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Chen P, Li S, Nagaoka K, Kakimi K, Kataoka K, Cabral H. Nanoenabled IL-15 Superagonist via Conditionally Stabilized Protein-Protein Interactions Eradicates Solid Tumors by Precise Immunomodulation. J Am Chem Soc 2024. [PMID: 39356776 DOI: 10.1021/jacs.4c08327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2024]
Abstract
Protein complexes are crucial structures that control many biological processes. Harnessing these structures could be valuable for therapeutic therapy. However, their instability and short lifespans need to be addressed for effective use. Here, we propose an innovative approach based on a functional polymeric cloak that coordinately anchors different domains of protein complexes and assembles them into a stabilized nanoformulation. As the polymer-protein association in the cloak is pH sensitive, the nanoformulation also allows targeting the release of the protein complexes to the acidic microenvironment of tumors for aiding their therapeutic performance. Building on this strategy, we developed an IL-15 nanosuperagonist (Nano-SA) by encapsulating the interleukin-15 (IL-15)/IL-15 Receptor α (IL-15Rα) complex (IL-15cx) for fostering synergistic transpresentation in tumors. Upon intravenous administration, Nano-SA stably circulated in the bloodstream, safeguarding the integrity of IL-15cx until reaching the tumor site, where it selectively released the active complex. Thus, Nano-SA significantly amplified the antitumor immune signals while diminishing systemic off-target effects. In murine colon cancer models, Nano-SA achieved potent immunotherapeutic effects, eradicating tumors without adverse side effects. These findings highlight the transformative potential of nanotechnology for advancing protein complex-based therapies.
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Affiliation(s)
- Pengwen Chen
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Shangwei Li
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Koji Nagaoka
- Department of Immunotherapeutics, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Kazuhiro Kakimi
- Department of Immunotherapeutics, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Kazunori Kataoka
- Innovation Center of NanoMedicine (iCONM), Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Horacio Cabral
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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2
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Chang SH, Jung S, Chae JJ, Kim JY, Kim SU, Choi JY, Han HJ, Kim HT, Kim HJ, Kim HJ, Park WY, Sparks JA, Lee EY, Lee JS. Therapeutic single-cell landscape: methotrexate exacerbates interstitial lung disease by compromising the stemness of alveolar epithelial cells under systemic inflammation. EBioMedicine 2024; 108:105339. [PMID: 39303666 PMCID: PMC11437874 DOI: 10.1016/j.ebiom.2024.105339] [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: 03/01/2024] [Revised: 08/21/2024] [Accepted: 08/30/2024] [Indexed: 09/22/2024] Open
Abstract
BACKGROUND Interstitial lung disease (ILD) poses a serious threat in patients with rheumatoid arthritis (RA). However, the impact of cornerstone drugs, including methotrexate (MTX) and TNF inhibitor, on RA-associated ILD (RA-ILD) remains controversial. METHODS Using an SKG mouse model and single-cell transcriptomics, we investigated the effects of MTX and TNF blockade on ILD. FINDINGS Our study revealed that MTX exacerbates pulmonary inflammation by promoting immune cell infiltration, Th17 activation, and fibrosis. In contrast, TNF inhibitor ameliorates these features and inhibits ILD progression. Analysis of data from a human RA-ILD cohort revealed that patients with ILD progression had persistently higher systemic inflammation than those without progression, particularly among the subgroup undergoing MTX treatment. INTERPRETATION These findings highlight the need for personalized therapeutic approaches in RA-ILD, given the divergent outcomes of MTX and TNF inhibitor. FUNDING This work was funded by GENINUS Inc., and the National Research Foundation of Korea, and Seoul National University Hospital.
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Affiliation(s)
- Sung Hae Chang
- Division of Rheumatology, Department of Internal Medicine, Soonchunhyang University College of Medicine, Cheonan, 31151, South Korea
| | - Seyoung Jung
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Jeong Jun Chae
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea; Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, 06351, South Korea
| | - Jeong Yeon Kim
- Inocras, Inc., San Diego, CA, 92121, USA; Division of Rheumatology, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Seon Uk Kim
- Division of Rheumatology, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Ji Yong Choi
- Division of Rheumatology, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Hye-Jeong Han
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, Cheonan, 31151, Republic of Korea
| | - Hyun Taek Kim
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, Cheonan, 31151, Republic of Korea
| | - Hak-Jae Kim
- Department of Clinical Pharmacology, College of Medicine, Soonchunhyang University, Cheonan, 31151, Republic of Korea
| | - Hyun Je Kim
- Department of Biomedical Science, Seoul National University, Seoul, 03080, Republic of Korea
| | - Woong Yang Park
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Jeffrey A Sparks
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Eun Young Lee
- Division of Rheumatology, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
| | - Jeong Seok Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea; Inocras, Inc., San Diego, CA, 92121, USA.
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Strickland LN, Liu W, Hussein U, Mardik N, Chen X, Mills T, Vornik LA, Savage MI, Sei S, Clifford J, Eltzschig HK, Brown PH, Zhao Z, McAllister F, Bailey-Lundberg JM. Preventive Treatment with a CD73 Small Molecule Inhibitor Enhances Immune Surveillance in K-Ras Mutant Pancreatic Intraepithelial Neoplasia. Cancer Prev Res (Phila) 2024; 17:457-470. [PMID: 39099209 PMCID: PMC11443214 DOI: 10.1158/1940-6207.capr-24-0200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/25/2024] [Accepted: 08/01/2024] [Indexed: 08/06/2024]
Abstract
Immunoprevention is an emerging consideration for solid tumors, including pancreatic ductal adenocarcinoma (PDAC). We and others have shown that Kras mutations in genetic models of spontaneous pancreatic intraepithelial neoplasia (PanIN), which is a precursor to PDAC, results in CD73 expression in the neoplastic epithelium and some populations of infiltrating immune cells, including macrophages and CD8 T cells. CD73 is an ecto-enzyme that converts extracellular adenosine monophosphate to adenosine, a critical immune inhibitory molecule in PDAC. We hypothesized inhibition of CD73 would reduce the incidence of PanIN formation and alter the immune microenvironment. To test our hypothesis, we used the KrasG12D; PdxCre1 (KC) genetically engineered mouse model and tested the utility of AB-680, a small molecule inhibitor targeting CD73, to inhibit PanIN progression. AB-680, or vehicle control, was administered using oral gavage delivery 3 days/week at 10 mg/kg, beginning when the mice were 2 months old and lasting 3 months. We euthanized the mice at 5 months old. In the KC model, we quantified significantly less pancreatitis, early and advanced PanIN, and quantified a significant increase in M1 macrophages in AB-680-treated mice. Single-cell RNA sequencing (scRNA-seq) of pancreata of AB-680-treated mice revealed increased infiltration of CD4+ T cells, CD8+ T cells, and mature B cells. The scRNA-seq analysis showed that CD73 inhibition reduced M2 macrophages, acinar, and PanIN cell populations. CD73 inhibition enhanced immune surveillance and expanded unique clonotypes of TCR and BCR, indicating that inhibition of CD73 augments adaptive immunity early in the neoplastic microenvironment. Prevention Relevance: Previous studies found PanIN lesions in healthy pancreata. Not all progress to PDAC, suggesting a window for enhanced antitumor immunity through immunoprevention therapy. CD73 inhibition in our study prevents PanIN progression, reduces immune-suppressive macrophages and expands TCR and BCR unique clonotypes, highlighting an encouraging therapeutic avenue for high-risk individuals.
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Affiliation(s)
- Lincoln N. Strickland
- Department of Anesthesiology, Critical Care and Pain Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas.
| | - Wendao Liu
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, Texas.
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas.
| | - Usama Hussein
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas.
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Nicolette Mardik
- Department of Anesthesiology, Critical Care and Pain Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas.
| | - Xian Chen
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas.
| | - Tingting Mills
- Department of Biochemistry, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas.
| | - Lana A. Vornik
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Michelle I. Savage
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Shizuko Sei
- Division of Cancer Prevention, National Cancer Institute, Rockville, Maryland.
| | - John Clifford
- Division of Cancer Prevention, National Cancer Institute, Rockville, Maryland.
| | - Holger K. Eltzschig
- Department of Anesthesiology, Critical Care and Pain Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas.
| | - Powel H. Brown
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Zhongming Zhao
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas.
| | - Florencia McAllister
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas.
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Jennifer M. Bailey-Lundberg
- Department of Anesthesiology, Critical Care and Pain Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas.
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, Texas.
- Department of Pathology, Microbiology and Immunology, The University of Nebraska Medical Center, Omaha, Nebraska.
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4
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Maliah A, Santana-Magal N, Parikh S, Gordon S, Reshef K, Sade Y, Khateeb A, Richter A, Gutwillig A, Parikh R, Golan T, Krissi M, Na M, Binshtok G, Manich P, Elkoshi N, Grisaru-Tal S, Zemser-Werner V, Brenner R, Vaknine H, Nizri E, Moyal L, Amitay-Laish I, Rosemberg L, Munitz A, Kronfeld-Schor N, Shifrut E, Kobiler O, Madi A, Geiger T, Carmi Y, Levy C. Crosslinking of Ly6a metabolically reprograms CD8 T cells for cancer immunotherapy. Nat Commun 2024; 15:8354. [PMID: 39333093 PMCID: PMC11437002 DOI: 10.1038/s41467-024-52079-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/25/2024] [Indexed: 09/29/2024] Open
Abstract
T cell inhibitory mechanisms prevent autoimmune reactions, while cancer immunotherapy aims to remove these inhibitory signals. Chronic ultraviolet (UV) exposure attenuates autoimmunity through promotion of poorly understood immune-suppressive mechanisms. Here we show that mice with subcutaneous melanoma are not responsive to anti-PD1 immunotherapy following chronic UV irradiation, given prior to tumor injection, due to the suppression of T cell killing ability in skin-draining lymph nodes. Using mass cytometry and single-cell RNA-sequencing analyzes, we discover that skin-specific, UV-induced suppression of T-cells killing activity is mediated by upregulation of a Ly6ahigh T-cell subpopulation. Independently of the UV effect, Ly6ahigh T cells are induced by chronic type-1 interferon in the tumor microenvironment. Treatment with an anti-Ly6a antibody enhances the anti-tumoral cytotoxic activity of T cells and reprograms their mitochondrial metabolism via the Erk/cMyc axis. Treatment with an anti-Ly6a antibody inhibits tumor growth in mice resistant to anti-PD1 therapy. Applying our findings in humans could lead to an immunotherapy treatment for patients with resistance to existing treatments.
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Affiliation(s)
- Avishai Maliah
- Department of Human Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nadine Santana-Magal
- Department of Pathology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shivang Parikh
- The Ragon Institute of Mass General, MIT and Harvard 600/625 Main Street, Cambridge, MA, USA
| | - Sagi Gordon
- Department of Human Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Keren Reshef
- Department of Pathology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yuval Sade
- Department of Human Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Aseel Khateeb
- Department of Pathology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Alon Richter
- Department of Pathology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amit Gutwillig
- Department of Pathology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Roma Parikh
- Department of Human Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tamar Golan
- Department of Human Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Matan Krissi
- Department of Human Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Manho Na
- Department of Pathology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Gal Binshtok
- Department of Human Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Paulee Manich
- Department of Human Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nadav Elkoshi
- Department of Human Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sharon Grisaru-Tal
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Ronen Brenner
- Institute of Oncology, E. Wolfson Medical Center, Holon, Israel
| | - Hananya Vaknine
- Institute of Pathology, E. Wolfson Medical Center, Holon, Israel
| | - Eran Nizri
- Peritoneal Surface Malignancies and Melanoma Unit, Department of Surgery A, Tel-Aviv Sourasky Medical Center, Tel Aviv University, Tel Aviv, Israel
| | - Lilach Moyal
- Felsenstein Medical Research Center, Tel-Aviv University and the Division of Dermatology, Rabin Medical Center, Petach Tikva, Israel
| | - Iris Amitay-Laish
- Felsenstein Medical Research Center, Tel-Aviv University and the Division of Dermatology, Rabin Medical Center, Petach Tikva, Israel
| | - Luiza Rosemberg
- School of Zoology, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Ariel Munitz
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Eric Shifrut
- Department of Pathology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Faculty of Life Sciences, School of Neurobiology, Biochemistry and Biophysics, Tel Aviv University, Tel Aviv, Israel
- Dotan Center for Advanced Therapies, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Oren Kobiler
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Asaf Madi
- Department of Pathology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tamar Geiger
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yaron Carmi
- Department of Pathology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Carmit Levy
- Department of Human Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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5
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Lacagnina MJ, Willcox KF, Boukelmoune N, Bavencoffe A, Sankaranarayanan I, Barratt DT, Zuberi YA, Dayani D, Chavez MV, Lu JT, Farinotti AB, Shiers S, Barry AM, Mwirigi JM, Tavares-Ferreira D, Funk GA, Cervantes AM, Svensson CI, Walters ET, Hutchinson MR, Heijnen CJ, Price TJ, Fiore NT, Grace PM. B cells drive neuropathic pain-related behaviors in mice through IgG-Fc gamma receptor signaling. Sci Transl Med 2024; 16:eadj1277. [PMID: 39321269 PMCID: PMC11479571 DOI: 10.1126/scitranslmed.adj1277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 03/06/2024] [Accepted: 09/03/2024] [Indexed: 09/27/2024]
Abstract
Neuroimmune interactions are essential for the development of neuropathic pain, yet the contributions of distinct immune cell populations have not been fully unraveled. Here, we demonstrate the critical role of B cells in promoting mechanical hypersensitivity (allodynia) after peripheral nerve injury in male and female mice. Depletion of B cells with a single injection of anti-CD20 monoclonal antibody at the time of injury prevented the development of allodynia. B cell-deficient (muMT) mice were similarly spared from allodynia. Nerve injury was associated with increased immunoglobulin G (IgG) accumulation in ipsilateral lumbar dorsal root ganglia (DRGs) and dorsal spinal cords. IgG was colocalized with sensory neurons and macrophages in DRGs and microglia in spinal cords. IgG also accumulated in DRG samples from human donors with chronic pain, colocalizing with a marker for macrophages and satellite glia. RNA sequencing revealed a B cell population in naive mouse and human DRGs. A B cell transcriptional signature was enriched in DRGs from human donors with neuropathic pain. Passive transfer of IgG from injured mice induced allodynia in injured muMT recipient mice. The pronociceptive effects of IgG are likely mediated through immune complexes interacting with Fc gamma receptors (FcγRs) expressed by sensory neurons, microglia, and macrophages, given that both mechanical allodynia and hyperexcitability of dissociated DRG neurons were abolished in nerve-injured FcγR-deficient mice. Consistently, the pronociceptive effects of IgG passive transfer were lost in FcγR-deficient mice. These data reveal that a B cell-IgG-FcγR axis is required for the development of neuropathic pain in mice.
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Affiliation(s)
- Michael J. Lacagnina
- Laboratories of Neuroimmunology, Department of Symptom Research, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kendal F. Willcox
- Laboratories of Neuroimmunology, Department of Symptom Research, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nabila Boukelmoune
- Laboratories of Neuroimmunology, Department of Symptom Research, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alexis Bavencoffe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77225, USA
| | - Ishwarya Sankaranarayanan
- Department of Neuroscience and Center for Advanced Pain Studies, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Daniel T. Barratt
- School of Biomedicine, University of Adelaide, Adelaide, SA 5005, Australia
- Davies Livestock Research Centre, University of Adelaide, Roseworthy, SA 5371, Australia
| | - Younus A. Zuberi
- Laboratories of Neuroimmunology, Department of Symptom Research, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dorsa Dayani
- Laboratories of Neuroimmunology, Department of Symptom Research, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Melissa V. Chavez
- Laboratories of Neuroimmunology, Department of Symptom Research, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jonathan T. Lu
- Laboratories of Neuroimmunology, Department of Symptom Research, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Stephanie Shiers
- Department of Neuroscience and Center for Advanced Pain Studies, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Allison M. Barry
- Department of Neuroscience and Center for Advanced Pain Studies, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Juliet M. Mwirigi
- Department of Neuroscience and Center for Advanced Pain Studies, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Diana Tavares-Ferreira
- Department of Neuroscience and Center for Advanced Pain Studies, University of Texas at Dallas, Richardson, TX 75080, USA
| | | | | | - Camilla I. Svensson
- Department of Physiology and Pharmacology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Edgar T. Walters
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77225, USA
| | - Mark R. Hutchinson
- School of Biomedicine, University of Adelaide, Adelaide, SA 5005, Australia
- Davies Livestock Research Centre, University of Adelaide, Roseworthy, SA 5371, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, Adelaide, SA 5005, Australia
| | - Cobi J. Heijnen
- Department of Psychological Sciences, Rice University, Houston, TX 77005, USA
| | - Theodore J. Price
- Department of Neuroscience and Center for Advanced Pain Studies, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Nathan T. Fiore
- Laboratories of Neuroimmunology, Department of Symptom Research, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Peter M. Grace
- Laboratories of Neuroimmunology, Department of Symptom Research, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Cruz-Granados P, Frejo L, Perez-Carpena P, Amor-Dorado JC, Dominguez-Duran E, Fernandez-Nava MJ, Batuecas-Caletrio A, Haro-Hernandez E, Martinez-Martinez M, Lopez-Escamez JA. Multiomic-based immune response profiling in migraine, vestibular migraine and Meniere's disease. Immunology 2024. [PMID: 39294737 DOI: 10.1111/imm.13863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Accepted: 09/04/2024] [Indexed: 09/21/2024] Open
Abstract
Migraine (MI) is the most common neurological disease, affecting with 20% of the world population. A subset of 25% of MI patients showcase concurrent vestibular symptoms, which may classify as vestibular migraine (VM). Meniere's disease (MD) is a complex inner ear disorder defined by episodes of vertigo associated with tinnitus and sensorineural hearing loss with a significant autoimmune/autoinflammatory contribution, which symptoms overlap with VM. Blood samples from 18 patients with MI (5), VM (5) and MD (8) and 6 controls were collected and compared in a case-control study. Droplet-isolated nuclei from mononuclear cells used to generate scRNAseq and scATACseq data sets from MI, VM and MD. MI and VM have no differences in their immune transcriptome; therefore, they were considered as a single cluster for further analyses. Natural Killer (NK) cells transcriptomic data support a polarisation triggered by Type 1 innate immune cells via the release of interleukin (IL)-12, IL-15 and IL-18. According to the monocyte scRNAseq data, there were two MD clusters, one inactive and one driven by monocytes. The unique pathways of the MI + VM cluster were cellular responses to metal ions, whereas MD monocyte-driven cluster pathways showed responses to biotic stimuli. MI and MD have different immune responses. These findings support that MI and VM have a Type 1 immune lymphoid cell response, and that there are two clusters of MD patients, one inactive and one Monocyte-driven.
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Affiliation(s)
- Pablo Cruz-Granados
- Meniere Disease Neuroscience Research Program, Faculty of Medicine and Health, School of Medical Sciences, The Kolling Institute, University of Sydney, Sydney, New South Wales, Australia
| | - Lidia Frejo
- Meniere Disease Neuroscience Research Program, Faculty of Medicine and Health, School of Medical Sciences, The Kolling Institute, University of Sydney, Sydney, New South Wales, Australia
- Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
| | - Patricia Perez-Carpena
- Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
- Department of Otolaryngology, Hospital Universitario San Cecilio, Instituto de Investigación Biosanitaria, ibs.GRANADA, Granada, Spain
| | | | | | - Maria Jose Fernandez-Nava
- Department of Otolaryngology, Hospital Universitario Salamanca, Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Division of Otolaryngology, Department of Surgery, Universidad de Salamanca, Salamanca, Spain
| | - Angel Batuecas-Caletrio
- Department of Otolaryngology, Hospital Universitario Salamanca, Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Division of Otolaryngology, Department of Surgery, Universidad de Salamanca, Salamanca, Spain
| | - Elisheba Haro-Hernandez
- Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
- Department of Otorhinolaryngology, Hospital de Baza, Granada, Spain
| | - Marta Martinez-Martinez
- Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
| | - Jose A Lopez-Escamez
- Meniere Disease Neuroscience Research Program, Faculty of Medicine and Health, School of Medical Sciences, The Kolling Institute, University of Sydney, Sydney, New South Wales, Australia
- Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
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7
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Sweet MJ, Ramnath D, Singhal A, Kapetanovic R. Inducible antibacterial responses in macrophages. Nat Rev Immunol 2024:10.1038/s41577-024-01080-y. [PMID: 39294278 DOI: 10.1038/s41577-024-01080-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2024] [Indexed: 09/20/2024]
Abstract
Macrophages destroy bacteria and other microorganisms through phagocytosis-coupled antimicrobial responses, such as the generation of reactive oxygen species and the delivery of hydrolytic enzymes from lysosomes to the phagosome. However, many intracellular bacteria subvert these responses, escaping to other cellular compartments to survive and/or replicate. Such bacterial subversion strategies are countered by a range of additional direct antibacterial responses that are switched on by pattern-recognition receptors and/or host-derived cytokines and other factors, often through inducible gene expression and/or metabolic reprogramming. Our understanding of these inducible antibacterial defence strategies in macrophages is rapidly evolving. In this Review, we provide an overview of the broad repertoire of antibacterial responses that can be engaged in macrophages, including LC3-associated phagocytosis, metabolic reprogramming and antimicrobial metabolites, lipid droplets, guanylate-binding proteins, antimicrobial peptides, metal ion toxicity, nutrient depletion, autophagy and nitric oxide production. We also highlight key inducers, signalling pathways and transcription factors involved in driving these different antibacterial responses. Finally, we discuss how a detailed understanding of the molecular mechanisms of antibacterial responses in macrophages might be exploited for developing host-directed therapies to combat antibiotic-resistant bacterial infections.
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Affiliation(s)
- Matthew J Sweet
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
| | - Divya Ramnath
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Amit Singhal
- Infectious Diseases Labs (ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Ronan Kapetanovic
- INRAE, Université de Tours, Infectiologie et Santé Publique (ISP), Nouzilly, France
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8
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Gottschalk RA, Germain RN. Linking signal input, cell state, and spatial context to inflammatory responses. Curr Opin Immunol 2024; 91:102462. [PMID: 39265520 DOI: 10.1016/j.coi.2024.102462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 08/21/2024] [Accepted: 08/24/2024] [Indexed: 09/14/2024]
Abstract
Signal integration is central to a causal understanding of appropriately scaled inflammatory responses. Here, we discuss recent progress in our understanding of the stimulus-response linkages downstream of pro-inflammatory inputs, with special attention to (1) the impact of cell state on the specificity of evoked gene expression and (2) the critical role of the spatial context of stimulus exposure. Advances in these directions are emerging from new tools for inferring cell-cell interactions and the activities of cytokines and transcription factors in complex microenvironments, enabling analysis of signal integration in tissue settings. Building on data-driven elucidation of factors driving inflammatory outcomes, mechanistic modeling can then contribute to a quantitative understanding of regulatory events that balance protective versus pathological inflammation.
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Affiliation(s)
- Rachel A Gottschalk
- Department of Immunology, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Center for Systems Immunology, University of Pittsburgh, Pittsburgh, PA, USA.
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9
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Pu Z, Chen S, Lu Y, Wu Z, Cai Z, Mou L. Exploring the molecular mechanisms of macrophages in islet transplantation using single-cell analysis. Front Immunol 2024; 15:1407118. [PMID: 39267737 PMCID: PMC11391485 DOI: 10.3389/fimmu.2024.1407118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 08/02/2024] [Indexed: 09/15/2024] Open
Abstract
Background Islet transplantation is a promising treatment for type 1 diabetes that aims to restore insulin production and improve glucose control, but long-term graft survival remains a challenge due to immune rejection. Methods ScRNA-seq data from syngeneic and allogeneic islet transplantation grafts were obtained from GSE198865. Seurat was used for filtering and clustering, and UMAP was used for dimension reduction. Differentially expressed genes were analyzed between syngeneic and allogeneic islet transplantation grafts. Gene set variation analysis (GSVA) was performed on the HALLMARK gene sets from MSigDB. Monocle 2 was used to reconstruct differentiation trajectories, and cytokine signature enrichment analysis was used to compare cytokine responses between syngeneic and allogeneic grafts. Results Three distinct macrophage clusters (Mø-C1, Mø-C2, and Mø-C3) were identified, revealing complex interactions and regulatory mechanisms within macrophage populations. The significant activation of macrophages in allogeneic transplants was marked by the upregulation of allograft rejection-related genes and pathways involved in inflammatory and interferon responses. GSVA revealed eight pathways significantly upregulated in the Mø-C2 cluster. Trajectory analysis revealed that Mø-C3 serves as a common progenitor, branching into Mø-C1 and Mø-C2. Cytokine signature enrichment analysis revealed significant differences in cytokine responses, highlighting the distinct immunological environments created by syngeneic and allogeneic grafts. Conclusion This study significantly advances the understanding of macrophage roles within the context of islet transplantation by revealing the interactions between immune pathways and cellular fate processes. The findings highlight potential therapeutic targets for enhancing graft survival and function, emphasizing the importance of understanding the immunological aspects of transplant acceptance and longevity.
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Affiliation(s)
- Zuhui Pu
- Imaging Department, Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, Guangdong, China
- MetaLife Lab, Shenzhen Institute of Translational Medicine, Shenzhen, Guangdong, China
| | - Shujuan Chen
- Department of Endocrinology, Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, Guangdong, China
| | - Ying Lu
- MetaLife Lab, Shenzhen Institute of Translational Medicine, Shenzhen, Guangdong, China
| | - Zijing Wu
- MetaLife Lab, Shenzhen Institute of Translational Medicine, Shenzhen, Guangdong, China
| | - Zhiming Cai
- BGI Medical Group, Shenzhen, Guangdong, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China
| | - Lisha Mou
- MetaLife Lab, Shenzhen Institute of Translational Medicine, Shenzhen, Guangdong, China
- Department of Endocrinology, Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, Guangdong, China
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10
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Yousefpour P, Zhang YJ, Maiorino L, Melo MB, Arainga Ramirez MA, Kumarapperuma SC, Xiao P, Silva M, Li N, Michaels KK, Georgeson E, Eskandarzadeh S, Kubitz M, Groschel B, Qureshi K, Fontenot J, Hangartner L, Nedellec R, Love JC, Burton DR, Schief WR, Villinger FJ, Irvine DJ. Modulation of antigen delivery and lymph node activation in non-human primates by saponin adjuvant SMNP. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.28.608716. [PMID: 39253464 PMCID: PMC11383317 DOI: 10.1101/2024.08.28.608716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Saponin-based vaccine adjuvants are potent in preclinical animal models and humans, but their mechanisms of action remain poorly understood. Here, using a stabilized HIV envelope trimer immunogen, we carried out studies in non-human primates (NHPs) comparing the most common clinical adjuvant alum with Saponin/MPLA Nanoparticles (SMNP), a novel ISCOMs-like adjuvant. SMNP elicited substantially stronger humoral immune responses than alum, including 7-fold higher peak antigen-specific germinal center B cell responses, 18-fold higher autologous neutralizing antibody titers, and higher levels of antigen-specific plasma and memory B cells. PET-CT imaging in live NHPs showed that, unlike alum, SMNP promoted rapid antigen accumulation in both proximal and distal lymph nodes (LNs). SMNP also induced strong type I interferon transcriptional signatures, expansion of innate immune cells, and increased antigen presenting cell activation in LNs. These findings indicate that SMNP promotes multiple facets of the early immune response relevant for enhanced immunity to vaccination.
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Affiliation(s)
- Parisa Yousefpour
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
| | - Yiming J Zhang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
| | - Laura Maiorino
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Mariane B Melo
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
| | | | - Sidath C Kumarapperuma
- Research Imaging Institute, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Peng Xiao
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA 70560, USA
| | - Murillo Silva
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
| | - Na Li
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Katarzyna K Michaels
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Erik Georgeson
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Saman Eskandarzadeh
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Kubitz
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bettina Groschel
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kashif Qureshi
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jane Fontenot
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA 70560, USA
| | - Lars Hangartner
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rebecca Nedellec
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - J Christopher Love
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Dennis R Burton
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - William R Schief
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Moderna Inc., Cambridge, MA 02139, USA
| | - Francois J Villinger
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA 70560, USA
- Department of Biology, University of Louisiana at Lafayette, New Iberia, LA 70560 USA
| | - Darrell J Irvine
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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11
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Bessell E, Finlay RE, James LK, Ludewig B, Harris NL, Krebs P, Hepworth MR, Dubey LK. Stromal cell and B cell dialogue potentiates IL-33-enriched lymphoid niches to support eosinophil recruitment and function during type 2 immunity. Cell Rep 2024; 43:114620. [PMID: 39141517 DOI: 10.1016/j.celrep.2024.114620] [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: 11/08/2023] [Revised: 05/27/2024] [Accepted: 07/25/2024] [Indexed: 08/16/2024] Open
Abstract
Eosinophils are involved in host protection against multicellular organisms. However, their recruitment to the mesenteric lymph node (mLN) during type 2 immunity is understudied. Our results demonstrate that eosinophil association with lymphoid stromal niches constructed by fibroblastic reticular cells (FRCs) and lymphatic endothelial cells is diminished in mice selectively lacking interleukin (IL)-4Rα or lymphotoxin-β (LTβ) expression on B cells. Furthermore, eosinophil survival, activation, and enhanced Il1rl1 receptor expression are driven by stromal cell and B cell dialogue. The ligation of lymphotoxin-β receptor (LTβR) on FRCs improves eosinophil survival and significantly augments IL-33 expression and eosinophil homing to the mLN, thus confirming the significance of lymphotoxin signaling for granulocyte recruitment. Eosinophil-deficient ΔdblGATA-1 mice show diminished mLN expansion, reduced interfollicular region (IFR) alarmin expression, and delayed helminth clearance, elucidating their importance in type 2 immunity. These findings provide insight into dialogue between stromal cells and B cells, which govern mLN eosinophilia, and the relevance of these mechanisms during type 2 immunity.
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Affiliation(s)
- Emily Bessell
- William Harvey Research Institute (WHRI), Barts & The London School of Medicine & Dentistry, Queen Mary University of London (QMUL), London, UK; Institute of Tissue Medicine and Pathology, University of Bern, Bern, Switzerland; Institute of Parasitology, Vetsuisse Faculty, University of Bern, Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Rachel E Finlay
- Division of Immunology, Immunity to Infection and Respiratory Medicine, Faculty of Biology, Medicine and Health, Lydia Becker Institute of Immunology and Inflammation, The University of Manchester, Manchester, UK
| | - Louisa K James
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, UK
| | - Burkhard Ludewig
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Nicola L Harris
- Department of Immunology and Pathology, Central Clinical School, Monash University, The Alfred Centre, Melbourne, VIC, Australia
| | - Philippe Krebs
- Institute of Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
| | - Matthew R Hepworth
- Division of Immunology, Immunity to Infection and Respiratory Medicine, Faculty of Biology, Medicine and Health, Lydia Becker Institute of Immunology and Inflammation, The University of Manchester, Manchester, UK
| | - Lalit Kumar Dubey
- William Harvey Research Institute (WHRI), Barts & The London School of Medicine & Dentistry, Queen Mary University of London (QMUL), London, UK; Institute of Tissue Medicine and Pathology, University of Bern, Bern, Switzerland.
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12
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Liu W, Zhao Z. Scupa: Single-cell unified polarization assessment of immune cells using the single-cell foundation model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.15.608093. [PMID: 39229048 PMCID: PMC11370394 DOI: 10.1101/2024.08.15.608093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Immune cells undergo cytokine-driven polarization in respond to diverse stimuli. This process significantly modulates their transcriptional profiles and functional states. Although single-cell RNA sequencing (scRNA-seq) has advanced our understanding of immune responses across various diseases or conditions, currently there lacks a method to systematically examine cytokine effects and immune cell polarization. To address this gap, we developed Single-cell unified polarization assessment (Scupa), the first computational method for comprehensive immune cell polarization analysis. Scupa is trained on data from the Immune Dictionary, which characterizes 66 cytokine-driven polarization states across 14 immune cell types. By leveraging the cell embeddings from the Universal Cell Embeddings model, Scupa effectively identifies polarized cells in new datasets generated from different species and experimental conditions. Applications of Scupa in independent datasets demonstrated its accuracy in classifying polarized cells and further revealed distinct polarization profiles in tumor-infiltrating myeloid cells across cancers. Scupa complements conventional single-cell data analysis by providing new insights into immune cell polarization, and it holds promise for assessing molecular effects or identifying therapeutic targets in cytokine-based therapies.
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Affiliation(s)
- Wendao Liu
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Zhongming Zhao
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
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13
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Jia D, Salazar-Cavazos E, West T, Liang SH, Costa R, Clavijo-Salomon M, Huang A, Trinchieri G, Lionakis M, Mukherjee R, Altan-Bonnet G. Chaotic dynamics for homeostatic hematopoiesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.16.608266. [PMID: 39372763 PMCID: PMC11451746 DOI: 10.1101/2024.08.16.608266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
Abstract
Hematopoiesis is a highly dynamical and stochastic process, challenging our understanding of homeostasis. Clinical studies of leukemia or neutropenic patients revealed that multiple blood cell types fluctuate spontaneously with large yet regular oscillations of their frequencies. Yet the stability of hematopoiesis in healthy individuals remains understudied. Here we report on both cross-sectional and longitudinal studies of dozens of healthy mice, through high-dimensional mass and spectral cytometry, to understand hematopoiesis at homeostasis. We found that all cell types in the bone marrow, blood, and spleen exhibit large variations of frequency (e.g., with coefficients of variation larger than 1). While the frequencies of individual cell type fluctuate, there existed extensive and robust correlations/anti-correlations between cell types, exemplified by the pronounced anti-correlation between blood neutrophils and B cells. Through longitudinal study of the blood content of healthy mice, we found that leukocyte fluctuations are ergodic yet subject to chaotic behaviors characterized by a broad spectrum of characteristic timescales. We then built a minimal mathematical model to capture these dynamical features of hematopoiesis (fluctuations, correlations, and chaos) and explain how the accumulation of B cells (e.g. during lymphoma development) would transition the blood cell dynamics from chaos to oscillations (as observed clinically). Finally, we demonstrated the ubiquity and consistency of the correlated fluctuations in hematopoiesis by comparing mouse cohorts of different genetic backgrounds and ages. To conclude, we discuss how study of hematopoiesis must factor in the newfound chaotic dynamics at homeostasis, towards better modeling the responses to perturbations.
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14
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Paton V, Ramirez Flores RO, Gabor A, Badia-I-Mompel P, Tanevski J, Garrido-Rodriguez M, Saez-Rodriguez J. Assessing the impact of transcriptomics data analysis pipelines on downstream functional enrichment results. Nucleic Acids Res 2024; 52:8100-8111. [PMID: 38943333 DOI: 10.1093/nar/gkae552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 06/03/2024] [Accepted: 06/19/2024] [Indexed: 07/01/2024] Open
Abstract
Transcriptomics is widely used to assess the state of biological systems. There are many tools for the different steps, such as normalization, differential expression, and enrichment. While numerous studies have examined the impact of method choices on differential expression results, little attention has been paid to their effects on further downstream functional analysis, which typically provides the basis for interpretation and follow-up experiments. To address this, we introduce FLOP, a comprehensive nextflow-based workflow combining methods to perform end-to-end analyses of transcriptomics data. We illustrate FLOP on datasets ranging from end-stage heart failure patients to cancer cell lines. We discovered effects not noticeable at the gene-level, and observed that not filtering the data had the highest impact on the correlation between pipelines in the gene set space. Moreover, we performed three benchmarks to evaluate the 12 pipelines included in FLOP, and confirmed that filtering is essential in scenarios of expected moderate-to-low biological signal. Overall, our results underscore the impact of carefully evaluating the consequences of the choice of preprocessing methods on downstream enrichment analyses. We envision FLOP as a valuable tool to measure the robustness of functional analyses, ultimately leading to more reliable and conclusive biological findings.
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Affiliation(s)
- Victor Paton
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
| | - Ricardo Omar Ramirez Flores
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
| | - Attila Gabor
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
| | - Pau Badia-I-Mompel
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
| | - Jovan Tanevski
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
| | - Martin Garrido-Rodriguez
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
- European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
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15
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Shanley M, Daher M, Dou J, Li S, Basar R, Rafei H, Dede M, Gumin J, Pantaleόn Garcίa J, Nunez Cortes AK, He S, Jones CM, Acharya S, Fowlkes NW, Xiong D, Singh S, Shaim H, Hicks SC, Liu B, Jain A, Zaman MF, Miao Q, Li Y, Uprety N, Liu E, Muniz-Feliciano L, Deyter GM, Mohanty V, Zhang P, Evans SE, Shpall EJ, Lang FF, Chen K, Rezvani K. Interleukin-21 engineering enhances NK cell activity against glioblastoma via CEBPD. Cancer Cell 2024; 42:1450-1466.e11. [PMID: 39137729 PMCID: PMC11370652 DOI: 10.1016/j.ccell.2024.07.007] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/31/2024] [Accepted: 07/17/2024] [Indexed: 08/15/2024]
Abstract
Glioblastoma (GBM) is an aggressive brain cancer with limited therapeutic options. Natural killer (NK) cells are innate immune cells with strong anti-tumor activity and may offer a promising treatment strategy for GBM. We compared the anti-GBM activity of NK cells engineered to express interleukin (IL)-15 or IL-21. Using multiple in vivo models, IL-21 NK cells were superior to IL-15 NK cells both in terms of safety and long-term anti-tumor activity, with locoregionally administered IL-15 NK cells proving toxic and ineffective at tumor control. IL-21 NK cells displayed a unique chromatin accessibility signature, with CCAAT/enhancer-binding proteins (C/EBP), especially CEBPD, serving as key transcription factors regulating their enhanced function. Deletion of CEBPD resulted in loss of IL-21 NK cell potency while its overexpression increased NK cell long-term cytotoxicity and metabolic fitness. These results suggest that IL-21, through C/EBP transcription factors, drives epigenetic reprogramming of NK cells, enhancing their anti-tumor efficacy against GBM.
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Affiliation(s)
- Mayra Shanley
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - May Daher
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Jinzhuang Dou
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Sufang Li
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Rafet Basar
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Hind Rafei
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Merve Dede
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Joy Gumin
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Jezreel Pantaleόn Garcίa
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Ana Karen Nunez Cortes
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Shan He
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Corry M Jones
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Sunil Acharya
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Natalie W Fowlkes
- Department of Veterinary Medicine and Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Donghai Xiong
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Sanjay Singh
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Hila Shaim
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Samantha Claire Hicks
- Department of Veterinary Medicine and Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Bin Liu
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Abhinav Jain
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Mohammad Fayyad Zaman
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Qi Miao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Ye Li
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Nadima Uprety
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Enli Liu
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Luis Muniz-Feliciano
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Gary M Deyter
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Vakul Mohanty
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Patrick Zhang
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Scott E Evans
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Elizabeth J Shpall
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Frederick F Lang
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Katayoun Rezvani
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA.
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16
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Rael VE, Yano JA, Huizar JP, Slayden LC, Weiss MA, Turcotte EA, Terry JM, Zuo W, Thiffault I, Pastinen T, Farrow EG, Jenkins JL, Becker ML, Wong SC, Stevens AM, Otten C, Allenspach EJ, Bonner DE, Bernstein JA, Wheeler MT, Saxton RA, Liu B, Majer O, Barton GM. Large-scale mutational analysis identifies UNC93B1 variants that drive TLR-mediated autoimmunity in mice and humans. J Exp Med 2024; 221:e20232005. [PMID: 38780621 PMCID: PMC11116816 DOI: 10.1084/jem.20232005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/21/2024] [Accepted: 04/17/2024] [Indexed: 05/25/2024] Open
Abstract
Nucleic acid-sensing Toll-like receptors (TLR) 3, 7/8, and 9 are key innate immune sensors whose activities must be tightly regulated to prevent systemic autoimmune or autoinflammatory disease or virus-associated immunopathology. Here, we report a systematic scanning-alanine mutagenesis screen of all cytosolic and luminal residues of the TLR chaperone protein UNC93B1, which identified both negative and positive regulatory regions affecting TLR3, TLR7, and TLR9 responses. We subsequently identified two families harboring heterozygous coding mutations in UNC93B1, UNC93B1+/T93I and UNC93B1+/R336C, both in key negative regulatory regions identified in our screen. These patients presented with cutaneous tumid lupus and juvenile idiopathic arthritis plus neuroinflammatory disease, respectively. Disruption of UNC93B1-mediated regulation by these mutations led to enhanced TLR7/8 responses, and both variants resulted in systemic autoimmune or inflammatory disease when introduced into mice via genome editing. Altogether, our results implicate the UNC93B1-TLR7/8 axis in human monogenic autoimmune diseases and provide a functional resource to assess the impact of yet-to-be-reported UNC93B1 mutations.
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Affiliation(s)
- Victoria E. Rael
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Julian A. Yano
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - John P. Huizar
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Leianna C. Slayden
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Madeleine A. Weiss
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Elizabeth A. Turcotte
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Jacob M. Terry
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Wenqi Zuo
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Isabelle Thiffault
- Department of Pathology and Laboratory Medicine, Children’s Mercy Hospital, Kansas City, MO, USA
- Genomic Medicine Center, Children’s Mercy Hospital, Kansas City, MO, USA
- University of Missouri Kansas City School of Medicine, Kansas City, MO, USA
| | - Tomi Pastinen
- Genomic Medicine Center, Children’s Mercy Hospital, Kansas City, MO, USA
- University of Missouri Kansas City School of Medicine, Kansas City, MO, USA
| | - Emily G. Farrow
- Department of Pathology and Laboratory Medicine, Children’s Mercy Hospital, Kansas City, MO, USA
- Genomic Medicine Center, Children’s Mercy Hospital, Kansas City, MO, USA
- University of Missouri Kansas City School of Medicine, Kansas City, MO, USA
| | - Janda L. Jenkins
- Department of Genetics, Children’s Mercy Hospital, Kansas City, MO, USA
| | - Mara L. Becker
- Division of Rheumatology, Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Stephen C. Wong
- Division of Rheumatology, Department of Pediatrics, Seattle Children’s Hospital, Seattle, WA, USA
| | - Anne M. Stevens
- Division of Rheumatology, Department of Pediatrics, Seattle Children’s Hospital, Seattle, WA, USA
- Johnson & Johnson Innovative Medicine, Spring House, PA, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Catherine Otten
- Division of Pediatric Neurology, Department of Neurology, Seattle Children’s Hospital, University of Washington, Seattle, WA, USA
| | - Eric J. Allenspach
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Devon E. Bonner
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
- Division of Medical Genetics, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jonathan A. Bernstein
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
- Division of Medical Genetics, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew T. Wheeler
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Robert A. Saxton
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Bo Liu
- Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Olivia Majer
- Max Planck Institute for Infection Biology, Berlin, Germany
| | - Gregory M. Barton
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
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17
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Albakova Z. HSP90 multi-functionality in cancer. Front Immunol 2024; 15:1436973. [PMID: 39148727 PMCID: PMC11324539 DOI: 10.3389/fimmu.2024.1436973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 07/18/2024] [Indexed: 08/17/2024] Open
Abstract
The 90-kDa heat shock proteins (HSP90s) are molecular chaperones essential for folding, unfolding, degradation and activity of a wide range of client proteins. HSP90s and their cognate co-chaperones are subject to various post-translational modifications, functional consequences of which are not fully understood in cancer. Intracellular and extracellular HSP90 family members (HSP90α, HSP90β, GRP94 and TRAP1) promote cancer by sustaining various hallmarks of cancer, including cell death resistance, replicative immortality, tumor immunity, angiogenesis, invasion and metastasis. Given the importance of HSP90 in tumor progression, various inhibitors and HSP90-based vaccines were developed for the treatment of cancer. Further understanding of HSP90 functions in cancer may provide new opportunities and novel therapeutic strategies for the treatment of cancer.
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Affiliation(s)
- Zarema Albakova
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
- Chokan Limited Liability Partnership, Almaty, Kazakhstan
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18
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Manea M, Mărunțelu I, Constantinescu I. Extended analysis on peripheral blood cytokines correlated with hepatitis B virus viral load in chronically infected patients - a systematic review and meta-analysis. Front Med (Lausanne) 2024; 11:1429926. [PMID: 39149606 PMCID: PMC11325457 DOI: 10.3389/fmed.2024.1429926] [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: 05/09/2024] [Accepted: 07/08/2024] [Indexed: 08/17/2024] Open
Abstract
Background Hepatitis B Virus (HBV) can affect life quality. Monitoring and understanding the fluctuations of the HBV level of viremia related to the intricate immune activity of the host helps in the development of new treatment strategies and evaluation patterns. This meta-analysis presents the correlations between cytokines and the level of viremia in chronic HBV patients for a better comprehension of the immune mechanisms behind this infection. Methods We used PRISMA guidelines for this meta-analysis. The databases assessed were PUBMED, WEB OF SCIENCE, SCOPUS, and Cochrane Library. ZOTERO and PlotDigitizer helped the systematic research process. We extracted information related to the correlations between cytokines and the HBV-DNA level. Effect measures included comparisons between standardized mean differences and correlation coefficients. We evaluated retrieved articles with the Newcastle-Ottawa Quality Assessment Scale (NOS). The R 4.2.2 software displayed the statistical calculation and graphical representations. Results From 58,169 records, we extracted 16 articles with 32 different cytokine determinations. The main interleukins included in detection panels were IL-10 and IL-21. The meta-correlation analysis comprised 1,199 chronic HBV patients. The standardized mean difference between cytokine levels in HBV patients and healthy controls was 0.82 (95% CI = [-0.19, 1.84], p = 0.11). We observed a significant, fair, pooled correlation coefficient between IL-10, IL-9, and the viral load (r = 0.52, 95% CI = [0.19, 0.85]). Conclusion This meta-analysis brings novelty because it gives a first rigorous systematic look at multiple studies with many cytokines. Our research approaches a debatable issue and gives a possible solution for settling controversies. Future studies can arise towards understanding the immune disruption in HBV and the development of new, improved assays for prognosis.
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Affiliation(s)
- Marina Manea
- Immunology and Transplant Immunology, University of Medicine and Pharmacy "Carol Davila", Bucharest, Romania
| | - Ion Mărunțelu
- Immunology and Transplant Immunology, University of Medicine and Pharmacy "Carol Davila", Bucharest, Romania
- Center of Immunogenetics and Virology, Fundeni Clinical Institute, Bucharest, Romania
| | - Ileana Constantinescu
- Immunology and Transplant Immunology, University of Medicine and Pharmacy "Carol Davila", Bucharest, Romania
- Center of Immunogenetics and Virology, Fundeni Clinical Institute, Bucharest, Romania
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19
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Tsai CY, Oo M, Peh JH, Yeo BCM, Aptekmann A, Lee B, Liu JJJ, Tsao WS, Dick T, Fink K, Gengenbacher M. Splenic marginal zone B cells restrict Mycobacterium tuberculosis infection by shaping the cytokine pattern and cell-mediated immunity. Cell Rep 2024; 43:114426. [PMID: 38959109 PMCID: PMC11307145 DOI: 10.1016/j.celrep.2024.114426] [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: 12/14/2023] [Revised: 04/29/2024] [Accepted: 06/17/2024] [Indexed: 07/05/2024] Open
Abstract
Understanding the role of B cells in tuberculosis (TB) is crucial for developing new TB vaccines. However, the changes in B cell immune landscapes during TB and their functional implications remain incompletely explored. Using high-dimensional flow cytometry to map the immune landscape in response to Mycobacterium tuberculosis (Mtb) infection, our results show an accumulation of marginal zone B (MZB) cells and other unconventional B cell subsets in the lungs and spleen, shaping an unconventional B cell landscape. These MZB cells exhibit activated and memory-like phenotypes, distinguishing their functional profiles from those of conventional B cells. Notably, functional studies show that MZB cells produce multiple cytokines and contribute to systemic protection against TB by shaping cytokine patterns and cell-mediated immunity. These changes in the immune landscape are reversible upon successful TB chemotherapy. Our study suggests that, beyond antibody production, targeting the regulatory function of B cells may be a valuable strategy for TB vaccine development.
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Affiliation(s)
- Chen-Yu Tsai
- Center for Discovery and Innovation (CDI), Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA
| | - Myo Oo
- Center for Discovery and Innovation (CDI), Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA
| | - Jih Hou Peh
- Biosafety Level 3 Core, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Level 15, Centre for Translational Medicine (MD6), NUS, 14 Medical Drive, Singapore 117599, Singapore
| | - Benjamin C M Yeo
- Infectious Diseases Translational Research Programme and Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Level 2, Blk MD4, 5 Science Drive 2, Singapore 117545, Singapore
| | - Ariel Aptekmann
- Center for Discovery and Innovation (CDI), Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA
| | - Bernett Lee
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research, Biopolis, 8A Biomedical Grove, Level 3 & 4, Immunos Building, Singapore 138648, Singapore; Centre for Biomedical Informatics, Lee Kong Chian School of Medicine, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore; A(∗)STAR Infectious Diseases Labs, Agency for Science, Technology and Research, 8A Biomedical Grove #05-13, Immunos, Singapore 138648, Singapore
| | - Joe J J Liu
- Biosafety Level 3 Core, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Level 15, Centre for Translational Medicine (MD6), NUS, 14 Medical Drive, Singapore 117599, Singapore
| | - Wen-Shan Tsao
- Center for Discovery and Innovation (CDI), Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA
| | - Thomas Dick
- Center for Discovery and Innovation (CDI), Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA; Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA
| | - Katja Fink
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research, Biopolis, 8A Biomedical Grove, Level 3 & 4, Immunos Building, Singapore 138648, Singapore
| | - Martin Gengenbacher
- Center for Discovery and Innovation (CDI), Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA; Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA.
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20
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Tarannum M, Dinh K, Vergara J, Birch G, Abdulhamid YZ, Kaplan IE, Ay O, Maia A, Beaver O, Sheffer M, Shapiro R, Ali AK, Dong H, Ham JD, Bobilev E, James S, Cameron AB, Nguyen QD, Ganapathy S, Chayawatto C, Koreth J, Paweletz CP, Gokhale PC, Barbie DA, Matulonis UA, Soiffer RJ, Ritz J, Porter RL, Chen J, Romee R. CAR memory-like NK cells targeting the membrane proximal domain of mesothelin demonstrate promising activity in ovarian cancer. SCIENCE ADVANCES 2024; 10:eadn0881. [PMID: 38996027 PMCID: PMC11244547 DOI: 10.1126/sciadv.adn0881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 06/10/2024] [Indexed: 07/14/2024]
Abstract
Epithelial ovarian cancer (EOC) remains one of the most lethal gynecological cancers. Cytokine-induced memory-like (CIML) natural killer (NK) cells have shown promising results in preclinical and early-phase clinical trials. In the current study, CIML NK cells demonstrated superior antitumor responses against a panel of EOC cell lines, increased expression of activation receptors, and up-regulation of genes involved in cell cycle/proliferation and down-regulation of inhibitory/suppressive genes. CIML NK cells transduced with a chimeric antigen receptor (CAR) targeting the membrane-proximal domain of mesothelin (MSLN) further improved the antitumor responses against MSLN-expressing EOC cells and patient-derived xenograft tumor cells. CAR arming of the CIML NK cells subtanstially reduced their dysfunction in patient-derived ascites fluid with transcriptomic changes related to altered metabolism and tonic signaling as potential mechanisms. Lastly, the adoptive transfer of MSLN-CAR CIML NK cells demonstrated remarkable inhibition of tumor growth and prevented metastatic spread in xenograft mice, supporting their potential as an effective therapeutic strategy in EOC.
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MESH Headings
- Animals
- Female
- Humans
- Mice
- Carcinoma, Ovarian Epithelial/metabolism
- Carcinoma, Ovarian Epithelial/pathology
- Carcinoma, Ovarian Epithelial/immunology
- Carcinoma, Ovarian Epithelial/therapy
- Cell Line, Tumor
- GPI-Linked Proteins/metabolism
- GPI-Linked Proteins/genetics
- Immunologic Memory
- Immunotherapy, Adoptive/methods
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Mesothelin
- Ovarian Neoplasms/metabolism
- Ovarian Neoplasms/pathology
- Ovarian Neoplasms/immunology
- Ovarian Neoplasms/therapy
- Protein Domains
- Receptors, Chimeric Antigen/metabolism
- Receptors, Chimeric Antigen/immunology
- Receptors, Chimeric Antigen/genetics
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Mubin Tarannum
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Khanhlinh Dinh
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Juliana Vergara
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Grace Birch
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Yasmin Z. Abdulhamid
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Isabel E. Kaplan
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Oyku Ay
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Andreia Maia
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Owen Beaver
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Michal Sheffer
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Roman Shapiro
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Alaa Kassim Ali
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Han Dong
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - James Dongjoo Ham
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Eden Bobilev
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Sydney James
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Amy B. Cameron
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Quang-De Nguyen
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Suthakar Ganapathy
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Chayapatou Chayawatto
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - John Koreth
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Cloud P. Paweletz
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Prafulla C. Gokhale
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - David A. Barbie
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Division of Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ursula A. Matulonis
- Division of Gynecologic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Robert J. Soiffer
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jerome Ritz
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Rebecca L. Porter
- Division of Gynecologic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jianzhu Chen
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rizwan Romee
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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21
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Gleeson TA, Kaiser C, Lawrence CB, Brough D, Allan SM, Green JP. The NLRP3 inflammasome is essential for IL-18 production in a murine model of macrophage activation syndrome. Dis Model Mech 2024; 17:dmm050762. [PMID: 38775430 DOI: 10.1242/dmm.050762] [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: 02/26/2024] [Accepted: 05/13/2024] [Indexed: 06/04/2024] Open
Abstract
Hyperinflammatory disease is associated with an aberrant immune response resulting in cytokine storm. One such instance of hyperinflammatory disease is known as macrophage activation syndrome (MAS). The pathology of MAS can be characterised by significantly elevated serum levels of interleukin-18 (IL-18) and interferon gamma (IFNγ). Given the role for IL-18 in MAS, we sought to establish the role of inflammasomes in the disease process. Using a murine model of CpG-oligonucleotide-induced MAS, we discovered that the expression of the NLRP3 inflammasome was increased and correlated with IL-18 production. Inhibition of the NLRP3 inflammasome or the downstream caspase-1 prevented MAS-mediated upregulation of IL-18 in the plasma but, interestingly, did not alleviate key features of hyperinflammatory disease including hyperferritinaemia and splenomegaly. Furthermore blockade of IL-1 receptor with its antagonist IL-1Ra did not prevent the development of CpG-induced MAS, despite being clinically effective in the treatment of MAS. These data demonstrate that, during the development of MAS, the NLRP3 inflammasome was essential for the elevation in plasma IL-18 - a key cytokine in clinical cases of MAS - but was not a driving factor in the pathogenesis of CpG-induced MAS.
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Affiliation(s)
- Tara A Gleeson
- Division of Neuroscience, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
- Geoffrey Jefferson Brain Research Centre, The Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Manchester M6 8HD, UK
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester M13 9PL, UK
| | | | - Catherine B Lawrence
- Division of Neuroscience, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
- Geoffrey Jefferson Brain Research Centre, The Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Manchester M6 8HD, UK
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester M13 9PL, UK
| | - David Brough
- Division of Neuroscience, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
- Geoffrey Jefferson Brain Research Centre, The Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Manchester M6 8HD, UK
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester M13 9PL, UK
| | - Stuart M Allan
- Division of Neuroscience, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
- Geoffrey Jefferson Brain Research Centre, The Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Manchester M6 8HD, UK
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester M13 9PL, UK
| | - Jack P Green
- Division of Neuroscience, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
- Geoffrey Jefferson Brain Research Centre, The Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Manchester M6 8HD, UK
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester M13 9PL, UK
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22
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He S, Gubin MM, Rafei H, Basar R, Dede M, Jiang X, Liang Q, Tan Y, Kim K, Gillison ML, Rezvani K, Peng W, Haymaker C, Hernandez S, Solis LM, Mohanty V, Chen K. Elucidating immune-related gene transcriptional programs via factorization of large-scale RNA-profiles. iScience 2024; 27:110096. [PMID: 38957791 PMCID: PMC11217617 DOI: 10.1016/j.isci.2024.110096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 04/03/2024] [Accepted: 05/21/2024] [Indexed: 07/04/2024] Open
Abstract
Recent developments in immunotherapy, including immune checkpoint blockade (ICB) and adoptive cell therapy (ACT), have encountered challenges such as immune-related adverse events and resistance, especially in solid tumors. To advance the field, a deeper understanding of the molecular mechanisms behind treatment responses and resistance is essential. However, the lack of functionally characterized immune-related gene sets has limited data-driven immunological research. To address this gap, we adopted non-negative matrix factorization on 83 human bulk RNA sequencing (RNA-seq) datasets and constructed 28 immune-specific gene sets. After rigorous immunologist-led manual annotations and orthogonal validations across immunological contexts and functional omics data, we demonstrated that these gene sets can be applied to refine pan-cancer immune subtypes, improve ICB response prediction and functionally annotate spatial transcriptomic data. These functional gene sets, informing diverse immune states, will advance our understanding of immunology and cancer research.
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Affiliation(s)
- Shan He
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Matthew M. Gubin
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hind Rafei
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rafet Basar
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Merve Dede
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xianli Jiang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Qingnan Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yukun Tan
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kunhee Kim
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maura L. Gillison
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Katayoun Rezvani
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Weiyi Peng
- Department of Biology and Biochemistry, The University of Houston, Houston, TX, USA
| | - Cara Haymaker
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sharia Hernandez
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Luisa M. Solis
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vakul Mohanty
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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23
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Kwon JJ, Pan J, Gonzalez G, Hahn WC, Zitnik M. On knowing a gene: A distributional hypothesis of gene function. Cell Syst 2024; 15:488-496. [PMID: 38810640 PMCID: PMC11189734 DOI: 10.1016/j.cels.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 02/25/2024] [Accepted: 04/30/2024] [Indexed: 05/31/2024]
Abstract
As words can have multiple meanings that depend on sentence context, genes can have various functions that depend on the surrounding biological system. This pleiotropic nature of gene function is limited by ontologies, which annotate gene functions without considering biological contexts. We contend that the gene function problem in genetics may be informed by recent technological leaps in natural language processing, in which representations of word semantics can be automatically learned from diverse language contexts. In contrast to efforts to model semantics as "is-a" relationships in the 1990s, modern distributional semantics represents words as vectors in a learned semantic space and fuels current advances in transformer-based models such as large language models and generative pre-trained transformers. A similar shift in thinking of gene functions as distributions over cellular contexts may enable a similar breakthrough in data-driven learning from large biological datasets to inform gene function.
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Affiliation(s)
- Jason J Kwon
- Dana-Farber Cancer Institute and Harvard Medical School, Department of Medical Oncology, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Joshua Pan
- Dana-Farber Cancer Institute and Harvard Medical School, Department of Medical Oncology, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Guadalupe Gonzalez
- Department of Computing, Faculty of Engineering, Imperial College, London SW7 2AZ, UK
| | - William C Hahn
- Dana-Farber Cancer Institute and Harvard Medical School, Department of Medical Oncology, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Marinka Zitnik
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Department of Biomedical Informatics, Boston, MA 02115, USA; Harvard Data Science Initiative, Harvard University, Cambridge, MA 02138, USA; Kempner Institute for the Study of Natural and Artificial Intelligence, Harvard University, Allston, MA 02134, USA.
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24
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Schonblum A, Ali Naser D, Ovadia S, Egbaria M, Puyesky S, Epshtein A, Wald T, Mercado-Medrez S, Ashery-Padan R, Landsman L. Beneficial islet inflammation in health depends on pericytic TLR/MyD88 signaling. J Clin Invest 2024; 134:e179335. [PMID: 38885342 PMCID: PMC11245159 DOI: 10.1172/jci179335] [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: 01/11/2024] [Accepted: 05/24/2024] [Indexed: 06/20/2024] Open
Abstract
While inflammation is beneficial for insulin secretion during homeostasis, its transformation adversely affects β cells and contributes to diabetes. However, the regulation of islet inflammation for maintaining glucose homeostasis remains largely unknown. Here, we identified pericytes as pivotal regulators of islet immune and β cell function in health. Islets and pancreatic pericytes express various cytokines in healthy humans and mice. To interfere with the pericytic inflammatory response, we selectively inhibited the TLR/MyD88 pathway in these cells in transgenic mice. The loss of MyD88 impaired pericytic cytokine production. Furthermore, MyD88-deficient mice exhibited skewed islet inflammation with fewer cells, an impaired macrophage phenotype, and reduced IL-1β production. This aberrant pericyte-orchestrated islet inflammation was associated with β cell dedifferentiation and impaired glucose response. Additionally, we found that Cxcl1, a pericytic MyD88-dependent cytokine, promoted immune IL-1β production. Treatment with either Cxcl1 or IL-1β restored the mature β cell phenotype and glucose response in transgenic mice, suggesting a potential mechanism through which pericytes and immune cells regulate glucose homeostasis. Our study revealed pericyte-orchestrated islet inflammation as a crucial element in glucose regulation, implicating this process as a potential therapeutic target for diabetes.
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Affiliation(s)
- Anat Schonblum
- Department of Cell and Development Biology, Faculty of Medical and Health Sciences and
| | - Dunia Ali Naser
- Department of Cell and Development Biology, Faculty of Medical and Health Sciences and
| | - Shai Ovadia
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medical and Health Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Mohammed Egbaria
- Department of Cell and Development Biology, Faculty of Medical and Health Sciences and
| | - Shani Puyesky
- Department of Cell and Development Biology, Faculty of Medical and Health Sciences and
| | - Alona Epshtein
- Department of Cell and Development Biology, Faculty of Medical and Health Sciences and
| | - Tomer Wald
- Department of Cell and Development Biology, Faculty of Medical and Health Sciences and
| | - Sophia Mercado-Medrez
- Department of Cell and Development Biology, Faculty of Medical and Health Sciences and
| | - Ruth Ashery-Padan
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medical and Health Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Limor Landsman
- Department of Cell and Development Biology, Faculty of Medical and Health Sciences and
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25
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Belean A, Xue E, Cisneros B, Roberson EDO, Paley MA, Bigley TM. Transcriptomic profiling of thymic dysregulation and viral tropism after neonatal roseolovirus infection. Front Immunol 2024; 15:1375508. [PMID: 38895117 PMCID: PMC11183875 DOI: 10.3389/fimmu.2024.1375508] [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: 01/23/2024] [Accepted: 05/10/2024] [Indexed: 06/21/2024] Open
Abstract
Introduction Herpesviruses, including the roseoloviruses, have been linked to autoimmune disease. The ubiquitous and chronic nature of these infections have made it difficult to establish a causal relationship between acute infection and subsequent development of autoimmunity. We have shown that murine roseolovirus (MRV), which is highly related to human roseoloviruses, induces thymic atrophy and disruption of central tolerance after neonatal infection. Moreover, neonatal MRV infection results in development of autoimmunity in adult mice, long after resolution of acute infection. This suggests that MRV induces durable immune dysregulation. Methods In the current studies, we utilized single-cell RNA sequencing (scRNAseq) to study the tropism of MRV in the thymus and determine cellular processes in the thymus that were disrupted by neonatal MRV infection. We then utilized tropism data to establish a cell culture system. Results Herein, we describe how MRV alters the thymic transcriptome during acute neonatal infection. We found that MRV infection resulted in major shifts in inflammatory, differentiation and cell cycle pathways in the infected thymus. We also observed shifts in the relative number of specific cell populations. Moreover, utilizing expression of late viral transcripts as a proxy of viral replication, we identified the cellular tropism of MRV in the thymus. This approach demonstrated that double negative, double positive, and CD4 single positive thymocytes, as well as medullary thymic epithelial cells were infected by MRV in vivo. Finally, by applying pseudotime analysis to viral transcripts, which we refer to as "pseudokinetics," we identified viral gene transcription patterns associated with specific cell types and infection status. We utilized this information to establish the first cell culture systems susceptible to MRV infection in vitro. Conclusion Our research provides the first complete picture of roseolovirus tropism in the thymus after neonatal infection. Additionally, we identified major transcriptomic alterations in cell populations in the thymus during acute neonatal MRV infection. These studies offer important insight into the early events that occur after neonatal MRV infection that disrupt central tolerance and promote autoimmune disease.
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Affiliation(s)
- Andrei Belean
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Eden Xue
- Division of Rheumatology, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States
| | - Benjamin Cisneros
- Division of Rheumatology, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States
| | - Elisha D. O. Roberson
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
- Division of Rheumatology, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Michael A. Paley
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Tarin M. Bigley
- Division of Rheumatology, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States
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26
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He S, Gubin MM, Rafei H, Basar R, Dede M, Jiang X, Liang Q, Tan Y, Kim K, Gillison ML, Rezvani K, Peng W, Haymaker C, Hernandez S, Solis LM, Mohanty V, Chen K. Elucidating immune-related gene transcriptional programs via factorization of large-scale RNA-profiles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.10.593433. [PMID: 38798470 PMCID: PMC11118452 DOI: 10.1101/2024.05.10.593433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Recent developments in immunotherapy, including immune checkpoint blockade (ICB) and adoptive cell therapy, have encountered challenges such as immune-related adverse events and resistance, especially in solid tumors. To advance the field, a deeper understanding of the molecular mechanisms behind treatment responses and resistance is essential. However, the lack of functionally characterized immune-related gene sets has limited data-driven immunological research. To address this gap, we adopted non-negative matrix factorization on 83 human bulk RNA-seq datasets and constructed 28 immune-specific gene sets. After rigorous immunologist-led manual annotations and orthogonal validations across immunological contexts and functional omics data, we demonstrated that these gene sets can be applied to refine pan-cancer immune subtypes, improve ICB response prediction and functionally annotate spatial transcriptomic data. These functional gene sets, informing diverse immune states, will advance our understanding of immunology and cancer research.
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27
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van Hees EP, Morton LT, Remst DFG, Wouters AK, Van den Eynde A, Falkenburg JHF, Heemskerk MH. Self-sufficient primary natural killer cells engineered to express T cell receptors and interleukin-15 exhibit improved effector function and persistence. Front Immunol 2024; 15:1368290. [PMID: 38690288 PMCID: PMC11058644 DOI: 10.3389/fimmu.2024.1368290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/03/2024] [Indexed: 05/02/2024] Open
Abstract
Background NK cells can be genetically engineered to express a transgenic T-cell receptor (TCR). This approach offers an alternative strategy to target heterogenous tumors, as NK:TCR cells can eradicate both tumor cells with high expression of HLA class I and antigen of interest or HLA class I negative tumors. Expansion and survival of NK cells relies on the presence of IL-15. Therefore, autonomous production of IL-15 by NK:TCR cells might improve functional persistence of NK cells. Here we present an optimized NK:TCR product harnessed with a construct encoding for soluble IL-15 (NK:TCR/IL-15), to support their proliferation, persistence and cytotoxic capabilities. Methods Expression of tumor-specific TCRs in peripheral blood derived NK-cells was achieved following retroviral transduction. NK:TCR/IL-15 cells were compared with NK:TCR cells for autonomous cytokine production, proliferation and survival. NK:BOB1-TCR/IL-15 cells, expressing a HLA-B*07:02-restricted TCR against BOB1, a B-cell lineage specific transcription factor highly expressed in all B-cell malignancies, were compared with control NK:BOB1-TCR and NK:CMV-TCR/IL-15 cells for effector function against TCR antigen positive malignant B-cell lines in vitro and in vivo. Results Viral incorporation of the interleukin-15 gene into engineered NK:TCR cells was feasible and high expression of the TCR was maintained, resulting in pure NK:TCR/IL-15 cell products generated from peripheral blood of multiple donors. Self-sufficient secretion of IL-15 by NK:TCR cells enables engineered NK cells to proliferate in vitro without addition of extra cytokines. NK:TCR/IL-15 demonstrated a marked enhancement of TCR-mediated cytotoxicity as well as enhanced NK-mediated cytotoxicity resulting in improved persistence and performance of NK:BOB1-TCR/IL-15 cells in an orthotopic multiple myeloma mouse model. However, in contrast to prolonged anti-tumor reactivity by NK:BOB1-TCR/IL-15, we observed in one of the experiments an accumulation of NK:BOB1-TCR/IL-15 cells in several organs of treated mice, leading to unexpected death 30 days post-NK infusion. Conclusion This study showed that NK:TCR/IL-15 cells secrete low levels of IL-15 and can proliferate in an environment lacking cytokines. Repeated in vitro and in vivo experiments confirmed the effectiveness and target specificity of our product, in which addition of IL-15 supports TCR- and NK-mediated cytotoxicity.
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Affiliation(s)
- Els P. van Hees
- Department of Hematology, Leiden University Medical Centre (LUMC), Leiden, Netherlands
| | - Laura T. Morton
- Department of Hematology, Leiden University Medical Centre (LUMC), Leiden, Netherlands
| | - Dennis F. G. Remst
- Department of Hematology, Leiden University Medical Centre (LUMC), Leiden, Netherlands
| | - Anne K. Wouters
- Department of Hematology, Leiden University Medical Centre (LUMC), Leiden, Netherlands
| | - Astrid Van den Eynde
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), Antwerp, Belgium
| | | | - Mirjam H.M. Heemskerk
- Department of Hematology, Leiden University Medical Centre (LUMC), Leiden, Netherlands
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28
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Wood EK, Reid BM, Sheerar DS, Donzella B, Gunnar MR, Coe CL. Lingering Effects of Early Institutional Rearing and Cytomegalovirus Infection on the Natural Killer Cell Repertoire of Adopted Adolescents. Biomolecules 2024; 14:456. [PMID: 38672472 PMCID: PMC11047877 DOI: 10.3390/biom14040456] [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: 02/13/2024] [Revised: 03/26/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Adversity during infancy can affect neurobehavioral development and perturb the maturation of physiological systems. Dysregulated immune and inflammatory responses contribute to many of the later effects on health. Whether normalization can occur following a transition to more nurturing, benevolent conditions is unclear. To assess the potential for recovery, blood samples were obtained from 45 adolescents adopted by supportive families after impoverished infancies in institutional settings (post-institutionalized, PI). Their immune profiles were compared to 39 age-matched controls raised by their biological parents (non-adopted, NA). Leukocytes were immunophenotyped, and this analysis focuses on natural killer (NK) cell populations in circulation. Cytomegalovirus (CMV) seropositivity was evaluated to determine if early infection contributed to the impact of an atypical rearing. Associations with tumor necrosis factor-alpha (TNF-α) and interferon-gamma (IFN-γ), two cytokines released by activated NK cells, were examined. Compared to the NA controls, PI adolescents had a lower percent of CD56bright NK cells in circulation, higher TNF-α levels, and were more likely to be infected with CMV. PI adolescents who were latent carriers of CMV expressed NKG2C and CD57 surface markers on more NK cells, including CD56dim lineages. The NK cell repertoire revealed lingering immune effects of early rearing while still maintaining an overall integrity and resilience.
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Affiliation(s)
- Elizabeth K. Wood
- Department of Psychiatry, Oregon Health & Science University, Portland, OR 97239, USA
| | - Brie M. Reid
- Department of Psychiatry and Human Behavior, Brown University, Providence, RI 02906, USA;
| | - Dagna S. Sheerar
- Wisconsin Institute of Medical Research, University of Wisconsin Comprehensive Carbone Cancer Center, Madison, WI 53706, USA;
| | - Bonny Donzella
- Institute of Child Development, University of Minnesota, Minneapolis, MN 55455, USA; (B.D.); (M.R.G.)
| | - Megan R. Gunnar
- Institute of Child Development, University of Minnesota, Minneapolis, MN 55455, USA; (B.D.); (M.R.G.)
| | - Christopher L. Coe
- Department of Psychology, University of Wisconsin-Madison, Madison, WI 54706, USA;
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29
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Dong J, Zhao J, Wu Z, Liu J, Wang B, Qi X. The Predictive Value of Neutrophil Extracellular Trap-Related Risk Score in Prognosis and Immune Microenvironment of Colorectal Cancer Patients. Mol Biotechnol 2024:10.1007/s12033-024-01135-4. [PMID: 38580851 DOI: 10.1007/s12033-024-01135-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/23/2024] [Indexed: 04/07/2024]
Abstract
Colorectal cancer (CRC) has brought great healthy burden for patients. Neutrophil extracellular traps (NETs) have been explored in several tumors, while it remains largely unclear in CRC. CRC-related data were downloaded from Cancer Genome Atlas and Gene Expression Omnibus databases. Then, a NET risk score was built after univariate Cox and LASSO Cox regression analysis. Prognostic value was evaluated via survival analysis, stratification analysis, and ROC analysis. The functional enrichment analysis was conducted basing on bulk and scRNA-seq data. The immune landscape difference was analyzed using CIBERSORT, XCell, and MCPcounter portals. NET risk score was built for CRC patients, basing on G0S2, HIST1H2BC, CRISPLD2, and IL17A. In TCGA-CRC and validation datasets, regardless of age or gender, high-risk CRC patients had significantly worse prognosis, besides higher NET risk score was mainly found in samples with MSI-H and advanced T, N, and M stages. Employing multiple databases, we noticed that M0 and M2 Macrophages infiltrated the most in high-risk CRC patients, besides M2 Macrophages and neutrophils showed positive correlation with NET risk score. A novel reliable prognostic NET risk score was developed for CRC patients, and high-risk patients had unfavorable prognosis with advanced disease status.
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Affiliation(s)
- Jiuxing Dong
- Department of Oncology, Hebei Petrochina Central Hospital, NO. 51 Xinkai Road, Langfang, 065000, Hebei, China
| | - Jia Zhao
- Department of Oncology, Hebei Petrochina Central Hospital, NO. 51 Xinkai Road, Langfang, 065000, Hebei, China
| | - Zhenming Wu
- Department of Oncology, Hebei Petrochina Central Hospital, NO. 51 Xinkai Road, Langfang, 065000, Hebei, China
| | - Jun Liu
- Department of Oncology, Hebei Petrochina Central Hospital, NO. 51 Xinkai Road, Langfang, 065000, Hebei, China
| | - Baoxin Wang
- Department of Oncology, Hebei Petrochina Central Hospital, NO. 51 Xinkai Road, Langfang, 065000, Hebei, China
| | - Xiuheng Qi
- Department of Oncology, Hebei Petrochina Central Hospital, NO. 51 Xinkai Road, Langfang, 065000, Hebei, China.
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30
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Li X, Sun S, Zhang W, Liang Z, Fang Y, Sun T, Wan Y, Ma X, Zhang S, Xu Y, Tian R. Identification of genetic modifiers enhancing B7-H3-targeting CAR T cell therapy against glioblastoma through large-scale CRISPRi screening. J Exp Clin Cancer Res 2024; 43:95. [PMID: 38561797 PMCID: PMC10986136 DOI: 10.1186/s13046-024-03027-6] [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: 01/19/2024] [Accepted: 03/24/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Glioblastoma multiforme (GBM) is a highly aggressive brain tumor with a poor prognosis. Current treatment options are limited and often ineffective. CAR T cell therapy has shown success in treating hematologic malignancies, and there is growing interest in its potential application in solid tumors, including GBM. However, current CAR T therapy lacks clinical efficacy against GBM due to tumor-related resistance mechanisms and CAR T cell deficiencies. Therefore, there is a need to improve CAR T cell therapy efficacy in GBM. METHODS We conducted large-scale CRISPR interference (CRISPRi) screens in GBM cell line U87 MG cells co-cultured with B7-H3 targeting CAR T cells to identify genetic modifiers that can enhance CAR T cell-mediated tumor killing. Flow cytometry-based tumor killing assay and CAR T cell activation assay were performed to validate screening hits. Bioinformatic analyses on bulk and single-cell RNA sequencing data and the TCGA database were employed to elucidate the mechanism underlying enhanced CAR T efficacy upon knocking down the selected screening hits in U87 MG cells. RESULTS We established B7-H3 as a targetable antigen for CAR T therapy in GBM. Through large-scale CRISPRi screening, we discovered genetic modifiers in GBM cells, including ARPC4, PI4KA, ATP6V1A, UBA1, and NDUFV1, that regulated the efficacy of CAR T cell-mediated tumor killing. Furthermore, we discovered that TNFSF15 was upregulated in both ARPC4 and NDUFV1 knockdown GBM cells and revealed an immunostimulatory role of TNFSF15 in modulating tumor-CAR T interaction to enhance CAR T cell efficacy. CONCLUSIONS Our study highlights the power of CRISPR-based genetic screening in investigating tumor-CAR T interaction and identifies potential druggable targets in tumor cells that confer resistance to CAR T cell killing. Furthermore, we devised targeted strategies that synergize with CAR T therapy against GBM. These findings shed light on the development of novel combinatorial strategies for effective immunotherapy of GBM and other solid tumors.
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Affiliation(s)
- Xing Li
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518055, China
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518055, China
| | - Shiyu Sun
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518055, China
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710004, China
| | - Wansong Zhang
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518055, China
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518055, China
| | - Ziwei Liang
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518055, China
| | - Yitong Fang
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518055, China
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518055, China
| | - Tianhu Sun
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518055, China
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518055, China
| | - Yong Wan
- Department of Neurosurgery, Shenzhen People's Hospital, Shenzhen, Guangdong, 518020, China
| | - Xingcong Ma
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710004, China
| | - Shuqun Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710004, China.
| | - Yang Xu
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518055, China.
| | - Ruilin Tian
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518055, China.
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518055, China.
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31
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Schäfer PSL, Dimitrov D, Villablanca EJ, Saez-Rodriguez J. Integrating single-cell multi-omics and prior biological knowledge for a functional characterization of the immune system. Nat Immunol 2024; 25:405-417. [PMID: 38413722 DOI: 10.1038/s41590-024-01768-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 01/16/2024] [Indexed: 02/29/2024]
Abstract
The immune system comprises diverse specialized cell types that cooperate to defend the host against a wide range of pathogenic threats. Recent advancements in single-cell and spatial multi-omics technologies provide rich information about the molecular state of immune cells. Here, we review how the integration of single-cell and spatial multi-omics data with prior knowledge-gathered from decades of detailed biochemical studies-allows us to obtain functional insights, focusing on gene regulatory processes and cell-cell interactions. We present diverse applications in immunology and critically assess underlying assumptions and limitations. Finally, we offer a perspective on the ongoing technological and algorithmic developments that promise to get us closer to a systemic mechanistic understanding of the immune system.
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Affiliation(s)
- Philipp Sven Lars Schäfer
- Institute for Computational Bioscience, Faculty of Medicine and Heidelberg University Hospital, Heidelberg University, Heidelberg, Germany
| | - Daniel Dimitrov
- Institute for Computational Bioscience, Faculty of Medicine and Heidelberg University Hospital, Heidelberg University, Heidelberg, Germany
| | - Eduardo J Villablanca
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
- Center of Molecular Medicine, Stockholm, Sweden
| | - Julio Saez-Rodriguez
- Institute for Computational Bioscience, Faculty of Medicine and Heidelberg University Hospital, Heidelberg University, Heidelberg, Germany.
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32
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Landuzzi L, Ruzzi F, Pellegrini E, Lollini PL, Scotlandi K, Manara MC. IL-1 Family Members in Bone Sarcomas. Cells 2024; 13:233. [PMID: 38334625 PMCID: PMC10854900 DOI: 10.3390/cells13030233] [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: 12/30/2023] [Revised: 01/17/2024] [Accepted: 01/24/2024] [Indexed: 02/10/2024] Open
Abstract
IL-1 family members have multiple pleiotropic functions affecting various tissues and cells, including the regulation of the immune response, hematopoietic homeostasis, bone remodeling, neuronal physiology, and synaptic plasticity. Many of these activities are involved in various pathological processes and immunological disorders, including tumor initiation and progression. Indeed, IL-1 family members have been described to contribute to shaping the tumor microenvironment (TME), determining immune evasion and drug resistance, and to sustain tumor aggressiveness and metastasis. This review addresses the role of IL-1 family members in bone sarcomas, particularly the highly metastatic osteosarcoma (OS) and Ewing sarcoma (EWS), and discusses the IL-1-family-related mechanisms that play a role in bone metastasis development. We also consider the therapeutic implications of targeting IL-1 family members, which have been proposed as (i) relevant targets for anti-tumor and anti-metastatic drugs; (ii) immune checkpoints for immune suppression; and (iii) potential antigens for immunotherapy.
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Affiliation(s)
- Lorena Landuzzi
- Experimental Oncology Laboratory, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy; (E.P.); (K.S.); (M.C.M.)
| | - Francesca Ruzzi
- Laboratory of Immunology and Biology of Metastasis, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy;
| | - Evelin Pellegrini
- Experimental Oncology Laboratory, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy; (E.P.); (K.S.); (M.C.M.)
| | - Pier-Luigi Lollini
- Laboratory of Immunology and Biology of Metastasis, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy;
| | - Katia Scotlandi
- Experimental Oncology Laboratory, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy; (E.P.); (K.S.); (M.C.M.)
| | - Maria Cristina Manara
- Experimental Oncology Laboratory, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy; (E.P.); (K.S.); (M.C.M.)
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33
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Essouma M. Autoimmune inflammatory myopathy biomarkers. Clin Chim Acta 2024; 553:117742. [PMID: 38176522 DOI: 10.1016/j.cca.2023.117742] [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: 07/18/2023] [Revised: 12/21/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024]
Abstract
The autoimmune inflammatory myopathy disease spectrum, commonly known as myositis, is a group of systemic diseases that mainly affect the muscles, skin and lungs. Biomarker assessment helps in understanding disease mechanisms, allowing for the implementation of precise strategies in the classification, diagnosis, and management of these diseases. This review examines the pathogenic mechanisms and highlights current data on blood and tissue biomarkers of autoimmune inflammatory myopathies.
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Affiliation(s)
- Mickael Essouma
- Network of Immunity in Infections, Malignancy and Autoimmunity, Universal Scientific Education and Research Network, Cameroon
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Huang M, Wang L, Zhang Q, Zhou L, Liao R, Wu A, Wang X, Luo J, Huang F, Zou W, Wu J. Interleukins in Platelet Biology: Unraveling the Complex Regulatory Network. Pharmaceuticals (Basel) 2024; 17:109. [PMID: 38256942 PMCID: PMC10820339 DOI: 10.3390/ph17010109] [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: 12/20/2023] [Revised: 01/04/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Interleukins, a diverse family of cytokines produced by various cells, play crucial roles in immune responses, immunoregulation, and a wide range of physiological and pathological processes. In the context of megakaryopoiesis, thrombopoiesis, and platelet function, interleukins have emerged as key regulators, exerting significant influence on the development, maturation, and activity of megakaryocytes (MKs) and platelets. While the therapeutic potential of interleukins in platelet-related diseases has been recognized for decades, their clinical application has been hindered by limitations in basic research and challenges in drug development. Recent advancements in understanding the molecular mechanisms of interleukins and their interactions with MKs and platelets, coupled with breakthroughs in cytokine engineering, have revitalized the field of interleukin-based therapeutics. These breakthroughs have paved the way for the development of more effective and specific interleukin-based therapies for the treatment of platelet disorders. This review provides a comprehensive overview of the effects of interleukins on megakaryopoiesis, thrombopoiesis, and platelet function. It highlights the potential clinical applications of interleukins in regulating megakaryopoiesis and platelet function and discusses the latest bioengineering technologies that could improve the pharmacokinetic properties of interleukins. By synthesizing the current knowledge in this field, this review aims to provide valuable insights for future research into the clinical application of interleukins in platelet-related diseases.
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Affiliation(s)
- Miao Huang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; (M.H.); (Q.Z.)
| | - Long Wang
- Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China; (L.W.); (L.Z.); (R.L.); (A.W.); (F.H.)
| | - Qianhui Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; (M.H.); (Q.Z.)
| | - Ling Zhou
- Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China; (L.W.); (L.Z.); (R.L.); (A.W.); (F.H.)
| | - Rui Liao
- Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China; (L.W.); (L.Z.); (R.L.); (A.W.); (F.H.)
| | - Anguo Wu
- Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China; (L.W.); (L.Z.); (R.L.); (A.W.); (F.H.)
| | - Xinle Wang
- Department of Physiology, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China; (X.W.); (J.L.)
| | - Jiesi Luo
- Department of Physiology, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China; (X.W.); (J.L.)
| | - Feihong Huang
- Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China; (L.W.); (L.Z.); (R.L.); (A.W.); (F.H.)
| | - Wenjun Zou
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; (M.H.); (Q.Z.)
| | - Jianming Wu
- Department of Physiology, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China; (X.W.); (J.L.)
- The Key Laboratory of Medical Electrophysiology, Institute of Cardiovascular Research, Ministry of Education of China, Luzhou 646000, China
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