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El-Dehaibi F, Zamora R, Radder J, Yin J, Shah AM, Namas RA, Situ M, Zhao Y, Bain W, Morris A, McVerry BJ, Barclay DA, Billiar TR, Zhang Y, Kitsios GD, Vodovotz Y. A common single nucleotide polymorphism is associated with inflammation and critical illness outcomes. iScience 2023; 26:108333. [PMID: 38034362 PMCID: PMC10684809 DOI: 10.1016/j.isci.2023.108333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 08/25/2023] [Accepted: 10/22/2023] [Indexed: 12/02/2023] Open
Abstract
Acute inflammation is heterogeneous in critical illness and predictive of outcome. We hypothesized that genetic variability in novel, yet common, gene variants contributes to this heterogeneity and could stratify patient outcomes. We searched algorithmically for significant differences in systemic inflammatory mediators associated with any of 551,839 SNPs in one derivation (n = 380 patients with blunt trauma) and two validation (n = 75 trauma and n = 537 non-trauma patients) cohorts. This analysis identified rs10404939 in the LYPD4 gene. Trauma patients homozygous for the A allele (rs10404939AA; 27%) had different trajectories of systemic inflammation along with persistently elevated multiple organ dysfunction (MOD) indices vs. patients homozygous for the G allele (rs10404939GG; 26%). rs10404939AA homozygotes in the trauma validation cohort had elevated MOD indices, and non-trauma patients displayed more complex inflammatory networks and worse 90-day survival compared to rs10404939GG homozygotes. Thus, rs10404939 emerged as a common, broadly prognostic SNP in critical illness.
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Affiliation(s)
- Fayten El-Dehaibi
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Ruben Zamora
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Josiah Radder
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jinling Yin
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Ashti M. Shah
- Physician Scientist Training Program, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Rami A. Namas
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Michelle Situ
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Yanwu Zhao
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - William Bain
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Bryan J. McVerry
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Derek A. Barclay
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Timothy R. Billiar
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Georgios D. Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Yoram Vodovotz
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Center for Inflammation and Regeneration Modeling, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Center for Systems Immunology, University of Pittsburgh, Pittsburgh, PA 15213, USA
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Fu L, Huang Q, Wu Y, Chen D. Prognostic analysis of uveal melanoma based on the characteristic genes of M2-type macrophages in the tumor microenvironment. BMC Bioinformatics 2023; 24:280. [PMID: 37434120 DOI: 10.1186/s12859-023-05396-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/23/2023] [Indexed: 07/13/2023] Open
Abstract
Uveal melanoma arises from stromal melanocytes and is the most prevalent primary intraocular tumor in adults. It poses a significant diagnostic and therapeutic challenge due to its high malignancy and early onset of metastases. In recent years, there has been a growing interest in the role of diverse immune cells in tumor cell development and metastasis. Using The Cancer Genome Atlas and the gene expression omnibus databases, and the CIBERSORT method, we investigated the topography of intra-tumor immune infiltration in uveal melanoma in this research. We evaluated the prognosis of uveal melanoma patients using the M2 macrophage immune cell infiltration score in conjunction with clinical tumor patient data. We built a prognostic model based on the distinctive genes of M2 macrophages and combined it with patients' clinical data in the database; we ran a survival prognostic analysis to authenticate the model's accuracy. The functional study revealed the importance of macrophage-associated genes in the development of uveal melanoma. Moreover, the reliability of our prediction model was verified by combining tumor mutational load, immune checkpoint, and drug sensitivity, respectively. Our study provides a reference for the follow-up study of uveal melanoma.
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Affiliation(s)
- Li Fu
- Department of Ophthalmology, Jian Yang Hospital of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Qun Huang
- Department of Ophthalmology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Yongfeng Wu
- Department of Ophthalmology, Jian Yang Hospital of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Diang Chen
- Department of Andrology, Hospital of Chengdu University of Traditional Chinese Medicine, Sichuan, Chengdu, China.
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Yang W, Wei C, Cheng J, Ding R, Li Y, Wang Y, Yang Y, Wang J. BTG2 and SerpinB5, a novel gene pair to evaluate the prognosis of lung adenocarcinoma. Front Immunol 2023; 14:1098700. [PMID: 37006240 PMCID: PMC10064863 DOI: 10.3389/fimmu.2023.1098700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/07/2023] [Indexed: 03/19/2023] Open
Abstract
IntroductionLung adenocarcinoma (LUAD), as the most frequent pathological subtype of non−small cell lung cancer, is often characterized by poor prognosis and low 5-year survival rate. Exploriton of new biomarkers and accurate molecular mechanisms for effectively predicting the prognosis of LUAD patients is still necessary. Presently, BTG2 and SerpinB5, which play important roles in tumors, are studied as a gene pair for the first time with the aim of exploring whether they can be used as potential prognostic markers.MethodsUsing the bioinformatics method to explore whether BTG2 and SerpinB5 can become independent prognostic factors, and explore their clinical application value and whether they can be used as immunotherapeutic markers. In addition, we also verify the conclusions obtained from external datasets, molecular docking, and SqRT-PCR.ResultsThe results show that compared with normal lung tissue, BTG2 expression level was down-regulated and SerpinB5 was up-regulated in LUAD. Additionally, Kaplan–Meier survival analysis demonstrate that the prognosis of low expression level of BTG2 was poor, and that of high expression level of SerpinB5 was poor, suggesting that both of them can be used as independent prognostic factors. Moreover, the prognosis models of the two genes were constructed respectively in this study, and their prediction effect was verified by external data. Besides, ESTIMATE algorithm reveals the relationship between this gene pair and the immune microenvironment. Furthermore, patients with a high expression level of BTG2 and a low expression level of SerpinB5 have higher immunophenoscore for CTLA-4 and PD-1 inhibitors than patients with a low expression level of BTG2 and a high expression level of SerpinB5, indicating that such patients have a more obvious effect of immunotherapy.DiscussionCollectively, all the results demonstrate that BTG2 and SerpinB5 might serve as potential prognostic biomarkers and novel therapeutic targets for LUAD.
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Affiliation(s)
- Wanting Yang
- School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Chunli Wei
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Jingliang Cheng
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Ran Ding
- School of Medical Informatics Engineering, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Yan Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Faculty of Chemical, Environmental and Biological Science and Technology, Dalian University of Technology, Dalian, Liaoning, China
| | - Yonghua Wang
- College of Life Sciences, Northwest University, Shaanxi, China
| | - Yinfeng Yang
- School of Medical Informatics Engineering, Anhui University of Chinese Medicine, Hefei, Anhui, China
- *Correspondence: Yinfeng Yang, ; Jinghui Wang,
| | - Jinghui Wang
- School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
- *Correspondence: Yinfeng Yang, ; Jinghui Wang,
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Cao W, Zhou W, Li M, Zhang Z, Zhang X, Yang K, Yang S, Cao G, Chen B, Xiong M. A novel signature based on CeRNA and immune status predicts prognostic risk and drug sensitivity in gastric cancer patients. Front Immunol 2022; 13:951135. [PMID: 36483555 PMCID: PMC9723231 DOI: 10.3389/fimmu.2022.951135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 11/07/2022] [Indexed: 11/24/2022] Open
Abstract
Background At present, there is increasing evidence that both competitive endogenous RNAs (ceRNAs) and immune status in the tumor microenvironment (TME) can affect the progression of gastric cancer (GC), and are closely related to the prognosis of patients. However, few studies have linked the two to jointly determine the prognosis of patients with GC. This study aimed to develop a combined prognostic model based on ceRNAs and immune biomarkers. Methods First, the gene expression profiles and clinical information were downloaded from TCGA and GEO databases. Then two ceRNA networks were constructed on the basis of circRNA. Afterwards, the key genes were screened by univariate Cox regression analysis and Lasso regression analysis, and the ceRNA-related prognostic model was constructed by multivariate Cox regression analysis. Next, CIBERSORT and ESTIMATE algorithms were utilized to obtain the immune cell infiltration abundance and stromal/immune score in TME. Furthermore, the correlation between ceRNAs and immunity was found out through co-expression analysis, and another immune-related prognosis model was established. Finally, combining these two models, a comprehensive prognostic model was built and visualized with a nomogram. Results The (circRNA, lncRNA)-miRNA-mRNA regulatory network of GC was constructed. The predictive power of ceRNA-related and immune-related prognosis models was moderate. Co-expression analysis showed that the ceRNA network was correlated with immunity. The integrated model of combined ceRNAs and immunity in the TCGA training set, the AUC values of 1, 3, and 5-year survival rates were 0.78, 0.76, and 0.78, respectively; in the independent external validation set GSE62254, they were 0.81, 0.79, and 0.78 respectively; in GSE15459, they were 0.84, 0.88 and 0.89 respectively. Besides, the prognostic score of the comprehensive model can predict chemotherapeutic drug resistance. Moreover, we found that plasma variant translocation 1 (PVT1) and infiltrating immune cells (mast cells) are worthy of further investigation as independent prognostic factors. Conclusions Two ceRNA regulatory networks were constructed based on circRNA. At the same time, a comprehensive prognosis model was established, which has a high clinical significance for prognosis prediction and chemotherapy drug selection of GC patients.
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Affiliation(s)
- Wei Cao
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Weiguo Zhou
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Mengying Li
- Laboratory for Reproductive Immunology, Hospital of Obstetrics and Gynecology, Shanghai Medical School, Fudan University, Shanghai, China
| | - Zehua Zhang
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xun Zhang
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Kang Yang
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China,Department of General Surgery, Anhui Public Health Clinical Center, Hefei, China
| | - Shiyi Yang
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Guodong Cao
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China,*Correspondence: Guodong Cao, ; Bo Chen, ; Maoming Xiong,
| | - Bo Chen
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China,Department of Surgery, The People’s Hospital of Hanshan County, Ma’anshan, China,*Correspondence: Guodong Cao, ; Bo Chen, ; Maoming Xiong,
| | - Maoming Xiong
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China,*Correspondence: Guodong Cao, ; Bo Chen, ; Maoming Xiong,
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Gao Y, Wang K, Tang XX, Niu JL, Wang J. A Pilot Study of Prognostic Value of Metastatic Lymph Node Count and Size in Patients with Different Stages of Gastric Carcinoma. Cancer Manag Res 2022; 14:2055-2064. [PMID: 35761822 PMCID: PMC9233543 DOI: 10.2147/cmar.s352334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 06/13/2022] [Indexed: 12/23/2022] Open
Abstract
Background The correlation between the preoperative lymph node count (LNC) on multidetector computed tomography (MDCT) and the prognosis of gastric carcinoma (GC) remains to be defined. This research aims to evaluate the prognostic value of LNC on MDCT in GC patients based on tumor-node-metastasis (TNM) staging, using different size criteria for counting. Methods The clinical data of 126 patients with gastric adenocarcinoma undergoing gastrectomy were retrospectively analyzed. Lymph nodes greater than 8mm and 5mm on MDCT were counted and recorded. The prognostic implications of LNC on MDCT for patient survival were analyzed according to different size criteria for counting and tumor TNM staging. Results When 8mm was used as the counting criterion, LNC on MDCT had no significant effect on the overall survival (OS) of the entire cohort. In addition, the OS of T1–T2 GC patients with LNC on MDCT ≥1 was significantly worse than that of patients with LNC on MDCT <1. When 5mm was used as the counting criterion, LNC on MDCT was found to be significantly associated with the OS of the entire cohort. In the subgroup analysis, patients with relatively advanced (T3-T4, N+ and III) GC with LNC on MDCT >7 showed a significantly worse OS than those with LNC on MDCT ≤7. LNC on MDCT >7 with 5mm as the counting criterion and Stage III were independent risk factors for adverse prognosis. Conclusion The prognostic value of LNC on MDCT based on different size criteria varies in patients with different stages of GC. LNC of a smaller size (5mm) on MDCT may be a prognostic factor for patients with relatively advanced GC.
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Affiliation(s)
- Yong Gao
- Department of Medical Imaging, Shanxi Medical University, Taiyuan, 030001, People’s Republic of China
- Department of Radiology, Shanxi Provincial People’s Hospital, Taiyuan, 030012, People’s Republic of China
| | - Kun Wang
- Department of Hepatopathy, Third People Hospital of Taiyuan City, Taiyuan, 030001, People’s Republic of China
| | - Xiao-Xian Tang
- Department of Radiology, Shanxi Provincial People’s Hospital, Taiyuan, 030012, People’s Republic of China
| | - Jin-Liang Niu
- Department of Radiology, 2nd Hospital, Shanxi Medical University, Taiyuan, 030001, People’s Republic of China
| | - Jun Wang
- Department of Medical Imaging, Shanxi Medical University, Taiyuan, 030001, People’s Republic of China
- Correspondence: Jun Wang, Department of Medical Imaging, Shanxi Medical University, Taiyuan, 030001, People’s Republic of China, Tel +86-351-488-5199, Fax +86-351-496-0092, Email
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