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Hao L, Khajouei F, Rodriguez J, Kim S, Lee EJA. Unlocking the Promise of Decellularized Pancreatic Tissue: A Novel Approach to Support Angiogenesis in Engineered Tissue. Bioengineering (Basel) 2024; 11:183. [PMID: 38391669 PMCID: PMC10886056 DOI: 10.3390/bioengineering11020183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/08/2024] [Accepted: 02/12/2024] [Indexed: 02/24/2024] Open
Abstract
Advancements in regenerative medicine have highlighted the potential of decellularized extracellular matrix (ECM) as a scaffold for organ bioengineering. Although the potential of ECM in major organ systems is well-recognized, studies focusing on the angiogenic effects of pancreatic ECM are limited. This study investigates the capabilities of pancreatic ECM, particularly its role in promoting angiogenesis. Using a Triton-X-100 solution, porcine pancreas was successfully decellularized, resulting in a significant reduction in DNA content (97.1% removal) while preserving key pancreatic ECM components. A three-dimensional ECM hydrogel was then created from this decellularized tissue and used for cell culture. Biocompatibility tests demonstrated enhanced adhesion and proliferation of mouse embryonic stem cell-derived endothelial cells (mES-ECs) and human umbilical vein endothelial cells (HUVECs) in this hydrogel compared to conventional scaffolds. The angiogenic potential was evaluated through tube formation assays, wherein the cells showed superior tube formation capabilities in ECM hydrogel compared to rat tail collagen. The RT-PCR analysis further confirmed the upregulation of pro-angiogenic genes in HUVECs cultured within the ECM hydrogel. Specifically, HUVECs cultured in the ECM hydrogel exhibited a significant upregulation in the expression of MMP2, VEGF and PAR-1, compared to those cultured in collagen hydrogel or in a monolayer condition. The identification of ECM proteins, specifically PRSS2 and Decorin, further supports the efficacy of pancreatic ECM hydrogel as an angiogenic scaffold. These findings highlight the therapeutic promise of pancreatic ECM hydrogel as a candidate for vascularized tissue engineering application.
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Affiliation(s)
- Lei Hao
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - Fariba Khajouei
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - Jaselin Rodriguez
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - Soojin Kim
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - Eun Jung A Lee
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA
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2
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Doherty DT, Khambalia HA, van Dellen D, Jennings RE, Piper Hanley K. Unlocking the post-transplant microenvironment for successful islet function and survival. Front Endocrinol (Lausanne) 2023; 14:1250126. [PMID: 37711891 PMCID: PMC10497759 DOI: 10.3389/fendo.2023.1250126] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/07/2023] [Indexed: 09/16/2023] Open
Abstract
Islet transplantation (IT) offers the potential to restore euglycemia for patients with type 1 diabetes mellitus (T1DM). Despite improvements in islet isolation techniques and immunosuppressive regimes, outcomes remain suboptimal with UK five-year graft survivals (5YGS) of 55% and most patients still requiring exogenous insulin after multiple islet infusions. Native islets have a significant non-endocrine component with dense extra-cellular matrix (ECM), important for islet development, cell survival and function. Collagenase isolation necessarily disrupts this complex islet microenvironment, leaving islets devoid of a supporting framework and increasing vulnerability of transplanted islets. Following portal venous transplantation, a liver injury response is potentially induced, which typically results in inflammation and ECM deposition from liver specific myofibroblasts. The impact of this response may have important impact on islet survival and function. A fibroblast response and ECM deposition at the kidney capsule and eye chamber alongside other implantation sites have been shown to be beneficial for survival and function. Investigating the implantation site microenvironment and the interactions of transplanted islets with ECM proteins may reveal therapeutic interventions to improve IT and stem-cell derived beta-cell therapy.
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Affiliation(s)
- Daniel T. Doherty
- Faculty of Biology, Medicine & Health, University of Manchester, Manchester, United Kingdom
- Department of Renal & Pancreatic Transplantation, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Hussein A. Khambalia
- Faculty of Biology, Medicine & Health, University of Manchester, Manchester, United Kingdom
- Department of Renal & Pancreatic Transplantation, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - David van Dellen
- Faculty of Biology, Medicine & Health, University of Manchester, Manchester, United Kingdom
- Department of Renal & Pancreatic Transplantation, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Rachel E. Jennings
- Faculty of Biology, Medicine & Health, University of Manchester, Manchester, United Kingdom
- Department of Endocrinology, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Karen Piper Hanley
- Faculty of Biology, Medicine & Health, University of Manchester, Manchester, United Kingdom
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3
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Glorieux L, Vandooren L, Derclaye S, Pyr Dit Ruys S, Oncina-Gil P, Salowka A, Herinckx G, Aajja E, Lemoine P, Spourquet C, Lefort H, Henriet P, Tyteca D, Spagnoli FM, Alsteens D, Vertommen D, Pierreux CE. In-Depth Analysis of the Pancreatic Extracellular Matrix during Development for Next-Generation Tissue Engineering. Int J Mol Sci 2023; 24:10268. [PMID: 37373416 DOI: 10.3390/ijms241210268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/04/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
The pancreas is a complex organ consisting of differentiated cells and extracellular matrix (ECM) organized adequately to enable its endocrine and exocrine functions. Although much is known about the intrinsic factors that control pancreas development, very few studies have focused on the microenvironment surrounding pancreatic cells. This environment is composed of various cells and ECM components, which play a critical role in maintaining tissue organization and homeostasis. In this study, we applied mass spectrometry to identify and quantify the ECM composition of the developing pancreas at the embryonic (E) day 14.5 and postnatal (P) day 1 stages. Our proteomic analysis identified 160 ECM proteins that displayed a dynamic expression profile with a shift in collagens and proteoglycans. Furthermore, we used atomic force microscopy to measure the biomechanical properties and found that the pancreatic ECM was soft (≤400 Pa) with no significant change during pancreas maturation. Lastly, we optimized a decellularization protocol for P1 pancreatic tissues, incorporating a preliminary crosslinking step, which effectively preserved the 3D organization of the ECM. The resulting ECM scaffold proved suitable for recellularization studies. Our findings provide insights into the composition and biomechanics of the pancreatic embryonic and perinatal ECM, offering a foundation for future studies investigating the dynamic interactions between the ECM and pancreatic cells.
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Affiliation(s)
- Laura Glorieux
- Cell Biology Unit, de Duve Institute, UCLouvain, 1200 Brussels, Belgium
| | - Laura Vandooren
- Cell Biology Unit, de Duve Institute, UCLouvain, 1200 Brussels, Belgium
| | - Sylvie Derclaye
- Nanobiophysics Lab, Louvain Institute of Biomolecular Science and Technology, UCLouvain, 1348 Louvain-la-Neuve, Belgium
| | | | - Paloma Oncina-Gil
- Nanobiophysics Lab, Louvain Institute of Biomolecular Science and Technology, UCLouvain, 1348 Louvain-la-Neuve, Belgium
| | - Anna Salowka
- Centre for Gene Therapy and Regenerative Medicine, King's College London, Great Maze Pond, London SE1 9RT, UK
| | - Gaëtan Herinckx
- de Duve Institute and MASSPROT Platform, UCLouvain, 1200 Brussels, Belgium
| | - Elias Aajja
- Cell Biology Unit, de Duve Institute, UCLouvain, 1200 Brussels, Belgium
| | - Pascale Lemoine
- Cell Biology Unit, de Duve Institute, UCLouvain, 1200 Brussels, Belgium
| | | | - Hélène Lefort
- Cell Biology Unit, de Duve Institute, UCLouvain, 1200 Brussels, Belgium
| | - Patrick Henriet
- Cell Biology Unit, de Duve Institute, UCLouvain, 1200 Brussels, Belgium
| | - Donatienne Tyteca
- Cell Biology Unit, de Duve Institute, UCLouvain, 1200 Brussels, Belgium
| | - Francesca M Spagnoli
- Centre for Gene Therapy and Regenerative Medicine, King's College London, Great Maze Pond, London SE1 9RT, UK
| | - David Alsteens
- Nanobiophysics Lab, Louvain Institute of Biomolecular Science and Technology, UCLouvain, 1348 Louvain-la-Neuve, Belgium
| | - Didier Vertommen
- de Duve Institute and MASSPROT Platform, UCLouvain, 1200 Brussels, Belgium
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Ha BG, Jang YJ, Lee E, Kim BG, Myung K, Sun W, Jeong SJ. Isolation and identification of extracellular matrix proteins from oil-based CASPERized mouse brains for matrisomal analysis. Heliyon 2023; 9:e14777. [PMID: 37025807 PMCID: PMC10070542 DOI: 10.1016/j.heliyon.2023.e14777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 03/02/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023] Open
Abstract
The extracellular matrix (ECM) components present within all tissues and organs help to maintain the cytoskeletal architecture and tissue morphology. Although the ECM plays a role in cellular events and signaling pathways, it has not been well studied due its insolubility and complexity. Brain tissue has a higher cell density and weaker mechanical strength than other tissues in the body. When removing cells using a general decellularization method to produce scaffolds and obtain ECM proteins, various problems must be considered because tissues are easily damaged. To retain the brain shape and ECM components, we performed decellularization in combination with polymerization. We immersed mouse brains in oil for polymerization and decellularization via O-CASPER (Oil-based Clinically and Experimentally Applicable Acellular Tissue Scaffold Production for Tissue Engineering and Regenerative Medicine) and then isolated ECM components using sequential matrisome preparation reagents (SMPRs), namely, RIPA, PNGase F, and concanavalin A. Adult mouse brains were preserved with our decellularization method. Western blot and LC-MS/MS analyses revealed that ECM components, including collagen and laminin, were isolated efficiently from decellularized mouse brains using SMPRs. Our method will be useful to obtain matrisomal data and perform functional studies using adult mouse brains and other tissues.
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Affiliation(s)
- Byung Geun Ha
- Research Group of Developmental Disorders and Rare Diseases, Korea Brain Research Institute (KBRI), Daegu, 41062, Republic of Korea
| | - Yu-Jin Jang
- Research Group of Developmental Disorders and Rare Diseases, Korea Brain Research Institute (KBRI), Daegu, 41062, Republic of Korea
| | - EunSoo Lee
- Fluorescence Core Imaging Center, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Byung-Gyu Kim
- Center for Genomic Integrity, Institute for Basic Science, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Woong Sun
- Department of Anatomy, Brain Korea 21 Plus Program for Biomedical Science, Korea University College of Medicine, Seoul, 02841, Republic of Korea
| | - Sung-Jin Jeong
- Research Group of Developmental Disorders and Rare Diseases, Korea Brain Research Institute (KBRI), Daegu, 41062, Republic of Korea
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Republic of Korea
- Corresponding author.Research Group of Developmental Disorders and Rare Diseases, Korea Brain Research Institute (KBRI), Daegu, 41062, Republic of Korea.
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Pantoja BTDS, Carvalho RC, Miglino MA, Carreira ACO. The Canine Pancreatic Extracellular Matrix in Diabetes Mellitus and Pancreatitis: Its Essential Role and Therapeutic Perspective. Animals (Basel) 2023; 13:ani13040684. [PMID: 36830471 PMCID: PMC9952199 DOI: 10.3390/ani13040684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/27/2022] [Accepted: 11/29/2022] [Indexed: 02/18/2023] Open
Abstract
Diabetes mellitus and pancreatitis are common pancreatic diseases in dogs, affecting the endocrine and exocrine portions of the organ. Dogs have a significant role in the history of research related to genetic diseases, being considered potential models for the study of human diseases. This review discusses the importance of using the extracellular matrix of the canine pancreas as a model for the study of diabetes mellitus and pancreatitis, in addition to focusing on the importance of using extracellular matrix in new regenerative techniques, such as decellularization and recellularization. Unlike humans, rabbits, mice, and pigs, there are no reports in the literature characterizing the healthy pancreatic extracellular matrix in dogs, in addition to the absence of studies related to matrix components that are involved in triggering diabetes melittus and pancreatitis. The extracellular matrix plays the role of physical support for the cells and allows the regulation of various cellular processes. In this context, it has already been demonstrated that physiologic and pathologic pancreatic changes lead to ECM remodeling, highlighting the importance of an in-depth study of the changes associated with pancreatic diseases.
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Affiliation(s)
- Bruna Tássia dos Santos Pantoja
- Department of Surgery, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Sao Paulo 05508-270, SP, Brazil
| | - Rafael Cardoso Carvalho
- Department of Animal Science, Center for Agricultural and Environmental Sciences, Federal University of Maranhao, Chapadinha 65500-000, MA, Brazil
| | - Maria Angelica Miglino
- Department of Surgery, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Sao Paulo 05508-270, SP, Brazil
| | - Ana Claudia Oliveira Carreira
- Department of Surgery, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Sao Paulo 05508-270, SP, Brazil
- Center for Natural and Human Sciences, Federal University of ABC, Santo Andre 09280-550, SP, Brazil
- Correspondence: or ; Tel.: +55-11-983229615
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6
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Tissue engineering of decellularized pancreas scaffolds for regenerative medicine in diabetes. Acta Biomater 2023; 157:49-66. [PMID: 36427686 DOI: 10.1016/j.actbio.2022.11.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 11/27/2022]
Abstract
Diabetes mellitus is a global disease requiring long-term treatment and monitoring. At present, pancreas or islet transplantation is the only reliable treatment for achieving stable euglycemia in Type I diabetes patients. However, the shortage of viable pancreata for transplantation limits the use of this therapy for the majority of patients. Organ decellularization and recellularization is emerging as a promising solution to overcome the shortage of viable organs for transplantation by providing a potential alternative source of donor organs. Several studies on decellularization and recellularization of rodent, porcine, and human pancreata have been performed, and show promise for generating usable decellularized pancreas scaffolds for subsequent recellularization and transplantation. In this state-of-the-art review, we provide an overview of the latest advances in pancreas decellularization, recellularization, and revascularization. We also discuss clinical considerations such as potential transplantation sites, donor source, and immune considerations. We conclude with an outlook on the remaining work that needs to be done in order to realize the goal of using this technology to create bioengineered pancreata for transplantation in diabetes patients. STATEMENT OF SIGNIFICANCE: Pancreas or islet transplantation is a means of providing insulin-independence in diabetes patients. However, due to the shortage of viable pancreata, whole-organ decellularization and recellularization is emerging as a promising solution to overcome organ shortage for transplantation. Several studies on decellularization and recellularization of rodent, porcine, and human pancreata have shown promise for generating usable decellularized pancreas scaffolds for subsequent recellularization and transplantation. In this state-of-the-art review, we highlight the latest advances in pancreas decellularization, recellularization, and revascularization. We also discuss clinical considerations such as potential transplantation sites, donor source, and immune considerations. We conclude with future work that needs to be done in order to realize clinical translation of bioengineered pancreata for transplantation in diabetes patients.
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7
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Paragomi P, Wang R, Huang JY, Midttun Ø, Ulvik A, Ueland PM, Koh WP, Yuan JM, Luu HN. The Association Between Serum Riboflavin and Flavin Mononucleotide With Pancreatic Cancer: Findings From a Prospective Cohort Study. Pancreas 2023; 52:e127-e134. [PMID: 37523604 PMCID: PMC10399971 DOI: 10.1097/mpa.0000000000002220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
OBJECTIVES Vitamin B2 (riboflavin) has a prime role in metabolic reactions imperative to cell cycle and proliferation. We investigated the associations between serum concentrations of riboflavin flavin mononucleotide with the risk of pancreatic cancer in a nested case-control study involving 58 cases and 104 matched controls. METHODS The Singapore Chinese Health Study, an ongoing prospective cohort study of 63,257 Chinese Singaporeans. Conditional logistic regression method was used to evaluate these associations with adjustment for potential confounders including the level of education, body mass index, smoking status, alcohol consumption, history of diabetes, serum cotinine and pyridoxal 5'-phosphate, estimated glomerular filtration rate, and total methyl donors (ie, the sum of serum choline, betaine, and methionine). RESULTS The risk of pancreatic cancer increased with increasing level of serum riboflavin in a dose-dependent manner, especially in men (Ptrend = 0.003). The odds ratio (95% confidence intervals) of pancreatic cancer for the second and third tertiles of serum riboflavin, compared with the lowest tertile, were 9.92 (1.65-59.77) and 25.59 (3.09-212.00), respectively. This positive association was stronger in individuals with a longer follow-up period (≥7 years). CONCLUSIONS The findings suggest a potential role of riboflavin in the development of pancreatic cancer, especially in men.
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Affiliation(s)
- Pedram Paragomi
- From the UPMC Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Renwei Wang
- From the UPMC Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Joyce Y Huang
- From the UPMC Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA
| | | | - Arve Ulvik
- Laboratory of Clinical Biochemistry, Haukeland University Hospital, Bergen, Norway
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Singh G, Senapati S, Satpathi S, Behera PK, Das B, Nayak B. Establishment of decellularized extracellular matrix scaffold derived from caprine pancreas as a novel alternative template over porcine pancreatic scaffold for prospective biomedical application. FASEB J 2022; 36:e22574. [PMID: 36165227 DOI: 10.1096/fj.202200807r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 08/25/2022] [Accepted: 09/16/2022] [Indexed: 11/11/2022]
Abstract
In this study, the caprine pancreas has been presented as an alternative to the porcine organ for pancreatic xenotransplantation with lesser risk factors. The obtained caprine pancreas underwent a systematic cycle of detergent perfusion for decellularization. It was perfused using anionic (0.5% w/v sodium dodecyl sulfate) as well as non-ionic (0.1% v/v triton X-100, t-octyl phenoxy polyethoxy ethanol) detergents and washed intermittently with 1XPBS supplemented with 0.1% v/v antibiotic and nucleases in a gravitation-driven set-up. After 48 h, a white decellularized pancreas was obtained, and its extracellular matrix (ECM) content was examined for scaffold-like properties. The ECM content was assessed for removal of cellular content, and nuclear material was evaluated with temporal H&E staining. Quantified DNA was found to be present in a negligible amount in the resultant decellularized pancreas tissue (DPT), thus prohibiting it from triggering any immunogenicity. Collagen and fibronectin were confirmed to be preserved upon trichrome and immunohistochemical staining, respectively. SEM and AFM images reveal interconnected collagen fibril networks in the DPT, confirming that collagen was unaffected. sGAG was visualized using Prussian blue staining and quantified with DMMB assay, where DPT has effectively retained this ECM component. Uniaxial tensile analysis revealed that DPT possesses better elasticity than NPT (native pancreatic tissue). Physical parameters like tensile strength, stiffness, biodegradation, and swelling index were retained in the DPT with negligible loss. The cytocompatibility analysis of DPT has shown no cytotoxic effect for up to 72 h on normal insulin-producing cells (MIN-6) and cancerous glioblastoma (LN229) cells in vitro. The scaffold was recellularized using isolated mouse islets, which have established in vitro cell proliferation for up to 9 days. The scaffold received at the end of the decellularization cycle was found to be non-toxic to the cells, retained biological and physical properties of the native ECM, suitable for recellularization, and can be used as a safer and better alternative as a transplantable organ from a xenogeneic source.
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Affiliation(s)
- Garima Singh
- Immunology and Molecular Medicine Laboratory, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Shantibhusan Senapati
- Tumor Microenvironment and Animal Models Laboratory, Institute of Life Sciences, Bhubaneswar, India
| | | | | | - Biswajit Das
- Tumor Microenvironment and Animal Models Laboratory, Institute of Life Sciences, Bhubaneswar, India
| | - Bismita Nayak
- Immunology and Molecular Medicine Laboratory, Department of Life Science, National Institute of Technology, Rourkela, India
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Tremmel DM, Sackett SD, Feeney AK, Mitchell SA, Schaid MD, Polyak E, Chlebeck PJ, Gupta S, Kimple ME, Fernandez LA, Odorico JS. A human pancreatic ECM hydrogel optimized for 3-D modeling of the islet microenvironment. Sci Rep 2022; 12:7188. [PMID: 35504932 PMCID: PMC9065104 DOI: 10.1038/s41598-022-11085-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 04/04/2022] [Indexed: 02/07/2023] Open
Abstract
Extracellular matrix (ECM) plays a multitude of roles, including supporting cells through structural and biochemical interactions. ECM is damaged in the process of isolating human islets for clinical transplantation and basic research. A platform in which islets can be cultured in contact with natural pancreatic ECM is desirable to better understand and support islet health, and to recapitulate the native islet environment. Our study demonstrates the derivation of a practical and durable hydrogel from decellularized human pancreas that supports human islet survival and function. Islets embedded in this hydrogel show increased glucose- and KCl-stimulated insulin secretion, and improved mitochondrial function compared to islets cultured without pancreatic matrix. In extended culture, hydrogel co-culture significantly reduced levels of apoptosis compared to suspension culture and preserved controlled glucose-responsive function. Isolated islets displayed altered endocrine and non-endocrine cell arrangement compared to in situ islets; hydrogel preserved an islet architecture more similar to that observed in situ. RNA sequencing confirmed that gene expression differences between islets cultured in suspension and hydrogel largely fell within gene ontology terms related to extracellular signaling and adhesion. Natural pancreatic ECM improves the survival and physiology of isolated human islets.
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Affiliation(s)
- Daniel M Tremmel
- Division of Transplantation, Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.
| | - Sara Dutton Sackett
- Division of Transplantation, Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.
| | - Austin K Feeney
- Division of Transplantation, Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Samantha A Mitchell
- Division of Transplantation, Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael D Schaid
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA.,William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
| | - Erzsebet Polyak
- Division of Transplantation, Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Peter J Chlebeck
- Division of Transplantation, Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Sakar Gupta
- Division of Transplantation, Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Michelle E Kimple
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA.,William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
| | | | - Jon S Odorico
- Division of Transplantation, Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
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Proteomic and Bioinformatic Analysis of Decellularized Pancreatic Extracellular Matrices. Molecules 2021; 26:molecules26216740. [PMID: 34771149 PMCID: PMC8588251 DOI: 10.3390/molecules26216740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 11/04/2021] [Accepted: 11/06/2021] [Indexed: 01/15/2023] Open
Abstract
Tissue microenvironments are rich in signaling molecules. However, factors in the tissue matrix that can serve as tissue-specific cues for engineering pancreatic tissues have not been thoroughly identified. In this study, we performed a comprehensive proteomic analysis of porcine decellularized pancreatic extracellular matrix (dpECM). By profiling dpECM collected from subjects of different ages and genders, we showed that the detergent-free decellularization method developed in this study permits the preservation of approximately 62.4% more proteins than a detergent-based method. In addition, we demonstrated that dpECM prepared from young pigs contained approximately 68.5% more extracellular matrix proteins than those prepared from adult pigs. Furthermore, we categorized dpECM proteins by biological process, molecular function, and cellular component through gene ontology analysis. Our study results also suggested that the protein composition of dpECM is significantly different between male and female animals while a KEGG enrichment pathway analysis revealed that dpECM protein profiling varies significantly depending on age. This study provides the proteome of pancreatic decellularized ECM in different animal ages and genders, which will help identify the bioactive molecules that are pivotal in creating tissue-specific cues for engineering tissues in vitro.
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Al-Saggaf UM, Usman M, Naseem I, Moinuddin M, Jiman AA, Alsaggaf MU, Alshoubaki HK, Khan S. ECM-LSE: Prediction of Extracellular Matrix Proteins Using Deep Latent Space Encoding of k-Spaced Amino Acid Pairs. Front Bioeng Biotechnol 2021; 9:752658. [PMID: 34722479 PMCID: PMC8552119 DOI: 10.3389/fbioe.2021.752658] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/13/2021] [Indexed: 12/26/2022] Open
Abstract
Extracelluar matrix (ECM) proteins create complex networks of macromolecules which fill-in the extracellular spaces of living tissues. They provide structural support and play an important role in maintaining cellular functions. Identification of ECM proteins can play a vital role in studying various types of diseases. Conventional wet lab-based methods are reliable; however, they are expensive and time consuming and are, therefore, not scalable. In this research, we propose a sequence-based novel machine learning approach for the prediction of ECM proteins. In the proposed method, composition of k-spaced amino acid pair (CKSAAP) features are encoded into a classifiable latent space (LS) with the help of deep latent space encoding (LSE). A comprehensive ablation analysis is conducted for performance evaluation of the proposed method. Results are compared with other state-of-the-art methods on the benchmark dataset, and the proposed ECM-LSE approach has shown to comprehensively outperform the contemporary methods.
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Affiliation(s)
- Ubaid M. Al-Saggaf
- Center of Excellence in Intelligent Engineering Systems, King Abdulaziz University, Jeddah, Saudi Arabia
- Electrical and Computer Engineering Department, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muhammad Usman
- Department of Computer Engineering, Chosun University, Gwangju, South Korea
| | - Imran Naseem
- Research and Development, Love For Data, Karachi, Pakistan
- School of Electrical, Electronic and Computer Engineering, The University of Western Australia, Perth, WA, Australia
- College of Engineering, Karachi Institute of Economics and Technology, Korangi Creek, Karachi, Pakistan
| | - Muhammad Moinuddin
- Center of Excellence in Intelligent Engineering Systems, King Abdulaziz University, Jeddah, Saudi Arabia
- Electrical and Computer Engineering Department, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmad A. Jiman
- Electrical and Computer Engineering Department, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammed U. Alsaggaf
- Center of Excellence in Intelligent Engineering Systems, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Radiology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hitham K. Alshoubaki
- Center of Excellence in Intelligent Engineering Systems, King Abdulaziz University, Jeddah, Saudi Arabia
- Electrical and Computer Engineering Department, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Shujaat Khan
- Department of Bio and Brain Engineering, Daejeon, South Korea
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12
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Tabang DN, Cui Y, Tremmel DM, Ford M, Li Z, Sackett SD, Odorico JS, Li L. Analysis of pancreatic extracellular matrix protein post-translational modifications via electrostatic repulsion-hydrophilic interaction chromatography coupled with mass spectrometry. Mol Omics 2021; 17:652-664. [PMID: 34318855 PMCID: PMC8511275 DOI: 10.1039/d1mo00104c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The pancreas is a vital organ with digestive and endocrine roles, and diseases of the pancreas affect millions of people yearly. A better understanding of the pancreas proteome and its dynamic post-translational modifications (PTMs) is necessary to engineer higher fidelity tissue analogues for use in transplantation. The extracellular matrix (ECM) has major roles in binding and signaling essential to the viability of insulin-producing islets of Langerhans. To characterize PTMs in the pancreas, native and decellularized tissues from four donors were analyzed. N-Glycosylated and phosphorylated peptides were simultaneously enriched via electrostatic repulsion-hydrophilic interaction chromatography and analyzed with mass spectrometry, maximizing PTM information from one workflow. A modified surfactant and chaotropic agent assisted sequential extraction/on-pellet digestion was used to maximize solubility of the ECM. The analysis resulted in the confident identification of 3650 proteins, including 517 N-glycoproteins and 148 phosphoproteins. We identified 214 ECM proteins, of which 99 were N-glycosylated, 18 were phosphorylated, and 9 were found to have both modifications. Collagens, a major component of the ECM, were the most highly glycosylated of the ECM proteins and several were also heavily phosphorylated, raising the possibility of structural and thus functional changes resulting from these modifications. To our knowledge, this work represents the first characterization of PTMs in pancreatic ECM proteins. This work provides a basal profile of PTMs in the healthy human pancreatic ECM, laying the foundation for future investigations to determine disease-specific changes such as in diabetes and pancreatic cancer, and potentially helping to guide the development of tissue replacement constructs. Data are available via ProteomeXchange with identifier PXD025048.
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Affiliation(s)
- Dylan Nicholas Tabang
- Department of Chemistry, University of Wisconsin-Madison, 777 Highland Ave., Madison, WI, 53706, USA.
| | - Yusi Cui
- Department of Chemistry, University of Wisconsin-Madison, 777 Highland Ave., Madison, WI, 53706, USA.
| | - Daniel M Tremmel
- Department of Surgery, Division of Transplantation, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Megan Ford
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Zihui Li
- Department of Chemistry, University of Wisconsin-Madison, 777 Highland Ave., Madison, WI, 53706, USA.
| | - Sara Dutton Sackett
- Department of Surgery, Division of Transplantation, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jon S Odorico
- Department of Surgery, Division of Transplantation, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 777 Highland Ave., Madison, WI, 53706, USA.
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
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13
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Hashemi J, Kajbafzadeh AM, Ghorbani F, Soleimani M, Arefian E, Khorramirouz R, Enderami SE, Pasalar P. Application of iPSCs derived pancreatic β-like cells using pancreatic bio-scaffold. Exp Cell Res 2021; 405:112667. [PMID: 34107273 DOI: 10.1016/j.yexcr.2021.112667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 11/17/2022]
Abstract
This study aimed toengineer a pancreatic tissue. Intact rat pancreases were successfully decellularized, and were reseeded with human-induced pluripotent stem cells using different 2D and 3D culture growth factors. The differentiation process was assessed for the presence of a pancreas-like tissue. The histology and SEM analysis revealed cell attachment in all samples, except for the Exp4, and the Flow-cytometry provided 87% viability for the differentiated cells. In Exp1, PDX1 with the positive expression of 2.87±0.06 was dramatically higher than Exp2 with a 2.44±0.06 reaction. NGN3-reactions were 8±0.1 and 6.6±0.2 in Exp1 and Exp2 at P < 0.05, respectively. C-peptide with the expression of 7.5±0.7 in Exp3 was almost equal to that in Exp1 and Exp2. Glucagon (5.1±1) and PDX1 (3.2±0.82) in Exp3 indicated no significant difference. The significant upregulations of pancreatic endocrine markers (PDX1 and NGN3), and the cell-specific glucose transporter (GLUT2) were observed in the differentiated IPCs in the 3D culture of Exp2 after 21 days. The highest insulin and C-peptide concentrations were observed in Exp2. In Exp3, insulin secretion in response to high glucose and 10 mM arginine was 42.43 ±6.34 μU/ml. A decellularized pancreas in the presence of hiPSCs and growth factors could be efficiently used as a natural scaffold.
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Affiliation(s)
- Javad Hashemi
- Department of Pathobiology and Laboratory Sciences, Faculty of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Abdol-Mohammad Kajbafzadeh
- Pediatric Urology and Regenerative Medicine Research Center, Section of Tissue Engineering and Stem Cells Therapy, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Fariba Ghorbani
- Tracheal Diseases Research Center (TDRC), National Research Institute of Tuberculosis & Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoud Soleimani
- Department of Hematology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ehsan Arefian
- Molecular Virology Lab, Department of Microbiology, School of Biology, College of Science, University of Tehran, Iran
| | - Reza Khorramirouz
- Pediatric Urology and Regenerative Medicine Research Center, Section of Tissue Engineering and Stem Cells Therapy, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Ehsan Enderami
- Molecular and cell biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Parvin Pasalar
- Department of Clinical Biochemistry, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
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14
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Li X, Zhang S, Wong KC. Deep embedded clustering with multiple objectives on scRNA-seq data. Brief Bioinform 2021; 22:6209682. [PMID: 33822877 DOI: 10.1093/bib/bbab090] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/17/2021] [Accepted: 02/25/2021] [Indexed: 12/19/2022] Open
Abstract
In recent years, single-cell RNA sequencing (scRNA-seq) technologies have been widely adopted to interrogate gene expression of individual cells; it brings opportunities to understand the underlying processes in a high-throughput manner. Deep embedded clustering (DEC) was demonstrated successful in high-dimensional sparse scRNA-seq data by joint feature learning and cluster assignment for identifying cell types simultaneously. However, the deep network architecture for embedding clustering is not trivial to optimize. Therefore, we propose an evolutionary multiobjective DEC by synergizing the multiobjective evolutionary optimization to simultaneously evolve the hyperparameters and architectures of DEC in an automatic manner. Firstly, a denoising autoencoder is integrated into the DEC to project the high-dimensional sparse scRNA-seq data into a low-dimensional space. After that, to guide the evolution, three objective functions are formulated to balance the model's generality and clustering performance for robustness. Meanwhile, migration and mutation operators are proposed to optimize the objective functions to select the suitable hyperparameters and architectures of DEC in the multiobjective framework. Multiple comparison analyses are conducted on twenty synthetic data and eight real data from different representative single-cell sequencing platforms to validate the effectiveness. The experimental results reveal that the proposed algorithm outperforms other state-of-the-art clustering methods under different metrics. Meanwhile, marker genes identification, gene ontology enrichment and pathology analysis are conducted to reveal novel insights into the cell type identification and characterization mechanisms.
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Affiliation(s)
- Xiangtao Li
- School of Artificial Intelligence Jilin University, Jilin, China
| | - Shixiong Zhang
- Department of Computer science City University of Hong Kong, Hong Kong SAR
| | - Ka-Chun Wong
- Department of Computer science City University of Hong Kong, Hong Kong SAR
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15
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Proteome-wide and matrisome-specific alterations during human pancreas development and maturation. Nat Commun 2021; 12:1020. [PMID: 33589611 PMCID: PMC7884717 DOI: 10.1038/s41467-021-21261-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 01/19/2021] [Indexed: 01/31/2023] Open
Abstract
The extracellular matrix (ECM) is unique to each tissue and capable of guiding cell differentiation, migration, morphology, and function. The ECM proteome of different developmental stages has not been systematically studied in the human pancreas. In this study, we apply mass spectrometry-based quantitative proteomics strategies using N,N-dimethyl leucine isobaric tags to delineate proteome-wide and ECM-specific alterations in four age groups: fetal (18-20 weeks gestation), juvenile (5-16 years old), young adults (21-29 years old) and older adults (50-61 years old). We identify 3,523 proteins including 185 ECM proteins and quantify 117 of them. We detect previously unknown proteome and matrisome features during pancreas development and maturation. We also visualize specific ECM proteins of interest using immunofluorescent staining and investigate changes in ECM localization within islet or acinar compartments. This comprehensive proteomics analysis contributes to an improved understanding of the critical roles that ECM plays throughout human pancreas development and maturation.
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16
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Burganova G, Bridges C, Thorn P, Landsman L. The Role of Vascular Cells in Pancreatic Beta-Cell Function. Front Endocrinol (Lausanne) 2021; 12:667170. [PMID: 33981287 PMCID: PMC8109179 DOI: 10.3389/fendo.2021.667170] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/08/2021] [Indexed: 12/13/2022] Open
Abstract
Insulin-producing β-cells constitute the majority of the cells in the pancreatic islets. Dysfunction of these cells is a key factor in the loss of glucose regulation that characterizes type 2 diabetes. The regulation of many of the functions of β-cells relies on their close interaction with the intra-islet microvasculature, comprised of endothelial cells and pericytes. In addition to providing islet blood supply, cells of the islet vasculature directly regulate β-cell activity through the secretion of growth factors and other molecules. These factors come from capillary mural pericytes and endothelial cells, and have been shown to promote insulin gene expression, insulin secretion, and β-cell proliferation. This review focuses on the intimate crosstalk of the vascular cells and β-cells and its role in glucose homeostasis and diabetes.
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Affiliation(s)
- Guzel Burganova
- Department of Cell and Development Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Claire Bridges
- Charles Perkins Centre, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, Australia
| | - Peter Thorn
- Charles Perkins Centre, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, Australia
| | - Limor Landsman
- Department of Cell and Development Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- *Correspondence: Limor Landsman,
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17
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Asthana A, Tamburrini R, Chaimov D, Gazia C, Walker SJ, Van Dyke M, Tomei A, Lablanche S, Robertson J, Opara EC, Soker S, Orlando G. Comprehensive characterization of the human pancreatic proteome for bioengineering applications. Biomaterials 2020; 270:120613. [PMID: 33561625 DOI: 10.1016/j.biomaterials.2020.120613] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/27/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023]
Abstract
Interactions between the pancreatic extracellular matrix (ECM) and islet cells are known to regulate multiple aspects of islet physiology, including survival, proliferation, and glucose-stimulated insulin secretion. Recognizing the essential role of ECM in islet survival and function, various engineering approaches have been developed that aim to utilize ECM-based materials to recreate a native-like microenvironment. However, a major impediment to the success of these approaches has been the lack of a robust and comprehensive characterization of the human pancreatic proteome. Herein, by combining mass spectrometry (MS) and multiplex ELISA, we have provided an improved workflow for the in-depth profiling of the proteome, including minor constituents that are generally underrepresented. Moreover, we have further validated the effectiveness of our detergent-free decellularization protocol in the removal of cellular proteins and retention of the matrisome. It has also been established that the decellularized ECM and its derivatives can provide more tissue-specific cues than traditionally used biological scaffolds and are therefore more physiologically relevant for the development of hydrogels, bioinks and medium additives, in order to create a pancreatic niche. The data generated in this study would contribute significantly to the efforts of comprehensively defining the ECM atlas and also serve as a standard for the human pancreatic proteome to provide further guidance for design and engineering strategies for improved tissue engineering scaffolds.
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Affiliation(s)
- Amish Asthana
- Department of Surgery, Wake Forest Baptist Medical Center, Medical Center Boulevard, Winston Salem, USA; Wake Forest Institute for Regenerative Medicine, Winston Salem, USA; Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, USA
| | - Riccardo Tamburrini
- Department of Surgery, Wake Forest Baptist Medical Center, Medical Center Boulevard, Winston Salem, USA; Wake Forest Institute for Regenerative Medicine, Winston Salem, USA; Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, USA
| | - Deborah Chaimov
- Department of Surgery, Wake Forest Baptist Medical Center, Medical Center Boulevard, Winston Salem, USA; Wake Forest Institute for Regenerative Medicine, Winston Salem, USA; Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, USA
| | - Carlo Gazia
- Department of Surgery, Wake Forest Baptist Medical Center, Medical Center Boulevard, Winston Salem, USA; Wake Forest Institute for Regenerative Medicine, Winston Salem, USA; Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, USA
| | - Stephen J Walker
- Wake Forest Institute for Regenerative Medicine, Winston Salem, USA; Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, USA
| | - Mark Van Dyke
- Department of Biomedical Engineering and Mechanics, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Alice Tomei
- Diabetes Research Institute, University of Miami, Miami, USA
| | - Sandrine Lablanche
- Grenoble Alps University, Laboratory of Fundamental and Applied Bioenergetics (LBFA), And Environmental and System Biology (BEeSy), Grenoble, France; Inserm, U1055, Grenoble, France
| | - John Robertson
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA, USA
| | - Emmanuel C Opara
- Wake Forest Institute for Regenerative Medicine, Winston Salem, USA; Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, USA
| | - Shay Soker
- Wake Forest Institute for Regenerative Medicine, Winston Salem, USA; Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, USA
| | - Giuseppe Orlando
- Department of Surgery, Wake Forest Baptist Medical Center, Medical Center Boulevard, Winston Salem, USA; Wake Forest Institute for Regenerative Medicine, Winston Salem, USA; Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, USA.
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18
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Choi SR, Yang Y, Huang KY, Kong HJ, Flick MJ, Han B. Engineering of biomaterials for tumor modeling. MATERIALS TODAY. ADVANCES 2020; 8:100117. [PMID: 34541484 PMCID: PMC8448271 DOI: 10.1016/j.mtadv.2020.100117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Development of biomaterials mimicking tumor and its microenvironment has recently emerged for the use of drug discovery, precision medicine, and cancer biology. These biomimetic models have developed by reconstituting tumor and stroma cells within the 3D extracellular matrix. The models are recently extended to recapitulate the in vivo tumor microenvironment, including biological, chemical, and mechanical conditions tailored for specific cancer type and its microenvironment. In spite of the recent emergence of various innovative engineered tumor models, many of these models are still early stage to be adapted for cancer research. In this article, we review the current status of biomaterials engineering for tumor models considering three main aspects - cellular engineering, matrix engineering, and engineering for microenvironmental conditions. Considering cancer-specific variability in these aspects, our discussion is focused on pancreatic cancer, specifically pancreatic ductal adenocarcinoma (PDAC). In addition, we further discussed the current challenges and future opportunities to create reliable and relevant tumor models.
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Affiliation(s)
- Sae Rome Choi
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, USA
| | - Yi Yang
- Department of Pathology and Laboratory Medicine, Lineberger Comprehensive Cancer Center, and Blood Research Center, University of North Carolina, Chapel Hill, NC, USA
| | - Kai-Yu Huang
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hyun Joon Kong
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Matthew J. Flick
- Department of Pathology and Laboratory Medicine, Lineberger Comprehensive Cancer Center, and Blood Research Center, University of North Carolina, Chapel Hill, NC, USA
| | - Bumsoo Han
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, USA
- Weldon School of Biomedical Engineering and Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, USA
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19
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Knott SJ, Brown KA, Josyer H, Carr A, Inman D, Jin S, Friedl A, Ponik SM, Ge Y. Photocleavable Surfactant-Enabled Extracellular Matrix Proteomics. Anal Chem 2020; 92:15693-15698. [PMID: 33232116 DOI: 10.1021/acs.analchem.0c03104] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The extracellular matrix (ECM) provides an architectural meshwork that surrounds and supports cells. The dysregulation of heavily post-translationally modified ECM proteins directly contributes to various diseases. Mass spectrometry (MS)-based proteomics is an ideal tool to identify ECM proteins and characterize their post-translational modifications, but ECM proteomics remains challenging owing to the extremely low solubility of the ECM. Herein, enabled by effective solubilization of ECM proteins using our recently developed photocleavable surfactant, Azo, we have developed a streamlined ECM proteomic strategy that allows fast tissue decellularization, efficient extraction and enrichment of ECM proteins, and rapid digestion prior to reversed-phase liquid chromatography (RPLC)-MS analysis. A total of 173 and 225 unique ECM proteins from mouse mammary tumors have been identified using 1D and 2D RPLC-MS/MS, respectively. Moreover, 87 (from 1DLC-MS/MS) and 229 (from 2DLC-MS/MS) post-translational modifications of ECM proteins, including glycosylation, phosphorylation, and hydroxylation, were identified and localized. This Azo-enabled ECM proteomics strategy will streamline the analysis of ECM proteins and promote the study of ECM biology.
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Affiliation(s)
- Samantha J Knott
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Kyle A Brown
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Harini Josyer
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Austin Carr
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - David Inman
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Andreas Friedl
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, 1685 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Suzanne M Ponik
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States.,Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, Wisconsin 53705, United States.,Human Proteomics Program, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, Wisconsin 53705, United States
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20
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Sanders KL, Edwards JL. Nano-liquid chromatography-mass spectrometry and recent applications in omics investigations. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:4404-4417. [PMID: 32901622 PMCID: PMC7530103 DOI: 10.1039/d0ay01194k] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Liquid chromatography coupled to mass spectrometry (LC-MS) is one of the most powerful tools in identifying and quantitating molecular species. Decreasing column diameter from the millimeter to micrometer scale is now a well-developed method which allows for sample limited analysis. Specific fabrication of capillary columns is required for proper implementation and optimization when working in the nanoflow regime. Coupling the capillary column to the mass spectrometer for electrospray ionization (ESI) requires reduction of the subsequent emitter tip. Reduction of column diameter to capillary scale can produce improved chromatographic efficiency and the reduction of emitter tip size increased sensitivity of the electrospray process. This improved sensitivity and ionization efficiency is valuable in analysis of precious biological samples where analytes vary in size, ion affinity, and concentration. In this review we will discuss common approaches and challenges in implementing nLC-MS methods and how the advantages can be leveraged to investigate a wide range of biomolecules.
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21
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Meier RPH, Meyer J, Muller YD, Szot GL, Bédat B, Andres A, Massé N, Lablanche S, Puppa G, Bosco D, Berney T. Pancreas collagen digestion during islet of Langerhans isolation-a prospective study. Transpl Int 2020; 33:1516-1528. [PMID: 32852857 DOI: 10.1111/tri.13725] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/03/2020] [Accepted: 08/20/2020] [Indexed: 12/12/2022]
Abstract
The success of pancreas islet isolation largely depends on donor characteristics, including extracellular matrix composition of which collagen is the main element. We hypothesized that isolation yields are proportional to collagen digestion percentage, and aimed to determine a threshold that predicts isolation success. The amount of pancreas collagen (I-V) was determined using colorimetry prior to and after the digestion process in 52 human islet isolations. Collagen I-V and VI were also assessed histologically. We identified a collagen digestion threshold of ≥ 60% as an independent factor beyond which an islet preparation has a ninefold increased odds of yielding ≥ 250 000 islet equivalents (IEQ) (P = 0.009) and a sixfold increased odds of being transplanted (P = 0.015). Preparations with ≥ 60% collagen digestion (n = 35) yielded 283 017 ± 164 214 IEQ versus 180 142 ± 85 397 in the < 60% collagen digestion group (n = 17) (P = 0.016); respectively 62.9% versus 29.4% of those were transplanted (P = 0.024). Common donor characteristics, initial collagen content, enzyme blend, and digestion times were not associated with collagen digestion percentage variations. Donor age positively correlated with the amount of collagen VI (P = 0.013). There was no difference in islet graft survival between high and low digestion groups. We determined that a 60% pancreas collagen digestion is the threshold beyond which an islet isolation is likely to be successful and transplanted.
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Affiliation(s)
- Raphael P H Meier
- Cell Isolation and Transplantation Center, Department of Surgery, University of Geneva Hospitals and School of Medicine, Geneva, Switzerland.,Department of Surgery, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jeremy Meyer
- Cell Isolation and Transplantation Center, Department of Surgery, University of Geneva Hospitals and School of Medicine, Geneva, Switzerland
| | - Yannick D Muller
- Cell Isolation and Transplantation Center, Department of Surgery, University of Geneva Hospitals and School of Medicine, Geneva, Switzerland.,Transplant Surgery, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Gregory L Szot
- Transplant Surgery, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Benoît Bédat
- Cell Isolation and Transplantation Center, Department of Surgery, University of Geneva Hospitals and School of Medicine, Geneva, Switzerland
| | - Axel Andres
- Cell Isolation and Transplantation Center, Department of Surgery, University of Geneva Hospitals and School of Medicine, Geneva, Switzerland.,Division of Transplantation, Department of Surgery, University of Geneva Hospitals and School of Medicine, Geneva, Switzerland
| | - Nathalie Massé
- Division of Transplantation, Department of Surgery, University of Geneva Hospitals and School of Medicine, Geneva, Switzerland
| | - Sandrine Lablanche
- Grenoble Alpes University, Grenoble, France.,Laboratory of Fundamental and Applied Bioenergetics Grenoble, Inserm U1055, Grenoble, France
| | - Giacomo Puppa
- Diagnostic Department, Geneva University Hospital, Geneva, Switzerland.,Department of Pathology and Immunology, University of Geneva Medical School, Geneva, Switzerland
| | - Domenico Bosco
- Cell Isolation and Transplantation Center, Department of Surgery, University of Geneva Hospitals and School of Medicine, Geneva, Switzerland
| | - Thierry Berney
- Cell Isolation and Transplantation Center, Department of Surgery, University of Geneva Hospitals and School of Medicine, Geneva, Switzerland.,Division of Transplantation, Department of Surgery, University of Geneva Hospitals and School of Medicine, Geneva, Switzerland
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22
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The human liver matrisome - Proteomic analysis of native and fibrotic human liver extracellular matrices for organ engineering approaches. Biomaterials 2020; 257:120247. [PMID: 32739662 DOI: 10.1016/j.biomaterials.2020.120247] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 07/05/2020] [Accepted: 07/16/2020] [Indexed: 02/06/2023]
Abstract
The production of biomaterials that endow significant morphogenic and microenvironmental cues for the constitution of cell integration and regeneration remains a key challenge in the successful implementation of functional organ replacements. Despite the vast development in the production of biological and architecturally native matrices, the complex compositions and pivotal figures by which the human matrisome mediates many of its essential functions are yet to be defined. Here we present a thorough analysis of the native human liver proteomic landscape using decellularization and defatting protocols to create extracellular matrix scaffolds of natural origin that can further be used in both bottom-up and top-down approaches in tissue engineering based organ replacements. Furthermore, by analyzing human liver extracellular matrices in different stages of fibrosis and cirrhosis, we have identified distinct attributes of these tissues that could potentially be exploited therapeutically and thus require further investigation. The general experimental pipeline presented in this study is applicable to any type of tissue and can be widely used for different approaches in regenerative medicine and in the construction of novel biomaterials for organ engineering approaches.
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23
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24
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Prediction of Extracellular Matrix Proteins by Fusing Multiple Feature Information, Elastic Net, and Random Forest Algorithm. MATHEMATICS 2020. [DOI: 10.3390/math8020169] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Extracellular matrix (ECM) proteins play an important role in a series of biological processes of cells. The study of ECM proteins is helpful to further comprehend their biological functions. We propose ECMP-RF (extracellular matrix proteins prediction by random forest) to predict ECM proteins. Firstly, the features of the protein sequence are extracted by combining encoding based on grouped weight, pseudo amino-acid composition, pseudo position-specific scoring matrix, a local descriptor, and an autocorrelation descriptor. Secondly, the synthetic minority oversampling technique (SMOTE) algorithm is employed to process the class imbalance data, and the elastic net (EN) is used to reduce the dimension of the feature vectors. Finally, the random forest (RF) classifier is used to predict the ECM proteins. Leave-one-out cross-validation shows that the balanced accuracy of the training and testing datasets is 97.3% and 97.9%, respectively. Compared with other state-of-the-art methods, ECMP-RF is significantly better than other predictors.
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25
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Lammert E, Thorn P. The Role of the Islet Niche on Beta Cell Structure and Function. J Mol Biol 2019; 432:1407-1418. [PMID: 31711959 DOI: 10.1016/j.jmb.2019.10.032] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 01/15/2023]
Abstract
The islets of Langerhans or pancreatic islets are pivotal in the control of blood glucose and are complex microorgans embedded within the larger volume of the exocrine pancreas. Humans can have ~3.2 million islets [1] which, to our current knowledge, function in a similar manner to sense circulating blood glucose levels and respond with the secretion of a mix of different hormones that act to maintain glucose concentrations around a specific set point [2]. At a cellular level, the control of hormone secretion by glucose and other secretagogues is well-understood [3]. The key signal cascades have been identified and many details of the secretory process are known. However, if we shift focus from single cells and consider cells within intact islets, we do not have a comprehensive model as to how the islet environment influences cell function and how the islets work as a whole. This is important because there is overwhelming evidence that the structure and function of the individual endocrine cells are dramatically affected by the islet environment [4,5]. Uncovering the influence of this islet niche might drive future progress in treatments for Type 2 diabetes [6] and cell replacement therapies for Type 1 diabetes [7]. In this review, we focus on the insulin secreting beta cells and their interactions with the immediate environment that surrounds them including endocrine-endocrine interactions and contacts with capillaries.
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Affiliation(s)
- Eckhard Lammert
- Institute of Metabolic Physiology, Heinrich Heine University, Düsseldorf, Germany; Institute for Vascular and Islet Cell Biology, German Diabetes Center, Leibniz Center for Diabetes Research, Heinrich Heine University, Düsseldorf, Germany; German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Peter Thorn
- Charles Perkins Centre, School of Medical Sciences, University of Sydney, Camperdown, NSW 2006, Australia.
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