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Saito S, Shahbaz S, Osman M, Redmond D, Bozorgmehr N, Rosychuk RJ, Lam G, Sligl W, Cohen Tervaert JW, Elahi S. Diverse immunological dysregulation, chronic inflammation, and impaired erythropoiesis in long COVID patients with chronic fatigue syndrome. J Autoimmun 2024; 147:103267. [PMID: 38797051 DOI: 10.1016/j.jaut.2024.103267] [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: 10/30/2023] [Revised: 05/16/2024] [Accepted: 05/22/2024] [Indexed: 05/29/2024]
Abstract
A substantial number of patients recovering from acute SARS-CoV-2 infection present serious lingering symptoms, often referred to as long COVID (LC). However, a subset of these patients exhibits the most debilitating symptoms characterized by ongoing myalgic encephalomyelitis or chronic fatigue syndrome (ME/CFS). We specifically identified and studied ME/CFS patients from two independent LC cohorts, at least 12 months post the onset of acute disease, and compared them to the recovered group (R). ME/CFS patients had relatively increased neutrophils and monocytes but reduced lymphocytes. Selective T cell exhaustion with reduced naïve but increased terminal effector T cells was observed in these patients. LC was associated with elevated levels of plasma pro-inflammatory cytokines, chemokines, Galectin-9 (Gal-9), and artemin (ARTN). A defined threshold of Gal-9 and ARTN concentrations had a strong association with LC. The expansion of immunosuppressive CD71+ erythroid cells (CECs) was noted. These cells may modulate the immune response and contribute to increased ARTN concentration, which correlated with pain and cognitive impairment. Serology revealed an elevation in a variety of autoantibodies in LC. Intriguingly, we found that the frequency of 2B4+CD160+ and TIM3+CD160+ CD8+ T cells completely separated LC patients from the R group. Our further analyses using a multiple regression model revealed that the elevated frequency/levels of CD4 terminal effector, ARTN, CEC, Gal-9, CD8 terminal effector, and MCP1 but lower frequency/levels of TGF-β and MAIT cells can distinguish LC from the R group. Our findings provide a new paradigm in the pathogenesis of ME/CFS to identify strategies for its prevention and treatment.
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Affiliation(s)
- Suguru Saito
- School of Dentistry, Division of Foundational Sciences, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, T6G 2E1, AB, Canada
| | - Shima Shahbaz
- School of Dentistry, Division of Foundational Sciences, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, T6G 2E1, AB, Canada
| | - Mohammed Osman
- Department of Medicine, Division of Rheumatology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, T6G 2E1, AB, Canada
| | - Desiree Redmond
- Department of Medicine, Division of Rheumatology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, T6G 2E1, AB, Canada
| | - Najmeh Bozorgmehr
- School of Dentistry, Division of Foundational Sciences, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, T6G 2E1, AB, Canada
| | - Rhonda J Rosychuk
- Department of Pediatrics, Division of Infectious Disease, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, T6G 2E1, AB, Canada
| | - Grace Lam
- Department of Medicine, Division of Pulmonary Medicine, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, T6G 2E1, AB, Canada
| | - Wendy Sligl
- Department of Critical Care Medicine, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, T6G 2E1, AB, Canada; Department of Medicine, Division of Infectious Diseases, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, T6G 2E1, AB, Canada
| | - Jan Willem Cohen Tervaert
- Department of Medicine, Division of Rheumatology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, T6G 2E1, AB, Canada
| | - Shokrollah Elahi
- School of Dentistry, Division of Foundational Sciences, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, T6G 2E1, AB, Canada; Department of Oncology, University of Alberta, Edmonton, T6G 2E1, AB, Canada; Faculty of Medicine & Dentistry, University of Alberta, Edmonton, T6G 2E1, AB, Canada; Li Ka Shing Institute of Virology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, T6G 2E1, AB, Canada.
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Fan X, Peng H, Wang X, Sun Y, Dong Y, Zhou J, Chen J, Huang S. Tumor-associated CD8 +T cell tolerance induced by erythroid progenitor cells. Front Immunol 2024; 15:1381919. [PMID: 38799424 PMCID: PMC11116624 DOI: 10.3389/fimmu.2024.1381919] [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: 02/04/2024] [Accepted: 04/23/2024] [Indexed: 05/29/2024] Open
Abstract
Introduction CD8+T cell tolerance plays an important role in tumor escape. Recent studies have shown that CD45+ erythroid progenitor cells (CD45+EPCs) generated through splenic extramedullary erythropoiesis suppress tumor immunity. However, the mechanism underlying how CD45+EPCs mediate CD8+T cell tolerance remains incompletely understood and requires further research. Methods In this study, the antigen-processing abilities of CD45+EPCs was verified through both in vitro and in vivo experiments. We have used the method of co-culture in vitro and adoptive transfer experiments in vivo to explore the effects of CD45+EPCs on CD8+T cell tolerance. RNA-sequencing analysis and blocking experiments were used to evaluate the role of ROS in the CD45+EPC mediated tolerance of CD8+T cells. Finally, we incorporated uric acid into the adoptive transfer experiments to rescue the CD45+EPC mediated tumor-promoting effect. Results and discussion We found that CD45+EPCs take up soluble proteins, present antigenic epitopes on their surface, and induce antigen-specific CD8+T cell anergy. In addition, we found that CD45+EPC directly nitrates tyrosine within the TCR/CD8 complex via the production of reactive oxygen species and peroxynitrite, preventing CD8+ T cells from responding to their specific peptide antigens. Furthermore, uric acid treatment effectively abolished the immunosuppressive effects of CD45+EPCs during CD8+T cell adoptive transfer, thereby enhancing the anti-tumor efficacy. These results demonstrated that CD8+T cell tolerance in tumor-bearing mice is induced by CD45+EPCs. The results of this study have direct implications for tumor immunotherapy.
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Affiliation(s)
- Xue Fan
- Department of Oncology and Southwest Cancer Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Radiation Treatment Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Endocrinology/Osteoporosis Department, West China School of Public Health and West China Forth Hospital, Sichuan University, Chengdu, China
| | - Han Peng
- Department of Oncology and Southwest Cancer Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Radiation Treatment Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Xuesong Wang
- Department of Oncology and Southwest Cancer Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Radiation Treatment Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yixin Sun
- Department of Oncology and Southwest Cancer Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Radiation Treatment Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yan Dong
- Department of Oncology and Southwest Cancer Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Radiation Treatment Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Jie Zhou
- Department of Oncology and Southwest Cancer Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Radiation Treatment Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Jianfang Chen
- Department of Oncology and Southwest Cancer Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Radiation Treatment Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Shuo Huang
- Department of Oncology and Southwest Cancer Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Radiation Treatment Centre, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
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Bozorgmehr N, Syed H, Mashhouri S, Walker J, Elahi S. Transcriptomic profiling of peripheral blood cells in HPV-associated carcinoma patients receiving combined valproic acid and avelumab. Mol Oncol 2024; 18:1209-1230. [PMID: 37681284 PMCID: PMC11077001 DOI: 10.1002/1878-0261.13519] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/27/2023] [Accepted: 09/05/2023] [Indexed: 09/09/2023] Open
Abstract
Human papillomavirus (HPV)-associated cancer continues to evade the immune system by promoting a suppressive tumor microenvironment. Therefore, immunotherapy appears to be a promising approach for targeting HPV-associated tumors. We hypothesized that valproic acid (VA) as an epigenetic agent combined with avelumab may enhance the antitumor immunity in HPV-associated solid tumors. We performed bulk RNA-sequencing (RNA-Seq) on total peripheral blood mononuclear cells (PBMCs) of seven nonresponders (NRs) and four responders (Rs). A total of 39 samples (e.g., pretreatment, post-VA, postavelumab, and endpoint) were analyzed. Also, we quantified plasma analytes and performed flow cytometry. We observed a differential pattern in immune response following treatment with VA and/or avelumab in NRs vs. Rs. A significant upregulation of transcripts associated with NETosis [the formation of neutrophil extracellular traps (NETs)] and neutrophil degranulation pathways was linked to the presence of a myeloid-derived suppressor cell signature in NRs. We noted the elevation of IL-8/IL-18 cytokines and a distinct transcriptome signature at the baseline and endpoint in NRs. By using the receiver operator characteristics, we identified a cutoff value for the plasma IL-8/IL-18 to discriminate NRs from Rs. We found differential therapeutic effects for VA and avelumab in NRs vs. Rs. Thus, our results imply that measuring the plasma IL-8/IL-18 and bulk RNA-Seq of PBMCs may serve as valuable biomarkers to predict immunotherapy outcomes.
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Affiliation(s)
- Najmeh Bozorgmehr
- Division of Foundational Sciences, School of DentistryUniversity of AlbertaEdmontonABCanada
| | - Hussain Syed
- Division of Foundational Sciences, School of DentistryUniversity of AlbertaEdmontonABCanada
| | - Siavash Mashhouri
- Division of Foundational Sciences, School of DentistryUniversity of AlbertaEdmontonABCanada
| | - John Walker
- Department of Medical OncologyUniversity of AlbertaEdmontonABCanada
| | - Shokrollah Elahi
- Division of Foundational Sciences, School of DentistryUniversity of AlbertaEdmontonABCanada
- Department of Medical OncologyUniversity of AlbertaEdmontonABCanada
- Faculty of Medicine and DentistryLi Ka Shing Institute of VirologyUniversity of AlbertaEdmontonABCanada
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Mashhouri S, Rahmati A, Azimi A, Fava RA, Ismail IH, Walker J, Elahi S. Targeting Dectin-1 and or VISTA enhances anti-tumor immunity in melanoma but not colorectal cancer model. Cell Oncol (Dordr) 2024:10.1007/s13402-024-00950-w. [PMID: 38668817 DOI: 10.1007/s13402-024-00950-w] [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] [Accepted: 04/11/2024] [Indexed: 06/27/2024] Open
Abstract
PURPOSE Acquired resistance to immune checkpoint blockers (ICBs) is a major barrier in cancer treatment, emphasizing the need for innovative strategies. Dectin-1 (gene Clec7a) is a C-type lectin receptor best known for its ability to recognize β-glucan-rich structures in fungal cell walls. While Dectin-1 is expressed in myeloid cells and tumor cells, its significance in cancer remains the subject of controversy. METHODS Using Celc7a-/- mice and curdlan administration to stimulate Dectin-1 signaling, we explored its impact. VISTA KO mice were employed to assess VISTA's role, and bulk RNAseq analyzed curdlan effects on neutrophils. RESULTS Our findings reveal myeloid cells as primary Dectin-1 expressing cells in the tumor microenvironment (TME), displaying an activated phenotype. Strong Dectin-1 co-expression/co-localization with VISTA and PD-L1 in TME myeloid cells was observed. While Dectin-1 deletion lacked protective effects, curdlan stimulation significantly curtailed B16-F10 tumor progression. RNAseq and pathway analyses supported curdlan's role in triggering a cascade of events leading to increased production of pro-inflammatory mediators, potentially resulting in the recruitment and activation of immune cells. Moreover, we identified a heterogeneous subset of Dectin-1+ effector T cells in the TME. Similar to mice, human myeloid cells are the prominent cells expressing Dectin-1 in cancer patients. CONCLUSION Our study proposes Dectin-1 as a potential adjunctive target with ICBs, orchestrating a comprehensive engagement of innate and adaptive immune responses in melanoma. This innovative approach holds promise for overcoming acquired resistance to ICBs in cancer treatment, offering avenues for further exploration and development.
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Affiliation(s)
- Siavash Mashhouri
- Department of Dentistry, Division of Foundational Sciences, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
| | - Amirhossein Rahmati
- Department of Dentistry, Division of Foundational Sciences, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
| | - Ako Azimi
- Department of Dentistry, Division of Foundational Sciences, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
| | - Roy A Fava
- Department of Veterans Affairs Medical Center, Research Service, White River Junction, VT, USA
- Department of Medicine, Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA
| | - Ismail Hassan Ismail
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
- Biophysics Department, Faculty of Science, Cairo University, Giza, 12613, Egypt
| | - John Walker
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
| | - Shokrollah Elahi
- Department of Dentistry, Division of Foundational Sciences, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada.
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada.
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada.
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Yin M, Zhang Y, Li X, Li X. Unveiling the impact of maternal gestational diabetes mellitus on cord blood CD71+ erythroid cell transcriptome. Pediatr Res 2024:10.1038/s41390-024-03139-x. [PMID: 38519796 DOI: 10.1038/s41390-024-03139-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/15/2024] [Accepted: 03/01/2024] [Indexed: 03/25/2024]
Abstract
IMPACT This study reveals the effects of maternal gestational diabetes mellitus (GDM) on the transcriptome of CD71+ erythroid cells (CECs) in cord blood. It highlights the role of CECs in immunosuppressive function and identifies potential mechanisms linking GDM to adverse outcomes in offspring. This understanding might lead to improved strategies for managing and preventing adverse outcomes in infants born to mothers with GDM.
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Affiliation(s)
- Min Yin
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Yan Zhang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xinyu Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xia Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China.
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Marin D, Li Y, Basar R, Rafei H, Daher M, Dou J, Mohanty V, Dede M, Nieto Y, Uprety N, Acharya S, Liu E, Wilson J, Banerjee P, Macapinlac HA, Ganesh C, Thall PF, Bassett R, Ammari M, Rao S, Cao K, Shanley M, Kaplan M, Hosing C, Kebriaei P, Nastoupil LJ, Flowers CR, Moseley SM, Lin P, Ang S, Popat UR, Qazilbash MH, Champlin RE, Chen K, Shpall EJ, Rezvani K. Safety, efficacy and determinants of response of allogeneic CD19-specific CAR-NK cells in CD19 + B cell tumors: a phase 1/2 trial. Nat Med 2024; 30:772-784. [PMID: 38238616 PMCID: PMC10957466 DOI: 10.1038/s41591-023-02785-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/20/2023] [Indexed: 01/28/2024]
Abstract
There is a pressing need for allogeneic chimeric antigen receptor (CAR)-immune cell therapies that are safe, effective and affordable. We conducted a phase 1/2 trial of cord blood-derived natural killer (NK) cells expressing anti-CD19 chimeric antigen receptor and interleukin-15 (CAR19/IL-15) in 37 patients with CD19+ B cell malignancies. The primary objectives were safety and efficacy, defined as day 30 overall response (OR). Secondary objectives included day 100 response, progression-free survival, overall survival and CAR19/IL-15 NK cell persistence. No notable toxicities such as cytokine release syndrome, neurotoxicity or graft-versus-host disease were observed. The day 30 and day 100 OR rates were 48.6% for both. The 1-year overall survival and progression-free survival were 68% and 32%, respectively. Patients who achieved OR had higher levels and longer persistence of CAR-NK cells. Receiving CAR-NK cells from a cord blood unit (CBU) with nucleated red blood cells ≤ 8 × 107 and a collection-to-cryopreservation time ≤ 24 h was the most significant predictor for superior outcome. NK cells from these optimal CBUs were highly functional and enriched in effector-related genes. In contrast, NK cells from suboptimal CBUs had upregulation of inflammation, hypoxia and cellular stress programs. Finally, using multiple mouse models, we confirmed the superior antitumor activity of CAR/IL-15 NK cells from optimal CBUs in vivo. These findings uncover new features of CAR-NK cell biology and underscore the importance of donor selection for allogeneic cell therapies. ClinicalTrials.gov identifier: NCT03056339 .
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Affiliation(s)
- David Marin
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ye Li
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rafet Basar
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hind Rafei
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - May Daher
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jinzhuang Dou
- Department of Bioinformatics and Computational Biology, 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, USA
| | - Merve Dede
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yago Nieto
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nadima Uprety
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sunil Acharya
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Enli Liu
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jeffrey Wilson
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pinaki Banerjee
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Homer A Macapinlac
- Department of Nuclear Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christina Ganesh
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Peter F Thall
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Roland Bassett
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mariam Ammari
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sheetal Rao
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kai Cao
- Department of Laboratory Medicine, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mayra Shanley
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mecit Kaplan
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chitra Hosing
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Partow Kebriaei
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Loretta J Nastoupil
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher R Flowers
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sadie Mae Moseley
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paul Lin
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sonny Ang
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Uday R Popat
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Muzaffar H Qazilbash
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Richard E Champlin
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Elizabeth J Shpall
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Katayoun Rezvani
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Shahbaz S, Sligl W, Osman M, Elahi S. Immunological responses in SARS-CoV-2 and HIV co-infection versus SARS-CoV-2 mono-infection: case report of the interplay between SARS-CoV-2 and HIV. ALLERGY, ASTHMA, AND CLINICAL IMMUNOLOGY : OFFICIAL JOURNAL OF THE CANADIAN SOCIETY OF ALLERGY AND CLINICAL IMMUNOLOGY 2023; 19:91. [PMID: 37848967 PMCID: PMC10583436 DOI: 10.1186/s13223-023-00846-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 10/08/2023] [Indexed: 10/19/2023]
Abstract
BACKGROUND There is an urgent need to understand the interplay between SARS-CoV-2 and HIV to inform risk-mitigation approaches for HIV-infected individuals. OBJECTIVES We conclude that people living with HIV (PLWH) who are antiretroviral therapy (ART) naïve could be at a greater risk of morbidity or mortality once co-infected with SARS-CoV-2. METHODS Here, we performed extensive immune phenotyping using flow cytometry. Moreover, to compare the range of values observed in the co-infected case, we have included a larger number of mono-infected cases with SARS-CoV-2. We also quantified soluble co-inhibitory/co-stimulatory molecules in the plasma of our patients. RESULTS We noted a robust immune activation characterized by the expansion of CD8+ T cells expressing co-inhibitory/stimulatory molecules (e.g. PD-1, TIM-3, 2B4, TIGIT, CD39, and ICOS) and activation markers (CD38, CD71, and HLA-DR) in the co-infected case. We further found that neutrophilia was more pronounced at the expense of lymphopenia in the co-infected case. In particular, naïve and central memory CD8+ T cells were scarce as a result of switching to effector and effector memory in the co-infected case. CD8+ T cell effector functions such as cytokine production (e.g. TNF-α and IFN-γ) and cytolytic molecules expression (granzyme B and perforin) following anti-CD3/CD28 or the Spike peptide pool stimulation were more prominent in the co-infected case versus the mono-infected case. We also observed that SARS-CoV-2 alters T cell exhaustion commonly observed in PLWH. CONCLUSION These findings imply that inadequate immune reconstitution and/or lack of access to ART could dysregulate immune response against SARS-CoV-2 infection, which can result in poor clinical outcomes in PLWH. Our study has implications for prioritizing PLWH in the vaccination program/access to ART in resource-constrained settings.
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Affiliation(s)
- Shima Shahbaz
- School of Dentistry, Division of Foundational Sciences, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Wendy Sligl
- Department of Critical Care Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- Department of Medicine, Division of Infectious Diseases, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Mohammed Osman
- Department of Medicine, Division of Rheumatology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Shokrollah Elahi
- School of Dentistry, Division of Foundational Sciences, University of Alberta, Edmonton, AB, T6G 2E1, Canada.
- Department of Oncology, University of Alberta, Edmonton, AB, T6G 2E1, Canada.
- Li Ka Shing Institute of Virology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, T6G 2E1, Canada.
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Toufiq M, Rinchai D, Bettacchioli E, Kabeer BSA, Khan T, Subba B, White O, Yurieva M, George J, Jourde-Chiche N, Chiche L, Palucka K, Chaussabel D. Harnessing large language models (LLMs) for candidate gene prioritization and selection. J Transl Med 2023; 21:728. [PMID: 37845713 PMCID: PMC10580627 DOI: 10.1186/s12967-023-04576-8] [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: 08/28/2023] [Accepted: 09/28/2023] [Indexed: 10/18/2023] Open
Abstract
BACKGROUND Feature selection is a critical step for translating advances afforded by systems-scale molecular profiling into actionable clinical insights. While data-driven methods are commonly utilized for selecting candidate genes, knowledge-driven methods must contend with the challenge of efficiently sifting through extensive volumes of biomedical information. This work aimed to assess the utility of large language models (LLMs) for knowledge-driven gene prioritization and selection. METHODS In this proof of concept, we focused on 11 blood transcriptional modules associated with an Erythroid cells signature. We evaluated four leading LLMs across multiple tasks. Next, we established a workflow leveraging LLMs. The steps consisted of: (1) Selecting one of the 11 modules; (2) Identifying functional convergences among constituent genes using the LLMs; (3) Scoring candidate genes across six criteria capturing the gene's biological and clinical relevance; (4) Prioritizing candidate genes and summarizing justifications; (5) Fact-checking justifications and identifying supporting references; (6) Selecting a top candidate gene based on validated scoring justifications; and (7) Factoring in transcriptome profiling data to finalize the selection of the top candidate gene. RESULTS Of the four LLMs evaluated, OpenAI's GPT-4 and Anthropic's Claude demonstrated the best performance and were chosen for the implementation of the candidate gene prioritization and selection workflow. This workflow was run in parallel for each of the 11 erythroid cell modules by participants in a data mining workshop. Module M9.2 served as an illustrative use case. The 30 candidate genes forming this module were assessed, and the top five scoring genes were identified as BCL2L1, ALAS2, SLC4A1, CA1, and FECH. Researchers carefully fact-checked the summarized scoring justifications, after which the LLMs were prompted to select a top candidate based on this information. GPT-4 initially chose BCL2L1, while Claude selected ALAS2. When transcriptional profiling data from three reference datasets were provided for additional context, GPT-4 revised its initial choice to ALAS2, whereas Claude reaffirmed its original selection for this module. CONCLUSIONS Taken together, our findings highlight the ability of LLMs to prioritize candidate genes with minimal human intervention. This suggests the potential of this technology to boost productivity, especially for tasks that require leveraging extensive biomedical knowledge.
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Affiliation(s)
- Mohammed Toufiq
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Eleonore Bettacchioli
- INSERM UMR1227, Lymphocytes B et Autoimmunité, Université de Bretagne Occidentale, Brest, France
- Service de Rhumatologie, CHU de Brest, Brest, France
| | | | - Taushif Khan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Bishesh Subba
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Olivia White
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Marina Yurieva
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Joshy George
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Laurent Chiche
- Service de Médecine Interne, Hôpital Européen, Marseille, France
| | - Karolina Palucka
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
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Shevchenko JA, Nazarov KV, Alshevskaya AA, Sennikov SV. Erythroid Cells as Full Participants in the Tumor Microenvironment. Int J Mol Sci 2023; 24:15141. [PMID: 37894821 PMCID: PMC10606658 DOI: 10.3390/ijms242015141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/07/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
The tumor microenvironment is an important factor that can determine the success or failure of antitumor therapy. Cells of hematopoietic origin are one of the most important mediators of the tumor-host interaction and, depending on the cell type and functional state, exert pro- or antitumor effects in the tumor microenvironment or in adjacent tissues. Erythroid cells can be full members of the tumor microenvironment and exhibit immunoregulatory properties. Tumor growth is accompanied by the need to obtain growth factors and oxygen, which stimulates the appearance of the foci of extramedullary erythropoiesis. Tumor cells create conditions to maintain the long-term proliferation and viability of erythroid cells. In turn, tumor erythroid cells have a number of mechanisms to suppress the antitumor immune response. This review considers current data on the existence of erythroid cells in the tumor microenvironment, formation of angiogenic clusters, and creation of optimal conditions for tumor growth. Despite being the most important life-support function of the body, erythroid cells support tumor growth and do not work against it. The study of various signaling mechanisms linking tumor growth with the mobilization of erythroid cells and the phenotypic and functional differences between erythroid cells of different origin allows us to identify potential targets for immunotherapy.
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Affiliation(s)
- Julia A. Shevchenko
- Laboratory of Molecular Immunology, Federal State Budgetary Scientific Institution, Research Institute of Fundamental and Clinical Immunology, 630099 Novosibirsk, Russia; (J.A.S.); (K.V.N.)
- Laboratory of Immune Engineering, Federal State Autonomous Educational Institution, Ministry of Health of the Russian Federation, Higher Education I.M. Sechenov First Moscow State Medical University, Sechenov University, 119048 Moscow, Russia;
| | - Kirill V. Nazarov
- Laboratory of Molecular Immunology, Federal State Budgetary Scientific Institution, Research Institute of Fundamental and Clinical Immunology, 630099 Novosibirsk, Russia; (J.A.S.); (K.V.N.)
| | - Alina A. Alshevskaya
- Laboratory of Immune Engineering, Federal State Autonomous Educational Institution, Ministry of Health of the Russian Federation, Higher Education I.M. Sechenov First Moscow State Medical University, Sechenov University, 119048 Moscow, Russia;
| | - Sergey V. Sennikov
- Laboratory of Molecular Immunology, Federal State Budgetary Scientific Institution, Research Institute of Fundamental and Clinical Immunology, 630099 Novosibirsk, Russia; (J.A.S.); (K.V.N.)
- Laboratory of Immune Engineering, Federal State Autonomous Educational Institution, Ministry of Health of the Russian Federation, Higher Education I.M. Sechenov First Moscow State Medical University, Sechenov University, 119048 Moscow, Russia;
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