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Zhong T, Cheng X, Gu Q, Fu G, Wang Y, Jiang Y, Xu J, Jiang Z. Integrated analyses reveal the diagnostic and predictive values of COL5A2 and association with immune environment in Crohn's disease. Genes Immun 2024; 25:209-218. [PMID: 38789829 PMCID: PMC11178494 DOI: 10.1038/s41435-024-00276-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 05/03/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024]
Abstract
The pathogenesis of Crohn's disease (CD) involves abnormal immune cell infiltration and dysregulated immune response. Therefore, thorough research on immune cell abnormalities in CD is crucial for improved treatment of this disease. Single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data of CD were obtained from the Gene Expression Omnibus (GEO) database. Cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT), weighted gene co-expression network analysis (WGCNA), protein-protein interaction (PPI) networks evaluated the proportion of immune infiltrating cells, constructed co-expression network and identified key genes, respectively. Based on the dataset (GSE134809), 15 cell clusters were defined and labeled as different cell types. Among the 11 modules, the yellow module had the closest relationship with plasma cells (cluster 5). Confirmed using RNA sequencing and IHC assay, the expression of COL5A2 in CD samples was higher than that in control samples. Furthermore, the COL5A2 protein expression remarkably decreased in the group of patients who responded to anti-tumor necrosis factor (TNF) treatments, compared to the non-response group. The comprehensive analyses described here provided novel insight into the landscape of CD-associated immune environment. In addition, COL5A2 were identified as potential diagnostic indicators for CD, as well as promising predictive markers for CD patients.
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Affiliation(s)
- Tingting Zhong
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoqing Cheng
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qianru Gu
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Guoxiang Fu
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yihong Wang
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yujie Jiang
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiaqi Xu
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Zhinong Jiang
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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Cao H, Huang P, Qiu J, Gong X, Cao H. Immune landscape of hepatocellular carcinoma tumor microenvironment identifies a prognostic relevant model. Heliyon 2024; 10:e24861. [PMID: 38317886 PMCID: PMC10839619 DOI: 10.1016/j.heliyon.2024.e24861] [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: 08/04/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 02/07/2024] Open
Abstract
Background Various studies highlighted that immune cell-mediated inflammatory processes play crucial roles in the progression and treatment of hepatocellular carcinoma (HCC). However, the immune microenvironment of HCC is still poorly characterized. Exploring the role of immune-related genes (IRGs) and describing the immune landscape in HCC would provide insights into tumor-immune co-evolution along HCC progression. Methods We integrated the datasets with complete prognostic information from the Cancer Genome Atlas (TCGA) database and GEO DataSets (GSE14520, GSE76427, and GSE54236) to construct a novel immune landscape based on the Cibersort algorithm and reveal the prognostic signature in HCC patients. Results To describe the tumor microenvironment (TME) in HCC, immune infiltration patterns were defined using the CIBERSORT method, and a prognostic signature contains 5 types of immune cells, including 3 high-risk immune cells (T.cells. CD4. memory. resting, Macrophages.M0, Macrophages.M2) and 2 low-risk immune cells (Plasma. cells, T.cells.CD8), were finally constructed. A novel prognostic index, based on prognostic immune risk score (pIRG), was developed using the univariate Cox regression analyses and LASSO Cox regression algorithm. Furthermore, the ROC curve and KM curve showed that the TME signatures had a stable value in predicting the prognosis of HCC patients in the internal training cohort, internal validation, and external validation cohort. Differential genes analysis and qPCR experiment showed that the expression levels of AKR1B10, LAPTM4B, MMP9, and SPP1 were significantly increased in high-risk patients, while the expression of CD5L was lower. Further analysis found that AKR1B10 and MMP9 were associated with higher M0 macrophage infiltration, while CD5L was associated with higher plasma cell infiltration. Conclusions Taken together, we performed a comprehensive evaluation of the immune landscape of HCC and constructed a novel and robust prognostic prediction model. AKR1B10, LAPTM4B, MMP9, SPP1, and CD5L were involved in important processes in the HCC tumor microenvironment and were expected to become HCC prediction markers and potential targets of treatment.
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Affiliation(s)
- Hongru Cao
- Department of Nephrology, Affiliated Hospital of Chifeng University, Chifeng City, Inner Mongolia, 024000, PR China
| | - Ping Huang
- Infectious Disease Prevention and Control Hospital of Chifeng City, Chifeng City, Inner Mongolia, 024000, PR China
| | - Jiawei Qiu
- Institute of Cardiovascular Disease of Chifeng University, Chifeng City, Inner Mongolia, 024000, PR China
| | - Xiaohui Gong
- Department of Emergency Medicine, Affiliated Hospital of Chifeng University, Chifeng City, Inner Mongolia, 024000, PR China
- Institute of Cardiovascular Disease of Chifeng University, Chifeng City, Inner Mongolia, 024000, PR China
| | - Hongfei Cao
- Department of Gastroenterology, Affiliated Hospital of Chifeng University, Chifeng City, Inner Mongolia, 024000, PR China
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Yao S, Huang Z, Wei C, Wang Y, Xiao H, Chen S, Huang Z. CD79A work as a potential target for the prognosis of patients with OSCC: analysis of immune cell infiltration in oral squamous cell carcinoma based on the CIBERSORTx deconvolution algorithm. BMC Oral Health 2023; 23:411. [PMID: 37344840 DOI: 10.1186/s12903-023-02936-w] [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: 10/18/2022] [Accepted: 04/04/2023] [Indexed: 06/23/2023] Open
Abstract
OBJECTIVE To analyze the abundance of infiltrating tumor immune cells in patients with oral squamous cell carcinoma (OSCC) and to search for potential targets that can predict patient prognosis. METHODS A total of 400 samples from 210 patients with OSCC were collected using The Cancer Genome Atlas (TCGA) database. CIBERSORTx was used to evaluate the infiltration abundance of tumor immune cells. Potential target genes were searched to predict patient prognosis through case grouping, differential analysis, and enrichment analysis. Surgical excisional tissue sections of patients with oral squamous cell carcinoma admitted to the Department of Oral and Maxillofacial Surgery, Second Affiliated Hospital of Shantou University Medical College, from 2015 to 2018 were collected and followed up. RESULTS The CIBERSORTx deconvolution algorithm was used to analyze the infiltration abundance of immune cells in the samples. Cases with a high infiltration abundance of naive and memory B lymphocytes improved the prognosis of OSCC patients. The prognosis of patients with low CD79A expression was significantly better than that of patients with high CD79A expression. CONCLUSION CD79A can predict the infiltration abundance of B lymphocytes in the tumor microenvironment of patients with OSCC. CD79A is a potential target for predicting the prognosis of patients with OSCC. This study provides novel ideas for the treatment of OSCC and for predicting patient prognosis.
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Affiliation(s)
- Shucong Yao
- Department of Oral and Maxillofacial Surgery, Second Affiliated Hospital of Shantou University Medical College, 69 Dongxia North Road, Shantou, 515000, Guangdong, China
- Nanhai Translational Innovation Center of Precision Immunology, Sun Yat-Sen Memorial Hospital, Guangzhou, China
| | - Zixian Huang
- Nanhai Translational Innovation Center of Precision Immunology, Sun Yat-Sen Memorial Hospital, Guangzhou, China
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Changji Wei
- Department of Oral and Maxillofacial Surgery, Second Affiliated Hospital of Shantou University Medical College, 69 Dongxia North Road, Shantou, 515000, Guangdong, China
| | - Yuepeng Wang
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hongwei Xiao
- Department of Oral and Maxillofacial Surgery, Second Affiliated Hospital of Shantou University Medical College, 69 Dongxia North Road, Shantou, 515000, Guangdong, China
| | - Shisheng Chen
- Department of Oral and Maxillofacial Surgery, Second Affiliated Hospital of Shantou University Medical College, 69 Dongxia North Road, Shantou, 515000, Guangdong, China.
| | - Zhiquan Huang
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.
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Lin XH, Li DP, Liu ZY, Zhang S, Tang WQ, Chen RX, Weng SQ, Tseng YJ, Xue RY, Dong L. Six immune-related promising biomarkers may promote hepatocellular carcinoma prognosis: a bioinformatics analysis and experimental validation. Cancer Cell Int 2023; 23:52. [PMID: 36959615 PMCID: PMC10035283 DOI: 10.1186/s12935-023-02888-9] [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: 12/07/2021] [Accepted: 02/23/2023] [Indexed: 03/25/2023] Open
Abstract
Background Abnormal miRNA and mRNA expression and dysregulated immune microenvironment have been found to frequently induce the progression of hepatocellular carcinoma (HCC) in recent reports. In particular, the immune-related competing endogenous RNAs (ceRNA) mechanism plays a crucial role in HCC progression. However, the underlying mechanisms remain unclear. Methods Differentially expressed immune-related genes were obtained from the Immport, GEO, and TCGA databases. The mRNA and protein expression levels in HCC tissues and adjacent normal tissues were confirmed, and we further investigated the methylation levels of these biomarkers to explore their function. Then, the TIMER and TISCH databases were used to assess the relationship between immune infiltration and hub genes. Survival analysis and univariate and multivariate Cox models were used to evaluate the association between hub genes and HCC diagnosis. Hub gene expression was experimentally validated in six HCC cell lines and 15 HCC samples using qRT-PCR and immunohistochemistry. The hub genes were uploaded to DSigDB for drug prediction enrichment analysis. Results We identified that patients with abnormal miRNAs (hsa-miR-125b-5p and hsa-miR-21-5p) and their targeted genes (NTF3, PSMD14, CD320, and SORT1) had a worse prognosis. Methylation analysis of miRNA-targeted genes suggested that alteration of methylation levels is also a factor in the induction of tumorigenesis. We also found that the development of HCC progression caused by miRNA-mRNA interactions may be closely correlated with the infiltration of immunocytes. Moreover, the GSEA, GO, and KEGG analysis suggested that several common immune-related biological processes and pathways were related to miRNA-targeted genes. The results of qRT-PCR, immunohistochemistry, and western blotting were consistent with our bioinformatics results, suggesting that abnormal miRNAs and their targeted genes may affect HCC progression. Conclusions Briefly, our study systematically describes the mechanisms of miRNA-mRNA interactions in HCC and predicts promising biomarkers that are associated with immune filtration for HCC progression. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-023-02888-9.
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Affiliation(s)
- Xia-Hui Lin
- grid.8547.e0000 0001 0125 2443Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032 China
- grid.413087.90000 0004 1755 3939Shanghai Institute of Liver Disease, Shanghai, 200032 China
| | - Dong-ping Li
- grid.8547.e0000 0001 0125 2443Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032 China
- grid.413087.90000 0004 1755 3939Shanghai Institute of Liver Disease, Shanghai, 200032 China
| | - Zhi-Yong Liu
- grid.8547.e0000 0001 0125 2443Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032 China
- grid.413087.90000 0004 1755 3939Shanghai Institute of Liver Disease, Shanghai, 200032 China
| | - Si Zhang
- grid.8547.e0000 0001 0125 2443Key Laboratory of Glycoconjugate Research Ministry of Public Health, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032 China
| | - Wen-qing Tang
- grid.8547.e0000 0001 0125 2443Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032 China
- grid.413087.90000 0004 1755 3939Shanghai Institute of Liver Disease, Shanghai, 200032 China
| | - Rong-xin Chen
- grid.8547.e0000 0001 0125 2443Key Laboratory of Carcinogenesis and Cancer Invasion, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032 China
| | - Shu-qiang Weng
- grid.8547.e0000 0001 0125 2443Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032 China
- grid.413087.90000 0004 1755 3939Shanghai Institute of Liver Disease, Shanghai, 200032 China
| | - Yu-jen Tseng
- grid.8547.e0000 0001 0125 2443Department of Digestive Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Middle Road, Shanghai, 200040 China
| | - Ru-yi Xue
- grid.8547.e0000 0001 0125 2443Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032 China
- grid.413087.90000 0004 1755 3939Shanghai Institute of Liver Disease, Shanghai, 200032 China
| | - Ling Dong
- grid.8547.e0000 0001 0125 2443Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032 China
- grid.413087.90000 0004 1755 3939Shanghai Institute of Liver Disease, Shanghai, 200032 China
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Yao S, Huang Z, Wei C, Wang Y, Xiao H, Chen S, Huang Z. CD79A Work as a Potential Target For The Prognosis of Patients With HNSCC: Analysis of Immune Cell Infiltration In Head and Neck Squamous Cell Carcinoma Based on The CIBERSORTx Deconvolution Algorithm.. [DOI: 10.21203/rs.3.rs-2177047/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
Objective
To analyze the abundance of infiltrating tumor immune cells in patients with head and neck squamous cell carcinoma (HNSCC) and to search for potential targets that can predict patient prognosis.
Methods
A total of 400 samples from 210 patients with HNSCC were collected using The Cancer Genome Atlas (TCGA) database. CIBERSORTx was used to evaluate the infiltration abundance of tumor immune cells. Potential target genes were searched to predict patient prognosis through case grouping, differential analysis, and enrichment analysis. The correlation between target genes and tumor immune cell infiltration was verified using the TIMER2.0 database. Surgical excisional tissue sections of patients with head and neck squamous cell carcinoma admitted to the Department of Oral and Maxillofacial Surgery, Second Affiliated Hospital of Shantou University Medical College, from 2015 to 2018 were collected and followed up.
Results
The CIBERSORTx deconvolution algorithm was used to analyze the infiltration abundance of immune cells in the samples. Cases with a high infiltration abundance of naive and memory B lymphocytes exhibited a significantly improved prognosis. The prognosis of patients with high CD79A expression was significantly better than that of patients with low CD79A expression. In addition, CD79A expression was significantly correlated with B lymphocyte infiltration in the tumor microenvironment.
Conclusion
CD79A can predict the infiltration abundance of B lymphocytes in the tumor microenvironment of patients with HNSCC. CD79A is a potential target for predicting the prognosis of patients with HNSCC. This study provides novel ideas for the treatment of HNSCC and for predicting patient prognosis.
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Affiliation(s)
- Shucong Yao
- Second Affiliated Hospital of Shantou University Medical College
| | - Zixian Huang
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University
| | - Changji Wei
- Second Affiliated Hospital of Shantou University Medical College
| | - Yuepeng Wang
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University
| | - Hongwei Xiao
- Second Affiliated Hospital of Shantou University Medical College
| | - Shisheng Chen
- Second Affiliated Hospital of Shantou University Medical College
| | - Zhiquan Huang
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University
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Hu X, Zhu H, Feng S, Wang C, Ye Y, Xiong X. Transmembrane and coiled-coil domains 3 is a diagnostic biomarker for predicting immune checkpoint blockade efficacy in hepatocellular carcinoma. Front Genet 2022; 13:1006357. [PMID: 36246598 PMCID: PMC9556949 DOI: 10.3389/fgene.2022.1006357] [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: 07/29/2022] [Accepted: 09/14/2022] [Indexed: 02/03/2023] Open
Abstract
Liver hepatocellular carcinoma (LIHC) is a malignancy with a high mortality and morbidity rate worldwide. However, the pathogenesis of LIHC has still not been thoroughly studied. Transmembrane and coiled-coil domains 3 (TMCO3) encodes a monovalent cation, a member of the proton transducer 2 (CPA2) family of transporter proteins. In the present study, TMCO3 expression and its relationship with cancer prognosis, as well as its immunological role in LIHC were studied by bioinformatic analysis. We found the significant overexpression of TMCO3 in LIHC in the TCGA, HCCDB, and GEO databases. In LIHC patients, high TMCO3 expression was related to poorer overall survival (OS) and TMCO3 had good predictive accuracy for prognosis. Moreover, TMCO3 was linked to the infiltrates of certain immune cells in LIHC. The correlation of TMCO3 with immune checkpoints was also revealed. Moreover, patients with LIHC with low TMCO3 expression showed a better response to immune checkpoint blockade (ICB) than those with LIHC with high TMCO3 expression. GO and KEGG enrichment analyses indicated that TMCO3 was probably involved in the microtubule cytoskeleton organization involved in mitosis, small GTPase mediated signal transduction, and TGF-β pathway. In conclusion, TMCO3 may be a potential biomarker for LIHC prognosis and immunotherapy.
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Affiliation(s)
- Xinyao Hu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Hua Zhu
- Department of Neurosurgery, The Affiliated Huzhou Hospital, Zhejiang University School of Medicine (Huzhou Central Hospital), Huzhou, China,Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Shi Feng
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Chaoqun Wang
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Yingze Ye
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China,*Correspondence: Yingze Ye, ; Xiaoxing Xiong,
| | - Xiaoxing Xiong
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China,Department of Neurosurgery, The Affiliated Huzhou Hospital, Zhejiang University School of Medicine (Huzhou Central Hospital), Huzhou, China,Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China,*Correspondence: Yingze Ye, ; Xiaoxing Xiong,
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Zhou L, Chen G, Liu T, Liu X, Yang C, Jiang J. MJDs family members: Potential prognostic targets and immune-associated biomarkers in hepatocellular carcinoma. Front Genet 2022; 13:965805. [PMID: 36159990 PMCID: PMC9500549 DOI: 10.3389/fgene.2022.965805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/10/2022] [Indexed: 11/21/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common gastrointestinal malignancies. It is not easy to be diagnosed in the early stage and is prone to relapse, with a very poor prognosis. And immune cell infiltration and tumor microenvironment play important roles in predicting therapeutic response and prognosis of HCC. Machado-Joseph domain-containing proteases (MJDs), as a gene family extensively involved in tumor progression, has pro-cancer and anti-cancer effects. However, the relationship between MJDs family members and immune cell infiltration and tumor microenvironment in HCC remains unclear. Therefore, cBio Cancer Genomics Portal (cBioPortal), The Cancer Genome Atlas (TCGA), UALCAN, Human Protein Atlas (HPA), MethSurv, and Tumor Immune Estimation Resource (TIMER) databases were performed to investigate the mRNA expression, DNA methylation, clinicopathologic features, immune cell infiltration and other related functions of MJDs family members in HCC. The results indicated that the expression of ATXN3, JOSD1, and JOSD2 was dramatically increased in HCC tissues and cell lines, and was correlated with histological grade, specimen type, TP53 mutation, lymph node metastatic, gender, and age of patients with HCC. Meanwhile, these genes also showed clinical value in improving the overall survival (OS), disease-specific survival (DSS), progression free survival (PFS), and relapse-free survival (RFS) in patients with HCC. The prognostic model indicated that the worse survival was associated with overall high expression of MJDs members. Next, the results suggested that promotor methylation levels of the MJDs family were closely related to these family mRNA expression levels, clinicopathologic features, and prognostic values in HCC. Moreover, the MJDs family were significantly correlated with CD4+ T cells, CD8+ T cells, B cells, neutrophils, macrophages, and DCs. And MJDs family members’ expression were substantially associated with the levels of several lymphocytes, immunomoinhibitors, immunomostimulators, chemokine ligands, and chemokine receptors. In addition, the expression levels of MJDs family were significantly correlated with cancer-related signaling pathways. Taken together, our results indicated that the aberrant expression of MJDs family in HCC played a critical role in clinical feature, prognosis, tumor microenvironment, immune-related molecules, mutation, gene copy number, and promoter methylation level. And MJDs family may be effective immunotherapeutic targets for patients with HCC and have the potential to be prognostic biomarkers.
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Affiliation(s)
- Lei Zhou
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Guojie Chen
- Hunan YoBon Biotechnology Limited Company, Changsha, China
| | - Tao Liu
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Xinyuan Liu
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Chengxiao Yang
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Jianxin Jiang
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
- Department of Hepatobiliary Surgery, Renmin Hospital of Wuhan University, Wuhan, China
- *Correspondence: Jianxin Jiang,
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Hao X, Zheng Z, Liu H, Zhang Y, Kang J, Kong X, Rong D, Sun G, Sun G, Liu L, Yu H, Tang W, Wang X. Inhibition of APOC1 promotes the transformation of M2 into M1 macrophages via the ferroptosis pathway and enhances anti-PD1 immunotherapy in hepatocellular carcinoma based on single-cell RNA sequencing. Redox Biol 2022; 56:102463. [PMID: 36108528 PMCID: PMC9482117 DOI: 10.1016/j.redox.2022.102463] [Citation(s) in RCA: 96] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/28/2022] [Accepted: 08/28/2022] [Indexed: 11/04/2022] Open
Abstract
Single-cell RNA-sequencing (scRNA-seq) presents better insights into cell behavior in the context of a complex tumor microenvironment by profiling single-cell populations. However, the mechanisms underlying treatment failure in hepatocellular carcinoma (HCC) are poorly understood. In this study, we performed deep scRNA-seq on immune cells under the isolation in peripheral blood, cancer tissues, and nearby common tissues of four HCC cases and two non-cancer controls, and 212,494 cells were included in the analysis. We identified distinct immune cell subtypes, enriched pathways for differential genes, and delineated associated developmentally relevant trajectories. APOC1 was found over-expressed in tumor-associated macrophages (TAMs) of HCC tissues than in normal tissues. Inhibition of APOC1 reversed the M2 phenotype to the M1 phenotype via the ferroptosis pathway in TAMs from HCC. Tumors in APOC1 −/− C57BL/6 mice demonstrated consistent attenuation compared to wild-type (WT) mice. Mass spectrometry results revealed that the relative proportion of M2 macrophages, B cells, and CD4+ T cells in the APOC1 −/− group exhibited a downward expression compared with the WT group, whereas CD8+ T cells, M1 macrophages, and NK cells exhibited an upward trend. Finally, APOC1 was found to be negatively correlated with the expression of PD1/PD-L1 in human HCC samples. In conclusion, the present study demonstrated that inhibiting APOC1 can promote the transformation of M2 macrophages into M1 macrophages via the ferroptosis pathway, thereby reshaping the tumor immune microenvironment and improving the anti-PD1 immunotherapy for HCC, providing a new strategy for improving the therapeutic effect of anti-PD1, and bringing new hope to HCC patients.
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A Novel Prognostic Signature Revealed the Interaction of Immune Cells in Tumor Microenvironment Based on Single-Cell RNA Sequencing for Lung Adenocarcinoma. J Immunol Res 2022; 2022:6555810. [PMID: 35812244 PMCID: PMC9270162 DOI: 10.1155/2022/6555810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/12/2022] [Accepted: 06/15/2022] [Indexed: 11/18/2022] Open
Abstract
Background The tumor immune microenvironment (TIME) played an important role in immunotherapy prognosis and treatment response. Immune cells constitute a large part of the tumor microenvironment and regulate tumor progression. Our research is dedicated to studying the infiltrating immune cell in lung adenocarcinoma (LUAD) and seeking potential targets. Methods The scRNA-seq data were collected from our FDZSH and two public datasets. The code for cell-type mapping algorithms was downloaded from the CIBERSORTx portal. The bioinformatics data of LUAD patients could be approached from The Cancer Genome Atlas (TCGA) portal. Weighted gene coexpression network analysis (WGCNA) and least absolute shrinkage and selection operator (LASSO) analyses were performed to construct a risk model. TIMER2 and TIDE helped with the immune infiltration estimation, while PROGENy helped the cancer-related pathways' enrichment analysis. GSE31210 dataset and IMVigor ICB therapy cohort validated our findings as the external validation datasets. Results We clustered the scRNA-seq dataset (integrating our FDZSH datasets and other public datasets) into 23 subpopulations. After curated cell annotation, we implemented Cibersort and WGCNA analysis to anchor the brown module and natural killer cell cluster1 due to the most relationship with tumor trait. The overlap of the brown module gene, natural killer cell signature, and DEGs of tumor and adjacent normal samples was screened by LASSO Cox regression. The obtained 5-gene risk model showed an excellent prognostic performance in the validation dataset. Furthermore, there was a correlation between risk score and tumor-infiltrating immune cells and tumor genomics abnormity. Patients with higher risk scores had a significantly lower immunotherapy response rate. Conclusion Our observations implied that immune cells played a pivotal role in TIME and established a 5-gene signature (including IDH2, ADRB2, SFTPC, CCDC69, and CCND2) on the basement of nature killer markers targeted by WGCNA analysis. The significance of clinical outcome and immunotherapy response prediction was validated robustly.
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NOL12 as an Oncogenic Biomarker Promotes Hepatocellular Carcinoma Growth and Metastasis. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:6891155. [PMID: 35693698 PMCID: PMC9184182 DOI: 10.1155/2022/6891155] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 05/03/2022] [Accepted: 05/12/2022] [Indexed: 12/11/2022]
Abstract
Hepatocellular carcinoma (HCC) is a common malignancy with a poor prognosis worldwide. However, the pathogenesis of HCC remains poorly understood. In this study, we found that NOL12 was significantly overexpressed in independent HCC datasets from TCGA database. We confirmed that the expression level of NOL12 was upregulated in human HCC tissues and cell lines by RT-qPCR. High expression of NOL12 is associated with worse reduced overall survival (OS), high pathological grade, node metastasis, and advanced clinical stage in patients with HCC. Moreover, knockdown of NOL12 dramatically inhibits the proliferation and metastasis of HCC cells in vitro and in vivo. CIBERSORTx analysis revealed that twelve types of tumor-infiltrating immune cells (TICs) are correlated with NOL12 expression. The risk signature based on 8 NOL12-related genes is an independent prognostic factor for patients with HCC. The OS rate of patients in the low-risk score group was better than that in the high-risk score group. In addition, the total tumor mutation burden (TMB) in the high-risk score group increased significantly, and the risk scores could be used as an alternative indicator of immune checkpoint inhibitor (ICI) response. In conclusion, our findings indicated that NOL12 might be involved in the progression of HCC and can be used as a potential therapeutic target. Moreover, the NOL12-related risk signature may have predictive relevance with regard to ICI therapy.
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Vadapalli S, Abdelhalim H, Zeeshan S, Ahmed Z. Artificial intelligence and machine learning approaches using gene expression and variant data for personalized medicine. Brief Bioinform 2022; 23:6590150. [PMID: 35595537 DOI: 10.1093/bib/bbac191] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/02/2022] [Accepted: 04/26/2022] [Indexed: 12/16/2022] Open
Abstract
Precision medicine uses genetic, environmental and lifestyle factors to more accurately diagnose and treat disease in specific groups of patients, and it is considered one of the most promising medical efforts of our time. The use of genetics is arguably the most data-rich and complex components of precision medicine. The grand challenge today is the successful assimilation of genetics into precision medicine that translates across different ancestries, diverse diseases and other distinct populations, which will require clever use of artificial intelligence (AI) and machine learning (ML) methods. Our goal here was to review and compare scientific objectives, methodologies, datasets, data sources, ethics and gaps of AI/ML approaches used in genomics and precision medicine. We selected high-quality literature published within the last 5 years that were indexed and available through PubMed Central. Our scope was narrowed to articles that reported application of AI/ML algorithms for statistical and predictive analyses using whole genome and/or whole exome sequencing for gene variants, and RNA-seq and microarrays for gene expression. We did not limit our search to specific diseases or data sources. Based on the scope of our review and comparative analysis criteria, we identified 32 different AI/ML approaches applied in variable genomics studies and report widely adapted AI/ML algorithms for predictive diagnostics across several diseases.
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Affiliation(s)
- Sreya Vadapalli
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, 112 Paterson St, New Brunswick, NJ, USA
| | - Habiba Abdelhalim
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, 112 Paterson St, New Brunswick, NJ, USA
| | - Saman Zeeshan
- Rutgers Cancer Institute of New Jersey, Rutgers University, 195 Little Albany St, New Brunswick, NJ, USA
| | - Zeeshan Ahmed
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, 112 Paterson St, New Brunswick, NJ, USA.,Department of Medicine, Robert Wood Johnson Medical School, Rutgers Biomedical and Health Sciences, 125 Paterson St, New Brunswick, NJ, USA
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Wang ZZ, Meng T, Yang MY, Wang W, Zhang Y, Liu Y, Han AQ, Wu J, Wang HX, Qian B, Zhu LX. ALYREF associated with immune infiltration is a prognostic biomarker in hepatocellular carcinoma. Transl Oncol 2022; 21:101441. [PMID: 35523010 PMCID: PMC9079359 DOI: 10.1016/j.tranon.2022.101441] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 04/07/2022] [Accepted: 04/22/2022] [Indexed: 11/21/2022] Open
Abstract
ALYREF is a potential prognostic marker for hepatocellular carcinoma. ALYREF affects the biological function of hepatocellular carcinoma cells. ALYREF is associated with immune infiltration in hepatocellular carcinoma. The model constructed based on ALYREF-related immune genes provides a reference for the evaluation of immunotherapy.
Background Although ALYREF has been demonstrated to have a role in a number of malignancies, its role in hepatocellular carcinoma (HCC) has received little attention. Our objective was to research at the prognostic value, biological role and relevance of ALYREF to the immune system in HCC. Methods The expression of ALYREF and its relationship with clinical parameters of HCC patients were analyzed by liver cancer cohort (LIHC) of The Cancer Genome Atlas. The expression and prognosis were verified by immunohistochemistry experiments. Gene transfection, CCK-8, scratch healing, transwell invasion and flow cytometry were used to assess the molecular function of ALYREF in vitro. The TIMER and TISIDB online data portals were used to assess the relevance of ALYREF to immunization. Stepwise regression analysis of ALYREF-related immune genes in the LIHC training set was used to construct a prognostic risk prediction model. Also, construct a nomogram to predict patient survival. The testing set for internal verification. Results Knockdown of ALYREF changed the biological phenotypes of HCC cells, such as proliferation, apoptosis, and invasion. In addition, the expression of ALYREF in HCC affected the level of immune cell infiltration and correlated with the overall survival time of patients. The constructed immune prognostic model allows for a valid assessment of patients. Conclusion ALYREF is increased in HCC, has an impact on cellular function and the immune system, and might be used as a prognostic marker.
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Affiliation(s)
- Zhen-Zhen Wang
- Department of General Surgery, Central Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Tao Meng
- Department of General Surgery, The First People's Hospital of Hefei, Hefei 230000, China
| | - Ming-Ya Yang
- Department of Haematology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Wei Wang
- Department of General Surgery, Central Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Yan Zhang
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Yu Liu
- Department of General Surgery, Central Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - An-Qi Han
- Department of General Surgery, Central Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Jin Wu
- Department of General Surgery, Central Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Hui-Xiao Wang
- Department of Medicine, The Second People's Hospital of Anhui Province, Hefei 230000, China.
| | - Bo Qian
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230022, China.
| | - Li-Xin Zhu
- Department of General Surgery, Central Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China.
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Wu X, Zhao X, Xiong Y, Zheng M, Zhong C, Zhou Y. Deciphering Cell-Type-Specific Gene Expression Signatures of Cardiac Diseases Through Reconstruction of Bulk Transcriptomes. Front Cell Dev Biol 2022; 10:792774. [PMID: 35252172 PMCID: PMC8894713 DOI: 10.3389/fcell.2022.792774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/12/2022] [Indexed: 12/14/2022] Open
Abstract
Cardiac diseases compose a fatal disease category worldwide. Over the past decade, high-throughput transcriptome sequencing of bulk heart tissues has widened our understanding of the onset and progression of cardiac diseases. The recent rise of single-cell RNA sequencing (scRNA-seq) technology further enables deep explorations of their molecular mechanisms in a cell-type-specific manner. However, due to technical difficulties in performing scRNA-seq on heart tissues, there are still few scRNA-seq studies on cardiac diseases. In this study, we demonstrate that an effective alternative could be cell-type-specific computational reconstruction of bulk transcriptomes. An integrative bulk transcriptome dataset covering 110 samples from 12 studies was first constructed by re-analysis of raw sequencing data derived from the heart tissues of four common cardiac disease mouse models (myocardial infarction, dilated cardiomyopathy, hypertrophic cardiomyopathy, and arrhythmogenic right ventricular cardiomyopathy). Based on the single-cell reference covering four major cardiac component cell types and 22 immune cell subtypes, for each sample, the bulk transcriptome was reconstructed into cellular compositions and cell-type-specific expression profiles by CIBERSORTx. Variations in the estimated cell composition revealed elevated abundances of fibroblast and monocyte during myocardial infarction, which were further verified by our flow cytometry experiment. Moreover, through cell-type-specific differential gene expression and pathway enrichment analysis, we observed a series of signaling pathways that mapped to specific cell type in diseases, like MAPK and EGFR1 signaling pathways in fibroblasts in myocardial infarction. We also found an increased expression of several secretory proteins in monocytes which may serve as regulatory factors in cardiac fibrosis. Finally, a ligand–receptor analysis identified key cell types which may serve as hubs in cellular communication in cardiac diseases. Our results provide novel clues for the cell-type-specific signatures of cardiac diseases that would promote better understanding of their pathophysiological mechanisms.
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Affiliation(s)
- Xiaobin Wu
- Department of Biomedical Informatics, Center for Noncoding RNA Medicine, School of Basic Medical Sciences, Peking University, Beijing, China
- MOE Key Laboratory of Molecular Cardiovascular Sciences, Peking University, Beijing, China
| | - Xingyu Zhao
- Beijing Key Laboratory of Tumor Systems Biology, Department of Immunology, School of Basic Medical Sciences, Institute of Systems Biomedicine, Peking University, Beijing, China
| | - Yufei Xiong
- MOE Key Laboratory of Molecular Cardiovascular Sciences, Peking University, Beijing, China
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Ming Zheng
- MOE Key Laboratory of Molecular Cardiovascular Sciences, Peking University, Beijing, China
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Chao Zhong
- Beijing Key Laboratory of Tumor Systems Biology, Department of Immunology, School of Basic Medical Sciences, Institute of Systems Biomedicine, Peking University, Beijing, China
- *Correspondence: Chao Zhong, ; Yuan Zhou,
| | - Yuan Zhou
- Department of Biomedical Informatics, Center for Noncoding RNA Medicine, School of Basic Medical Sciences, Peking University, Beijing, China
- MOE Key Laboratory of Molecular Cardiovascular Sciences, Peking University, Beijing, China
- *Correspondence: Chao Zhong, ; Yuan Zhou,
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Lu J, Chen Y, Zhang X, Guo J, Xu K, Li L. A novel prognostic model based on single-cell RNA sequencing data for hepatocellular carcinoma. Cancer Cell Int 2022; 22:38. [PMID: 35078458 PMCID: PMC8787928 DOI: 10.1186/s12935-022-02469-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/13/2022] [Indexed: 12/24/2022] Open
Abstract
Background The tumour heterogeneous make-up of immune cell infiltrates is a key factor for the therapy response and prognosis of hepatocellular carcinoma (HCC). However, it is still a major challenge to comprehensively understand the tumour immune microenvironment (TIME) at the genetic and cellular levels. Methods HCC single-cell RNA sequencing (scRNA-seq) data were downloaded from the Gene Expression Omnibus (GEO) database, and gene expression data were retrieved from The Cancer Genome Atlas (TCGA) database and International Cancer Genome Consortium (ICGC) database. Cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT) was performed to evaluate the abundance of immune infiltrating cells. We employed weighted gene coexpression network analysis (WGCNA) to construct a gene coexpression network. Univariate Cox and least absolute shrinkage and selection operator (LASSO) analyses were further used to construct a risk model. Moreover, the expression levels of model genes were assessed by qPCR. Results We defined 25 cell clusters based on the scRNA-seq dataset (GSE149614), and the clusters were labelled as various cell types by marker genes. Then, we constructed a weighted coexpression network and identified a total of 6 modules, among which the brown module was most highly correlated with tumours. Moreover, we found that the brown module was most closely related to monocytes (cluster 21). Through univariate Cox and LASSO analyses, we constructed a 3-gene risk model (RiskScore = 0.257*Expression CSTB + 0.263* Expression TALDO1 + 0.313* Expression CLTA). This risk model showed excellent predictive efficacy for prognosis in the TCGA-LIHC and ICGC cohorts. Additionally, patients with high risk scores were found to be less likely to benefit from immunotherapy. Conclusions We developed a 3-gene signature (including CLTA, TALDO1 and CSTB) based on the heterogeneity of the TIME to predict the survival outcome and immunotherapy response. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-022-02469-2.
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Le T, Su S, Shahriyari L. Immune classification of osteosarcoma. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2021; 18:1879-1897. [PMID: 33757216 PMCID: PMC7992873 DOI: 10.3934/mbe.2021098] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Tumor immune microenvironment has been shown to be important in predicting the tumor progression and the outcome of treatments. This work aims to identify different immune patterns in osteosarcoma and their clinical characteristics. We use the latest and best performing deconvolution method, CIBERSORTx, to obtain the relative abundance of 22 immune cells. Then we cluster patients based on their estimated immune abundance and study the characteristics of these clusters, along with the relationship between immune infiltration and outcome of patients. We find that abundance of CD8 T cells, NK cells and M1 Macrophages have a positive association with prognosis, while abundance of γδ T cells, Mast cells, M0 Macrophages and Dendritic cells have a negative association with prognosis. Accordingly, the cluster with the lowest proportion of CD8 T cells, M1 Macrophages and highest proportion of M0 Macrophages has the worst outcome among clusters. By grouping patients with similar immune patterns, we are also able to suggest treatments that are specific to the tumor microenvironment.
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Affiliation(s)
- Trang Le
- Department of Mathematics and Statistics, University of Massachusetts Amherst, Amherst, MA MA 01003-9305, USA
| | - Sumeyye Su
- Department of Mathematics and Statistics, University of Massachusetts Amherst, Amherst, MA MA 01003-9305, USA
| | - Leili Shahriyari
- Department of Mathematics and Statistics, University of Massachusetts Amherst, Amherst, MA MA 01003-9305, USA
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