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Rosin NL, Winstone TML, Kelley M, Biernaskie J, Dufour A, Orton DJ. Targeted proteomic approach for quantification of collagen type I and type III in formalin-fixed paraffin-embedded tissue. Sci Rep 2024; 14:17769. [PMID: 39090134 PMCID: PMC11294326 DOI: 10.1038/s41598-024-68377-9] [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: 03/05/2024] [Accepted: 07/23/2024] [Indexed: 08/04/2024] Open
Abstract
Collagen is the most abundant protein in mammals and a major structural component of the extracellular matrix (ECM). Changes to ECM composition occur as a result of numerous physiological and pathophysiological causes, and a common means to evaluate these changes is the collagen 3 (Col3) to collagen 1 (Col1) ratio. Current methods to measure the Col3/1 ratio suffer from a lack of specificity and often under- or over-estimate collagen composition and quantity. This manuscript presents a targeted liquid chromatography tandem mass spectrometry (LC-MS/MS) method for quantification of Col3 and Col1 in FFPE tissues. Using surrogate peptides to generate calibration curves, Col3 and Col1 are readily quantified in FFPE tissue sections with high accuracy and precision. The method is applied to several tissue types from both human and reindeer sources, demonstrating its generalizability. In addition, the targeted LC-MS/MS method permits quantitation of the hydroxyprolinated form of Col3, which has significant implications for understanding not only the quantity of Col3 in tissue, but also understanding of the pathophysiology underlying many causes of ECM changes. This manuscript presents a straightforward, accurate, precise, and generalizable method for quantifying the Col3/1 ratio in a variety of tissue types and organisms.
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Affiliation(s)
- Nicole L Rosin
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Tara M L Winstone
- Department of Pathology and Laboratory Medicine, University of Calgary, 3535 Research Rd NW, Room 1E-415, Calgary, AB, T2I 2K8, Canada
| | - Margaret Kelley
- Department of Pathology and Laboratory Medicine, University of Calgary, 3535 Research Rd NW, Room 1E-415, Calgary, AB, T2I 2K8, Canada
| | - Jeff Biernaskie
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- Department of Surgery, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Antoine Dufour
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada
| | - Dennis J Orton
- Department of Pathology and Laboratory Medicine, University of Calgary, 3535 Research Rd NW, Room 1E-415, Calgary, AB, T2I 2K8, Canada.
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2
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Faktor J, Kote S, Bienkowski M, Hupp TR, Marek-Trzonkowska N. Novel FFPE proteomics method suggests prolactin induced protein as hormone induced cytoskeleton remodeling spatial biomarker. Commun Biol 2024; 7:708. [PMID: 38851810 PMCID: PMC11162451 DOI: 10.1038/s42003-024-06354-8] [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: 01/20/2023] [Accepted: 05/20/2024] [Indexed: 06/10/2024] Open
Abstract
Robotically assisted proteomics provides insights into the regulation of multiple proteins achieving excellent spatial resolution. However, developing an effective method for spatially resolved quantitative proteomics of formalin fixed paraffin embedded tissue (FFPE) in an accessible and economical manner remains challenging. We introduce non-robotic In-insert FFPE proteomics approach, combining glass insert FFPE tissue processing with spatial quantitative data-independent mass spectrometry (DIA). In-insert approach identifies 450 proteins from a 5 µm thick breast FFPE tissue voxel with 50 µm lateral dimensions covering several tens of cells. Furthermore, In-insert approach associated a keratin series and moesin (MOES) with prolactin-induced protein (PIP) indicating their prolactin and/or estrogen regulation. Our data suggest that PIP is a spatial biomarker for hormonally triggered cytoskeletal remodeling, potentially useful for screening hormonally affected hotspots in breast tissue. In-insert proteomics represents an alternative FFPE processing method, requiring minimal laboratory equipment and skills to generate spatial proteotype repositories from FFPE tissue.
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Affiliation(s)
- Jakub Faktor
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822, Gdansk, Poland.
| | - Sachin Kote
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822, Gdansk, Poland.
| | - Michal Bienkowski
- Medical University of Gdansk, University of Gdansk, Mariana Smoluchowskiego 17, 80-214, Gdansk, Poland
| | - Ted R Hupp
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822, Gdansk, Poland
| | - Natalia Marek-Trzonkowska
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822, Gdansk, Poland
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3
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Ambli M, Deracinois B, Jenequin AS, Ravallec R, Cudennec B, Flahaut C. Impact of Bioinformatics Search Parameters for Peptides' Identification and Their Post-Translational Modifications: A Case Study of Proteolysed Gelatines from Beef, Pork, and Fish. Foods 2023; 12:2524. [PMID: 37444262 DOI: 10.3390/foods12132524] [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: 04/22/2023] [Revised: 06/16/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
Bioinformatics software, allowing the identification of peptides by the comparison of peptide fragmentation spectra obtained by mass spectrometry versus targeted databases or directly by de novo sequencing, is now mandatory in peptidomics/proteomics approaches. Programming the identification software requires specifying, among other things, the mass measurement accuracy of the instrument and the digestion enzyme used with the number of missed cleavages allowed. Moreover, these software algorithms are able to identify a large number of post-translational modifications (PTMs). However, peptide and PTM identifications are challenging in the agrofood field due to non-specific cleavage sites of physiological- or food-grade enzymes and the number and location of PTMs. In this study, we show the importance of customized software programming to obtain a better peptide and PTM identification rate in the agrofood field. A gelatine product and one industrial gelatine hydrolysate from three different sources (beef, pork, and fish), each digested by simulated gastrointestinal digestion, MS-grade trypsin, or both, were used to perform the comparisons. Two main points are illustrated: (i) the impact of the set-up of specific enzyme versus no specific enzyme use and (ii) the impact of a maximum of six PTMs allowed per peptide versus the standard of three. Prior knowledge of the composition of the raw proteins is an important asset for better identification of peptide sequences.
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Affiliation(s)
- Mouna Ambli
- UMR Transfrontalière BioEcoAgro-INRAe N° 1158, Univ. Artois, Univ. Lille, INRAe, Univ. Liège, UPJV, JUNIA, Univ. Littoral Côte d'Opale, ICV-Institut Charles Viollette, 62300 Lens, France
| | - Barbara Deracinois
- UMR Transfrontalière BioEcoAgro-INRAe N° 1158, Univ. Artois, Univ. Lille, INRAe, Univ. Liège, UPJV, JUNIA, Univ. Littoral Côte d'Opale, ICV-Institut Charles Viollette, 62300 Lens, France
| | - Anne-Sophie Jenequin
- UMR Transfrontalière BioEcoAgro-INRAe N° 1158, Univ. Artois, Univ. Lille, INRAe, Univ. Liège, UPJV, JUNIA, Univ. Littoral Côte d'Opale, ICV-Institut Charles Viollette, 62300 Lens, France
| | - Rozenn Ravallec
- UMR Transfrontalière BioEcoAgro-INRAe N° 1158, Univ. Artois, Univ. Lille, INRAe, Univ. Liège, UPJV, JUNIA, Univ. Littoral Côte d'Opale, ICV-Institut Charles Viollette, 62300 Lens, France
| | - Benoit Cudennec
- UMR Transfrontalière BioEcoAgro-INRAe N° 1158, Univ. Artois, Univ. Lille, INRAe, Univ. Liège, UPJV, JUNIA, Univ. Littoral Côte d'Opale, ICV-Institut Charles Viollette, 62300 Lens, France
| | - Christophe Flahaut
- UMR Transfrontalière BioEcoAgro-INRAe N° 1158, Univ. Artois, Univ. Lille, INRAe, Univ. Liège, UPJV, JUNIA, Univ. Littoral Côte d'Opale, ICV-Institut Charles Viollette, 62300 Lens, France
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4
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Anohova V, Asyakina L, Babich O, Dikaya O, Goikhman A, Maksimova K, Grechkina M, Korobenkov M, Burkova D, Barannikov A, Narikovich A, Chupakhin E, Snigirev A, Antipov S. The Dosidicus gigas Collagen for Scaffold Preparation and Cell Cultivation: Mechanical and Physicochemical Properties, Morphology, Composition and Cell Viability. Polymers (Basel) 2023; 15:1220. [PMID: 36904464 PMCID: PMC10006952 DOI: 10.3390/polym15051220] [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: 12/06/2022] [Revised: 01/19/2023] [Accepted: 01/30/2023] [Indexed: 03/04/2023] Open
Abstract
Directed formation of the structure of the culture of living cells is the most important task of tissue engineering. New materials for 3D scaffolds of living tissue are critical for the mass adoption of regenerative medicine protocols. In this manuscript, we demonstrate the results of the molecular structure study of collagen from Dosidicus gigas and reveal the possibility of obtaining a thin membrane material. The collagen membrane is characterized by high flexibility and plasticity as well as mechanical strength. The technology of obtaining collagen scaffolds, as well as the results of studies of its mechanical properties, surface morphology, protein composition, and the process of cell proliferation on its surface, are shown in the given manuscript. The investigation of living tissue culture grown on the surface of a collagen scaffold by X-ray tomography on a synchrotron source made it possible to remodel the structure of the extracellular matrix. It was found that the scaffolds obtained from squid collagen are characterized by a high degree of fibril ordering and high surface roughness and provide efficient directed growth of the cell culture. The resulting material provides the formation of the extracellular matrix and is characterized by a short time to living tissue sorption.
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Affiliation(s)
- Veronika Anohova
- Immanuel Kant Baltic Federal University, Nevskogo 14, Kaliningrad 236006, Russia
| | - Lyudmila Asyakina
- Immanuel Kant Baltic Federal University, Nevskogo 14, Kaliningrad 236006, Russia
| | - Olga Babich
- Immanuel Kant Baltic Federal University, Nevskogo 14, Kaliningrad 236006, Russia
| | - Olga Dikaya
- Immanuel Kant Baltic Federal University, Nevskogo 14, Kaliningrad 236006, Russia
| | - Aleksandr Goikhman
- Immanuel Kant Baltic Federal University, Nevskogo 14, Kaliningrad 236006, Russia
| | - Ksenia Maksimova
- Immanuel Kant Baltic Federal University, Nevskogo 14, Kaliningrad 236006, Russia
| | | | - Maxim Korobenkov
- Immanuel Kant Baltic Federal University, Nevskogo 14, Kaliningrad 236006, Russia
| | - Diana Burkova
- Voronezh State University, 1, University Square, Voronezh 394063, Russia
| | - Aleksandr Barannikov
- Immanuel Kant Baltic Federal University, Nevskogo 14, Kaliningrad 236006, Russia
| | - Anton Narikovich
- Immanuel Kant Baltic Federal University, Nevskogo 14, Kaliningrad 236006, Russia
| | - Evgeny Chupakhin
- Immanuel Kant Baltic Federal University, Nevskogo 14, Kaliningrad 236006, Russia
- Saint Petersburg State University, Saint Petersburg 199034, Russia
| | - Anatoly Snigirev
- Immanuel Kant Baltic Federal University, Nevskogo 14, Kaliningrad 236006, Russia
| | - Sergey Antipov
- Immanuel Kant Baltic Federal University, Nevskogo 14, Kaliningrad 236006, Russia
- Voronezh State University, 1, University Square, Voronezh 394063, Russia
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5
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Proteomics-Based Identification of Dysregulated Proteins in Breast Cancer. Proteomes 2022; 10:proteomes10040035. [PMID: 36278695 PMCID: PMC9590004 DOI: 10.3390/proteomes10040035] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/10/2022] [Accepted: 10/18/2022] [Indexed: 11/18/2022] Open
Abstract
Immunohistochemistry (IHC) is still widely used as a morphology-based assay for in situ analysis of target proteins as specific tumor antigens. However, as a very heterogeneous collection of neoplastic diseases, breast cancer (BC) requires an accurate identification and characterization of larger panels of candidate biomarkers, beyond ER, PR, and HER2 proteins, for diagnosis and personalized treatment, without the limited availability of antibodies that are required to identify specific proteins. Top-down, middle-down, and bottom-up mass spectrometry (MS)-based proteomics approaches complement traditional histopathological tissue analysis to examine expression, modification, and interaction of hundreds to thousands of proteins simultaneously. In this review, we discuss the proteomics-based identification of dysregulated proteins in BC that are essential for the following issues: discovery and validation of new biomarkers by analysis of solid and liquid/non-invasive biopsies, cell lines, organoids and xenograft models; identification of panels of biomarkers for early detection and accurate discrimination between cancer, benign and normal tissues; identification of subtype-specific and stage-specific protein expression profiles in BC grading and measurement of disease progression; characterization of new subtypes of BC; characterization and quantitation of post-translational modifications (PTMs) and aberrant protein-protein interactions (PPI) involved in tumor development; characterization of the global remodeling of BC tissue homeostasis, diagnosis and prognostic information; and deciphering of molecular functions, biological processes and mechanisms through which the dysregulated proteins cause tumor initiation, invasion, and treatment resistance.
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6
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Circulating proteins as predictive and prognostic biomarkers in breast cancer. Clin Proteomics 2022; 19:25. [PMID: 35818030 PMCID: PMC9275040 DOI: 10.1186/s12014-022-09362-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 06/28/2022] [Indexed: 11/22/2022] Open
Abstract
Breast cancer (BC) is the most common cancer and among the leading causes of cancer death in women. It is a heterogeneous group of tumours with numerous morphological and molecular subtypes, making predictions of disease evolution and patient outcomes difficult. Therefore, biomarkers are needed to help clinicians choose the best treatment for each patient. For the last years, studies have increasingly focused on biomarkers obtainable by liquid biopsy. Circulating proteins (from serum or plasma) can be used for inexpensive and minimally invasive determination of disease risk, early diagnosis, treatment adjusting, prognostication and disease progression monitoring. We provide here a review of the main published studies on serum proteins in breast cancer and elaborate on the potential of circulating proteins to be predictive and/or prognostic biomarkers in breast cancer.
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7
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Riengvirodkij N, Roytrakul S, Jaresitthikunchai J, Phaonakrop N, Charoenlappanich S, Sakcamduang W. Peptide barcodes in dogs affected by mitral valve disease with and without pulmonary hypertension using MALDI-TOF MS and LC-MS/MS. PLoS One 2021; 16:e0255611. [PMID: 34383793 PMCID: PMC8360550 DOI: 10.1371/journal.pone.0255611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 07/19/2021] [Indexed: 11/20/2022] Open
Abstract
Mitral valve disease (MVD) is an important and most frequently acquired heart disease found in dogs. MVD is classified into different stages according to its severity. There is a challenge in differentiation between asymptomatic and symptomatic stages of the MVD. Moreover, pulmonary hypertension (PH) is a common complication in dogs affected by MVD. In clinical practice, there are also some limitations to identify PH. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a technique that can characterize specific patterns of peptide mass called peptide barcodes from various samples. Besides, in combination with liquid chromatography-tandem mass spectrometry (LC-MS/MS), potential peptide sequences associated with specific conditions could be identified. The present study aimed to use MALDI-TOF coupled with LC-MS/MS to characterize specific peptide barcodes and potential peptide candidates in serum samples from healthy dogs, dogs with MVD stage B (MVD B, asymptomatic stage), MVD stage C (MVD C, symptomatic stage), MVD stage B with PH (MVD B PH), and MVD stage C with PH (MVD C PH). Discrete clusters of the 5 sample groups were identified by 3D plot analysis. Peptide barcodes also revealed differences in peptide patterns among the 5 groups. Six amino acid sequences of peptide candidates at 1,225.60, 1,363.85, 1,688.71, 1789.52, 2020.21, and 2156.42 Da were identified as part of the proteins CLCN1, CLUL1, EDNRA, PTEN, SLC39A7, and CLN6, respectively. The network interactions between these discovered proteins and common cardiovascular drugs were also investigated. These results demonstrate that MALDI-TOF MS has promise as an optional technique for diagnosing dogs affected by asymptomatic and symptomatic stages of MVD with and without PH. Further studies are required to identify peptide barcodes in dogs with other diseases to create peptide barcode databases in veterinary medicine before using this method as a novel diagnostic tool in the future.
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Affiliation(s)
- Nattapon Riengvirodkij
- Prasu-Arthorn Animal Hospital, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
| | - Sittiruk Roytrakul
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Janthima Jaresitthikunchai
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Narumon Phaonakrop
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sawanya Charoenlappanich
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Walasinee Sakcamduang
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
- * E-mail:
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8
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Taga Y, Tanaka K, Hattori S, Mizuno K. In-depth correlation analysis demonstrates that 4-hydroxyproline at the Yaa position of Gly-Xaa-Yaa repeats dominantly stabilizes collagen triple helix. Matrix Biol Plus 2021; 10:100067. [PMID: 34195597 PMCID: PMC8233474 DOI: 10.1016/j.mbplus.2021.100067] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/18/2021] [Accepted: 04/19/2021] [Indexed: 12/29/2022] Open
Abstract
4Hyp at the Yaa position of Gly-Xaa-Yaa repeats has the highest correlation with collagen denaturation temperature (Td), especially in vertebrates. Significant correlation with Td exists for Gly-Xaa-4Hyp tripeptides, but not for Gly-Pro-Yaa tripeptides. The in-depth correlation analysis demonstrates the dominating role of Yaa position 4Hyp for collagen stability.
There is a general consensus that collagen stability is largely maintained by Pro and its major hydroxylated form, 4-hydroxyproline (4Hyp). However, positional difference in their stabilizing effect at the Xaa or Yaa position of collagenous Gly-Xaa-Yaa sequences has remained inconclusive. Here, we position-specifically evaluated the correlation of imino acid contents to denaturation temperature (Td) of collagen among various vertebrate and invertebrate species, using a recently developed LC–MS methodology. 4Hyp at the Yaa position showed the highest positive correlation with Td, followed by Pro at the Xaa position, which was even further increased by excluding invertebrates. We confirmed that Gly-Pro-4Hyp liberated after bacterial collagenase digestion was highly positively correlated with Td. Furthermore, other tripeptides with Yaa position 4Hyp also had comparable positive correlation, excepting negative correlation of Gly-Gly-4Hyp, while tripeptides with Xaa position Pro did not. These data provide evidence that 4Hyp dominantly contributes to thermal stability of collagen depending on its sequence position, especially in vertebrates.
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Affiliation(s)
- Yuki Taga
- Nippi Research Institute of Biomatrix, 520-11 Kuwabara, Toride, Ibaraki 302-0017, Japan
| | - Keisuke Tanaka
- Nippi Research Institute of Biomatrix, 520-11 Kuwabara, Toride, Ibaraki 302-0017, Japan
| | - Shunji Hattori
- Nippi Research Institute of Biomatrix, 520-11 Kuwabara, Toride, Ibaraki 302-0017, Japan
| | - Kazunori Mizuno
- Nippi Research Institute of Biomatrix, 520-11 Kuwabara, Toride, Ibaraki 302-0017, Japan
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9
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Millard AR, Annis RG, Caffell AC, Dodd LL, Fischer R, Gerrard CM, Graves CP, Hendy J, Mackenzie L, Montgomery J, Nowell GM, Radini A, Beaumont J, Koon HEC, Speller CF. Scottish soldiers from the Battle of Dunbar 1650: A prosopographical approach to a skeletal assemblage. PLoS One 2020; 15:e0243369. [PMID: 33347451 PMCID: PMC7751964 DOI: 10.1371/journal.pone.0243369] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 11/20/2020] [Indexed: 11/18/2022] Open
Abstract
After the Battle Dunbar between English and Scottish forces in 1650, captured Scottish soldiers were imprisoned in Durham and many hundreds died there within a few weeks. The partial skeletal remains of 28 of these men were discovered in 2013. Building on previous osteological work, here we report wide-ranging scientific studies of the remains to address the following questions: Did they have comparable diet, health and disease throughout their lives? Did they have common histories of movement (or lack of movement) during their childhoods? Can we create a collective biography of these men? Strontium and oxygen isotope analysis of tooth enamel investigated childhood movement. Carbon and nitrogen isotope analysis of incrementally sampled dentine addressed childhood diet and nutrition. Metaproteomic analysis of dental calculus investigated oral microbiomes and food residues; this was complemented by microscopic analysis of debris in calculus from ingested materials. Selected individuals were examined for dental microwear. The extent of hydroxylation of proline in collagen was examined as a potential biomarker for scurvy. An osteobiography for each man was created using the full range of data generated about him, and these were synthesised using an approach based on the historical method for a collective biography or prosopography. The childhood residences of the men were primarily within the Midland Valley of Scotland, though some spent parts of their childhood outside the British Isles. This is concordant with the known recruitment areas of the Scottish army in 1650. Their diets included oats, brassicas and milk but little seafood, as expected for lowland rather than highland diets of the period. Childhood periods of starvation or illness were almost ubiquitous, but not simultaneous, suggesting regionally variable food shortages in the 1620s and 1630s. It is likely there was widespread low-level scurvy, ameliorating in later years of life, which suggests historically unrecorded shortages of fruit and vegetables in the early 1640s. Almost all men were exposed to burnt plant matter, probably as inhaled soot, and this may relate to the high proportion of them with of sinusitis. Interpersonal violence causing skeletal trauma was rare. Based on commonalities in their osteobiographies, we argue that these men were drawn from the same stratum of society. This study is perhaps the most extensive to date of individuals from 17th century Scotland. Combined with a precise historical context it allows the lives of these men to be investigated and compared to the historical record with unprecedented precision. It illustrates the power of archaeological science methods to confirm, challenge and complement historical evidence.
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Affiliation(s)
- Andrew R. Millard
- Department of Archaeology, Durham University, Durham, United Kingdom
- * E-mail:
| | - Richard G. Annis
- Archaeological Services, Durham University, Durham, United Kingdom
| | - Anwen C. Caffell
- Department of Archaeology, Durham University, Durham, United Kingdom
| | - Laura L. Dodd
- Department of Archaeology, Durham University, Durham, United Kingdom
- KDK Archaeology Ltd, Leighton Buzzard, United Kingdom
| | - Roman Fischer
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | | | - C. Pamela Graves
- Department of Archaeology, Durham University, Durham, United Kingdom
| | - Jessica Hendy
- Department of Archaeology, University of York, York, United Kingdom
| | - Lisa Mackenzie
- Department of Archaeology, University of York, York, United Kingdom
| | - Janet Montgomery
- Department of Archaeology, Durham University, Durham, United Kingdom
| | - Geoff M. Nowell
- Department of Earth Sciences, Durham University, Durham, United Kingdom
| | - Anita Radini
- Department of Archaeology, University of York, York, United Kingdom
| | - Julia Beaumont
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford, United Kingdom
| | - Hannah E. C. Koon
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford, United Kingdom
| | - Camilla F. Speller
- Department of Anthropology, University of British Columbia, Vancouver, British Columbia, Canada
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10
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Zhang S, Lu X, Hu C, Li Y, Yang H, Yan H, Fan J, Xu G, Abnet CC, Qiao Y. Serum Metabolomics for Biomarker Screening of Esophageal Squamous Cell Carcinoma and Esophageal Squamous Dysplasia Using Gas Chromatography-Mass Spectrometry. ACS OMEGA 2020; 5:26402-26412. [PMID: 33110968 PMCID: PMC7581083 DOI: 10.1021/acsomega.0c02600] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/30/2020] [Indexed: 05/14/2023]
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC) is one of the most common malignancies with poor diagnosis. Esophageal squamous dysplasia (ESD) is considered as an immediate precancerous lesion of ESCC. Lack of biomarkers for discriminating ESCC and ESD from healthy subjects limits the early diagnosis and treatment of ESCC. Therefore, a serum metabolomic strategy was conducted to identify and validate potential metabolic markers for the screening of ESCC and ESD subjects. METHODS A total of 74 patients with ESCC, 72 patients with ESD, and 75 normal control (NC) subjects were enrolled in this study. Gas chromatography-mass spectrometry was used to acquire serum metabolic profiles. Pathway analysis was conducted to uncover the fluctuated metabolic pathways during ESCC. Multivariate analyses were used to screen and validate the biomarkers. RESULTS ESCC, ESD, and NC subjects revealed progressively altered metabolic profiles, in which amino acids globally increased, while fatty acids decreased in ESCCs compared with the control groups. Pathway analysis demonstrated the activated biosynthesis of amino acids and inhibited desaturation of saturated fatty acids. The panel constructed with propanoic acid, linoleic acid, glycerol-3-phosphate, and l-glutamine showed the area under the curve (AUC), sensitivity, and specificity of 0.817, 0.75, and 0.74, respectively, in the discrimination of ESCC/ESD patients from NC subjects. The panel constructed by propanoic acid, l-leucine, and hydroxyproline revealed the AUC, sensitivity, and specificity of 0.819, 0.76, and 0.72, respectively, in the discrimination of ESD from NC subjects. The combination of hypoxanthine, 2-ketoisocaproic acid, l-glutamate, and l-aspartate showed the AUC, sensitivity, and specificity of 0.818, 0.83, and 0.74, respectively, in the discrimination of ESCC patients from ESD subjects. CONCLUSIONS Our study revealed the systematic landscape for metabolic alterations in sera of ESD and ESCC patients. The defined metabolite markers showed reasonable performance in the discrimination of ESCC and ESD patients, and may provide helpful reference for clinicians and biologists.
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Affiliation(s)
- Su Zhang
- Department
of Cancer Epidemiology, National Cancer Center/National Clinical Research
Center for Cancer/Cancer Hospital, Chinese
Academy of Medical Sciences and Peking Union Medical College, 17 South Panjiayuan Lane, Beijing 100021, China
| | - Xin Lu
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy
of Sciences, Dalian 116023, China
| | - Chunxiu Hu
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy
of Sciences, Dalian 116023, China
| | - Yanli Li
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy
of Sciences, Dalian 116023, China
| | - Huan Yang
- Department
of Cancer Epidemiology, National Cancer Center/National Clinical Research
Center for Cancer/Cancer Hospital, Chinese
Academy of Medical Sciences and Peking Union Medical College, 17 South Panjiayuan Lane, Beijing 100021, China
| | - Huijiao Yan
- Department
of Cancer Epidemiology, National Cancer Center/National Clinical Research
Center for Cancer/Cancer Hospital, Chinese
Academy of Medical Sciences and Peking Union Medical College, 17 South Panjiayuan Lane, Beijing 100021, China
| | - Jinhu Fan
- Department
of Cancer Epidemiology, National Cancer Center/National Clinical Research
Center for Cancer/Cancer Hospital, Chinese
Academy of Medical Sciences and Peking Union Medical College, 17 South Panjiayuan Lane, Beijing 100021, China
- . Tel: 010-87787423
| | - Guowang Xu
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy
of Sciences, Dalian 116023, China
- . Tel/Fax: 0086-422-84379530
| | - Christian C. Abnet
- Division
of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Youlin Qiao
- Department
of Cancer Epidemiology, National Cancer Center/National Clinical Research
Center for Cancer/Cancer Hospital, Chinese
Academy of Medical Sciences and Peking Union Medical College, 17 South Panjiayuan Lane, Beijing 100021, China
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11
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van Huizen NA, Burgers PC, van Rosmalen J, Doukas M, IJzermans JNM, Luider TM. Down-Regulation of Collagen Hydroxylation in Colorectal Liver Metastasis. Front Oncol 2020; 10:557737. [PMID: 33117689 PMCID: PMC7561380 DOI: 10.3389/fonc.2020.557737] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/27/2020] [Indexed: 11/21/2022] Open
Abstract
Collagen is significantly upregulated in colorectal liver metastasis (CRLM) compared to liver tissue. Expression levels of specific collagen types in CRLM resemble those in colorectal cancer (CRC) and colon tissue. We investigated whether the collagen hydroxylation pattern from the primary tumor also migrates with the metastatic tumor. The degree of collagen alpha-1(I) hydroxylation in colon, CRC, liver, and CRLM tissue of the same individuals (n = 14) was studied with mass spectrometry. The degree of hydroxylation was investigated in 36 collagen alpha-1(I) peptides, covering 54% of the triple helical region. The degree of hydroxylation in liver tissue was similar to that in colon tissue. The overall degree of hydroxylation was significantly lower (9 ± 14%) in CRC tissue and also significantly lower (12 ± 22%) in CRLM tissue compared to colon. Furthermore, eleven peptides with a specific number of hydroxylations are significantly different between CRLM and liver tissue; these peptides could be candidates for the detection of CRLM. For one of these eleven peptides, a matching naturally occurring peptide in urine has been identified as being significantly different between patients suffering from CRLM and healthy controls. The hydroxylation pattern in CRLM resembles partly the pattern in liver, primary colorectal cancer and colon.
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Affiliation(s)
- Nick A. van Huizen
- Department of Surgery, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Neurology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Peter C. Burgers
- Department of Neurology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Joost van Rosmalen
- Department of Biostatistics, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Michail Doukas
- Department of Pathology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Jan N. M. IJzermans
- Department of Surgery, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Theo M. Luider
- Department of Neurology, Erasmus University Medical Center, Rotterdam, Netherlands
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12
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van Huizen NA, Ijzermans JNM, Burgers PC, Luider TM. Collagen analysis with mass spectrometry. MASS SPECTROMETRY REVIEWS 2020; 39:309-335. [PMID: 31498911 DOI: 10.1002/mas.21600] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 07/17/2019] [Accepted: 07/17/2019] [Indexed: 06/10/2023]
Abstract
Mass spectrometry-based techniques can be applied to investigate collagen with respect to identification, quantification, supramolecular organization, and various post-translational modifications. The continuous interest in collagen research has led to a shift from techniques to analyze the physical characteristics of collagen to methods to study collagen abundance and modifications. In this review, we illustrate the potential of mass spectrometry for in-depth analyses of collagen.
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Affiliation(s)
- Nick A van Huizen
- Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Surgery, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Jan N M Ijzermans
- Department of Surgery, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Peter C Burgers
- Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Theo M Luider
- Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
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13
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Taga Y, Kusubata M, Mizuno K. Quantitative Analysis of the Positional Distribution of Hydroxyproline in Collagenous Gly-Xaa-Yaa Sequences by LC-MS with Partial Acid Hydrolysis and Precolumn Derivatization. Anal Chem 2020; 92:8427-8434. [PMID: 32437599 DOI: 10.1021/acs.analchem.0c01098] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Collagen is extensively modified by various enzymes, including prolyl hydroxylases. Pro residues at the Yaa position of repeating Gly-Xaa-Yaa amino acid sequences are mostly hydroxylated to 4-hydroxyproline (4Hyp), which is essential for the thermal stability of collagen triple helix. In contrast, Pro residues at the Xaa position are rarely modified to 3Hyp and 4Hyp, the biological function of which is poorly understood. Overall estimation of prolyl hydroxylation with discrimination of the position (Xaa or Yaa) and hydroxylation type (4Hyp or 3Hyp) has been difficult to perform using traditional methods. In the present study, we developed a novel position-specific analytical method featuring LC-MS detection of collagenous Gly-containing dipeptides, including Gly-Pro, Pro-Gly, Gly-4Hyp, Gly-3Hyp, and 4Hyp-Gly, after partial acid hydrolysis and precolumn derivatization using 3-aminopyridyl-N-hydroxysuccinimidyl carbamate (APDS). We performed acid hydrolysis at 55 °C with HCl/trifluoroacetic acid/water (2:1:1, v/v) to avoid peptide inversion and imbalanced peptide generation observed for collagenous model peptides. The positional distribution of Pro, 4Hyp, and 3Hyp can be calculated from the relative concentrations of the APDS-derivatized dipeptides, and in combination with amino acid analysis, we can determine their absolute contents at the Xaa and Yaa positions. Bovine type I, III, and V collagens were analyzed by the established method, and the amount of 4Hyp was higher than that of 3Hyp at the Xaa position in type I and III collagens. In addition, we clearly showed that collagen extracted from earthworm cuticles has an extremely high content of Xaa position 4Hyp, reaching over 10% of the total amino acids.
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Affiliation(s)
- Yuki Taga
- Nippi Research Institute of Biomatrix, 520-11 Kuwabara, Toride, Ibaraki 302-0017, Japan
| | - Masashi Kusubata
- Nippi Research Institute of Biomatrix, 520-11 Kuwabara, Toride, Ibaraki 302-0017, Japan
| | - Kazunori Mizuno
- Nippi Research Institute of Biomatrix, 520-11 Kuwabara, Toride, Ibaraki 302-0017, Japan
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14
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Pouliquen DL, Boissard A, Coqueret O, Guette C. Biomarkers of tumor invasiveness in proteomics (Review). Int J Oncol 2020; 57:409-432. [PMID: 32468071 PMCID: PMC7307599 DOI: 10.3892/ijo.2020.5075] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/07/2020] [Indexed: 12/13/2022] Open
Abstract
Over the past two decades, quantitative proteomics has emerged as an important tool for deciphering the complex molecular events involved in cancers. The number of references involving studies on the cancer metastatic process has doubled since 2010, while the last 5 years have seen the development of novel technologies combining deep proteome coverage capabilities with quantitative consistency and accuracy. To highlight key findings within this huge amount of information, the present review identified a list of tumor invasive biomarkers based on both the literature and data collected on a biocollection of experimental cell lines, tumor models of increasing invasiveness and tumor samples from patients with colorectal or breast cancer. Crossing these different data sources led to 76 proteins of interest out of 1,245 mentioned in the literature. Information on these proteins can potentially be translated into clinical prospects, since they represent potential targets for the development and evaluation of innovative therapies, alone or in combination. Herein, a systematical review of the biology of each of these proteins, including their specific subcellular/extracellular or multiple localizations is presented. Finally, as an important advantage of quantitative proteomics is the ability to provide data on all these molecules simultaneously in cell pellets, body fluids or paraffin‑embedded sections of tumors/invaded tissues, the significance of some of their interconnections is discussed.
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Affiliation(s)
| | - Alice Boissard
- Paul Papin ICO Cancer Center, CRCINA, Inserm, Université d'Angers, F‑44000 Nantes, France
| | | | - Catherine Guette
- Paul Papin ICO Cancer Center, CRCINA, Inserm, Université d'Angers, F‑44000 Nantes, France
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15
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van Huizen NA, Burgers PC, Saintmont F, Brocorens P, Gerbaux P, Stingl C, Dekker LJM, IJzermans JNM, Luider TM. Identification of 4-Hydroxyproline at the Xaa Position in Collagen by Mass Spectrometry. J Proteome Res 2019; 18:2045-2051. [PMID: 30945869 DOI: 10.1021/acs.jproteome.8b00930] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Collagen has a triple helix form, structured by a [-Gly-Xaa-Yaa-] repetition, where Xaa and Yaa are amino acids. This repeating unit can be post-translationally modified by enzymes, where proline is often hydroxylated into hydroxyproline (Hyp). Two Hyp isomers occur in collagen: 4-hydroxyproline (4Hyp, Gly-Xaa-Pro, substrate for 4-prolyl hydroxylase) and 3-hydroxyproline (3Hyp, Gly-Pro-4Hyp, substrate for 3-prolyl hydroxylase). If 4Hyp is lacking at the Yaa position, then Pro at the Xaa position should remain unmodified. Nevertheless, in literature 41 positions have been described where Hyp occurs at the Xaa position (?xHyp) lacking an adjacent 4Hyp. We report four additional positions in liver and colorectal liver metastasis tissue (CRLM). We studied the sequence commonalities between the 45 known positions of ?xHyp. Alanine and glutamine were frequently present adjacent to ?xHyp. We showed that proline, position 584 in COL1A2, had a lower rate of modification in CRLM than in healthy liver. The isomeric identity of ?xHyp, that is, 3- and/or 4Hyp, remains unknown. We present a proof of principle identification of ?xHyp. This identification is based on liquid chromatography retention time differences and mass spectrometry using ETD-HCD fragmentation, complemented by ab initio calculations. Both techniques identify ?xHyp at position 584 in COL1A2 as 4-hydroxyproline (4xHyp).
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Affiliation(s)
| | | | - Fabrice Saintmont
- Organic Synthesis & Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), Center of Innovation and Research in Materials and Polymers (CIRMAP) , University of Mons - UMONS , 23 Place du Parc , 7000 Mons , Belgium.,Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, Research Institute for Science and Engineering of Materials , University of Mons, UMONS , 23 Place du Parc , 7000 Mons , Belgium
| | - Patrick Brocorens
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, Research Institute for Science and Engineering of Materials , University of Mons, UMONS , 23 Place du Parc , 7000 Mons , Belgium
| | - Pascal Gerbaux
- Organic Synthesis & Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), Center of Innovation and Research in Materials and Polymers (CIRMAP) , University of Mons - UMONS , 23 Place du Parc , 7000 Mons , Belgium
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16
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Barcus CE, Keely PJ, Eliceiri KW, Schuler LA. Prolactin signaling through focal adhesion complexes is amplified by stiff extracellular matrices in breast cancer cells. Oncotarget 2018; 7:48093-48106. [PMID: 27344177 PMCID: PMC5217003 DOI: 10.18632/oncotarget.10137] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 06/06/2016] [Indexed: 11/25/2022] Open
Abstract
Estrogen receptor α positive (ERα+) breast cancer accounts for most breast cancer deaths. Both prolactin (PRL) and extracellular matrix (ECM) stiffness/density have been implicated in metastatic progression of this disease. We previously demonstrated that these factors cooperate to fuel processes involved in cancer progression. Culture of ERα+ breast cancer cells in dense/stiff 3D collagen-I matrices shifts the repertoire of PRL signals, and increases crosstalk between PRL and estrogen to promote proliferation and invasion. However, previous work did not distinguish ECM stiffness and collagen density. In order to dissect the ECM features that control PRL signals, we cultured T47D and MCF-7 cells on polyacrylamide hydrogels of varying elastic moduli (stiffness) with varying collagen-I concentrations (ligand density). Increasing stiffness from physiological to pathological significantly augmented PRL-induced phosphorylation of ERK1/2 and the SFK target, FAK-Y925, with only modest effects on pSTAT5. In contrast, higher collagen-I ligand density lowered PRL-induced pSTAT5 with no effect on pERK1/2 or pFAK-Y925. Disrupting focal adhesion signaling decreased PRL signals and PRL/estrogen-induced proliferation more efficiently in stiff, compared to compliant, extracellular environments. These data indicate that matrix stiffness shifts the balance of PRL signals from physiological (JAK2/STAT5) to pathological (FAK/SFK/ERK1/2) by increasing PRL signals through focal adhesions. Together, our studies suggest that PRL signaling to FAK and SFKs may be useful targets in clinical aggressive ERα+ breast carcinomas.
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Affiliation(s)
- Craig E Barcus
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI 53706, USA.,Cellular and Molecular Biology Program, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Patricia J Keely
- Cellular and Molecular Biology Program, University of Wisconsin-Madison, Madison, WI 53706, USA.,Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA.,Laboratory for Cellular and Molecular Biology and Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, WI 53706, USA.,University of Wisconsin Paul P. Carbone Comprehensive Cancer Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kevin W Eliceiri
- Laboratory for Cellular and Molecular Biology and Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, WI 53706, USA.,University of Wisconsin Paul P. Carbone Comprehensive Cancer Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Linda A Schuler
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI 53706, USA.,Cellular and Molecular Biology Program, University of Wisconsin-Madison, Madison, WI 53706, USA.,University of Wisconsin Paul P. Carbone Comprehensive Cancer Center, University of Wisconsin-Madison, Madison, WI 53706, USA
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17
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Povedano JM, Martinez P, Serrano R, Tejera Á, Gómez-López G, Bobadilla M, Flores JM, Bosch F, Blasco MA. Therapeutic effects of telomerase in mice with pulmonary fibrosis induced by damage to the lungs and short telomeres. eLife 2018; 7:31299. [PMID: 29378675 PMCID: PMC5818250 DOI: 10.7554/elife.31299] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 01/23/2018] [Indexed: 12/31/2022] Open
Abstract
Pulmonary fibrosis is a fatal lung disease characterized by fibrotic foci and inflammatory infiltrates. Short telomeres can impair tissue regeneration and are found both in hereditary and sporadic cases. We show here that telomerase expression using AAV9 vectors shows therapeutic effects in a mouse model of pulmonary fibrosis owing to a low-dose bleomycin insult and short telomeres. AAV9 preferentially targets regenerative alveolar type II cells (ATII). AAV9-Tert-treated mice show improved lung function and lower inflammation and fibrosis at 1–3 weeks after viral treatment, and improvement or disappearance of the fibrosis at 8 weeks after treatment. AAV9-Tert treatment leads to longer telomeres and increased proliferation of ATII cells, as well as lower DNA damage, apoptosis, and senescence. Transcriptome analysis of ATII cells confirms downregulation of fibrosis and inflammation pathways. We provide a proof-of-principle that telomerase activation may represent an effective treatment for pulmonary fibrosis provoked or associated with short telomeres. Idiopathic pulmonary fibrosis (or IPF for short) is a rare disease that scars the lungs. The condition gets worse over time, making it harder and harder to breathe, and eventually leading to death. Patients typically only survive for a few years after being diagnosed with IPF. This is because, as yet, there is no cure; the available treatments only act to lessen the symptoms. Several risk factors have linked to the development of IPF, among them, the presence of short telomeres. Like the plastic tips on shoelaces, telomeres are protective structures at the ends of chromosomes. Telomeres shorten with age, and when they become too short the cell stops dividing and often dies in a process known as apoptosis. IPF can develop when the telomeres in the cells that repair everyday wear and tear in the lungs (known as ATII cells) become too short. This means that the damage goes unrepaired, triggering an immune reaction and uncontrolled scarring. Telomerase is an enzyme that can lengthen short telomeres, and Povedano, Martínez et al. set out to develop a new treatment approach that would use this enzyme to correct the short telomeres, and cure the scarring seen in IPF. Gene therapy was used to introduce the gene for telomerase into mice that had scarring in their lungs due to short telomeres. Povedano, Martínez et al. found that, when injected into the mice, the telomerase gene therapy was able to reach ATII cells and could help to heal the lungs. At the level of individual cells, mice treated with telomerase had longer telomeres, meaning that more of their ATII cells stayed alive and kept dividing to regenerate the lung tissue. Consistent with previous studies, the telomerase gene therapy caused no negative side effects in the mice; for example, there was no increased risk of cancer. These findings may possibly lead to new treatments for those patients suffering from IPF associated with short telomeres. Developing this approach into a clinical trial could in the future benefit many IPF patients who currently have very limited treatment options.
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Affiliation(s)
- Juan Manuel Povedano
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre, Madrid, Spain
| | - Paula Martinez
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre, Madrid, Spain
| | - Rosa Serrano
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre, Madrid, Spain
| | - Águeda Tejera
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre, Madrid, Spain
| | - Gonzalo Gómez-López
- Bioinformatics Core Unit, Structural Biology and Biocomputing Program, Spanish National Cancer Centre, Madrid, Spain
| | - Maria Bobadilla
- Roche Pharma Research and Early Development (pRED), Neuroscience, Ophthalmology and Rare Disease, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland.,Roche Partnering, EIN, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Juana Maria Flores
- Animal Surgery and Medicine Department, Faculty of Veterinary Science, Complutense University of Madrid, Madrid, Spain
| | - Fátima Bosch
- Centre of Animal Biotechnology and Gene Therapy, Department of Biochemistry and Molecular Biology, School of Veterinary Medicine, Autonomous University of Barcelona, Bellaterra, Spain
| | - Maria A Blasco
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre, Madrid, Spain
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18
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Design of Fiber Networks for Studying Metastatic Invasion. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1092:289-318. [DOI: 10.1007/978-3-319-95294-9_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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19
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Label-free relative quantification applied to LC-MALDI acquisition for rapid analysis of chondrocyte secretion modulation. J Proteomics 2015; 114:263-73. [DOI: 10.1016/j.jprot.2014.10.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 10/10/2014] [Accepted: 10/22/2014] [Indexed: 11/21/2022]
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20
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Gopalakrishnan R, Azhagiya Singam ER, Vijaya Sundar J, Subramanian V. Interaction of collagen like peptides with gold nanosurfaces: a molecular dynamics investigation. Phys Chem Chem Phys 2015; 17:5172-86. [DOI: 10.1039/c4cp04969a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, an attempt has been made to understand the interaction between collagen like peptides (CPs) with a gold nanosurface (AuNS) using a classical molecular dynamics simulation.
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Affiliation(s)
- R. Gopalakrishnan
- Chemical laboratory
- Council of Scientific and Industrial Research
- Central Leather Research Institute
- Chennai-600020
- India
| | - E. R. Azhagiya Singam
- Chemical laboratory
- Council of Scientific and Industrial Research
- Central Leather Research Institute
- Chennai-600020
- India
| | - J. Vijaya Sundar
- Chemical laboratory
- Council of Scientific and Industrial Research
- Central Leather Research Institute
- Chennai-600020
- India
| | - V. Subramanian
- Chemical laboratory
- Council of Scientific and Industrial Research
- Central Leather Research Institute
- Chennai-600020
- India
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21
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Wang J, Nain AS. Suspended micro/nanofiber hierarchical biological scaffolds fabricated using non-electrospinning STEP technique. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:13641-9. [PMID: 25310055 DOI: 10.1021/la503011u] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Extracellular matrix (ECM) is a fibrous natural cell environment, possessing complicated micro- and nanoarchitectures, which provide extracellular signaling cues and influence cell behaviors. Mimicking this three-dimensional microenvironment in vitro is a challenge in developmental and disease biology. Here, suspended multilayer hierarchical nanofiber assemblies (diameter from micrometers to less than 100 nm) with accurately controlled fiber orientation and spacing are demonstrated as biological scaffolds fabricated using the non-electrospinning STEP (Spinneret based Tunable Engineered Parameter) fiber manufacturing technique. Micro/nanofiber arrays were manufactured with high parallelism (relative angles between fibers were maintained less than 6°) and well controlled interfiber spacing (<15%). Using these controls, we demonstrate a bottom up hierarchical assembly of suspended six layer structures of progressively reduced diameters and spacing from several polymer systems. We then demonstrate use of STEP scaffolds to study single and multicell arrangement at high magnifications. Specifically, using double layer divergent (0°-90°) suspended nanofibers assemblies, we show precise quantitative control of cell geometry (change in shape index from 0.15 to 0.57 at similar cell areas), and through design of scaffold porosity (80 × 80 μm(2) to 5 × 5 μm(2)) quadruple the cell attachment density. Furthermore, using unidirectional or crisscross patterns of sparse and dense fiber arrays, we are able to control the cell spread area from ∼400 to ∼700 μm(2), while the nucleus shape index increases from 0.75 to 0.99 with cells nearly doubling their focal adhesion cluster lengths (∼15 μm) on widely spaced nanofiber arrays. The platform developed in this study allows a wide parametric investigation of biophysical cues which influence cell behaviors with implications in tissue engineering, developmental biology, and disease biology.
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Affiliation(s)
- Ji Wang
- Department of Mechanical Engineering and †Department of Biomedical Engineering and Mechanics, Virginia Tech , Blacksburg, Virginia 24061, United States
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22
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Li PL, Zhang X, Li TF, Wang LL, Du LT, Yang YM, Li J, Wang HY, Zhang Y, Wang CX. Combined detection of sialic acid and hydroxyproline in diagnosis of ovarian cancer and its comparison with human epididymis protein 4 and carbohydrate antigen 125. Clin Chim Acta 2014; 439:148-53. [PMID: 25445414 DOI: 10.1016/j.cca.2014.10.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 10/13/2014] [Accepted: 10/17/2014] [Indexed: 12/27/2022]
Abstract
BACKGROUND Elevated serum sialic acid (SA) and hydroxyproline (Hyp) concentrations have been found in a variety of malignant cancers. We simultaneously detect serum concentrations of SA and Hyp (SA&Hyp) in ovarian cancer, and compare its diagnostic value with classic tumor markers-human epididymis protein 4 (HE4) and carbohydrate antigen 125 (CA125). METHODS Serum concentrations of SA&Hyp, HE4 and CA125A were detected in a total of 767 serum samples collected from 484 patients with gynecologic diseases, 180 healthy individuals, 45 pregnant women and 58 patients with renal failure using chemical colorimetry and electrochemiluminescence immunoassay (ECLIA), respectively. Risk of ovarian malignancy algorithm (ROMA) was calculated based on HE4 and CA125 values. RESULTS Serum SA&Hyp concentrations were influenced significantly by renal failure and pregnancy but not age and menopausal status. The median concentrations of SA&Hyp, HE4 and CA125 in patients with ovarian cancer were 119.0 U/ml, 190.2 pmol/l and 366.0 pmol/l, which were significantly higher than concentrations in patients with benign gynecologic diseases (P<0.001). SA&Hyp showed a significantly higher AUC than HE4 and CA125 in the diagnosis of gynecologic malignancies (P<0.001), while no significance was found when compared with ROMA. Specially, SA&Hyp in 48.3% subjects (29/60) diagnosed as positive before primary surgery showed negative after surgery. CONCLUSIONS Renal failure and pregnancy are the main source for increased false positive of SA and Hyp. Compared with HE4 and CA125, SA&Hyp shows a better diagnosis value and can be used in the diagnosis and dynamic monitoring of gynecologic pelvic malignancies, while no statistical significance was found compared with ROMA.
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Affiliation(s)
- Pei-long Li
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, 107 Wenhua West Road, Jinan 250012, Shandong Province, China
| | - Xin Zhang
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, 107 Wenhua West Road, Jinan 250012, Shandong Province, China
| | - Tong-fu Li
- Qingdao Bo-Xin Biotechnology Co. Ltd, Qingdao 266101, Shandong Province, China
| | - Li-li Wang
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, 107 Wenhua West Road, Jinan 250012, Shandong Province, China
| | - Lu-tao Du
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, 107 Wenhua West Road, Jinan 250012, Shandong Province, China
| | - Yong-mei Yang
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, 107 Wenhua West Road, Jinan 250012, Shandong Province, China
| | - Juan Li
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, 107 Wenhua West Road, Jinan 250012, Shandong Province, China
| | - Hai-yan Wang
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, 107 Wenhua West Road, Jinan 250012, Shandong Province, China
| | - Yi Zhang
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, 107 Wenhua West Road, Jinan 250012, Shandong Province, China.
| | - Chuan-xin Wang
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, 107 Wenhua West Road, Jinan 250012, Shandong Province, China.
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23
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Rodrigo MAM, Zitka O, Krizkova S, Moulick A, Adam V, Kizek R. MALDI-TOF MS as evolving cancer diagnostic tool: a review. J Pharm Biomed Anal 2014; 95:245-55. [PMID: 24699369 DOI: 10.1016/j.jpba.2014.03.007] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 03/03/2014] [Accepted: 03/06/2014] [Indexed: 02/09/2023]
Abstract
Recent developments in mass spectrometry have introduced clinical proteomics to the forefront of diseases diagnosis, offering reliable, robust and efficient analytical method for biomarker discovery and monitoring. MALDI-TOF is a powerful tool for surveying proteins and peptides comprising the realm for clinical analysis. MALDI-TOF has the potential to revolutionize cancer diagnostics by facilitating biomarker discovery, enabling tissue imaging and quantifying biomarker levels. Healthy (control) and cancerous tissues can be analyzed on the basis of mass spectrometry (MALDI-TOF) imaging to identify cancer-specific changes that may prove to be clinically useful. We review MALDI-TOF profiling techniques as tools for detection of cancer biomarkers in various cancers. We mainly discuss recent advances including period from 2011 to 2013.
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Affiliation(s)
- Miguel Angel Merlos Rodrigo
- Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic
| | - Ondrej Zitka
- Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic
| | - Sona Krizkova
- Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic
| | - Amitava Moulick
- Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic
| | - Rene Kizek
- Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic.
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