1
|
Baruah B, Dutta MP, Banerjee S, Bhattacharyya DK. EnsemBic: An effective ensemble of biclustering to identify potential biomarkers of esophageal squamous cell carcinoma. Comput Biol Chem 2024; 110:108090. [PMID: 38759483 DOI: 10.1016/j.compbiolchem.2024.108090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 03/28/2024] [Accepted: 04/29/2024] [Indexed: 05/19/2024]
Abstract
The development of functionally enriched and biologically competent biclustering algorithm is essential for extracting hidden information from massive biological datasets. This paper presents a novel biclustering ensemble called EnsemBic based on p-value, which calculates the functional similarity of genetic associations. To validate the effectiveness and robustness of EnsemBic, we apply three well-known biclustering techniques, viz. Laplace Prior, iBBiG, and xMotif to implement EnsemBic and have been compared using different leading parameters. It is observed that the EnsemBic outperforms its competing algorithms in several prominent functional and biological measures. Next, the biclusters obtained from EnsemBic are used to identify potential biomarkers of Esophageal Squamous Cell Carcinoma (ESCC) by exploring topological and biological relevance with reference to the elite genes, attained from genecards. Finally, we discover that the genes F2RL3, APPL1, CALM1, IFNGR1, LPAR1, ANGPT2, ARPC2, CGN, CLDN7, ATP6V1C2, CEACAM1, FTL, PLAU,PSMB4, and EPHB2 carry both the topological and biological significance of previously established ESCC elite genes. Therefore, we declare the aforementioned genes as potential biomarkers of ESCC.
Collapse
Affiliation(s)
- Bikash Baruah
- Dept. of Computer Science and Engineering, NIT Arunachal Pradesh, India
| | - Manash P Dutta
- Dept. of Computer Science & Information Technology, Cotton University, Guwahati, Assam, India.
| | | | - Dhruba K Bhattacharyya
- Dept. of Computer Science and Engineering, Tezpur University, School of Engineering, Tezpur, India
| |
Collapse
|
2
|
Kostecki KL, Iida M, Crossman BE, Salgia R, Harari PM, Bruce JY, Wheeler DL. Immune Escape Strategies in Head and Neck Cancer: Evade, Resist, Inhibit, Recruit. Cancers (Basel) 2024; 16:312. [PMID: 38254801 PMCID: PMC10814769 DOI: 10.3390/cancers16020312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Head and neck cancers (HNCs) arise from the mucosal lining of the aerodigestive tract and are often associated with alcohol use, tobacco use, and/or human papillomavirus (HPV) infection. Over 600,000 new cases of HNC are diagnosed each year, making it the sixth most common cancer worldwide. Historically, treatments have included surgery, radiation, and chemotherapy, and while these treatments are still the backbone of current therapy, several immunotherapies have recently been approved by the Food and Drug Administration (FDA) for use in HNC. The role of the immune system in tumorigenesis and cancer progression has been explored since the early 20th century, eventually coalescing into the current three-phase model of cancer immunoediting. During each of the three phases-elimination, equilibrium, and escape-cancer cells develop and utilize multiple strategies to either reach or remain in the final phase, escape, at which point the tumor is able to grow and metastasize with little to no detrimental interference from the immune system. In this review, we summarize the many strategies used by HNC to escape the immune system, which include ways to evade immune detection, resist immune cell attacks, inhibit immune cell functions, and recruit pro-tumor immune cells.
Collapse
Affiliation(s)
- Kourtney L. Kostecki
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA; (K.L.K.); (M.I.); (B.E.C.)
| | - Mari Iida
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA; (K.L.K.); (M.I.); (B.E.C.)
| | - Bridget E. Crossman
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA; (K.L.K.); (M.I.); (B.E.C.)
| | - Ravi Salgia
- Department of Medical Oncology and Experimental Therapeutics, Comprehensive Cancer Center, City of Hope, Duarte, CA 91010, USA;
| | - Paul M. Harari
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA; (K.L.K.); (M.I.); (B.E.C.)
- University of Wisconsin Carbone Cancer Center, Madison, WI 53705, USA;
| | - Justine Y. Bruce
- University of Wisconsin Carbone Cancer Center, Madison, WI 53705, USA;
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Deric L. Wheeler
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA; (K.L.K.); (M.I.); (B.E.C.)
- University of Wisconsin Carbone Cancer Center, Madison, WI 53705, USA;
| |
Collapse
|
3
|
Götz L, Rueckschloss U, Balk G, Pfeiffer V, Ergün S, Kleefeldt F. The role of carcinoembryonic antigen-related cell adhesion molecule 1 in cancer. Front Immunol 2023; 14:1295232. [PMID: 38077351 PMCID: PMC10704240 DOI: 10.3389/fimmu.2023.1295232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/08/2023] [Indexed: 12/18/2023] Open
Abstract
The Carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1), also known as CD66a, is a member of the immunoglobulin superfamily. CEACAM1 was shown to be a prognostic marker in patients suffering from cancer. In this review, we summarize pre-clinical and clinical evidence linking CEACAM1 to tumorigenicity and cancer progression. Furthermore, we discuss potential CEACAM1-based mechanisms that may affect cancer biology.
Collapse
Affiliation(s)
- Lisa Götz
- Institute of Anatomy and Cell Biology, Julius‐Maximilians‐University Würzburg, Würzburg, Germany
| | - Uwe Rueckschloss
- Institute of Anatomy and Cell Biology, Julius‐Maximilians‐University Würzburg, Würzburg, Germany
| | - Gözde Balk
- Institute of Anatomy and Cell Biology, Julius‐Maximilians‐University Würzburg, Würzburg, Germany
| | - Verena Pfeiffer
- Institute of Anatomy and Cell Biology, Julius‐Maximilians‐University Würzburg, Würzburg, Germany
| | - Süleyman Ergün
- Institute of Anatomy and Cell Biology, Julius‐Maximilians‐University Würzburg, Würzburg, Germany
| | - Florian Kleefeldt
- Institute of Anatomy and Cell Biology, Julius‐Maximilians‐University Würzburg, Würzburg, Germany
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, United States
| |
Collapse
|
4
|
Liu C, Li X, Xiong F, Wang L, Chen K, Wu P, Hua L, Zhang Z. Down-regulation of MLLT1 super elongation complex subunit impairs the anti-tumor activity of natural killer cells in esophageal cancer. Immunobiology 2022; 227:152238. [PMID: 35763909 DOI: 10.1016/j.imbio.2022.152238] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/09/2022] [Accepted: 06/14/2022] [Indexed: 11/05/2022]
Abstract
Natural killer (NK) cells actively participate in anti-tumor immunity and are thus regarded as a promising tool in immunotherapy against esophageal cancer (EC). However, the mechanisms regulating NK cell activation and exhaustion have not been completely elucidated. In this study, we characterized the expression and function of MLLT1 super elongation complex subunit (MLLT1) in esophageal NK cells in a mouse EC model. MLLT1 was down-regulated in esophageal NK cells, especially NK cells expressing both T cell immunoglobulin and mucin-domain containing-3 (TIM-3) and lymphocyte activation gene3(LAG-3). In vitro knockdown of MLLT1 in NK cells resulted in significant decreases in the expression of IFN-γ and perforin, as well as impaired NK cell cytotoxicity on tumor cells. Adoptive transfer of MLLT-deficient NK cells into EC-bearing mice showed consistent impairment of NK cell anti-tumor activity, as evidenced by decreases in IFN-γ and perforin but not granzyme B. Furthermore, EC tissue cells, which were enriched from the esophagus of EC-bearing mice, induced down-regulation of MLLT1 in splenic NK cells. This down-regulation was partially restored by a TIM-3 blocking antibody. Therefore, this study indicated that TIM-3 signaling down-regulated MLLT1 in esophageal NK cells, and MLLT1 down-regulation undermined the tumoricidal function of NK cells in EC. Our study unveils a novel mechanism underlying NK cell exhaustion/dysfunction in the EC microenvironment. MLLT1 could be a potential target in future NK cell-mediated immunotherapy against EC.
Collapse
Affiliation(s)
- Chong Liu
- The Department of Thoracic Surgery, Tongren Hospital of Wuhan University, 241 Pengliuyang Road, Wuchang District, Wuhan, Hubei Province 430060, China
| | - Xueman Li
- The Department of Thoracic Surgery, Tongren Hospital of Wuhan University, 241 Pengliuyang Road, Wuchang District, Wuhan, Hubei Province 430060, China
| | - Fei Xiong
- The Department of Thoracic Surgery, Tongren Hospital of Wuhan University, 241 Pengliuyang Road, Wuchang District, Wuhan, Hubei Province 430060, China
| | - Lingying Wang
- The Department of Thoracic Surgery, Tongren Hospital of Wuhan University, 241 Pengliuyang Road, Wuchang District, Wuhan, Hubei Province 430060, China
| | - Kang Chen
- The Department of Thoracic Surgery, Tongren Hospital of Wuhan University, 241 Pengliuyang Road, Wuchang District, Wuhan, Hubei Province 430060, China
| | - Pingshang Wu
- The Department of Thoracic Surgery, Tongren Hospital of Wuhan University, 241 Pengliuyang Road, Wuchang District, Wuhan, Hubei Province 430060, China
| | - Li Hua
- The Department of Thoracic Surgery, Tongren Hospital of Wuhan University, 241 Pengliuyang Road, Wuchang District, Wuhan, Hubei Province 430060, China
| | - Zhuo Zhang
- The Department of Thoracic Surgery, Tongren Hospital of Wuhan University, 241 Pengliuyang Road, Wuchang District, Wuhan, Hubei Province 430060, China.
| |
Collapse
|
5
|
Serum Level of CEACAM1 in Patients with Nonsmall Cell Lung Cancer and Its Clinical Significance in Cancer Tissue. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:7948010. [PMID: 35449849 PMCID: PMC9018175 DOI: 10.1155/2022/7948010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/16/2022] [Accepted: 03/18/2022] [Indexed: 12/23/2022]
Abstract
Objective To analyze the expression of CEACAM1 in serum of patients with nonsmall cell lung cancer (NSCLC) and to explore the correlation and clinical significance between the expression of CEACAM1 and pathological parameters of NSCLC tissue. Methods A total of 100 patients with NSCLC who underwent tumor resection were screened. Another 100 healthy patients in physical examination department were selected as control group. Venous blood and cancer tissue samples were collected. The expression of CEACAM1, TGF-β, VEGF-A, and IL-8 was detected. Results The results of various indicators in the lung cancer group were much higher than those in the healthy group; CEACAM1 was significantly positively correlated with TGF-β expression. The later the clinical stage and the higher the degree of differentiation of cancer tissue specimens, the more the expression of CEACAM1 in serum samples. Conclusions The expression level of CEACAM1 in the serum of NSCLC patients is strongly correlated with TGF-β, VEGF-A, and IL-8, indicating that serum CEACAM1 and TGF-β levels can predict the occurrence, progression, and prognosis of lung cancer and provide a target for future targeted therapy of lung cancer.
Collapse
|