

8 Publications

  • Page 1 of 1

Tissue-specific parameters for the design of ECM-mimetic biomaterials.

Acta Biomater 2021 Apr 18. Epub 2021 Apr 18.

Paul M. Rady Department of Mechanical Engineering, University of Colorado - Boulder, 1111 Engineering Center, 427 UCB, Boulder, CO 80309, United States. Electronic address:

The extracellular matrix (ECM) is a complex network of biomolecules that mechanically and biochemically directs cell behavior and is crucial for maintaining tissue function and health. The heterogeneous organization and composition of the ECM varies within and between tissue types, directing mechanics, aiding in cell-cell communication, and facilitating tissue assembly and reassembly during development, injury and disease. As technologies like 3D printing rapidly advance, researchers are better able to recapitulate in vivo tissue properties in vitro; however, tissue-specific variations in ECM composition and organization are not given enough consideration. This is in part due to a lack of information regarding how the ECM of many tissues varies in both homeostatic and diseased states. To address this gap, we describe the components and organization of the ECM, and provide examples for different tissues at various states of disease. While many aspects of ECM biology remain unknown, our goal is to highlight the complexity of various tissues and inspire engineers to incorporate unique components of the native ECM into in vitro platform design and fabrication. Ultimately, we anticipate that the use of biomaterials that incorporate key tissue-specific ECM will lead to in vitro models that better emulate human pathologies. STATEMENT OF SIGNIFICANCE: Biomaterial development primarily emphasizes the engineering of new materials and therapies at the expense of identifying key parameters of the tissue that is being emulated. This can be partially attributed to the difficulty in defining the 3D composition, organization, and mechanics of the ECM within different tissues and how these material properties vary as a function of homeostasis and disease. In this review, we highlight a range of tissues throughout the body and describe how ECM content, cell diversity, and mechanical properties change in diseased tissues and influence cellular behavior. Accurately mimicking the tissue of interest in vitro by using ECM specific to the appropriate state of homeostasis or pathology in vivo will yield results more translatable to humans.
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http://dx.doi.org/10.1016/j.actbio.2021.04.017DOI Listing
April 2021

3D Mapping Reveals a Complex and Transient Interstitial Matrix During Murine Kidney Development.

J Am Soc Nephrol 2021 Apr 19. Epub 2021 Apr 19.

Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana

Background: The extracellular matrix (ECM) is a network of proteins and glycosaminoglycans that provides structural and biochemical cues to cells. In the kidney, the ECM is critical for nephrogenesis; however, the dynamics of ECM composition and how it relates to 3D structure during development is unknown.

Methods: Using embryonic day 14.5 (E14.5), E18.5, postnatal day 3 (P3), and adult kidneys, we fractionated proteins based on differential solubilities, performed liquid chromatography-tandem mass spectrometry, and identified changes in ECM protein content (matrisome). Decellularized kidneys were stained for ECM proteins and imaged in 3D using confocal microscopy.

Results: We observed an increase in interstitial ECM that connects the stromal mesenchyme to the basement membrane (TNXB, COL6A1, COL6A2, COL6A3) between the embryo and adult, and a transient elevation of interstitial matrix proteins (COL5A2, COL12A1, COL26A1, ELN, EMID1, FBN1, LTBP4, THSD4) at perinatal time points. Basement membrane proteins critical for metanephric induction (FRAS1, FREM2) were highest in abundance in the embryo, whereas proteins necessary for integrity of the glomerular basement membrane (COL4A3, COL4A4, COL4A5, LAMB2) were more abundant in the adult. 3D visualization revealed a complex interstitial matrix that dramatically changed over development, including the perinatal formation of fibrillar structures that appear to support the medullary rays.

Conclusion: By correlating 3D ECM spatiotemporal organization with global protein abundance, we revealed novel changes in the interstitial matrix during kidney development. This new information regarding the ECM in developing kidneys offers the potential to inform the design of regenerative scaffolds that can guide nephrogenesis .
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http://dx.doi.org/10.1681/ASN.2020081204DOI Listing
April 2021

Comparative Analysis of the Extracellular Matrix Proteome across the Myotendinous Junction.

J Proteome Res 2020 10 14;19(10):3955-3967. Epub 2020 Sep 14.

Purdue University Interdisciplinary Life Science Program, 155 S. Grant Street, West Lafayette, Indiana 47907, United States.

The myotendinous junction is a highly interdigitated interface designed to transfer muscle-generated force to tendon. Understanding how this interface is formed and organized, as well as identifying tendon- and muscle-specific extracellular matrix (ECM), is critical for designing effective regenerative therapies to restore functionality to damaged muscle-tendon units. However, a comparative analysis of the ECM proteome across this interface has not been conducted. The goal of this study was to resolve the distribution of ECM proteins that are uniformly expressed as well as those specific to each of the muscle, tendon, and junction tissues. The soleus muscles from 5-month-old wild-type C57BL/6 mice were harvested and dissected into the central muscle (M) away from tendon, the junction between muscle and tendon (J) and the tendon (T). Tissues were processed by either homogenizing in guanidine hydrochloride or fractionating to isolate the ECM from more soluble intracellular components and then analyzed using liquid chromatography-tandem mass spectrometry. Overall, we found that both tissue processing methods generated similar ECM profiles. Many ECM were found across the muscle-tendon unit, including type I collagen and associated fibril-regulating proteins. The ECM identified exclusively in M were primarily related to the basal lamina, whereas those specific to T and J tissue included thrombospondins and other matricellular ECM. Type XXII collagen (COL22A1) was restricted to J, and we identified COL5A3 as a potential marker of the muscle-tendon interface. Immunohistochemical analysis of key proteins confirmed the restriction of some basal lamina proteins to M, tenascin-C to T, and COL22A1 to J. COL5A3, PRELP, and POSTN were visualized in the tissue surrounding the junction, suggesting that these proteins play a role in stabilizing the interface. This comparative map provides a guide for tissue-specific ECM that can facilitate the spatial visualization of M, J, and T tissues and inform musculoskeletal regenerative therapies.
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http://dx.doi.org/10.1021/acs.jproteome.0c00248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8325396PMC
October 2020

Computational Hemodynamic Modeling of Arterial Aneurysms: A Mini-Review.

Front Physiol 2020 12;11:454. Epub 2020 May 12.

Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, United States.

Arterial aneurysms are pathological dilations of blood vessels, which can be of clinical concern due to thrombosis, dissection, or rupture. Aneurysms can form throughout the arterial system, including intracranial, thoracic, abdominal, visceral, peripheral, or coronary arteries. Currently, aneurysm diameter and expansion rates are the most commonly used metrics to assess rupture risk. Surgical or endovascular interventions are clinical treatment options, but are invasive and associated with risk for the patient. For aneurysms in locations where thrombosis is the primary concern, diameter is also used to determine the level of therapeutic anticoagulation, a treatment that increases the possibility of internal bleeding. Since simple diameter is often insufficient to reliably determine rupture and thrombosis risk, computational hemodynamic simulations are being developed to help assess when an intervention is warranted. Created from subject-specific data, computational models have the potential to be used to predict growth, dissection, rupture, and thrombus-formation risk based on hemodynamic parameters, including wall shear stress, oscillatory shear index, residence time, and anomalous blood flow patterns. Generally, endothelial damage and flow stagnation within aneurysms can lead to coagulation, inflammation, and the release of proteases, which alter extracellular matrix composition, increasing risk of rupture. In this review, we highlight recent work that investigates aneurysm geometry, model parameter assumptions, and other specific considerations that influence computational aneurysm simulations. By highlighting modeling validation and verification approaches, we hope to inspire future computational efforts aimed at improving our understanding of aneurysm pathology and treatment risk stratification.
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http://dx.doi.org/10.3389/fphys.2020.00454DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7235429PMC
May 2020

Kidney Histopathology and Prediction of Kidney Failure: A Retrospective Cohort Study.

Am J Kidney Dis 2020 09 24;76(3):350-360. Epub 2020 Apr 24.

Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN. Electronic address:

Rationale & Objective: The use of kidney histopathology for predicting kidney failure is not established. We hypothesized that the use of histopathologic features of kidney biopsy specimens would improve prediction of clinical outcomes made using demographic and clinical variables alone.

Study Design: Retrospective cohort study and development of a clinical prediction model.

Setting & Participants: All 2,720 individuals from the Biopsy Biobank Cohort of Indiana who underwent kidney biopsy between 2002 and 2015 and had at least 2 years of follow-up.

New Predictors & Established Predictors: Demographic variables, comorbid conditions, baseline clinical characteristics, and histopathologic features.

Outcomes: Time to kidney failure, defined as sustained estimated glomerular filtration rate ≤ 10mL/min/1.73m.

Analytical Approach: Multivariable Cox regression model with internal validation by bootstrapping. Models including clinical and demographic variables were fit with the addition of histopathologic features. To assess the impact of adding a histopathology variable, the amount of variance explained (r) and the C index were calculated. The impact on prediction was assessed by calculating the net reclassification index for each histopathologic variable and for all combined.

Results: Median follow-up was 3.1 years. Within 5 years of biopsy, 411 (15.1%) patients developed kidney failure. Multivariable analyses including demographic and clinical variables revealed that severe glomerular obsolescence (adjusted HR, 2.03; 95% CI, 1.51-2.03), severe interstitial fibrosis and tubular atrophy (adjusted HR, 1.99; 95% CI, 1.52-2.59), and severe arteriolar hyalinosis (adjusted HR, 1.53; 95% CI, 1.14-2.05) were independently associated with the primary outcome. The addition of all histopathologic variables to the clinical model yielded a net reclassification index for kidney failure of 5.1% (P < 0.001) with a full model C statistic of 0.915. Analyses addressing the competing risk for death, optimism, or shrinkage did not significantly change the results.

Limitations: Selection bias from the use of clinically indicated biopsies and exclusion of patients with less than 2 years of follow-up, as well as reliance on surrogate indicators of kidney failure onset.

Conclusions: A model incorporating histopathologic features from kidney biopsy specimens improved prediction of kidney failure and may be valuable clinically. Future studies will be needed to understand whether even more detailed characterization of kidney tissue may further improve prognostication about the future trajectory of estimated glomerular filtration rate.
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http://dx.doi.org/10.1053/j.ajkd.2019.12.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7483298PMC
September 2020

Mapping the Nephron Exercise Incorporates Multiple Learning Strategies.

MedEdPORTAL 2017 09 28;13:10635. Epub 2017 Sep 28.

First-year Medical Student, Indiana University School of Medicine.

Introduction: Understanding the location and action of nephron transporters and channels is important to the understanding of renal function. As each region of the nephron is unique in its inclusion of specific transporters and channels, mapping of the nephron is an effective first step in understanding overall nephron processing. We describe a small-group, active-learning exercise that facilitates students' ability to understand renal processing within each region of the nephron.

Methods: Following an overview lecture on renal transporters and channels, small groups of students worked cooperatively to map the nephron. This 2-hour, collaborative exercise was developed to reinforce key concepts in renal processing of ions and nutrients and, at the same time, utilize effective learning strategies. Learning strategies incorporated in this exercise include small-group collaboration, peer teaching, retrieval practice using an audience response system, and elaboration through discussion.

Results: Written examination was used to assess student understanding. Students demonstrated higher performance on a subset of questions related to this learning activity compared to the overall exam. Highly positive feedback was provided by a convenience sample of students completing an anonymous survey.

Discussion: This nephron-mapping exercise was an effective means to promote synthesis and analysis of lecture content and engage students in methods that enhance learning.
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http://dx.doi.org/10.15766/mep_2374-8265.10635DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6338137PMC
September 2017

Integrative FourD omics approach profiles the target network of the carbon storage regulatory system.

Nucleic Acids Res 2017 02;45(4):1673-1686

McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, USA.

Multi-target regulators represent a largely untapped area for metabolic engineering and anti-bacterial development. These regulators are complex to characterize because they often act at multiple levels, affecting proteins, transcripts and metabolites. Therefore, single omics experiments cannot profile their underlying targets and mechanisms. In this work, we used an Integrative FourD omics approach (INFO) that consists of collecting and analyzing systems data throughout multiple time points, using multiple genetic backgrounds, and multiple omics approaches (transcriptomics, proteomics and high throughput sequencing crosslinking immunoprecipitation) to evaluate simultaneous changes in gene expression after imposing an environmental stress that accentuates the regulatory features of a network. Using this approach, we profiled the targets and potential regulatory mechanisms of a global regulatory system, the well-studied carbon storage regulatory (Csr) system of Escherichia coli, which is widespread among bacteria. Using 126 sets of proteomics and transcriptomics data, we identified 136 potential direct CsrA targets, including 50 novel ones, categorized their behaviors into distinct regulatory patterns, and performed in vivo fluorescence-based follow up experiments. The results of this work validate 17 novel mRNAs as authentic direct CsrA targets and demonstrate a generalizable strategy to integrate multiple lines of omics data to identify a core pool of regulator targets.
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http://dx.doi.org/10.1093/nar/gkx048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389547PMC
February 2017

Adaptation of Tri-molecular fluorescence complementation allows assaying of regulatory Csr RNA-protein interactions in bacteria.

Biotechnol Bioeng 2015 Feb 26;112(2):365-75. Epub 2014 Sep 26.

The University of Texas at Austin, McKetta Department of Chemical Engineering 200 E. Dean Keeton St. Stop C0400 Austin, Texas, USA 78712.

sRNAs play a significant role in controlling and regulating cellular metabolism. One of the more interesting aspects of certain sRNAs is their ability to make global changes in the cell by interacting with regulatory proteins. In this work, we demonstrate the use of an in vivo Tri-molecular Fluorescence Complementation assay to detect and visualize the central regulatory sRNA-protein interaction of the Carbon Storage Regulatory system in E. coli. The Carbon Storage Regulator consists primarily of an RNA binding protein, CsrA, that alters the activity of mRNA targets and of an sRNA, CsrB, that modulates the activity of CsrA. We describe the construction of a fluorescence complementation system that detects the interactions between CsrB and CsrA. Additionally, we demonstrate that the intensity of the fluorescence of this system is able to detect changes in the affinity of the CsrB-CsrA interaction, as caused by mutations in the protein sequence of CsrA. While previous methods have adopted this technique to study mRNA or RNA localization, this is the first attempt to use this technique to study the sRNA-protein interaction directly in bacteria. This method presents a potentially powerful tool to study complex bacterial RNA protein interactions in vivo.
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http://dx.doi.org/10.1002/bit.25351DOI Listing
February 2015
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