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Jaiswal S, Joshi B, Chen J, Wang F, Dame MK, Spence JR, Newsome GM, Katz EL, Shah YM, Ramakrishnan SK, Li G, Lee M, Appelman HD, Kuick R, Wang TD. Membrane Bound Peroxiredoxin-1 Serves as a Biomarker for In Vivo Detection of Sessile Serrated Adenomas. Antioxid Redox Signal 2022; 36:39-56. [PMID: 34409853 PMCID: PMC8792500 DOI: 10.1089/ars.2020.8244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Aim: Sessile serrated adenomas (SSAs) are premalignant lesions driven by the BRAFV600E mutation to give rise to colorectal cancers (CRCs). They are often missed during white light colonoscopy because of their subtle appearance. Previously, a fluorescently labeled 7mer peptide KCCFPAQ was shown to detect SSAs in vivo. We aim to identify the target of this peptide. Results: Peroxiredoxin-1 (Prdx1) was identified as the binding partner of the peptide ligand. In vitro binding assays and immunofluorescence staining of human colon specimens ex vivo supported this result. Prdx1 was overexpressed on the membrane of cells with the BRAFV600E mutation, and this effect was dependent on oxidative stress. RKO cells harboring the BRAFV600E mutation and human SSA specimens showed higher oxidative stress as well as elevated levels of Prdx1 on the cell membrane. Innovation and Conclusion: These results suggest that Prdx1 is overexpressed on the cell surface in the presence of oxidative stress and can serve as an imaging biomarker for in vivo detection of SSAs. Antioxid. Redox Signal. 36, 39-56.
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Affiliation(s)
- Sangeeta Jaiswal
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Bishnu Joshi
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Jing Chen
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Fa Wang
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael K Dame
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Jason R Spence
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA.,Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Gina M Newsome
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Erica L Katz
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Yatrik M Shah
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.,Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Sadeesh K Ramakrishnan
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Gaoming Li
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Miki Lee
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Henry D Appelman
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Rork Kuick
- Department of Biostatistics, and University of Michigan, Ann Arbor, Michigan, USA
| | - Thomas D Wang
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA.,Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, USA
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Dame MK, Attili D, McClintock SD, Dedhia PH, Ouillette P, Hardt O, Chin AM, Xue X, Laliberte J, Katz EL, Newsome GM, Hill DR, Miller AJ, Tsai YH, Agorku D, Altheim CH, Bosio A, Simon B, Samuelson LC, Stoerker JA, Appelman HD, Varani J, Wicha MS, Brenner DE, Shah YM, Spence JR, Colacino JA. Identification, isolation and characterization of human LGR5-positive colon adenoma cells. Development 2018; 145:dev.153049. [PMID: 29467240 DOI: 10.1242/dev.153049] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 02/06/2018] [Indexed: 01/02/2023]
Abstract
The intestine is maintained by stem cells located at the base of crypts and distinguished by the expression of LGR5. Genetically engineered mouse models have provided a wealth of information about intestinal stem cells, whereas less is known about human intestinal stem cells owing to difficulty detecting and isolating these cells. We established an organoid repository from patient-derived adenomas, adenocarcinomas and normal colon, which we analyzed for variants in 71 colorectal cancer (CRC)-associated genes. Normal and neoplastic colon tissue organoids were analyzed by immunohistochemistry and fluorescent-activated cell sorting for LGR5. LGR5-positive cells were isolated from four adenoma organoid lines and were subjected to RNA sequencing. We found that LGR5 expression in the epithelium and stroma was associated with tumor stage, and by integrating functional experiments with LGR5-sorted cell RNA sequencing data from adenoma and normal organoids, we found correlations between LGR5 and CRC-specific genes, including dickkopf WNT signaling pathway inhibitor 4 (DKK4) and SPARC-related modular calcium binding 2 (SMOC2). Collectively, this work provides resources, methods and new markers to isolate and study stem cells in human tissue homeostasis and carcinogenesis.
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Affiliation(s)
- Michael K Dame
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Durga Attili
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Priya H Dedhia
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter Ouillette
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Olaf Hardt
- Miltenyi Biotec GmbH, Bergisch Gladbach, 51429, Germany
| | - Alana M Chin
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiang Xue
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Julie Laliberte
- Department of Research and Development, Progenity, Inc., Ann Arbor, MI 48109, USA
| | - Erica L Katz
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Gina M Newsome
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - David R Hill
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Alyssa J Miller
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yu-Hwai Tsai
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - David Agorku
- Miltenyi Biotec GmbH, Bergisch Gladbach, 51429, Germany
| | - Christopher H Altheim
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andreas Bosio
- Miltenyi Biotec GmbH, Bergisch Gladbach, 51429, Germany
| | - Becky Simon
- BioCentury Publications, Redwood City, CA 94065, USA
| | - Linda C Samuelson
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jay A Stoerker
- Department of Research and Development, Progenity, Inc., Ann Arbor, MI 48109, USA
| | - Henry D Appelman
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - James Varani
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Max S Wicha
- Department of Internal Medicine, Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Dean E Brenner
- Department of Internal Medicine, Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yatrik M Shah
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jason R Spence
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Justin A Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA .,Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
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Laliberte JC, Dame MK, Attili D, Islam B, Kim K, Zhang J, Katz EL, Newsome GM, Dedhia PH, Kruger A, Mann T, Goodman T, Buis J, Brenner DE, Varani J, Spence JR, Colacino JA, Stoerker J. Abstract LB-093: Simultaneous measurement of global methylation and copy number alterations in human colorectal cancer samples. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-lb-093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Epigenomic changes are commonly observed in cancer. We developed a next-generation sequencing (NGS) assay which can identify subtle changes in global methylation as well as copy number alterations (CNAs). The assay measures the methylation level of some repeat elements, covering over 25% of all CpG in the genome.
Genomic DNA extracted from 18 pairs of matched colorectal tumor to normal tissue was tested (four adenocarcinomas, including one associated with inflammatory bowel disease, and fourteen adenomas, including one adenoma from a Lynch syndrome patient, one familial adenomatous polyposis (FAP) and two sessile serrated adenomas (SSA)). We also assayed organoids established from these tissues at early (2 month) and late (more than 6 months) timepoints in culture. Briefly, bisulfite conversion and enrichment of the repeats was performed. The Illumina compatible products were sequenced on a HiSEQ 2500. Analysis was performed using Bismark (Krueger F., Babraham institute) and Nexus copy number (BioDiscovery) to determine the global methylation and the CNAs, respectively. Finally, somatic and germline variants were determined by targeted sequencing of 71 genes using the QIAseq colorectal cancer panel (QIAGEN).
Our data showed that all adenocarcinoma presented hypomethylation and CNAs as well as multiple somatic variants in APC, KRAS, TP53, SMAD4 and PIK3CA. Six out of the fourteen adenomas presented CNAs and nine showed hypomethylation. The most frequently observed copy number gain affected the chromosomes 8q and 13. Eight adenomas presenting somatic mutations in APC also exhibited distinct global hypomethylation. Previous publications have reported that mutations in APC precede global hypomethylation. Interestingly, one adenoma showed significant hypomethylation but no detectable CNAs or APC mutations. The two SSA samples showed the characteristic BRAF V600E mutations and the FAP sample presented germline mutation in APC. The FAP and the SSA samples did not show hypomethylation or CNAs. Most organoids presented CNAs and somatic mutations similar to their matched tissue even after 2 years in culture. However, few organoids developed new CNAs and somatic variants. Monitoring the changes in organoid may provide important information on tumor progression.
This assay measured CNAs and methylation in colorectal cancer samples, findings which may assist in determining the status of the disease and provide guidance to the appropriate action. Our NGS assay interrogates a significant portion of the genome leading to a more accurate and sensitive evaluation of the state of these cancer cells.
Note: This abstract was not presented at the meeting.
Citation Format: Julie C. Laliberte, Michael K. Dame, Durga Attili, Bodrul Islam, Kevin Kim, Jessica Zhang, Erica L. Katz, Gina M. Newsome, Priya H. Dedhia, Adele Kruger, Tobias Mann, Tom Goodman, Jeffrey Buis, Dean E. Brenner, James Varani, Jason R. Spence, Justin A. Colacino, Jay Stoerker. Simultaneous measurement of global methylation and copy number alterations in human colorectal cancer samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-093. doi:10.1158/1538-7445.AM2017-LB-093
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Affiliation(s)
| | - Michael K. Dame
- 2Department of Pathology, University of Michigan Medical School, Ann Arbor, MI
| | - Durga Attili
- 2Department of Pathology, University of Michigan Medical School, Ann Arbor, MI
| | - Bodrul Islam
- 2Department of Pathology, University of Michigan Medical School, Ann Arbor, MI
| | - Kevin Kim
- 2Department of Pathology, University of Michigan Medical School, Ann Arbor, MI
| | - Jessica Zhang
- 2Department of Pathology, University of Michigan Medical School, Ann Arbor, MI
| | - Erica L. Katz
- 2Department of Pathology, University of Michigan Medical School, Ann Arbor, MI
| | - Gina M. Newsome
- 2Department of Pathology, University of Michigan Medical School, Ann Arbor, MI
| | - Priya H. Dedhia
- 3Department of Surgery, University of Michigan, Ann Arbor, MI
| | | | | | | | | | - Dean E. Brenner
- 4Department of Pharmacology, Department of Internal Medicine, Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI
| | - James Varani
- 2Department of Pathology, University of Michigan Medical School, Ann Arbor, MI
| | - Jason R. Spence
- 5Department of Internal Medicine, Division of Gastroenterology, Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Justin A. Colacino
- 6Department of Environmental Health Sciences, Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI
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