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Kattelus R, Starskaia I, Lindén M, Batkulwar K, Pietilä S, Moulder R, Marson A, Rasool O, Suomi T, Elo LL, Lahesmaa R, Buchacher T. Phenotypic profiling of human induced regulatory T cells at early differentiation: insights into distinct immunosuppressive potential. Cell Mol Life Sci 2024; 81:399. [PMID: 39264416 PMCID: PMC11393232 DOI: 10.1007/s00018-024-05429-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 08/20/2024] [Accepted: 08/27/2024] [Indexed: 09/13/2024]
Abstract
Regulatory T cells (Tregs) play a key role in suppressing systemic effector immune responses, thereby preventing autoimmune diseases but also potentially contributing to tumor progression. Thus, there is great interest in clinically manipulating Tregs, but the precise mechanisms governing in vitro-induced Treg (iTreg) differentiation are not yet fully understood. Here, we used multiparametric mass cytometry to phenotypically profile human iTregs during the early stages of in vitro differentiation at single-cell level. A panel of 25 metal-conjugated antibodies specific to markers associated with human Tregs was used to characterize these immunomodulatory cells. We found that iTregs highly express the transcription factor FOXP3, as well as characteristic Treg-associated surface markers (e.g. CD25, PD1, CD137, CCR4, CCR7, CXCR3, and CD103). Expression of co-inhibitory factors (e.g. TIM3, LAG3, and TIGIT) increased slightly at late stages of iTreg differentiation. Further, CD103 was upregulated on a subpopulation of iTregs with greater suppressive capacity than their CD103- counterparts. Using mass-spectrometry-based proteomics, we showed that sorted CD103+ iTregs express factors associated with immunosuppression. Overall, our study highlights that during early stages of differentiation, iTregs resemble memory-like Treg features with immunosuppressive activity, and provides opportunities for further investigation into the molecular mechanisms underlying Treg function.
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Affiliation(s)
- Roosa Kattelus
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku, Finland
| | - Inna Starskaia
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku, Finland
| | - Markus Lindén
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Kedar Batkulwar
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Sami Pietilä
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Robert Moulder
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, 94158, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Omid Rasool
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Tomi Suomi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Riitta Lahesmaa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland.
- Institute of Biomedicine, University of Turku, Turku, Finland.
| | - Tanja Buchacher
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland.
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2
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Kalim UU, Biradar R, Junttila S, Khan MM, Tripathi S, Khan MH, Smolander J, Kanduri K, Envall T, Laiho A, Marson A, Rasool O, Elo LL, Lahesmaa R. A proximal enhancer regulates RORA expression during early human Th17 cell differentiation. Clin Immunol 2024; 264:110261. [PMID: 38788884 DOI: 10.1016/j.clim.2024.110261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/19/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024]
Abstract
Gene regulatory elements, such as enhancers, greatly influence cell identity by tuning the transcriptional activity of specific cell types. Dynamics of enhancer landscape during early human Th17 cell differentiation remains incompletely understood. Leveraging ATAC-seq-based profiling of chromatin accessibility and comprehensive analysis of key histone marks, we identified a repertoire of enhancers that potentially exert control over the fate specification of Th17 cells. We found 23 SNPs associated with autoimmune diseases within Th17-enhancers that precisely overlapped with the binding sites of transcription factors actively engaged in T-cell functions. Among the Th17-specific enhancers, we identified an enhancer in the intron of RORA and demonstrated that this enhancer positively regulates RORA transcription. Moreover, CRISPR-Cas9-mediated deletion of a transcription factor binding site-rich region within the identified RORA enhancer confirmed its role in regulating RORA transcription. These findings provide insights into the potential mechanism by which the RORA enhancer orchestrates Th17 differentiation.
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Affiliation(s)
- Ubaid Ullah Kalim
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland; InFLAMES Research Flagship Center, University of Turku, Turku, Finland.
| | - Rahul Biradar
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland; InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Sini Junttila
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland; InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Mohd Moin Khan
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Subhash Tripathi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Meraj Hasan Khan
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Johannes Smolander
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland; InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Kartiek Kanduri
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Tapio Envall
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Asta Laiho
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland; InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Omid Rasool
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland; InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland; InFLAMES Research Flagship Center, University of Turku, Turku, Finland; Institute of Biomedicine, University of Turku, Turku, Finland
| | - Riitta Lahesmaa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland; InFLAMES Research Flagship Center, University of Turku, Turku, Finland; Institute of Biomedicine, University of Turku, Turku, Finland.
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3
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Andrabi SBA, Kalim UU, Palani S, Khan MM, Khan MH, Fagersund J, Orpana J, Paulin N, Batkulwar K, Junttila S, Buchacher T, Grönroos T, Toikka L, Ammunet T, Sen P, Orešič M, Kumpulainen V, Tuomisto JEE, Sinha R, Marson A, Rasool O, Elo LL, Lahesmaa R. Long noncoding RNA LIRIL2R modulates FOXP3 levels and suppressive function of human CD4 + regulatory T cells by regulating IL2RA. Proc Natl Acad Sci U S A 2024; 121:e2315363121. [PMID: 38805281 PMCID: PMC11161746 DOI: 10.1073/pnas.2315363121] [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: 09/08/2023] [Accepted: 04/24/2024] [Indexed: 05/30/2024] Open
Abstract
Regulatory T cells (Tregs) are central in controlling immune responses, and dysregulation of their function can lead to autoimmune disorders or cancer. Despite extensive studies on Tregs, the basis of epigenetic regulation of human Treg development and function is incompletely understood. Long intergenic noncoding RNAs (lincRNA)s are important for shaping and maintaining the epigenetic landscape in different cell types. In this study, we identified a gene on the chromosome 6p25.3 locus, encoding a lincRNA, that was up-regulated during early differentiation of human Tregs. The lincRNA regulated the expression of interleukin-2 receptor alpha (IL2RA), and we named it the lincRNA regulator of IL2RA (LIRIL2R). Through transcriptomics, epigenomics, and proteomics analysis of LIRIL2R-deficient Tregs, coupled with global profiling of LIRIL2R binding sites using chromatin isolation by RNA purification, followed by sequencing, we identified IL2RA as a target of LIRIL2R. This nuclear lincRNA binds upstream of the IL2RA locus and regulates its epigenetic landscape and transcription. CRISPR-mediated deletion of the LIRIL2R-bound region at the IL2RA locus resulted in reduced IL2RA expression. Notably, LIRIL2R deficiency led to reduced expression of Treg-signature genes (e.g., FOXP3, CTLA4, and PDCD1), upregulation of genes associated with effector T cells (e.g., SATB1 and GATA3), and loss of Treg-mediated suppression.
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Affiliation(s)
- Syed Bilal Ahmad Andrabi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- InFLAMES – Innovation Ecosystem Based on the Immune System Flagship University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Ubaid Ullah Kalim
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- InFLAMES – Innovation Ecosystem Based on the Immune System Flagship University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Senthil Palani
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Mohd Moin Khan
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- InFLAMES – Innovation Ecosystem Based on the Immune System Flagship University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Meraj Hasan Khan
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- InFLAMES – Innovation Ecosystem Based on the Immune System Flagship University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Jimmy Fagersund
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- InFLAMES – Innovation Ecosystem Based on the Immune System Flagship University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Julius Orpana
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- InFLAMES – Innovation Ecosystem Based on the Immune System Flagship University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Niklas Paulin
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- InFLAMES – Innovation Ecosystem Based on the Immune System Flagship University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Kedar Batkulwar
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- InFLAMES – Innovation Ecosystem Based on the Immune System Flagship University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Sini Junttila
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- InFLAMES – Innovation Ecosystem Based on the Immune System Flagship University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Tanja Buchacher
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- InFLAMES – Innovation Ecosystem Based on the Immune System Flagship University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Toni Grönroos
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Lea Toikka
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Tea Ammunet
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- InFLAMES – Innovation Ecosystem Based on the Immune System Flagship University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Partho Sen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Matej Orešič
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- InFLAMES – Innovation Ecosystem Based on the Immune System Flagship University of Turku and Åbo Akademi University, 20520, Turku, Finland
- School of Medical Sciences, Örebro University, Örebro702 81, Sweden
| | - Venla Kumpulainen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Johanna E. E. Tuomisto
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA94305
| | - Alexander Marson
- Gladstone-University of California San Francisco Institute of Genomic Immunology, San Francisco, CA94158
| | - Omid Rasool
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- InFLAMES – Innovation Ecosystem Based on the Immune System Flagship University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Laura L. Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- InFLAMES – Innovation Ecosystem Based on the Immune System Flagship University of Turku and Åbo Akademi University, 20520, Turku, Finland
- Institute of Biomedicine, University of Turku, 20520Turku, Finland
| | - Riitta Lahesmaa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- InFLAMES – Innovation Ecosystem Based on the Immune System Flagship University of Turku and Åbo Akademi University, 20520, Turku, Finland
- Institute of Biomedicine, University of Turku, 20520Turku, Finland
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4
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Jiang Y, Yu Y, Pan Z, Glandorff C, Sun M. Ferroptosis: a new hunter of hepatocellular carcinoma. Cell Death Discov 2024; 10:136. [PMID: 38480712 PMCID: PMC10937674 DOI: 10.1038/s41420-024-01863-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/06/2024] [Accepted: 02/12/2024] [Indexed: 03/17/2024] Open
Abstract
Ferroptosis is an iron ion-dependent, regulatory cell death modality driven by intracellular lipid peroxidation that plays a key role in the development of HCC. Studies have shown that various clinical agents (e.g., sorafenib) have ferroptosis inducer-like effects and can exert therapeutic effects by modulating different key factors in the ferroptosis pathway. This implies that targeting tumor cell ferroptosis may be a very promising strategy for tumor therapy. In this paper, we summarize the prerequisites and defense systems for the occurrence of ferroptosis and the regulatory targets of drug-mediated ferroptosis action in HCC, the differences and connections between ferroptosis and other programmed cell deaths. We aim to summarize the theoretical basis, classical inducers of ferroptosis and research progress of ferroptosis in HCC cells, clued to the treatment of HCC by regulating ferroptosis network. Further investigation of the specific mechanisms of ferroptosis and the development of hepatocellular carcinoma and interventions at different stages of hepatocellular carcinoma will help us to deepen our understanding of hepatocellular carcinoma, with a view to providing new and more precise preventive as well as therapeutic measures for patients.
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Affiliation(s)
- Yulang Jiang
- Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Key Laboratory of Liver and Kidney Diseases, Institute of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yongxin Yu
- Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Key Laboratory of Liver and Kidney Diseases, Institute of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Ziyang Pan
- Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Key Laboratory of Liver and Kidney Diseases, Institute of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Christian Glandorff
- Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Key Laboratory of Liver and Kidney Diseases, Institute of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- University Clinic of Hamburg at the HanseMerkur Center of TCM, Hamburg, Germany
| | - Mingyu Sun
- Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
- Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
- Key Laboratory of Liver and Kidney Diseases, Institute of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
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5
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Annanya A, Priyadharshini B, Suresh V, Dilipan E. Computational Analysis of Single Nucleotide Polymorphisms in Human HIC1 Gene. Cureus 2024; 16:e56664. [PMID: 38646326 PMCID: PMC11032261 DOI: 10.7759/cureus.56664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 03/21/2024] [Indexed: 04/23/2024] Open
Abstract
Background A putative tumor suppressor gene called HIC1 (hypermethylated in cancer) is situated at 17p13.3, a locus where the allelic loss occurs often in human malignancies, including breast cancer. Hypermethylated in cancer 1 protein is a protein that in humans is encoded by the HIC1 gene and it's a Homo sapiens (Human). This gene functions as a growth regulatory and tumor repressor gene. The molecular function of HIC1 gene includes DNA-binding transcription factor activity, sequence-specific DNA binding, DNA binding, histone deacetylase binding, protein binding, metal ion binding, nucleic acid binding, DNA-binding transcription repressor activity, RNA polymerase II-specific, DNA-binding transcription factor activity, RNA polymerase II-specific. The biological process of HIC1 gene includes multicellular organism development, negative regulation of Wnt signaling pathway, positive regulation of DNA damage response, signal transduction by p53 class mediator regulation of transcription, DNA-templated, negative regulation of transcription by RNA polymerase II, Wnt signaling pathway, transcription, DNA-templated, intrinsic apoptotic signaling pathway in response to DNA damage, cellular response to DNA damage stimulus. The study aimed to predict the stability and structure of the protein that will arise from single nucleotide polymorphisms (SNPs) in the human HIC1 gene. Methodology To investigate the possible negative effects associated with these SNPs, bioinformatic analysis is typically essential. The following tools were employed for forecasting harmful SNPs: scale-invariant feature transform (SIFT), Protein Analysis Through Evolutionary Relationships (PANTHER), nonsynonymous SNP by Protein Variation Effect Analyzer (PROVEAN), and nonsynonymous SNP by Single Nucleotide Polymorphism Annotation Platform (SNAP). Results The present study identified a total of 36 SNPs using the SIFT approach, which were shown to have functional significance. Twenty-six were determined to be tolerable, whereas 10 were shown to be detrimental. Out of 20 SNPs, seven (P370A, P646S, R654P, A476T, S400S, D666N, D7V) SNPs were predicted as "Possibly damaging" and seven (L9F, G468R, G490R, L482R, S12W, G489D, S12P) were identified as "probably benign", and six (R725G, G620S, A56V, E463D, D394N, L338V) were identified as "probably damaging" according to the predictions made by PANTHER tools. The majority of the pixels on the strip were red, indicating that the gene changes may have dangerous consequences. These results highlight the need for more research to fully comprehend how these mutations affect the hic1 protein's function, which is essential for the emergence of different types of cancer. Conclusion The current research has provided us with essential information about how SNPs might be used as a diagnostic marker for cancer, given that SNPs may be candidates for cellular changes caused by mutations linked to cancer.
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Affiliation(s)
- Arora Annanya
- Physiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai, IND
| | - Boopathi Priyadharshini
- Physiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai, IND
| | - Vasugi Suresh
- Medical Physiology, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, IND
| | - Elangovan Dilipan
- Physiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai, IND
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Rade M, Böhlen S, Neuhaus V, Löffler D, Blumert C, Merz M, Köhl U, Dehmel S, Sewald K, Reiche K. A time-resolved meta-analysis of consensus gene expression profiles during human T-cell activation. Genome Biol 2023; 24:287. [PMID: 38098113 PMCID: PMC10722659 DOI: 10.1186/s13059-023-03120-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 11/22/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND The coordinated transcriptional regulation of activated T-cells is based on a complex dynamic behavior of signaling networks. Given an external stimulus, T-cell gene expression is characterized by impulse and sustained patterns over the course. Here, we analyze the temporal pattern of activation across different T-cell populations to develop consensus gene signatures for T-cell activation. RESULTS Here, we identify and verify general biomarker signatures robustly evaluating T-cell activation in a time-resolved manner. We identify time-resolved gene expression profiles comprising 521 genes of up to 10 disjunct time points during activation and different polarization conditions. The gene signatures include central transcriptional regulators of T-cell activation, representing successive waves as well as sustained patterns of induction. They cover sustained repressed, intermediate, and late response expression rates across multiple T-cell populations, thus defining consensus biomarker signatures for T-cell activation. In addition, intermediate and late response activation signatures in CAR T-cell infusion products are correlated to immune effector cell-associated neurotoxicity syndrome. CONCLUSION This study is the first to describe temporally resolved gene expression patterns across T-cell populations. These biomarker signatures are a valuable source, e.g., monitoring transcriptional changes during T-cell activation with a reasonable number of genes, annotating T-cell states in single-cell transcriptome studies, or assessing dysregulated functions of human T-cell immunity.
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Affiliation(s)
- Michael Rade
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103, Leipzig, Germany.
| | - Sebastian Böhlen
- Department of Preclinical Pharmacology and In-Vitro Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, ITEM, Nikolai-Fuchs-Strasse 1, 30625, Hannover, Germany
| | - Vanessa Neuhaus
- Department of Preclinical Pharmacology and In-Vitro Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, ITEM, Nikolai-Fuchs-Strasse 1, 30625, Hannover, Germany
| | - Dennis Löffler
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103, Leipzig, Germany
| | - Conny Blumert
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103, Leipzig, Germany
| | - Maximilian Merz
- Department of Hematology, Cellular Therapy, Hemostaseology and Infectiology, University Hospital of Leipzig, Leipzig, Germany
| | - Ulrike Köhl
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103, Leipzig, Germany
- Institute for Clinical Immunology, Leipzig University, Johannisallee 30, 04103, Leipzig, Germany
| | - Susann Dehmel
- Department of Preclinical Pharmacology and In-Vitro Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, ITEM, Nikolai-Fuchs-Strasse 1, 30625, Hannover, Germany
| | - Katherina Sewald
- Department of Preclinical Pharmacology and In-Vitro Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, ITEM, Nikolai-Fuchs-Strasse 1, 30625, Hannover, Germany
| | - Kristin Reiche
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103, Leipzig, Germany
- Institute for Clinical Immunology, Leipzig University, Johannisallee 30, 04103, Leipzig, Germany
- Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), Dresden, Leipzig, Germany
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7
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Andrabi SBA, Batkulwar K, Bhosale SD, Moulder R, Khan MH, Buchacher T, Khan MM, Arnkil I, Rasool O, Marson A, Kalim UU, Lahesmaa R. HIC1 interacts with FOXP3 multi protein complex: Novel pleiotropic mechanisms to regulate human regulatory T cell differentiation and function. Immunol Lett 2023; 263:123-132. [PMID: 37838026 DOI: 10.1016/j.imlet.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 10/16/2023]
Abstract
Transcriptional repressor, hypermethylated in cancer 1 (HIC1) participates in a range of important biological processes, such as tumor repression, immune suppression, embryonic development and epigenetic gene regulation. Further to these, we previously demonstrated that HIC1 provides a significant contribution to the function and development of regulatory T (Treg) cells. However, the mechanism by which it regulates these processes was not apparent. To address this question, we used affinity-purification mass spectrometry to characterize the HIC1 interactome in human Treg cells. Altogether 61 high-confidence interactors were identified, including IKZF3, which is a key transcription factor in the development of Treg cells. The biological processes associated with these interacting proteins include protein transport, mRNA processing, non-coding (ncRNA) transcription and RNA metabolism. The results revealed that HIC1 is part of a FOXP3-RUNX1-CBFB protein complex that regulates Treg signature genes thus improving our understanding of HIC1 function during early Treg cell differentiation.
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Affiliation(s)
- Syed Bilal Ahmad Andrabi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; InFLAMES Research Flagship Center, University of Turku
| | - Kedar Batkulwar
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; InFLAMES Research Flagship Center, University of Turku
| | - Santosh D Bhosale
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; Precision Biomarker Laboratories, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Robert Moulder
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; InFLAMES Research Flagship Center, University of Turku
| | - Meraj Hasan Khan
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; InFLAMES Research Flagship Center, University of Turku
| | - Tanja Buchacher
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; InFLAMES Research Flagship Center, University of Turku
| | - Mohd Moin Khan
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; InFLAMES Research Flagship Center, University of Turku
| | - Ilona Arnkil
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; InFLAMES Research Flagship Center, University of Turku
| | - Omid Rasool
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; InFLAMES Research Flagship Center, University of Turku
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Ubaid Ullah Kalim
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; InFLAMES Research Flagship Center, University of Turku
| | - Riitta Lahesmaa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; InFLAMES Research Flagship Center, University of Turku; Institute of Biomedicine, University of Turku.
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8
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Abstract
Cytotoxic CD8+ T cells recognize and eliminate infected or cancerous cells. A subset of CD8+ memory T cells called tissue-resident memory T cells (TRM ) resides in peripheral tissues, monitors the periphery for pathogen invasion, and offers a rapid and potent first line of defense at potential sites of re-infection. TRM cells are found in almost all tissues and are transcriptionally and epigenetically distinct from circulating memory populations, which shows their ability to acclimate to the tissue environment to allow for long-term survival. Recent work and the broader availability of single-cell profiling have highlighted TRM heterogeneity among different tissues, as well as identified specialized subsets within individual tissues, that are time and infection dependent. TRM cell phenotypic and transcriptional heterogeneity has implications for understanding TRM function and longevity. This review aims to summarize and discuss the latest findings on CD8+ TRM heterogeneity using single-cell molecular profiling and explore the potential implications for immune protection and the design of immune therapies.
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Affiliation(s)
- Maximilian Heeg
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Ananda W Goldrath
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, California, USA
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9
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Wu Y, Lin Z, Tang X, Tong Z, Ji Y, Xu Y, Zhou Z, Yang J, Li Z, Liu T. Ferroptosis-related gene HIC1 in the prediction of the prognosis and immunotherapeutic efficacy with immunological activity. Front Immunol 2023; 14:1182030. [PMID: 37388742 PMCID: PMC10300279 DOI: 10.3389/fimmu.2023.1182030] [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: 03/08/2023] [Accepted: 05/31/2023] [Indexed: 07/01/2023] Open
Abstract
Background Hypermethylated in Cancer 1 (HIC1) was originally confirmed as a tumor suppressor and has been found to be hypermethylated in human cancers. Although growing evidence has supported the critical roles of HIC1 in cancer initiation and development, its roles in tumor immune microenvironment and immunotherapy are still unclear, and no comprehensive pan-cancer analysis of HIC1 has been conducted. Methods HIC1 expression in pan-cancer, and differential HIC1 expression between tumor and normal samples were investigated. Immunohistochemistry (IHC) was employed to validate HIC1 expression in different cancers by our clinical cohorts, including lung cancer, sarcoma (SARC), breast cancer, and kidney renal clear cell carcinoma (KIRC). The prognostic value of HIC1 was illustrated by Kaplan-Meier curves and univariate Cox analysis, followed by the genetic alteration analysis of HIC1 in pan-cancer. Gene Set Enrichment Analysis (GSEA) was conducted to illustrate the signaling pathways and biological functions of HIC1. The correlations between HIC1 and tumor mutation burden (TMB), microsatellite instability (MSI), and the immunotherapy efficacy of PD-1/PD-L1 inhibitors were analyzed by Spearman correlation analysis. Drug sensitivity analysis of HIC1 was performed by extracting data from the CellMiner™ database. Results HIC1 expression was abnormally expressed in most cancers, and remarkable associations between HIC1 expression and prognostic outcomes of patients in pan-cancer were detected. HIC1 was significantly correlated with T cells, macrophages, and mast cell infiltration in different cancers. Moreover, GSEA revealed that HIC1 was significantly involved in immune-related biological functions and signaling pathways. There was a close relationship of HIC1 with TMB and MSI in different cancers. Furthermore, the most exciting finding was that HIC1 expression was significantly correlated with the response to PD-1/PD-L1 inhibitors in cancer treatment. We also found that HIC1 was significantly correlated with the sensitivity of several anti-cancer drugs, such as axitinib, batracylin, and nelarabine. Finally, our clinical cohorts further validated the expression pattern of HIC1 in cancers. Conclusions Our investigation provided an integrative understanding of the clinicopathological significance and functional roles of HIC1 in pan-cancer. Our findings suggested that HIC1 can function as a potential biomarker for predicting the prognosis, immunotherapy efficacy, and drug sensitivity with immunological activity in cancers.
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Affiliation(s)
- Yanlin Wu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhengjun Lin
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xianzhe Tang
- Department of Orthopedics, Chenzhou No.1 People’s Hospital, Chenzhou, Hunan, China
| | - Zhongyi Tong
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yuqiao Ji
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yingting Xu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ziting Zhou
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jing Yang
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhihong Li
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Tang Liu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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10
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Erber J, Herndler-Brandstetter D. Regulation of T cell differentiation and function by long noncoding RNAs in homeostasis and cancer. Front Immunol 2023; 14:1181499. [PMID: 37346034 PMCID: PMC10281531 DOI: 10.3389/fimmu.2023.1181499] [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: 03/07/2023] [Accepted: 05/02/2023] [Indexed: 06/23/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) increase in genomes of complex organisms and represent the largest group of RNA genes transcribed in mammalian cells. Previously considered only transcriptional noise, lncRNAs comprise a heterogeneous class of transcripts that are emerging as critical regulators of T cell-mediated immunity. Here we summarize the lncRNA expression landscape of different T cell subsets and highlight recent advances in the role of lncRNAs in regulating T cell differentiation, function and exhaustion during homeostasis and cancer. We discuss the different molecular mechanisms of lncRNAs and highlight lncRNAs that can serve as novel targets to modulate T cell function or to improve the response to cancer immunotherapies by modulating the immunosuppressive tumor microenvironment.
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11
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Bhokisham N, Laudermilch E, Traeger LL, Bonilla TD, Ruiz-Estevez M, Becker JR. CRISPR-Cas System: The Current and Emerging Translational Landscape. Cells 2023; 12:cells12081103. [PMID: 37190012 DOI: 10.3390/cells12081103] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023] Open
Abstract
CRISPR-Cas technology has rapidly changed life science research and human medicine. The ability to add, remove, or edit human DNA sequences has transformative potential for treating congenital and acquired human diseases. The timely maturation of the cell and gene therapy ecosystem and its seamless integration with CRISPR-Cas technologies has enabled the development of therapies that could potentially cure not only monogenic diseases such as sickle cell anemia and muscular dystrophy, but also complex heterogenous diseases such as cancer and diabetes. Here, we review the current landscape of clinical trials involving the use of various CRISPR-Cas systems as therapeutics for human diseases, discuss challenges, and explore new CRISPR-Cas-based tools such as base editing, prime editing, CRISPR-based transcriptional regulation, CRISPR-based epigenome editing, and RNA editing, each promising new functionality and broadening therapeutic potential. Finally, we discuss how the CRISPR-Cas system is being used to understand the biology of human diseases through the generation of large animal disease models used for preclinical testing of emerging therapeutics.
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Affiliation(s)
| | - Ethan Laudermilch
- Corporate Research Material Labs, 3M Center, 3M Company, Maplewood, MN 55144, USA
| | - Lindsay L Traeger
- Corporate Research Material Labs, 3M Center, 3M Company, Maplewood, MN 55144, USA
| | - Tonya D Bonilla
- Corporate Research Material Labs, 3M Center, 3M Company, Maplewood, MN 55144, USA
| | | | - Jordan R Becker
- Corporate Research Material Labs, 3M Center, 3M Company, Maplewood, MN 55144, USA
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12
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Zhang D, Ye Y, Hu X. A non-invasive piTreg-related gene signature for spontaneous tolerance in renal transplantation. Gene X 2023; 848:146901. [DOI: 10.1016/j.gene.2022.146901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/11/2022] [Accepted: 09/13/2022] [Indexed: 10/14/2022] Open
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13
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Shao Y, Saaoud F, Cornwell W, Xu K, Kirchhoff A, Lu Y, Jiang X, Wang H, Rogers TJ, Yang X. Cigarette Smoke and Morphine Promote Treg Plasticity to Th17 via Enhancing Trained Immunity. Cells 2022; 11:2810. [PMID: 36139385 PMCID: PMC9497420 DOI: 10.3390/cells11182810] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/02/2022] [Accepted: 09/04/2022] [Indexed: 11/23/2022] Open
Abstract
CD4+ regulatory T cells (Tregs) respond to environmental cues to permit or suppress inflammation, and atherosclerosis weakens Treg suppression and promotes plasticity. However, the effects of smoking plus morphine (SM + M) on Treg plasticity remain unknown. To determine whether SM + M promotes Treg plasticity to T helper 17 (Th17) cells, we analyzed the RNA sequencing data from SM, M, and SM + M treated Tregs and performed knowledge-based and IPA analysis. We demonstrated that (1) SM + M, M, and SM upregulated the transcripts of cytokines, chemokines, and clusters of differentiation (CDs) and modulated the transcripts of kinases and phosphatases in Tregs; (2) SM + M, M, and SM upregulated the transcripts of immunometabolism genes, trained immunity genes, and histone modification enzymes; (3) SM + M increased the transcripts of Th17 transcription factor (TF) RORC and Tfh factor CXCR5 in Tregs; M increased the transcripts of T helper cell 1 (Th1) TF RUNX3 and Th1-Th9 receptor CXCR3; and SM inhibited Treg TGIF1 transcript; (4) six genes upregulated in SM + M Tregs were matched with the top-ranked Th17 pathogenic genes; and 57, 39 genes upregulated in SM + M Tregs were matched with groups II and group III Th17 pathogenic genes, respectively; (5) SM + M upregulated the transcripts of 70 IPA-TFs, 11 iTregs-specific TFs, and 4 iTregs-Th17 shared TFs; and (6) SM + M, M, and SM downregulated Treg suppression TF Rel (c-Rel); and 35 SM + M downregulated genes were overlapped with Rel-/- Treg downregulated genes. These results provide novel insights on the roles of SM + M in reprogramming Treg transcriptomes and Treg plasticity to Th17 cells and novel targets for future therapeutic interventions involving immunosuppression in atherosclerotic cardiovascular diseases, autoimmune diseases, transplantation, and cancers.
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Affiliation(s)
- Ying Shao
- Department of Cardiovascular Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Fatma Saaoud
- Department of Cardiovascular Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - William Cornwell
- Center for Inflammation and Lung Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Keman Xu
- Department of Cardiovascular Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Aaron Kirchhoff
- Center for Inflammation and Lung Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Yifan Lu
- Department of Cardiovascular Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Xiaohua Jiang
- Department of Cardiovascular Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Hong Wang
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Thomas J. Rogers
- Center for Inflammation and Lung Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Xiaofeng Yang
- Department of Cardiovascular Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
- Center for Inflammation and Lung Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
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14
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Li FJ, Long HZ, Zhou ZW, Luo HY, Xu SG, Gao LC. System Xc−/GSH/GPX4 axis: An important antioxidant system for the ferroptosis in drug-resistant solid tumor therapy. Front Pharmacol 2022; 13:910292. [PMID: 36105219 PMCID: PMC9465090 DOI: 10.3389/fphar.2022.910292] [Citation(s) in RCA: 79] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
The activation of ferroptosis is a new effective way to treat drug-resistant solid tumors. Ferroptosis is an iron-mediated form of cell death caused by the accumulation of lipid peroxides. The intracellular imbalance between oxidant and antioxidant due to the abnormal expression of multiple redox active enzymes will promote the produce of reactive oxygen species (ROS). So far, a few pathways and regulators have been discovered to regulate ferroptosis. In particular, the cystine/glutamate antiporter (System Xc−), glutathione peroxidase 4 (GPX4) and glutathione (GSH) (System Xc−/GSH/GPX4 axis) plays a key role in preventing lipid peroxidation-mediated ferroptosis, because of which could be inhibited by blocking System Xc−/GSH/GPX4 axis. This review aims to present the current understanding of the mechanism of ferroptosis based on the System Xc−/GSH/GPX4 axis in the treatment of drug-resistant solid tumors.
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Affiliation(s)
- Feng-Jiao Li
- School of Pharmacy, University of South China, Phase I Clinical Trial Centre, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang, China
| | - Hui-Zhi Long
- School of Pharmacy, University of South China, Phase I Clinical Trial Centre, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang, China
| | - Zi-Wei Zhou
- School of Pharmacy, University of South China, Phase I Clinical Trial Centre, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang, China
| | - Hong-Yu Luo
- School of Pharmacy, University of South China, Phase I Clinical Trial Centre, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang, China
| | - Shuo-Guo Xu
- School of Pharmacy, University of South China, Phase I Clinical Trial Centre, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang, China
| | - Li-Chen Gao
- School of Pharmacy, University of South China, Phase I Clinical Trial Centre, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang, China
- *Correspondence: Li-Chen Gao,
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15
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Ibarra IL, Ratnu VS, Gordillo L, Hwang I, Mariani L, Weinand K, Hammarén HM, Heck J, Bulyk ML, Savitski MM, Zaugg JB, Noh K. Comparative chromatin accessibility upon BDNF stimulation delineates neuronal regulatory elements. Mol Syst Biol 2022; 18:e10473. [PMID: 35996956 PMCID: PMC9396287 DOI: 10.15252/msb.202110473] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 12/30/2022] Open
Abstract
Neuronal stimulation induced by the brain-derived neurotrophic factor (BDNF) triggers gene expression, which is crucial for neuronal survival, differentiation, synaptic plasticity, memory formation, and neurocognitive health. However, its role in chromatin regulation is unclear. Here, using temporal profiling of chromatin accessibility and transcription in mouse primary cortical neurons upon either BDNF stimulation or depolarization (KCl), we identify features that define BDNF-specific chromatin-to-gene expression programs. Enhancer activation is an early event in the regulatory control of BDNF-treated neurons, where the bZIP motif-binding Fos protein pioneered chromatin opening and cooperated with co-regulatory transcription factors (Homeobox, EGRs, and CTCF) to induce transcription. Deleting cis-regulatory sequences affect BDNF-mediated Arc expression, a regulator of synaptic plasticity. BDNF-induced accessible regions are linked to preferential exon usage by neurodevelopmental disorder-related genes and the heritability of neuronal complex traits, which were validated in human iPSC-derived neurons. Thus, we provide a comprehensive view of BDNF-mediated genome regulatory features using comparative genomic approaches to dissect mammalian neuronal stimulation.
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Affiliation(s)
- Ignacio L Ibarra
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL)HeidelbergGermany
- Faculty of BiosciencesCollaboration for Joint PhD Degree between EMBL and Heidelberg UniversityHeidelbergGermany
- Institute of Computational BiologyHelmholtz Center MunichOberschleißheimGermany
| | - Vikram S Ratnu
- Genome Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Lucia Gordillo
- Faculty of BiosciencesCollaboration for Joint PhD Degree between EMBL and Heidelberg UniversityHeidelbergGermany
- Genome Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - In‐Young Hwang
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL)HeidelbergGermany
- Genome Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Luca Mariani
- Division of Genetics, Department of MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMAUSA
| | - Kathryn Weinand
- Division of Genetics, Department of MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMAUSA
| | - Henrik M Hammarén
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL)HeidelbergGermany
- Genome Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Jennifer Heck
- Genome Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Martha L Bulyk
- Division of Genetics, Department of MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMAUSA
- Department of PathologyBrigham and Women's Hospital and Harvard Medical SchoolBostonMAUSA
| | - Mikhail M Savitski
- Genome Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Judith B Zaugg
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Kyung‐Min Noh
- Genome Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
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16
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Khan MM, Khan MH, Kalim UU, Khan S, Junttila S, Paulin N, Kong L, Rasool O, Elo LL, Lahesmaa R. Long Intergenic Noncoding RNA MIAT as a Regulator of Human Th17 Cell Differentiation. Front Immunol 2022; 13:856762. [PMID: 35784351 PMCID: PMC9242727 DOI: 10.3389/fimmu.2022.856762] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 05/10/2022] [Indexed: 11/13/2022] Open
Abstract
T helper 17 (Th17) cells protect against fungal and bacterial infections and are implicated in autoimmunity. Several long intergenic noncoding RNAs (lincRNA) are induced during Th17 differentiation, however, their contribution to Th17 differentiation is poorly understood. We aimed to characterize the function of the lincRNA Myocardial Infarction Associated Transcript (MIAT) during early human Th17 cell differentiation. We found MIAT to be upregulated early after induction of human Th17 cell differentiation along with an increase in the chromatin accessibility at the gene locus. STAT3, a key regulator of Th17 differentiation, directly bound to the MIAT promoter and induced its expression during the early stages of Th17 cell differentiation. MIAT resides in the nucleus and regulates the expression of several key Th17 genes, including IL17A, IL17F, CCR6 and CXCL13, possibly by altering the chromatin accessibility of key loci, including IL17A locus. Further, MIAT regulates the expression of protein kinase C alpha (PKCα), an upstream regulator of IL17A. A reanalysis of published single-cell RNA-seq data showed that MIAT was expressed in T cells from the synovium of RA patients. Our results demonstrate that MIAT contributes to human Th17 differentiation by upregulating several genes implicated in Th17 differentiation. High MIAT expression in T cells of RA patient synovia suggests a possible role of MIAT in Th17 mediated autoimmune pathologies.
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Affiliation(s)
- Mohd Moin Khan
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,InFLAMES Research Flagship Center , University of Turku, Turku, Finland.,Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku, Finland
| | - Meraj Hasan Khan
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,InFLAMES Research Flagship Center , University of Turku, Turku, Finland
| | - Ubaid Ullah Kalim
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,InFLAMES Research Flagship Center , University of Turku, Turku, Finland
| | - Sofia Khan
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,InFLAMES Research Flagship Center , University of Turku, Turku, Finland
| | - Sini Junttila
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,InFLAMES Research Flagship Center , University of Turku, Turku, Finland
| | - Niklas Paulin
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,InFLAMES Research Flagship Center , University of Turku, Turku, Finland
| | - Lingjia Kong
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,The Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, United States.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, United States
| | - Omid Rasool
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,InFLAMES Research Flagship Center , University of Turku, Turku, Finland
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,InFLAMES Research Flagship Center , University of Turku, Turku, Finland.,Institute of Biomedicine, University of Turku, Turku, Finland
| | - Riitta Lahesmaa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,InFLAMES Research Flagship Center , University of Turku, Turku, Finland.,Institute of Biomedicine, University of Turku, Turku, Finland
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17
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Yang JM, Ren Y, Kumar A, Xiong X, Das JK, Peng HY, Wang L, Ren X, Zhang Y, Ji C, Cheng Y, Zhang L, Alaniz RC, de Figueiredo P, Fang D, Zhou H, Liu X, Wang J, Song J. NAC1 modulates autoimmunity by suppressing regulatory T cell-mediated tolerance. SCIENCE ADVANCES 2022; 8:eabo0183. [PMID: 35767626 PMCID: PMC9242588 DOI: 10.1126/sciadv.abo0183] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/12/2022] [Indexed: 05/28/2023]
Abstract
We report here that nucleus accumbens-associated protein-1 (NAC1), a nuclear factor of the Broad-complex, Tramtrack, Bric-a-brac/poxvirus and zinc finger (BTB/POZ) gene family, is a negative regulator of FoxP3 in regulatory T cells (Tregs) and a critical determinant of immune tolerance. Phenotypically, NAC1-/- mice showed substantial tolerance to the induction of autoimmunity and generated a larger amount of CD4+ Tregs that exhibit a higher metabolic profile and immune-suppressive activity, increased acetylation and expression of FoxP3, and slower turnover of this transcription factor. Treatment of Tregs with the proinflammatory cytokines interleukin-1β or tumor necrosis factor-α induced a robust up-regulation of NAC1 but evident down-regulation of FoxP3 as well as the acetylated FoxP3. These findings imply that NAC1 acts as a trigger of the immune response through destabilization of Tregs and suppression of tolerance induction, and targeting of NAC1 warrants further exploration as a potential tolerogenic strategy for treatment of autoimmune disorders.
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Affiliation(s)
- Jin-Ming Yang
- Department of Toxicology and Cancer Biology, Department of Pharmacology and Nutritional Science, and Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Yijie Ren
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Anil Kumar
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Xiaofang Xiong
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Jugal Kishore Das
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Hao-Yun Peng
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Liqing Wang
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Xingcong Ren
- Department of Toxicology and Cancer Biology, Department of Pharmacology and Nutritional Science, and Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Yi Zhang
- Department of Toxicology and Cancer Biology, Department of Pharmacology and Nutritional Science, and Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Cheng Ji
- Department of Toxicology and Cancer Biology, Department of Pharmacology and Nutritional Science, and Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Yan Cheng
- Department of Toxicology and Cancer Biology, Department of Pharmacology and Nutritional Science, and Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Li Zhang
- Department of Toxicology and Cancer Biology, Department of Pharmacology and Nutritional Science, and Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Robert C. Alaniz
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Paul de Figueiredo
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77845, USA
- Norman Borlaug Center, Texas A&M University, College Station, TX 77845, USA
| | - Deyu Fang
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Hongwei Zhou
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xiaoqi Liu
- Department of Toxicology and Cancer Biology, Department of Pharmacology and Nutritional Science, and Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Jianlong Wang
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jianxun Song
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
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18
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Shetty A, Tripathi SK, Junttila S, Buchacher T, Biradar R, Bhosale S, Envall T, Laiho A, Moulder R, Rasool O, Galande S, Elo L, Lahesmaa R. A systematic comparison of FOSL1, FOSL2 and BATF-mediated transcriptional regulation during early human Th17 differentiation. Nucleic Acids Res 2022; 50:4938-4958. [PMID: 35511484 PMCID: PMC9122603 DOI: 10.1093/nar/gkac256] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 03/30/2022] [Accepted: 04/19/2022] [Indexed: 12/21/2022] Open
Abstract
Th17 cells are essential for protection against extracellular pathogens, but their aberrant activity can cause autoimmunity. Molecular mechanisms that dictate Th17 cell-differentiation have been extensively studied using mouse models. However, species-specific differences underscore the need to validate these findings in human. Here, we characterized the human-specific roles of three AP-1 transcription factors, FOSL1, FOSL2 and BATF, during early stages of Th17 differentiation. Our results demonstrate that FOSL1 and FOSL2 co-repress Th17 fate-specification, whereas BATF promotes the Th17 lineage. Strikingly, FOSL1 was found to play different roles in human and mouse. Genome-wide binding analysis indicated that FOSL1, FOSL2 and BATF share occupancy over regulatory regions of genes involved in Th17 lineage commitment. These AP-1 factors also share their protein interacting partners, which suggests mechanisms for their functional interplay. Our study further reveals that the genomic binding sites of FOSL1, FOSL2 and BATF harbour hundreds of autoimmune disease-linked SNPs. We show that many of these SNPs alter the ability of these transcription factors to bind DNA. Our findings thus provide critical insights into AP-1-mediated regulation of human Th17-fate and associated pathologies.
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Affiliation(s)
| | | | | | | | - Rahul Biradar
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku 20520, Finland
| | - Santosh D Bhosale
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
- Department of Biochemistry and Molecular Biology, Protein Research Group, University of Southern Denmark, Campusvej 55, Odense M, DK 5230, Denmark
| | - Tapio Envall
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Asta Laiho
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku 20520, Finland
| | - Robert Moulder
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku 20520, Finland
| | - Omid Rasool
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku 20520, Finland
| | - Sanjeev Galande
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008, India
- Department of Life Sciences, Shiv Nadar University, Delhi-NCR
| | - Laura L Elo
- Correspondence may also be addressed to Laura Elo. Tel: +358 29 450 2090;
| | - Riitta Lahesmaa
- To whom correspondence should be addressed. Tel: +358 29 450 2415;
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19
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Wang H, Cheng Q, Chang K, Bao L, Yi X. Integrated Analysis of Ferroptosis-Related Biomarker Signatures to Improve the Diagnosis and Prognosis Prediction of Ovarian Cancer. Front Cell Dev Biol 2022; 9:807862. [PMID: 35071242 PMCID: PMC8766510 DOI: 10.3389/fcell.2021.807862] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/08/2021] [Indexed: 12/24/2022] Open
Abstract
Ovarian cancer remains the most lethal gynecological malignancy. Ferroptosis, a specialized form of iron-dependent, nonapoptotic cell death, plays a crucial role in various cancers. However, the contribution of ferroptosis to ovarian cancer is poorly understood. Here, we characterized the diagnostic, prognostic, and therapeutic value of ferroptosis-related genes in ovarian cancer by analyzing transcriptomic data from The Cancer Genome Atlas and Gene Expression Omnibus databases. A reliable 10-gene ferroptosis signature (HIC1, ACSF2, MUC1, etc.) for the diagnosis of ovarian cancer was identified. Notably, we constructed and validated a novel prognostic signature including three FRGs: HIC1, LPCAT3, and DUOX1. We also further developed a risk score model based on these three genes which divided ovarian cancer patients into two risk groups. Functional analysis revealed that immune response and immune-related pathways were enriched in the high-risk group. Meanwhile, the tumor microenvironment was distinct between the two groups, with more M2 Macrophage infiltration and higher expression of key immune checkpoint molecules in the high-risk group than in the other group. Low-risk patients exhibited more favorable immunotherapy and chemotherapy responses. We conclude that crosstalk between ferroptosis and immunity may contribute to the worse prognosis of patients in the high-risk group. In particular, HIC1 showed both diagnostic and prognostic value in ovarian cancer. In vitro experiments demonstrated that inhibition of HIC1 improved drug sensitivity of chemotherapy and immunotherapy agents by inducing ferroptosis. Our findings provide new insights into the potential role of FRGs in the early detection, prognostic prediction, and individualized treatment decision-making for ovarian cancer patients.
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Affiliation(s)
- Huan Wang
- Department of Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China.,Department of Gynecology, Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, Shanghai, China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Qi Cheng
- Department of Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Kaikai Chang
- Department of Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Lingjie Bao
- Department of Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Xiaofang Yi
- Department of Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
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20
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Sen P, Andrabi SBA, Buchacher T, Khan MM, Kalim UU, Lindeman TM, Alves MA, Hinkkanen V, Kemppainen E, Dickens AM, Rasool O, Hyötyläinen T, Lahesmaa R, Orešič M. Quantitative genome-scale metabolic modeling of human CD4 + T cell differentiation reveals subset-specific regulation of glycosphingolipid pathways. Cell Rep 2021; 37:109973. [PMID: 34758307 DOI: 10.1016/j.celrep.2021.109973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/26/2021] [Accepted: 10/19/2021] [Indexed: 02/04/2023] Open
Abstract
T cell activation, proliferation, and differentiation involve metabolic reprogramming resulting from the interplay of genes, proteins, and metabolites. Here, we aim to understand the metabolic pathways involved in the activation and functional differentiation of human CD4+ T cell subsets (T helper [Th]1, Th2, Th17, and induced regulatory T [iTreg] cells). Here, we combine genome-scale metabolic modeling, gene expression data, and targeted and non-targeted lipidomics experiments, together with in vitro gene knockdown experiments, and show that human CD4+ T cells undergo specific metabolic changes during activation and functional differentiation. In addition, we confirm the importance of ceramide and glycosphingolipid biosynthesis pathways in Th17 differentiation and effector functions. Through in vitro gene knockdown experiments, we substantiate the requirement of serine palmitoyltransferase (SPT), a de novo sphingolipid pathway in the expression of proinflammatory cytokines (interleukin [IL]-17A and IL17F) by Th17 cells. Our findings provide a comprehensive resource for selective manipulation of CD4+ T cells under disease conditions characterized by an imbalance of Th17/natural Treg (nTreg) cells.
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Affiliation(s)
- Partho Sen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; School of Medical Sciences, Örebro University, 702 81 Örebro, Sweden.
| | | | - Tanja Buchacher
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Mohd Moin Khan
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Ubaid Ullah Kalim
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Tuomas Mikael Lindeman
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Marina Amaral Alves
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Victoria Hinkkanen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Esko Kemppainen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Alex M Dickens
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; Department of Chemistry, University of Turku, 20520 Turku, Finland
| | - Omid Rasool
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | | | - Riitta Lahesmaa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland.
| | - Matej Orešič
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; School of Medical Sciences, Örebro University, 702 81 Örebro, Sweden.
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21
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Cheng ZY, He TT, Gao XM, Zhao Y, Wang J. ZBTB Transcription Factors: Key Regulators of the Development, Differentiation and Effector Function of T Cells. Front Immunol 2021; 12:713294. [PMID: 34349770 PMCID: PMC8326903 DOI: 10.3389/fimmu.2021.713294] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 07/06/2021] [Indexed: 12/12/2022] Open
Abstract
The development and differentiation of T cells represents a long and highly coordinated, yet flexible at some points, pathway, along which the sequential and dynamic expressions of different transcriptional factors play prominent roles at multiple steps. The large ZBTB family comprises a diverse group of transcriptional factors, and many of them have emerged as critical factors that regulate the lineage commitment, differentiation and effector function of hematopoietic-derived cells as well as a variety of other developmental events. Within the T-cell lineage, several ZBTB proteins, including ZBTB1, ZBTB17, ZBTB7B (THPOK) and BCL6 (ZBTB27), mainly regulate the development and/or differentiation of conventional CD4/CD8 αβ+ T cells, whereas ZBTB16 (PLZF) is essential for the development and function of innate-like unconventional γδ+ T & invariant NKT cells. Given the critical role of T cells in host defenses against infections/tumors and in the pathogenesis of many inflammatory disorders, we herein summarize the roles of fourteen ZBTB family members in the development, differentiation and effector function of both conventional and unconventional T cells as well as the underlying molecular mechanisms.
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Affiliation(s)
- Zhong-Yan Cheng
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Ting-Ting He
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Xiao-Ming Gao
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Ying Zhao
- Department of Pathophysiology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Jun Wang
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
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22
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Bernshtein B, Nachshon A, Shnayder M, Stern L, Avdic S, Blyth E, Gottlieb D, Abendroth A, Slobedman B, Stern-Ginossar N, Schwartz M. Profiling the Blood Compartment of Hematopoietic Stem Cell Transplant Patients During Human Cytomegalovirus Reactivation. Front Cell Infect Microbiol 2021; 10:607470. [PMID: 33489936 PMCID: PMC7820775 DOI: 10.3389/fcimb.2020.607470] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/27/2020] [Indexed: 11/16/2022] Open
Abstract
Human cytomegalovirus (HCMV) is a widespread pathogen establishing a latent infection in its host. HCMV reactivation is a major health burden in immunocompromised individuals, and is a major cause of morbidity and mortality following hematopoietic stem cell transplantation (HSCT). Here we determined HCMV genomic levels using droplet digital PCR in different peripheral blood mononuclear cell (PBMC) populations in HCMV reactivating HSCT patients. This high sensitivity approach revealed that all PBMC populations harbored extremely low levels of viral DNA at the peak of HCMV DNAemia. Transcriptomic analysis of PBMCs from high-DNAemia samples revealed elevated expression of genes typical of HCMV specific T cells, while regulatory T cell enhancers as well as additional genes related to immune response were downregulated. Viral transcript levels in these samples were extremely low, but remarkably, the detected transcripts were mainly immediate early viral genes. Overall, our data indicate that HCMV DNAemia is associated with distinct signatures of immune response in the blood compartment, however it is not necessarily accompanied by substantial infection of PBMCs and the residual infected PBMCs are not productively infected.
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Affiliation(s)
- Biana Bernshtein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Aharon Nachshon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Miri Shnayder
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Lauren Stern
- Discipline of Infectious Diseases and Immunology, Faculty of Medicine and Health, Charles Perkins Centre, University of Sydney, Camperdown, NSW, Australia
| | - Selmir Avdic
- Sydney Cellular Therapies Laboratory, Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Emily Blyth
- Sydney Cellular Therapies Laboratory, Westmead Institute for Medical Research, Westmead, NSW, Australia.,BMT and Cell Therapies Unit, Westmead Hospital, Sydney, NSW, Australia.,Westmead Institute for Medical Research at the University of Sydney, Westmead, NSW, Australia.,Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, Australia
| | - David Gottlieb
- BMT and Cell Therapies Unit, Westmead Hospital, Sydney, NSW, Australia.,Westmead Institute for Medical Research at the University of Sydney, Westmead, NSW, Australia.,Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, Australia
| | - Allison Abendroth
- Discipline of Infectious Diseases and Immunology, Faculty of Medicine and Health, Charles Perkins Centre, University of Sydney, Camperdown, NSW, Australia
| | - Barry Slobedman
- Discipline of Infectious Diseases and Immunology, Faculty of Medicine and Health, Charles Perkins Centre, University of Sydney, Camperdown, NSW, Australia
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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23
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Andersen L, Gülich AF, Alteneder M, Preglej T, Orola MJ, Dhele N, Stolz V, Schebesta A, Hamminger P, Hladik A, Floess S, Krausgruber T, Faux T, Andrabi SBA, Huehn J, Knapp S, Sparwasser T, Bock C, Laiho A, Elo LL, Rasool O, Lahesmaa R, Sakaguchi S, Ellmeier W. The Transcription Factor MAZR/PATZ1 Regulates the Development of FOXP3 + Regulatory T Cells. Cell Rep 2020; 29:4447-4459.e6. [PMID: 31875552 DOI: 10.1016/j.celrep.2019.11.089] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 10/24/2019] [Accepted: 11/21/2019] [Indexed: 01/22/2023] Open
Abstract
Forkhead box protein P3+ (FOXP3+) regulatory T cells (Treg cells) play a key role in maintaining tolerance and immune homeostasis. Here, we report that a T cell-specific deletion of the transcription factor MAZR (also known as PATZ1) leads to an increased frequency of Treg cells, while enforced MAZR expression impairs Treg cell differentiation. Further, MAZR expression levels are progressively downregulated during thymic Treg cell development and during in-vitro-induced human Treg cell differentiation, suggesting that MAZR protein levels are critical for controlling Treg cell development. However, MAZR-deficient Treg cells show only minor transcriptional changes ex vivo, indicating that MAZR is not essential for establishing the transcriptional program of peripheral Treg cells. Finally, the loss of MAZR reduces the clinical score in dextran-sodium sulfate (DSS)-induced colitis, suggesting that MAZR activity in T cells controls the extent of intestinal inflammation. Together, these data indicate that MAZR is part of a Treg cell-intrinsic transcriptional network that modulates Treg cell development.
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Affiliation(s)
- Liisa Andersen
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Alexandra Franziska Gülich
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Marlis Alteneder
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Teresa Preglej
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Maria Jonah Orola
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Narendra Dhele
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Valentina Stolz
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Alexandra Schebesta
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Patricia Hamminger
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Anastasiya Hladik
- Laboratory of Infection Biology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Stefan Floess
- Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Thomas Krausgruber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Thomas Faux
- Medical Bioinformatics Centre, Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Syed Bilal Ahmad Andrabi
- Molecular Systems Immunology, Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Jochen Huehn
- Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sylvia Knapp
- Laboratory of Infection Biology, Department of Medicine I, Medical University of Vienna, Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tim Sparwasser
- Department of Medical Microbiology and Hygiene, Medical Center of the Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Asta Laiho
- Medical Bioinformatics Centre, Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Laura L Elo
- Medical Bioinformatics Centre, Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Omid Rasool
- Molecular Systems Immunology, Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Riitta Lahesmaa
- Molecular Systems Immunology, Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Shinya Sakaguchi
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Wilfried Ellmeier
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria.
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24
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Ray H, Chang C. The transcription factor Hypermethylated in Cancer 1 (Hic1) regulates neural crest migration via interaction with Wnt signaling. Dev Biol 2020; 463:169-181. [PMID: 32502469 DOI: 10.1016/j.ydbio.2020.05.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 05/20/2020] [Accepted: 05/20/2020] [Indexed: 01/20/2023]
Abstract
The transcription factor Hypermethylated in Cancer 1 (HIC1) is associated with both tumorigenesis and the complex human developmental disorder Miller-Dieker Syndrome. While many studies have characterized HIC1 as a tumor suppressor, HIC1 function in development is less understood. Loss-of-function mouse alleles show embryonic lethality accompanied with developmental defects, including craniofacial abnormalities that are reminiscent of human Miller-Dieker Syndrome patients. However, the tissue origin of the defects has not been reported. In this study, we use the power of the Xenopus laevis model system to explore Hic1 function in early development. We show that hic1 mRNA is expressed throughout early Xenopus development and has a spatial distribution within the neural plate border and in migrating neural crest cells in branchial arches. Targeted manipulation of hic1 levels in the dorsal ectoderm that gives rise to neural and neural crest tissues reveals that both overexpression and knockdown of hic1 result in craniofacial defects with malformations of the craniofacial cartilages. Neural crest specification is not affected by altered hic1 levels, but migration of the cranial neural crest is impaired both in vivo and in tissue explants. Mechanistically, we find that Hic1 regulates cadherin expression profiles and canonical Wnt signaling. Taken together, these results identify Hic1 as a novel regulator of the canonical Wnt pathway during neural crest migration.
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Affiliation(s)
- Heather Ray
- Dept. of Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, MCLM 338, 1918 University Dr. Birmingham, AL, 35294, USA.
| | - Chenbei Chang
- Dept. of Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, MCLM 338, 1918 University Dr. Birmingham, AL, 35294, USA
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25
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Single-cell transcriptomics identifies an effectorness gradient shaping the response of CD4 + T cells to cytokines. Nat Commun 2020; 11:1801. [PMID: 32286271 PMCID: PMC7156481 DOI: 10.1038/s41467-020-15543-y] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/18/2020] [Indexed: 12/14/2022] Open
Abstract
Naïve CD4+ T cells coordinate the immune response by acquiring an effector phenotype in response to cytokines. However, the cytokine responses in memory T cells remain largely understudied. Here we use quantitative proteomics, bulk RNA-seq, and single-cell RNA-seq of over 40,000 human naïve and memory CD4+ T cells to show that responses to cytokines differ substantially between these cell types. Memory T cells are unable to differentiate into the Th2 phenotype, and acquire a Th17-like phenotype in response to iTreg polarization. Single-cell analyses show that T cells constitute a transcriptional continuum that progresses from naïve to central and effector memory T cells, forming an effectorness gradient accompanied by an increase in the expression of chemokines and cytokines. Finally, we show that T cell activation and cytokine responses are influenced by the effectorness gradient. Our results illustrate the heterogeneity of T cell responses, furthering our understanding of inflammation. Cytokines critically control the differentiation and functions of activated naïve and memory T cells. Here the authors show, using multi-omics and single-cell analyses, that naïve and memory T cells exhibit distinct cytokine responses, in which an ‘effectorness gradient’ is depicted by a transcriptional continuum, which shapes the downstream genetic programs.
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26
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Khan MM, Ullah U, Khan MH, Kong L, Moulder R, Välikangas T, Bhosale SD, Komsi E, Rasool O, Chen Z, Elo LL, Westermarck J, Lahesmaa R. CIP2A Constrains Th17 Differentiation by Modulating STAT3 Signaling. iScience 2020; 23:100947. [PMID: 32171124 PMCID: PMC7068643 DOI: 10.1016/j.isci.2020.100947] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/10/2020] [Accepted: 02/21/2020] [Indexed: 02/06/2023] Open
Abstract
Cancerous Inhibitor of Protein Phosphatase 2A (CIP2A) is an oncogene and a potential cancer therapy target protein. Accordingly, a better understanding of the physiological function of CIP2A, especially in the context of immune cells, is a prerequisite for its exploitation in cancer therapy. Here, we report that CIP2A negatively regulates interleukin (IL)-17 production by Th17 cells in human and mouse. Interestingly, concomitant with increased IL-17 production, CIP2A-deficient Th17 cells had increased strength and duration of STAT3 phosphorylation. We analyzed the interactome of phosphorylated STAT3 in CIP2A-deficient and CIP2A-sufficient Th17 cells and indicated together with genome-wide gene expression profiling, a role of Acylglycerol Kinase (AGK) in the regulation of Th17 differentiation by CIP2A. We demonstrated that CIP2A regulates the strength of the interaction between AGK and STAT3, and thereby modulates STAT3 phosphorylation and expression of IL-17 in Th17 cells.
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Affiliation(s)
- Mohd Moin Khan
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6A, Turku, Finland; Turku Doctoral Programme of Molecular Medicine (TuDMM), University of Turku, Turku, Finland
| | - Ubaid Ullah
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6A, Turku, Finland
| | - Meraj H Khan
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6A, Turku, Finland
| | - Lingjia Kong
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6A, Turku, Finland; The Broad Institute of MIT and Harvard, Cambridge, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, USA
| | - Robert Moulder
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6A, Turku, Finland
| | - Tommi Välikangas
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6A, Turku, Finland; Doctoral Programme in Mathematics and Computer Sciences (MATTI), University of Turku, Turku, Finland
| | - Santosh Dilip Bhosale
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6A, Turku, Finland
| | - Elina Komsi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6A, Turku, Finland
| | - Omid Rasool
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6A, Turku, Finland
| | - Zhi Chen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6A, Turku, Finland; Faculty of Biochemistry and Molecular Medicine, University of Oulu
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6A, Turku, Finland
| | - Jukka Westermarck
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6A, Turku, Finland; Institute of Biomedicine, University of Turku, Turku, Finland
| | - Riitta Lahesmaa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6A, Turku, Finland.
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Hudson WH, Gensheimer J, Hashimoto M, Wieland A, Valanparambil RM, Li P, Lin JX, Konieczny BT, Im SJ, Freeman GJ, Leonard WJ, Kissick HT, Ahmed R. Proliferating Transitory T Cells with an Effector-like Transcriptional Signature Emerge from PD-1 + Stem-like CD8 + T Cells during Chronic Infection. Immunity 2019; 51:1043-1058.e4. [PMID: 31810882 PMCID: PMC6920571 DOI: 10.1016/j.immuni.2019.11.002] [Citation(s) in RCA: 351] [Impact Index Per Article: 70.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 08/06/2019] [Accepted: 11/01/2019] [Indexed: 01/01/2023]
Abstract
T cell dysfunction is a characteristic feature of chronic viral infection and cancer. Recent studies in chronic lymphocytic choriomeningitis virus (LCMV) infection have defined a PD-1+ Tcf-1+ CD8+ T cell subset capable of self-renewal and differentiation into more terminally differentiated cells that downregulate Tcf-1 and express additional inhibitory molecules such as Tim3. Here, we demonstrated that expression of the glycoprotein CD101 divides this terminally differentiated population into two subsets. Stem-like Tcf-1+ CD8+ T cells initially differentiated into a transitory population of CD101-Tim3+ cells that later converted into CD101+ Tim3+ cells. Recently generated CD101-Tim3+ cells proliferated in vivo, contributed to viral control, and were marked by an effector-like transcriptional signature including expression of the chemokine receptor CX3CR1, pro-inflammatory cytokines, and granzyme B. PD-1 pathway blockade increased the numbers of CD101-Tim3+ CD8+ T cells, suggesting that these newly generated transitional cells play a critical role in PD-1-based immunotherapy.
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Affiliation(s)
- William H Hudson
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30033, USA
| | - Julia Gensheimer
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30033, USA
| | - Masao Hashimoto
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30033, USA
| | - Andreas Wieland
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30033, USA
| | - Rajesh M Valanparambil
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30033, USA
| | - Peng Li
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1674, USA
| | - Jian-Xin Lin
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1674, USA
| | - Bogumila T Konieczny
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30033, USA
| | - Se Jin Im
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30033, USA
| | - Gordon J Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Warren J Leonard
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1674, USA
| | - Haydn T Kissick
- Department of Urology, Emory University School of Medicine, Atlanta, GA 30033, USA
| | - Rafi Ahmed
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30033, USA.
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Wu Y, Chang YM, Stell AJ, Priestnall SL, Sharma E, Goulart MR, Gribben J, Xia D, Garden OA. Phenotypic characterisation of regulatory T cells in dogs reveals signature transcripts conserved in humans and mice. Sci Rep 2019; 9:13478. [PMID: 31530890 PMCID: PMC6748983 DOI: 10.1038/s41598-019-50065-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/05/2019] [Indexed: 12/12/2022] Open
Abstract
Regulatory T cells (Tregs) are a double-edged regulator of the immune system. Aberrations of Tregs correlate with pathogenesis of inflammatory, autoimmune and neoplastic disorders. Phenotypically and functionally distinct subsets of Tregs have been identified in humans and mice on the basis of their extensive portfolios of monoclonal antibodies (mAb) against Treg surface antigens. As an important veterinary species, dogs are increasingly recognised as an excellent model for many human diseases. However, insightful study of canine Tregs has been restrained by the limited availability of mAb. We therefore set out to characterise CD4+CD25high T cells isolated ex vivo from healthy dogs and showed that they possess a regulatory phenotype, function, and transcriptomic signature that resembles those of human and murine Tregs. By launching a cross-species comparison, we unveiled a conserved transcriptomic signature of Tregs and identified that transcript hip1 may have implications in Treg function.
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Affiliation(s)
- Ying Wu
- Royal Veterinary College, London, UK
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | - Eshita Sharma
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Michelle R Goulart
- Royal Veterinary College, London, UK
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - John Gribben
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Dong Xia
- Royal Veterinary College, London, UK
| | - Oliver A Garden
- Royal Veterinary College, London, UK.
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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29
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CRISPR/Cas9 guided genome and epigenome engineering and its therapeutic applications in immune mediated diseases. Semin Cell Dev Biol 2019; 96:32-43. [PMID: 31112800 DOI: 10.1016/j.semcdb.2019.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 12/21/2022]
Abstract
Recent developments in the nucleic acid editing technologies have provided a powerful tool to precisely engineer the genome and epigenome for studying many aspects of immune cell differentiation and development as well as several immune mediated diseases (IMDs) including autoimmunity and cancer. Here, we discuss the recent technological achievements of the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-based RNA-guided genome and epigenome editing toolkit and provide an insight into how CRISPR/Cas9 (CRISPR Associated Protein 9) toolbox could be used to examine genetic and epigenetic mechanisms underlying IMDs. In addition, we will review the progress in CRISPR/Cas9-based genome-wide genome and epigenome screens in various cell types including immune cells. Finally, we will discuss the potential of CRISPR/Cas9 in defining the molecular function of disease associated SNPs overlapping gene regulatory elements.
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30
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Zhang X, Du L, Qiao Y, Zhang X, Zheng W, Wu Q, Chen Y, Zhu G, Liu Y, Bian Z, Guo S, Yang Y, Ma L, Yu Y, Pan Q, Sun F, Wang J. Ferroptosis is governed by differential regulation of transcription in liver cancer. Redox Biol 2019; 24:101211. [PMID: 31108460 PMCID: PMC6526247 DOI: 10.1016/j.redox.2019.101211] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 04/22/2019] [Accepted: 04/28/2019] [Indexed: 12/20/2022] Open
Abstract
Ferroptosis is an outcome of metabolic disorders and closely linked to liver cancer. However, the mechanism underlying the fine regulation of ferroptosis in liver cancer remains unclear. Here, we have identified two categories of genes: ferroptosis up-regulated factors (FUF) and ferroptosis down-regulated factors (FDF), which stimulate and suppress ferroptosis by affecting the synthesis of GSH. Furthermore, FUF are controlled by one transcription factor HIC1, while FDF controlled by another transcription factor HNF4A. Occurrence of ferroptosis might depend on the histone acetyltransferase KAT2B. Upon stimulation of ferroptosis, dissociation of KAT2B prevents HNF4A from binding to the FDF promoter. This effect happens prior to the recruitment of KAT2B to the FUF promoter, which facilitates HIC1 binding to transcribe FUF. Clinically, HIC1 and HNF4A conversely correlate with tumor stage in liver cancer. Patients with lower HIC1 and higher HNF4A exhibit poorer prognostic outcomes. Disrupting the balance between HIC1 and HNF4A might be helpful in treating liver cancer. Opposite gene expression profiles trigged by ferroptosis are identified. Reduction of GSH is the major cause of inducing ferroptosis in liver cancer cells. Genes related to ferroptosis are controlled by transcription factors HIC1 and HNF4A. Stimulation of ferroptosis breaks the balance between HIC1 and HNF4A. Lower HIC1 with higher HNF4A has poorer clinical outcomes in liver cancer patients.
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Affiliation(s)
- Xiao Zhang
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China
| | - Lutao Du
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, 250033, Shandong province, China
| | - Yongxia Qiao
- School of Public Health, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Xiaobai Zhang
- School of Life Science and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai, 200092, China
| | - Weisheng Zheng
- School of Life Science and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai, 200092, China
| | - Qi Wu
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China
| | - Yan Chen
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China
| | - Guoqing Zhu
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China
| | - Ya Liu
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China
| | - Zhixuan Bian
- Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China
| | - Susu Guo
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China
| | - Yueyue Yang
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China
| | - Lifang Ma
- Shanghai Institute of Thoracic Tumors, Shanghai Chest Hospital, Shanghai, 200030, China
| | - Yongchun Yu
- Shanghai Chest Hospital, Shanghai, 200030, China
| | - Qiuhui Pan
- Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China.
| | - Fenyong Sun
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China.
| | - Jiayi Wang
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China; Advanced Institute of Translational Medicine, Tongji University, Shanghai, 200092, China.
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31
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Hoeppli RE, MacDonald KN, Leclair P, Fung VCW, Mojibian M, Gillies J, Rahavi SMR, Campbell AIM, Gandhi SK, Pesenacker AM, Reid G, Lim CJ, Levings MK. Tailoring the homing capacity of human Tregs for directed migration to sites of Th1-inflammation or intestinal regions. Am J Transplant 2019; 19:62-76. [PMID: 29766641 DOI: 10.1111/ajt.14936] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 04/17/2018] [Accepted: 05/06/2018] [Indexed: 01/25/2023]
Abstract
Cell-based therapy with CD4+ FOXP3+ regulatory T cells (Tregs) is a promising strategy to limit organ rejection and graft-vs-host disease. Ongoing clinical applications have yet to consider how human Tregs could be modified to direct their migration to specific inflammation sites and/or tissues for more targeted immunosuppression. We show here that stable, homing-receptor-tailored human Tregs can be generated from thymic Tregs isolated from pediatric thymus or adult blood. To direct migration to Th1-inflammatory sites, addition of interferon-γ and IL-12 during Treg expansion produced suppressive, epigenetically stable CXCR3+ TBET+ FOXP3+ T helper (Th)1-Tregs. CXCR3 remained expressed after injection in vivo and Th1-Tregs migrated efficiently towards CXCL10 in vitro. To induce tissue-specific migration, addition of retinoic acid (RA) during Treg expansion induced expression of the gut-homing receptors α4β7-integrin and CCR9. FOXP3+ RA-Tregs had elevated expression of the functional markers latency-associated peptide and glycoprotein A repetitions predominant, increased suppressive capacity in vitro and migrated efficiently to healthy and inflamed intestine after injection into mice. Homing-receptor-tailored Tregs were epigenetically stable even after long-term exposure to inflammatory conditions, suppressive in vivo and characterized by Th1- or gut-homing-specific transcriptomes. Tailoring human thymic Treg homing during in vitro expansion offers a new and clinically applicable approach to improving the potency and specificity of Treg therapy.
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Affiliation(s)
- R E Hoeppli
- Department of Surgery, University of British Columbia & British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - K N MacDonald
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - P Leclair
- Department of Pediatrics, University of British Columbia & British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - V C W Fung
- Department of Surgery, University of British Columbia & British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - M Mojibian
- Department of Surgery, University of British Columbia & British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - J Gillies
- Department of Surgery, University of British Columbia & British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - S M R Rahavi
- Department of Pediatrics, University of British Columbia & British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - A I M Campbell
- Department of Surgery, University of British Columbia & British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - S K Gandhi
- Department of Surgery, University of British Columbia & British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - A M Pesenacker
- Department of Surgery, University of British Columbia & British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - G Reid
- Department of Pediatrics, University of British Columbia & British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - C J Lim
- Department of Pediatrics, University of British Columbia & British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - M K Levings
- Department of Surgery, University of British Columbia & British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada.,School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
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Nousiainen K, Kanduri K, Ricaño-Ponce I, Wijmenga C, Lahesmaa R, Kumar V, Lähdesmäki H. snpEnrichR: analyzing co-localization of SNPs and their proxies in genomic regions. Bioinformatics 2018; 34:4112-4114. [PMID: 29878048 PMCID: PMC6247941 DOI: 10.1093/bioinformatics/bty460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/05/2018] [Indexed: 12/02/2022] Open
Abstract
Motivation Co-localization of trait associated SNPs for specific transcription-factor binding sites or regulatory regions in the genome can yield profound insight into underlying causal mechanisms. Analysis is complicated because the truly causal SNPs are generally unknown and can be either SNPs reported in GWAS studies or other proxy SNPs in their linkage disequilibrium. Hence, a comprehensive pipeline for SNP co-localization analysis that utilizes all relevant information about both the genotyped SNPs and their proxies is needed. Results We developed an R package snpEnrichR for SNP co-localization analysis. The software integrates different tools for random SNP generation and genome co-localization analysis to automatize and help users to create custom SNP co-localization analysis. We show via an example that including proxy SNPs in SNP co-localization analysis enhances the sensitivity of co-localization detection. Availability and implementation The software is available at https://github.com/kartiek/snpEnrichR.
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Affiliation(s)
- Kari Nousiainen
- Department of Computer Science, Aalto University School of Science, FI-00076 Aalto, Finland
- To whom correspondence should be addressed. E-mail: or
| | - Kartiek Kanduri
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
- To whom correspondence should be addressed. E-mail: or
| | - Isis Ricaño-Ponce
- Department of Genetics, UMCG, University of Groningen, AB Groningen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, UMCG, University of Groningen, AB Groningen, the Netherlands
- Department of Immunology, K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Vinod Kumar
- Department of Genetics, UMCG, University of Groningen, AB Groningen, the Netherlands
- Department of Internal Medicine, Radboud University Medical Center, GA Nijmegen, the Netherlands
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University School of Science, FI-00076 Aalto, Finland
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
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Yang J, Wu C, Yu Y, Mao H, Bao Y, Kang Y, Qi Z. A mongolian pine specific endoplasmic reticulum localized CALMODULIN-LIKE calcium binding protein enhances arabidopsis growth. JOURNAL OF PLANT PHYSIOLOGY 2018; 226:1-11. [PMID: 29689429 DOI: 10.1016/j.jplph.2018.04.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 04/07/2018] [Accepted: 04/10/2018] [Indexed: 06/08/2023]
Abstract
Stress-adapted wild plants are natural sources of novel genes for molecular breeding. Here, we conducted a transcriptional analysis of Pinus sylvestris var. mongolica Litv, an evergreen pine in northeastern China, to identify a novel CALMODULIN-LIKE protein-encoding gene, PsCML1, no significant homologs found in other plant species. PsCML1 encodes a protein predicted to have a single trans-membrane domain at its N-terminal. Four EF-hand motifs (calcium [Ca]-binding structures) are located at its C-terminal and showed Ca2+-specific affinity in isothermal titration calorimetric analysis. Transient expression of PsCML1 in Nicotiana benthamiana showed that the PsCML1 localizes to the endoplasmic reticulum (ER). Heterologous expression of PsCML1 in Arabidopsis significantly promoted seedling growth, and increased resistance to stress from NaCl and Ca2+ deficiency. The roots of the transgenic seedlings had higher contents of cellulose and pectin, but less hemicellulose than those of the wild type (WT). The biosynthesis of cell wall components is linked with protein glycosylation in the ER and reactive oxygen species (ROS) homeostasis. No significant difference was found in the extent of protein glycosylation between the transgenic and WT plants. However, the transgenic roots had higher steady-state levels of ROS, NADPH oxidase activity, and endo-membrane dynamics than those of the WT. A working model was proposed to delineate the interaction among Ca2+, ROS homeostasis, and cell wall loosening-dependent cell division.
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Affiliation(s)
- Jia Yang
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010021, PR China; Inner Mongolia HeSheng Institute of Ecological Sciences & Technology, Hohhot, 011517, PR China
| | - Caili Wu
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010021, PR China
| | - Yahui Yu
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010021, PR China
| | - Huiping Mao
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010021, PR China
| | - Yuying Bao
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010021, PR China.
| | - Yan Kang
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010021, PR China.
| | - Zhi Qi
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010021, PR China.
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Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3. BMC Biol 2018; 16:47. [PMID: 29730990 PMCID: PMC5937035 DOI: 10.1186/s12915-018-0518-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 04/10/2018] [Indexed: 02/08/2023] Open
Abstract
Background Regulatory T cells (Tregs) expressing the transcription factor FOXP3 are crucial mediators of self-tolerance, preventing autoimmune diseases but possibly hampering tumor rejection. Clinical manipulation of Tregs is of great interest, and first-in-man trials of Treg transfer have achieved promising outcomes. Yet, the mechanisms governing induced Treg (iTreg) differentiation and the regulation of FOXP3 are incompletely understood. Results To gain a comprehensive and unbiased molecular understanding of FOXP3 induction, we performed time-series RNA sequencing (RNA-Seq) and proteomics profiling on the same samples during human iTreg differentiation. To enable the broad analysis of universal FOXP3-inducing pathways, we used five differentiation protocols in parallel. Integrative analysis of the transcriptome and proteome confirmed involvement of specific molecular processes, as well as overlap of a novel iTreg subnetwork with known Treg regulators and autoimmunity-associated genes. Importantly, we propose 37 novel molecules putatively involved in iTreg differentiation. Their relevance was validated by a targeted shRNA screen confirming a functional role in FOXP3 induction, discriminant analyses classifying iTregs accordingly, and comparable expression in an independent novel iTreg RNA-Seq dataset. Conclusion The data generated by this novel approach facilitates understanding of the molecular mechanisms underlying iTreg generation as well as of the concomitant changes in the transcriptome and proteome. Our results provide a reference map exploitable for future discovery of markers and drug candidates governing control of Tregs, which has important implications for the treatment of cancer, autoimmune, and inflammatory diseases. Electronic supplementary material The online version of this article (10.1186/s12915-018-0518-3) contains supplementary material, which is available to authorized users.
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