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Cao X, Huber S, Ahari AJ, Traube FR, Seifert M, Oakes CC, Secheyko P, Vilov S, Scheller IF, Wagner N, Yépez VA, Blombery P, Haferlach T, Heinig M, Wachutka L, Hutter S, Gagneur J. Analysis of 3760 hematologic malignancies reveals rare transcriptomic aberrations of driver genes. Genome Med 2024; 16:70. [PMID: 38769532 PMCID: PMC11103968 DOI: 10.1186/s13073-024-01331-6] [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: 09/29/2023] [Accepted: 04/04/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Rare oncogenic driver events, particularly affecting the expression or splicing of driver genes, are suspected to substantially contribute to the large heterogeneity of hematologic malignancies. However, their identification remains challenging. METHODS To address this issue, we generated the largest dataset to date of matched whole genome sequencing and total RNA sequencing of hematologic malignancies from 3760 patients spanning 24 disease entities. Taking advantage of our dataset size, we focused on discovering rare regulatory aberrations. Therefore, we called expression and splicing outliers using an extension of the workflow DROP (Detection of RNA Outliers Pipeline) and AbSplice, a variant effect predictor that identifies genetic variants causing aberrant splicing. We next trained a machine learning model integrating these results to prioritize new candidate disease-specific driver genes. RESULTS We found a median of seven expression outlier genes, two splicing outlier genes, and two rare splice-affecting variants per sample. Each category showed significant enrichment for already well-characterized driver genes, with odds ratios exceeding three among genes called in more than five samples. On held-out data, our integrative modeling significantly outperformed modeling based solely on genomic data and revealed promising novel candidate driver genes. Remarkably, we found a truncated form of the low density lipoprotein receptor LRP1B transcript to be aberrantly overexpressed in about half of hairy cell leukemia variant (HCL-V) samples and, to a lesser extent, in closely related B-cell neoplasms. This observation, which was confirmed in an independent cohort, suggests LRP1B as a novel marker for a HCL-V subclass and a yet unreported functional role of LRP1B within these rare entities. CONCLUSIONS Altogether, our census of expression and splicing outliers for 24 hematologic malignancy entities and the companion computational workflow constitute unique resources to deepen our understanding of rare oncogenic events in hematologic cancers.
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Affiliation(s)
- Xueqi Cao
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Graduate School of Quantitative Biosciences (QBM), Munich, Germany
| | - Sandra Huber
- Munich Leukemia Laboratory (MLL), Munich, Germany
| | - Ata Jadid Ahari
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Franziska R Traube
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Marc Seifert
- Department of Haematology, Oncology and Clinical Immunology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Christopher C Oakes
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Polina Secheyko
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Faculty of Biology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Sergey Vilov
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany
| | - Ines F Scheller
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany
| | - Nils Wagner
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Helmholtz Association - Munich School for Data Science (MUDS), Munich, Germany
| | - Vicente A Yépez
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Piers Blombery
- Peter MacCallum Cancer Centre, Melbourne, Australia
- University of Melbourne, Melbourne, Australia
- Torsten Haferlach Leukämiediagnostik Stiftung, Munich, Germany
| | | | - Matthias Heinig
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany
| | - Leonhard Wachutka
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.
| | | | - Julien Gagneur
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.
- Graduate School of Quantitative Biosciences (QBM), Munich, Germany.
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany.
- Institute of Human Genetics, School of Medicine and Health, Technical University of Munich, Munich, Germany.
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Wang S, Wang R, Hu D, Zhang C, Cao P, Huang J. Machine learning reveals diverse cell death patterns in lung adenocarcinoma prognosis and therapy. NPJ Precis Oncol 2024; 8:49. [PMID: 38409471 PMCID: PMC10897292 DOI: 10.1038/s41698-024-00538-5] [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: 07/13/2023] [Accepted: 02/08/2024] [Indexed: 02/28/2024] Open
Abstract
Cancer cell growth, metastasis, and drug resistance pose significant challenges in the management of lung adenocarcinoma (LUAD). However, there is a deficiency in optimal predictive models capable of accurately forecasting patient prognoses and guiding the selection of targeted treatments. Programmed cell death (PCD) pathways play a pivotal role in the development and progression of various cancers, offering potential as prognostic indicators and drug sensitivity markers for LUAD patients. The development and validation of predictive models were conducted by integrating 13 PCD patterns with comprehensive analysis of bulk RNA, single-cell RNA transcriptomics, and pertinent clinicopathological details derived from TCGA-LUAD and six GEO datasets. Utilizing the machine learning algorithms, we identified ten critical differentially expressed genes associated with PCD in LUAD, namely CHEK2, KRT18, RRM2, GAPDH, MMP1, CHRNA5, TMPRSS4, ITGB4, CD79A, and CTLA4. Subsequently, we conducted a programmed cell death index (PCDI) based on these genes across the aforementioned cohorts and integrated this index with relevant clinical features to develop several prognostic nomograms. Furthermore, we observed a significant correlation between the PCDI and immune features in LUAD, including immune cell infiltration and the expression of immune checkpoint molecules. Additionally, we found that patients with a high PCDI score may exhibit resistance to immunotherapy and standard adjuvant chemotherapy regimens; however, they may benefit from other FDA-supported drugs such as docetaxel and dasatinib. In conclusion, the PCDI holds potential as a prognostic signature and can facilitate personalized treatment for LUAD patients.
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Affiliation(s)
- Shun Wang
- Department of Respiratory Medicine, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Fudan University, Shanghai, 200031, China
| | - Ruohuang Wang
- Department of Otolaryngology, the Second Affiliated Hospital of the Naval Military Medical University (Shanghai Changzheng Hospital), Shanghai, 200003, China
| | - Dingtao Hu
- Clinical Cancer Institute, Center for Translational Medicine, Naval Medical University, Shanghai, 200433, China
| | - Caoxu Zhang
- Department of Molecular Diagnostics, The Core Laboratory in Medical Center of Clinical Research, Department of Endocrinology, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiaotong University School of Medicine, Shanghai, 200011, China
| | - Peng Cao
- Department of Interventional Pulmonology, Anhui Chest Hospital, Hefei, Anhui, 230022, China
| | - Jie Huang
- Department of Respiratory Medicine, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Fudan University, Shanghai, 200031, 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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Li Z, Lu Z, Hu C, Zhang Y, Chen Y, Zhang J, Guo F, Wang J, Tang Z, Tang F, He Z. A Machine Learning Analysis of Prognostic Genes Associated With Allograft Tolerance After Renal Transplantation. Cell Transplant 2023; 32:9636897231195116. [PMID: 37650419 PMCID: PMC10475226 DOI: 10.1177/09636897231195116] [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: 05/03/2023] [Revised: 07/22/2023] [Accepted: 08/01/2023] [Indexed: 09/01/2023] Open
Abstract
In this study, we aimed to identify transplantation tolerance (TOL)-related gene signature and use it to predict the different types of renal allograft rejection performances in kidney transplantation. Gene expression data were obtained from the Gene Expression Omnibus (GEO) database, differently expressed genes (DEGs) were performed, and the gene ontology (GO) function enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were also conducted. The machine learning methods were combined to analyze the feature TOL-related genes and verify their predictive performance. Afterward, the gene expression levels and predictive performances of TOL-related genes were conducted in the context of acute rejection (AR), chronic rejection (CR), and graft loss through heatmap plots and the receiver operating characteristic (ROC) curves, and their respective immune infiltration results were also performed. Furthermore, the TOL-related gene signature for graft survival was conducted to discover gene immune cell enrichment. A total of 25 TOL-related DEGs were founded, and the GO and KEGG results indicated that DEGs mainly enriched in B cell-related functions and pathways. 7 TOL-related gene signature was constructed and performed delightedly in TOL groups and different types of allograft rejection. The immune infiltration analysis suggested that gene signature was correlated with different types of immune cells. The Kaplan-Meier (KM) survival analysis demonstrated that BLNK and MZB1 were the prognostic TOL-related genes. Our study proposed a novel gene signature that may influence TOL in kidney transplantation, providing possible guidance for immunosuppressive therapy in kidney transplant patients.
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Affiliation(s)
- Zhibiao Li
- Department of Urology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Zechao Lu
- Department of Urology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Chuxian Hu
- The Sixth Clinical College of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yixin Zhang
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Clinical Research Center for Urological Diseases, Guangzhou, Guangdong, China
| | - Yushu Chen
- Department of Urology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Jiahao Zhang
- Department of Urology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Feng Guo
- Department of Urology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Jinjin Wang
- Department of Urology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Zhicheng Tang
- Department of Urology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Fucai Tang
- Department of Urology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Zhaohui He
- Department of Urology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
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Yao PA, Sun HJ, Li XY. Identification of key genes in late-onset major depressive disorder through a co-expression network module. Front Genet 2022; 13:1048761. [PMID: 36561317 PMCID: PMC9763307 DOI: 10.3389/fgene.2022.1048761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
Late-onset major depressive disorder (LOD) increases the risk of disability and suicide in elderly patients. However, the complex pathological mechanism of LOD still remains unclear. We selected 10 LOD patients and 12 healthy control samples from the GSE76826 dataset for statistical analysis. Under the screening criteria, 811 differentially expressed genes (DEGs) were screened. We obtained a total of two most clinically significant modules through the weighted gene co-expression network analysis (WGCNA). Functional analysis of the genes in the most clinically significant modules was performed to explore the potential mechanism of LOD, followed by protein-protein interaction (PPI) analysis and hub gene identification in the core area of the PPI network. Furthermore, we identified immune infiltrating cells using the cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT) algorithm between healthy subjects and LOD patients with the GSE98793 dataset. Next, six hub genes (CD27, IL7R, CXCL1, CCR7, IGLL5, and CD79A) were obtained by intersecting hub genes with DEGs, followed by verifying the diagnostic accuracy with the receiver operating characteristic curve (ROC). In addition, we constructed the least absolute shrinkage and selection operator (LASSO) regression model for hub gene cross-validation. Finally, we found that CD27 and IGLL5 were good diagnostic indicators of LOD, and CD27 may be the key gene of immune function change in LOD. In conclusion, our research shows that the changes in the immune function may be an important mechanism in the development of LOD, which can provide some guidance for the related research of LOD in the future.
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Affiliation(s)
- Ping-An Yao
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China,Department of Neurobiology and Acupuncture Research, The Third Clinical Medical College, Zhejiang Chinese Medical University, Key Laboratory of Acupuncture and Neurology of Zhejiang Province, Hangzhou, China
| | - Hai-Ju Sun
- Department of Neurobiology and Acupuncture Research, The Third Clinical Medical College, Zhejiang Chinese Medical University, Key Laboratory of Acupuncture and Neurology of Zhejiang Province, Hangzhou, China
| | - Xiao-Yu Li
- Department of Neurobiology and Acupuncture Research, The Third Clinical Medical College, Zhejiang Chinese Medical University, Key Laboratory of Acupuncture and Neurology of Zhejiang Province, Hangzhou, China,The Third Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China,*Correspondence: Xiao-Yu Li,
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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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Zhao X, Ma Y, Bian H, Liu Z. CD20 expression is closely associated with Epstein–Barr virus infection and an inferior survival in nodular sclerosis classical Hodgkin lymphoma. Front Oncol 2022; 12:993768. [PMID: 36147921 PMCID: PMC9486205 DOI: 10.3389/fonc.2022.993768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/17/2022] [Indexed: 11/17/2022] Open
Abstract
Background Nodular sclerosis classical Hodgkin lymphoma (NSCHL) is a rare disease in which Epstein–Barr virus (EBV) and CD20 can be detected. The clinical significance of EBV infection, CD20 expression and their relationship are still unclear in NSCHL presently. The aim of this research was to systematically explore the clinical significance of EBV infection, expression of CD20 and their relationship in NSCHL. Methods 109 NSCHL patients diagnosed in Qingdao University’s Affiliated Hospital were chosen from January 2010 to July 2019, and the clinical and survival data of all patients were collected retrospectively. Results Among 109 patients, 33 patients were assigned to the group of EBV-positives, following the results of the EBV-encoded RNA (EBER1). Compared with EBV-negative group patients, those in the group of EBV-positive were older (P=0.004) and their β2-microglobulin (β2-MG) levels were higher (P=0.006). The CD20 positivity rate in the group of EBV-positive was substantially higher than that in the EBV-negative group (54.5% vs 27.6%, P=0.007). Among 109 patients, EBV+ and CD20+ double positive patients acquired the least overall survival (OS), and patients with EBV- and CD20- double negative had the best OS (P < 0.001). Although old age, gender, EBV infection and CD20 positive were the risk factors for OS in NSCHL, multivariate analysis showed that CD20 positivity was the only characteristic that showed to be an independent risk factor for OS in NSCHL patients. Conclusion CD20 was found to be strongly expressed in NSCHL patients who had been infected with EBV, and it was found to be an independent risk factor for NSCHL patients’ survival.
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Affiliation(s)
- Xia Zhao
- Department of Lymphoma, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yushuo Ma
- Department of Medicine, Medical College of Qingdao University, Qingdao, China
| | - Haiyan Bian
- Department of Medicine, Medical College of Qingdao University, Qingdao, China
| | - Zhihe Liu
- Department of Lymphoma, The Affiliated Hospital of Qingdao University, Qingdao, China
- *Correspondence: Zhihe Liu,
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Su P, Peng Z, Xu B, Yang B, Jin F. Establishment and validation of an individualized macrophage-related gene signature to predict overall survival in patients with triple negative breast cancer. PeerJ 2021; 9:e12383. [PMID: 34900411 PMCID: PMC8621725 DOI: 10.7717/peerj.12383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 10/04/2021] [Indexed: 12/31/2022] Open
Abstract
Background Recently, researchers have classified highly heterogeneous triple negative breast cancer (TNBC) into different subtypes from different perspectives and investigated the characteristics of different subtypes to pursue individualized treatment. With the increase of immunotherapy and its preliminary application in TNBC treatment, the value of immune-related strategies in the treatment of TNBC has been initially reflected. Based thereon, this study plans to classify and further explore TNBC from the perspective of immune cell infiltration. Method The fractions of immune cells of TNBC patients were assessed by six immune component analysis methods in The Cancer Genome Atlas (TCGA) database. Hub genes significantly related to poor prognosis were verified by weighted gene co-expression network analysis (WGCNA) analysis, Lasso analysis, and univariate KM analysis. Two cohorts of TNBC patients with complete prognosis information were collected for validation analysis. Finally, the Genomics of Drug Sensitivity in Cancer (GDSC) database was adopted to ascertain the sensitivity differences of different populations based on hub-gene grouping to different chemotherapy drugs. Results Five hub genes (CD79A, CXCL13, IGLL5, LHFPL2, and PLEKHF1) of the key co-expression gene module could divide TNBC patients into two groups (Cluster A and Cluster B) based on consistency cluster analysis. The patients with Cluster A were responsible for significantly worse prognosis than the patients with Cluster B (P = 0.023). In addition, another classification method, PCoA, and two other datasets (GSE103091 and GSE76124), were used to obtain consistent results with previous findings, which verified the stability of the classification method and dataset in this study. The grouping criteria based on the previous results were developed and the accuracy of the cut-off values was validated. A prognosis model of TNBC patients was then constructed based on the grouping results of five hub genes and N staging as prognostic factors. The results of ROC and decision curve analyses showed that this model had high prediction accuracy and patients could benefit therefrom. Finally, GDSC database analysis proved that patients in Cluster A were more sensitive to Vinorelbine. Separate analysis of the sensitivity of patients in Cluster A to Gemcitabine and Vinorelbine showed that the patients in Cluster A exhibited higher sensitivity to Vinorelbine. We hypothesized that these five genes were related to gemcitabine resistance and they could serve as biomarkers for clinical drug decision-making after anthracene resistance and taxane resistance in patients with advanced TNBC. Conclusion This study found five hub prognostic genes associated with macrophages, and a prognostic model was established to predict the survival of TNBC patients. Finally, these five genes were related to gemcitabine resistance in TNBC patients.
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Affiliation(s)
- Peng Su
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Ziqi Peng
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Boyang Xu
- Gastroenterology Department, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Bowen Yang
- Department of Medical Oncology, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Feng Jin
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
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Chen M, Fu M, Wang A, Wu X, Zhen J, Gong M, Zhang X, Yue G, Du Q, Zhao W, Zhao Y, Lu P, Wang H. Cytoplasmic CD79a is a promising biomarker for B lymphoblastic leukemia follow up post CD19 CAR-T therapy. Leuk Lymphoma 2021; 63:426-434. [PMID: 34672246 DOI: 10.1080/10428194.2021.1980214] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Minimal residual disease (MRD) detection is an important prognostic parameter in patients with refractory or relapsed B-cell acute lymphoblastic leukemia (R/R B-ALL). CD79a has been reported to exhibit a high degree of linage-specificity for B-cell differentiation, with a specificity of 88% and a sensitivity of 100%. In this study, we investigated the efficiency and prognostic role of cytoplasmic CD79a (cCD79a) antibody-gated multicolor flow cytometry (MFC) in MRD detection in patients with B-ALL who received CD19-targeted chimeric antigen receptor (CAR) T-cell therapy bridging to allogeneic hematopoietic stem cell transplantation (allo-HSCT). The retrospective analysis was carried on to 59 patients who accepted allo-HSCT after CD19-CAR-T infusion from June 2016 to May 2017. The MFC MRD statuses before and after allo-HSCT were both strongly correlated with the transplantation prognosis, the MFC panel with cCD79a gating can effectively monitor MRD after CD19 CAR T-cell therapy and predict the prognosis after allo-HSCT. Trial registration: ClinicalTrials#: ChiCTR-IIh-16008711.gov: NCT03173417. Registered 30 May 2017 - retrospectively registered, https://www.clinicaltrials.gov/.
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Affiliation(s)
- Man Chen
- Department of Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, Langfang, China
| | - Minjing Fu
- Department of Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, Langfang, China
| | - Aixian Wang
- Department of Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, Langfang, China
| | - Xueying Wu
- Department of Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, Langfang, China
| | - Junyi Zhen
- Department of Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, Langfang, China
| | - Meiwei Gong
- Department of Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, Langfang, China
| | - Xian Zhang
- Department of Haematology, Hebei Yanda Lu Daopei Hospital, Langfang, China
| | - Guanlan Yue
- Department of Stem Cell Transplantation, Hebei Yanda Lu Daopei Hospital, Langfang, China
| | - Qing Du
- Department of Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, Langfang, China
| | - Wei Zhao
- Department of Stem Cell Transplantation, Hebei Yanda Lu Daopei Hospital, Langfang, China
| | - Yanli Zhao
- Department of Stem Cell Transplantation, Hebei Yanda Lu Daopei Hospital, Langfang, China
| | - Peihua Lu
- Department of Stem Cell Transplantation, Hebei Yanda Lu Daopei Hospital, Langfang, China
| | - Hui Wang
- Department of Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, Langfang, China
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