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Pan-cancer landscape of AID-related mutations, composite mutations, and their potential role in the ICI response. NPJ Precis Oncol 2022; 6:89. [PMID: 36456685 PMCID: PMC9715662 DOI: 10.1038/s41698-022-00331-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 11/02/2022] [Indexed: 12/03/2022] Open
Abstract
Activation-induced cytidine deaminase, AICDA or AID, is a driver of somatic hypermutation and class-switch recombination in immunoglobulins. In addition, this deaminase belonging to the APOBEC family may have off-target effects genome-wide, but its effects at pan-cancer level are not well elucidated. Here, we used different pan-cancer datasets, totaling more than 50,000 samples analyzed by whole-genome, whole-exome, or targeted sequencing. AID mutations are present at pan-cancer level with higher frequency in hematological cancers and higher presence at transcriptionally active TAD domains. AID synergizes initial hotspot mutations by a second composite mutation. AID mutational load was found to be independently associated with a favorable outcome in immune-checkpoint inhibitors (ICI) treated patients across cancers after analyzing 2000 samples. Finally, we found that AID-related neoepitopes, resulting from mutations at more frequent hotspots if compared to other mutational signatures, enhance CXCL13/CCR5 expression, immunogenicity, and T-cell exhaustion, which may increase ICI sensitivity.
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2
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Wu C, Zhong L, Li W, Liu B, Huang B, Luo Z, Wu Y. Study on the mechanism of Mycoplasma gallisepticum infection on chicken tracheal mucosa injury. Avian Pathol 2022; 51:361-373. [PMID: 35503522 DOI: 10.1080/03079457.2022.2068997] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
ABSTRACTMycoplasma gallisepticum (MG) is a pathogenic microorganism that causes serious harm to the poultry industry. It is mainly adsorbed on the cilia and mucosa of respiratory epithelial cells, causing tracheal mucosal damage or cilia loss, causing chronic respiratory disease (CRD). In order to study the effect of MG infection on chicken tracheal mucosa injury and explore its possible mechanism, specific-pathogen-free (SPF) chickens were challenged with Mycoplasma gallisepticum wild-type strain MG-HY. Then, transcriptome sequencing analysis was performed to study the mechanism of MG tracheal mucosal damage. During infection, MG localizes and proliferates in the chicken trachea, and induces mucosal damage. A total of 3112 significantly (P < 0.01) differentially expressed genes (DEGs) were selected by RNA-seq, including 1646 up-regulated genes and 1466 down-regulated genes. Functional analysis showed increased expression levels of genes involved in immune defense response and mechanical barrier of tracheal mucosa in infected chicks. The expression level of pro-inflammatory cytokines (TNF-α) increased, activating the upstream protein Ras of the ERK-MLCK signaling pathway, Ras causing ERK phosphorylation levels to rise and MLCK activation, thus causing phosphationalization of MLC, and further regulating the expression and mucous distribution of tight junction protein (TJ), leading to tracheal mucosal injury in chicks. The results of qRT-PCR assay and immunohistochemical analysis were consistent with the results of transcriptome analysis. Overall, Our findings provide a basis for further research on the underlying mechanism of chick tracheal mucosal damage caused by MG infection, and help to understand how MG induces respiratory immune damage in birds.
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Affiliation(s)
- Chunlin Wu
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou 8 350002, People's Republic of China
| | - Lemiao Zhong
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou 8 350002, People's Republic of China
| | - Wenji Li
- ZooKo biochec technology Co. Ltd, Nanping 354200, People's Republic of China
| | - Binhui Liu
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou 8 350002, People's Republic of China.,Fujian Vocational College of Agriculture, Fuzhou 350002, People's Republic of China
| | - Baoqin Huang
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou 8 350002, People's Republic of China.,Fujian Sunner Development Co. Ltd, Nanping 354100, People's Republic of China
| | - Zhongbao Luo
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou 8 350002, People's Republic of China.,Fujian Sunner Development Co. Ltd, Nanping 354100, People's Republic of China
| | - Yijian Wu
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou 8 350002, People's Republic of China.,Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal 10 Health (Fujian Agricultural and Forestry University), Fuzhou 350002, People's 11 Republic of China
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3
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Kaur R, Chauhan A, Bhat SA, Chatterjee D, Ghoshal S, Pal A. Gene of the month: Cornulin. J Clin Pathol 2021; 75:289-291. [PMID: 34969781 DOI: 10.1136/jclinpath-2021-208011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2021] [Indexed: 11/04/2022]
Abstract
Cornulin (CRNN) gene encodes a 495 amino acid long protein and is located on chromosome 1q21.3. Primarily, it functions as the marker of differentiation. Initially, it was found to be specific for the squamous cells of oesophagus. However, later on, several studies have revealed the presence of Cornulin downregulation in various epithelial squamous cell carcinomas of the head and neck, oesophagus and cervix and clinically associated it with worsening of cancer and the poor prognosis. Cornulin levels also showed dysregulation in other diseases such as Eczema and Psoriasis. Besides the differentiation marker, it was identified to be involved in the stress response. The studies, in psoriasis and oesophageal squamous cell carcinoma, has elucidated that the dysregulation in the Cornulin is associated with the cell cycle events such as G1/S transition. However, the actual function of Cornulin is still yet to be explored in detail.
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Affiliation(s)
- Rajandeep Kaur
- Biochemistry, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Anshika Chauhan
- Biochemistry, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Shabir Ahmad Bhat
- Biochemistry, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Debajyoti Chatterjee
- Histopathology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Sushmita Ghoshal
- Radiotherapy, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Arnab Pal
- Biochemistry, Post Graduate Institute of Medical Education and Research, Chandigarh, India
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4
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Expression of Ki-67, Cornulin and ISG15 in non-involved mucosal surgical margins as predictive markers for relapse in oral squamous cell carcinoma (OSCC). PLoS One 2021; 16:e0261575. [PMID: 34941961 PMCID: PMC8700009 DOI: 10.1371/journal.pone.0261575] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 12/03/2021] [Indexed: 11/19/2022] Open
Abstract
Background
Local relapse of oral squamous cell carcinoma in non-involved mucosal surgical margins indicated possibility of field alteration in the margins, which could be predicted with certain biomarkers. The objectives were to evaluate the expression of Ki-67, Cornulin and ISG15 in non-involved mucosal surgical margins and the association of clinicopathological prognosticators with local relapse in oral squamous cell carcinoma.
Methods
Surgical margins from the study (relapse) group (n = 23), control (non-relapse) group (n = 32) and normal oral mucosa (n = 5) were immunohistochemically stained using Ki-67, Cornulin and ISG15 antibodies. Association between expression of markers and clinicopathological prognosticators with local relapse in oral squamous cell carcinoma was analyzed statistically.
Results
The study group surgical margins demonstrated significantly decreased Cornulin expression (p = 0.032). Low Cornulin expression was significantly associated with local relapse (p = 0.004) and non-tongue primary tumor (p = 0.013). Although not significantly associated with local relapse, expression of Ki-67 was significantly reduced in female patients (p = 0.041). Age above 57.5 years, Chinese & Indian ethnicity, alcohol consumption, epithelial dysplasia in surgical margins, and type III and IV patterns of invasion of tumor were also significantly related to local relapse. Regression analysis showed low expression of Cornulin (p = 0.018), and increased patient’s age (p = 0.008) were predictors of local relapse in oral squamous cell carcinoma, with 34-fold risk and 18-fold risk, respectively. Expression of Ki-67 and ISG15 did not show significant association with local relapse in oral squamous cell carcinoma.
Conclusion
Low expression of Cornulin is an independent predictor of relapse in oral squamous cell carcinoma.
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5
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Identification of crucial long non-coding RNAs and mRNAs along with related regulatory networks through microarray analysis in esophageal carcinoma. Funct Integr Genomics 2021; 21:377-391. [PMID: 33864185 DOI: 10.1007/s10142-021-00784-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 03/22/2021] [Accepted: 04/06/2021] [Indexed: 02/01/2023]
Abstract
Esophageal carcinoma (EC) is a tremendous threat to human health and life worldwide. Long non-coding RNAs (lncRNAs) have been identified as crucial players in carcinomas including EC. An in-depth understanding on regulatory networks of lncRNAs contributes to the better management of EC. In this text, 2052 lncRNAs and 3240 mRNAs were found to be differentially expressed in 5 EC tumor tissues versus adjacent normal tissues by microarray analysis. Moreover, 297 carcinoma-related genes were screened out according to pathway and disease annotation analyses. In addition, 410 potential lncRNA-mRNA cis-regulation pairs and 395 lncRNA-mRNA trans-regulation pairs were screened out. Among these genes, 14 trans-regulated and 19 cis-regulated genes were found to be related with carcinomas. Additionally, 42 possible lncRNA-mRNA trans-regulation pairs and 26 cis-regulation pairs were found to be related with carcinomas. Also, 4 differentially expressed transcription factors in EC and lncRNAs possibly regulated by these transcription factors were screened out. Moreover, plenty of common upregulated or downregulated lncRNAs and mRNAs in EC were identified by comparative analysis for our microarray outcomes and previous high-throughput data. Furthermore, we demonstrated that ENST00000437781.1 knockdown inhibited cell proliferation and facilitated cell apoptosis by downregulating SIX homeobox 4 (SIX4) and ENST00000524987.1 knockdown had no influence on anoctamin 1 calcium activated chloride channel (ANO1) expression in EC cells. In conclusion, we identified some crucial lncRNAs and genes along with potential regulatory networks of lncRNAs/genes, deepening our understanding on pathogenesis of EC.
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6
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Lin Y, Zhang Y, Chen Y, Liu Z. Promoter methylation and clinical significance of GPX3 in esophageal squamous cell carcinoma. Pathol Res Pract 2019; 215:152676. [PMID: 31610903 DOI: 10.1016/j.prp.2019.152676] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 09/17/2019] [Accepted: 09/27/2019] [Indexed: 02/05/2023]
Abstract
BACKGROUND Glutathione peroxidase 3 (GPX3) provides critical protection against reactive oxygen species (ROS) in cells. Downregulation of GPX3 may contribute to carcinogenesis of esophageal squamous cell carcinoma (ESCC), but the mechanisms are not clear. MATERIALS AND METHODS We examined the differences in gene expression between ESCC and normal esophageal epithelial, by using GEO datasets, and collected 136 ESCC tumors and adjacent normal tissues to confirm our findings. GPX3 expression was measured, at the mRNA and protein levels, by qRT-PCR, Western Blot and immunohistochemistry (IHC). RESULTS GPX3 mRNA and protein levels were 3.3-fold higher in normal epithelium compared with case-matched ESCC tissues. There was no significant correlation between clinical parameters and expression levels of GPX3 in ESCC. Promoter methylation of the GPX3 gene correlated with decreased expression. CONCLUSION Downregulation of GPX3 might be a key factor in the process of ESCC carcinogenesis.
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Affiliation(s)
- Youbin Lin
- Department of Orthopaedics, First Affiliated Hospital of Shantou University Medical College, No. 57 Changping Road, Shantou, Guangdong 515041, China
| | - Ying Zhang
- Department of Pathology, Sun Yat-Sen University Cancer Center, 651 Dongfeng East Road, Guangzhou 510060, China.
| | - Yelong Chen
- Department of Orthopaedics, First Affiliated Hospital of Shantou University Medical College, No. 57 Changping Road, Shantou, Guangdong 515041, China
| | - Zhaoyong Liu
- Department of Orthopaedics, First Affiliated Hospital of Shantou University Medical College, No. 57 Changping Road, Shantou, Guangdong 515041, China.
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Qadir F, Lalli A, Dar HH, Hwang S, Aldehlawi H, Ma H, Dai H, Waseem A, Teh MT. Clinical correlation of opposing molecular signatures in head and neck squamous cell carcinoma. BMC Cancer 2019; 19:830. [PMID: 31443700 PMCID: PMC6708230 DOI: 10.1186/s12885-019-6059-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 08/19/2019] [Indexed: 12/12/2022] Open
Abstract
Background The concept of head and neck cancers (HNSCC) having unique molecular signatures is well accepted but relating this to clinical presentation and disease behaviour is essential for patient benefit. Currently the clinical significance of HNSCC molecular subtypes is uncertain therefore personalisation of HNSCC treatment is not yet possible. Methods We performed meta-analysis on 8 microarray studies and identified six significantly up- (PLAU, FN1, CDCA5) and down-regulated (CRNN, CLEC3B and DUOX1) genes which were subsequently quantified by RT-qPCR in 100 HNSCC patient margin and core tumour samples. Results Retrospective correlation with sociodemographic and clinicopathological patient details identified two subgroups of opposing molecular signature (+q6 and -q6) that correlated to two recognised high-risk HNSCC populations in the UK. The +q6 group were older, male, and excessive alcohol users whilst the –q6 group were younger, female, paan-chewers and predominantly Bangladeshi. Additionally, all patients with tumour recurrence were in the latter subgroup. Conclusions We provide the first evidence linking distinct molecular signatures in HNSCC with clinical presentations. Prospective trials are required to determine the correlation between these distinct genotypes and disease progression or treatment response. This is an important step towards the ultimate goal of improving outcomes by utilising personalised molecular-signature-guided treatments for HNSCC patients.
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Affiliation(s)
- Fatima Qadir
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, The Blizard Building, 4, Newark Street, London, England, E1 2AT, UK
| | - Anand Lalli
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, The Blizard Building, 4, Newark Street, London, England, E1 2AT, UK
| | - Huma Habib Dar
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, The Blizard Building, 4, Newark Street, London, England, E1 2AT, UK
| | - Sungjae Hwang
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, The Blizard Building, 4, Newark Street, London, England, E1 2AT, UK
| | - Hebah Aldehlawi
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, The Blizard Building, 4, Newark Street, London, England, E1 2AT, UK
| | - Hong Ma
- China-British Joint Molecular Head and Neck Cancer Research Laboratory, Affiliated Stomatological Hospital of Guizhou Medical University, Guizhou, China
| | - Haiyan Dai
- China-British Joint Molecular Head and Neck Cancer Research Laboratory, Affiliated Stomatological Hospital of Guizhou Medical University, Guizhou, China
| | - Ahmad Waseem
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, The Blizard Building, 4, Newark Street, London, England, E1 2AT, UK
| | - Muy-Teck Teh
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, The Blizard Building, 4, Newark Street, London, England, E1 2AT, UK. .,China-British Joint Molecular Head and Neck Cancer Research Laboratory, Affiliated Stomatological Hospital of Guizhou Medical University, Guizhou, China. .,Cancer Research Institute, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China.
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8
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Escribano D, Horvatić A, Contreras-Aguilar MD, Guillemin N, Cerón JJ, Tecles F, Martinez-Miró S, Eckersall PD, Manteca X, Mrljak V. Changes in saliva proteins in two conditions of compromised welfare in pigs: An experimental induced stress by nose snaring and lameness. Res Vet Sci 2019; 125:227-234. [PMID: 31284225 DOI: 10.1016/j.rvsc.2019.06.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/03/2019] [Accepted: 06/18/2019] [Indexed: 12/12/2022]
Abstract
The aim of this study was to identify biological pathways and proteins differentially expressed in saliva of pigs in two conditions of compromised welfare: an acute stress consisting of restraint with a nose snare and in pigs with lameness which is a highly frequent problem in the swine industry. For this purpose, high-resolution quantitative proteomics based on Tandem Mass Tags labelling was used. Four proteins showed significant differences in the conditions of compromised welfare, namely cornulin, the heat shock protein 27 and lactate dehydrogenase (LDH), that showed significant increases, whereas immunoglobulin J chain showed a significant decrease. LDH, which was the protein that showed the highest differences, was selected for validation and clinical evaluation as a diagnostic biomarker. Significant changes in this protein were observed between pigs restrained with a nose snare and pigs with lameness compared with healthy pigs when measured with available commercial assays in a larger population of pigs. In conclusion, this study reports that in situations of compromised welfare on farm, such as acute stress and lameness in pigs, there are changes in proteins and metabolic pathways in saliva, and describes a series of proteins that could potentially be used as biomarkers for both short term acute stress and longer term chronic stress of lameness. These biomarkers would have the advantage of being measured in saliva by a noninvasive and not stressful collection sampling procedure.
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Affiliation(s)
- Damián Escribano
- Department of Animal and Food Science, School of Veterinary Science, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain.
| | - Anita Horvatić
- ERA Chair FP7, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia
| | - Maria Dolores Contreras-Aguilar
- Interdisciplinary Laboratory of Clinical Analysis Interlab-UMU, Regional Campus of International Excellence 'Campus Mare Nostrum', University of Murcia, Campus de Espinardo s/n, 30100 Espinardo, Murcia, Spain
| | - Nicolas Guillemin
- ERA Chair FP7, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia
| | - Jose Joaquín Cerón
- Interdisciplinary Laboratory of Clinical Analysis Interlab-UMU, Regional Campus of International Excellence 'Campus Mare Nostrum', University of Murcia, Campus de Espinardo s/n, 30100 Espinardo, Murcia, Spain
| | - Fernando Tecles
- Interdisciplinary Laboratory of Clinical Analysis Interlab-UMU, Regional Campus of International Excellence 'Campus Mare Nostrum', University of Murcia, Campus de Espinardo s/n, 30100 Espinardo, Murcia, Spain
| | - Silvia Martinez-Miró
- Department of Animal Production, Veterinary school, Campus of Excellence Mare Nostrum, University of Murcia, Campus de Espinardo s/n, 30100 Espinardo, Murcia, Spain
| | - Peter David Eckersall
- ERA Chair FP7, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia; Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Bearsden Rd, Glasgow G61 1QH, UK
| | - Xavier Manteca
- Department of Animal and Food Science, School of Veterinary Science, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Vladimir Mrljak
- ERA Chair FP7, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia
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9
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Abdo J, Wichman CS, Dietz NE, Ciborowski P, Fleegel J, Mittal SK, Agrawal DK. Discovery of Novel and Clinically Relevant Markers in Formalin-Fixed Paraffin-Embedded Esophageal Cancer Specimen. Front Oncol 2018; 8:157. [PMID: 29868478 PMCID: PMC5954028 DOI: 10.3389/fonc.2018.00157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 04/25/2018] [Indexed: 12/26/2022] Open
Abstract
Due to the ineffectiveness of chemoradiation and targeted therapy in esophageal anticancer care and the subsequent low survival rates, we constructed a high throughput method to discover and investigate new markers with prognostic, diagnostic, and therapeutic clinical utility. This was accomplished by developing a quick, inexpensive, and dependable platform to simultaneously quantify thousands of proteins which subsequently revealed novel markers involved in the pathogenesis of esophageal adenocarcinoma (EAC) via discovery mass spectrometry paired with conservative biostatistics. Our method uncovered a perfect storm of tumor suppressors being downregulated, proliferation markers ramped up, and chemoresistance markers overexpressed—many of which could serve as new therapy targets for EAC. The 12 markers discovered by this method are novel regarding their involvement in the pathogenesis of EAC. The molecular oncology arena now has a dozen new proteomic targets suitable for validation and elucidation of their clinical utility via gene knockdown in cellular and animal models. This new method can be replicated and applied to other cancers or disease states for research and development and discovery-based investigations. Our findings, which serve as a proof of concept, will hopefully motivate research groups to further expound on the molecular processes involved in the aggressiveness of EAC and other solid tumor diseases, ultimately leading to improved patient management strategies.
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Affiliation(s)
- Joe Abdo
- Department of Clinical and Translational Science, Creighton University School of Medicine, Omaha, NE, United States
| | - Christopher S Wichman
- Department of Biostatistics, College of Public Health, University of Nebraska Medical Center, Omaha, NE, United States
| | - Nicholas E Dietz
- Department of Clinical and Translational Science, Creighton University School of Medicine, Omaha, NE, United States.,Department of Pathology, CHI Health Creighton University Medical Center, College of Medicine, Omaha, NE, United States
| | - Pawel Ciborowski
- Department of Pharmacology, University of Nebraska Medical Center, Omaha, NE, United States
| | - John Fleegel
- Department of Clinical and Translational Science, Creighton University School of Medicine, Omaha, NE, United States
| | - Sumeet K Mittal
- Department of Clinical and Translational Science, Creighton University School of Medicine, Omaha, NE, United States.,Norton Thoracic Institute, St. Joseph's Hospital and Medical Center, Dignity Health, Phoenix, AZ, United States
| | - Devendra K Agrawal
- Department of Clinical and Translational Science, Creighton University School of Medicine, Omaha, NE, United States
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10
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Sundkvist A, Myte R, Bodén S, Enroth S, Gyllensten U, Harlid S, van Guelpen B. Targeted plasma proteomics identifies a novel, robust association between cornulin and Swedish moist snuff. Sci Rep 2018; 8:2320. [PMID: 29396534 PMCID: PMC5797131 DOI: 10.1038/s41598-018-20794-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 01/24/2018] [Indexed: 01/08/2023] Open
Abstract
Lifestyle behaviors are believed to influence the body’s inflammatory state. Chronic low-grade inflammation contributes to the development of major non-communicable diseases such as diabetes, cardiovascular disease and cancer. Inflammation may thus be an important link between lifestyle and disease. We evaluated self-reported physical activity, tobacco use and alcohol consumption in relation to plasma levels of 160 validated inflammatory and cancer biomarkers. The study included 138 participants from a population-based cohort, all with repeated sampling of plasma and data ten years apart, allowing consideration of both intra- and inter-individual variation. Of 17 relationships identified, the strongest was an independent, positive association between cornulin (CRNN) and Swedish moist snuff (snus) use. We replicated the finding in a second cohort of 501 individuals, in which a dose-response relationship was also observed. Snus explained approximately one fifth of the variance in CRNN levels in both sample sets (18% and 23%). In conclusion, we identified a novel, independent, dose-dependent association between CRNN and snus use. Further study is warranted, to evaluate the performance of CRNN as a potential snus biomarker. The putative importance of lifestyle behaviors on a wide range of protein biomarkers illustrates the need for more personalized biomarker cut-offs.
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Affiliation(s)
- Anneli Sundkvist
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Robin Myte
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Stina Bodén
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Stefan Enroth
- Department of Immunology, Genetics, and Pathology, Biomedical Center, Science for Life Laboratory Uppsala University, Uppsala, Sweden
| | - Ulf Gyllensten
- Department of Immunology, Genetics, and Pathology, Biomedical Center, Science for Life Laboratory Uppsala University, Uppsala, Sweden
| | - Sophia Harlid
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
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11
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Dai Y, Wang Q, Gonzalez Lopez A, Anders M, Malfertheiner P, Vieth M, Kemmner W. Genome-Wide Analysis of Barrett's Adenocarcinoma. A First Step Towards Identifying Patients at Risk and Developing Therapeutic Paths. Transl Oncol 2017; 11:116-124. [PMID: 29223109 PMCID: PMC6002392 DOI: 10.1016/j.tranon.2017.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/12/2017] [Accepted: 10/23/2017] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND: Barrett's esophagus metaplasia is the key precursor lesion of esophageal adenocarcinoma. The aim of this study was to find a subset of markers that may allow the identification of patients at risk for esophageal adenocarcinoma, and to determine genes differentially expressed in esophageal squamous cell carcinoma. METHODS: Laser capture microdissection technique was applied to procure cells from defined regions. Genome-wide RNA profiling was performed on esophageal adenocarcinoma (n = 21), Barrett's esophagus (n = 20), esophageal squamous carcinoma (n = 9) and healthy esophageal biopsies (n = 18) using the Affymetrix Human Genome U133plus 2.0 array. Microarray results were validated by quantitative real-time polymerase chain reaction in a second and independent cohort and by immunohistochemistry of two putative markers in a third independent cohort. RESULTS: Through unsupervised hierarchical clustering and principal component analysis, samples were separated into four distinct groups that match perfectly with histology. Many genes down-regulated in esophageal cancers belong to the epidermal differentiation complex or the related GO-group “cornified envelope” of terminally differentiated keratinocytes. Similarly, retinol metabolism was strongly down-regulated. Genes showing strong overexpression in esophageal carcinomas belong to the GO groups extracellular region /matrix such as MMP1, CTHRC1, and INHBA. According to an analysis of genes strongly up-regulated in both esophageal adenocarcinoma and Barrett's esophagus, REG4 might be of particular interest as an early marker for esophageal adenocarcinoma. CONCLUSIONS: Our study provides high quality data, which could serve for identification of potential biomarkers of Barrett's esophagus at risk of esophageal adenocarcinoma progression.
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Affiliation(s)
- Yiyang Dai
- Translational Oncology, Experimental Clinical Research Center (ECRC), Charité Campus Buch, 13125 Berlin, Germany
| | - Qing Wang
- Translational Oncology, Experimental Clinical Research Center (ECRC), Charité Campus Buch, 13125 Berlin, Germany
| | - Adrian Gonzalez Lopez
- Department of Anesthesiology and Operative Intensive Care Medicine, Charité Campus Virchow-Klinikum, 13353 Berlin, Germany
| | - Mario Anders
- Gastroenterologie und Interdisziplinäre Endoskopie, Vivantes Wenckebach-Klinikum, 12099 Berlin, Germany
| | - Peter Malfertheiner
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Magdeburg, 39120 Magdeburg, Germany
| | - Michael Vieth
- Institute of Pathology, Klinikum Bayreuth, 95445 Bayreuth, Germany
| | - Wolfgang Kemmner
- Translational Oncology, Experimental Clinical Research Center (ECRC), Charité Campus Buch, 13125 Berlin, Germany.
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12
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Li S, Xu Y, Sun Z, Feng L, Shang D, Zhang C, Shi X, Han J, Su F, Yang H, Zhao J, Song C, Zhang Y, Li C, Li X. Identification of a lncRNA involved functional module for esophageal cancer subtypes. MOLECULAR BIOSYSTEMS 2017; 12:3312-3323. [PMID: 27539139 DOI: 10.1039/c6mb00101g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Esophageal cancer (EC) is the sixth most common cause of death from cancer and has two principal histological subtypes: esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC). In addition, Barrett's esophagus (BE), due to its strong association with EAC, is generally considered to be a premalignant condition of EAC. lncRNAs are believed to function in initiation and progression of multiple cancers, and therefore should play prominent, but unknown roles in the determination and behavior of different EC subtypes. In this study, by using expression profile re-annotation and differential expression (DE) analysis, we identified DE-lncRNAs and DE-protein-coding genes (DE-PCGs), and then constructed a lncRNA-PCG network, using co-expressed DE-lncRNAs (550) and DE-PCGs (5236), which was also annotated for EC subtypes. After module mining of the network, we obtained twenty candidate lncRNA-PCG modules that were ranked by gene expression and subtype-specification. Within the top four modules, we identified an ESCC specific module, two EAC-BE-specific modules and a heterologous module. Novel candidate lncRNAs were identified, in addition to lncRNAs known to be functionally connected to EC, and could be responsible for the subtype disparities in the GO biological process and at pathway levels.
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Affiliation(s)
- Shang Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
| | - Yanjun Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
| | - Zeguo Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
| | - Li Feng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
| | - Desi Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
| | - Chunlong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
| | - Xinrui Shi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
| | - Junwei Han
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
| | - Fei Su
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
| | - Haixiu Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
| | - Jianmei Zhao
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Chao Song
- School of Pharmacology, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
| | - Chunquan Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China. and School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
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Salahshourifar I, Vincent-Chong VK, Chang HY, Ser HL, Ramanathan A, Kallarakkal TG, Rahman ZAA, Ismail SM, Prepageran N, Mustafa WMW, Abraham MT, Tay KK, Zain RB. Downregulation of CRNN gene and genomic instability at 1q21.3 in oral squamous cell carcinoma. Clin Oral Investig 2015; 19:2273-83. [DOI: 10.1007/s00784-015-1467-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 03/23/2015] [Indexed: 12/14/2022]
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