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Gkantaras A, Kotzamanidis C, Kyriakidis K, Farmaki E, Makedou K, Tzimagiorgis G, Bekeschus S, Malousi A. Multi-Cohort Transcriptomic Profiling of Medical Gas Plasma-Treated Cancers Reveals the Role of Immunogenic Cell Death. Cancers (Basel) 2024; 16:2186. [PMID: 38927892 PMCID: PMC11201794 DOI: 10.3390/cancers16122186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
The therapeutic potential of cold physical gas plasma operated at atmospheric pressure in oncology has been thoroughly demonstrated in numerous preclinical studies. The cytotoxic effect on malignant cells has been attributed mainly to biologically active plasma-generated compounds, namely, reactive oxygen and nitrogen species. The intracellular accumulation of reactive oxygen and nitrogen species interferes strongly with the antioxidant defense system of malignant cells, activating multiple signaling cascades and inevitably leading to oxidative stress-induced cell death. This study aims to determine whether plasma-induced cancer cell death operates through a universal molecular mechanism that is independent of the cancer cell type. Using whole transcriptome data, we sought to investigate the activation mechanism of plasma-treated samples in patient-derived prostate cell cultures, melanoma, breast, lymphoma, and lung cancer cells. The results from the standardized single-cohort gene expression analysis and parallel multi-cohort meta-analysis strongly indicate that plasma treatment globally induces cancer cell death through immune-mediated mechanisms, such as interleukin signaling, Toll-like receptor cascades, and MyD88 activation leading to pro-inflammatory cytokine release and tumor antigen presentation.
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Affiliation(s)
- Antonios Gkantaras
- Laboratory of Biological Chemistry, Medical School, Aristotle University, 54124 Thessaloniki, Greece; (A.G.); (K.M.); (G.T.)
- Pediatric Immunology and Rheumatology Referral Center, 1st Department of Pediatrics, Aristotle University, 54124 Thessaloniki, Greece;
| | | | | | - Evangelia Farmaki
- Pediatric Immunology and Rheumatology Referral Center, 1st Department of Pediatrics, Aristotle University, 54124 Thessaloniki, Greece;
| | - Kali Makedou
- Laboratory of Biological Chemistry, Medical School, Aristotle University, 54124 Thessaloniki, Greece; (A.G.); (K.M.); (G.T.)
| | - Georgios Tzimagiorgis
- Laboratory of Biological Chemistry, Medical School, Aristotle University, 54124 Thessaloniki, Greece; (A.G.); (K.M.); (G.T.)
| | - Sander Bekeschus
- ZIK Plasmatis, Leibniz Institute for Plasma Science and Technology (INP), 17489 Greifswald, Germany;
- Clinic and Policlinic for Dermatology and Venerology, Rostock University Medical Center, 18057 Rostock, Germany
| | - Andigoni Malousi
- Laboratory of Biological Chemistry, Medical School, Aristotle University, 54124 Thessaloniki, Greece; (A.G.); (K.M.); (G.T.)
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Akaho R, Kiyoura Y, Tamai R. Synergistic effect of Toll-like receptor 2 ligands and alendronate on proinflammatory cytokine production in mouse macrophage-like RAW-ASC cells is accompanied by upregulation of MyD88 expression. J Oral Biosci 2024; 66:412-419. [PMID: 38614429 DOI: 10.1016/j.job.2024.04.003] [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: 12/11/2023] [Revised: 04/05/2024] [Accepted: 04/07/2024] [Indexed: 04/15/2024]
Abstract
OBJECTIVES Toll-like receptors (TLRs) recognize whole cells or components of microorganisms. Alendronate (ALN) is an anti-bone-resorptive drug that has inflammatory side effects. The aim in this study was to examine whether ALN augments TLR2 ligand-induced proinflammatory cytokine production using mouse macrophage-like RAW264.7 cells transfected with murine apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC) gene (hereafter, referred to as "RAW-ASC cells"). METHODS RAW-ASC cells were pretreated with or without ALN and then incubated with or without TLR2 ligands. The levels of secreted mouse IL-1α, IL-1β, IL-6, and tumor necrosis factor-α (TNF-α) in culture supernatants and the activation of activator protein-1 (AP-1) or nuclear factor-κB (NF-κB) were measured using enzyme-linked immunosorbent assay (ELISA). The expressions of myeloid differentiation factor 88 (MyD88), caspase-11, nucleotide-binding oligomerization domain-like receptor family pyrin domain-containing 3 (NLRP3), ASC, NF-κB p65, and actin were analyzed via Western blotting. TLR2 expression was analyzed using flow cytometry. RESULTS ALN substantially upregulated the Pam3CSK4-induced release of IL-1α, IL-1β, IL-6, and TNF-α and MyD88 expression in RAW-ASC cells. ST-2825, a MyD88 inhibitor, inhibited the ALN-augmented release of these cytokines. Pretreatment with ALN augmented Pam3CSK4-induced NF-κB activation in RAW-ASC cells and upregulated AP-1 activation. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) S protein and ALN synergically upregulated the release of IL-1α, IL-1β, IL-6 and TNF-α in RAW-ASC cells. CONCLUSIONS Our findings suggest that ALN augments TLR2 ligand-induced proinflammatory cytokine production via the upregulation of MyD88 expression, and this augmentation is accompanied by the activation of NF-κB and AP-1 in RAW-ASC cells.
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Affiliation(s)
- Reiko Akaho
- Department of Infectious Diseases, Ohu University Graduate School of Dentistry, 31-1 Misumido, Tomitamachi, Koriyama, Fukushima, 963-8611, Japan
| | - Yusuke Kiyoura
- Department of Infectious Diseases, Ohu University Graduate School of Dentistry, 31-1 Misumido, Tomitamachi, Koriyama, Fukushima, 963-8611, Japan; Department of Oral Medical Science, Ohu University School of Dentistry, 31-1 Misumido, Tomitamachi, Koriyama, Fukushima, 963-8611, Japan
| | - Riyoko Tamai
- Department of Infectious Diseases, Ohu University Graduate School of Dentistry, 31-1 Misumido, Tomitamachi, Koriyama, Fukushima, 963-8611, Japan; Department of Oral Medical Science, Ohu University School of Dentistry, 31-1 Misumido, Tomitamachi, Koriyama, Fukushima, 963-8611, Japan.
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Schiroli G, Kartha V, Duarte FM, Kristiansen TA, Mayerhofer C, Shrestha R, Earl A, Hu Y, Tay T, Rhee C, Buenrostro JD, Scadden DT. Cell of origin epigenetic priming determines susceptibility to Tet2 mutation. Nat Commun 2024; 15:4325. [PMID: 38773071 PMCID: PMC11109152 DOI: 10.1038/s41467-024-48508-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 04/30/2024] [Indexed: 05/23/2024] Open
Abstract
Hematopoietic stem cell (HSC) mutations can result in clonal hematopoiesis (CH) with heterogeneous clinical outcomes. Here, we investigate how the cell state preceding Tet2 mutation impacts the pre-malignant phenotype. Using an inducible system for clonal analysis of myeloid progenitors, we find that the epigenetic features of clones at similar differentiation status are highly heterogeneous and functionally respond differently to Tet2 mutation. Cell differentiation stage also influences Tet2 mutation response indicating that the cell of origin's epigenome modulates clone-specific behaviors in CH. Molecular features associated with higher risk outcomes include Sox4 that sensitizes cells to Tet2 inactivation, inducing dedifferentiation, altered metabolism and increasing the in vivo clonal output of mutant cells, as confirmed in primary GMP and HSC models. Our findings validate the hypothesis that epigenetic features can predispose specific clones for dominance, explaining why identical genetic mutations can result in different phenotypes.
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Affiliation(s)
- Giulia Schiroli
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Vinay Kartha
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Fabiana M Duarte
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Trine A Kristiansen
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Christina Mayerhofer
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Rojesh Shrestha
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Andrew Earl
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Yan Hu
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Tristan Tay
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Catherine Rhee
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Jason D Buenrostro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - David T Scadden
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
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Leary JR, Bacher R. Interpretable trajectory inference with single-cell Linear Adaptive Negative-binomial Expression (scLANE) testing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.19.572477. [PMID: 38187622 PMCID: PMC10769309 DOI: 10.1101/2023.12.19.572477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The rapid proliferation of trajectory inference methods for single-cell RNA-seq data has allowed researchers to investigate complex biological processes by examining underlying gene expression dynamics. After estimating a latent cell ordering, statistical models are used to determine which genes exhibit changes in expression that are significantly associated with progression through the biological trajectory. While a few techniques for performing trajectory differential expression exist, most rely on the flexibility of generalized additive models in order to account for the inherent nonlinearity of changes in gene expression. As such, the results can be difficult to interpret, and biological conclusions often rest on subjective visual inspections of the most dynamic genes. To address this challenge, we propose scLANE testing, which is built around an interpretable generalized linear model and handles nonlinearity with basis splines chosen empirically for each gene. In addition, extensions to estimating equations and mixed models allow for reliable trajectory testing under complex experimental designs. After validating the accuracy of scLANE under several different simulation scenarios, we apply it to a set of diverse biological datasets and display its ability to provide novel biological information when used downstream of both pseudotime and RNA velocity estimation methods.
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Affiliation(s)
- Jack R. Leary
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, FL 32610, USA
| | - Rhonda Bacher
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, FL 32610, USA
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Avagyan S, Zon LI. Clonal hematopoiesis and inflammation - the perpetual cycle. Trends Cell Biol 2023; 33:695-707. [PMID: 36593155 PMCID: PMC10310890 DOI: 10.1016/j.tcb.2022.12.001] [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: 10/03/2022] [Revised: 12/04/2022] [Accepted: 12/08/2022] [Indexed: 01/01/2023]
Abstract
Acquired genetic or cytogenetic alterations in a blood stem cell that confer clonal fitness promote its relative expansion leading to clonal hematopoiesis (CH). Despite a largely intact hematopoietic output, CH is associated with a heightened risk of progression to hematologic malignancies and with non-hematologic health manifestations, including cardiovascular disease and overall mortality. We focus on the evidence for the role of inflammation in establishing, maintaining and reciprocally being affected by CH. We describe the known pro-inflammatory signals associated with CH and preclinical studies that elucidated the cellular mechanisms involved. We review the evolving literature on early-onset CH in germline predisposition conditions and the possible role of immune dysregulation in this context.
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Affiliation(s)
- Serine Avagyan
- Dana-Farber/Boston Children's Hospital Cancer and Blood Disorders Center, Boston, MA, USA.
| | - Leonard I Zon
- Boston Children's Hospital, Boston, MA 02215, USA; Howard Hughes Medical Institute, USA
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Erra Diaz F, Mazzitelli I, Bleichmar L, Melucci C, Thibodeau A, Dalotto Moreno T, Marches R, Rabinovich GA, Ucar D, Geffner J. Concomitant inhibition of PPARγ and mTORC1 induces the differentiation of human monocytes into highly immunogenic dendritic cells. Cell Rep 2023; 42:112156. [PMID: 36842088 DOI: 10.1016/j.celrep.2023.112156] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/29/2022] [Accepted: 02/08/2023] [Indexed: 02/27/2023] Open
Abstract
Monocytes can differentiate into macrophages (Mo-Macs) or dendritic cells (Mo-DCs). The cytokine granulocyte-macrophage colony-stimulating factor (GM-CSF) induces the differentiation of monocytes into Mo-Macs, while the combination of GM-CSF/interleukin (IL)-4 is widely used to generate Mo-DCs for clinical applications and to study human DC biology. Here, we report that pharmacological inhibition of the nuclear receptor peroxisome proliferator-activated receptor gamma (PPARγ) in the presence of GM-CSF and the absence of IL-4 induces monocyte differentiation into Mo-DCs. Remarkably, we find that simultaneous inhibition of PPARγ and the nutrient sensor mammalian target of rapamycin complex 1 (mTORC1) induces the differentiation of Mo-DCs with stronger phenotypic stability, superior immunogenicity, and a transcriptional profile characterized by a strong type I interferon (IFN) signature, a lower expression of a large set of tolerogenic genes, and the differential expression of several transcription factors compared with GM-CSF/IL-4 Mo-DCs. Our findings uncover a pathway that tailors Mo-DC differentiation with potential implications in the fields of DC vaccination and cancer immunotherapy.
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Affiliation(s)
- Fernando Erra Diaz
- Facultad de Medicina, Instituto de Investigaciones Biomédicas en Retrovirus y SIDA, Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina
| | - Ignacio Mazzitelli
- Facultad de Medicina, Instituto de Investigaciones Biomédicas en Retrovirus y SIDA, Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina
| | - Lucía Bleichmar
- Facultad de Medicina, Instituto de Investigaciones Biomédicas en Retrovirus y SIDA, Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina
| | - Claudia Melucci
- Facultad de Medicina, Instituto de Investigaciones Biomédicas en Retrovirus y SIDA, Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina
| | - Asa Thibodeau
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Tomás Dalotto Moreno
- Laboratorio de Glicomedicina, Instituto de Biología y Medicina Experimental (IBYME-CONICET), Buenos Aires, Argentina
| | - Radu Marches
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Gabriel A Rabinovich
- Laboratorio de Glicomedicina, Instituto de Biología y Medicina Experimental (IBYME-CONICET), Buenos Aires, Argentina; Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA; Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06030, USA.
| | - Jorge Geffner
- Facultad de Medicina, Instituto de Investigaciones Biomédicas en Retrovirus y SIDA, Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina.
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7
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Huang D, Berglund M, Damdimopoulos A, Antonson P, Lindskog C, Enblad G, Amini RM, Okret S. Sex- and Female Age-Dependent Differences in Gene Expression in Diffuse Large B-Cell Lymphoma-Possible Estrogen Effects. Cancers (Basel) 2023; 15:cancers15041298. [PMID: 36831639 PMCID: PMC9954534 DOI: 10.3390/cancers15041298] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/09/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
For most lymphomas, including diffuse large B-cell lymphoma (DLBCL), the male incidence is higher, and the prognosis is worse compared to females. The reasons are unclear; however, epidemiological and experimental data suggest that estrogens are involved. With this in mind, we analyzed gene expression data from a publicly available cohort (EGAD00001003600) of 746 DLBCL samples based on RNA sequencing. We found 1293 genes to be differentially expressed between males and females (adj. p-value < 0.05). Few autosomal genes and pathways showed common sex-regulated expression between germinal center B-cell (GCB) and activated B-cell lymphoma (ABC) DLBCL. Analysis of differentially expressed genes between pre- vs. postmenopausal females identified 208 GCB and 345 ABC genes, with only 5 being shared. When combining the differentially expressed genes between females vs. males and pre- vs. postmenopausal females, nine putative estrogen-regulated genes were identified in ABC DLBCL. Two of them, NR4A2 and MUC5B, showed induced and repressed expression, respectively. Interestingly, NR4A2 has been reported as a tumor suppressor in lymphoma. We show that ABC DLBCL females with a high NR4A2 expression showed better survival. Inversely, MUC5B expression causes a more malignant phenotype in several cancers. NR4A2 and MUC5B were confirmed to be estrogen-regulated when the ABC cell line U2932 was grafted to mice. The results demonstrate sex- and female reproductive age-dependent differences in gene expression between DLBCL subtypes, likely due to estrogens. This may contribute to the sex differences in incidence and prognosis.
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Affiliation(s)
- Dan Huang
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 83 Huddinge, Sweden
| | - Mattias Berglund
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 83 Huddinge, Sweden
| | - Anastasios Damdimopoulos
- Bioinformatics and Expression Core Facility, Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 83 Huddinge, Sweden
| | - Per Antonson
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 83 Huddinge, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Gunilla Enblad
- Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Rose-Marie Amini
- Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Sam Okret
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 83 Huddinge, Sweden
- Correspondence: ; Tel.: +46-8-524-81069
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