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Sarkar S, Hill DD, Rosenberg AF, Eaton EF, Kutsch O, Kobie JJ. Injection Drug Use Alters Plasma Regulation of the B Cell Response. Cells 2024; 13:1011. [PMID: 38920641 PMCID: PMC11202061 DOI: 10.3390/cells13121011] [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: 04/26/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/27/2024] Open
Abstract
The opioid epidemic continues to be a major public health issue that includes millions of people who inject drugs (PWID). PWID have increased incidence of serious infections, including HIV as well as metabolic and inflammatory sequelae. We sought to discern the extent of systemic alterations in humoral immunity associated with injection drug use, including alterations in the plasma proteome and its regulation of B cell responsiveness. Comprehensive plasma proteomics analysis of HIV negative/hepatitis C negative individuals with a history of recent injection heroin use was performed using mass spectrometry and ELISA. The effects of plasma from PWID and healthy controls on the in vitro proliferation and transcriptional profile of B cell responses to stimulation were determined by flow cytometry and RNA-Seq. The plasma proteome of PWID was distinct from healthy control individuals, with numerous immune-related analytes significantly altered in PWID, including complement (C3, C5, C9), immunoglobulin (IgD, IgM, kappa light chain), and other inflammatory mediators (CXCL4, LPS binding protein, C-reactive protein). The plasma of PWID suppressed the in vitro proliferation of B cells. Transcriptome analysis indicated that PWID plasma treatment increased B cell receptor and CD40 signaling and shifted B cell differentiation from plasma cell-like toward germinal center B cell-like transcriptional profiles. These results indicate that the systemic inflammatory milieu is substantially altered in PWID and may impact their B cell responses.
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Affiliation(s)
- Sanghita Sarkar
- Infectious Diseases Division, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35249, USA
| | - Dave D. Hill
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35249, USA
| | - Alexander F. Rosenberg
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35249, USA
| | - Ellen F. Eaton
- Infectious Diseases Division, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35249, USA
| | - Olaf Kutsch
- Infectious Diseases Division, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35249, USA
| | - James J. Kobie
- Infectious Diseases Division, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35249, USA
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Mei N, Gong S, Wang L, Wang L, Wang J, Li J, Bao Y, Zhang H, Wang H. Identification of a Prognostic Model Based on NK Cell-Related Genes in Multiple Myeloma Using Single-Cell and Transcriptomic Data Analysis. Blood Lymphat Cancer 2024; 14:31-48. [PMID: 38854627 PMCID: PMC11162243 DOI: 10.2147/blctt.s461529] [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: 03/06/2024] [Accepted: 05/21/2024] [Indexed: 06/11/2024]
Abstract
Background Multiple myeloma (MM), an incurable plasma cell malignancy. The significance of the relationship between natural killer (NK) cell-related genes and clinical factors in MM remains unclear. Methods Initially, we extracted NK cell-related genes from peripheral blood mononuclear cells (PBMC) of healthy donors and MM samples by employing single-cell transcriptome data analysis in TISCH2. Subsequently, we screened NK cell-related genes with prognostic significance through univariate Cox regression analysis and protein-protein interaction (PPI) network analysis. Following the initial analyses, we developed potential subtypes and prognostic models for MM using consensus clustering and lasso regression analysis. Additionally, we conducted a correlation analysis to explore the relationship between clinical features and risk scores. Finally, we constructed a weighted gene co-expression network analysis (WGCNA) and identified differentially expressed genes (DEGs) within the MM cohort. Results We discovered that 153 NK cell-related genes were significantly associated with the prognosisof MM patients (P <0.05). Patients in NK cluster A exhibited poorer survival outcomes compared to those in cluster B. Furthermore, our NK cell-related genes risk model revealed that patients with a high risk score had significantly worse prognoses (P <0.05). Patients with a high risk score were more likely to exhibit adverse clinical markers. Additionally, the nomogram based on NK cell-related genes demonstrated strong prognostic performance. The enrichment analysis indicated that immune-related pathways were significantly correlated with both the NK subtypes and the NK cell-related genes risk model. Ultimately, through the combined use of WGCNA and DEGs analysis, and by employing Venn diagrams, we determined that ITM2C is an independent prognostic marker for MM patients. Conclusion In this study, we developed a novel model based on NK cell-related genes to stratify the prognosis of MM patients. Notably, higher expression levels of ITM2C were associated with more favorable survival outcomes in these patients.
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Affiliation(s)
- Nan Mei
- Department of Hematology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, People’s Republic of China
| | - Sha Gong
- Department of Hematology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, People’s Republic of China
| | - Lizhao Wang
- Department of Breast Surgery, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, People’s Republic of China
| | - Lu Wang
- Department of Hematology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, People’s Republic of China
| | - Jincheng Wang
- Department of Hematology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, People’s Republic of China
| | - Jianpeng Li
- Department of Urology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, People’s Republic of China
| | - Yingying Bao
- Institute of Gene and Cell Therapy, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, People’s Republic of China
| | - Huanming Zhang
- Department of Hematology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, People’s Republic of China
| | - Huaiyu Wang
- Department of Hematology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, People’s Republic of China
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Ye X, Yang S, Tu J, Xu L, Wang Y, Chen H, Yu R, Huang P. Leveraging baseline transcriptional features and information from single-cell data to power the prediction of influenza vaccine response. Front Cell Infect Microbiol 2024; 14:1243586. [PMID: 38384303 PMCID: PMC10879619 DOI: 10.3389/fcimb.2024.1243586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 01/11/2024] [Indexed: 02/23/2024] Open
Abstract
Introduction Vaccination is still the primary means for preventing influenza virus infection, but the protective effects vary greatly among individuals. Identifying individuals at risk of low response to influenza vaccination is important. This study aimed to explore improved strategies for constructing predictive models of influenza vaccine response using gene expression data. Methods We first used gene expression and immune response data from the Immune Signatures Data Resource (IS2) to define influenza vaccine response-related transcriptional expression and alteration features at different time points across vaccination via differential expression analysis. Then, we mapped these features to single-cell resolution using additional published single-cell data to investigate the possible mechanism. Finally, we explored the potential of these identified transcriptional features in predicting influenza vaccine response. We used several modeling strategies and also attempted to leverage the information from single-cell RNA sequencing (scRNA-seq) data to optimize the predictive models. Results The results showed that models based on genes showing differential expression (DEGs) or fold change (DFGs) at day 7 post-vaccination performed the best in internal validation, while models based on DFGs had a better performance in external validation than those based on DEGs. In addition, incorporating baseline predictors could improve the performance of models based on days 1-3, while the model based on the expression profile of plasma cells deconvoluted from the model that used DEGs at day 7 as predictors showed an improved performance in external validation. Conclusion Our study emphasizes the value of using combination modeling strategy and leveraging information from single-cell levels in constructing influenza vaccine response predictive models.
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Affiliation(s)
- Xiangyu Ye
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Sheng Yang
- Department of Biostatistics, National Vaccine Innovation Platform, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Junlan Tu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Lei Xu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yifan Wang
- Department of Infectious Disease, Jurong Hospital Affiliated to Jiangsu University, Jurong, China
| | - Hongbo Chen
- Department of Infectious Disease, Jurong Hospital Affiliated to Jiangsu University, Jurong, China
| | - Rongbin Yu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Peng Huang
- Department of Epidemiology, National Vaccine Innovation Platform, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
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Diao H, Xue WQ, Wang TM, Yang DW, Deng CM, Li DH, Zhang WL, Liao Y, Wu YX, Chen XY, Zhou T, Li XZ, Zhang PF, Zheng XH, Zhang SD, Hu YZ, Cao SM, Liu Q, Ye WM, He YQ, Jia WH. The interaction and mediation effects between the host genetic factors and Epstein-Barr virus VCA-IgA in the risk of nasopharyngeal carcinoma. J Med Virol 2023; 95:e29224. [PMID: 37970759 DOI: 10.1002/jmv.29224] [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: 07/16/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/17/2023]
Abstract
Previous studies have demonstrated strong associations between host genetic factors and Epstein-Barr virus (EBV) VCA-IgA with the risk of nasopharyngeal carcinoma (NPC). However, the specific interplay between host genetics and EBV VCA-IgA on NPC risk is not well understood. In this two-stage case-control study (N = 4804), we utilized interaction and mediation analysis to investigate the interplay between host genetics (genome-wide association study-derived polygenic risk score [PRS]) and EBV VCA-IgA antibody level in the NPC risk. We employed a four-way decomposition analysis to assess the extent to which the genetic effect on NPC risk is mediated by or interacts with EBV VCA-IgA. We consistently found a significant interaction between the PRS and EBV VCA-IgA on NPC risk (discovery population: synergy index [SI] = 2.39, 95% confidence interval [CI] = 1.85-3.10; replication population: SI = 3.10, 95% CI = 2.17-4.44; all pinteraction < 0.001). Moreover, the genetic variants included in the PRS demonstrated similar interactions with EBV VCA-IgA antibody. We also observed an obvious dose-response relationship between the PRS and EBV VCA-IgA antibody on NPC risk (all ptrend < 0.001). Furthermore, our decomposition analysis revealed that a substantial proportion (approximately 90%) of the genetic effects on NPC risk could be attributed to host genetic-EBV interaction, while the risk effects mediated by EBV VCA-IgA antibody were weak and statistically insignificant. Our study provides compelling evidence for an interaction between host genetics and EBV VCA-IgA antibody in the development of NPC. These findings emphasize the importance of implementing measures to control EBV infection as a crucial strategy for effectively preventing NPC, particularly in individuals at high genetic risk.
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Affiliation(s)
- Hua Diao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
- School of Public Health, Sun Yat-Sen University, Guangzhou, China
| | - Wen-Qiong Xue
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Tong-Min Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Da-Wei Yang
- School of Public Health, Sun Yat-Sen University, Guangzhou, China
| | - Chang-Mi Deng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Dan-Hua Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Wen-Li Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Ying Liao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Yan-Xia Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Xue-Yin Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Ting Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Xi-Zhao Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Pei-Fen Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Xiao-Hui Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Shao-Dan Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Ye-Zhu Hu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Su-Mei Cao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Department of Cancer Prevention Center, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Qing Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Department of Cancer Prevention Center, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Wei-Min Ye
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Epidemiology and Health Statistics and Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Yong-Qiao He
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
- School of Public Health, Sun Yat-Sen University, Guangzhou, China
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Awazu Y, Fukuda T, Noda T, Uchikura E, Nanno S, Imai K, Yamauchi M, Yasui T, Sumi T. CLPTM1L expression predicts recurrence of patients with intermediate‑ and high‑risk stage IB‑IIB cervical cancer undergoing radical hysterectomy followed by TP as adjuvant chemotherapy. Oncol Lett 2023; 26:353. [PMID: 37545614 PMCID: PMC10398629 DOI: 10.3892/ol.2023.13939] [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: 04/10/2023] [Accepted: 06/14/2023] [Indexed: 08/08/2023] Open
Abstract
According to the National Comprehensive Cancer Network clinical practice guidelines of cervical cancer, concurrent chemoradiotherapy or radiotherapy is suggested for patients who receive radical hysterectomy and have intermediate- and high-risk cervical cancer. However, adjuvant chemotherapy has been increasingly chosen given the adverse events associated with chemoradiotherapy or radiotherapy and the increase in evidence regarding the efficacy of adjuvant chemotherapy. Given that adjuvant chemotherapy is not a standard treatment at present, if recurrence after adjuvant chemotherapy could be predicted, it would assist the decision of gynecological oncologists selecting which adjuvant therapy (chemotherapy or radiation therapy) to use. Cleft lip and palate transmembrane protein 1-like protein (CLPTM1L; also known as cisplatin resistance-related protein 9) is associated with apoptotic mechanisms and is related to the proliferation of the tumor cells and resistance against chemotherapy. In the present study, the association between CLPTM1L expression and recurrence of intermediate- and high-risk stage IB-IIB cervical cancer in patients undergoing radical hysterectomy followed by treatment with cisplatin and paclitaxel (TP) as adjuvant chemotherapy was determined. Patients were divided into two groups: Recurrence group and no-recurrence group. CLPTM1L expression was examined using immunohistochemistry in paraffin-embedded sections using weighted scores. Regarding the characteristics of the patients, a histology of non-squamous cell carcinoma, lymph node metastasis and parametrium invasion were more common in the recurrence group compared with the non-recurrence group. In the recurrence group, CLPTM1L expression was significantly higher than that in the no-recurrence group. Next, patients were divided into low and high-expression groups based on the weighted score with a cut-off value of 6. In the high expression group, patients exhibited a higher rate of recurrence (37.5 vs. 5.1%) and had worse overall survival. Multivariate analysis revealed that high CLPTM1L expression was independently related to recurrence. In in vitro analysis, small interfering RNA-mediated knockdown of CLPTM1L enhanced the sensitivity of cervical cancer cells to cisplatin. In conclusion, the present study revealed that CLPTM1L expression may be a predictive biomarker of recurrence of intermediate- and high-risk stage IB-IIB cervical cancer in patients undergoing radical hysterectomy followed by TP as adjuvant chemotherapy.
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Affiliation(s)
- Yuichiro Awazu
- Department of Obstetrics and Gynecology, Osaka City University Graduate School of Medicine, Osaka, Osaka 5454-8585, Japan
| | - Takeshi Fukuda
- Department of Obstetrics and Gynecology, Osaka Metropolitan University Graduate School of Medicine, Osaka, Osaka 5454-8585, Japan
| | - Takuya Noda
- Department of Obstetrics and Gynecology, Osaka City University Graduate School of Medicine, Osaka, Osaka 5454-8585, Japan
| | - Eijiro Uchikura
- Department of Obstetrics and Gynecology, Osaka City University Graduate School of Medicine, Osaka, Osaka 5454-8585, Japan
| | - Shigenori Nanno
- Department of Obstetrics and Gynecology, Osaka City University Graduate School of Medicine, Osaka, Osaka 5454-8585, Japan
| | - Kenji Imai
- Department of Obstetrics and Gynecology, Osaka Metropolitan University Graduate School of Medicine, Osaka, Osaka 5454-8585, Japan
| | - Makoto Yamauchi
- Department of Obstetrics and Gynecology, Osaka Metropolitan University Graduate School of Medicine, Osaka, Osaka 5454-8585, Japan
| | - Tomoyo Yasui
- Department of Obstetrics and Gynecology, Osaka Metropolitan University Graduate School of Medicine, Osaka, Osaka 5454-8585, Japan
| | - Toshiyuki Sumi
- Department of Obstetrics and Gynecology, Osaka Metropolitan University Graduate School of Medicine, Osaka, Osaka 5454-8585, Japan
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Cheng RYH, de Rutte J, Ito CEK, Ott AR, Bosler L, Kuo WY, Liang J, Hall BE, Rawlings DJ, Di Carlo D, James RG. SEC-seq: association of molecular signatures with antibody secretion in thousands of single human plasma cells. Nat Commun 2023; 14:3567. [PMID: 37322036 PMCID: PMC10272111 DOI: 10.1038/s41467-023-39367-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 06/07/2023] [Indexed: 06/17/2023] Open
Abstract
The secreted products of cells drive many functions in vivo; however, methods to link this functional information to surface markers and transcriptomes have been lacking. By accumulating secretions close to secreting cells held within cavity-containing hydrogel nanovials, we demonstrate workflows to analyze the amount of IgG secreted from single human B cells and link this information to surface markers and transcriptomes from the same cells. Measurements using flow cytometry and imaging flow cytometry corroborate the association between IgG secretion and CD38/CD138. By using oligonucleotide-labeled antibodies we find that upregulation of pathways for protein localization to the endoplasmic reticulum and mitochondrial oxidative phosphorylation are most associated with high IgG secretion, and uncover surrogate plasma cell surface markers (e.g., CD59) defined by the ability to secrete IgG. Altogether, this method links quantity of secretion with single-cell sequencing (SEC-seq) and enables researchers to fully explore the links between genome and function, laying the foundation for discoveries in immunology, stem cell biology, and beyond.
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Affiliation(s)
- Rene Yu-Hong Cheng
- Center of Immunotherapy and Immunity, Seattle Children Research Institute, Seattle, WA, 98101, USA
- Molecular Engineering and Science Institute, University of Washington, Seattle, WA, 98195, USA
| | | | - Cade Ellis K Ito
- Center of Immunotherapy and Immunity, Seattle Children Research Institute, Seattle, WA, 98101, USA
- Department of Lab Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Andee R Ott
- Center of Immunotherapy and Immunity, Seattle Children Research Institute, Seattle, WA, 98101, USA
| | - Lucie Bosler
- Partillion Bioscience, Los Angeles, CA, 90095, USA
| | - Wei-Ying Kuo
- Partillion Bioscience, Los Angeles, CA, 90095, USA
| | - Jesse Liang
- Partillion Bioscience, Los Angeles, CA, 90095, USA
| | | | - David J Rawlings
- Center of Immunotherapy and Immunity, Seattle Children Research Institute, Seattle, WA, 98101, USA
- Department of Immunology, University of Washington, Seattle, WA, 98195, USA
- Departments of Pediatrics, University of Washington, Seattle, WA, 98195, USA
| | - Dino Di Carlo
- Partillion Bioscience, Los Angeles, CA, 90095, USA.
- Department of Bioengineering, University of California - Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Mechanical and Aerospace Engineering, Los Angeles, CA, 90095, USA.
- California NanoSystems Institute (CNSI), University of California - Los Angeles, Los Angeles, CA, 90095, USA.
| | - Richard G James
- Center of Immunotherapy and Immunity, Seattle Children Research Institute, Seattle, WA, 98101, USA.
- Molecular Engineering and Science Institute, University of Washington, Seattle, WA, 98195, USA.
- Department of Lab Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA.
- Departments of Pediatrics, University of Washington, Seattle, WA, 98195, USA.
- Department of Pharmacology, University of Washington, Seattle, WA, 98195, USA.
- Brotman-Baty Institute for Precision Medicine, Seattle, WA, 98195, USA.
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Lan M, Zhang S, Gao L. Efficient Generation of Paired Single-Cell Multiomics Profiles by Deep Learning. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023:e2301169. [PMID: 37114830 PMCID: PMC10375161 DOI: 10.1002/advs.202301169] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/08/2023] [Indexed: 06/19/2023]
Abstract
Recent advances in single-cell sequencing technology have made it possible to measure multiple paired omics simultaneously in a single cell such as cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) and single-nucleus chromatin accessibility and mRNA expression sequencing (SNARE-seq). However, the widespread application of these single-cell multiomics profiling technologies has been limited by their experimental complexity, noise in nature, and high cost. In addition, single-omics sequencing technologies have generated tremendous and high-quality single-cell datasets but have yet to be fully utilized. Here, single-cell multiomics generation (scMOG), a deep learning-based framework to generate single-cell assay for transposase-accessible chromatin (ATAC) data in silico is developed from experimentally available single-cell RNA-seq measurements and vice versa. The results demonstrate that scMOG can accurately perform cross-omics generation between RNA and ATAC, and generate paired multiomics data with biological meanings when one omics is experimentally unavailable and out of training datasets. The generated ATAC, either alone or in combination with measured RNA, exhibits equivalent or superior performance to that of the experimentally measured counterparts throughout multiple downstream analyses. scMOG is also applied to human lymphoma data, which proves to be more effective in identifying tumor samples than the experimentally measured ATAC data. Finally, the performance of scMOG is investigated in other omics such as proteomics and it still shows robust performance on surface protein generation.
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Affiliation(s)
- Meng Lan
- School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi, 710071, China
| | - Shixiong Zhang
- School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi, 710071, China
| | - Lin Gao
- School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi, 710071, China
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8
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Regional immunity of chicken adipose tissue responds to secondary immunity induced by Newcastle disease vaccine via promoting immune activation and weakening lipid metabolism. Poult Sci 2023; 102:102646. [PMID: 37031585 PMCID: PMC10105486 DOI: 10.1016/j.psj.2023.102646] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Adipose tissue (AT) is considered as a regional immune organ and plays an important role in the anti-infection immune response. However, the function and mechanism of chicken AT in response to secondary immune response remain poorly understood. Here, we used mRNA and microRNA (miRNA) sequencing technology to survey the transcriptomic landscape of chicken abdominal adipose tissue (AAT) during the first and second immunization with Newcastle disease virus (NDV) vaccine, and carried out bioinformatics analysis, such as Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis, protein-protein interaction (PPI) analysis, and miRNA-mRNA integrated analysis. The results indicated that chicken AAT actively responded to the secondary immune response. DNA replication and cytoskeleton regulation as the regulatory functions of immune activation changed significantly, and weakened lipid metabolism was an effective strategy for the secondary immunity. Mechanically, the regulatory network between the differentially expressed miRNAs (DEMs) and their targeted differentially expressed genes (DEGs), such as miR-206/miR-499-5p-nuclear receptor subfamily 4 group A member 3 (NR4A3)/methylsterol monooxygenase 1 (MSMO1) pathway, was one of the potential key mechanisms by which AAT responded to the secondary immune response. In conclusion, regional immunity of chicken AT responds to secondary immunity by promoting immune activation and weakening lipid metabolism, and this study can instruct future research on antiviral strategy.
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Trezise S, Kong IY, Hawkins ED, Herold MJ, Willis SN, Nutt SL. An arrayed CRISPR screen of primary B cells reveals the essential elements of the antibody secretion pathway. Front Immunol 2023; 14:1089243. [PMID: 36860866 PMCID: PMC9969136 DOI: 10.3389/fimmu.2023.1089243] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/25/2023] [Indexed: 02/15/2023] Open
Abstract
Background Humoral immunity depends on the differentiation of B cells into antibody secreting cells (ASCs). Excess or inappropriate ASC differentiation can lead to antibody-mediated autoimmune diseases, while impaired differentiation results in immunodeficiency. Methods We have used CRISPR/Cas9 technology in primary B cells to screen for regulators of terminal differentiation and antibody production. Results We identified several new positive (Sec61a1, Hspa5) and negative (Arhgef18, Pold1, Pax5, Ets1) regulators that impacted on the differentiation process. Other genes limited the proliferative capacity of activated B cells (Sumo2, Vcp, Selk). The largest number of genes identified in this screen (35) were required for antibody secretion. These included genes involved in endoplasmic reticulum-associated degradation and the unfolded protein response, as well as post-translational protein modifications. Discussion The genes identified in this study represent weak links in the antibody-secretion pathway that are potential drug targets for antibody-mediated diseases, as well as candidates for genes whose mutation results in primary immune deficiency.
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Affiliation(s)
- Stephanie Trezise
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.,Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Harvard University, Boston, MA, United States
| | - Isabella Y Kong
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.,Department of Pediatrics, Division of Pediatric Hematology/Oncology, Weill Cornell Medicine, New York, NY, United States
| | - Edwin D Hawkins
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Marco J Herold
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Simon N Willis
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Stephen L Nutt
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
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10
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Boiarsky R, Haradhvala NJ, Alberge JB, Sklavenitis-Pistofidis R, Mouhieddine TH, Zavidij O, Shih MC, Firer D, Miller M, El-Khoury H, Anand SK, Aguet F, Sontag D, Ghobrial IM, Getz G. Single cell characterization of myeloma and its precursor conditions reveals transcriptional signatures of early tumorigenesis. Nat Commun 2022; 13:7040. [PMID: 36396631 PMCID: PMC9672303 DOI: 10.1038/s41467-022-33944-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 10/03/2022] [Indexed: 11/18/2022] Open
Abstract
Multiple myeloma is a plasma cell malignancy almost always preceded by precursor conditions, but low tumor burden of these early stages has hindered the study of their molecular programs through bulk sequencing technologies. Here, we generate and analyze single cell RNA-sequencing of plasma cells from 26 patients at varying disease stages and 9 healthy donors. In silico dissection and comparison of normal and transformed plasma cells from the same bone marrow biopsy enables discovery of patient-specific transcriptional changes. Using Non-Negative Matrix Factorization, we discover 15 gene expression signatures which represent transcriptional modules relevant to myeloma biology, and identify a signature that is uniformly lost in abnormal cells across disease stages. Finally, we demonstrate that tumors contain heterogeneous subpopulations expressing distinct transcriptional patterns. Our findings characterize transcriptomic alterations present at the earliest stages of myeloma, providing insight into the molecular underpinnings of disease initiation.
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Affiliation(s)
- Rebecca Boiarsky
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- CSAIL and IMES, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicholas J Haradhvala
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Graduate Program in Biophysics, Cambridge, MA, USA
| | - Jean-Baptiste Alberge
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Romanos Sklavenitis-Pistofidis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Tarek H Mouhieddine
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Oksana Zavidij
- Constellation Pharmaceuticals a MorphoSys Company, Cambridge, MA, USA
| | - Ming-Chieh Shih
- CSAIL and IMES, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Mendy Miller
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Habib El-Khoury
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - David Sontag
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- CSAIL and IMES, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Irene M Ghobrial
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
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11
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Mountz JD, Gao M, Ponder DM, Liu S, Sun CW, Alduraibi F, Sullivan K, Pat B, Dell'Italia LJ, Hsu HC. IL-4 receptor blockade is a global repressor of naïve B cell development and responses in a dupilumab-treated patient. Clin Immunol 2022; 244:109130. [PMID: 36189576 PMCID: PMC9741950 DOI: 10.1016/j.clim.2022.109130] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/14/2022] [Accepted: 09/14/2022] [Indexed: 12/14/2022]
Abstract
Here, we report a case of atopic dermatitis (AD) in a patient who received biweekly doses of dupilumab, an antibody against the IL-4 receptor α chain (IL-4Rα). Single cell RNA-sequencing showed that naïve B cells expressed the highest levels of IL4R compared to other B cell subpopulations. Compared to controls, the dupilumab-treated patient exhibited diminished percentages of IL4R+IGHD+ naïve B cells and down-regulation of IL4R, FCER2 (CD23), and IGHD. Dupilumab treatment resulted in upregulation of genes associated with apoptosis and inhibition of B cell receptor signaling and down-regulation of class-switch and memory B cell development genes. The dupilumab-treated patient exhibited a rapid decline in COVID-19 anti-spike and anti-receptor binding domain antibodies between 4 and 8 and 11 months post COVID-19 vaccination. Our data suggest that intact and persistent IL-4 signaling is necessary for maintaining robust survival and development of naïve B cells, and maintaining a long term vaccine response.
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Affiliation(s)
- John D Mountz
- Division of Clinical Immunology and Rheumatology, Department of Medicine, The University of Alabama at Birmingham, USA; Department of Veterans Affairs Health Care System, Birmingham, AL, USA.
| | - Min Gao
- Informatics Institute, The University of Alabama at Birmingham, USA
| | - David M Ponder
- Division of Clinical Immunology and Rheumatology, Department of Medicine, The University of Alabama at Birmingham, USA
| | - Shanrun Liu
- Division of Clinical Immunology and Rheumatology, Department of Medicine, The University of Alabama at Birmingham, USA
| | - Chiao-Wang Sun
- Division of Clinical Immunology and Rheumatology, Department of Medicine, The University of Alabama at Birmingham, USA
| | - Fatima Alduraibi
- Division of Clinical Immunology and Rheumatology, Department of Medicine, The University of Alabama at Birmingham, USA
| | - Kathryn Sullivan
- Division of Clinical Immunology and Rheumatology, Department of Medicine, The University of Alabama at Birmingham, USA
| | - Betty Pat
- Department of Veterans Affairs Health Care System, Birmingham, AL, USA; Department of Medicine, Division of Cardiovascular Disease, the University of Alabama at Birmingham, Birmingham, AL, USA
| | - Louis J Dell'Italia
- Department of Veterans Affairs Health Care System, Birmingham, AL, USA; Department of Medicine, Division of Cardiovascular Disease, the University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hui-Chen Hsu
- Division of Clinical Immunology and Rheumatology, Department of Medicine, The University of Alabama at Birmingham, USA.
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12
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Li X, Wang R, Wang S, Wang L, Yu J. Construction of a B cell-related gene pairs signature for predicting prognosis and immunotherapeutic response in non-small cell lung cancer. Front Immunol 2022; 13:989968. [PMID: 36389757 PMCID: PMC9647047 DOI: 10.3389/fimmu.2022.989968] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 10/05/2022] [Indexed: 03/30/2024] Open
Abstract
BACKGROUND Accumulating evidence indicates that the B cells play important roles in anti-tumor immunity and shaping tumor development. This study aimed to explore the expression profiles of B cell marker genes and construct a B cell-related gene pairs (BRGPs) signature associated with the prognosis and immunotherapeutic efficiency in non-small cell lung cancer (NSCLC) patients. METHODS B cell-related marker genes in NSCLC were identified using single-cell RNA sequencing data. TCGA and GEO datasets were utilized to identify the prognostic BRGPs based on a novel algorithm of cyclically single pairing along with a 0-or-1 matrix. BRGPs signature was then constructed using Lasso-Cox regression model. Its prognostic value, associated immunogenomic features, putative molecular mechanism and predictive ability to immunotherapy were investigated in NSCLC patients. RESULTS The BRGPs signature was composed of 23 BRGPs including 28 distinct B cell-related genes. This predictive signature demonstrated remarkable power in distinguishing good or poor prognosis and can serve as an independent prognostic factor for NSCLC patients in both training and validation cohorts. Furthermore, BRGPs signature was significantly associated with immune scores, tumor purity, clinicopathological characteristics and various tumor-infiltrating immune cells. Besides, we demonstrated that the tumor mutational burden scores and TIDE scores were positively correlated with the risk score of the model implying immune checkpoint blockade therapy may be more effective in NSCLC patients with high-risk scores. CONCLUSIONS This novel BRGPs signature can be used to assess the prognosis of NSCLC patients and may be useful in guiding immune checkpoint inhibitor treatment in our clinical practice.
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Affiliation(s)
- Xuanzong Li
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Ruozheng Wang
- Department of Radiation Oncology, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, China
| | - Shijiang Wang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Linlin Wang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Jinming Yu
- Department of Radiation Oncology and Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- Research Unit of Radiation Oncology, Chinese Academy of Medical Sciences, Jinan, China
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13
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Genome-wide CRISPR screen reveals CLPTM1L as a lipid scramblase required for efficient glycosylphosphatidylinositol biosynthesis. Proc Natl Acad Sci U S A 2022; 119:e2115083119. [PMID: 35344438 PMCID: PMC9169118 DOI: 10.1073/pnas.2115083119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Scramblases translocate lipids across the lipid bilayer without consumption of ATP, thereby regulating lipid distributions in cellular membranes. Cytosol-to-lumen translocation across the endoplasmic reticulum (ER) membrane is a common process among lipid glycoconjugates involved in posttranslational protein modifications in eukaryotes. These translocations are thought to be mediated by specific ER-resident scramblases, but the identity of these proteins and the underlying molecular mechanisms have been elusive. Here, we show that CLPTM1L, an integral membrane protein with eight putative transmembrane domains, is the major lipid scramblase involved in efficient glycosylphosphatidylinositol biosynthesis in the ER membrane. Our results validate the long-standing hypothesis that lipid scramblases ensure the efficient translocations of lipid glycoconjugates across the ER membrane for protein glycosylation pathways. Glycosylphosphatidylinositols (GPIs) are complex glycolipids that act as membrane anchors of many eukaryotic cell surface proteins. Biosynthesis of GPIs is initiated at the cytosolic face of the endoplasmic reticulum (ER) by generation of N-acetylglucosaminyl-phosphatidylinositol (GlcNAc-PI). The second intermediate, glucosaminyl-phosphatidylinositol (GlcN-PI), is translocated across the membrane to the luminal face for later biosynthetic steps and attachment to proteins. The mechanism of the luminal translocation of GlcN-PI is unclear. Here, we report a genome-wide CRISPR knockout screen of genes required for rescuing GPI-anchored protein expression after addition of chemically synthesized GlcNAc-PI to PIGA-knockout cells that cannot synthesize GlcNAc-PI. We identified CLPTM1L (cleft lip and palate transmembrane protein 1-like), an ER-resident multipass membrane protein, as a GlcN-PI scramblase required for efficient biosynthesis of GPIs. Knockout of CLPTM1L in PIGA-knockout cells impaired the efficient utilization of chemically synthesized GlcNAc-PI and GlcN-PI for GPI biosynthesis. Purified CLPTM1L scrambled GlcN-PI, GlcNAc-PI, PI, and several other phospholipids in vitro. CLPTM1L, a member of the PQ-loop family of proteins, represents a type of lipid scramblase having no structural similarity to known lipid scramblases. Knockout of CLPTM1L in various wild-type mammalian cultured cells partially decreased the level of GPI-anchored proteins. These results suggest that CLPTM1L is the major lipid scramblase involved in cytosol-to-lumen translocation of GlcN-PI across the ER membrane for efficient GPI biosynthesis.
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14
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Henning AN, Green D, Baumann R, Grandinetti P, Highfill SL, Zhou H, De Giorgi V. Immunomagnetic B cell isolation as a tool to study blood cell subsets and enrich B cell transcripts. BMC Res Notes 2021; 14:418. [PMID: 34794498 PMCID: PMC8600718 DOI: 10.1186/s13104-021-05833-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/03/2021] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Transcriptional profiling of immune cells is an indispensable tool in biomedical research; however, heterogenous sample types routinely used in transcriptomic studies may mask important cell type-specific transcriptional differences. Techniques to isolate desired cell types are used to overcome this limitation. We sought to evaluate the use of immunomagnetic B cell isolation on RNA quality and transcriptional output. Additionally, we aimed to develop a B cell gene signature representative of a freshly isolated B cell population to be used as a tool to verify isolation efficacy and to provide a transcriptional standard for evaluating maintenance or deviation from traditional B cell identity. RESULTS We found RNA quality and RNA-sequencing output to be comparable between donor-matched PBMC, whole blood, and B cells following negative selection by immunomagnetic B cell isolation. Transcriptional analysis enabled the development of an 85 gene B cell signature. This signature effectively clustered isolated B cells from heterogeneous sample types in our study and naïve and memory B cells when applied to transcriptional data from a published source. Additionally, by identifying B cell signature genes whose functional role in B cells is currently unknown, our gene signature has uncovered areas for future investigation.
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Affiliation(s)
- Amanda N. Henning
- Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, MD USA
| | - Daniel Green
- Women’s Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Ryan Baumann
- Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, MD USA
| | - Patrick Grandinetti
- Experimental Transplantation and Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Steven L. Highfill
- Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, MD USA
| | - Huizhi Zhou
- Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, MD USA
| | - Valeria De Giorgi
- Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, MD USA
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15
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Parashar D, Geethadevi A, McAllister D, Ebben J, Peterson FC, Jensen DR, Bishop E, Pradeep S, Volkman BF, Dwinell MB, Chaluvally-Raghavan P, James MA. Targeted biologic inhibition of both tumor cell-intrinsic and intercellular CLPTM1L/CRR9-mediated chemotherapeutic drug resistance. NPJ Precis Oncol 2021; 5:16. [PMID: 33654182 PMCID: PMC7925570 DOI: 10.1038/s41698-021-00152-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 01/06/2021] [Indexed: 02/07/2023] Open
Abstract
Recurrence of therapy-resistant tumors is a principal problem in solid tumor oncology, particularly in ovarian cancer. Despite common complete responses to first line, platinum-based therapies, most women with ovarian cancer recur, and eventually, nearly all with recurrent disease develop platinum resistance. Likewise, both intrinsic and acquired resistance contribute to the dismal prognosis of pancreatic cancer. Our previous work and that of others has established CLPTM1L (cleft lip and palate transmembrane protein 1-like)/CRR9 (cisplatin resistance related protein 9) as a cytoprotective oncofetal protein that is present on the tumor cell surface. We show that CLPTM1L is broadly overexpressed and accumulated on the plasma membrane of ovarian tumor cells, while weakly or not expressed in normal tissues. High expression of CLPTM1L is associated with poor outcome in ovarian serous adenocarcinoma. Robust re-sensitization of resistant ovarian cancer cells to platinum-based therapy was achieved using human monoclonal biologics inhibiting CLPTM1L in both orthotopic isografts and patient-derived cisplatin resistant xenograft models. Furthermore, we demonstrate that in addition to cell-autonomous cytoprotection by CLPTM1L, extracellular CLPTM1L confers resistance to chemotherapeutic killing in an ectodomain-dependent fashion, and that this intercellular resistance mechanism is inhibited by anti-CLPTM1L biologics. Specifically, exosomal CLPTM1L from cisplatin-resistant ovarian carcinoma cell lines conferred resistance to cisplatin in drug-sensitive parental cell lines. CLPTM1L is present in extracellular vesicle fractions of tumor culture supernatants and in patients' serum with increasing abundance upon chemotherapy treatment. These findings have encouraging implications for the use of anti-CLPTM1L targeted biologics in the treatment of therapy-resistant tumors.
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Affiliation(s)
- Deepak Parashar
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Anjali Geethadevi
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Donna McAllister
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Johnathan Ebben
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | | | - Davin R Jensen
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Erin Bishop
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Sunila Pradeep
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Brian F Volkman
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Michael B Dwinell
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA
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16
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Inoue K, Hatano K, Hanamatsu Y, Saigo C, Kito Y, Bunai K, Shibata T, Takeuchi T. Pathobiological role of cleft palate transmembrane protein 1 family proteins in oral squamous cell carcinoma. J Cancer Res Clin Oncol 2019; 145:851-859. [DOI: 10.1007/s00432-019-02843-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/04/2019] [Indexed: 12/13/2022]
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17
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Cell Lineage Choice during Haematopoiesis: In Honour of Professor Antonius Rolink. Int J Mol Sci 2018; 19:ijms19092798. [PMID: 30227647 PMCID: PMC6163508 DOI: 10.3390/ijms19092798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 09/12/2018] [Accepted: 09/13/2018] [Indexed: 11/29/2022] Open
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