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Book ; Online ; Thesis: Biomarker discovery and confirmation using statistical and machine learning approaches in transcriptomics

Rade, Michael [Verfasser]

2024

Author's details	Michael Rade
Keywords	Medizin, Gesundheit ; Medicine, Health
Subject code	sg610
Language	English
Publisher	Universitätsbibliothek Leipzig
Publishing place	Leipzig
Document type	Book ; Online ; Thesis
Database	Digital theses on the web

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Article ; Online: A time-resolved meta-analysis of consensus gene expression profiles during human T-cell activation.

Rade, Michael / Böhlen, Sebastian / Neuhaus, Vanessa / Löffler, Dennis / Blumert, Conny / Merz, Maximilian / Köhl, Ulrike / Dehmel, Susann / Sewald, Katherina / Reiche, Kristin

Genome biology

2023 Volume 24, Issue 1, Page(s) 287

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 ... ...

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.
MeSH term(s)	Humans ; Transcriptome ; Gene Expression Profiling ; Consensus ; Gene Expression Regulation ; Biomarkers
Chemical Substances	Biomarkers
Language	English
Publishing date	2023-12-14
Publishing country	England
Document type	Meta-Analysis ; Journal Article
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-023-03120-7
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Transcriptional states of CAR-T infusion relate to neurotoxicity - lessons from high-resolution single-cell SOM expression portraying.

Loeffler-Wirth, Henry / Rade, Michael / Arakelyan, Arsen / Kreuz, Markus / Loeffler, Markus / Koehl, Ulrike / Reiche, Kristin / Binder, Hans

Frontiers in immunology

2022 Volume 13, Page(s) 994885

Abstract: Anti-CD19 CAR-T cell immunotherapy is a hopeful treatment option for patients with B cell lymphomas, however it copes with partly severe adverse effects like neurotoxicity. Single-cell resolved molecular data sets in combination with clinical ... ...

Abstract	Anti-CD19 CAR-T cell immunotherapy is a hopeful treatment option for patients with B cell lymphomas, however it copes with partly severe adverse effects like neurotoxicity. Single-cell resolved molecular data sets in combination with clinical parametrization allow for comprehensive characterization of cellular subpopulations, their transcriptomic states, and their relation to the adverse effects. We here present a re-analysis of single-cell RNA sequencing data of 24 patients comprising more than 130,000 cells with focus on cellular states and their association to immune cell related neurotoxicity. For this, we developed a single-cell data portraying workflow to disentangle the transcriptional state space with single-cell resolution and its analysis in terms of modularly-composed cellular programs. We demonstrated capabilities of single-cell data portraying to disentangle transcriptional states using intuitive visualization, functional mining, molecular cell stratification, and variability analyses. Our analysis revealed that the T cell composition of the patient's infusion product as well as the spectrum of their transcriptional states of cells derived from patients with low ICANS grade do not markedly differ from those of cells from high ICANS patients, while the relative abundancies, particularly that of cycling cells, of LAG3-mediated exhaustion and of CAR positive cells, vary. Our study provides molecular details of the transcriptomic landscape with possible impact to overcome neurotoxicity.
MeSH term(s)	Antigens, CD19 ; Humans ; Immunotherapy, Adoptive/adverse effects ; Neurotoxicity Syndromes/genetics ; Receptors, Chimeric Antigen/genetics ; T-Lymphocytes
Chemical Substances	Antigens, CD19 ; Receptors, Chimeric Antigen
Language	English
Publishing date	2022-09-28
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2022.994885
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A reliable transcriptomic risk-score applicable to formalin-fixed paraffin-embedded biopsies improves outcome prediction in localized prostate cancer.

Rade, Michael / Kreuz, Markus / Borkowetz, Angelika / Sommer, Ulrich / Blumert, Conny / Füssel, Susanne / Bertram, Catharina / Löffler, Dennis / Otto, Dominik J / Wöller, Livia A / Schimmelpfennig, Carolin / Köhl, Ulrike / Gottschling, Ann-Cathrin / Hönscheid, Pia / Baretton, Gustavo B / Wirth, Manfred / Thomas, Christian / Horn, Friedemann / Reiche, Kristin

Molecular medicine (Cambridge, Mass.)

2024 Volume 30, Issue 1, Page(s) 19

Abstract: Background: Clinical manifestation of prostate cancer (PCa) is highly variable. Aggressive tumors require radical treatment while clinically non-significant ones may be suitable for active surveillance. We previously developed the prognostic ProstaTrend ...

Abstract	Background: Clinical manifestation of prostate cancer (PCa) is highly variable. Aggressive tumors require radical treatment while clinically non-significant ones may be suitable for active surveillance. We previously developed the prognostic ProstaTrend RNA signature based on transcriptome-wide microarray and RNA-sequencing (RNA-Seq) analyses, primarily of prostatectomy specimens. An RNA-Seq study of formalin-fixed paraffin-embedded (FFPE) tumor biopsies has now allowed us to use this test as a basis for the development of a novel test that is applicable to FFPE biopsies as a tool for early routine PCa diagnostics. Methods: All patients of the FFPE biopsy cohort were treated by radical prostatectomy and median follow-up for biochemical recurrence (BCR) was 9 years. Based on the transcriptome data of 176 FFPE biopsies, we filtered ProstaTrend for genes susceptible to FFPE-associated degradation via regression analysis. ProstaTrend was additionally restricted to genes with concordant prognostic effects in the RNA-Seq TCGA prostate adenocarcinoma (PRAD) cohort to ensure robust and broad applicability. The prognostic relevance of the refined Transcriptomic Risk Score (TRS) was analyzed by Kaplan-Meier curves and Cox-regression models in our FFPE-biopsy cohort and 9 other public datasets from PCa patients with BCR as primary endpoint. In addition, we developed a prostate single-cell atlas of 41 PCa patients from 5 publicly available studies to analyze gene expression of ProstaTrend genes in different cell compartments. Results: Validation of the TRS using the original ProstaTrend signature in the cohort of FFPE biopsies revealed a relevant impact of FFPE-associated degradation on gene expression and consequently no significant association with prognosis (Cox-regression, p-value > 0.05) in FFPE tissue. However, the TRS based on the new version of the ProstaTrend-ffpe signature, which included 204 genes (of originally 1396 genes), was significantly associated with BCR in the FFPE biopsy cohort (Cox-regression p-value < 0.001) and retained prognostic relevance when adjusted for Gleason Grade Groups. We confirmed a significant association with BCR in 9 independent cohorts including 1109 patients. Comparison of the prognostic performance of the TRS with 17 other prognostically relevant PCa panels revealed that ProstaTrend-ffpe was among the best-ranked panels. We generated a PCa cell atlas to associate ProstaTrend genes with cell lineages or cell types. Tumor-specific luminal cells have a significantly higher TRS than normal luminal cells in all analyzed datasets. In addition, TRS of epithelial and luminal cells was correlated with increased Gleason score in 3 studies. Conclusions: We developed a prognostic gene-expression signature for PCa that can be applied to FFPE biopsies and may be suitable to support clinical decision-making.
MeSH term(s)	Male ; Humans ; Transcriptome ; Paraffin Embedding ; Gene Expression Profiling ; Prostatic Neoplasms/genetics ; Prostatic Neoplasms/pathology ; Risk Factors ; Formaldehyde ; RNA ; Biopsy
Chemical Substances	Formaldehyde (1HG84L3525) ; RNA (63231-63-0)
Language	English
Publishing date	2024-02-01
Publishing country	England
Document type	Journal Article
ZDB-ID	1283676-x
ISSN	1528-3658 ; 1076-1551
ISSN (online)	1528-3658
ISSN	1076-1551
DOI	10.1186/s10020-024-00789-9
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Book ; Article ; Online: A time-resolved meta-analysis of consensus gene expression profiles during human T-cell activation

Rade, Michael / Böhlen, Sebastian / Neuhaus, Vanessa / Löffler, Dennis / Blumert, Conny / Köhl, Ulrike / Dehmel, Susann / Sewald, Katherina / Reiche, Kristin

2023

Abstract: Background: The coordinated transcriptional regulation of activated T-cells is based on the complex dynamic behavior of signaling networks. Given an external stimulus, T-cell gene expression is characterized by impulse and sustained patterns over the ... ...

Abstract	Background: The coordinated transcriptional regulation of activated T-cells is based on the 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 analyzed the temporal pattern of activation across different T-cell populations to develop consensus gene signatures for T-cell activation. Methods: We applied a meta-analysis of anti-CD3/CD28 induced CD4+ T-cell activation kinetics of publicly available transcriptomewide time series using a random effects model. We used non-negative matrix factorization, an unsupervised deconvolution method, to infer changes in biological patterns over time. For verification and to further map a wider variety of the T-cell landscape, we performed a time series of transcriptome-wide RNA sequencing on activated blood T-cells. Lastly, we matched the identified consensus biomarker signatures to single-cell RNA sequencing (scRNA-Seq) data of autologous anti-CD19 chimeric antigen receptor (CAR) T-cells from 24 patients with large B cell lymphoma (LBCL) to characterize activation status of the cell product before infusion. Results: We identified 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 early, intermediate, and late response expression rates across multiple T-cell populations, thus defining consensus biomarker signatures for T-cell activation. Intermediate and late response activation signatures in CAR T-cell infusion products were correlated to immune effector cell-associated neurotoxicity syndrome. Conclusion: In conclusion, we describe temporally resolved gene expression patterns across T-cell populations. These biomarker signatures are a valuable source for e.g., monitoring transcriptional ...
Subject code	570
Language	English
Publishing country	de
Document type	Book ; Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: RNA sequencing of glioblastoma tissue slice cultures reveals the effects of treatment at the transcriptional level

Haehnel, Susann / Rade, Michael / Kaiser, Nicole / Reiche, Kristin / Horn, Andreas / Loeffler, Dennis / Blumert, Conny / Rapp, Felicitas / Horn, Friedemann / Meixensberger, Juergen / Renner, Christof / Mueller, Wolf / Gaunitz, Frank / Bechmann, Ingo / Winter, Karsten

FEBS Open Bio. 2022 Feb., v. 12, no. 2

2022

Abstract: One of the major challenges in cancer research is finding models that closely resemble tumors within patients. Human tissue slice cultures are a promising approach to provide a model of the patient's tumor biology ex vivo. Recently, it was shown that ... ...

Abstract	One of the major challenges in cancer research is finding models that closely resemble tumors within patients. Human tissue slice cultures are a promising approach to provide a model of the patient's tumor biology ex vivo. Recently, it was shown that these slices can be successfully analyzed by whole transcriptome sequencing as well as automated histochemistry, increasing their usability as preclinical model. Glioblastoma multiforme (GBM) is a highly malignant brain tumor with poor prognosis and little is known about its genetic background and heterogeneity regarding therapy success. In this study, tissue from the tumors of 25 patients with primary GBM was processed into slice cultures and treated with standard therapy (irradiation and temozolomide). Total RNA sequencing and automated histochemistry were performed to enable analysis of treatment effects at a transcriptional and histological level. Slice cultures from long‐term survivors (overall survival [OS] > 24 months) exhibited more apoptosis than cultures from patients with shorter OS. Proliferation within these slices was slightly increased in contrast to other groups, but not significantly. Among all samples, 58 protein‐coding genes were upregulated and 32 downregulated in treated vs. untreated slice cultures. In general, an upregulation of DNA damage‐related and cell cycle checkpoint genes as well as enrichment of genotoxicity pathways and p53‐dependent signaling was found after treatment. Overall, the current study reproduces knowledge from former studies regarding the feasibility of transcriptomic analyses and automated histology in tissue slice cultures. We further demonstrate that the experimental data merge with the clinical follow‐up of the patients, which improves the applicability of our model system.
Keywords	DNA ; RNA ; apoptosis ; automation ; brain neoplasms ; cell cycle checkpoints ; genetic background ; genotoxicity ; glioblastoma ; histochemistry ; humans ; irradiation ; models ; patients ; prognosis ; therapeutics ; transcription (genetics) ; transcriptome ; transcriptomics
Language	English
Dates of publication	2022-02
Size	p. 480-493.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2651702-4
ISSN	2211-5463
ISSN	2211-5463
DOI	10.1002/2211-5463.13353
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Transcriptional states of CAR-T infusion relate to neurotoxicity - lessons from high-resolution single-cell SOM expression portraying

Loeffler-Wirth, Henry / Rade, Michael / Arakelyan, Arsen / Kreuz, Markus / Löffler, Markus W. / Köhl, Ulrike / Reiche, Kristin / Binder, Hans

2022

Abstract	Anti-CD19 CAR-T cell immunotherapy is a hopeful treatment option for patients with B cell lymphomas, however it copes with partly severe adverse effects like neurotoxicity. Single-cell resolved molecular data sets in combination with clinical parametrization allow for comprehensive characterization of cellular subpopulations, their transcriptomic states, and their relation to the adverse effects. We here present a re-analysis of single-cell RNA sequencing data of 24 patients comprising more than 130,000 cells with focus on cellular states and their association to immune cell related neurotoxicity. For this, we developed a single-cell data portraying workflow to disentangle the transcriptional state space with single-cell resolution and its analysis in terms of modularly-composed cellular programs. We demonstrated capabilities of single-cell data portraying to disentangle transcriptional states using intuitive visualization, functional mining, molecular cell stratification, and variability analyses. Our analysis revealed that the T cell composition of the patient’s infusion product as well as the spectrum of their transcriptional states of cells derived from patients with low ICANS grade do not markedly differ from those of cells from high ICANS patients, while the relative abundancies, particularly that of cycling cells, of LAG3-mediated exhaustion and of CAR positive cells, vary. Our study provides molecular details of the transcriptomic landscape with possible impact to overcome neurotoxicity. 13
Keywords	Single-cell transcriptomics ; CAR-T cell immunotherapy ; Data portraying ; Transcriptional states ; Bioinformatics workflow
Subject code	610
Language	English
Publishing country	de
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Characterization and evaluation of gene fusions as a measure of genetic instability and disease prognosis in prostate cancer.

Schimmelpfennig, Carolin / Rade, Michael / Füssel, Susanne / Löffler, Dennis / Blumert, Conny / Bertram, Catharina / Borkowetz, Angelika / Otto, Dominik J / Puppel, Sven-Holger / Hönscheid, Pia / Sommer, Ulrich / Baretton, Gustavo B / Köhl, Ulrike / Wirth, Manfred / Thomas, Christian / Horn, Friedemann / Kreuz, Markus / Reiche, Kristin

BMC cancer

2023 Volume 23, Issue 1, Page(s) 575

Abstract: Background: Prostate cancer (PCa) is one of the most prevalent cancers worldwide. The clinical manifestations and molecular characteristics of PCa are highly variable. Aggressive types require radical treatment, whereas indolent ones may be suitable for ...

Abstract	Background: Prostate cancer (PCa) is one of the most prevalent cancers worldwide. The clinical manifestations and molecular characteristics of PCa are highly variable. Aggressive types require radical treatment, whereas indolent ones may be suitable for active surveillance or organ-preserving focal therapies. Patient stratification by clinical or pathological risk categories still lacks sufficient precision. Incorporating molecular biomarkers, such as transcriptome-wide expression signatures, improves patient stratification but so far excludes chromosomal rearrangements. In this study, we investigated gene fusions in PCa, characterized potential novel candidates, and explored their role as prognostic markers for PCa progression. Methods: We analyzed 630 patients in four cohorts with varying traits regarding sequencing protocols, sample conservation, and PCa risk group. The datasets included transcriptome-wide expression and matched clinical follow-up data to detect and characterize gene fusions in PCa. With the fusion calling software Arriba, we computationally predicted gene fusions. Following detection, we annotated the gene fusions using published databases for gene fusions in cancer. To relate the occurrence of gene fusions to Gleason Grading Groups and disease prognosis, we performed survival analyses using the Kaplan-Meier estimator, log-rank test, and Cox regression. Results: Our analyses identified two potential novel gene fusions, MBTTPS2,L0XNC01::SMS and AMACR::AMACR. These fusions were detected in all four studied cohorts, providing compelling evidence for the validity of these fusions and their relevance in PCa. We also found that the number of gene fusions detected in a patient sample was significantly associated with the time to biochemical recurrence in two of the four cohorts (log-rank test, p-value < 0.05 for both cohorts). This was also confirmed after adjusting the prognostic model for Gleason Grading Groups (Cox regression, p-values < 0.05). Conclusions: Our gene fusion characterization workflow revealed two potential novel fusions specific for PCa. We found evidence that the number of gene fusions was associated with the prognosis of PCa. However, as the quantitative correlations were only moderately strong, further validation and assessment of clinical value is required before potential application.
MeSH term(s)	Male ; Humans ; Prognosis ; Prostatic Neoplasms/pathology ; Neoplasm Grading ; Transcriptome ; Gene Fusion ; Biomarkers, Tumor/genetics ; Biomarkers, Tumor/metabolism
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2023-06-22
Publishing country	England
Document type	Journal Article
ZDB-ID	2041352-X
ISSN	1471-2407 ; 1471-2407
ISSN (online)	1471-2407
ISSN	1471-2407
DOI	10.1186/s12885-023-11019-6
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: RNA sequencing of glioblastoma tissue slice cultures reveals the effects of treatment at the transcriptional level.

FEBS open bio

2021 Volume 12, Issue 2, Page(s) 480–493

Abstract	One of the major challenges in cancer research is finding models that closely resemble tumors within patients. Human tissue slice cultures are a promising approach to provide a model of the patient's tumor biology ex vivo. Recently, it was shown that these slices can be successfully analyzed by whole transcriptome sequencing as well as automated histochemistry, increasing their usability as preclinical model. Glioblastoma multiforme (GBM) is a highly malignant brain tumor with poor prognosis and little is known about its genetic background and heterogeneity regarding therapy success. In this study, tissue from the tumors of 25 patients with primary GBM was processed into slice cultures and treated with standard therapy (irradiation and temozolomide). Total RNA sequencing and automated histochemistry were performed to enable analysis of treatment effects at a transcriptional and histological level. Slice cultures from long-term survivors (overall survival [OS] > 24 months) exhibited more apoptosis than cultures from patients with shorter OS. Proliferation within these slices was slightly increased in contrast to other groups, but not significantly. Among all samples, 58 protein-coding genes were upregulated and 32 downregulated in treated vs. untreated slice cultures. In general, an upregulation of DNA damage-related and cell cycle checkpoint genes as well as enrichment of genotoxicity pathways and p53-dependent signaling was found after treatment. Overall, the current study reproduces knowledge from former studies regarding the feasibility of transcriptomic analyses and automated histology in tissue slice cultures. We further demonstrate that the experimental data merge with the clinical follow-up of the patients, which improves the applicability of our model system.
MeSH term(s)	Brain Neoplasms/genetics ; Glioblastoma/metabolism ; Humans ; Sequence Analysis, RNA ; Temozolomide/pharmacology ; Temozolomide/therapeutic use ; Whole Exome Sequencing
Chemical Substances	Temozolomide (YF1K15M17Y)
Language	English
Publishing date	2021-12-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2651702-4
ISSN	2211-5463 ; 2211-5463
ISSN (online)	2211-5463
ISSN	2211-5463
DOI	10.1002/2211-5463.13353
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Single-cell multiomic dissection of response and resistance to chimeric antigen receptor T cells against BCMA in relapsed multiple myeloma.

Rade, Michael / Grieb, Nora / Weiss, Ronald / Sia, Jaren / Fischer, Luise / Born, Patrick / Boldt, Andreas / Fricke, Stephan / Franz, Paul / Scolnick, Jonathan / Venkatraman, Lakshmi / Xu, Stacy / Kloetzer, Christina / Heyn, Simone / Kubasch, Anne Sophie / Baber, Ronny / Wang, Song Yau / Bach, Enrica / Hoffmann, Sandra /

Ussmann, Jule / Schetschorke, Birthe / Hell, Saskia / Schwind, Sebastian / Metzeler, Klaus H / Herling, Marco / Jentzsch, Madlen / Franke, Georg-Nikolaus / Sack, Ulrich / Köhl, Ulrike / Platzbecker, Uwe / Reiche, Kristin / Vucinic, Vladan / Merz, Maximilian

Nature cancer

2024

Abstract: Markers that predict response and resistance to chimeric antigen receptor (CAR) T cells in relapsed/refractory multiple myeloma are currently missing. We subjected mononuclear cells isolated from peripheral blood and bone marrow before and after the ... ...

Abstract	Markers that predict response and resistance to chimeric antigen receptor (CAR) T cells in relapsed/refractory multiple myeloma are currently missing. We subjected mononuclear cells isolated from peripheral blood and bone marrow before and after the application of approved B cell maturation antigen-directed CAR T cells to single-cell multiomic analyses to identify markers associated with resistance and early relapse. Differences between responders and nonresponders were identified at the time of leukapheresis. Nonresponders showed an immunosuppressive microenvironment characterized by increased numbers of monocytes expressing the immune checkpoint molecule CD39 and suppressed CD8
Language	English
Publishing date	2024-04-19
Publishing country	England
Document type	Journal Article
ISSN	2662-1347
ISSN (online)	2662-1347
DOI	10.1038/s43018-024-00763-8
Database	MEDical Literature Analysis and Retrieval System OnLINE

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