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Quansah E, Shaik TA, Çevik E, Wang X, Höppener C, Meyer-Zedler T, Deckert V, Schmitt M, Popp J, Krafft C. Investigating biochemical and structural changes of glycated collagen using multimodal multiphoton imaging, Raman spectroscopy, and atomic force microscopy. Anal Bioanal Chem 2023; 415:6257-6267. [PMID: 37640827 PMCID: PMC10558391 DOI: 10.1007/s00216-023-04902-5] [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: 06/07/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 08/31/2023]
Abstract
Advanced glycation end products (AGEs) form extracellular crosslinking with collagenous proteins, which contributes to the development of diabetic complications. In this study, AGEs-related pentosidine (PENT) crosslinks-induced structural and biochemical changes are studied using multimodal multiphoton imaging, Raman spectroscopy and atomic force microscopy (AFM). Decellularized equine pericardium (EP) was glycated with four ribose concentrations ranging between 5 and 200 mM and monitored for up to 30 days. Two-photon excited fluorescence (TPEF) and second harmonic generation (SHG) microscopic imaging probed elastin and collagen fibers, respectively. The glycated EP showed a decrease in the SHG intensities associated with loss of non-centrosymmetry of collagen and an increase of TPEF intensities associated with PENT crosslinks upon glycation. TPEF signals from elastin fibers were unaffected. A three-dimensional reconstruction with SHG + TPEF z-stack images visualized the distribution of collagen and elastin within the EP volume matrix. In addition, Raman spectroscopy (RS) detected changes in collagen-related bands and discriminated glycated from untreated EP. Furthermore, AFM scans showed that the roughness increases and the D-unit structure of fibers remained unchanged during glycation. The PENT crosslinked-induced changes are discussed in the context of previous studies of glutaraldehyde- and genipin-induced crosslinking and collagenase-induced digestion of collagen. We conclude that TPEF, SHG, RS, and AFM are effective, label-free, and non-destructive methods to investigate glycated tissues, differentiate crosslinking processes, and characterize general collagen-associated and disease-related changes, in particular by their RS fingerprints.
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Affiliation(s)
- Elsie Quansah
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Member of the Leibniz Center for Photonics in Infectious Research (LPI), Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany
- Leibniz Institute of Photonic Technology (IPHT), Member of Leibniz Health Technologies, Member of the Leibniz Center for Photonics in Infectious Research (LPI), Albert-Einstein-Straße 9, 07745, Jena, Germany
| | - Tanveer Ahmed Shaik
- Leibniz Institute of Photonic Technology (IPHT), Member of Leibniz Health Technologies, Member of the Leibniz Center for Photonics in Infectious Research (LPI), Albert-Einstein-Straße 9, 07745, Jena, Germany
| | - Ecehan Çevik
- Leibniz Institute of Photonic Technology (IPHT), Member of Leibniz Health Technologies, Member of the Leibniz Center for Photonics in Infectious Research (LPI), Albert-Einstein-Straße 9, 07745, Jena, Germany
| | - Xinyue Wang
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Member of the Leibniz Center for Photonics in Infectious Research (LPI), Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany
- Leibniz Institute of Photonic Technology (IPHT), Member of Leibniz Health Technologies, Member of the Leibniz Center for Photonics in Infectious Research (LPI), Albert-Einstein-Straße 9, 07745, Jena, Germany
| | - Christiane Höppener
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Member of the Leibniz Center for Photonics in Infectious Research (LPI), Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany
- Leibniz Institute of Photonic Technology (IPHT), Member of Leibniz Health Technologies, Member of the Leibniz Center for Photonics in Infectious Research (LPI), Albert-Einstein-Straße 9, 07745, Jena, Germany
| | - Tobias Meyer-Zedler
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Member of the Leibniz Center for Photonics in Infectious Research (LPI), Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany
- Leibniz Institute of Photonic Technology (IPHT), Member of Leibniz Health Technologies, Member of the Leibniz Center for Photonics in Infectious Research (LPI), Albert-Einstein-Straße 9, 07745, Jena, Germany
| | - Volker Deckert
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Member of the Leibniz Center for Photonics in Infectious Research (LPI), Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany
- Leibniz Institute of Photonic Technology (IPHT), Member of Leibniz Health Technologies, Member of the Leibniz Center for Photonics in Infectious Research (LPI), Albert-Einstein-Straße 9, 07745, Jena, Germany
| | - Michael Schmitt
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Member of the Leibniz Center for Photonics in Infectious Research (LPI), Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany
- Leibniz Institute of Photonic Technology (IPHT), Member of Leibniz Health Technologies, Member of the Leibniz Center for Photonics in Infectious Research (LPI), Albert-Einstein-Straße 9, 07745, Jena, Germany
| | - Jürgen Popp
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Member of the Leibniz Center for Photonics in Infectious Research (LPI), Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany
- Leibniz Institute of Photonic Technology (IPHT), Member of Leibniz Health Technologies, Member of the Leibniz Center for Photonics in Infectious Research (LPI), Albert-Einstein-Straße 9, 07745, Jena, Germany
| | - Christoph Krafft
- Leibniz Institute of Photonic Technology (IPHT), Member of Leibniz Health Technologies, Member of the Leibniz Center for Photonics in Infectious Research (LPI), Albert-Einstein-Straße 9, 07745, Jena, Germany.
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Shortreed NA, Panicker AJ, Mangalaparthi KK, Zhong J, Pandey A, Griffiths LG. Optimization of a high-throughput shotgun immunoproteomics pipeline for antigen identification. J Proteomics 2023; 281:104906. [PMID: 37059220 PMCID: PMC10399726 DOI: 10.1016/j.jprot.2023.104906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/28/2023] [Accepted: 04/11/2023] [Indexed: 04/16/2023]
Abstract
Identification of proteins which initiate and/or perpetuate adaptive immune responses has potential to greatly impact pre-clinical and clinical work across numerous fields. To date, however, the methodologies available to identify antigens responsible for driving adaptive immune responses have been plagued by numerous issues which have drastically limited their widespread adoption. Therefore, in this study, we sought to optimize a shotgun immunoproteomics approach to alleviate these persistent issues and create a high-throughput, quantitative methodology for antigen identification. Three individual components of a previously published approach, namely the protein extraction, antigen elution, and LC-MS/MS analysis steps, were optimized in a systematic manner. These studies determined that preparation of protein extracts using a one-step tissue disruption method in immunoprecipitation (IP) buffer, eluting antigens from affinity chromatography columns with 1% trifluoroacetic acid (TFA), and TMT-labeling & multiplexing equal volumes of eluted samples for LC-MS/MS analysis, resulted in quantitative longitudinal antigen identification, with reduced variability between replicates and increased total number of antigens identified. This optimized pipeline provides a multiplexed, highly reproducible, and fully quantitative approach to antigen identification which is broadly applicable to determine the role of antigenic proteins in inciting (i.e., primary antigens) and perpetuating (i.e., secondary antigens) a wide range of diseases. SIGNIFICANCE: Using a systematic, hypothesis-driven approach, we identified potential improvements for three individual steps of a previously published approach for antigen-identification. Optimization of each step created a methodology which resolved many of the persistent issues associated with previous antigen identification approaches. The optimized high-throughput shotgun immunoproteomics approach described herein identifies more than five times as many unique antigens as the previously published method, greatly reduces protocol cost and mass spectrometry time per experiment, minimizes both inter- and intra-experimental variability, and ensures each experiment is fully quantitative. Ultimately, this optimized antigen identification approach has the potential to facilitate novel antigen identification studies, allowing evaluation of the adaptive immune response in a longitudinal manner and encourage innovations in a wide array of fields.
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Affiliation(s)
- Nicholas A Shortreed
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA; Department of Immunology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA; Department of Cardiovascular Medicine, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA.
| | - Anjali J Panicker
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA; Department of Immunology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA; Department of Cardiovascular Medicine, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA.
| | - Kiran K Mangalaparthi
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA.
| | - Jun Zhong
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA.
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA; Center for Individualized Medicine, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA.
| | - Leigh G Griffiths
- Department of Cardiovascular Medicine, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA; Department of Physiology & Biomedical Engineering, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA.
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Shaik TA, Baria E, Wang X, Korinth F, Lagarto JL, Höppener C, Pavone FS, Deckert V, Popp J, Cicchi R, Krafft C. Structural and Biochemical Changes in Pericardium upon Genipin Cross-Linking Investigated Using Nondestructive and Label-Free Imaging Techniques. Anal Chem 2022; 94:1575-1584. [PMID: 35015512 DOI: 10.1021/acs.analchem.1c03348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tissue cross-linking represents an important and often used technique to enhance the mechanical properties of biomaterials. For the first time, we investigated biochemical and structural properties of genipin (GE) cross-linked equine pericardium (EP) using optical imaging techniques in tandem with quantitative atomic force microscopy (AFM). EP was cross-linked with GE at 37 °C, and its biochemical and biomechanical properties were observed at various time points up to 24 h. GE cross-linked EP was monitored by the normalized ratio between its second-harmonic generation (SHG) and two-photon autofluorescence emissions and remained unchanged for untreated EP; however, a decreasing ratio due to depleted SHG and elevated autofluorescence and a fluorescence band at 625 nm were found for GE cross-linked EP. The mean autofluorescence lifetime of GE cross-linked EP also decreased. The biochemical signature of GE cross-linker and shift in collagen bands were detected and quantified using shifted excitation Raman difference spectroscopy as an innovative approach for tackling artifacts with high fluorescence backgrounds. AFM images indicated a higher and increasing Young's modulus correlated with cross-linking, as well as collagen structural changes in GE cross-linked EP, qualitatively explaining the observed decrease in the second-harmonic signal. In conclusion, we obtained detailed information about the biochemical, structural, and biomechanical effects of GE cross-linked EP using a unique combination of optical and force microscopy techniques in a nondestructive and label-free manner.
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Affiliation(s)
- Tanveer Ahmed Shaik
- Leibniz Institute of Photonic Technology and Member of Leibniz Research Alliance "Health Technologies", Albert-Einstein-Strasse 9, 07745 Jena, Germany
| | - Enrico Baria
- National Institute of Optics, National Research Council (CNR-INO), Largo E. Fermi 6, 50125 Florence, Italy.,European Laboratory for Non-Linear Spectroscopy (LENS), University of Florence, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
| | - Xinyue Wang
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University, Helmholtzweg 4, 07743 Jena, Germany
| | - Florian Korinth
- Leibniz Institute of Photonic Technology and Member of Leibniz Research Alliance "Health Technologies", Albert-Einstein-Strasse 9, 07745 Jena, Germany
| | - João L Lagarto
- National Institute of Optics, National Research Council (CNR-INO), Largo E. Fermi 6, 50125 Florence, Italy.,European Laboratory for Non-Linear Spectroscopy (LENS), University of Florence, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
| | - Christiane Höppener
- Leibniz Institute of Photonic Technology and Member of Leibniz Research Alliance "Health Technologies", Albert-Einstein-Strasse 9, 07745 Jena, Germany.,Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University, Helmholtzweg 4, 07743 Jena, Germany
| | - Francesco S Pavone
- National Institute of Optics, National Research Council (CNR-INO), Largo E. Fermi 6, 50125 Florence, Italy.,European Laboratory for Non-Linear Spectroscopy (LENS), University of Florence, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
| | - Volker Deckert
- Leibniz Institute of Photonic Technology and Member of Leibniz Research Alliance "Health Technologies", Albert-Einstein-Strasse 9, 07745 Jena, Germany.,Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University, Helmholtzweg 4, 07743 Jena, Germany
| | - Jürgen Popp
- Leibniz Institute of Photonic Technology and Member of Leibniz Research Alliance "Health Technologies", Albert-Einstein-Strasse 9, 07745 Jena, Germany.,Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University, Helmholtzweg 4, 07743 Jena, Germany
| | - Riccardo Cicchi
- National Institute of Optics, National Research Council (CNR-INO), Largo E. Fermi 6, 50125 Florence, Italy.,European Laboratory for Non-Linear Spectroscopy (LENS), University of Florence, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
| | - Christoph Krafft
- Leibniz Institute of Photonic Technology and Member of Leibniz Research Alliance "Health Technologies", Albert-Einstein-Strasse 9, 07745 Jena, Germany
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Korinth F, Shaik TA, Popp J, Krafft C. Assessment of shifted excitation Raman difference spectroscopy in highly fluorescent biological samples. Analyst 2021; 146:6760-6767. [PMID: 34704561 DOI: 10.1039/d1an01376a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Shifted excitation Raman difference spectroscopy (SERDS) can be used as an instrumental baseline correction technique to retrieve Raman bands in highly fluorescent samples. Genipin (GE) cross-linked equine pericardium (EP) was used as a model system since a blue pigment is formed upon cross-linking, which results in a strong fluorescent background in the Raman spectra. EP was cross-linked with 0.25% GE solution for 0.5 h, 2 h, 4 h, 6 h, 12 h, and 24 h, and compared with corresponding untreated EP. Raman spectra were collected with three different excitation wavelengths. For the assessment of the SERDS technique, the preprocessed SERDS spectra of two excitation wavelengths (784 nm-786 nm) were compared with the mathematical baseline-corrected Raman spectra at 785 nm excitation using extended multiplicative signal correction, rubberband, the sensitive nonlinear iterative peak and polynomial fitting algorithms. Whereas each baseline correction gave poor quality spectra beyond 6 h GE crosslinking with wave-like artefacts, the SERDS technique resulted in difference spectra, that gave superior reconstructed spectra with clear collagen and resonance enhanced GE pigment bands with lower standard deviation. Key for this progress was an advanced difference optimization approach that is described here. Furthermore, the results of the SERDS technique were independent of the intensity calibration because the system transfer response was compensated by calculating the difference spectrum. We conclude that this SERDS strategy can be transferred to Raman studies on biological and non-biological samples with a strong fluorescence background at 785 nm and also shorter excitation wavelengths which benefit from more intense scattering intensities and higher quantum efficiencies of CCD detectors.
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Affiliation(s)
- Florian Korinth
- Leibniz Institute of Photonic Technology and Member of Leibniz Research Alliance "Health Technologies", 07745 Jena, Germany. .,Leibniz Institute for Astrophysics Potsdam and Member of Leibniz Research Alliance "Health Technologies", 14482 Potsdam, Germany
| | - Tanveer Ahmed Shaik
- Leibniz Institute of Photonic Technology and Member of Leibniz Research Alliance "Health Technologies", 07745 Jena, Germany.
| | - Jürgen Popp
- Leibniz Institute of Photonic Technology and Member of Leibniz Research Alliance "Health Technologies", 07745 Jena, Germany. .,Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, 07743 Jena, Germany
| | - Christoph Krafft
- Leibniz Institute of Photonic Technology and Member of Leibniz Research Alliance "Health Technologies", 07745 Jena, Germany.
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Shaik TA, Lagarto JL, Baria E, Goktas M, Onoja PI, Blank KG, Pavone FS, Popp J, Krafft C, Cicchi R. Monitoring Changes in Biochemical and Biomechanical Properties of Collagenous Tissues Using Label-Free and Nondestructive Optical Imaging Techniques. Anal Chem 2021; 93:3813-3821. [PMID: 33596051 DOI: 10.1021/acs.analchem.0c04306] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We demonstrate the ability of nondestructive optical imaging techniques such as second-harmonic generation (SHG), two-photon fluorescence (TPF), fluorescence lifetime imaging (FLIM), and Raman spectroscopy (RS) to monitor biochemical and mechanical alterations in tissues upon collagen degradation. Decellularized equine pericardium (EP) was treated with 50 μg/mL bacterial collagenase at 37 °C for 8, 16, 24, and 32 h. The SHG ratio (defined as the normalized ratio between SHG and TPF signals) remained unchanged for untreated EP (stored in phosphate-buffered solution (PBS)), whereas treated EP showed a trend of a decreasing SHG ratio with increasing collagen degradation. In the fluorescence domain, treated EP experienced a red-shifted emission and the fluorescence lifetime had a trend of decreasing lifetime with increasing collagen digestion. RS monitors collagen degradation, the spectra had less intense Raman bands at 814, 852, 938, 1242, and 1270 cm-1. Non-negative least-squares (NNLS) modeling quantifies collagen loss and relative increase of elastin. The Young's modulus, derived from atomic force microscope-based nanoindentation experiments, showed a rapid decrease within the first 8 h of collagen degradation, whereas more gradual changes were observed for optical modalities. We conclude that optical imaging techniques like SHG, RS, and FLIM can monitor collagen degradation in a label-free manner and coarsely access mechanical properties in a nondestructive manner.
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Affiliation(s)
- Tanveer Ahmed Shaik
- Leibniz Institute of Photonic Technology, Albert-Einstein-Strasse 9, 07745 Jena, Germany
| | - João L Lagarto
- National Institute of Optics (INO), National Research Council (CNR), Largo E. Fermi 6, 50125 Florence, Italy.,European Laboratory for Non-Linear Spectroscopy (LENS), University of Florence, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
| | - Enrico Baria
- National Institute of Optics (INO), National Research Council (CNR), Largo E. Fermi 6, 50125 Florence, Italy.,European Laboratory for Non-Linear Spectroscopy (LENS), University of Florence, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
| | - Melis Goktas
- Mechano(bio)chemistry, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Patrick Igoche Onoja
- Leibniz Institute of Photonic Technology, Albert-Einstein-Strasse 9, 07745 Jena, Germany
| | - Kerstin G Blank
- Mechano(bio)chemistry, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Francesco S Pavone
- National Institute of Optics (INO), National Research Council (CNR), Largo E. Fermi 6, 50125 Florence, Italy.,European Laboratory for Non-Linear Spectroscopy (LENS), University of Florence, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
| | - Jürgen Popp
- Leibniz Institute of Photonic Technology, Albert-Einstein-Strasse 9, 07745 Jena, Germany.,Institute of Physical Chemistry, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany.,Abbe Center of Photonics, Friedrich Schiller University, Albert-Einstein-Strasse 6, 07745 Jena, Germany
| | - Christoph Krafft
- Leibniz Institute of Photonic Technology, Albert-Einstein-Strasse 9, 07745 Jena, Germany
| | - Riccardo Cicchi
- National Institute of Optics (INO), National Research Council (CNR), Largo E. Fermi 6, 50125 Florence, Italy.,European Laboratory for Non-Linear Spectroscopy (LENS), University of Florence, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
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