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Keshavarz F, Soltanshahi M, Khosravani F, Bakhshiyan F, Ghanbari A, Hassanzadeh S, Amirpour M, Ghalamfarsa G. Thymol-loaded liposomes effectively induced apoptosis and decreased EGFR expression in colorectal cancer cells. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:5157-5165. [PMID: 38240780 DOI: 10.1007/s00210-024-02945-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/09/2024] [Indexed: 06/12/2024]
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most common and deadly cancers worldwide. Different factors, such as environmental and genetic factors and lifestyle, affect it. Owing to the presence of phenolic, alkaloid, antioxidant, and terpenoid compounds, herbal compounds can be effective in the treatment of various cancers. Thymol is a natural monoterpene phenol that is abundant in some plants and exerts several biological effects. The aim of this study was to investigate the apoptotic, anti-proliferative effect and EGFR gene expression under the influence of thymol-loaded nanoliposome in SW84 and SW111 cell lines derived from colorectal cancer. MATERIALS AND METHODS The lipid thin-film hydration method was used to synthesize thymol-loaded liposomes, and their characterization was performed using TEM, DLS, and HPLC analyses. SW84 and SW1111 cells were treated with thymol- and thymol-loaded liposomes at different doses, the inhibition of cell proliferation was evaluated using an MTT assay, the rate of apoptosis induction was assessed using flow cytometry, and EGFR gene expression was measured using real-time PCR. RESULTS The nanoparticles produced were spherical, uniform, and 200 ± 10 nm in size. HPLC analysis showed that approximately 98% thymol was loaded into the nanoliposome. The results of the MTT assay showed that thymol and thymol-nanoliposomes decreased the proliferation of SW84 and SW1111 cells in a concentration-dependent manner. The IC50 of thymol and thymol-nanoliposomes were 18 and 14.2 µg/ml for the SW48 cell line (P = 0.04) and 10.5 and 6.4 µg/ml for the SW1116 cell line (P = 0.001). Thymol-nanoliposomes significantly inhibited the proliferation of cancer cells compared to free thymol. Flow cytometry showed an increase in the percentage of apoptotic cells, especially in the thymol-nanoliposome group in the treated cells. Real-time PCR results also showed that thymol and thymol-nanoliposome both caused a decrease in the expression of EGFR genes in both cell lines, but this effect of decreasing gene expression was significantly higher in the thymol-nanoliposome group. CONCLUSIONS Our results showed that thymol-nanoliposomes reduced proliferation, increased apoptosis, and decreased EGFR expression in colorectal cancer-derived cell lines.
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Affiliation(s)
- Fatemeh Keshavarz
- Department of Immunology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohsen Soltanshahi
- Department of Immunology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Khosravani
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Farzaneh Bakhshiyan
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Amir Ghanbari
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Sajad Hassanzadeh
- Department of Internal Medicine, School of Medicine, Yasuj University of Medical Sciences, Shahid Dr. Ghorban Ali Jalil Street, Yasuj, Iran
| | - Mozhgan Amirpour
- Department of Hematology and Blood Banking, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ghasem Ghalamfarsa
- Medicinal Plants Research Center, Yasuj University of Medical Sciences, Yasuj, Iran.
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Schaaf CR, Polkoff KM, Carter A, Stewart AS, Sheahan B, Freund J, Ginzel J, Snyder JC, Roper J, Piedrahita JA, Gonzalez LM. A LGR5 reporter pig model closely resembles human intestine for improved study of stem cells in disease. FASEB J 2023; 37:e22975. [PMID: 37159340 PMCID: PMC10446885 DOI: 10.1096/fj.202300223r] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/12/2023] [Accepted: 05/01/2023] [Indexed: 05/11/2023]
Abstract
Intestinal epithelial stem cells (ISCs) are responsible for intestinal epithelial barrier renewal; thereby, ISCs play a critical role in intestinal pathophysiology research. While transgenic ISC reporter mice are available, advanced translational studies lack a large animal model. This study validates ISC isolation in a new porcine Leucine Rich Repeat Containing G Protein-Coupled Receptor 5 (LGR5) reporter line and demonstrates the use of these pigs as a novel colorectal cancer (CRC) model. We applied histology, immunofluorescence, fluorescence-activated cell sorting, flow cytometry, gene expression quantification, and 3D organoid cultures to whole tissue and single cells from the duodenum, jejunum, ileum, and colon of LGR5-H2B-GFP and wild-type pigs. Ileum and colon LGR5-H2B-GFP, healthy human, and murine biopsies were compared by mRNA fluorescent in situ hybridization (FISH). To model CRC, adenomatous polyposis coli (APC) mutation was induced by CRISPR/Cas9 editing in porcine LGR5-H2B-GFP colonoids. Crypt-base, green fluorescent protein (GFP) expressing cells co-localized with ISC biomarkers. LGR5-H2B-GFPhi cells had significantly higher LGR5 expression (p < .01) and enteroid forming efficiency (p < .0001) compared with LGR5-H2B-GFPmed/lo/neg cells. Using FISH, similar LGR5, OLFM4, HOPX, LYZ, and SOX9 expression was identified between human and LGR5-H2B-GFP pig crypt-base cells. LGR5-H2B-GFP/APCnull colonoids had cystic growth in WNT/R-spondin-depleted media and significantly upregulated WNT/β-catenin target gene expression (p < .05). LGR5+ ISCs are reproducibly isolated in LGR5-H2B-GFP pigs and used to model CRC in an organoid platform. The known anatomical and physiologic similarities between pig and human, and those shown by crypt-base FISH, underscore the significance of this novel LGR5-H2B-GFP pig to translational ISC research.
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Affiliation(s)
- Cecilia R. Schaaf
- Department of Clinical Sciences, College of Veterinary MedicineNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Kathryn M. Polkoff
- Department of Molecular Biomedical Sciences, College of Veterinary MedicineNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Amber Carter
- Department of Molecular Biomedical Sciences, College of Veterinary MedicineNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Amy S. Stewart
- Department of Clinical Sciences, College of Veterinary MedicineNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Breanna Sheahan
- Department of Molecular Biomedical Sciences, College of Veterinary MedicineNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - John Freund
- Department of Clinical Sciences, College of Veterinary MedicineNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Joshua Ginzel
- Department of SurgeryDuke UniversityDurhamNorth CarolinaUSA
| | - Joshua C. Snyder
- Department of SurgeryDuke UniversityDurhamNorth CarolinaUSA
- Department of Cell BiologyDuke UniversityDurhamNorth CarolinaUSA
| | - Jatin Roper
- Department of Medicine, Division of GastroenterologyDuke UniversityDurhamNorth CarolinaUSA
- Department of Pharmacology and Cancer BiologyDuke UniversityDurhamNorth CarolinaUSA
| | - Jorge A. Piedrahita
- Department of Molecular Biomedical Sciences, College of Veterinary MedicineNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Liara M. Gonzalez
- Department of Clinical Sciences, College of Veterinary MedicineNorth Carolina State UniversityRaleighNorth CarolinaUSA
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3
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Jaitner S, Pretzsch E, Neumann J, Schäffauer A, Schiemann M, Angele M, Kumbrink J, Schwitalla S, Greten FR, Brandl L, Klauschen F, Horst D, Kirchner T, Jung A. Olfactomedin 4 associates with expression of differentiation markers but not with properties of cancer stemness, EMT nor metastatic spread in colorectal cancer. J Pathol Clin Res 2023; 9:73-85. [PMID: 36349502 PMCID: PMC9732686 DOI: 10.1002/cjp2.300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 10/06/2022] [Accepted: 10/13/2022] [Indexed: 11/11/2022]
Abstract
Tumor stem cells play a pivotal role in carcinogenesis and metastatic spread in colorectal cancer (CRC). Olfactomedin 4 (OLFM4) is co-expressed with the established stem cell marker leucine-rich repeat-containing G protein-coupled receptor 5 at the bottom of intestinal crypts and has been suggested as a surrogate for cancer stemness and a biomarker in gastrointestinal tumors associated with prognosis. Therefore, it was the aim of the present study to clarify whether OLFM4 is involved in carcinogenesis and metastatic spread in CRC. We used a combined approach of functional assays using forced OLFM4 overexpression in human CRC cell lines, xenograft mice, and an immunohistochemical approach using patient tissues to investigate the impact of OLFM4 on stemness, canonical Wnt signaling, properties of metastasis and differentiation as well as prognosis. OLFM4 expression correlated weakly with tumor grade in one patient cohort (metastasis collection: p = 0.05; pooled analysis of metastasis collection and survival collection: p = 0.19) and paralleled the expression of differentiation markers (FABP2, MUC2, and CK20) (p = 0.002) but did not correlate with stemness-associated markers. Further analyses in CRC cells lines as well as xenograft mice including forced overexpression of OLFM4 revealed that OLFM4 neither altered the expression of markers of stemness nor epithelial-mesenchymal transition, nor did OLFM4 itself drive proliferation, migration, or colony formation, which are all prerequisites of carcinogenesis and tumor progression. In line with this, we found no significant correlation between OLFM4 expression, metastasis, and patient survival. In summary, expression of OLFM4 in human CRC seems to be characteristic of differentiation marker expression in CRC but is not a driver of carcinogenesis nor metastatic spread.
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Affiliation(s)
- Stefanie Jaitner
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Elise Pretzsch
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-Universität München, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Partner Site Munich, Heidelberg, Germany
| | - Jens Neumann
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Partner Site Munich, Heidelberg, Germany
| | - Achim Schäffauer
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Matthias Schiemann
- Institute of Medical Microbiology, Immunology and Hygiene, Technische Universität München, Munich, Germany.,Clinical Cooperation Group Immune Monitoring, Helmholtz Center Munich (Neuherberg) and Technische Universität München, Munich, Germany
| | - Martin Angele
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jörg Kumbrink
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Partner Site Munich, Heidelberg, Germany
| | - Sarah Schwitalla
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt, Germany
| | - Florian R Greten
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Partner Site Munich, Heidelberg, Germany.,Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt, Germany
| | - Lydia Brandl
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Frederick Klauschen
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Partner Site Munich, Heidelberg, Germany
| | - David Horst
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Kirchner
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Partner Site Munich, Heidelberg, Germany
| | - Andreas Jung
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Partner Site Munich, Heidelberg, Germany
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4
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McCool EN, Xu T, Chen W, Beller NC, Nolan SM, Hummon AB, Liu X, Sun L. Deep top-down proteomics revealed significant proteoform-level differences between metastatic and nonmetastatic colorectal cancer cells. SCIENCE ADVANCES 2022; 8:eabq6348. [PMID: 36542699 PMCID: PMC9770947 DOI: 10.1126/sciadv.abq6348] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 11/18/2022] [Indexed: 05/23/2023]
Abstract
Understanding cancer metastasis at the proteoform level is crucial for discovering previously unknown protein biomarkers for cancer diagnosis and drug development. We present the first top-down proteomics (TDP) study of a pair of isogenic human nonmetastatic and metastatic colorectal cancer (CRC) cell lines (SW480 and SW620). We identified 23,622 proteoforms of 2332 proteins from the two cell lines, representing nearly fivefold improvement in the number of proteoform identifications (IDs) compared to previous TDP datasets of human cancer cells. We revealed substantial differences between the SW480 and SW620 cell lines regarding proteoform and single amino acid variant (SAAV) profiles. Quantitative TDP unveiled differentially expressed proteoforms between the two cell lines, and the corresponding genes had diversified functions and were closely related to cancer. Our study represents a pivotal advance in TDP toward the characterization of human proteome in a proteoform-specific manner, which will transform basic and translational biomedical research.
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Affiliation(s)
- Elijah N. McCool
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Tian Xu
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Wenrong Chen
- Department of BioHealth Informatics, Indiana University–Purdue University Indianapolis, 719 Indiana Avenue, Indianapolis, IN 46202, USA
| | - Nicole C. Beller
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
| | - Scott M. Nolan
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Amanda B. Hummon
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
- The Comprehensive Cancer Center, The Ohio State University, 500 West 12th Avenue, Columbus, OH 43210, USA
| | - Xiaowen Liu
- Deming Department of Medicine, School of Medicine, Tulane University, 1441 Canal Street, New Orleans, LA 70112, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
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5
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Munro MJ, Wickremesekera SK, Tan ST, Peng L. Proteomic analysis of low- and high-grade human colon adenocarcinoma tissues and tissue-derived primary cell lines reveals unique biological functions of tumours and new protein biomarker candidates. Clin Proteomics 2022; 19:27. [PMID: 35842572 PMCID: PMC9287856 DOI: 10.1186/s12014-022-09364-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/22/2022] [Indexed: 11/10/2022] Open
Abstract
Background Colon cancer is the third most common cancer and second highest cause of cancer deaths worldwide. The aim of the study was to find new biomarkers for diagnosis, prognosis and therapeutic drug targets for this disease. Methods Four low-grade and four high-grade human colon adenocarcinoma tumours with patient-matched normal colon tissues were analysed. Additionally, tissue-derived primary cell lines were established from each tumour tissue. The cell lines were validated using DNA sequencing to confirm that they are a suitable in vitro model for colon adenocarcinoma based on conserved gene mutations. Label-free quantitation proteomics was performed to compare the proteomes of colon adenocarcinoma samples to normal colon samples, and of colon adenocarcinoma tissues to tissue-derived cell lines to find significantly differentially abundant proteins. The functions enriched within the differentially expressed proteins were assessed using STRING. Proteomics data was validated by Western blotting. Results A total of 4767 proteins were identified across all tissues, and 4711 across primary tissue-derived cell lines. Of these, 3302 proteins were detected in both the tissues and the cell lines. On average, primary cell lines shared about 70% of proteins with their parent tissue, and they retained mutations to key colon adenocarcinoma-related genes and did not diverge far genetically from their parent tissues. Colon adenocarcinoma tissues displayed upregulation of RNA processing, steroid biosynthesis and detoxification, and downregulation of cytoskeletal organisation and loss of normal muscle function. Tissue-derived cell lines exhibited increased interferon-gamma signalling and aberrant ferroptosis. Overall, 318 proteins were significantly up-regulated and 362 proteins significantly down-regulated by comparisons of high-grade with low-grade tumours and low-grade tumour with normal colon tissues from both sample types. Conclusions The differences exhibited between tissues and cell lines highlight the additional information that can be obtained from patient-derived primary cell lines. DNA sequencing and proteomics confirmed that these cell lines can be considered suitable in vitro models of the parent tumours. Various potential biomarkers for colon adenocarcinoma initiation and progression and drug targets were identified and discussed, including seven novel markers: ACSL4, ANK2, AMER3, EXOSC1, EXOSC6, GCLM, and TFRC. Supplementary Information The online version contains supplementary material available at 10.1186/s12014-022-09364-y.
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Affiliation(s)
- Matthew J Munro
- School of Biological Sciences and Centre for Biodiscovery, Victoria University of Wellington, Wellington, 6140, New Zealand.,Gillies McIndoe Research Institute, Newtown, PO Box 7184, Wellington, 6242, New Zealand
| | - Susrutha K Wickremesekera
- Gillies McIndoe Research Institute, Newtown, PO Box 7184, Wellington, 6242, New Zealand.,Upper Gastrointestinal, Hepatobiliary & Pancreatic Section, Department of General Surgery, Wellington Regional Hospital, Wellington, 6021, New Zealand
| | - Swee T Tan
- Gillies McIndoe Research Institute, Newtown, PO Box 7184, Wellington, 6242, New Zealand. .,Wellington Regional Plastic, Maxillofacial & Burns Unit, Hutt Hospital, Lower Hutt, 5040, New Zealand. .,Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Melbourne, VIC, 3050, Australia.
| | - Lifeng Peng
- School of Biological Sciences and Centre for Biodiscovery, Victoria University of Wellington, Wellington, 6140, New Zealand.
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6
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Liu W, Rodgers GP. Olfactomedin 4 Is Not a Precise Marker for Human Intestinal Stem Cells, But Is Involved in Intestinal Carcinogenesis. Gastroenterology 2022; 162:1001-1004. [PMID: 34906535 DOI: 10.1053/j.gastro.2021.11.041] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/24/2021] [Accepted: 11/24/2021] [Indexed: 12/02/2022]
Affiliation(s)
- Wenli Liu
- Molecular and Clinical Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Griffin P Rodgers
- Molecular and Clinical Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
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Sheahan BJ, Theriot CM, Cortes JE, Dekaney CM. Prolonged oral antimicrobial administration prevents doxorubicin-induced loss of active intestinal stem cells. Gut Microbes 2022; 14:2018898. [PMID: 35012435 PMCID: PMC8757478 DOI: 10.1080/19490976.2021.2018898] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Acute intestinal mucositis is a common off-target effect of chemotherapy, leading to co-morbidities such as vomiting, diarrhea, sepsis, and death. We previously demonstrated that the presence of enteric bacteria modulates the extent of jejunal epithelial damage induced by doxorubicin (DXR) in mice. Despite conventional thinking of the crypt as a sterile environment, recent evidence suggests that bacterial signaling influences aISC function. In this study, we labeled aISCs using transgenic Lgr5-driven fluorescence or with immunostaining for OLFM4. We examined the effect of DXR in both germ free (GF) mice and mice depleted of microbiota using an established antimicrobial treatment protocol (AMBx). We found differences in DXR-induced loss of aISCs between GF mice and mice treated with AMBx. aISCs were decreased after DXR in GF mice, whereas AMBx mice retained aISC expression after DXR. Neither group of mice exhibited an inflammatory response to DXR, suggesting the difference in aISC retention was not due to differences in local tissue inflammation. Therefore, we suspected that there was a protective microbial signal present in the AMBx mice that was not present in the GF mice. 16S rRNA sequencing of jejunal luminal contents demonstrated that AMBx altered the fecal and jejunal microbiota. In the jejunal contents, AMBx mice had increased abundance of Ureaplasma and Burkholderia. These results suggest pro-survival signaling from microbiota in AMBx-treated mice to the aISCs, and that this signaling maintains aISCs in the face of chemotherapeutic injury. Manipulation of the enteric microbiota presents a therapeutic target for reducing the severity of chemotherapy-associated mucositis.
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Affiliation(s)
- Breanna J Sheahan
- Molecular Biomedical Sciences, College of Veterinary Medicine, NC State University, Raleigh, NCUSA,Department of Pharmacology and Cancer Biology, Duke University, Durham, NcUSA
| | - Casey M Theriot
- Population Health and Pathobiology, College of Veterinary Medicine, NC State University, Raleigh, NCUSA
| | - Jocsa E. Cortes
- Molecular Biomedical Sciences, College of Veterinary Medicine, NC State University, Raleigh, NCUSA
| | - Christopher M Dekaney
- Molecular Biomedical Sciences, College of Veterinary Medicine, NC State University, Raleigh, NCUSA,CONTACT Christopher M Dekaney Molecular Biomedical Sciences, College of Veterinary Medicine,NC State University1060 William Moore Drive, Campus Box 8401, Raleigh, North Carolina27607
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8
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Maarouf A, Boissard A, Henry C, Leman G, Coqueret O, Guette C, Lelièvre E. Anterior gradient protein 2 is a marker of tumor aggressiveness in breast cancer and favors chemotherapy‑induced senescence escape. Int J Oncol 2021; 60:5. [PMID: 34913074 PMCID: PMC8727137 DOI: 10.3892/ijo.2021.5295] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 11/09/2021] [Indexed: 11/05/2022] Open
Abstract
Among the different chemotherapies available, genotoxic drugs are widely used. In response to these drugs, particularly doxorubicin, tumor cells can enter into senescence. Chemotherapy‑induced senescence (CIS) is a complex response. Long described as a definitive arrest of cell proliferation, the present authors and various groups have shown that this state may not be complete and could allow certain cells to reproliferate. The mechanism could be due to the activation of new signaling pathways. In the laboratory, the proteins involved in these pathways and triggering cell proliferation were studied. The present study determined a new role for anterior gradient protein 2 (AGR2) in vivo in patients and in vitro in a senescence escape model. AGR2's implication in breast cancer patients and proliferation of senescent cells was assessed based on a SWATH‑MS proteomic study of patients' samples and RNA interference technology on cell lines. First, AGR2 was identified and it was found that its concentration is higher in the serum of patients with breast cancer and that this high concentration is associated with metastasis occurrence. An inverse correlation between intratumoral AGR2 expression and the senescence marker p16 was also observed. This observation led to the study of the role of AGR2 in the CIS escape model. In this model, it was found that AGR2 is overexpressed in cells during senescence escape and that its loss considerably reduces this phenomenon. Furthermore, it was shown that the extracellular form of AGR2 stimulated the reproliferation of senescent cells. The power of proteomic analysis based on the SWATH‑MS approach allowed the present study to highlight the mammalian target of rapamycin (mTOR)/AKT signaling pathway in the senescence escape mechanism mediated by AGR2. Analysis of the two signaling pathways revealed that AGR2 modulated RICTOR and AKT phosphorylation. All these results showed that AGR2 expression in sera and tumors of breast cancer patients is a marker of tumor progression and metastasis occurrence. They also showed that its overexpression regulates CIS escape via activation of the mTOR/AKT signaling pathway.
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Affiliation(s)
- Amine Maarouf
- Paul Papin ICO Cancer Center, CRCINA, INSERM U1232, Université de Nantes, Université d'Angers, 49055 Angers, France
| | - Alice Boissard
- Paul Papin ICO Cancer Center, CRCINA, INSERM U1232, Université de Nantes, Université d'Angers, 49055 Angers, France
| | - Cécile Henry
- Paul Papin ICO Cancer Center, CRCINA, INSERM U1232, Université de Nantes, Université d'Angers, 49055 Angers, France
| | - Géraldine Leman
- Paul Papin ICO Cancer Center, CRCINA, INSERM U1232, Université de Nantes, Université d'Angers, 49055 Angers, France
| | - Olivier Coqueret
- Paul Papin ICO Cancer Center, CRCINA, INSERM U1232, Université de Nantes, Université d'Angers, 49055 Angers, France
| | - Catherine Guette
- Paul Papin ICO Cancer Center, CRCINA, INSERM U1232, Université de Nantes, Université d'Angers, 49055 Angers, France
| | - Eric Lelièvre
- Paul Papin ICO Cancer Center, CRCINA, INSERM U1232, Université de Nantes, Université d'Angers, 49055 Angers, France
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9
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Xiao Q, Zhang F, Xu L, Yue L, Kon OL, Zhu Y, Guo T. High-throughput proteomics and AI for cancer biomarker discovery. Adv Drug Deliv Rev 2021; 176:113844. [PMID: 34182017 DOI: 10.1016/j.addr.2021.113844] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/13/2021] [Accepted: 06/15/2021] [Indexed: 02/08/2023]
Abstract
Biomarkers are assayed to assess biological and pathological status. Recent advances in high-throughput proteomic technology provide opportunities for developing next generation biomarkers for clinical practice aided by artificial intelligence (AI) based techniques. We summarize the advances and limitations of cancer biomarkers based on genomic and transcriptomic analysis, as well as classical antibody-based methodologies. Then we review recent progresses in mass spectrometry (MS)-based proteomics in terms of sample preparation, peptide fractionation by liquid chromatography (LC) and mass spectrometric data acquisition. We highlight applications of AI techniques in high-throughput clinical studies as compared with clinical decisions based on singular features. This review sets out our approach for discovering clinical biomarkers in studies using proteomic big data technology conjoined with computational and statistical methods.
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10
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Neyazi M, Bharadwaj SS, Bullers S, Varenyiova Z, Travis S, Arancibia-Cárcamo CV, Powrie F, Geremia A. Overexpression of Cancer-Associated Stem Cell Gene OLFM4 in the Colonic Epithelium of Patients With Primary Sclerosing Cholangitis. Inflamm Bowel Dis 2021; 27:1316-1327. [PMID: 33570127 PMCID: PMC8314119 DOI: 10.1093/ibd/izab025] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND To examine immune-epithelial interactions and their impact on epithelial transformation in primary sclerosing cholangitis-associated ulcerative colitis (PSC-UC) using patient-derived colonic epithelial organoid cultures (EpOCs). METHODS The EpOCs were originated from colonic biopsies from patients with PSC-UC (n = 12), patients with UC (n = 14), and control patients (n = 10) and stimulated with cytokines previously associated with intestinal inflammation (interferon (IFN) γ and interleukin (IL)-22). Markers of cytokine downstream pathways, stemness, and pluripotency were analyzed by real-time quantitative polymerase chain reaction and immunofluorescence. The OLFM4 expression in situ was assessed by RNAscope and immunohistochemistry. RESULTS A distinct expression of stem cell-associated genes was observed in EpOCs derived from patients with PSC-UC, with lower expression of the classical stem-cell marker LGR5 and overexpression of OLFM4, previously associated with pluripotency and early stages of neoplastic transformation in the gastrointestinal and biliary tracts. High levels of OLFM4 were also found ex vivo in colonic biopsies from patients with PSC-UC. In addition, IFNγ stimulation resulted in the downregulation of LGR5 in EpOCs, whereas higher expression of OLFM4 was observed after IL-22 stimulation. Interestingly, expression of the IL-22 receptor, IL22RA1, was induced by IFNγ, suggesting that a complex interplay between these cytokines may contribute to carcinogenesis in PSC-UC. CONCLUSIONS Higher expression of OLFM4, a cancer stemness gene induced by IL-22, is present in PSC-UC, suggesting that IL-22 responses may result in alterations of the intestinal stem-cell niche in these patients.
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Affiliation(s)
- Mastura Neyazi
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, and National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals National Health Services Foundation Trust, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Sraddha S Bharadwaj
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, and National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals National Health Services Foundation Trust, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Samuel Bullers
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, University of Oxford, Oxford, UK
| | - Zofia Varenyiova
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, and National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals National Health Services Foundation Trust, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Oxford IBD Cohort Study Investigators
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, and National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals National Health Services Foundation Trust, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Simon Travis
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, and National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals National Health Services Foundation Trust, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Carolina V Arancibia-Cárcamo
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, and National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals National Health Services Foundation Trust, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Fiona Powrie
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, University of Oxford, Oxford, UK
| | - Alessandra Geremia
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, and National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals National Health Services Foundation Trust, John Radcliffe Hospital, University of Oxford, Oxford, UK
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11
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Sheahan BJ, Freeman AN, Keeley TM, Samuelson LC, Roper J, Hasapis S, Lee CL, Dekaney CM. Epithelial Regeneration After Doxorubicin Arises Primarily From Early Progeny of Active Intestinal Stem Cells. Cell Mol Gastroenterol Hepatol 2021; 12:119-140. [PMID: 33571711 PMCID: PMC8082264 DOI: 10.1016/j.jcmgh.2021.01.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS aISCs (aISCs) are sensitive to acute insults including chemotherapy and irradiation. Regeneration after aISC depletion has primarily been explored in irradiation (IR). However, the cellular origin of epithelial regeneration after doxorubicin (DXR), a common chemotherapeutic, is poorly understood. METHODS We monitored DXR's effect on aISCs by enumerating Lgr5-eGFP+ and Olfm4+ crypts, cleaved caspase-3 (CASP3+) immunofluorescence, and time-lapse organoid imaging. Lineage tracing from previously identified regenerative cell populations (Bmi1+, Hopx+, Dll1+, and Defa6+) was performed with DXR damage. Lineage tracing from aISCs was compared with lineage tracing from early progeny cells (transit-amplifying cells arising from aISCs 1 day predamage) in the context of DXR and IR. We compared stem cell and DNA damage response (DDR) transcripts in isolated aISCs and early progeny cells 6 and 24 hours after DXR. RESULTS Epithelial regeneration after DXR primarily arose from early progeny cells generated by aISCs. Early progeny cells upregulated stem cell gene expression and lacked apoptosis induction (6 hours DXR: 2.5% of CASP3+ cells, p<0.0001). aISCs downregulated stem cell gene expression and underwent rapid apoptosis (6 hours DXR: 63.4% of CASP3+ cells). There was minimal regenerative contribution from Bmi1+, Hopx+, Dll1+, and Defa6+-expressing populations. In homeostasis, 48.4% of early progeny cells were BrdU+, and expressed low levels of DDR transcripts. CONCLUSIONS We show that DXR effectively depleted aISCs in the small intestine and subsequent epithelial regeneration depended on nonquiescent early progeny cells of aISCs. The chemoresistant phenotype of the early progeny cells may rely on a dampened DDR in contrast to aISCs' robust DDR, which facilitates expeditious apoptosis.
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Affiliation(s)
- Breanna J. Sheahan
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina
| | - Ally N. Freeman
- Department of Biological Sciences, College of Sciences, North Carolina State University, Raleigh, North Carolina
| | - Theresa M. Keeley
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan
| | - Linda C. Samuelson
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan
| | - Jatin Roper
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, North Carolina,Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina
| | - Stephanie Hasapis
- Department of Radiation Oncology, Duke University, Durham, North Carolina
| | - Chang-Lung Lee
- Department of Radiation Oncology, Duke University, Durham, North Carolina,Department of Pathology, Duke University, Durham, North Carolina
| | - Christopher M. Dekaney
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina,Correspondence Address requests for correspondence to: Christopher M. Dekaney, PhD, 1060 William Moore Drive, Campus Box 8401, Raleigh, North Carolina 27607.
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12
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Hagan RD, Langston MA. Molecular Subtyping and Outlier Detection in Human Disease Using the Paraclique Algorithm. ALGORITHMS 2021; 14:63. [PMID: 36092474 PMCID: PMC9455766 DOI: 10.3390/a14020063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Recent discoveries of distinct molecular subtypes have led to remarkable advances in treatment for a variety of diseases. While subtyping via unsupervised clustering has received a great deal of interest, most methods rely on basic statistical or machine learning methods. At the same time, techniques based on graph clustering, particularly clique-based strategies, have been successfully used to identify disease biomarkers and gene networks. A graph theoretical approach based on the paraclique algorithm is described that can easily be employed to identify putative disease subtypes and serve as an aid in outlier detection as well. The feasibility and potential effectiveness of this method is demonstrated on publicly available gene co-expression data derived from patient samples covering twelve different disease families.
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13
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Kuno R, Ito G, Kawamoto A, Hiraguri Y, Sugihara HY, Takeoka S, Nagata S, Takahashi J, Tsuchiya M, Anzai S, Mizutani T, Shimizu H, Yui S, Oshima S, Tsuchiya K, Watanabe M, Okamoto R. Notch and TNF-α signaling promote cytoplasmic accumulation of OLFM4 in intestinal epithelium cells and exhibit a cell protective role in the inflamed mucosa of IBD patients. Biochem Biophys Rep 2021; 25:100906. [PMID: 33490652 PMCID: PMC7808948 DOI: 10.1016/j.bbrep.2020.100906] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 12/30/2020] [Accepted: 12/30/2020] [Indexed: 12/12/2022] Open
Abstract
Notch signaling is activated in the intestinal epithelial cells (IECs) of patients with inflammatory bowel disease (IBD), and contributes to mucosal regeneration. Our previous study indicated that TNF-α and Notch signaling may synergistically promote the expression of the intestinal stem cell (ISC) marker OLFM4 in human IECs. In the present study, we investigated the gene regulation and function of OLFM4 in human IEC lines. We confirmed that TNF-α and Notch synergistically upregulate the mRNA expression of OLFM4. Luciferase reporter assay showed that OLFM4 transcription is regulated by the synergy of TNF-α and Notch. At the protein level, synergy between TNF-α and Notch promoted cytoplasmic accumulation of OLFM4, which has potential anti-apoptotic properties in human IECs. Analysis of patient-derived tissues and organoids consistently showed cytoplasmic accumulation of OLFM4 in response to NF-κB and Notch activation. Cytoplasmic accumulation of OLFM4 in human IECs is tightly regulated by Notch and TNF-α in synergy. Such cytoplasmic accumulation of OLFM4 may have a cell-protective role in the inflamed mucosa of patients with IBD. Notch and TNF-α signaling is important in IECs of patients with IBD. Notch and TNF-α signaling promotes the cytoplasmic accumulation of OLFM4. OLFM4 accumulation may have anti-apoptotic properties. OLFM4 could protect against mucosal inflammation in IBD.
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Key Words
- CD, Crohn's disease
- ChIP, chromatin immunoprecipitation
- DBZ, intestinal epithelial cells
- Dox, doxycycline
- IBD, inflammatory bowel disease
- IEC, dibenzazepine
- NICD, Notch intracellular domain
- Notch pathway
- OLFM4
- TNF-α, tumour necrosis factor α
- Tumour necrosis factor-α (TNF-α)
- UC, ulcerative colitis
- qRT-PCR, quantitative reverse transcription-polymerase chain reaction analysis
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Affiliation(s)
- Reiko Kuno
- Department of Gastroenterology and Hepatology, Japan
| | - Go Ito
- Advanced Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Ami Kawamoto
- Department of Gastroenterology and Hepatology, Japan
| | - Yui Hiraguri
- Department of Gastroenterology and Hepatology, Japan
| | | | | | - Sayaka Nagata
- Department of Gastroenterology and Hepatology, Japan
| | | | - Mao Tsuchiya
- Department of Gastroenterology and Hepatology, Japan
| | - Sho Anzai
- Department of Gastroenterology and Hepatology, Japan
| | | | - Hiromichi Shimizu
- Center for Stem Cell and Regenerative Medicine, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Shiro Yui
- Center for Stem Cell and Regenerative Medicine, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | | | | | - Mamoru Watanabe
- Advanced Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Ryuichi Okamoto
- Department of Gastroenterology and Hepatology, Japan.,Center for Stem Cell and Regenerative Medicine, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
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14
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Lindhorst PH, Hummon AB. Proteomics of Colorectal Cancer: Tumors, Organoids, and Cell Cultures-A Minireview. Front Mol Biosci 2020; 7:604492. [PMID: 33363210 PMCID: PMC7758474 DOI: 10.3389/fmolb.2020.604492] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/20/2020] [Indexed: 12/14/2022] Open
Abstract
Proteomics, the study of the complete protein composition of a sample, is an important field for cancer research. Changes in the proteome can serve as a biomarker of cancer or lead to the development of a targeted therapy. This minireview will focus on mass spectrometry-based proteomics studies applied specifically to colorectal cancer, particularly the variety of cancer model systems used, including tumor samples, two-dimensional (2D) and three-dimensional (3D) cell cultures such as spheroids and organoids. A thorough discussion of the application of these systems will accompany the review of the literature, as each provides distinct advantages and disadvantages for colorectal cancer research. Finally, we provide conclusions and future perspectives for the application of these model systems to cancer research as a whole.
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Affiliation(s)
- Philip H Lindhorst
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States.,The Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
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15
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Prognostic Significance and Functional Relevance of Olfactomedin 4 in Early-Stage Hepatocellular Carcinoma. Clin Transl Gastroenterol 2020; 11:e00124. [PMID: 31990698 PMCID: PMC7056049 DOI: 10.14309/ctg.0000000000000124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES Hepatocellular carcinoma (HCC) is a leading cancer-related cause of death. Unfortunately, recurrence is common even after curative treatment of early-stage patients, and no adjuvant treatment has yet been established. Aberrant expression of OLFM4 in human cancers has been reported; yet, its specific function during tumor development remains poorly understood, and its role in HCC is unknown. The purpose of this study is to examine the prognostic significance of OLFM4 and its functional relevance in determining recurrence in patients with early-stage HCC. METHODS Immunohistochemical staining to assess expression, cellular distribution, and prognostic significance of OLFM4 was performed in a tissue microarray comprising 157 HCC tissues and matched nontumor tissues. In addition, expression of OLFM4-coding mRNA was assessed in a separate patients' cohort. The findings were validated by in vitro functional studies using siRNA directed against OLFM4 to assess its effect on cell motility and proliferation. RESULTS The fraction of HCC samples exhibiting positive OLFM4 staining was higher in comparison with that observed in hepatocytes from matched nontumor tissue (61% vs 39%). However, cytoplasmic-only staining for OLFM4 was associated with vascular invasion (P = 0.048), MMP-7 expression (P = 0.002), and poorer survival (P = 0.008). A multivariate analysis confirmed the independent significance of OLFM4 in determining patients' outcome (5-year survival [58.3% vs 17.3%; HR: 2.135 {95% confidence interval: 1.135-4.015}; P = 0.019]). Correspondingly, inhibition of OLFM4 by siRNA modulated the expression of MMP-7 and E-cadherin, causing inhibition of cell proliferation, motility, and migration. DISCUSSION To the best of our knowledge, we provide the first report on the prognostic significance of OLFM4 in HCC and identify its mechanistic role as crucial mediator of MMP family protein and E-Cadherin in determining cell invasion and metastasis formation.
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16
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Dalal N, Jalandra R, Sharma M, Prakash H, Makharia GK, Solanki PR, Singh R, Kumar A. Omics technologies for improved diagnosis and treatment of colorectal cancer: Technical advancement and major perspectives. Biomed Pharmacother 2020; 131:110648. [PMID: 33152902 DOI: 10.1016/j.biopha.2020.110648] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/09/2020] [Accepted: 08/16/2020] [Indexed: 12/11/2022] Open
Abstract
Colorectal cancer (CRC) ranks third among the most commonly occurring cancers worldwide, and it causes half a million deaths annually. Alongside mechanistic study for CRC detection and treatment by conventional techniques, new technologies have been developed to study CRC. These technologies include genomics, transcriptomics, proteomics, and metabolomics which elucidate DNA markers, RNA transcripts, protein and, metabolites produced inside the colon and rectum part of the gut. All these approaches form the omics arena, which presents a remarkable opportunity for the discovery of novel prognostic, diagnostic and therapeutic biomarkers and also delineate the underlying mechanism of CRC causation, which may further help in devising treatment strategies. This review also mentions the latest developments in metagenomics and culturomics as emerging evidence suggests that metagenomics of gut microbiota has profound implications in the causation, prognosis, and treatment of CRC. A majority of bacteria cannot be studied as they remain unculturable, so culturomics has also been strengthened to develop culture conditions suitable for the growth of unculturable bacteria and identify unknown bacteria. The overall purpose of this review is to succinctly evaluate the application of omics technologies in colorectal cancer research for improving the diagnosis and treatment strategies.
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Affiliation(s)
- Nishu Dalal
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi 110067, India; Department of Environmental Science, Satyawati College, Delhi University, Delhi 110052, India
| | - Rekha Jalandra
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi 110067, India; Department of Zoology, Maharshi Dayanand University, Rohtak 124001, India
| | - Minakshi Sharma
- Department of Zoology, Maharshi Dayanand University, Rohtak 124001, India
| | - Hridayesh Prakash
- Amity Institute of Virology and Immunology, Amity University, Sector 125, Noida 201313, Uttar Pradesh, India
| | - Govind K Makharia
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Pratima R Solanki
- Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rajeev Singh
- Department of Environmental Science, Satyawati College, Delhi University, Delhi 110052, India.
| | - Anil Kumar
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi 110067, India.
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17
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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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18
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Clinicopathological significance of olfactomedin-4 in extrahepatic bile duct carcinoma. Pathol Res Pract 2020; 216:152940. [PMID: 32276789 DOI: 10.1016/j.prp.2020.152940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/01/2020] [Accepted: 03/21/2020] [Indexed: 12/28/2022]
Abstract
The clinicopathological and prognostic significance of olfactomedin-4 (OLFM4) expression has not yet been elucidated in extrahepatic bile duct carcinomas (EBDCs). Immunohistochemical analysis of OLFM4 expression in 31 normal biliary epithelia, 33 biliary intraepithelial neoplasias (BilINs), and 180 surgically resected EBDCs (54 perihilar and 126 distal) was performed and was used to analyze clinicopathological variables including patient survival. The expression of OLFM4 showed a progressive increase from normal biliary epithelia (0.2 ± 0.4) to BilINs (2.8 ± 3.2) to EBDCs (4.6 ± 4.2; P < 0.001). OLFM4 was highly expressed in 26.1% (47/180) of the EBDC cases, and high OLFM4 levels were more frequently observed in tumors with nodular growth (P = 0.029), well differentiation (P = 0.011), and lower T-category (P = 0.025) and stage grouping (P = 0.013). Patients with EBDC having high expression of OLFM4 had better survival than those with low expression of OLFM4 (median, 43.3 vs. 29.2 months; P = 0.037). OLFM4 might play an important role in carcinogenesis and in the progression from BilINs to EBDCs. High OLFM4 expression predicted less aggressive clinical behavior in patients with EBDC.
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19
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Suzuki T, Yamazaki H, Honda K, Ryo E, Kaneko A, Ota Y, Mori T. Altered DNA methylation is associated with aberrant stemness gene expression in early‑stage HNSCC. Int J Oncol 2019; 55:915-924. [PMID: 31432153 DOI: 10.3892/ijo.2019.4857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 07/17/2019] [Indexed: 11/05/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is characterized by morphological and functional cellular heterogeneity, which are properties of progenitor cells, as opposed to cell alterations caused by accidental expression of stem cell‑related molecules. The expression levels of stemness molecules and their distribution in HNSCC are unclear. As regards sporadic cellular heterogeneity, methylation is an important factor for transcriptional regulation in tumors. Integrative screening analysis of mRNA expression and altered methylation status was performed with original microarrays in 12 tumor and non‑tumor pairs of oral squamous cell carcinoma (SCC) cases. From this data set, genes regulated via aberrant DNA methylation and classified proteins were validated by function clustering. Olfactomedin 4 (OLFM4), known as an intestinal stemness molecule and cell‑cell adhesion factor, was found to be highly expressed in tumors, with an mRNA expression ratio [tumor/normal (T/N)] of 40.7686 and low methylation (‑18.02%) in the promoter region. In addition, the OLFM4 expression levels increased following treatment with the demethylating agent 5‑azacytidine in two HNSCC cell lines. Furthermore, the expression levels of OLFM4 in 59 cases of early‑stage tongue SCC were analyzed using immunohistochemistry to examine protein expression corresponding to the histopathological definition of tumors and to evaluate prognosis. The aberrant stemness gene expression caused by altered DNA methylation appeared to regulate early‑stage HNSCC characteristics. The results of the present study indicated a correlation between OLFM4 expression and promoter methylation, and suggest that it plays an important role in tumor cell heterogeneity in HNSCC.
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Affiliation(s)
- Takatsugu Suzuki
- Department of Oral Surgery, Tokai University School of Medicine, Isehara, Kanagawa 259‑1193, Japan
| | - Hiroshi Yamazaki
- Department of Oral Surgery, Tokai University School of Medicine, Isehara, Kanagawa 259‑1193, Japan
| | - Kazufumi Honda
- Division of Biomarker for Cancer Early Detection, National Cancer Center Research Institute, Tokyo 104‑0045, Japan
| | - Eijitsu Ryo
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo 104‑0045, Japan
| | - Akihiro Kaneko
- Department of Oral Surgery, Tokai University School of Medicine, Isehara, Kanagawa 259‑1193, Japan
| | - Yoshihide Ota
- Department of Oral Surgery, Tokai University School of Medicine, Isehara, Kanagawa 259‑1193, Japan
| | - Taisuke Mori
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo 104‑0045, Japan
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20
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Valo I, Raro P, Boissard A, Maarouf A, Jézéquel P, Verriele V, Campone M, Coqueret O, Guette C. OLFM4 Expression in Ductal Carcinoma In Situ and in Invasive Breast Cancer Cohorts by a SWATH-Based Proteomic Approach. Proteomics 2019; 19:e1800446. [PMID: 31318138 DOI: 10.1002/pmic.201800446] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 07/04/2019] [Indexed: 12/13/2022]
Abstract
Human olfactomedin-4 (OLFM4) is a secreted protein involved in a variety of cellular functions including proliferation, differentiation, apoptosis, and cell adhesion. OLFM4 expression has been studied in several tumor types including gastric, colorectal, lung, and endometrioid cancers where it has been suggested to be an independent favorable or unfavorable prognostic marker. For breast cancer, the clinical significance of OLFM4 is still unclear. In the present study, SWATH-MS is used as a tool for the robust identification and quantification of breast tissue proteins. SWATH-MS data show that OLFM4 expression is higher in DCIS than in invasive breast cancer. In-depth analysis of the breast tumor proteome show that OLFM4 is a favorable pronostic marker. Serum OLFM4 levels in peripheral blood are also analyzed by ELISA in 825 cases, including 94 cases of healthy individuals, 61 cases of non-invasive breast tumor (DCIS) and 670 cases of breast cancer (BC). It is found that serum OLFM4 levels are significantly higher in the DCIS cohort and in the breast cancer cohort compared with the healthy controls. This result suggests that circulating OLFM4 could be an interesting biomarker of early breast cancer. Data are available via ProteomeXchange with identifier PXD014194.
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Affiliation(s)
- Isabelle Valo
- Paul Papin ICO Cancer Center, CRCINA, INSERM, 49055, Angers, France
| | - Pedro Raro
- Paul Papin ICO Cancer Center, CRCINA, INSERM, 49055, Angers, France
| | - Alice Boissard
- Paul Papin ICO Cancer Center, CRCINA, INSERM, 49055, Angers, France
| | - Amine Maarouf
- Paul Papin ICO Cancer Center, CRCINA, INSERM, 49055, Angers, France.,Paul Papin ICO Cancer Center, CRCINA, INSERM, Université de Nantes, Université d'Angers, 49100, Angers, France
| | - Pascal Jézéquel
- Paul Papin ICO Cancer Center, CRCINA, INSERM, Unité de Bioinfomique, 44805, Nantes, France.,SIRIC ILIAD, Angers, Nantes, France
| | | | - Mario Campone
- Paul Papin ICO Cancer Center, CRCINA, INSERM, 49055, Angers, France.,SIRIC ILIAD, Angers, Nantes, France
| | - Olivier Coqueret
- Paul Papin ICO Cancer Center, CRCINA, INSERM, Université de Nantes, Université d'Angers, 49100, Angers, France.,SIRIC ILIAD, Angers, Nantes, France
| | - Catherine Guette
- Paul Papin ICO Cancer Center, CRCINA, INSERM, 49055, Angers, France.,SIRIC ILIAD, Angers, Nantes, France
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21
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Li Q, Liu A, Gu X, Su Z. Olfactomedin domain-containing proteins: evolution, functional divergence, expression patterns and damaging SNPs. Mol Genet Genomics 2019; 294:875-885. [PMID: 30915543 DOI: 10.1007/s00438-019-01549-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/15/2019] [Indexed: 12/11/2022]
Abstract
Olfactomedin domain-containing proteins appear to facilitate neurodevelopment, cell adhesion, intercellular interactions, and protein-protein interactions, and the disruption of their expression will lead to dramatic developmental perturbations and lethality. The aim of the present work was to study how these genes evolved in metazoans and diverged after their duplication as well as to characterize their expression profiles and detrimental mutations. We conducted an exhaustive survey of olfactomedin domain-containing genes in genomic databases, identifying 235 olfactomedin-like (OLF) proteins in 29 representative species covering all the main metazoan lineages. Phylogenetic analyses allowed us to define nine different subfamilies of OLF genes, and subfamily IX, which specifically includes two immunoglobulin domains, was identified for the first time in arthropods. Functional divergence analysis suggested that the function of this arthropod-specific OLF subfamily might have diverged from that of other subfamilies. Expression pattern analysis of OLF genes in humans and rats showed that human OLF genes tended to be highly expressed in the brain, while rat OLF genes were inclined to be expressed in the ovary and brain. We used the SIFT and PolyPhen servers in dbNSFP to distinguish deleterious mutations from neutral mutations for each member of the OLF gene family. The results showed that OLFML2B contains the most destructive SNPs (up to 61), while none of the mutations in OLFM2, OLFM4 and LPHN2 were predicted to be harmful. Taken together, these findings may not only enhance understanding of the phylogenetic relationships of the OLF family but also aid future studies on OLF protein regulation of nervous system development and immune function.
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Affiliation(s)
- Qin Li
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China.,Fudan University Shanghai Cancer Center, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Ake Liu
- Faculty of Biological Science and Technology, Changzhi University, Changzhi, 046011, Shanxi, China
| | - Xun Gu
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Zhixi Su
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China. .,Singlera Genomics Inc, Shanghai, China.
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22
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Khowal S, Naqvi SH, Monga S, Jain SK, Wajid S. Assessment of cellular and serum proteome from tongue squamous cell carcinoma patient lacking addictive proclivities for tobacco, betel nut, and alcohol: Case study. J Cell Biochem 2018; 119:5186-5221. [PMID: 29236289 DOI: 10.1002/jcb.26554] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 11/30/2017] [Indexed: 02/06/2023]
Abstract
The intriguing molecular pathways involved in oral carcinogenesis are still ambiguous. The oral squamous cell carcinoma (OSCC) ranks as the most common type constituting more than 90% of the globally diagnosed oral cancers cases. The elevation in the OSCC incidence rate during past 10 years has an alarming impression on human healthcare. The major challenges associated with OSCC include delayed diagnosis, high metastatic rates, and low 5-year survival rates. The present work foundations on reverse genetic strategy and involves the identification of genes showing expressional variability in an OSCC case lacking addictive proclivities for tobacco, betel nut, and/or alcohol, major etiologies. The expression modulations in the identified genes were analyzed in 16 patients comprising oral pre-cancer and cancer histo-pathologies. The genes SCCA1 and KRT1 were found to down regulate while DNAJC13, GIPC2, MRPL17, IG-Vreg, SSFA2, and UPF0415 upregulated in the oral pre-cancer and cancer pathologies, implicating the genes as crucial players in oral carcinogenesis.
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Affiliation(s)
- Sapna Khowal
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Samar H Naqvi
- Molecular Diagnostics, Genetix Biotech Asia (P) Ltd., New Delhi, India
| | - Seema Monga
- Department of ENT, Hamdard Institute of Medical Sciences and Research, Jamia Hamdard, New Delhi, India
| | - Swatantra K Jain
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
- Department of Biochemistry, Hamdard Institute of Medical Sciences and Research, Jamia Hamdard, New Delhi, India
| | - Saima Wajid
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
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23
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Lee PY, Chin SF, Low TY, Jamal R. Probing the colorectal cancer proteome for biomarkers: Current status and perspectives. J Proteomics 2018; 187:93-105. [PMID: 29953962 DOI: 10.1016/j.jprot.2018.06.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 06/13/2018] [Accepted: 06/23/2018] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is one of the most prevalent malignancies worldwide. Biomarkers that can facilitate better clinical management of CRC are in high demand to improve patient outcome and to reduce mortality. In this regard, proteomic analysis holds a promising prospect in the hunt of novel biomarkers for CRC and in understanding the mechanisms underlying tumorigenesis. This review aims to provide an overview of the current progress of proteomic research, focusing on discovery and validation of diagnostic biomarkers for CRC. We will summarize the contributions of proteomic strategies to recent discoveries of protein biomarkers for CRC and also briefly discuss the potential and challenges of different proteomic approaches in biomarker discovery and translational applications.
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Affiliation(s)
- Pey Yee Lee
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000 Kuala Lumpur, Malaysia.
| | - Siok-Fong Chin
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000 Kuala Lumpur, Malaysia
| | - Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000 Kuala Lumpur, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000 Kuala Lumpur, Malaysia
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24
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Le Duff M, Gouju J, Jonchère B, Guillon J, Toutain B, Boissard A, Henry C, Guette C, Lelièvre E, Coqueret O. Regulation of senescence escape by the cdk4-EZH2-AP2M1 pathway in response to chemotherapy. Cell Death Dis 2018; 9:199. [PMID: 29415991 PMCID: PMC5833455 DOI: 10.1038/s41419-017-0209-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 11/28/2017] [Accepted: 12/07/2017] [Indexed: 02/07/2023]
Abstract
Senescence is a tumor suppressive mechanism that induces a permanent proliferative arrest in response to an oncogenic insult or to the genotoxic stress induced by chemotherapy. We have recently described that some cells can escape this arrest, either because senescence was incomplete or as a consequence of a phenotypic adaptation. Malignant cells which resisted senescence emerged as more transformed cells that resist anoikis and rely on survival pathways activated by Akt and Mcl-1. In this study, we further characterize senescence escape, investigating how emergent cells could reproliferate. During the initial step of chemotherapy-induced senescence (CIS), we found that cyclin D1 was upregulated and that cell emergence was prevented when its main partner cdk4 was inactivated. Results indicate that this kinase induced the upregulation of the EZH2 methylase, a component of the polycomb PRC2 complex. Downregulated during the early step of treatment, the methylase was reactivated in clones that escaped senescence. The inactivation of EZH2, either by siRNA or by specific inhibitors, led to a specific inhibition of cell emergence. We used quantitative proteomic analysis to identify new targets of the methylase involved in senescence escape. We identified proteins involved in receptor endocytosis and described new functions for the AP2M1 protein in the control of chemotherapy-mediated senescence. Our results indicate that AP2M1 is involved in the transmission of secreted signals produced by senescent cells, suggesting that this pathway might regulate specific receptors involved in the control of CIS escape. In light of these results, we therefore propose that the cdk4–EZH2–AP2M1 pathway plays an important role during chemotherapy resistance and senescence escape. Since targeted therapies are available against these proteins, we propose that they should be tested in the treatment of colorectal or breast cancers that become resistant to first-line genotoxic therapies.
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Affiliation(s)
- Mélanie Le Duff
- Paul Papin ICO Cancer Center, CRCINA, INSERM, Université d'Angers, Angers, France
| | - Julien Gouju
- Paul Papin ICO Cancer Center, CRCINA, INSERM, Université d'Angers, Angers, France
| | - Barbara Jonchère
- Paul Papin ICO Cancer Center, CRCINA, INSERM, Université d'Angers, Angers, France
| | - Jordan Guillon
- Paul Papin ICO Cancer Center, CRCINA, INSERM, Université d'Angers, Angers, France
| | - Bertrand Toutain
- Paul Papin ICO Cancer Center, CRCINA, INSERM, Université d'Angers, Angers, France
| | - Alice Boissard
- Paul Papin ICO Cancer Center, CRCINA, INSERM, Université d'Angers, Angers, France
| | - Cécile Henry
- Paul Papin ICO Cancer Center, CRCINA, INSERM, Université d'Angers, Angers, France
| | - Catherine Guette
- Paul Papin ICO Cancer Center, CRCINA, INSERM, Université d'Angers, Angers, France
| | - Eric Lelièvre
- Paul Papin ICO Cancer Center, CRCINA, INSERM, Université d'Angers, Angers, France
| | - Olivier Coqueret
- Paul Papin ICO Cancer Center, CRCINA, INSERM, Université d'Angers, Angers, France.
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25
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Zhao J, Li H, Min L, Han X, Shu P, Yang Y, Gan Q, Wang X, Wang H, Ruan Y, Qin J, Sun Y, Qin X. High expression of tumor necrosis factor receptor-associated factor 2 promotes tumor metastasis and is associated with unfavorable prognosis in gastric cancer. J Gastroenterol Hepatol 2018; 33:431-442. [PMID: 28482378 DOI: 10.1111/jgh.13818] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 04/14/2017] [Accepted: 05/01/2017] [Indexed: 12/25/2022]
Abstract
BACKGROUND Tumor necrosis factor receptor-associated factor 2 (TRAF2) is a key effector in the activation of nuclear factor kappa B (NF-κB). Nevertheless, the role of TRAF2 in gastric tumorigenesis remains little defined. METHODS Immunohistochemistry was used to find the relationship between TRAF2 expression and clinicopathological characteristics of gastric cancer patients, and nomogram was applied to predict the overall survival of patients. Besides, we performed transwell assays to detect the function of TRAF2 in promoting metastasis and explored the correlations between TRAF2, NF-κB, and interleukin-8 (IL-8) in vitro. In addition, we examined the correlation between TRAF2 and tumor microenvironment by immunohistochemistry staining. RESULTS In our study, we found that TRAF2 expression was markedly increased in gastric cancer tissues. High intratumoral TRAF2 staining, which was associated with tumor invasion and metastasis, was also an independent poor prognosticator for gastric cancer patients. In vitro studies revealed that TRAF2 enhanced NF-κB activation and subsequent IL-8 expression in gastric cancer cells. Inhibition of NF-κB or IL-8 signaling attenuated TRAF2-induced migration and invasion abilities. High TRAF2 expression was confirmed to be associated with both high intratumoral and serum levels of IL-8. In addition, TRAF2 expression was positively correlated with neutrophil and macrophage infiltration as well as microvessels formation in gastric cancer samples. CONCLUSIONS These results suggest that TRAF2 functions as an important modulator in tumor metastasis and tumor microenvironment formation and is a novel independent prognostic factor of gastric cancer.
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Affiliation(s)
- Junjie Zhao
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Haojie Li
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lingqiang Min
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xu Han
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ping Shu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yupeng Yang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qiangjun Gan
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xuefei Wang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hongshan Wang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yuanyuan Ruan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jing Qin
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yihong Sun
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xinyu Qin
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
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26
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Lim LC, Lim YM. Proteome Heterogeneity in Colorectal Cancer. Proteomics 2018; 18. [PMID: 29316255 DOI: 10.1002/pmic.201700169] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 12/17/2017] [Indexed: 01/26/2023]
Abstract
Tumor heterogeneity is an important feature of colorectal cancer (CRC) manifested by dynamic changes in gene expression, protein expression, and availability of different tumor subtypes. Recent publications in the past 10 years have revealed proteome heterogeneity between different colorectal tumors and within the same tumor site. This paper reviews recent research works on the proteome heterogeneity in CRC, which includes the heterogeneity within a single tumor (intratumor heterogeneity), between different anatomical sites at the same organ, and between primary and metastatic sites (intertumor heterogeneity). The potential use of proteome heterogeneity in precision medicine and its implications in biomarker discovery and therapeutic outcomes will be discussed. Identification of the unique proteome landscape between and within individual tumors is imperative for understanding cancer biology and the management of CRC patients.
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Affiliation(s)
- Lay Cheng Lim
- Centre for Cancer Research, Faculty of Medicine and Health Sciences, University of Tunku Abdul Rahman, Selangor, Malaysia
| | - Yang Mooi Lim
- Centre for Cancer Research, Faculty of Medicine and Health Sciences, University of Tunku Abdul Rahman, Selangor, Malaysia
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27
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Alnabulsi A, Murray GI. Proteomics for early detection of colorectal cancer: recent updates. Expert Rev Proteomics 2017; 15:55-63. [PMID: 29064727 DOI: 10.1080/14789450.2018.1396893] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Colorectal cancer (CRC) is a common type of cancer with a relatively poor survival rate. The survival rate of patients could be improved if CRC is detected early. Biomarkers associated with early stages of tumor development might provide useful tools for the early diagnosis of colorectal cancer. Areas covered: Online searches using PubMed and Google Scholar were performed using keywords and with a focus on recent proteomic studies. The aim of this review is to highlight the need for biomarkers to improve the detection rate of early CRC and provide an overview of proteomic technologies used for biomarker discovery and validation. This review will also discuss recent proteomic studies which focus on identifying biomarkers associated with the early stages of CRC development. Expert commentary: A large number of CRC biomarkers are increasingly being identified by proteomics using diverse approaches. However, the clinical relevance and introduction of these markers into clinical practice cannot be determined without a robust validation process. The size of validation cohorts remains a major limitation in many biomarker studies.
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Affiliation(s)
- Abdo Alnabulsi
- a Pathology, School of Medicine, Medical Sciences and Nutrition , University of Aberdeen , Aberdeen , UK
| | - Graeme I Murray
- a Pathology, School of Medicine, Medical Sciences and Nutrition , University of Aberdeen , Aberdeen , UK
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28
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Cruz-Acuña R, Quirós M, Farkas AE, Dedhia PH, Huang S, Siuda D, García-Hernández V, Miller AJ, Spence JR, Nusrat A, García AJ. Synthetic hydrogels for human intestinal organoid generation and colonic wound repair. Nat Cell Biol 2017; 19:1326-1335. [PMID: 29058719 PMCID: PMC5664213 DOI: 10.1038/ncb3632] [Citation(s) in RCA: 347] [Impact Index Per Article: 49.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 09/19/2017] [Indexed: 12/12/2022]
Abstract
In vitro differentiation of human intestinal organoids (HIOs) from pluripotent stem cells is an unparalleled system for creating complex, multicellular three-dimensional structures capable of giving rise to tissue analogous to native human tissue. Current methods for generating HIOs rely on growth in an undefined tumour-derived extracellular matrix (ECM), which severely limits the use of organoid technologies for regenerative and translational medicine. Here, we developed a fully defined, synthetic hydrogel based on a four-armed, maleimide-terminated poly(ethylene glycol) macromer that supports robust and highly reproducible in vitro growth and expansion of HIOs, such that three-dimensional structures are never embedded in tumour-derived ECM. We also demonstrate that the hydrogel serves as an injection vehicle that can be delivered into injured intestinal mucosa resulting in HIO engraftment and improved colonic wound repair. Together, these studies show proof-of-concept that HIOs may be used therapeutically to treat intestinal injury.
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Affiliation(s)
- Ricardo Cruz-Acuña
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Miguel Quirós
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48104, USA
| | - Attila E Farkas
- Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Szeged 6726, Hungary
| | - Priya H Dedhia
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, Michigan 48104, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan 48104, USA
- Center for Organogenesis, University of Michigan Medical School, Ann Arbor, Michigan 48104, USA
| | - Sha Huang
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, Michigan 48104, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan 48104, USA
- Center for Organogenesis, University of Michigan Medical School, Ann Arbor, Michigan 48104, USA
| | - Dorothée Siuda
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48104, USA
| | | | - Alyssa J Miller
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, Michigan 48104, USA
| | - Jason R Spence
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, Michigan 48104, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan 48104, USA
- Center for Organogenesis, University of Michigan Medical School, Ann Arbor, Michigan 48104, USA
| | - Asma Nusrat
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48104, USA
| | - Andrés J García
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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29
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Liu C, Guo Y, Wu W, Zhang Z, Xu L, Wu K, Hu W, Liu G, Shi J, Xu C, Bi J, Sheng Y. Plasma olfactomedin 4 level in peripheral blood and its association with clinical features of breast cancer. Oncol Lett 2017; 14:8106-8113. [PMID: 29344255 DOI: 10.3892/ol.2017.7193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 08/15/2017] [Indexed: 01/06/2023] Open
Abstract
The present study aimed to investigate the expression of olfactomedin 4 (OLFM4) in plasma of patients with breast cancer and its association with diagnosis, metastasis and prognosis of breast cancer. OLFM4 gene expression level of peripheral blood plasma in 60 patients with breast cancer and 26 healthy donors was examined by ELISA. The expression of OLFM4 in tumor tissues of patients with breast cancer was evaluated by immunohistochemistry (protein expression) and reverse transcription-quantitative polymerase chain reaction (mRNA expression), respectively. Circulating tumor cells (CTCs) were detected in a certain set of patients. The expression of OLFM4 in plasma of the overall healthy people was higher compared with patients with breast cancer. The plasma OLFM4 level in patients with breast cancer was consistent with the expression of OLFM4 protein in tumor tissues (R2=1), indicating that the level of plasma OLFM4 expression may represent the expression of OLFM4 in breast cancer tissues. The plasma OLFM4 level in patients with histological grade I was significantly lower compared with grade III (P<0.05). Breast cancer patients with positive CTC were associated with low level of plasma OLFM4. These results suggest that low OLFM4 expression in plasma or tissue specimens of breast cancer patients is more likely to represent low histological differentiation and decreased invasive/metastatic capabilities. Taken together, plasma OLFM4 level may be considered as a biomarker for diagnosis and prognosis of breast cancer for cases where there are difficulties in obtaining tumor tissue samples.
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Affiliation(s)
- Chaoqian Liu
- Department of Breast Surgery, Changhai Hospital, Second Military Medical University, Shanghai 200433, P.R. China
| | - Yan Guo
- Department of Endocrinology, Changhai Hospital, Second Military Medical University, Shanghai 200433, P.R. China
| | - Weiwei Wu
- Biotecan Medical Diagnostics Co., Ltd, Zhangjiang Center for Translational Medicine, Shanghai 200120, P.R. China
| | - Zhenzhen Zhang
- Department of Breast Surgery, Changhai Hospital, Second Military Medical University, Shanghai 200433, P.R. China.,Biotecan Medical Diagnostics Co., Ltd, Zhangjiang Center for Translational Medicine, Shanghai 200120, P.R. China
| | - Lu Xu
- Department of Breast Surgery, Changhai Hospital, Second Military Medical University, Shanghai 200433, P.R. China
| | - Kainan Wu
- Department of Breast Surgery, Changhai Hospital, Second Military Medical University, Shanghai 200433, P.R. China
| | - Wei Hu
- Department of Breast Surgery, Changhai Hospital, Second Military Medical University, Shanghai 200433, P.R. China
| | - Guoping Liu
- Department of Breast Surgery, Changhai Hospital, Second Military Medical University, Shanghai 200433, P.R. China
| | - Junyi Shi
- Department of Breast Surgery, Changhai Hospital, Second Military Medical University, Shanghai 200433, P.R. China
| | - Cheng Xu
- Biotecan Medical Diagnostics Co., Ltd, Zhangjiang Center for Translational Medicine, Shanghai 200120, P.R. China
| | - Jianwei Bi
- Department of General Surgery, Changhai Hospital, Second Military Medical University, Shanghai 200433, P.R. China
| | - Yuan Sheng
- Department of Breast Surgery, Changhai Hospital, Second Military Medical University, Shanghai 200433, P.R. China
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30
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Yang Q, Bavi P, Wang JY, Roehrl MH. Immuno-proteomic discovery of tumor tissue autoantigens identifies olfactomedin 4, CD11b, and integrin alpha-2 as markers of colorectal cancer with liver metastases. J Proteomics 2017; 168:53-65. [DOI: 10.1016/j.jprot.2017.06.021] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 06/03/2017] [Accepted: 06/26/2017] [Indexed: 11/29/2022]
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31
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Michelland S, Bourgoin-Voillard S, Cunin V, Tollance A, Bertolino P, Slais K, Seve M. Low-molecular-weight color pI markers to monitor on-line the peptide focusing process in OFFGEL fractionation. Electrophoresis 2017; 38:2034-2041. [DOI: 10.1002/elps.201700075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 05/19/2017] [Accepted: 05/19/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Sylvie Michelland
- Univ. Grenoble Alpes, Inserm, U1055, LBFA and BEeSy; PROMETHEE Proteomic Platform; Grenoble France
- CHU de Grenoble, Institut de Biologie et de Pathologie; PROMETHEE Proteomic Platform; Grenoble France
| | - Sandrine Bourgoin-Voillard
- Univ. Grenoble Alpes, Inserm, U1055, LBFA and BEeSy; PROMETHEE Proteomic Platform; Grenoble France
- CHU de Grenoble, Institut de Biologie et de Pathologie; PROMETHEE Proteomic Platform; Grenoble France
| | - Valérie Cunin
- Univ. Grenoble Alpes, Inserm, U1055, LBFA and BEeSy; PROMETHEE Proteomic Platform; Grenoble France
- CHU de Grenoble, Institut de Biologie et de Pathologie; PROMETHEE Proteomic Platform; Grenoble France
| | - Axel Tollance
- Univ. Grenoble Alpes, Inserm, U1055, LBFA and BEeSy; PROMETHEE Proteomic Platform; Grenoble France
- CHU de Grenoble, Institut de Biologie et de Pathologie; PROMETHEE Proteomic Platform; Grenoble France
| | | | - Karel Slais
- Institute of Analytical Chemistry of the Academy of Sciences of the Czech Republic v.v.i.; Brno Czech Republic
| | - Michel Seve
- Univ. Grenoble Alpes, Inserm, U1055, LBFA and BEeSy; PROMETHEE Proteomic Platform; Grenoble France
- CHU de Grenoble, Institut de Biologie et de Pathologie; PROMETHEE Proteomic Platform; Grenoble France
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32
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Genetics, Molecular, and Proteomics Advances in Filamentous Fungi. Curr Microbiol 2017; 74:1226-1236. [PMID: 28733909 DOI: 10.1007/s00284-017-1308-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 07/13/2017] [Indexed: 10/19/2022]
Abstract
Filamentous fungi play a dynamic role in health and the environment. In addition, their unique and complex hyphal structures are involved in their morphogenesis, integrity, synthesis, and degradation, according to environmental and physiological conditions and resource availability. However, in biotechnology, it has a great value in the production of enzymes, pharmaceuticals, and food ingredients. The beginning of nomenclature of overall fungi started in early 1990 after which the categorization, interior and exterior mechanism, function, molecular and genetics study took pace. This mini-review has emphasized some of the important aspects of filamentous fungi, their pattern of life cycle, history, and development of different strategic methods applied to exploit this unique organism. New trends and concepts that have been applied to overcome obstacle because of their basic structure related to genomics and systems biology has been presented. Furthermore, the future aspects and challenges that need to be deciphered to get a bigger and better picture of filamentous fungi have been discussed.
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Karki R, Malireddi RKS, Zhu Q, Kanneganti TD. NLRC3 regulates cellular proliferation and apoptosis to attenuate the development of colorectal cancer. Cell Cycle 2017; 16:1243-1251. [PMID: 28598238 DOI: 10.1080/15384101.2017.1317414] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Nucleotide-binding domain, leucine-rich-repeat-containing proteins (NLRs) are intracellular innate immune sensors of pathogen-associated and damage-associated molecular patterns. NLRs regulate diverse biologic processes such as inflammatory responses, cell proliferation and death, and gut microbiota to attenuate tumorigenesis. In a recent publication in Nature, we identified NLRC3 as a negative regulator of PI3K-mTOR signaling and characterized its potential tumor suppressor function. Enterocytes lacking NLRC3 cannot control cellular proliferation because they are unable to suppress activation of PI3K-mTOR signaling pathways. In this Extra-View, we explore possible mechanisms through which NLRC3 regulates cellular proliferation and cell death. Besides interacting with PI3K, NLRC3 associates with TRAF6 and mTOR, confirming our recent finding that NLRC3 negatively regulates the PI3K-mTOR axis. Herein, we show that NLRC3 suppresses c-Myc expression and activation of PI3K-AKT targets FoxO3a and FoxO1 in the colon of Nlrc3-/- mice, suggesting that additional signaling pathways contribute to increased cellular proliferation. Moreover, NLRC3 suppresses colorectal tumorigenesis by promoting cellular apoptosis. Genes encoding intestinal stem cell markers BMI1 and OLFM4 are upregulated in the colon of Nlrc3-/- mice. Herein, we discuss recent findings and explore mechanisms through which NLRC3 regulates PI3K-mTOR signaling. Our studies highlight the therapeutic potential of modulating NLRC3 to prevent and treat cancer.
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Affiliation(s)
- Rajendra Karki
- a Department of Immunology , St. Jude Children's Research Hospital , Memphis , TN , USA
| | | | - Qifan Zhu
- a Department of Immunology , St. Jude Children's Research Hospital , Memphis , TN , USA
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34
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Dick JM. Chemical composition and the potential for proteomic transformation in cancer, hypoxia, and hyperosmotic stress. PeerJ 2017; 5:e3421. [PMID: 28603672 PMCID: PMC5463988 DOI: 10.7717/peerj.3421] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 05/16/2017] [Indexed: 12/19/2022] Open
Abstract
The changes of protein expression that are monitored in proteomic experiments are a type of biological transformation that also involves changes in chemical composition. Accompanying the myriad molecular-level interactions that underlie any proteomic transformation, there is an overall thermodynamic potential that is sensitive to microenvironmental conditions, including local oxidation and hydration potential. Here, up- and down-expressed proteins identified in 71 comparative proteomics studies were analyzed using the average oxidation state of carbon (ZC) and water demand per residue (\documentclass[12pt]{minimal}
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}{}${\overline{n}}_{{\mathrm{H}}_{2}\mathrm{O}}$\end{document}n¯H2O), calculated using elemental abundances and stoichiometric reactions to form proteins from basis species. Experimental lowering of oxygen availability (hypoxia) or water activity (hyperosmotic stress) generally results in decreased ZC or \documentclass[12pt]{minimal}
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}{}${\overline{n}}_{{\mathrm{H}}_{2}\mathrm{O}}$\end{document}n¯H2O of up-expressed compared to down-expressed proteins. This correspondence of chemical composition with experimental conditions provides evidence for attraction of the proteomes to a low-energy state. An opposite compositional change, toward higher average oxidation or hydration state, is found for proteomic transformations in colorectal and pancreatic cancer, and in two experiments for adipose-derived stem cells. Calculations of chemical affinity were used to estimate the thermodynamic potentials for proteomic transformations as a function of fugacity of O2 and activity of H2O, which serve as scales of oxidation and hydration potential. Diagrams summarizing the relative potential for formation of up- and down-expressed proteins have predicted equipotential lines that cluster around particular values of oxygen fugacity and water activity for similar datasets. The changes in chemical composition of proteomes are likely linked with reactions among other cellular molecules. A redox balance calculation indicates that an increase in the lipid to protein ratio in cancer cells by 20% over hypoxic cells would generate a large enough electron sink for oxidation of the cancer proteomes. The datasets and computer code used here are made available in a new R package, canprot.
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Quesada-Calvo F, Massot C, Bertrand V, Longuespée R, Blétard N, Somja J, Mazzucchelli G, Smargiasso N, Baiwir D, De Pauw-Gillet MC, Delvenne P, Malaise M, Coimbra Marques C, Polus M, De Pauw E, Meuwis MA, Louis E. OLFM4, KNG1 and Sec24C identified by proteomics and immunohistochemistry as potential markers of early colorectal cancer stages. Clin Proteomics 2017; 14:9. [PMID: 28344541 PMCID: PMC5364649 DOI: 10.1186/s12014-017-9143-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 02/21/2017] [Indexed: 12/17/2022] Open
Abstract
Background Despite recent advances in colorectal cancer (CRC) diagnosis and population screening programs, the identification of patients with preneoplastic lesions or with early CRC stages remains challenging and is important for reducing CRC incidence and increasing patient’s survival.
Methods We analysed 76 colorectal tissue samples originated from early CRC stages, normal or inflamed mucosa by label-free proteomics. The characterisation of three selected biomarker candidates was performed by immunohistochemistry on an independent set of precancerous and cancerous lesions harbouring increasing CRC stages. Results Out of 5258 proteins identified, we obtained 561 proteins with a significant differential distribution among groups of patients and controls. KNG1, OLFM4 and Sec24C distributions were validated in tissues and showed different expression levels especially in the two early CRC stages compared to normal and preneoplastic tissues. Conclusion We highlighted three proteins that require further investigations to better characterise their role in early CRC carcinogenesis and their potential as early CRC markers. Electronic supplementary material The online version of this article (doi:10.1186/s12014-017-9143-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Florence Quesada-Calvo
- Gastroenterology Department, GIGA-R, Liège University Hospital CHU, ULg, GIGA CHU-B34 Avenue de l'Hôpital 11, 4000 Liège, Belgium
| | - Charlotte Massot
- Gastroenterology Department, GIGA-R, Liège University Hospital CHU, ULg, GIGA CHU-B34 Avenue de l'Hôpital 11, 4000 Liège, Belgium
| | - Virginie Bertrand
- Laboratory of Mass Spectrometry, Chemistry Department, GIGA-R, CART, ULg, 4000 Liège, Belgium
| | - Rémi Longuespée
- Laboratory of Mass Spectrometry, Chemistry Department, GIGA-R, CART, ULg, 4000 Liège, Belgium
| | - Noëlla Blétard
- Department of Anatomy and Pathology, GIGA-R, Liège University Hospital CHU, ULg, 4000 Liège, Belgium
| | - Joan Somja
- Department of Anatomy and Pathology, GIGA-R, Liège University Hospital CHU, ULg, 4000 Liège, Belgium
| | - Gabriel Mazzucchelli
- Laboratory of Mass Spectrometry, Chemistry Department, GIGA-R, CART, ULg, 4000 Liège, Belgium
| | - Nicolas Smargiasso
- Laboratory of Mass Spectrometry, Chemistry Department, GIGA-R, CART, ULg, 4000 Liège, Belgium
| | | | - Marie-Claire De Pauw-Gillet
- Mammalian Cell Culture Laboratory, Department of Preclinical and Biomedical Sciences, GIGA-R, ULg, 4000 Liège, Belgium
| | - Philippe Delvenne
- Department of Anatomy and Pathology, GIGA-R, Liège University Hospital CHU, ULg, 4000 Liège, Belgium
| | - Michel Malaise
- Department of Clinical Sciences, Rheumatology, Liège University Hospital CHU, 4000 Liège, Belgium
| | | | - Marc Polus
- Gastroenterology Department, GIGA-R, Liège University Hospital CHU, ULg, GIGA CHU-B34 Avenue de l'Hôpital 11, 4000 Liège, Belgium
| | - Edwin De Pauw
- Laboratory of Mass Spectrometry, Chemistry Department, GIGA-R, CART, ULg, 4000 Liège, Belgium
| | - Marie-Alice Meuwis
- Gastroenterology Department, GIGA-R, Liège University Hospital CHU, ULg, GIGA CHU-B34 Avenue de l'Hôpital 11, 4000 Liège, Belgium
| | - Edouard Louis
- Gastroenterology Department, GIGA-R, Liège University Hospital CHU, ULg, GIGA CHU-B34 Avenue de l'Hôpital 11, 4000 Liège, Belgium
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O'Neill JR, Pak HS, Pairo-Castineira E, Save V, Paterson-Brown S, Nenutil R, Vojtěšek B, Overton I, Scherl A, Hupp TR. Quantitative Shotgun Proteomics Unveils Candidate Novel Esophageal Adenocarcinoma (EAC)-specific Proteins. Mol Cell Proteomics 2017; 16:1138-1150. [PMID: 28336725 PMCID: PMC5461543 DOI: 10.1074/mcp.m116.065078] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 02/26/2017] [Indexed: 12/11/2022] Open
Abstract
Esophageal cancer is the eighth most common cancer worldwide and the majority of patients have systemic disease at presentation. Esophageal adenocarcinoma (OAC), the predominant subtype in western countries, is largely resistant to current chemotherapy regimens. Selective markers are needed to enhance clinical staging and to allow targeted therapies yet there are minimal proteomic data on this cancer type. After histological review, lysates from OAC and matched normal esophageal and gastric samples from seven patients were subjected to LC MS/MS after tandem mass tag labeling and OFFGEL fractionation. Patient matched samples of OAC, normal esophagus, normal stomach, lymph node metastases and uninvolved lymph nodes were used from an additional 115 patients for verification of expression by immunohistochemistry (IHC). Over six thousand proteins were identified and quantified across samples. Quantitative reproducibility was excellent between technical replicates and a moderate correlation was seen across samples with the same histology. The quantitative accuracy was verified across the dynamic range for seven proteins by immunohistochemistry (IHC) on the originating tissues. Multiple novel tumor-specific candidates are proposed and EPCAM was verified by IHC. This shotgun proteomic study of OAC used a comparative quantitative approach to reveal proteins highly expressed in specific tissue types. Novel tumor-specific proteins are proposed and EPCAM was demonstrated to be specifically overexpressed in primary tumors and lymph node metastases compared with surrounding normal tissues. This candidate and others proposed in this study could be developed as tumor-specific targets for novel clinical staging and therapeutic approaches.
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Affiliation(s)
- J Robert O'Neill
- From the ‡Edinburgh Cancer Research Centre at the Institute of Genetics and Molecular Medicine, Edinburgh University; Robert.o'.,§Department of Surgery, Royal Infirmary of Edinburgh
| | - Hui-Song Pak
- ¶Department of Human Protein Sciences, Faculty of Medicine, University of Geneva
| | - Erola Pairo-Castineira
- ‖Centre for Medical Informatics, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh.,**MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Edinburgh University
| | - Vicki Save
- ‡‡Department of Pathology, Royal Infirmary of Edinburgh
| | | | - Rudolf Nenutil
- §§Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno
| | - Bořivoj Vojtěšek
- §§Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno
| | - Ian Overton
- ‖Centre for Medical Informatics, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh.,**MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Edinburgh University
| | - Alex Scherl
- ¶Department of Human Protein Sciences, Faculty of Medicine, University of Geneva
| | - Ted R Hupp
- From the ‡Edinburgh Cancer Research Centre at the Institute of Genetics and Molecular Medicine, Edinburgh University.,§§Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno
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Comprehensive Proteomic Characterization of the Human Colorectal Carcinoma Reveals Signature Proteins and Perturbed Pathways. Sci Rep 2017; 7:42436. [PMID: 28181595 PMCID: PMC5299448 DOI: 10.1038/srep42436] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 01/10/2017] [Indexed: 02/07/2023] Open
Abstract
The global change in protein abundance in colorectal cancer (CRC) and its contribution to tumorigenesis have not been comprehensively analyzed. In this study, we conducted a comprehensive proteomic analysis of paired tumors and adjacent tissues (AT) using high-resolution Fourier-transform mass spectrometry and a novel algorithm of quantitative pathway analysis. 12380 proteins were identified and 740 proteins that presented a 4-fold change were considered a CRC proteomic signature. A significant pattern of changes in protein abundance was uncovered which consisted of an imbalance in protein abundance of inhibitory and activating regulators in key signal pathways, a significant elevation of proteins in chromatin modification, gene expression and DNA replication and damage repair, and a decreased expression of proteins responsible for core extracellular matrix architectures. Specifically, based on the relative abundance, we identified a panel of 11 proteins to distinguish CRC from AT. The protein that showed the greatest degree of overexpression in CRC compared to AT was Dipeptidase 1 (DPEP1). Knockdown of DPEP1 in SW480 and HCT116 cells significantly increased cell apoptosis and attenuated cell proliferation and invasion. Together, our results show one of largest dataset in CRC proteomic research and provide a molecular link from genomic abnormalities to the tumor phenotype.
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Liu Y, Wang F, Xu P. miR-590 accelerates lung adenocarcinoma migration and invasion through directly suppressing functional target OLFM4. Biomed Pharmacother 2017; 86:466-474. [DOI: 10.1016/j.biopha.2016.12.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 11/29/2016] [Accepted: 12/01/2016] [Indexed: 01/09/2023] Open
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Abstract
Olfactomedin 4 (OLFM4) is an olfactomedin domain-containing glycoprotein. Multiple signaling pathways and factors, including NF-κB, Wnt, Notch, PU.1, retinoic acids, estrogen receptor, and miR-486, regulate its expression. OLFM4 interacts with several other proteins, such as gene associated with retinoic-interferon-induced mortality 19 (GRIM-19), cadherins, lectins, nucleotide oligomerization domain-1 (NOD1) and nucleotide oligomerization domain-2 (NOD2), and cathepsins C and D, known to regulate important cellular functions. Recent investigations using Olfm4-deficient mouse models have provided important clues about its in vivo biological functions. Olfm4 inhibited Helicobacter pylori-induced NF-κB pathway activity and inflammation and facilitated H. pylori colonization in the mouse stomach. Olfm4-deficient mice exhibited enhanced immunity against Escherichia coli and Staphylococcus aureus infection. Olfm4 deletion in a chronic granulomatous disease mouse model rescued them from S. aureus infection. Olfm4 deletion in mice treated with azoxymethane/dextran sodium sulfate led to robust intestinal inflammation and intestinal crypt hyperplasia. Olfm4 deletion in Apc (Min/+) mice promoted intestinal polyp formation as well as adenocarcinoma development in the distal colon. Further, Olfm4-deficient mice spontaneously developed prostatic epithelial lesions as they age. OLFM4 expression is correlated with cancer differentiation, stage, metastasis, and prognosis in a variety of cancers, suggesting its potential clinical value as an early-stage cancer marker or a therapeutic target. Collectively, these data suggest that OLFM4 plays important roles in innate immunity against bacterial infection, gastrointestinal inflammation, and cancer. In this review, we have summarized OLFM4's initial characterization, expression, regulation, protein interactions, and biological functions.
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Casey TM, Khan JM, Bringans SD, Koudelka T, Takle PS, Downs RA, Livk A, Syme RA, Tan KC, Lipscombe RJ. Analysis of Reproducibility of Proteome Coverage and Quantitation Using Isobaric Mass Tags (iTRAQ and TMT). J Proteome Res 2016; 16:384-392. [PMID: 28152591 DOI: 10.1021/acs.jproteome.5b01154] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This study aimed to compare the depth and reproducibility of total proteome and differentially expressed protein coverage in technical duplicates and triplicates using iTRAQ 4-plex, iTRAQ 8-plex, and TMT 6-plex reagents. The analysis was undertaken because comprehensive comparisons of isobaric mass tag reproducibility have not been widely reported in the literature. The highest number of proteins was identified with 4-plex, followed by 8-plex and then 6-plex reagents. Quantitative analyses revealed that more differentially expressed proteins were identified with 4-plex reagents than 8-plex reagents and 6-plex reagents. Replicate reproducibility was determined to be ≥69% for technical duplicates and ≥57% for technical triplicates. The results indicate that running an 8-plex or 6-plex experiment instead of a 4-plex experiment resulted in 26 or 39% fewer protein identifications, respectively. When 4-plex spectra were searched with three software tools-ProteinPilot, Mascot, and Proteome Discoverer-the highest number of protein identifications were obtained with Mascot. The analysis of negative controls demonstrated the importance of running experiments as replicates. Overall, this study demonstrates the advantages of using iTRAQ 4-plex reagents over iTRAQ 8-plex and TMT 6-plex reagents, provides estimates of technical duplicate and triplicate reproducibility, and emphasizes the value of running replicate samples.
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Affiliation(s)
- Tammy M Casey
- Proteomics International , Perth, Western Australia 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, The University of Western Australia , Nedlands, Western Australia 6009, Australia
| | - Javed M Khan
- Proteomics International , Perth, Western Australia 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, The University of Western Australia , Nedlands, Western Australia 6009, Australia
| | - Scott D Bringans
- Proteomics International , Perth, Western Australia 6009, Australia
| | - Tomas Koudelka
- Proteomics International , Perth, Western Australia 6009, Australia
| | - Pari S Takle
- Proteomics International , Perth, Western Australia 6009, Australia
| | - Rachael A Downs
- Proteomics International , Perth, Western Australia 6009, Australia
| | - Andreja Livk
- Proteomics International , Perth, Western Australia 6009, Australia
| | - Robert A Syme
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University , Bentley, Western Australia 6102, Australia
| | - Kar-Chun Tan
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University , Bentley, Western Australia 6102, Australia
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Huang HC, Yan L, Shao MY, Chen ZC. Advances in proteomic study of colorectal cancer. Shijie Huaren Xiaohua Zazhi 2016; 24:3870-3876. [DOI: 10.11569/wcjd.v24.i27.3870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer is one of the most common malignant tumors and the fourth cause of cancer-related mortality. It is not easy to be found at the early stage and therefore has a poor prognosis. Thus, new molecular biomarkers are required to improve early diagnosis and discover new effective therapeutic targets. Advances in proteomic technologies have greatly enhanced our understanding of the pathogenesis of colorectal cancer at the protein level, and improved our ability of early diagnosis and treatment. Proteomic studies of colorectal tissues, serum and cell lines have identified differentially expressed proteins, new potential diagnostic biomarkers and clinical drug targets. This article reviews the advances in proteomic study of colorectal cancer in recent years.
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Guo LL, He ZC, Yang CQ, Qiao PT, Yin GL. Epigenetic silencing of olfactomedin-4 enhances gastric cancer cell invasion via activation of focal adhesion kinase signaling. BMB Rep 2016; 48:630-5. [PMID: 26303970 PMCID: PMC4911205 DOI: 10.5483/bmbrep.2015.48.11.130] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Indexed: 01/17/2023] Open
Abstract
Downregulation of olfactomedin-4 (OLFM4) is associated with tumor progression, lymph node invasion and metastases. However, whether or not downregulation of OLFM4 is associated with epigenetic silencing remains unknown. In this study, we investigate the role of OLFM4 in gastric cancer cell invasion. We confirm the previous result that OLFM4 expression is increased in gastric cancer tissues and decreases with an increasing number of metastatic lymph nodes, which are associated with OLFM4 promoter hypermethylation. Overexpression of OLFM4 in gastric cancer cells had an inhibitory effect on cell invasion. Furthermore, we found that focal adhesion kinase (FAK) was negatively correlated with OLFM4 in regards to lymph node metastasis in gastric cancer tissues. Also, inhibition of FAK induced by OLFM4 knockdown resulted in a decrease in cell invasion. Thus, our study demonstrates that epigenetic silencing of OLFM4 enhances gastric cancer cell invasion via activation of FAK signaling. [BMB Reports 2015; 48(11): 630-635]
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Affiliation(s)
- Li-Li Guo
- Department of Gastroenterology, Heping Hospital, Changzhi Medical College, Changzhi, Shanxi 046000, China
| | - Zhao-Cai He
- Department of General Surgery, Heping Hospital, Changzhi Medical College, Changzhi, Shanxi 046000, China
| | - Chang-Qing Yang
- Department of Gastroenterology, Heping Hospital, Changzhi Medical College, Changzhi, Shanxi 046000, China
| | - Pei-Tang Qiao
- Department of Gastroenterology, Heping Hospital, Changzhi Medical College, Changzhi, Shanxi 046000, China
| | - Guo-Ling Yin
- Department of radiotherapy, Heping Hospital, Changzhi Medical College, Changzhi, Shanxi 046000, China
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Quantitative proteomic analysis exploring progression of colorectal cancer: Modulation of the serpin family. J Proteomics 2016; 148:139-48. [PMID: 27492143 DOI: 10.1016/j.jprot.2016.07.031] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 07/04/2016] [Accepted: 07/28/2016] [Indexed: 12/12/2022]
Abstract
UNLABELLED Colorectal cancer (CRC) remains a major cause of cancer related-death in developed countries. The mortality risk is correlated with the stage of CRC determined at the primary diagnosis and early diagnosis is associated with enhanced survival rate. Currently, only faecal occult blood tests are used to screen for CRC. Consequently, there is an incentive to identify specific markers of CRC. We used quantitative proteomic analysis of serum samples to characterize protein profiles in adenoma, CRC and healthy control samples. We identified 89 distinct proteins modulated between normal, colorectal adenoma and carcinoma patients. This list emphasizes proteins involved in enzyme regulator activities and in particular the serpin family. In serum samples, protein profiles of three members of the serpin family (SERPINA1, SERPINA3 and SERPINC1) were confirmed by ELISA assays. We obtained sensitivity/specificity values of 95%/95% for both SERPINA1 and SERPINC1, and 95%/55% for SERPINA3. This study supports the idea that serum proteins can discriminate adenoma and CRC patients from unaffected patients and reveals a panel of regulated proteins that might be useful for selecting patients for colonoscopy. By evaluating SERPINA1, SERPINA3 and SERPINC1, we highlight the potential role of the serpin family during the development and progression of CRC. SIGNIFICANCE Colorectal cancer (CRC) remains a major cause of cancer mortality throughout the world. However, very few CRC biomarkers have satisfactory sensitivity and specificity in clinical practice. To the best of our knowledge our study is the first to profile sera proteomes between adenoma, CRC and healthy patients. We report a comprehensive list of proteins that may be used as early diagnostic biomarkers of CRC. It is noteworthy that 17% of these modulated proteins have been previously described as candidate biomarkers in CRC. Enzyme regulator activity was found to be the main molecular function among these proteins and, in particular, there was an enrichment of members of the serpin family. The subsequent verification on a new cohort by ELISA demonstrates that these serpins could be useful to discriminate healthy from colorectal carcinoma patients with a high sensitivity and specificity. The combination of these biomarkers should increase predictive powers of CRC diagnosis. The remaining candidates form a reserve for further evaluation of additional biomarkers for CRC diagnosis.
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Dick JM. Proteomic indicators of oxidation and hydration state in colorectal cancer. PeerJ 2016; 4:e2238. [PMID: 27547546 PMCID: PMC4958012 DOI: 10.7717/peerj.2238] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 06/20/2016] [Indexed: 12/15/2022] Open
Abstract
New integrative approaches are needed to harness the potential of rapidly growing datasets of protein expression and microbial community composition in colorectal cancer. Chemical and thermodynamic models offer theoretical tools to describe populations of biomacromolecules and their relative potential for formation in different microenvironmental conditions. The average oxidation state of carbon (ZC) can be calculated as an elemental ratio from the chemical formulas of proteins, and water demand per residue (\documentclass[12pt]{minimal}
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}{}${\overline{n}}_{{\mathrm{H}}_{2}\mathrm{O}}$\end{document}n¯H2O) is computed by writing the overall formation reactions of proteins from basis species. Using results reported in proteomic studies of clinical samples, many datasets exhibit higher mean ZC or \documentclass[12pt]{minimal}
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}{}${\overline{n}}_{{\mathrm{H}}_{2}\mathrm{O}}$\end{document}n¯H2O of proteins in carcinoma or adenoma compared to normal tissue. In contrast, average protein compositions in bacterial genomes often have lower ZC for bacteria enriched in fecal samples from cancer patients compared to healthy donors. In thermodynamic calculations, the potential for formation of the cancer-related proteins is energetically favored by changes in the chemical activity of H2O and fugacity of O2 that reflect the compositional differences. The compositional analysis suggests that a systematic change in chemical composition is an essential feature of cancer proteomes, and the thermodynamic descriptions show that the observed proteomic transformations in host tissue could be promoted by relatively high microenvironmental oxidation and hydration states.
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Zhao J, Shu P, Duan F, Wang X, Min L, Shen Z, Ruan Y, Qin J, Sun Y, Qin X. Loss of OLFM4 promotes tumor migration through inducing interleukin-8 expression and predicts lymph node metastasis in early gastric cancer. Oncogenesis 2016; 5:e234. [PMID: 27294866 PMCID: PMC4945743 DOI: 10.1038/oncsis.2016.42] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 01/15/2016] [Accepted: 05/11/2016] [Indexed: 12/26/2022] Open
Abstract
Endoscopic surgery is increasingly used for early gastric cancer (EGC) treatment worldwide, and lymph node metastasis remains the most important risk factor for endoscopic surgery in EGC patients. Olfactomedin 4 (OLFM4) is mainly expressed in the digestive system and upregulated in several types of tumors. However, the role of OLFM4 in EGC has not been explored. We evaluated OLFM4 expression by immunohistochemical staining in 105 patients with EGC who underwent gastrectomy. The clinicopathological factors and OLFM4 expression were co-analyzed to predict lymph node metastasis in EGC. The metastatic mechanism of OLFM4 in gastric cancer was also investigated. We found that OLFM4 was upregulated in EGC tumor sections, and relatively low expression of OLFM4 was observed in patients with lymph node metastasis. OLFM4 expression as well as tumor size and differentiation were identified as independent factors, which could be co-analyzed to generate a better model for predicting lymph node metastasis in EGC patients. In vitro studies revealed that knockdown of OLFM4 promoted the migration of gastric cancer cells through activating the NF-κB/interleukin-8 axis. Negative correlation between OLFM4 and interleukin-8 expression was also observed in EGC tumor samples. Our study implies that OLFM4 expression is a potential predictor of lymph node metastasis in EGC, and combing OLFM4 with tumor size and differentiation could better stratify EGC patients with different risks of lymph node metastasis.
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Affiliation(s)
- J Zhao
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - P Shu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - F Duan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - X Wang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - L Min
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Z Shen
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Y Ruan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - J Qin
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Y Sun
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - X Qin
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
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Peng F, Huang Y, Li MY, Li GQ, Huang HC, Guan R, Chen ZC, Liang SP, Chen YH. Dissecting characteristics and dynamics of differentially expressed proteins during multistage carcinogenesis of human colorectal cancer. World J Gastroenterol 2016; 22:4515-4528. [PMID: 27182161 PMCID: PMC4858633 DOI: 10.3748/wjg.v22.i18.4515] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 02/13/2016] [Accepted: 03/18/2016] [Indexed: 02/06/2023] Open
Abstract
AIM: To discover novel biomarkers for early diagnosis, prognosis or treatment of human colorectal cancer.
METHODS: iTRAQ 2D LC-MS/MS analysis was used to identify differentially expressed proteins (DEPs) in the human colonic epithelial carcinogenic process using laser capture microdissection-purified colonic epithelial cells from normal colon, adenoma, carcinoma in situ and invasive carcinoma tissues.
RESULTS: A total of 326 DEPs were identified, and four DEPs (DMBT1, S100A9, Galectin-10, and S100A8) with progressive alteration in the carcinogenic process were further validated by immunohistochemistry. The DEPs were involved in multiple biological processes including cell cycle, cell adhesion, translation, mRNA processing, and protein synthesis. Some of the DEPs involved in cellular process such as “translation” and “mRNA splicing” were progressively up-regulated, while some DEPs involved in other processes such as “metabolism” and “cell response to stress” was progressively down-regulated. Other proteins with up- or down-regulation at certain stages of carcinogenesis may play various roles at different stages of the colorectal carcinogenic process.
CONCLUSION: These findings give insights into our understanding of the mechanisms of colorectal carcinogenesis and provide clues for further investigation of carcinogenesis and identification of biomarkers.
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Wang D, Pan Y, Hao T, Chen Y, Qiu S, Chen L, Zhao J. Clinical and Prognostic Significance of ANCCA in Squamous Cell Lung Carcinoma Patients. Arch Med Res 2016; 47:89-95. [PMID: 27131099 DOI: 10.1016/j.arcmed.2016.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/06/2016] [Indexed: 02/01/2023]
Abstract
BACKGROUND AND AIMS AAA+ nuclear coregulatory cancer associated (ANCCA) has been demonstrated as playing important roles in diverse biological processes including tumorigenesis. However, the clinical and prognostic significance of ANCCA in squamous cell lung carcinoma (SCLC) patients is still unknown. The aim of this study is to identify the role of ANCCA in SCLC patients. METHODS ANCCA mRNA and protein expressions were detected in SCLC tissues and cell lines by real-time PCR and Western blot. We examined the ANCCA protein expression in 152 SCLC samples by immunohistochemistry and analyzed the association between the expression of ANCCA protein and clinicopathological characteristics of SCLC patients. RESULTS ANCCA mRNA and protein expression are increased in SCLC tissues and cell lines. Moreover, ANCCA protein overexpression was associated with differentiated degree, clinical stage, lymph node metastasis, and distant metastasis. In uni- and multivariate analyses, ANCCA protein overexpression was an independent poor prognostic factor for SCLC patients. CONCLUSIONS ANCCA act as a potential biomarker for therapeutic strategy and prognostic prediction for SCLC.
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Affiliation(s)
- Dingmiao Wang
- Department of Emergency Medicine, Xianning Central Hospital, Xianning City, Hubei Province, China; Department of Cardiothoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Yang Pan
- Department of Emergency Medicine, Xianning Central Hospital, Xianning City, Hubei Province, China
| | - Ting Hao
- Department of Emergency Medicine, Xianning Central Hospital, Xianning City, Hubei Province, China
| | - Yong Chen
- Department of Emergency Medicine, Xianning Central Hospital, Xianning City, Hubei Province, China
| | - Shiming Qiu
- Department of Emergency Medicine, Xianning Central Hospital, Xianning City, Hubei Province, China
| | - Ling Chen
- Department of Emergency Medicine, Xianning Central Hospital, Xianning City, Hubei Province, China
| | - Jinping Zhao
- Department of Cardiothoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province, China.
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Méplan C, Johnson IT, Polley ACJ, Cockell S, Bradburn DM, Commane DM, Arasaradnam RP, Mulholland F, Zupanic A, Mathers JC, Hesketh J. Transcriptomics and proteomics show that selenium affects inflammation, cytoskeleton, and cancer pathways in human rectal biopsies. FASEB J 2016; 30:2812-25. [PMID: 27103578 DOI: 10.1096/fj.201600251r] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 04/12/2016] [Indexed: 01/11/2023]
Abstract
Epidemiologic studies highlight the potential role of dietary selenium (Se) in colorectal cancer prevention. Our goal was to elucidate whether expression of factors crucial for colorectal homoeostasis is affected by physiologic differences in Se status. Using transcriptomics and proteomics followed by pathway analysis, we identified pathways affected by Se status in rectal biopsies from 22 healthy adults, including 11 controls with optimal status (mean plasma Se = 1.43 μM) and 11 subjects with suboptimal status (mean plasma Se = 0.86 μM). We observed that 254 genes and 26 proteins implicated in cancer (80%), immune function and inflammatory response (40%), cell growth and proliferation (70%), cellular movement, and cell death (50%) were differentially expressed between the 2 groups. Expression of 69 genes, including selenoproteins W1 and K, which are genes involved in cytoskeleton remodelling and transcription factor NFκB signaling, correlated significantly with Se status. Integrating proteomics and transcriptomics datasets revealed reduced inflammatory and immune responses and cytoskeleton remodelling in the suboptimal Se status group. This is the first study combining omics technologies to describe the impact of differences in Se status on colorectal expression patterns, revealing that suboptimal Se status could alter inflammatory signaling and cytoskeleton in human rectal mucosa and so influence cancer risk.-Méplan, C., Johnson, I. T., Polley, A. C. J., Cockell, S., Bradburn, D. M., Commane, D. M., Arasaradnam, R. P., Mulholland, F., Zupanic, A., Mathers, J. C., Hesketh, J. Transcriptomics and proteomics show that selenium affects inflammation, cytoskeleton, and cancer pathways in human rectal biopsies.
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Affiliation(s)
- Catherine Méplan
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, United Kingdom; School of Biomedical Sciences, Newcastle University, Newcastle-upon-Tyne, United Kingdom; Human Nutrition Research Centre, Newcastle University, Newcastle-upon-Tyne, United Kingdom; The Medical School, Newcastle University, Newcastle-upon-Tyne, United Kingdom;
| | - Ian T Johnson
- Institute of Food Research, Norwich Research Park, Norwich, United Kingdom
| | - Abigael C J Polley
- Institute of Food Research, Norwich Research Park, Norwich, United Kingdom
| | - Simon Cockell
- Bioinformatics Support Unit, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | | | - Daniel M Commane
- Human Nutrition Research Centre, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Ramesh P Arasaradnam
- School of Biomedical Sciences, Newcastle University, Newcastle-upon-Tyne, United Kingdom; Wansbeck General Hospital, Ashingon, United Kingdom; and **Institute of Cellular Medicine, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Francis Mulholland
- Institute of Food Research, Norwich Research Park, Norwich, United Kingdom
| | - Anze Zupanic
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - John C Mathers
- Human Nutrition Research Centre, Newcastle University, Newcastle-upon-Tyne, United Kingdom; **Institute of Cellular Medicine, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - John Hesketh
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, United Kingdom; Human Nutrition Research Centre, Newcastle University, Newcastle-upon-Tyne, United Kingdom; The Medical School, Newcastle University, Newcastle-upon-Tyne, United Kingdom
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49
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Olfactomedin 4 deletion induces colon adenocarcinoma in Apc Min/+ mice. Oncogene 2016; 35:5237-5247. [PMID: 26973250 PMCID: PMC5057043 DOI: 10.1038/onc.2016.58] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 01/27/2016] [Accepted: 02/02/2016] [Indexed: 12/13/2022]
Abstract
Colon carcinogenesis is a multiple-step process involving the accumulation of a series of genetic and epigenetic alterations. The most commonly initiating event of intestinal carcinogenesis is mutation of the adenomatous polyposis coli (APC) gene, which leads to activation of the Wnt/β-catenin pathway. Olfactomedin 4 (OLFM4) has emerged as an intestinal stem-cell marker, but its biological function in the intestine remains to be determined. Here we show that Olfm4 deletion induced colon adenocarcinoma in the distal colon of ApcMin/+ mice. Mechanistically, we found that OLFM4 is a target gene of the Wnt/β-catenin pathway and can downregulate β-catenin signaling by competing with Wnt ligands for binding to Frizzled receptors, as well as by inhibition of the Akt-GSK-3β (Akt-glycogen synthase kinase-3β) pathway. We have shown that both Wnt and nuclear factor-κB (NF-κB) signaling were boosted in tumor tissues of Apc Olfm4 double-mutant mice. These data establish OLFM4 as a critical negative regulator of the Wnt/β-catenin and NF-κB pathways that inhibits colon-cancer development initiated by APC mutation. In addition, Olfm4 deletion significantly enhanced intestinal-crypt proliferation and inflammation induced by azoxymethane/dextran sodium sulfate. Thus, OLFM4 has an important role in the regulation of intestinal inflammation and tumorigenesis, and could be a potential therapeutic target for intestinal malignant tumors. Unlike the human colonic epithelium, the mouse colonic epithelium does not express OLFM4, but nevertheless, systemic OLFM4 deletion promotes colon tumorigenesis and that loss from mucosal neutrophils may have a role to play.
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Ma H, Chen G, Guo M. Mass spectrometry based translational proteomics for biomarker discovery and application in colorectal cancer. Proteomics Clin Appl 2016; 10:503-15. [PMID: 26616366 DOI: 10.1002/prca.201500082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 11/17/2015] [Accepted: 11/25/2015] [Indexed: 12/29/2022]
Abstract
Colorectal cancer (CRC) is a leading cause of cancer-related death in the world. Clinically, early detection of the disease is the most effective approach to tackle this tough challenge. Discovery and development of reliable and effective diagnostic tools for the assessment of prognosis and prediction of response to drug therapy are urgently needed for personalized therapies and better treatment outcomes. Among many ongoing efforts in search for potential CRC biomarkers, MS-based translational proteomics provides a unique opportunity for the discovery and application of protein biomarkers toward better CRC early detection and treatment. This review updates most recent studies that use preclinical models and clinical materials for the identification of CRC-related protein markers. Some new advances in the development of CRC protein markers such as CRC stem cell related protein markers, SRM/MRM-MS and MS cytometry approaches are also discussed in order to address future directions and challenges from bench translational research to bedside clinical application of CRC biomarkers.
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Affiliation(s)
- Hong Ma
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-Africa Joint Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, P. R. China.,Haematology and Oncology Division, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Guilin Chen
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-Africa Joint Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, P. R. China.,University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Mingquan Guo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-Africa Joint Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, P. R. China
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