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Das A, Wang X, Devonshire K, Lyons EJ, Popescu I, Zhou Z, Li J, Sembrat J, Pilewski J, Zou C, Alder JK, Chen BB, Snyder ME, McDyer JF. IL-10 Is Critical for Regulation of Cytotoxic CD4+NKG7+ T Cells in Lung Allograft Rejection but Is Not Required for Allograft Acceptance. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 213:898-905. [PMID: 39072690 DOI: 10.4049/jimmunol.2400279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 07/08/2024] [Indexed: 07/30/2024]
Abstract
Lung transplant remains the primary therapeutic option for patients with end-stage lung disease, but long-term survival rates remain suboptimal compared with other solid organ transplants. Acute cellular rejection (ACR) is a significant challenge in lung transplant recipients, with T cell-mediated mechanisms playing a major role. IL-10 is known for its immunoregulatory function, although its specific role in lung allograft rejection remains unclear. Using the mouse orthotopic lung transplant model, we investigated the role of IL-10 in regulating alloeffector T cell responses. Unexpectedly, we found that IL-10 was not required for early costimulation blockade-induced allograft acceptance. However, IL-10 deficiency or blockade resulted in increased CD4+ T cell numbers, proliferation, graft infiltration, and alloeffector responses. In the absence of IL-10, CD4+ T cell responses predominated over CD8 responses during ACR in contrast to wild-type mice. Type 1 immunity (IFN-γ) responses along with elevated CD4+NKG7+ and CD4+CD107a+ responses predominated during ACR, highlighting a critical regulatory role for IL-10 in modulating CD4+ T cell alloimmune responses. We further demonstrated increased colocalization of NKG7 and CD107a in CD4+ T cells from IL-10-deficient allografts, suggesting coordination in cytotoxic activity. Together, our findings highlight a critical role for IL-10 in regulation of cytotoxic CD4+NKG7+ T cells, an effector population that needs further investigation to elucidate their role in lung allograft rejection.
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Affiliation(s)
- Antu Das
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Xingan Wang
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Kaitlyn Devonshire
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Emily J Lyons
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Iulia Popescu
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Zihe Zhou
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Jingmei Li
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - John Sembrat
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Joseph Pilewski
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Chunbin Zou
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Jonathan K Alder
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Bill B Chen
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Aging Institute, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Mark E Snyder
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - John F McDyer
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
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Lad M, Beniwal AS, Jain S, Shukla P, Kalistratova V, Jung J, Shah SS, Yagnik G, Saha A, Sati A, Babikir H, Nguyen AT, Gill S, Rios J, Young JS, Lui A, Salha D, Diaz A, Aghi MK. Glioblastoma induces the recruitment and differentiation of dendritic-like "hybrid" neutrophils from skull bone marrow. Cancer Cell 2024; 42:1549-1569.e16. [PMID: 39255776 DOI: 10.1016/j.ccell.2024.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/28/2024] [Accepted: 08/08/2024] [Indexed: 09/12/2024]
Abstract
Tumor-associated neutrophil (TAN) effects on glioblastoma (GBM) biology remain under-characterized. We show here that neutrophils with dendritic features-including morphological complexity, expression of antigen presentation genes, and the ability to process exogenous peptide and stimulate major histocompatibility complex (MHC)II-dependent T cell activation-accumulate intratumorally and suppress tumor growth in vivo. Trajectory analysis of patient TAN scRNA-seq identifies this "hybrid" dendritic-neutrophil phenotype as a polarization state that is distinct from canonical cytotoxic TANs, and which differentiates from local precursors. These hybrid-inducible immature neutrophils-which we identified in patient and murine glioblastomas-arise not from circulation, but from local skull marrow. Through labeled skull flap transplantation and targeted ablation, we characterize calvarial marrow as a contributor of antitumoral myeloid antigen-presenting cells (APCs), including TANs, which elicit T cell cytotoxicity and memory. As such, agents augmenting neutrophil egress from skull marrow-such as intracalvarial AMD3100, whose survival-prolonging effect in GBM we report-present therapeutic potential.
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Affiliation(s)
- Meeki Lad
- University of California, San Francisco (UCSF), Department of Neurosurgery, San Francisco, CA, USA
| | - Angad S Beniwal
- University of California, San Francisco (UCSF), Department of Neurosurgery, San Francisco, CA, USA
| | - Saket Jain
- University of California, San Francisco (UCSF), Department of Neurosurgery, San Francisco, CA, USA
| | - Poojan Shukla
- University of California, San Francisco (UCSF), Department of Neurosurgery, San Francisco, CA, USA
| | - Venina Kalistratova
- University of California, San Francisco (UCSF), Department of Neurosurgery, San Francisco, CA, USA
| | - Jangham Jung
- University of California, San Francisco (UCSF), Department of Neurosurgery, San Francisco, CA, USA
| | - Sumedh S Shah
- University of California, San Francisco (UCSF), Department of Neurosurgery, San Francisco, CA, USA
| | - Garima Yagnik
- University of California, San Francisco (UCSF), Department of Neurosurgery, San Francisco, CA, USA
| | - Atul Saha
- University of California, San Francisco (UCSF), Department of Neurosurgery, San Francisco, CA, USA
| | - Ankita Sati
- University of California, San Francisco (UCSF), Department of Neurosurgery, San Francisco, CA, USA
| | - Husam Babikir
- University of California, San Francisco (UCSF), Department of Neurosurgery, San Francisco, CA, USA
| | - Alan T Nguyen
- University of California, San Francisco (UCSF), Department of Neurosurgery, San Francisco, CA, USA
| | - Sabraj Gill
- University of California, San Francisco (UCSF), Department of Neurosurgery, San Francisco, CA, USA
| | - Jennifer Rios
- University of California, San Francisco (UCSF), Department of Neurosurgery, San Francisco, CA, USA
| | - Jacob S Young
- University of California, San Francisco (UCSF), Department of Neurosurgery, San Francisco, CA, USA
| | - Austin Lui
- University of California, San Francisco (UCSF), Department of Neurosurgery, San Francisco, CA, USA
| | - Diana Salha
- University of California, San Francisco (UCSF), Department of Neurosurgery, San Francisco, CA, USA
| | - Aaron Diaz
- University of California, San Francisco (UCSF), Department of Neurosurgery, San Francisco, CA, USA
| | - Manish K Aghi
- University of California, San Francisco (UCSF), Department of Neurosurgery, San Francisco, CA, USA.
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3
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Song EH, Garcia J, Xiong N. Dysbiosis-activated IL-17-producing T cells promote skin immunopathological progression in mice deficient of the Notch ligand Jag1 in keratinocytes. J Dermatol Sci 2024:S0923-1811(24)00189-0. [PMID: 39304389 DOI: 10.1016/j.jdermsci.2024.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
BACKGROUND The Notch signaling pathway is an evolutionarily conserved regulatory cascade critical in skin development and homeostasis. Mice deficient of Notch signaling molecules have impaired skin and hair follicle development associated with local tissue inflammation. However, mechanisms underlying skin inflammation and pathology resulting from defective Notch signals are not well understood. OBJECTIVE To dissect molecular and cellular mechanisms underlying development of skin immunopathology in mice defective of the Notch ligand Jagged-1 (Jag1). METHODS We assessed involvement of microbiota and immune cell subsets in skin pathogenic symptoms in Foxn1CreJag1fl/fl mice that were deficient of Jag1 in keratinocytes. We also used RNA-seq and 16S rRNA gene-seq analyses to identify molecular factors and bacterial species contributing to skin pathologic symptoms in Foxn1CreJag1fl/fl mice. RESULTS Compared to Jag1-sufficient littermate control mice, Foxn1CreJag1fl/fl mice had specific expansion of IL-17a-producing T cells accompanying follicular and epidermal hyperkeratosis and cyst formation while antibody blockage of IL-17a reduced the skin pathology. RNA-sequencing and 16S rRNA gene-sequencing analyses revealed dysregulated immune responses and altered microbiota compositions in the skin of Foxn1CreJag1fl/fl mice. Antibiotic treatment completely prevented over-activation of IL-17a-producing T cells and alleviated skin pathology in Foxn1CreJag1fl/fl mice. CONCLUSION Dysbiosis-induced over-activation of IL-17a-producing T cells is critically involved in development of skin pathology in Foxn1CreJag1fl/fl mice, establishing Foxn1CreJag1fl/fl mice as a useful model to study pathogenesis and therapeutic targets in microbiota-IL-17-mediated skin inflammatory diseases such as hidradenitis suppurativa (HS) and psoriasis.
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Affiliation(s)
- Eun Hyeon Song
- The Molecular, Cellular, and Integrative Biosciences (MCIBS) Graduate Program, The Pennsylvania State University, PA, USA; Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center San Antonio, TX, USA
| | - Juan Garcia
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center San Antonio, TX, USA
| | - Na Xiong
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center San Antonio, TX, USA; Department of Medicine-Division of Dermatology and Cutaneous Surgery, University of Texas Health Science Center San Antonio, TX , USA.
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4
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Hao X, Jiang B, Wu J, Xiang D, Xiong Z, Li C, Li Z, He S, Tu C, Li Z. Nanomaterials for bone metastasis. J Control Release 2024; 373:640-651. [PMID: 39084467 DOI: 10.1016/j.jconrel.2024.07.067] [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: 05/24/2024] [Revised: 07/23/2024] [Accepted: 07/28/2024] [Indexed: 08/02/2024]
Abstract
Bone metastasis, a prevalent occurrence in primary malignant tumors, is often associated with a grim prognosis. The bone microenvironment comprises various coexisting cell types, working together in a coordinated manner. This dynamic microenvironment plays a pivotal role in the initiation and progression of bone metastases. While cancer therapies have made advancements, the available options for addressing bone metastases remain insufficient. The advent of nanotechnology has ushered in a new era for managing and preventing bone metastases because of the physicochemical and adaptable advantages of nanoplatforms. In this review, we make an introduction of the underlying mechanisms and the current clinical therapies of bone metastases, highlighting the advances of intelligent nanosystems that can stimulate vascular regeneration, promote bone regeneration, eliminate tumor cells, minimize bone damage, and expedite bone healing. The innovation surrounding bone-targeting nanoplatforms presents a fresh approach to the theranostics of bone metastases.
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Affiliation(s)
- Xinyan Hao
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China; Xiangya School of Medicine, Central South University, Changsha, Hunan 410011, China; Department of Pharmacy, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Buchan Jiang
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China; Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Junyong Wu
- Department of Pharmacy, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Daxiong Xiang
- Department of Pharmacy, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Zijian Xiong
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China; Xiangya School of Medicine, Central South University, Changsha, Hunan 410011, China; Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Chenbei Li
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China; Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Zhaoqi Li
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China; Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Shasha He
- Department of Oncology, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China.
| | - Chao Tu
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China; Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China; Changsha Medical University, Changsha 410219, China.
| | - Zhihong Li
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China; Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China; Shenzhen Research Institute of Central South University, Guangdong 518063, China; FuRong Laboratory, Changsha 410078, Hunan, China.
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Brune Z, Lu A, Moss M, Brune L, Huang A, Matta B, Barnes BJ. IRF5 mediates adaptive immunity via altered glutamine metabolism, mTORC1 signaling and post-transcriptional regulation following T cell receptor activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.26.609422. [PMID: 39253451 PMCID: PMC11382993 DOI: 10.1101/2024.08.26.609422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Although dynamic alterations in transcriptional, translational, and metabolic programs have been described in T cells, the factors and pathways guiding these molecular shifts are poorly understood, with recent studies revealing a disassociation between transcriptional responses and protein expression following T cell receptor (TCR) stimulation. Previous studies identified interferon regulatory factor 5 (IRF5) in the transcriptional regulation of cytokines, chemotactic molecules and T effector transcription factors following TCR signaling. In this study, we identified T cell intrinsic IRF5 regulation of mTORC1 activity as a key modulator of CD40L protein expression. We further demonstrated a global shift in T cell metabolism, with alterations in glutamine metabolism accompanied by shifts in T cell populations at the single cell level due to loss of Irf5. T cell conditional Irf5 knockout mice in a murine model of experimental autoimmune encephalomyelitis (EAE) demonstrated protection from clinical disease with conserved defects in mTORC1 activity and glutamine regulation. Together, these findings expand our mechanistic understanding of IRF5 as an intrinsic regulator of T effector function(s) and support the therapeutic targeting of IRF5 in multiple sclerosis.
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Affiliation(s)
- Zarina Brune
- Center of Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
| | - Ailing Lu
- Center of Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Matthew Moss
- Center of Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Leianna Brune
- Center of Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Amanda Huang
- Center of Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Bharati Matta
- Center of Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Betsy J Barnes
- Center of Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
- Departments of Molecular Medicine and Pediatrics, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
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6
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Charoensuksira S, Tantiwong S, Pongklaokam J, Hanvivattanakul S, Surinlert P, Krajarng A, Thanasarnaksorn W, Hongeng S, Ponnikorn S. Disturbance of Immune Microenvironment in Androgenetic Alopecia through Spatial Transcriptomics. Int J Mol Sci 2024; 25:9031. [PMID: 39201715 PMCID: PMC11354591 DOI: 10.3390/ijms25169031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 08/11/2024] [Accepted: 08/15/2024] [Indexed: 09/03/2024] Open
Abstract
Androgenetic alopecia (AGA) is characterized by microinflammation and abnormal immune responses, particularly in the upper segment of hair follicles (HFs). However, the precise patterns of immune dysregulation remain unclear, partly due to limitations in current analysis techniques to preserve tissue architecture. The infundibulum, a major part of the upper segment of HFs, is associated with significant clusters of immune cells. In this study, we investigated immune cells around the infundibulum, referred to as peri-infundibular immune infiltration (PII). We employed spatial transcriptome profiling, a high-throughput analysis technology, to investigate the immunological disruptions within the PII region. Our comprehensive analysis included an evaluation of overall immune infiltrates, gene set enrichment analysis (GSEA), cellular deconvolution, differential expression analysis, over-representation analysis, protein-protein interaction (PPI) networks, and upstream regulator analysis to identify cell types and molecular dysregulation in immune cells. Our results demonstrated significant differences in immune signatures between the PII of AGA patients (PII-A) and the PII of control donors (PII-C). Specifically, PII-A exhibited an enrichment of CD4+ helper T cells, distinct immune response patterns, and a bias toward a T helper (Th) 2 response. Immunohistochemistry revealed disruptions in T cell subpopulations, with more CD4+ T cells displaying an elevated Th2 response and a reduced Th1-cytotoxic response compared to PII-C. These findings reveal the unique immune landscapes of PII-A and PII-C, suggesting potential for the development of innovative treatment approaches.
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Affiliation(s)
- Sasin Charoensuksira
- Division of Dermatology, Chulabhorn International College of Medicine, Thammasat University, Pathum Thani 12120, Thailand; (S.C.); (S.T.); (J.P.); (W.T.)
| | - Supasit Tantiwong
- Division of Dermatology, Chulabhorn International College of Medicine, Thammasat University, Pathum Thani 12120, Thailand; (S.C.); (S.T.); (J.P.); (W.T.)
| | - Juthapa Pongklaokam
- Division of Dermatology, Chulabhorn International College of Medicine, Thammasat University, Pathum Thani 12120, Thailand; (S.C.); (S.T.); (J.P.); (W.T.)
| | - Sirashat Hanvivattanakul
- Chulabhorn International College of Medicine, Thammasat University, Pathum Thani 12120, Thailand; (S.H.); (P.S.); (A.K.)
| | - Piyaporn Surinlert
- Chulabhorn International College of Medicine, Thammasat University, Pathum Thani 12120, Thailand; (S.H.); (P.S.); (A.K.)
- Research Unit in Synthesis and Applications of Graphene, Thammasat University, Pathum Thani 12120, Thailand
| | - Aungkana Krajarng
- Chulabhorn International College of Medicine, Thammasat University, Pathum Thani 12120, Thailand; (S.H.); (P.S.); (A.K.)
| | - Wilai Thanasarnaksorn
- Division of Dermatology, Chulabhorn International College of Medicine, Thammasat University, Pathum Thani 12120, Thailand; (S.C.); (S.T.); (J.P.); (W.T.)
- Division of Dermatology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Suradej Hongeng
- Division of Hematology and Oncology, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
| | - Saranyoo Ponnikorn
- Division of Dermatology, Chulabhorn International College of Medicine, Thammasat University, Pathum Thani 12120, Thailand; (S.C.); (S.T.); (J.P.); (W.T.)
- Chulabhorn International College of Medicine, Thammasat University, Pathum Thani 12120, Thailand; (S.H.); (P.S.); (A.K.)
- Thammasat University, Pattaya Campus, Bang Lamung 20150, Thailand
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7
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Ma ZL, Wang ZL, Zhang FY, Liu HX, Mao LH, Yuan L. Biomarkers of Parkinson's Disease: From Basic Research to Clinical Practice. Aging Dis 2024; 15:1813-1830. [PMID: 37815899 PMCID: PMC11272192 DOI: 10.14336/ad.2023.1005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/05/2023] [Indexed: 10/12/2023] Open
Abstract
Parkinson's disease (PD) is a common neurodegenerative disease characterized pathologically by dopaminergic neuron loss and the formation of Lewy bodies, which are enriched with aggregated α-synuclein (α-syn). PD currently has no cure, but therapeutic strategies are available to alleviate symptoms. Early diagnosis can greatly improve therapeutic interventions, but the clinical diagnosis of PD remains challenging and depends mainly on clinical features and imaging tests. Efficient and specific biomarkers are crucial for the diagnosis, monitoring, and evaluation of PD. Here, we reviewed the biomarkers of PD in different tissues and biofluids, along with the current clinical biochemical detection methods. We found that the sensitivity and specificity of single biomarkers are limited, and selecting appropriate indicators for combined detection can improve the diagnostic accuracy of PD.
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Affiliation(s)
| | | | - Fei-yue Zhang
- Laboratory of Research in Parkinson’s Disease and Related Disorders, Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, Health Sciences Institute, China Medical University, Shenyang, China
| | - Hong-xun Liu
- Laboratory of Research in Parkinson’s Disease and Related Disorders, Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, Health Sciences Institute, China Medical University, Shenyang, China
| | - Li-hong Mao
- Laboratory of Research in Parkinson’s Disease and Related Disorders, Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, Health Sciences Institute, China Medical University, Shenyang, China
| | - Lin Yuan
- Laboratory of Research in Parkinson’s Disease and Related Disorders, Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, Health Sciences Institute, China Medical University, Shenyang, China
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8
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Liang C, Spoerl S, Xiao Y, Habenicht KM, Haeusl SS, Sandner I, Winkler J, Strieder N, Eder R, Stanewsky H, Alexiou C, Dudziak D, Rosenwald A, Edinger M, Rehli M, Hoffmann P, Winkler TH, Berberich-Siebelt F. Oligoclonal CD4 +CXCR5 + T cells with a cytotoxic phenotype appear in tonsils and blood. Commun Biol 2024; 7:879. [PMID: 39025930 PMCID: PMC11258247 DOI: 10.1038/s42003-024-06563-1] [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: 09/15/2023] [Accepted: 07/05/2024] [Indexed: 07/20/2024] Open
Abstract
In clinical situations, peripheral blood accessible CD3+CD4+CXCR5+ T-follicular helper (TFH) cells may have to serve as a surrogate indicator for dysregulated germinal center responses in tissues. To determine the heterogeneity of TFH cells in peripheral blood versus tonsils, CD3+CD4+CD45RA-CXCR5+ cells of both origins were sorted. Transcriptomes, TCR repertoires and cell-surface protein expression were analysed by single-cell RNA sequencing, flow cytometry and immunohistochemistry. Reassuringly, all blood-circulating CD3+CD4+CXCR5+ T-cell subpopulations also appear in tonsils, there with some supplementary TFH characteristics, while peripheral blood-derived TFH cells display markers of proliferation and migration. Three further subsets of TFH cells, however, with bona fide T-follicular gene expression patterns, are exclusively found in tonsils. One additional, distinct and oligoclonal CD4+CXCR5+ subpopulation presents pronounced cytotoxic properties. Those 'killer TFH (TFK) cells' can be discovered in peripheral blood as well as among tonsillar cells but are located predominantly outside of germinal centers. They appear terminally differentiated and can be distinguished from all other TFH subsets by expression of NKG7 (TIA-1), granzymes, perforin, CCL5, CCR5, EOMES, CRTAM and CX3CR1. All in all, this study provides data for detailed CD4+CXCR5+ T-cell assessment of clinically available blood samples and extrapolation possibilities to their tonsil counterparts.
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Affiliation(s)
- Chunguang Liang
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, Julius-Maximilians-University Würzburg, Würzburg, Germany
- Institute of Immunology, Jena University Hospital, Friedrich-Schiller-University, Jena, Germany
| | - Silvia Spoerl
- Department of Internal Medicine 5, Hematology/Oncology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Yin Xiao
- Institute of Pathology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Katharina M Habenicht
- Division of Genetics, Department Biology, Nikolaus-Fiebiger-Center of Molecular Medicine, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Sigrun S Haeusl
- Institute of Pathology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Isabel Sandner
- Department of Internal Medicine 5, Hematology/Oncology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Julia Winkler
- Department of Internal Medicine 5, Hematology/Oncology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | | | - Rüdiger Eder
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | | | - Christoph Alexiou
- Department of Otorhinolaryngology, Head & Neck Surgery, Else Kröner-Fresenius-Foundation-Professorship, Section of Experimental Oncology & Nanomedicine (SEON), University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Diana Dudziak
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
- Institute of Immunology, Jena University Hospital, Friedrich-Schiller-University, Jena, Germany
| | - Andreas Rosenwald
- Institute of Pathology, Julius-Maximilians-University Würzburg, Würzburg, Germany
- Comprehensive Cancer Centre Mainfranken, Julius-Maximilians-University of Würzburg, Würzburg, Germany
| | - Matthias Edinger
- Leibniz Institute for Immunotherapy, Regensburg, Germany
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Michael Rehli
- Leibniz Institute for Immunotherapy, Regensburg, Germany
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Petra Hoffmann
- Leibniz Institute for Immunotherapy, Regensburg, Germany
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Thomas H Winkler
- Division of Genetics, Department Biology, Nikolaus-Fiebiger-Center of Molecular Medicine, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
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9
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Amancherla K, Schlendorf KH, Chow N, Sheng Q, Freedman JE, Rathmell JC. Single-cell RNA-sequencing identifies unique cell-specific gene expression profiles in high-grade cardiac allograft vasculopathy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.10.602989. [PMID: 39026730 PMCID: PMC11257508 DOI: 10.1101/2024.07.10.602989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Background Cardiac allograft vasculopathy (CAV), a diffuse thickening of the intima of the coronary arteries and microvasculature, is the leading cause of late graft failure and mortality after heart transplantation (HT). Diagnosis involves invasive coronary angiography, which carries substantial risk, and minimally-invasive approaches to CAV diagnosis are urgently needed. Using single-cell RNA-sequencing in peripheral blood mononuclear cells (PBMCs), we sought to identify cell-specific gene expression profiles in CAV. Methods Whole blood was collected from 22 HT recipients with angiographically-confirmed CAV and 18 HT recipients without CAV. PBMCs were isolated and subjected to single-cell RNA-sequencing using a 10X Genomics microfluidic platform. Downstream analyses focused on differential expression of genes, cell compositional changes, and T cell receptor repertoire analyses. Results Across 40 PBMC samples, we isolated 134,984 cells spanning 8 major clusters and 31 subclusters of cell types. Compositional analyses showed subtle, but significant increases in CD4+ T central memory cells, and CD14+ and CD16+ monocytes in high-grade CAV (CAV-2 and CAV-3) as compared to low-grade or absent CAV. After adjusting for age, gender, and prednisone use, 745 genes were differentially expressed in a cell-specific manner in high-grade CAV. Weighted gene co-expression network analyses showed enrichment for putative pathways involved in inflammation and angiogenesis. There were no significant differences in T cell clonality or diversity with increasing CAV severity. Conclusions Unbiased whole transcriptomic analyses at single-cell resolution identify unique, cell-specific gene expression patterns in CAV, suggesting the potential utility of peripheral gene expression biomarkers in diagnosing CAV.
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Huang D, Jiao X, Huang S, Liu J, Si H, Qi D, Pei X, Lu D, Wang Y, Li Z. Analysis of the heterogeneity and complexity of murine extraorbital lacrimal gland via single-cell RNA sequencing. Ocul Surf 2024; 34:60-95. [PMID: 38945476 DOI: 10.1016/j.jtos.2024.06.005] [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: 08/26/2022] [Revised: 06/22/2024] [Accepted: 06/26/2024] [Indexed: 07/02/2024]
Abstract
PURPOSE The lacrimal gland is essential for maintaining ocular surface health and avoiding external damage by secreting an aqueous layer of the tear film. However, a healthy lacrimal gland's inventory of cell types and heterogeneity remains understudied. METHODS Here, 10X Genome-based single-cell RNA sequencing was used to generate an unbiased classification of cellular diversity in the extraorbital lacrimal gland (ELG) of C57BL/6J mice. From 43,850 high-quality cells, we produced an atlas of cell heterogeneity and defined cell types using classic marker genes. The possible functions of these cells were analyzed through bioinformatics analysis. Additionally, the CellChat was employed for a preliminary analysis of the cell-cell communication network in the ELG. RESULTS Over 37 subclasses of cells were identified, including seven types of glandular epithelial cells, three types of fibroblasts, ten types of myeloid-derived immune cells, at least eleven types of lymphoid-derived immune cells, and five types of vascular-associated cell subsets. The cell-cell communication network analysis revealed that fibroblasts and immune cells play a pivotal role in the dense intercellular communication network within the mouse ELG. CONCLUSIONS This study provides a comprehensive transcriptome atlas and related database of the mouse ELG.
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Affiliation(s)
- Duliurui Huang
- Department of Ophthalmology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Xinwei Jiao
- Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, 450000, China
| | - Shenzhen Huang
- Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, 450000, China
| | - Jiangman Liu
- Department of Ophthalmology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Hongli Si
- Department of Ophthalmology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Di Qi
- Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, 450000, China
| | - Xiaoting Pei
- Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, 450000, China
| | - Dingli Lu
- Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, 450000, China
| | - Yimian Wang
- Division of Medicine, Faculty of Medical Sciences, University College London, Gower Street, London, WC1E 6BT, UK
| | - Zhijie Li
- Department of Ophthalmology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China; Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, 450000, China.
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11
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Huang Q, H J Cao W, Curio S, Yu H, Denman R, Chen E, Schreuder J, Dight J, Chaudhry M, Jacquelot N, Wimmer VC, Seillet C, Möröy T, Belz GT. GFI1B specifies developmental potential of innate lymphoid cell progenitors in the lungs. Sci Immunol 2024; 9:eadj2654. [PMID: 38820141 DOI: 10.1126/sciimmunol.adj2654] [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: 06/16/2023] [Accepted: 05/09/2024] [Indexed: 06/02/2024]
Abstract
Tissue-resident innate lymphoid cells (ILCs) play a vital role in the frontline defense of various tissues, including the lung. The development of type 2 ILCs (ILC2s) depends on transcription factors such as GATA3, RORα, GFI1, and Bcl11b; however, the factors regulating lung-resident ILC2s remain unclear. Through fate mapping analysis of the paralog transcription factors GFI1 and GFI1B, we show that GFI1 is consistently expressed during the transition from progenitor to mature ILC2s. In contrast, GFI1B expression is limited to specific subsets of bone marrow progenitors and lung-resident ILC progenitors. We found that GFI1B+ lung ILC progenitors represent a multi-lineage subset with tissue-resident characteristics and the potential to form lung-derived ILC subsets and liver-resident ILC1s. Loss of GFI1B in bone marrow progenitors led to the selective loss of lung-resident IL-18R+ ILCs and mature ILC2, subsequently preventing the emergence of effector ILCs that could protect the lung against inflammatory or tumor challenge.
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Affiliation(s)
- Qiutong Huang
- University of Queensland Frazer Institute, University of Queensland, Woolloongabba, QLD 4102, Australia
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Wang H J Cao
- University of Queensland Frazer Institute, University of Queensland, Woolloongabba, QLD 4102, Australia
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Sophie Curio
- University of Queensland Frazer Institute, University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Huiyang Yu
- University of Queensland Frazer Institute, University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Renae Denman
- University of Queensland Frazer Institute, University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Evelyn Chen
- University of Queensland Frazer Institute, University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Jaring Schreuder
- University of Queensland Frazer Institute, University of Queensland, Woolloongabba, QLD 4102, Australia
| | - James Dight
- University of Queensland Frazer Institute, University of Queensland, Woolloongabba, QLD 4102, Australia
| | - M Chaudhry
- University of Queensland Frazer Institute, University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Nicolas Jacquelot
- Department of Biochemistry and Molecular Biology; Department of Microbiology, Immunology and Infectious Diseases; Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Verena C Wimmer
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Cyril Seillet
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Tarik Möröy
- Institut de recherches cliniques de Montreal, Université de Montréal, Montreal, QC H2W 1R7, Canada
| | - Gabrielle T Belz
- University of Queensland Frazer Institute, University of Queensland, Woolloongabba, QLD 4102, Australia
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
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12
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Na J, Engwerda C. The role of CD4 + T cells in visceral leishmaniasis; new and emerging roles for NKG7 and TGFβ. Front Cell Infect Microbiol 2024; 14:1414493. [PMID: 38881737 PMCID: PMC11176485 DOI: 10.3389/fcimb.2024.1414493] [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: 04/09/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024] Open
Abstract
Visceral leishmaniasis is a potentially devastating neglected tropical disease caused by the protozoan parasites Leishmania donovani and L. infantum (chagasi). These parasites reside in tissue macrophages and survive by deploying a number of mechanisms aimed at subverting the host immune response. CD4+ T cells play an important role in controlling Leishmania parasites by providing help in the form of pro-inflammatory cytokines to activate microbiocidal pathways in infected macrophages. However, because these cytokines can also cause tissue damage if over-produced, regulatory immune responses develop, and the balance between pro-inflammatory and regulatory CD4+ T cells responses determines the outcomes of infection. Past studies have identified important roles for pro-inflammatory cytokines such as IFNγ and TNF, as well as regulatory co-inhibitory receptors and the potent anti-inflammatory cytokine IL-10. More recently, other immunoregulatory molecules have been identified that play important roles in CD4+ T cell responses during VL. In this review, we will discuss recent findings about two of these molecules; the NK cell granule protein Nkg7 and the anti-inflammatory cytokine TGFβ, and describe how they impact CD4+ T cell functions and immune responses during visceral leishmaniasis.
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Affiliation(s)
- Jinrui Na
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Medicine, University of Queensland, Brisbane, QLD, Australia
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13
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Ziblat A, Horton BL, Higgs EF, Hatogai K, Martinez A, Shapiro JW, Kim DEC, Zha Y, Sweis RF, Gajewski TF. Batf3 + DCs and the 4-1BB/4-1BBL axis are required at the effector phase in the tumor microenvironment for PD-1/PD-L1 blockade efficacy. Cell Rep 2024; 43:114141. [PMID: 38656869 PMCID: PMC11229087 DOI: 10.1016/j.celrep.2024.114141] [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: 08/30/2023] [Revised: 02/29/2024] [Accepted: 04/08/2024] [Indexed: 04/26/2024] Open
Abstract
The cellular source of positive signals that reinvigorate T cells within the tumor microenvironment (TME) for the therapeutic efficacy of programmed death-1 (PD-1)/programmed death-ligand 1 (PD-L1) blockade has not been clearly defined. We now show that Batf3-lineage dendritic cells (DCs) are essential in this process. Flow cytometric analysis, gene-targeted mice, and blocking antibody studies revealed that 4-1BBL is a major positive co-stimulatory signal provided by these DCs within the TME that translates to CD8+ T cell functional reinvigoration and tumor regression. Immunofluorescence and spatial transcriptomics on human tumor samples revealed clustering of Batf3+ DCs and CD8+ T cells, which correlates with anti-PD-1 efficacy. In addition, proximity to Batf3+ DCs within the TME is associated with CD8+ T cell transcriptional states linked to anti-PD-1 response. Our results demonstrate that Batf3+ DCs within the TME are critical for PD-1/PD-L1 blockade efficacy and indicate a major role for the 4-1BB/4-1BB ligand (4-1BBL) axis during this process.
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Affiliation(s)
- Andrea Ziblat
- Department of Pathology, Section of Hematology/Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Brendan L Horton
- Department of Pathology, Section of Hematology/Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Emily F Higgs
- Department of Pathology, Section of Hematology/Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Ken Hatogai
- Department of Pathology, Section of Hematology/Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Anna Martinez
- Department of Pathology, Section of Hematology/Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Jason W Shapiro
- Center for Research Informatics, University of Chicago, Chicago, IL 60637, USA
| | - Danny E C Kim
- Department of Pathology, Section of Hematology/Oncology, University of Chicago, Chicago, IL 60637, USA
| | - YuanYuan Zha
- Human Immunological Monitoring Facility, University of Chicago, Chicago, IL 60637, USA
| | - Randy F Sweis
- Department of Medicine, University of Chicago, Chicago, IL 60612, USA
| | - Thomas F Gajewski
- Department of Pathology, Section of Hematology/Oncology, University of Chicago, Chicago, IL 60637, USA; Department of Medicine, University of Chicago, Chicago, IL 60612, USA.
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14
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Anderko RR, DePuyt AE, Bronson R, Bullotta AC, Aga E, Bosch RJ, Jones RB, Eron JJ, Mellors JW, Gandhi RT, McMahon DK, Macatangay BJ, Rinaldo CR, Mailliard RB. Persistence of a Skewed Repertoire of NK Cells in People with HIV-1 on Long-Term Antiretroviral Therapy. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1564-1578. [PMID: 38551350 PMCID: PMC11073922 DOI: 10.4049/jimmunol.2300672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/11/2024] [Indexed: 04/05/2024]
Abstract
HIV-1 infection greatly alters the NK cell phenotypic and functional repertoire. This is highlighted by the expansion of a rare population of FcRγ- NK cells exhibiting characteristics of traditional immunologic memory in people with HIV (PWH). Although current antiretroviral therapy (ART) effectively controls HIV-1 viremia and disease progression, its impact on HIV-1-associated NK cell abnormalities remains unclear. To address this, we performed a longitudinal analysis detailing conventional and memory-like NK cell characteristics in n = 60 PWH during the first 4 y of ART. Throughout this regimen, a skewed repertoire of cytokine unresponsive FcRγ- memory-like NK cells persisted and accompanied an overall increase in NK surface expression of CD57 and KLRG1, suggestive of progression toward immune senescence. These traits were linked to elevated serum inflammatory biomarkers and increasing Ab titers to human CMV, with human CMV viremia detected in approximately one-third of PWH at years 1-4 of ART. Interestingly, 40% of PWH displayed atypical NK cell subsets, representing intermediate stages of NK-poiesis based on single-cell multiomic trajectory analysis. Our findings indicate that NK cell irregularities persist in PWH despite long-term ART, underscoring the need to better understand the causative mechanisms that prevent full restoration of immune health in PWH.
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Affiliation(s)
- Renee R. Anderko
- Department of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
| | - Allison E. DePuyt
- Department of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
| | - Rhianna Bronson
- Department of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
| | - Arlene C. Bullotta
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Evgenia Aga
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Ronald J. Bosch
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - R. Brad Jones
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Joseph J. Eron
- Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - John W. Mellors
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Rajesh T. Gandhi
- Infectious Disease Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Deborah K. McMahon
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Bernard J. Macatangay
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Charles R. Rinaldo
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Robbie B. Mailliard
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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15
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Wang CM, Jan Wu YJ, Zheng JW, Huang LY, Tan KP, Chen JY. T cell expressions of aberrant gene signatures and Co-inhibitory receptors (Co-IRs) as predictors of renal damage and lupus disease activity. J Biomed Sci 2024; 31:41. [PMID: 38650001 PMCID: PMC11034032 DOI: 10.1186/s12929-024-01024-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 04/01/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Systemic lupus erythematosus (SLE) is distinguished by an extensive range of clinical heterogeneity with unpredictable disease flares and organ damage. This research investigates the potential of aberrant signatures on T cell genes, soluble Co-IRs/ligands, and Co-IRs expression on T cells as biomarkers for lupus disease parameters. METHODS Comparative transcriptome profiling analysis of non-renal and end-stage renal disease (ESRD) phenotypes of SLE was performed using CD4 + and CD8 + cDNA microarrays of sorted T cells. Comparing the expression of Co-IRs on T cells and serum soluble mediators among healthy and SLE phenotypes. RESULTS SLE patients with ESRD were downregulated CD38, PLEK, interferon-γ, CX3CR1, FGFBP2, and SLCO4C1 transcripts on CD4 + and CD8 + T cells simultaneously and NKG7, FCRL6, GZMB/H, FcγRIII, ITGAM, Fas ligand, TBX21, LYN, granulysin, CCL4L1, CMKLR1, HLA-DRβ, KIR2DL3, and KLRD1 in CD8 T cells. Pathway enrichment and PPI network analyses revealed that the overwhelming majority of Differentially Expressed Genes (DEGs) have been affiliated with novel cytotoxic, antigen presentation, and chemokine-cell migration signature pathways. CD8 + GZMK + T cells that are varied in nature, including CD161 + Mucosal-associated invariant T (MAIT) cells and CD161- aged-associated T (Taa) cells and CD161-GZMK + GZMB + T cells might account for a higher level of GZMK in CD8 + T cells associated with ESRD. SLE patients have higher TIGIT + , PD1 + , and lower CD127 + cell percentages on CD4 + T cells, higher TIM3 + , TIGIT + , HLA-DR + cell frequency, and lower MFI expression of CD127, CD160 in CD8 T cells. Co-IRs expression in T cells was correlated with soluble PD-1, PDL-2, and TIM3 levels, as well as SLE disease activity, clinical phenotypes, and immune-therapy responses. CONCLUSION The signature of dysfunctional pathways defines a distinct immunity pattern in LN ESRD patients. Expression levels of Co-IRs in peripheral blood T cells and serum levels of soluble PD1/PDL-2/TIM3 can serve as biomarkers for evaluating clinical parameters and therapeutic responses.
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Affiliation(s)
- Chin-Man Wang
- Department of Rehabilitation, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, No. 5, Fu-Shin St. Kwei-Shan, Taoyuan, Republic of China
| | - Yeong-Jian Jan Wu
- Department of Medicine, Division of Allergy, Immunology and Rheumatology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan, No. 5, Fu-Shin St. Kwei-Shan, Republic of China
| | - Jian-Wen Zheng
- Department of Medicine, Division of Allergy, Immunology and Rheumatology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan, No. 5, Fu-Shin St. Kwei-Shan, Republic of China
| | - Li Yu Huang
- Department of Medicine, Division of Allergy, Immunology and Rheumatology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan, No. 5, Fu-Shin St. Kwei-Shan, Republic of China
| | - Keng Poo Tan
- Department of Medicine, Division of Allergy, Immunology and Rheumatology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan, No. 5, Fu-Shin St. Kwei-Shan, Republic of China
| | - Ji-Yih Chen
- Department of Medicine, Division of Allergy, Immunology and Rheumatology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan, No. 5, Fu-Shin St. Kwei-Shan, Republic of China.
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Huang F, Welner RS, Chen JY, Yue Z. PAGER-scFGA: unveiling cell functions and molecular mechanisms in cell trajectories through single-cell functional genomics analysis. FRONTIERS IN BIOINFORMATICS 2024; 4:1336135. [PMID: 38690527 PMCID: PMC11058213 DOI: 10.3389/fbinf.2024.1336135] [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: 11/10/2023] [Accepted: 04/01/2024] [Indexed: 05/02/2024] Open
Abstract
Background: Understanding how cells and tissues respond to stress factors and perturbations during disease processes is crucial for developing effective prevention, diagnosis, and treatment strategies. Single-cell RNA sequencing (scRNA-seq) enables high-resolution identification of cells and exploration of cell heterogeneity, shedding light on cell differentiation/maturation and functional differences. Recent advancements in multimodal sequencing technologies have focused on improving access to cell-specific subgroups for functional genomics analysis. To facilitate the functional annotation of cell groups and characterization of molecular mechanisms underlying cell trajectories, we introduce the Pathways, Annotated Gene Lists, and Gene Signatures Electronic Repository for Single-Cell Functional Genomics Analysis (PAGER-scFGA). Results: We have developed PAGER-scFGA, which integrates cell functional annotations and gene-set enrichment analysis into popular single-cell analysis pipelines such as Scanpy. Using differentially expressed genes (DEGs) from pairwise cell clusters, PAGER-scFGA infers cell functions through the enrichment of potential cell-marker genesets. Moreover, PAGER-scFGA provides pathways, annotated gene lists, and gene signatures (PAGs) enriched in specific cell subsets with tissue compositions and continuous transitions along cell trajectories. Additionally, PAGER-scFGA enables the construction of a gene subcellular map based on DEGs and allows examination of the gene functional compartments (GFCs) underlying cell maturation/differentiation. In a real-world case study of mouse natural killer (mNK) cells, PAGER-scFGA revealed two major stages of natural killer (NK) cells and three trajectories from the precursor stage to NK T-like mature stage within blood, spleen, and bone marrow tissues. As the trajectories progress to later stages, the DEGs exhibit greater divergence and variability. However, the DEGs in different trajectories still interact within a network during NK cell maturation. Notably, PAGER-scFGA unveiled cell cytotoxicity, exocytosis, and the response to interleukin (IL) signaling pathways and associated network models during the progression from precursor NK cells to mature NK cells. Conclusion: PAGER-scFGA enables in-depth exploration of functional insights and presents a comprehensive knowledge map of gene networks and GFCs, which can be utilized for future studies and hypothesis generation. It is expected to become an indispensable tool for inferring cell functions and detecting molecular mechanisms within cell trajectories in single-cell studies. The web app (accessible at https://au-singlecell.streamlit.app/) is publicly available.
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Affiliation(s)
- Fengyuan Huang
- Department of Biomedical Informatics and Data Science, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Robert S. Welner
- Hematology & Oncology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jake Y. Chen
- Department of Biomedical Informatics and Data Science, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Zongliang Yue
- Health Outcome Research and Policy Department, Harrison College of Pharmacy, Auburn University, Auburn, AL, United States
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Wang Y, Chen X, Tang N, Guo M, Ai D. Boosting Clear Cell Renal Carcinoma-Specific Drug Discovery Using a Deep Learning Algorithm and Single-Cell Analysis. Int J Mol Sci 2024; 25:4134. [PMID: 38612943 PMCID: PMC11012314 DOI: 10.3390/ijms25074134] [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: 02/17/2024] [Revised: 03/26/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Clear cell renal carcinoma (ccRCC), the most common subtype of renal cell carcinoma, has the high heterogeneity of a highly complex tumor microenvironment. Existing clinical intervention strategies, such as target therapy and immunotherapy, have failed to achieve good therapeutic effects. In this article, single-cell transcriptome sequencing (scRNA-seq) data from six patients downloaded from the GEO database were adopted to describe the tumor microenvironment (TME) of ccRCC, including its T cells, tumor-associated macrophages (TAMs), endothelial cells (ECs), and cancer-associated fibroblasts (CAFs). Based on the differential typing of the TME, we identified tumor cell-specific regulatory programs that are mediated by three key transcription factors (TFs), whilst the TF EPAS1/HIF-2α was identified via drug virtual screening through our analysis of ccRCC's protein structure. Then, a combined deep graph neural network and machine learning algorithm were used to select anti-ccRCC compounds from bioactive compound libraries, including the FDA-approved drug library, natural product library, and human endogenous metabolite compound library. Finally, five compounds were obtained, including two FDA-approved drugs (flufenamic acid and fludarabine), one endogenous metabolite, one immunology/inflammation-related compound, and one inhibitor of DNA methyltransferase (N4-methylcytidine, a cytosine nucleoside analogue that, like zebularine, has the mechanism of inhibiting DNA methyltransferase). Based on the tumor microenvironment characteristics of ccRCC, five ccRCC-specific compounds were identified, which would give direction of the clinical treatment for ccRCC patients.
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Affiliation(s)
| | | | | | | | - Dongmei Ai
- School of Mathematics and Physics, University of Science and Technology Beijing, Beijing 100083, China; (Y.W.); (X.C.); (N.T.); (M.G.)
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18
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Peng S, Lin A, Jiang A, Zhang C, Zhang J, Cheng Q, Luo P, Bai Y. CTLs heterogeneity and plasticity: implications for cancer immunotherapy. Mol Cancer 2024; 23:58. [PMID: 38515134 PMCID: PMC10956324 DOI: 10.1186/s12943-024-01972-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 02/26/2024] [Indexed: 03/23/2024] Open
Abstract
Cytotoxic T lymphocytes (CTLs) play critical antitumor roles, encompassing diverse subsets including CD4+, NK, and γδ T cells beyond conventional CD8+ CTLs. However, definitive CTLs biomarkers remain elusive, as cytotoxicity-molecule expression does not necessarily confer cytotoxic capacity. CTLs differentiation involves transcriptional regulation by factors such as T-bet and Blimp-1, although epigenetic regulation of CTLs is less clear. CTLs promote tumor killing through cytotoxic granules and death receptor pathways, but may also stimulate tumorigenesis in some contexts. Given that CTLs cytotoxicity varies across tumors, enhancing this function is critical. This review summarizes current knowledge on CTLs subsets, biomarkers, differentiation mechanisms, cancer-related functions, and strategies for improving cytotoxicity. Key outstanding questions include refining the CTLs definition, characterizing subtype diversity, elucidating differentiation and senescence pathways, delineating CTL-microbe relationships, and enabling multi-omics profiling. A more comprehensive understanding of CTLs biology will facilitate optimization of their immunotherapy applications. Overall, this review synthesizes the heterogeneity, regulation, functional roles, and enhancement strategies of CTLs in antitumor immunity, highlighting gaps in our knowledge of subtype diversity, definitive biomarkers, epigenetic control, microbial interactions, and multi-omics characterization. Addressing these questions will refine our understanding of CTLs immunology to better leverage cytotoxic functions against cancer.
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Affiliation(s)
- Shengkun Peng
- Department of Radiology, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Anqi Lin
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, Guangdong, China
| | - Aimin Jiang
- Department of Urology, Changhai hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Cangang Zhang
- Department of Pathogenic Microbiology and ImmunologySchool of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, Guangdong, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South University, Hunan, China.
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, Guangdong, China.
| | - Yifeng Bai
- Department of Oncology, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.
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19
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Radtke AJ, Postovalova E, Varlamova A, Bagaev A, Sorokina M, Kudryashova O, Meerson M, Polyakova M, Galkin I, Svekolkin V, Isaev S, Wiebe D, Sharun A, Sarachakov A, Perelman G, Lozinsky Y, Yaniv Z, Lowekamp BC, Speranza E, Yao L, Pittaluga S, Shaffer AL, Jonigk D, Phelan JD, Davies-Hill T, Huang DW, Ovcharov P, Nomie K, Nuzhdina E, Kotlov N, Ataullakhanov R, Fowler N, Kelly M, Muppidi J, Davis JL, Hernandez JM, Wilson WH, Jaffe ES, Staudt LM, Roschewski M, Germain RN. Multi-omic profiling of follicular lymphoma reveals changes in tissue architecture and enhanced stromal remodeling in high-risk patients. Cancer Cell 2024; 42:444-463.e10. [PMID: 38428410 PMCID: PMC10966827 DOI: 10.1016/j.ccell.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 12/04/2023] [Accepted: 02/05/2024] [Indexed: 03/03/2024]
Abstract
Follicular lymphoma (FL) is a generally incurable malignancy that evolves from developmentally blocked germinal center (GC) B cells. To promote survival and immune escape, tumor B cells undergo significant genetic changes and extensively remodel the lymphoid microenvironment. Dynamic interactions between tumor B cells and the tumor microenvironment (TME) are hypothesized to contribute to the broad spectrum of clinical behaviors observed among FL patients. Despite the urgent need, existing clinical tools do not reliably predict disease behavior. Using a multi-modal strategy, we examined cell-intrinsic and -extrinsic factors governing progression and therapeutic outcomes in FL patients enrolled onto a prospective clinical trial. By leveraging the strengths of each platform, we identify several tumor-specific features and microenvironmental patterns enriched in individuals who experience early relapse, the most high-risk FL patients. These features include stromal desmoplasia and changes to the follicular growth pattern present 20 months before first progression and first relapse.
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Affiliation(s)
- Andrea J Radtke
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Ziv Yaniv
- Bioinformatics and Computational Bioscience Branch, NIAID, NIH, Bethesda, MD 20892, USA
| | - Bradley C Lowekamp
- Bioinformatics and Computational Bioscience Branch, NIAID, NIH, Bethesda, MD 20892, USA
| | - Emily Speranza
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA; Florida Research and Innovation Center, Cleveland Clinic Lerner Research Institute, Port Saint Lucie, FL 34987, USA
| | - Li Yao
- Li Yao Visuals, Rockville, MD 20855, USA
| | | | - Arthur L Shaffer
- Lymphoid Malignancies Branch, NCI, NIH, Bethesda, MD 20892, USA; Tumor Targeted Delivery, Heme Malignancy Target Discovery Group, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Danny Jonigk
- Institute of Pathology, Aachen Medical University, RWTH Aachen, 52074 Aachen, Germany; German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), 30625 Hannover, Germany
| | - James D Phelan
- Lymphoid Malignancies Branch, NCI, NIH, Bethesda, MD 20892, USA
| | | | - Da Wei Huang
- Lymphoid Malignancies Branch, NCI, NIH, Bethesda, MD 20892, USA
| | | | | | | | | | | | | | - Michael Kelly
- CCR Single Analysis Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Bethesda, MD 20892, USA
| | - Jagan Muppidi
- Lymphoid Malignancies Branch, NCI, NIH, Bethesda, MD 20892, USA
| | - Jeremy L Davis
- Surgical Oncology Program, Metastasis Biology Section, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jonathan M Hernandez
- Surgical Oncology Program, Metastasis Biology Section, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | | | - Elaine S Jaffe
- Laboratory of Pathology, NCI, NIH, Bethesda, MD 20892, USA
| | - Louis M Staudt
- Lymphoid Malignancies Branch, NCI, NIH, Bethesda, MD 20892, USA
| | - Mark Roschewski
- Lymphoid Malignancies Branch, NCI, NIH, Bethesda, MD 20892, USA
| | - Ronald N Germain
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA
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20
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Hu X, Cao D, Zhou Z, Wang Z, Zeng J, Hong WX. Single-cell transcriptomic profiling reveals immune cell heterogeneity in acute myeloid leukaemia peripheral blood mononuclear cells after chemotherapy. Cell Oncol (Dordr) 2024; 47:97-112. [PMID: 37615858 PMCID: PMC10899424 DOI: 10.1007/s13402-023-00853-2] [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] [Accepted: 07/31/2023] [Indexed: 08/25/2023] Open
Abstract
PURPOSE Acute myeloid leukaemia (AML) is a heterogeneous disease characterised by the rapid clonal expansion of abnormally differentiated myeloid progenitor cells residing in a complex microenvironment. However, the immune cell types, status, and genome profile of the peripheral blood mononuclear cell (PBMC) microenvironment in AML patients after chemotherapy are poorly understood. In order to explore the immune microenvironment of AML patients after chemotherapy, we conducted this study for providing insights into precision medicine and immunotherapy of AML. METHODS In this study, we used single-cell RNA sequencing (scRNA-seq) to analyse the PBMC microenvironment from five AML patients treated with different chemotherapy regimens and six healthy donors. We compared the cell compositions in AML patients and healthy donors, and performed gene set enrichment analysis (GSEA), CellPhoneDB, and copy number variation (CNV) analysis. RESULTS Using scRNA-seq technology, 91,772 high quality cells of 44,950 PBMCs from AML patients and 46,822 PBMCs from healthy donors were classified as 14 major cell clusters. Our study revealed the sub-cluster diversity of T cells, natural killer (NK) cells, monocytes, dendritic cells (DCs), and haematopoietic stem cell progenitors (HSC-Prog) in AML patients under chemotherapy. NK cells and monocyte-DCs showed significant changes in transcription factor expression and chromosome copy number variation (CNV). We also observed significant heterogeneity in CNV and intercellular interaction networks in HSC-Prog cells. CONCLUSION Our results elucidated the PBMC single-cell landscape and provided insights into precision medicine and immunotherapy for treating AML.
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Affiliation(s)
- Xuqiao Hu
- Shenzhen Center for Chronic Disease Control and Prevention, Shenzhen Institute of Dermatology, Shenzhen, China.
- Second Clinical Medical College of Jinan University, First Affiliated Hospital of Southern University of Science and Technology (Shenzhen People's Hospital), Shenzhen, China.
| | - Dongyan Cao
- Department of Biliary-Pancreatic Surgery, the Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhenru Zhou
- Shenzhen Center for Chronic Disease Control and Prevention, Shenzhen Institute of Dermatology, Shenzhen, China
- Second Clinical Medical College of Jinan University, First Affiliated Hospital of Southern University of Science and Technology (Shenzhen People's Hospital), Shenzhen, China
| | - Zhaoyang Wang
- Shenzhen Center for Chronic Disease Control and Prevention, Shenzhen Institute of Dermatology, Shenzhen, China
- Second Clinical Medical College of Jinan University, First Affiliated Hospital of Southern University of Science and Technology (Shenzhen People's Hospital), Shenzhen, China
| | - Jieying Zeng
- Second Clinical Medical College of Jinan University, First Affiliated Hospital of Southern University of Science and Technology (Shenzhen People's Hospital), Shenzhen, China
| | - Wen-Xu Hong
- Shenzhen Center for Chronic Disease Control and Prevention, Shenzhen Institute of Dermatology, Shenzhen, China.
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21
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Fan Q, Yan R, Li Y, Lu L, Liu J, Li S, Fu T, Xue Y, Liu J, Li Z. Exploring Immune Cell Diversity in the Lacrimal Glands of Healthy Mice: A Single-Cell RNA-Sequencing Atlas. Int J Mol Sci 2024; 25:1208. [PMID: 38279208 PMCID: PMC10816500 DOI: 10.3390/ijms25021208] [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: 11/26/2023] [Revised: 01/05/2024] [Accepted: 01/09/2024] [Indexed: 01/28/2024] Open
Abstract
The lacrimal gland is responsible for maintaining the health of the ocular surface through the production of tears. However, our understanding of the immune system within the lacrimal gland is currently limited. Therefore, in this study, we utilized single-cell RNA sequencing and bioinformatic analysis to identify and analyze immune cells and molecules present in the lacrimal glands of normal mice. A total of 34,891 cells were obtained from the lacrimal glands of mice and classified into 18 distinct cell clusters using Seurat clustering. Within these cell populations, 26 different immune cell subpopulations were identified, including T cells, innate lymphocytes, macrophages, mast cells, dendritic cells, and B cells. Network analysis revealed complex cell-cell interactions between these immune cells, with particularly significant interactions observed among T cells, macrophages, plasma cells, and dendritic cells. Interestingly, T cells were found to be the main source of ligands for the Thy1 signaling pathway, while M2 macrophages were identified as the primary target of this pathway. Moreover, some of these immune cells were validated using immunohistological techniques. Collectively, these findings highlight the abundance and interactions of immune cells and provide valuable insights into the complexity of the lacrimal gland immune system and its relevance to associated diseases.
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Affiliation(s)
- Qiwei Fan
- Department of Pathology, School of Medicine, Jinan University, Guangzhou 510632, China; (Q.F.); (J.L.)
- International Ocular Surface Research Center, Key Laboratory for Regenerative Medicine, Institute of Ophthalmology, Jinan University, Guangzhou 510632, China; (R.Y.); (Y.L.); (L.L.); (S.L.); (T.F.); (Y.X.); (J.L.)
| | - Ruyu Yan
- International Ocular Surface Research Center, Key Laboratory for Regenerative Medicine, Institute of Ophthalmology, Jinan University, Guangzhou 510632, China; (R.Y.); (Y.L.); (L.L.); (S.L.); (T.F.); (Y.X.); (J.L.)
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510630, China
| | - Yan Li
- International Ocular Surface Research Center, Key Laboratory for Regenerative Medicine, Institute of Ophthalmology, Jinan University, Guangzhou 510632, China; (R.Y.); (Y.L.); (L.L.); (S.L.); (T.F.); (Y.X.); (J.L.)
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510630, China
| | - Liyuan Lu
- International Ocular Surface Research Center, Key Laboratory for Regenerative Medicine, Institute of Ophthalmology, Jinan University, Guangzhou 510632, China; (R.Y.); (Y.L.); (L.L.); (S.L.); (T.F.); (Y.X.); (J.L.)
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510630, China
| | - Jiangman Liu
- Department of Pathology, School of Medicine, Jinan University, Guangzhou 510632, China; (Q.F.); (J.L.)
- International Ocular Surface Research Center, Key Laboratory for Regenerative Medicine, Institute of Ophthalmology, Jinan University, Guangzhou 510632, China; (R.Y.); (Y.L.); (L.L.); (S.L.); (T.F.); (Y.X.); (J.L.)
| | - Senmao Li
- International Ocular Surface Research Center, Key Laboratory for Regenerative Medicine, Institute of Ophthalmology, Jinan University, Guangzhou 510632, China; (R.Y.); (Y.L.); (L.L.); (S.L.); (T.F.); (Y.X.); (J.L.)
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510630, China
| | - Ting Fu
- International Ocular Surface Research Center, Key Laboratory for Regenerative Medicine, Institute of Ophthalmology, Jinan University, Guangzhou 510632, China; (R.Y.); (Y.L.); (L.L.); (S.L.); (T.F.); (Y.X.); (J.L.)
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510630, China
| | - Yunxia Xue
- International Ocular Surface Research Center, Key Laboratory for Regenerative Medicine, Institute of Ophthalmology, Jinan University, Guangzhou 510632, China; (R.Y.); (Y.L.); (L.L.); (S.L.); (T.F.); (Y.X.); (J.L.)
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510630, China
| | - Jun Liu
- International Ocular Surface Research Center, Key Laboratory for Regenerative Medicine, Institute of Ophthalmology, Jinan University, Guangzhou 510632, China; (R.Y.); (Y.L.); (L.L.); (S.L.); (T.F.); (Y.X.); (J.L.)
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510630, China
| | - Zhijie Li
- International Ocular Surface Research Center, Key Laboratory for Regenerative Medicine, Institute of Ophthalmology, Jinan University, Guangzhou 510632, China; (R.Y.); (Y.L.); (L.L.); (S.L.); (T.F.); (Y.X.); (J.L.)
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510630, China
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22
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Yu T, Nie FQ, Zhang Q, Yu SK, Zhang ML, Wang Q, Wang EX, Lu KH, Sun M. Effects of methionine deficiency on B7H3-DAP12-CAR-T cells in the treatment of lung squamous cell carcinoma. Cell Death Dis 2024; 15:12. [PMID: 38182561 PMCID: PMC10770166 DOI: 10.1038/s41419-023-06376-w] [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: 02/20/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 01/07/2024]
Abstract
Lung squamous cell carcinoma (LUSC) is a subtype of lung cancer for which precision therapy is lacking. Chimeric antigen receptor T-cells (CAR-T) have the potential to eliminate cancer cells by targeting specific antigens. However, the tumor microenvironment (TME), characterized by abnormal metabolism could inhibit CAR-T function. Therefore, the aim of this study was to improve CAR-T efficacy in solid TME by investigating the effects of amino acid metabolism. We found that B7H3 was highly expressed in LUSC and developed DAP12-CAR-T targeting B7H3 based on our previous findings. When co-cultured with B7H3-overexpressing LUSC cells, B7H3-DAP12-CAR-T showed significant cell killing effects and released cytokines including IFN-γ and IL-2. However, LUSC cells consumed methionine (Met) in a competitive manner to induce a Met deficiency. CAR-T showed suppressed cell killing capacity, reduced cytokine release and less central memory T phenotype in medium with lower Met, while the exhaustion markers were up-regulated. Furthermore, the gene NKG7, responsible for T cell cytotoxicity, was downregulated in CAR-T cells at low Met concentration due to a decrease in m5C modification. NKG7 overexpression could partially restore the cytotoxicity of CAR-T in low Met. In addition, the anti-tumor efficacy of CAR-T was significantly enhanced when co-cultured with SLC7A5 knockdown LUSC cells at low Met concentration. In conclusion, B7H3 is a prospective target for LUSC, and B7H3-DAP12-CAR-T cells are promising for LUSC treatment. Maintaining Met levels in CAR-T may help overcome TME suppression and improve its clinical application potential.
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Affiliation(s)
- Tao Yu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, China
| | - Feng-Qi Nie
- Department of Oncology, The Second Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Qi Zhang
- Department of Oncology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
| | - Shao-Kun Yu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, China
| | - Mei-Ling Zhang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, China
| | - Qian Wang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, China
| | - En-Xiu Wang
- Nanjing CART Medical Technology Co., Ltd, Nanjing, China
| | - Kai-Hua Lu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, China.
| | - Ming Sun
- Suzhou Cancer Center Core Laboratory, Suzhou Municipal Hospital, Gusu School, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China.
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23
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Zou D, Yin Z, Yi SG, Wang G, Guo Y, Xiao X, Li S, Zhang X, Gonzalez NM, Minze LJ, Wang L, Wong STC, Osama Gaber A, Ghobrial RM, Li XC, Chen W. CD4 + T cell immunity is dependent on an intrinsic stem-like program. Nat Immunol 2024; 25:66-76. [PMID: 38168955 PMCID: PMC11064861 DOI: 10.1038/s41590-023-01682-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 10/11/2023] [Indexed: 01/05/2024]
Abstract
CD4+ T cells are central to various immune responses, but the molecular programs that drive and maintain CD4+ T cell immunity are not entirely clear. Here we identify a stem-like program that governs the CD4+ T cell response in transplantation models. Single-cell-transcriptomic analysis revealed that naive alloantigen-specific CD4+ T cells develop into TCF1hi effector precursor (TEP) cells and TCF1-CXCR6+ effectors in transplant recipients. The TCF1-CXCR6+CD4+ effectors lose proliferation capacity and do not reject allografts upon adoptive transfer into secondary hosts. By contrast, the TCF1hiCD4+ TEP cells have dual features of self-renewal and effector differentiation potential, and allograft rejection depends on continuous replenishment of TCF1-CXCR6+ effectors from TCF1hiCD4+ TEP cells. Mechanistically, TCF1 sustains the CD4+ TEP cell population, whereas the transcription factor IRF4 and the glycolytic enzyme LDHA govern the effector differentiation potential of CD4+ TEP cells. Deletion of IRF4 or LDHA in T cells induces transplant acceptance. These findings unravel a stem-like program that controls the self-renewal capacity and effector differentiation potential of CD4+ TEP cells and have implications for T cell-related immunotherapies.
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Affiliation(s)
- Dawei Zou
- Immunobiology & Transplant Science Center, Department of Surgery, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zheng Yin
- Systems Medicine and Bioengineering Department, Houston Methodist Neal Cancer Center, Houston, TX, USA
- Department of Radiology, Houston Methodist Hospital, Weill Cornell Medicine, Houston, TX, USA
| | - Stephanie G Yi
- Department of Surgery, J. C. Walter Jr. Transplant Center, Houston Methodist Hospital, Houston, TX, USA
- Department of Surgery, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Guohua Wang
- Immunobiology & Transplant Science Center, Department of Surgery, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
| | - Yang Guo
- Immunobiology & Transplant Science Center, Department of Surgery, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
| | - Xiang Xiao
- Immunobiology & Transplant Science Center, Department of Surgery, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
| | - Shuang Li
- Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX, USA
| | - Xiaolong Zhang
- Immunobiology & Transplant Science Center, Department of Surgery, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
| | - Nancy M Gonzalez
- Immunobiology & Transplant Science Center, Department of Surgery, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
| | - Laurie J Minze
- Immunobiology & Transplant Science Center, Department of Surgery, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
| | - Lin Wang
- Systems Medicine and Bioengineering Department, Houston Methodist Neal Cancer Center, Houston, TX, USA
| | - Stephen T C Wong
- Systems Medicine and Bioengineering Department, Houston Methodist Neal Cancer Center, Houston, TX, USA
- Department of Radiology, Houston Methodist Hospital, Weill Cornell Medicine, Houston, TX, USA
| | - A Osama Gaber
- Department of Surgery, J. C. Walter Jr. Transplant Center, Houston Methodist Hospital, Houston, TX, USA
- Department of Surgery, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Rafik M Ghobrial
- Department of Surgery, J. C. Walter Jr. Transplant Center, Houston Methodist Hospital, Houston, TX, USA
- Department of Surgery, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Xian C Li
- Immunobiology & Transplant Science Center, Department of Surgery, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
- Department of Surgery, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Wenhao Chen
- Immunobiology & Transplant Science Center, Department of Surgery, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA.
- Department of Surgery, Weill Cornell Medicine, Cornell University, New York, NY, USA.
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24
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Edwards CL, Engel JA, de Labastida Rivera F, Ng SS, Corvino D, Montes de Oca M, Frame TC, Chauhan SB, Singh SS, Kumar A, Wang Y, Na J, Mukhopadhyay P, Lee JS, Nylen S, Sundar S, Kumar R, Engwerda CR. A molecular signature for IL-10-producing Th1 cells in protozoan parasitic diseases. JCI Insight 2023; 8:e169362. [PMID: 37917177 PMCID: PMC10807716 DOI: 10.1172/jci.insight.169362] [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: 02/01/2023] [Accepted: 10/31/2023] [Indexed: 11/04/2023] Open
Abstract
Control of visceral leishmaniasis (VL) depends on proinflammatory Th1 cells that activate infected tissue macrophages to kill resident intracellular parasites. However, proinflammatory cytokines produced by Th1 cells can damage tissues and require tight regulation. Th1 cell IL-10 production is an important cell-autologous mechanism to prevent such damage. However, IL-10-producing Th1 (type 1 regulatory; Tr1) cells can also delay control of parasites and the generation of immunity following drug treatment or vaccination. To identify molecules to target in order to alter the balance between Th1 and Tr1 cells for improved antiparasitic immunity, we compared the molecular and phenotypic profiles of Th1 and Tr1 cells in experimental VL caused by Leishmania donovani infection of C57BL/6J mice. We also identified a shared Tr1 cell protozoan signature by comparing the transcriptional profiles of Tr1 cells from mice with experimental VL and malaria. We identified LAG3 as an important coinhibitory receptor in patients with VL and experimental VL, and we reveal tissue-specific heterogeneity of coinhibitory receptor expression by Tr1 cells. We also discovered a role for the transcription factor Pbx1 in suppressing CD4+ T cell cytokine production. This work provides insights into the development and function of CD4+ T cells during protozoan parasitic infections and identifies key immunoregulatory molecules.
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Affiliation(s)
- Chelsea L. Edwards
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
- University of Queensland, School of Medicine, Brisbane, Australia
| | | | | | - Susanna S. Ng
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Griffith University, School of Natural Sciences, Nathan, Australia
- Institute of Experimental Oncology, University of Bonn, Bonn, Germany
| | - Dillon Corvino
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Institute of Experimental Oncology, University of Bonn, Bonn, Germany
| | | | - Teija C.M. Frame
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
- University of Queensland, School of Medicine, Brisbane, Australia
| | | | | | - Awnish Kumar
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Yulin Wang
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Griffith University, School of Natural Sciences, Nathan, Australia
| | - Jinrui Na
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
- University of Queensland, School of Medicine, Brisbane, Australia
| | | | - Jason S. Lee
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
- University of Queensland, School of Medicine, Brisbane, Australia
| | - Susanne Nylen
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | | | - Rajiv Kumar
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
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25
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Frank D, Bergamasco M, Mlodzianoski MJ, Kueh A, Tsui E, Hall C, Kastrappis G, Voss AK, McLean C, Faux M, Rogers KL, Tran B, Vincan E, Komander D, Dewson G, Tran H. Trabid patient mutations impede the axonal trafficking of adenomatous polyposis coli to disrupt neurite growth. eLife 2023; 12:RP90796. [PMID: 38099646 PMCID: PMC10723793 DOI: 10.7554/elife.90796] [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] [Indexed: 12/17/2023] Open
Abstract
ZRANB1 (human Trabid) missense mutations have been identified in children diagnosed with a range of congenital disorders including reduced brain size, but how Trabid regulates neurodevelopment is not understood. We have characterized these patient mutations in cells and mice to identify a key role for Trabid in the regulation of neurite growth. One of the patient mutations flanked the catalytic cysteine of Trabid and its deubiquitylating (DUB) activity was abrogated. The second variant retained DUB activity, but failed to bind STRIPAK, a large multiprotein assembly implicated in cytoskeleton organization and neural development. Zranb1 knock-in mice harboring either of these patient mutations exhibited reduced neuronal and glial cell densities in the brain and a motor deficit consistent with fewer dopaminergic neurons and projections. Mechanistically, both DUB-impaired and STRIPAK-binding-deficient Trabid variants impeded the trafficking of adenomatous polyposis coli (APC) to microtubule plus-ends. Consequently, the formation of neuronal growth cones and the trajectory of neurite outgrowth from mutant midbrain progenitors were severely compromised. We propose that STRIPAK recruits Trabid to deubiquitylate APC, and that in cells with mutant Trabid, APC becomes hyperubiquitylated and mislocalized causing impaired organization of the cytoskeleton that underlie the neuronal and developmental phenotypes.
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Affiliation(s)
- Daniel Frank
- Ubiquitin Signalling Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Maria Bergamasco
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Michael J Mlodzianoski
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Centre for Dynamic Imaging, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Andrew Kueh
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Melbourne Advanced Genome Editing Centre, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, Australia
- School of Cancer Medicine, La Trobe University, Heidelberg, Australia
| | - Ellen Tsui
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Histology Facility, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Cathrine Hall
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Inflammation Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Georgios Kastrappis
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Anne Kathrin Voss
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Catriona McLean
- Department of Anatomical Pathology, The Alfred Hospital, Melbourne, Australia
| | - Maree Faux
- Neuro-Oncology Group, Murdoch Children's Research Institute, Parkville, Australia
| | - Kelly L Rogers
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Centre for Dynamic Imaging, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Bang Tran
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Elizabeth Vincan
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- The Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - David Komander
- Ubiquitin Signalling Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Grant Dewson
- Ubiquitin Signalling Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Hoanh Tran
- Ubiquitin Signalling Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
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26
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Furtado R, Paul M, Zhang J, Sung J, Karell P, Kim RS, Caillat-Zucman S, Liang L, Felgner P, Bauleni A, Gama S, Buchwald A, Taylor T, Seydel K, Laufer M, Delahaye F, Daily JP, Lauvau G. Cytolytic circumsporozoite-specific memory CD4 + T cell clones are expanded during Plasmodium falciparum infection. Nat Commun 2023; 14:7726. [PMID: 38001069 PMCID: PMC10673885 DOI: 10.1038/s41467-023-43376-y] [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: 08/02/2021] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Clinical immunity against Plasmodium falciparum infection develops in residents of malaria endemic regions, manifesting in reduced clinical symptoms during infection and in protection against severe disease but the mechanisms are not fully understood. Here, we compare the cellular and humoral immune response of clinically immune (0-1 episode over 18 months) and susceptible (at least 3 episodes) during a mild episode of Pf malaria infection in a malaria endemic region of Malawi, by analysing peripheral blood samples using high dimensional mass cytometry (CyTOF), spectral flow cytometry and single-cell transcriptomic analyses. In the clinically immune, we find increased proportions of circulating follicular helper T cells and classical monocytes, while the humoral immune response shows characteristic age-related differences in the protected. Presence of memory CD4+ T cell clones with a strong cytolytic ZEB2+ T helper 1 effector signature, sharing identical T cell receptor clonotypes and recognizing the Pf-derived circumsporozoite protein (CSP) antigen are found in the blood of the Pf-infected participants gaining protection. Moreover, in clinically protected participants, ZEB2+ memory CD4+ T cells express lower level of inhibitory and chemotactic receptors. We thus propose that clonally expanded ZEB2+ CSP-specific cytolytic memory CD4+ Th1 cells may contribute to clinical immunity against the sporozoite and liver-stage Pf malaria.
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Affiliation(s)
- Raquel Furtado
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, 10461, USA
- RF: BioNTech US, 40 Erie Street, Cambridge, MA, 02139, USA
| | - Mahinder Paul
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, 10461, USA
| | - Jinghang Zhang
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, 10461, USA
| | - Joowhan Sung
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, 10461, USA
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Paul Karell
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, 10461, USA
| | - Ryung S Kim
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, 10461, USA
| | - Sophie Caillat-Zucman
- Université de Paris, AP-HP, Hôpital Saint-Louis, Laboratoire d'Immunologie et Histocompatiblité, INSERM UMR976, 75010, Paris, France
| | - Li Liang
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Philip Felgner
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Andy Bauleni
- Malaria Alert Centre, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Syze Gama
- Blantyre Malaria Project, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Andrea Buchwald
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Terrie Taylor
- Blantyre Malaria Project, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Osteopathic Medical Specialties, Michigan State University, East Lansing, MI, 48824, USA
| | - Karl Seydel
- Blantyre Malaria Project, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Osteopathic Medical Specialties, Michigan State University, East Lansing, MI, 48824, USA
| | - Miriam Laufer
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Fabien Delahaye
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, 10461, USA
- FD: Precision Oncology, Sanofi, Vitry sur Seine, France
| | - Johanna P Daily
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, 10461, USA.
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, 10461, USA.
| | - Grégoire Lauvau
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, 10461, USA.
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27
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Schnell A, Huang L, Regan BML, Singh V, Vonficht D, Bollhagen A, Wang M, Hou Y, Bod L, Sobel RA, Chihara N, Madi A, Anderson AC, Regev A, Kuchroo VK. Targeting PGLYRP1 promotes antitumor immunity while inhibiting autoimmune neuroinflammation. Nat Immunol 2023; 24:1908-1920. [PMID: 37828379 PMCID: PMC10864036 DOI: 10.1038/s41590-023-01645-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 09/08/2023] [Indexed: 10/14/2023]
Abstract
Co-inhibitory and checkpoint molecules suppress T cell function in the tumor microenvironment, thereby rendering T cells dysfunctional. Although immune checkpoint blockade is a successful treatment option for multiple human cancers, severe autoimmune-like adverse effects can limit its application. Here, we show that the gene encoding peptidoglycan recognition protein 1 (PGLYRP1) is highly coexpressed with genes encoding co-inhibitory molecules, indicating that it might be a promising target for cancer immunotherapy. Genetic deletion of Pglyrp1 in mice led to decreased tumor growth and an increased activation/effector phenotype in CD8+ T cells, suggesting an inhibitory function of PGLYRP1 in CD8+ T cells. Surprisingly, genetic deletion of Pglyrp1 protected against the development of experimental autoimmune encephalomyelitis, a model of autoimmune disease in the central nervous system. PGLYRP1-deficient myeloid cells had a defect in antigen presentation and T cell activation, indicating that PGLYRP1 might function as a proinflammatory molecule in myeloid cells during autoimmunity. These results highlight PGLYRP1 as a promising target for immunotherapy that, when targeted, elicits a potent antitumor immune response while protecting against some forms of tissue inflammation and autoimmunity.
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Affiliation(s)
- Alexandra Schnell
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital and Harvard Medical School, Boston, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Linglin Huang
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Brianna M L Regan
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital and Harvard Medical School, Boston, MA, USA
| | - Vasundhara Singh
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dominik Vonficht
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital and Harvard Medical School, Boston, MA, USA
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Alina Bollhagen
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital and Harvard Medical School, Boston, MA, USA
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mona Wang
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital and Harvard Medical School, Boston, MA, USA
| | - Yu Hou
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital and Harvard Medical School, Boston, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Lloyd Bod
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital and Harvard Medical School, Boston, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Raymond A Sobel
- Palo Alto Veteran's Administration Health Care System and Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Norio Chihara
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Neurology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Asaf Madi
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Pathology, Faculty of Medicine, Tel-Aviv University, Tel Aviv-Yafo, Israel
| | - Ana C Anderson
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital and Harvard Medical School, Boston, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | - Vijay K Kuchroo
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital and Harvard Medical School, Boston, MA, USA.
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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28
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Shen P, Jia Y, Zhou W, Zheng W, Wu Y, Qu S, Du S, Wang S, Shi H, Sun J, Han X. A biomimetic liver cancer on-a-chip reveals a critical role of LIPOCALIN-2 in promoting hepatocellular carcinoma progression. Acta Pharm Sin B 2023; 13:4621-4637. [PMID: 37969730 PMCID: PMC10638501 DOI: 10.1016/j.apsb.2023.04.010] [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: 02/02/2023] [Revised: 04/03/2023] [Accepted: 04/15/2023] [Indexed: 11/17/2023] Open
Abstract
Hepatic stellate cells (HSCs) represent a significant component of hepatocellular carcinoma (HCC) microenvironments which play a critical role in tumor progression and drug resistance. Tumor-on-a-chip technology has provided a powerful in vitro platform to investigate the crosstalk between activated HSCs and HCC cells by mimicking physiological architecture with precise spatiotemporal control. Here we developed a tri-cell culture microfluidic chip to evaluate the impact of HSCs on HCC progression. On-chip analysis revealed activated HSCs contributed to endothelial invasion, HCC drug resistance and natural killer (NK) cell exhaustion. Cytokine array and RNA sequencing analysis were combined to indicate the iron-binding protein LIPOCALIN-2 (LCN-2) as a key factor in remodeling tumor microenvironments in the HCC-on-a-chip. LCN-2 targeted therapy demonstrated robust anti-tumor effects both in vitro 3D biomimetic chip and in vivo mouse model, including angiogenesis inhibition, sorafenib sensitivity promotion and NK-cell cytotoxicity enhancement. Taken together, the microfluidic platform exhibited obvious advantages in mimicking functional characteristics of tumor microenvironments and developing targeted therapies.
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Affiliation(s)
- Peiliang Shen
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Medicine & Holistic Integrative Medicine, Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yuanyuan Jia
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Medicine & Holistic Integrative Medicine, Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Weijia Zhou
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Medicine & Holistic Integrative Medicine, Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Weiwei Zheng
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Medicine & Holistic Integrative Medicine, Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yueyao Wu
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Medicine & Holistic Integrative Medicine, Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Suchen Qu
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Medicine & Holistic Integrative Medicine, Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Shiyu Du
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Medicine & Holistic Integrative Medicine, Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Siliang Wang
- Department of Pharmacy, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
- Nanjing Medical Center for Clinical Pharmacy, Nanjing 210008, China
| | - Huilian Shi
- Department of Infectious Diseases, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jia Sun
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Medicine & Holistic Integrative Medicine, Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Xin Han
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Medicine & Holistic Integrative Medicine, Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
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29
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Wang W, Gao X, Kang N, Wang C, Li C, Yu H, Zhang X. Shared biomarkers and immune cell infiltration signatures in ulcerative colitis and nonalcoholic steatohepatitis. Sci Rep 2023; 13:18497. [PMID: 37898694 PMCID: PMC10613305 DOI: 10.1038/s41598-023-44853-6] [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: 05/07/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023] Open
Abstract
The coexistence of ulcerative colitis (UC) and nonalcoholic steatohepatitis (NASH) involves a intricate interplay, though the precise pathophysiological mechanisms remain elusive. To shed light on this, our study endeavors to unravel the shared gene signatures and molecular mechanisms by employing quantitative bioinformatics analysis on a publicly available RNA-sequencing database. Gene expression profiles of UC (GSE87466) and NASH (GSE89632) were retrieved from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were analyzed using R software. After identifying common DEGs, functional enrichment analysis, protein-protein interaction (PPI) network analysis and module construction were performed to obtain candidate hub genes. GSE47908 for UC and GSE159676 for NASH were selected to validate the obtained candidate genes. A total of 119 common DEGs were found in NASH and UC patients. Functional and pathway analyses emphasized that viral infection, inflammation and immune response were enriched in these two diseases. After module construction and validation, CD2, CD8A, GNLY, IFI44, NKG7 and OAS2 were identified as hub genes. 6 hub genes and their combined prediction scores were found with an impressive accuracy and sensitivity. Functional estimation, gene set enrichment analysis and immune infiltration signature identification showed notable associations of the six hub genes with T cells, natural killer cells and type I interferon levels. In addition, we constructed UC combined with NASH mice model successfully with significantly higher expression of hub genes in both liver and colonic tissues than those in control group. Our study elucidates 6 hub genes of UC and NASH, which may participate in immune, inflammatory and antiviral effects. These findings provide some potential biochemical markers for further exploration of UC coexistence with NASH.
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Affiliation(s)
- Wenxin Wang
- Department of Gastroenterology and Hepatology, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Diseases, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
| | - Xin Gao
- Department of Gastroenterology and Hepatology, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Diseases, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
| | - Ning Kang
- Department of Gastroenterology and Hepatology, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Diseases, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
| | - Chen Wang
- Department of Gastroenterology and Hepatology, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Diseases, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
| | - Chenyang Li
- Department of Gastroenterology and Hepatology, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Diseases, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
| | - Huan Yu
- Department of Gastroenterology and Hepatology, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Diseases, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
| | - Xiaolan Zhang
- Department of Gastroenterology and Hepatology, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Diseases, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China.
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30
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Sarén T, Ramachandran M, Gammelgård G, Lövgren T, Mirabello C, Björklund ÅK, Wikström K, Hashemi J, Freyhult E, Ahlström H, Amini RM, Hagberg H, Loskog A, Enblad G, Essand M. Single-Cell RNA Analysis Reveals Cell-Intrinsic Functions of CAR T Cells Correlating with Response in a Phase II Study of Lymphoma Patients. Clin Cancer Res 2023; 29:4139-4152. [PMID: 37540566 PMCID: PMC10570681 DOI: 10.1158/1078-0432.ccr-23-0178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 06/22/2023] [Accepted: 08/02/2023] [Indexed: 08/06/2023]
Abstract
PURPOSE Although CD19 chimeric antigen receptor T cells (CAR-T) therapy has shown remarkable success in B-cell malignancies, a substantial fraction of patients do not obtain a long-term clinical response. This could be influenced by the quality of the individual CAR-T infusion product. To shed some light on this, clinical outcome was correlated to characteristics of CAR-T infusion products. PATIENTS AND METHODS In this phase II study, patients with B-cell lymphoma (n = 23) or leukemia (n = 1) received one or two infusions of third-generation CD19-directed CAR-Ts (2 × 108/m2). The clinical trial was registered at clinicaltrials.gov: NCT03068416. We investigated the transcriptional profile of individual CD19 CAR-T infusion products using targeted single-cell RNA sequencing and multicolor flow cytometry. RESULTS Two CAR-T infusions were not better than one in the settings used in this study. As for the CAR-T infusion products, we found that effector-like CD8+CAR-Ts with a high polyfunctionality, high cytotoxic and cytokine production profile, and low dysfunctional signature were associated with clinical response. An extended ex vivo expansion time during CAR-T manufacturing negatively influenced the proportion of effector CD8+CAR-Ts in the infusion product. CONCLUSIONS We identified cell-intrinsic characteristics of effector CD8+CAR-Ts correlating with response that could be used as an indicator for clinical outcome. The results in the study also serve as a guide to CAR-T manufacturing practices.
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Affiliation(s)
- Tina Sarén
- Department of Immunology, Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Mohanraj Ramachandran
- Department of Immunology, Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Gustav Gammelgård
- Department of Immunology, Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Tanja Lövgren
- Department of Immunology, Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Claudio Mirabello
- IFM Bioinformatics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Linköping University, Linköping, Sweden
| | - Åsa K. Björklund
- Department of Life Sciences, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Göteborg, Sweden
| | | | - Jamileh Hashemi
- Department of Immunology, Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Eva Freyhult
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Håkan Ahlström
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
- Antaros Medical AB, Mölndal, Sweden
| | - Rose-Marie Amini
- Department of Immunology, Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Hans Hagberg
- Department of Immunology, Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Angelica Loskog
- Department of Immunology, Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
- Lokon Pharma AB, Uppsala, Sweden
| | - Gunilla Enblad
- Department of Immunology, Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Magnus Essand
- Department of Immunology, Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
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31
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Guo M, Abd-Rabbo D, Bertol BC, Carew M, Lukhele S, Snell LM, Xu W, Boukhaled GM, Elsaesser H, Halaby MJ, Hirano N, McGaha TL, Brooks DG. Molecular, metabolic, and functional CD4 T cell paralysis in the lymph node impedes tumor control. Cell Rep 2023; 42:113047. [PMID: 37651234 PMCID: PMC10578141 DOI: 10.1016/j.celrep.2023.113047] [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: 11/23/2022] [Revised: 07/14/2023] [Accepted: 08/11/2023] [Indexed: 09/02/2023] Open
Abstract
CD4 T cells are central effectors of anti-cancer immunity and immunotherapy, yet the regulation of CD4 tumor-specific T (TTS) cells is unclear. We demonstrate that CD4 TTS cells are quickly primed and begin to divide following tumor initiation. However, unlike CD8 TTS cells or exhaustion programming, CD4 TTS cell proliferation is rapidly frozen in place by a functional interplay of regulatory T cells and CTLA4. Together these mechanisms paralyze CD4 TTS cell differentiation, redirecting metabolic circuits, and reducing their accumulation in the tumor. The paralyzed state is actively maintained throughout cancer progression and CD4 TTS cells rapidly resume proliferation and functional differentiation when the suppressive constraints are alleviated. Overcoming their paralysis established long-term tumor control, demonstrating the importance of rapidly crippling CD4 TTS cells for tumor progression and their potential restoration as therapeutic targets.
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Affiliation(s)
- Mengdi Guo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Diala Abd-Rabbo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Bruna C Bertol
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Madeleine Carew
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Sabelo Lukhele
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Laura M Snell
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Microbiology and Immunology and Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Wenxi Xu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Giselle M Boukhaled
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Heidi Elsaesser
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Marie Jo Halaby
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Naoto Hirano
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Tracy L McGaha
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - David G Brooks
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, Canada.
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Zhang L, Chun Y, Irizar H, Arditi Z, Grishina G, Grishin A, Vicencio A, Bunyavanich S. Integrated study of systemic and local airway transcriptomes in asthma reveals causal mediation of systemic effects by airway key drivers. Genome Med 2023; 15:71. [PMID: 37730635 PMCID: PMC10512627 DOI: 10.1186/s13073-023-01222-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/18/2023] [Indexed: 09/22/2023] Open
Abstract
BACKGROUND Systemic and local profiles have each been associated with asthma, but parsing causal relationships between system-wide and airway-specific processes can be challenging. We sought to investigate systemic and airway processes in asthma and their causal relationships. METHODS Three hundred forty-one participants with persistent asthma and non-asthmatic controls were recruited and underwent peripheral blood mononuclear cell (PBMC) collection and nasal brushing. Transcriptome-wide RNA sequencing of the PBMC and nasal samples and a series of analyses were then performed using a discovery and independent test set approach at each step to ensure rigor. Analytic steps included differential expression analyses, coexpression and probabilistic causal (Bayesian) network constructions, key driver analyses, and causal mediation models. RESULTS Among the 341 participants, the median age was 13 years (IQR = 10-16), 164 (48%) were female, and 200 (58.7%) had persistent asthma with mean Asthma Control Test (ACT) score 16.6 (SD = 4.2). PBMC genes associated with asthma were enriched in co-expression modules for NK cell-mediated cytotoxicity (fold enrichment = 4.5, FDR = 6.47 × 10-32) and interleukin production (fold enrichment = 2.0, FDR = 1.01 × 10-15). Probabilistic causal network and key driver analyses identified NK cell granule protein (NKG7, fold change = 22.7, FDR = 1.02 × 10-31) and perforin (PRF1, fold change = 14.9, FDR = 1.31 × 10-22) as key drivers predicted to causally regulate PBMC asthma modules. Nasal genes associated with asthma were enriched in the tricarboxylic acid (TCA) cycle module (fold enrichment = 7.5 FDR = 5.09 × 10-107), with network analyses identifying G3BP stress granule assembly factor 1 (G3BP1, fold change = 9.1 FDR = 2.77 × 10-5) and InaD-like protein (INADL, fold change = 5.3 FDR = 2.98 × 10-9) as nasal key drivers. Causal mediation analyses revealed that associations between PBMC key drivers and asthma are causally mediated by nasal key drivers (FDR = 0.0076 to 0.015). CONCLUSIONS Integrated study of the systemic and airway transcriptomes in a well-phenotyped asthma cohort identified causal key drivers of asthma among PBMC and nasal transcripts. Associations between PBMC key drivers and asthma are causally mediated by nasal key drivers.
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Affiliation(s)
- Lingdi Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
| | - Yoojin Chun
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
| | - Haritz Irizar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
| | - Zoe Arditi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
| | - Galina Grishina
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
| | - Alexander Grishin
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
| | - Alfin Vicencio
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
| | - Supinda Bunyavanich
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA.
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA.
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Dykema AG, Zhang J, Cheung LS, Connor S, Zhang B, Zeng Z, Cherry CM, Li T, Caushi JX, Nishimoto M, Munoz AJ, Ji Z, Hou W, Zhan W, Singh D, Zhang T, Rashid R, Mitchell-Flack M, Bom S, Tam A, Ionta N, Aye THK, Wang Y, Sawosik CA, Tirado LE, Tomasovic LM, VanDyke D, Spangler JB, Anagnostou V, Yang S, Spicer J, Rayes R, Taube J, Brahmer JR, Forde PM, Yegnasubramanian S, Ji H, Pardoll DM, Smith KN. Lung tumor-infiltrating T reg have divergent transcriptional profiles and function linked to checkpoint blockade response. Sci Immunol 2023; 8:eadg1487. [PMID: 37713507 PMCID: PMC10629528 DOI: 10.1126/sciimmunol.adg1487] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 07/25/2023] [Indexed: 09/17/2023]
Abstract
Regulatory T cells (Treg) are conventionally viewed as suppressors of endogenous and therapy-induced antitumor immunity; however, their role in modulating responses to immune checkpoint blockade (ICB) is unclear. In this study, we integrated single-cell RNA-seq/T cell receptor sequencing (TCRseq) of >73,000 tumor-infiltrating Treg (TIL-Treg) from anti-PD-1-treated and treatment-naive non-small cell lung cancers (NSCLC) with single-cell analysis of tumor-associated antigen (TAA)-specific Treg derived from a murine tumor model. We identified 10 subsets of human TIL-Treg, most of which have high concordance with murine TIL-Treg subsets. Only one subset selectively expresses high levels of TNFRSF4 (OX40) and TNFRSF18 (GITR), whose engangement by cognate ligand mediated proliferative programs and NF-κB activation, as well as multiple genes involved in Treg suppression, including LAG3. Functionally, the OX40hiGITRhi subset is the most highly suppressive ex vivo, and its higher representation among total TIL-Treg correlated with resistance to PD-1 blockade. Unexpectedly, in the murine tumor model, we found that virtually all TIL-Treg-expressing T cell receptors that are specific for TAA fully develop a distinct TH1-like signature over a 2-week period after entry into the tumor, down-regulating FoxP3 and up-regulating expression of TBX21 (Tbet), IFNG, and certain proinflammatory granzymes. Transfer learning of a gene score from the murine TAA-specific TH1-like Treg subset to the human single-cell dataset revealed a highly analogous subcluster that was enriched in anti-PD-1-responding tumors. These findings demonstrate that TIL-Treg partition into multiple distinct transcriptionally defined subsets with potentially opposing effects on ICB-induced antitumor immunity and suggest that TAA-specific TIL-Treg may positively contribute to antitumor responses.
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Affiliation(s)
- Arbor G. Dykema
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- The Mark Foundation Center for Advanced Genomics and Imaging, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jiajia Zhang
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- The Mark Foundation Center for Advanced Genomics and Imaging, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Laurene S. Cheung
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Sydney Connor
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Boyang Zhang
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Zhen Zeng
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- The Mark Foundation Center for Advanced Genomics and Imaging, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Taibo Li
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Justina X. Caushi
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Marni Nishimoto
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Andrew J. Munoz
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Zhicheng Ji
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Wenpin Hou
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Wentao Zhan
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Dipika Singh
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Tianbei Zhang
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Rufiaat Rashid
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Marisa Mitchell-Flack
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Sadhana Bom
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ada Tam
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Nick Ionta
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Thet H. K. Aye
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Yi Wang
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Camille A. Sawosik
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Lauren E. Tirado
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Luke M. Tomasovic
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Derek VanDyke
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
- Translational Tissue Engineering Center, Johns Hopkins University, Baltimore, MD, USA
| | - Jamie B. Spangler
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
- Translational Tissue Engineering Center, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Valsamo Anagnostou
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Stephen Yang
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Roni Rayes
- Department of Surgery, McGill University, Montreal, Canada
| | - Janis Taube
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- The Mark Foundation Center for Advanced Genomics and Imaging, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Julie R. Brahmer
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Patrick M. Forde
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Srinivasan Yegnasubramanian
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Drew M. Pardoll
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- The Mark Foundation Center for Advanced Genomics and Imaging, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Kellie N. Smith
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, USA
- The Mark Foundation Center for Advanced Genomics and Imaging, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
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Oh K, Yoo YJ, Torre-Healy LA, Rao M, Fassler D, Wang P, Caponegro M, Gao M, Kim J, Sasson A, Georgakis G, Powers S, Moffitt RA. Coordinated single-cell tumor microenvironment dynamics reinforce pancreatic cancer subtype. Nat Commun 2023; 14:5226. [PMID: 37633924 PMCID: PMC10460409 DOI: 10.1038/s41467-023-40895-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 08/14/2023] [Indexed: 08/28/2023] Open
Abstract
Bulk analyses of pancreatic ductal adenocarcinoma (PDAC) samples are complicated by the tumor microenvironment (TME), i.e. signals from fibroblasts, endocrine, exocrine, and immune cells. Despite this, we and others have established tumor and stroma subtypes with prognostic significance. However, understanding of underlying signals driving distinct immune and stromal landscapes is still incomplete. Here we integrate 92 single cell RNA-seq samples from seven independent studies to build a reproducible PDAC atlas with a focus on tumor-TME interdependence. Patients with activated stroma are synonymous with higher myofibroblastic and immunogenic fibroblasts, and furthermore show increased M2-like macrophages and regulatory T-cells. Contrastingly, patients with 'normal' stroma show M1-like recruitment, elevated effector and exhausted T-cells. To aid interoperability of future studies, we provide a pretrained cell type classifier and an atlas of subtype-based signaling factors that we also validate in mouse data. Ultimately, this work leverages the heterogeneity among single-cell studies to create a comprehensive view of the orchestra of signaling interactions governing PDAC.
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Affiliation(s)
- Ki Oh
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA
| | - Yun Jae Yoo
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA
| | - Luke A Torre-Healy
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA
| | - Manisha Rao
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA
- Department of Pathology, Stony Brook University, Stony Brook, NY, USA
| | - Danielle Fassler
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA
| | - Pei Wang
- Department of Cell Systems & Anatomy, University of Texas Health Science Center, San Antonio, TX, USA
| | - Michael Caponegro
- Department of Pharmacology, Stony Brook University, Stony Brook, NY, USA
| | - Mei Gao
- Department of Surgery, University of Kentucky and Markey Cancer Center, Lexington, KY, USA
| | - Joseph Kim
- Department of Surgery, University of Kentucky and Markey Cancer Center, Lexington, KY, USA
| | - Aaron Sasson
- Department of Surgery, Stony Brook University, Stony Brook, NY, USA
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA
| | - Georgios Georgakis
- Department of Surgery, Stony Brook University, Stony Brook, NY, USA
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA
| | - Scott Powers
- Department of Pathology, Stony Brook University, Stony Brook, NY, USA
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA
| | - Richard A Moffitt
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA.
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA, USA.
- Department of Biomedical Informatics, Emory University, Atlanta, GA, USA.
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Rudqvist NP, Charpentier M, Lhuillier C, Wennerberg E, Spada S, Sheridan C, Zhou XK, Zhang T, Formenti SC, Sims JS, Alonso A, Demaria S. Immunotherapy targeting different immune compartments in combination with radiation therapy induces regression of resistant tumors. Nat Commun 2023; 14:5146. [PMID: 37620372 PMCID: PMC10449830 DOI: 10.1038/s41467-023-40844-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 08/13/2023] [Indexed: 08/26/2023] Open
Abstract
Radiation therapy (RT) increases tumor response to CTLA-4 inhibition (CTLA4i) in mice and in some patients, yet deep responses are rare. To identify rational combinations of immunotherapy to improve responses we use models of triple negative breast cancer highly resistant to immunotherapy in female mice. We find that CTLA4i promotes the expansion of CD4+ T helper cells, whereas RT enhances T cell clonality and enriches for CD8+ T cells with an exhausted phenotype. Combination therapy decreases regulatory CD4+ T cells and increases effector memory, early activation and precursor exhausted CD8+ T cells. A combined gene signature comprising these three CD8+ T cell clusters is associated with survival in patients. Here we show that targeting additional immune checkpoints expressed by intratumoral T cells, including PD1, is not effective, whereas CD40 agonist therapy recruits resistant tumors into responding to the combination of RT and CTLA4i, indicating the need to target different immune compartments.
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Affiliation(s)
- Nils-Petter Rudqvist
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson, Houston, TX, 77030, USA
- Department of Immunology, University of Texas MD Anderson, Houston, TX, 77030, USA
| | - Maud Charpentier
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Claire Lhuillier
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Immuno-Oncology, Sanofi, 94403, Vitry-sur-Seine, France
| | - Erik Wennerberg
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY, 10065, USA
- Division of Radiotherapy and Imaging, Institute of Cancer Research, London, SM2 5NG, UK
| | - Sheila Spada
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Caroline Sheridan
- Department of Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Xi Kathy Zhou
- Division of Biostatistics, Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Tuo Zhang
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Silvia C Formenti
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Jennifer S Sims
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Alicia Alonso
- Department of Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Sandra Demaria
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY, 10065, USA.
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA.
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Venkatesh H, Tracy SI, Farrar MA. Cytotoxic CD4 T cells in the mucosa and in cancer. Front Immunol 2023; 14:1233261. [PMID: 37654482 PMCID: PMC10466411 DOI: 10.3389/fimmu.2023.1233261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 07/24/2023] [Indexed: 09/02/2023] Open
Abstract
CD4 T cells were initially described as helper cells that promote either the cellular immune response (Th1 cells) or the humoral immune response (Th2 cells). Since then, a plethora of functionally distinct helper and regulatory CD4 T cell subsets have been described. CD4 T cells with cytotoxic function were first described in the setting of viral infections and autoimmunity, and more recently in cancer and gut dysbiosis. Regulatory CD4 T cell subsets such as Tregs and T-regulatory type 1 (Tr1) cells have also been shown to have cytotoxic potential. Indeed, Tr1 cells have been shown to be important for maintenance of stem cell niches in the bone marrow and the gut. This review will provide an overview of cytotoxic CD4 T cell development, and discuss the role of inflammatory and Tr1-like cytotoxic CD4 T cells in maintenance of intestinal stem cells and in anti-cancer immune responses.
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Affiliation(s)
- Hrishi Venkatesh
- Center for Immunology, Masonic Cancer Center, Minneapolis, MN, United States
- University of Minnesota, Department of Laboratory Medicine and Pathology, Minneapolis, MN, United States
| | - Sean I. Tracy
- Center for Immunology, Masonic Cancer Center, Minneapolis, MN, United States
- Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Michael A. Farrar
- Center for Immunology, Masonic Cancer Center, Minneapolis, MN, United States
- University of Minnesota, Department of Laboratory Medicine and Pathology, Minneapolis, MN, United States
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Guo S, Yan M, Li X, Zhang S, Liu Z, Li K, Liu P, Liu Y, Sun G, Fu Q. Single-cell RNA-seq analysis reveals that immune cells induce human nucleus pulposus ossification and degeneration. Front Immunol 2023; 14:1224627. [PMID: 37638033 PMCID: PMC10449260 DOI: 10.3389/fimmu.2023.1224627] [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: 05/18/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023] Open
Abstract
Background and aims Determining the transcriptomes and molecular mechanism underlying human degenerative nucleus pulposus (NP) is of critical importance for treating intervertebral disc degeneration (IDD). Here, we aimed to elucidate the detailed molecular mechanism of NP ossification and IDD using single-cell RNA sequencing. Methods Single-cell RNA-seq and bioinformatic analysis were performed to identify NP cell populations with gene signatures, biological processes and pathways, and subpopulation analysis, RNA velocity analysis, and cell-to-cell communication analysis were performed in four IDD patients. We also verified the effects of immune cells on NP ossification using cultured NP cells and a well-established rat IDD model. Results We identified five cell populations with gene expression profiles in degenerative NP at single-cell resolution. GO database analysis showed that degenerative NP-associated genes were mainly enriched in extracellular matrix organization, immune response, and ossification. Gene set enrichment analysis showed that rheumatoid arthritis signaling, antigen processing and presentation signaling were activated in the blood cell cluster. We revealed that stromal cells, which are progenitor cells, differentiated toward an ossification phenotype and delineated interactions between immune cells (macrophages and T cells) and stromal cells. Immune factors such as TNF-α, CD74 and CCL-3 promoted the differentiation of stromal cells toward an ossification phenotype in vitro. Blocking TNF-α with a specific inhibitor successfully reversed NP ossification and modified NP morphology in vivo. Conclusion Our study revealed an increase in macrophages and T cells in degenerative NP, which induced stromal cell differentiation toward an ossification phenotype, and contributed to the identification of a novel therapeutic target to delay IDD.
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Affiliation(s)
- Song Guo
- Department of Spine Surgery, Shanghai Jiaotong University First People’s Hospital, Shanghai, China
| | - Meijun Yan
- Department of Spine Surgery, Shanghai Jiaotong University First People’s Hospital, Shanghai, China
| | - Xinhua Li
- Department of Spine Surgery, Shanghai Jiaotong University First People’s Hospital, Shanghai, China
| | - Shuya Zhang
- Department of Neurologic Surgery, Mayo Clinic, Rochester, MN, United States
| | - Zhong Liu
- Department of Spine Surgery, Shanghai Jiaotong University First People’s Hospital, Shanghai, China
| | - Kewei Li
- Department of Spine Surgery, Shanghai Jiaotong University First People’s Hospital, Shanghai, China
| | - Pengcheng Liu
- Department of Spine Surgery, Shanghai Jiaotong University First People’s Hospital, Shanghai, China
| | - Yanbin Liu
- Department of Spine Surgery, Shanghai Jiaotong University First People’s Hospital, Shanghai, China
| | - Guixin Sun
- Department of Traumatology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qiang Fu
- Department of Spine Surgery, Shanghai Jiaotong University First People’s Hospital, Shanghai, China
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Micevic G, Daniels A, Flem-Karlsen K, Park K, Talty R, McGeary M, Mirza H, Blackburn HN, Sefik E, Cheung JF, Hornick NI, Aizenbud L, Joshi NS, Kluger H, Iwasaki A, Bosenberg MW, Flavell RA. IL-7R licenses a population of epigenetically poised memory CD8 + T cells with superior antitumor efficacy that are critical for melanoma memory. Proc Natl Acad Sci U S A 2023; 120:e2304319120. [PMID: 37459511 PMCID: PMC10372654 DOI: 10.1073/pnas.2304319120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/08/2023] [Indexed: 07/20/2023] Open
Abstract
Recurrence of advanced melanoma after therapy is a major risk factor for reduced survival, and treatment options are limited. Antitumor immune memory plays a critical role in preventing melanoma recurrence and memory T cells could be a potent cell-based therapy, but the identity, and functional properties of the required immune cells are incompletely understood. Here, we show that an IL-7Rhi tumor-specific CD8+ population is critical for antitumor memory and can be epigenetically augmented to drive powerful antitumor immune responses. Using a model of functional antimelanoma memory, we found that high IL-7R expression selectively marks a CD8+ population in lymphoid organs that plays critical roles in maintaining tumor remission after immunotherapy or surgical resection. This population has intrinsic cytotoxic activity, lacks markers of exhaustion and has superior antitumor efficacy. IL-7Rhi cells have a functionally poised epigenetic landscape regulated by DNA methylation, which can be augmented by hypomethylating agents to confer improved survival and complete melanoma clearance in naive mice. Importantly, greater than 95% of tumor-specific T cells in draining lymph nodes after therapy express high levels of IL-7R. This overlap between IL-7Rhi and antigen-specific T cells allows for enrichment of a potent functional CD8+ population without determining antigen-specificity, which we demonstrate in a melanoma model without a known antigen. We identify that IL-7R expression in human melanoma is an independent prognostic factor of improved survival. These findings advance our basic understanding of antitumor memory and suggest a cell-based therapy using high IL-7R expression to enrich for a lymph node population with superior antitumor activity that can be augmented by hypomethylating agents.
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Affiliation(s)
- Goran Micevic
- Department of Immunobiology, Yale School of Medicine, New Haven, CT06520
- Department of Dermatology, Yale School of Medicine, New Haven, CT06520
| | - Andrew Daniels
- Department of Immunobiology, Yale School of Medicine, New Haven, CT06520
- Department of Pathology, Yale School of Medicine, New Haven, CT06520
| | | | - Koonam Park
- Department of Dermatology, Yale School of Medicine, New Haven, CT06520
| | - Ronan Talty
- Department of Pathology, Yale School of Medicine, New Haven, CT06520
| | - Meaghan McGeary
- Department of Pathology, Yale School of Medicine, New Haven, CT06520
| | - Haris Mirza
- Department of Immunobiology, Yale School of Medicine, New Haven, CT06520
- Department of Pathology, Yale School of Medicine, New Haven, CT06520
| | - Holly N. Blackburn
- Department of Immunobiology, Yale School of Medicine, New Haven, CT06520
- Department of Surgery, Yale School of Medicine, New Haven, CT06520
| | - Esen Sefik
- Department of Immunobiology, Yale School of Medicine, New Haven, CT06520
| | - Julie F. Cheung
- Department of Immunobiology, Yale School of Medicine, New Haven, CT06520
| | - Noah I. Hornick
- Department of Immunobiology, Yale School of Medicine, New Haven, CT06520
| | - Lilach Aizenbud
- Yale Cancer Center, Yale School of Medicine, New Haven, CT06520
- Department of Medicine (Medical Oncology), Yale School of Medicine, New Haven, CT06520
| | - Nikhil S. Joshi
- Department of Immunobiology, Yale School of Medicine, New Haven, CT06520
| | - Harriet Kluger
- Yale Cancer Center, Yale School of Medicine, New Haven, CT06520
- Department of Medicine (Medical Oncology), Yale School of Medicine, New Haven, CT06520
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT06520
| | - Akiko Iwasaki
- Department of Immunobiology, Yale School of Medicine, New Haven, CT06520
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT06520
- HHMI, Chevy Chase, MD20815
| | - Marcus W. Bosenberg
- Department of Immunobiology, Yale School of Medicine, New Haven, CT06520
- Department of Dermatology, Yale School of Medicine, New Haven, CT06520
- Department of Pathology, Yale School of Medicine, New Haven, CT06520
- Yale Cancer Center, Yale School of Medicine, New Haven, CT06520
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT06520
- Yale Center for Immuno-Oncology, Yale School of Medicine, New Haven, CT06520
| | - Richard A. Flavell
- Department of Immunobiology, Yale School of Medicine, New Haven, CT06520
- Yale Cancer Center, Yale School of Medicine, New Haven, CT06520
- HHMI, Chevy Chase, MD20815
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39
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Perriman L, Tavakolinia N, Jalali S, Li S, Hickey PF, Amann-Zalcenstein D, Ho WWH, Baldwin TM, Piers AT, Konstantinov IE, Anderson J, Stanley EG, Licciardi PV, Kannourakis G, Naik SH, Koay HF, Mackay LK, Berzins SP, Pellicci DG. A three-stage developmental pathway for human Vγ9Vδ2 T cells within the postnatal thymus. Sci Immunol 2023; 8:eabo4365. [PMID: 37450574 DOI: 10.1126/sciimmunol.abo4365] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/14/2023] [Indexed: 07/18/2023]
Abstract
Vγ9Vδ2 T cells are the largest population of γδ T cells in adults and can play important roles in providing effective immunity against cancer and infection. Many studies have suggested that peripheral Vγ9Vδ2 T cells are derived from the fetal liver and thymus and that the postnatal thymus plays little role in the development of these cells. More recent evidence suggested that these cells may also develop postnatally in the thymus. Here, we used high-dimensional flow cytometry, transcriptomic analysis, functional assays, and precursor-product experiments to define the development pathway of Vγ9Vδ2 T cells in the postnatal thymus. We identify three distinct stages of development for Vγ9Vδ2 T cells in the postnatal thymus that are defined by the progressive acquisition of functional potential and major changes in the expression of transcription factors, chemokines, and other surface markers. Furthermore, our analysis of donor-matched thymus and blood revealed that the molecular requirements for the development of functional Vγ9Vδ2 T cells are delivered predominantly by the postnatal thymus and not in the periphery. Tbet and Eomes, which are required for IFN-γ and TNFα expression, are up-regulated as Vγ9Vδ2 T cells mature in the thymus, and mature thymic Vγ9Vδ2 T cells rapidly express high levels of these cytokines after stimulation. Similarly, the postnatal thymus programs Vγ9Vδ2 T cells to express the cytolytic molecules, perforin, granzyme A, and granzyme K. This study provides a greater understanding of how Vγ9Vδ2 T cells develop in humans and may lead to opportunities to manipulate these cells to treat human diseases.
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Affiliation(s)
- Louis Perriman
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
- Fiona Elsey Cancer Research Institute, Ballarat, Australia
- Federation University Australia, Ballarat, Australia
| | - Naeimeh Tavakolinia
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Sedigheh Jalali
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Shuo Li
- Murdoch Children's Research Institute, Melbourne, Australia
| | - Peter F Hickey
- Advanced Genomics Facility and Single Cell Open Research Endeavour (SCORE), Advanced Technology and Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Daniela Amann-Zalcenstein
- Advanced Genomics Facility and Single Cell Open Research Endeavour (SCORE), Advanced Technology and Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - William Wing Ho Ho
- Advanced Genomics Facility and Single Cell Open Research Endeavour (SCORE), Advanced Technology and Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Tracey M Baldwin
- Advanced Genomics Facility and Single Cell Open Research Endeavour (SCORE), Advanced Technology and Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Adam T Piers
- Murdoch Children's Research Institute, Melbourne, Australia
- Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, Melbourne, Australia
| | - Igor E Konstantinov
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
- Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, Melbourne, Australia
- Cardiothoracic Surgery, Royal Children's Hospital, Melbourne, Australia
| | - Jeremy Anderson
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Edouard G Stanley
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Paul V Licciardi
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - George Kannourakis
- Fiona Elsey Cancer Research Institute, Ballarat, Australia
- Federation University Australia, Ballarat, Australia
| | - Shalin H Naik
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Hui-Fern Koay
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Laura K Mackay
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Stuart P Berzins
- Fiona Elsey Cancer Research Institute, Ballarat, Australia
- Federation University Australia, Ballarat, Australia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Daniel G Pellicci
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
- Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, Melbourne, Australia
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40
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Rashidfarrokhi A, Pillai R, Hao Y, Wu WL, Karadal-Ferrena B, Dimitriadoy SG, Cross M, Yeaton AH, Huang SM, Bhutkar AJ, Herrera A, Rajalingam S, Hayashi M, Huang KL, Bartnicki E, Zavitsanou AM, Wohlhieter CA, Leboeuf SE, Chen T, Loomis C, Mezzano V, Kulicke R, Davis FP, Stransky N, Smolen GA, Rudin CM, Moreira AL, Khanna KM, Pass HI, Wong KK, Koide S, Tsirigos A, Koralov SB, Papagiannakopoulos T. Tumor-intrinsic LKB1-LIF signaling axis establishes a myeloid niche to promote immune evasion and tumor growth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.15.549147. [PMID: 37502974 PMCID: PMC10370066 DOI: 10.1101/2023.07.15.549147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Tumor mutations can influence the surrounding microenvironment leading to suppression of anti-tumor immune responses and thereby contributing to tumor progression and failure of cancer therapies. Here we use genetically engineered lung cancer mouse models and patient samples to dissect how LKB1 mutations accelerate tumor growth by reshaping the immune microenvironment. Comprehensive immune profiling of LKB1 -mutant vs wildtype tumors revealed dramatic changes in myeloid cells, specifically enrichment of Arg1 + interstitial macrophages and SiglecF Hi neutrophils. We discovered a novel mechanism whereby autocrine LIF signaling in Lkb1 -mutant tumors drives tumorigenesis by reprogramming myeloid cells in the immune microenvironment. Inhibiting LIF signaling in Lkb1 -mutant tumors, via gene targeting or with a neutralizing antibody, resulted in a striking reduction in Arg1 + interstitial macrophages and SiglecF Hi neutrophils, expansion of antigen specific T cells, and inhibition of tumor progression. Thus, targeting LIF signaling provides a new therapeutic approach to reverse the immunosuppressive microenvironment of LKB1 -mutant tumors.
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41
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Wong P, Foltz JA, Chang L, Neal CC, Yao T, Cubitt CC, Tran J, Kersting-Schadek S, Palakurty S, Jaeger N, Russler-Germain DA, Marin ND, Gang M, Wagner JA, Zhou AY, Jacobs MT, Foster M, Schappe T, Marsala L, McClain E, Pence P, Becker-Hapak M, Fisk B, Petti AA, Griffith OL, Griffith M, Berrien-Elliott MM, Fehniger TA. T-BET and EOMES sustain mature human NK cell identity and antitumor function. J Clin Invest 2023; 133:e162530. [PMID: 37279078 PMCID: PMC10313375 DOI: 10.1172/jci162530] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 05/19/2023] [Indexed: 06/07/2023] Open
Abstract
Since the T-box transcription factors (TFs) T-BET and EOMES are necessary for initiation of NK cell development, their ongoing requirement for mature NK cell homeostasis, function, and molecular programming remains unclear. To address this, T-BET and EOMES were deleted in unexpanded primary human NK cells using CRISPR/Cas9. Deleting these TFs compromised in vivo antitumor response of human NK cells. Mechanistically, T-BET and EOMES were required for normal NK cell proliferation and persistence in vivo. NK cells lacking T-BET and EOMES also exhibited defective responses to cytokine stimulation. Single-cell RNA-Seq revealed a specific T-box transcriptional program in human NK cells, which was rapidly lost following T-BET and EOMES deletion. Further, T-BET- and EOMES-deleted CD56bright NK cells acquired an innate lymphoid cell precursor-like (ILCP-like) profile with increased expression of the ILC-3-associated TFs RORC and AHR, revealing a role for T-box TFs in maintaining mature NK cell phenotypes and an unexpected role of suppressing alternative ILC lineages. Our study reveals the critical importance of sustained EOMES and T-BET expression to orchestrate mature NK cell function and identity.
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Affiliation(s)
- Pamela Wong
- Department of Medicine, Division of Oncology
| | | | - Lily Chang
- Department of Medicine, Division of Oncology
| | | | - Tony Yao
- Department of Medicine, Division of Oncology
| | | | | | | | | | | | | | | | | | | | | | | | - Mark Foster
- Department of Medicine, Division of Oncology
| | | | | | | | | | | | - Bryan Fisk
- Department of Medicine, Division of Oncology
| | | | | | | | | | - Todd A. Fehniger
- Department of Medicine, Division of Oncology
- Siteman Cancer Center, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
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42
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Croft W, Pearce H, Margielewska-Davies S, Lim L, Nicol SM, Zayou F, Blakeway D, Marcon F, Powell-Brett S, Mahon B, Merard R, Zuo J, Middleton G, Roberts K, Brown RM, Moss P. Spatial determination and prognostic impact of the fibroblast transcriptome in pancreatic ductal adenocarcinoma. eLife 2023; 12:e86125. [PMID: 37350578 PMCID: PMC10361717 DOI: 10.7554/elife.86125] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 06/22/2023] [Indexed: 06/24/2023] Open
Abstract
Pancreatic ductal adenocarcinoma has a poor clinical outcome and responses to immunotherapy are suboptimal. Stromal fibroblasts are a dominant but heterogenous population within the tumor microenvironment and therapeutic targeting of stromal subsets may have therapeutic utility. Here, we combine spatial transcriptomics and scRNA-Seq datasets to define the transcriptome of tumor-proximal and tumor-distal cancer-associated fibroblasts (CAFs) and link this to clinical outcome. Tumor-proximal fibroblasts comprise large populations of myofibroblasts, strongly expressed podoplanin, and were enriched for Wnt ligand signaling. In contrast, inflammatory CAFs were dominant within tumor-distal subsets and expressed complement components and the Wnt-inhibitor SFRP2. Poor clinical outcome was correlated with elevated HIF-1α and podoplanin expression whilst expression of inflammatory and complement genes was predictive of extended survival. These findings demonstrate the extreme transcriptional heterogeneity of CAFs and its determination by apposition to tumor. Selective targeting of tumor-proximal subsets, potentially combined with HIF-1α inhibition and immune stimulation, may offer a multi-modal therapeutic approach for this disease.
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Affiliation(s)
- Wayne Croft
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of BirminghamBirminghamUnited Kingdom
- Centre for Computational Biology, University of BirminghamBirminghamUnited Kingdom
| | - Hayden Pearce
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of BirminghamBirminghamUnited Kingdom
| | - Sandra Margielewska-Davies
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of BirminghamBirminghamUnited Kingdom
| | - Lindsay Lim
- Cancer Research Horizons, The Francis Crick InstituteLondonUnited Kingdom
| | - Samantha M Nicol
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of BirminghamBirminghamUnited Kingdom
| | - Fouzia Zayou
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of BirminghamBirminghamUnited Kingdom
| | - Daniel Blakeway
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of BirminghamBirminghamUnited Kingdom
| | - Francesca Marcon
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital BirminghamBirminghamUnited Kingdom
| | - Sarah Powell-Brett
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital BirminghamBirminghamUnited Kingdom
| | - Brinder Mahon
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital BirminghamBirminghamUnited Kingdom
| | - Reena Merard
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital BirminghamBirminghamUnited Kingdom
| | - Jianmin Zuo
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of BirminghamBirminghamUnited Kingdom
| | - Gary Middleton
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of BirminghamBirminghamUnited Kingdom
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital BirminghamBirminghamUnited Kingdom
| | - Keith Roberts
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital BirminghamBirminghamUnited Kingdom
| | - Rachel M Brown
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital BirminghamBirminghamUnited Kingdom
| | - Paul Moss
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of BirminghamBirminghamUnited Kingdom
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital BirminghamBirminghamUnited Kingdom
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43
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Sung C, An J, Lee S, Park J, Lee KS, Kim IH, Han JY, Park YH, Kim JH, Kang EJ, Hong MH, Kim TY, Lee JC, Lee JL, Yoon S, Choi CM, Lee DH, Yoo C, Kim SW, Jeong JH, Seo S, Kim SY, Kong SY, Choi JK, Park SR. Integrative analysis of risk factors for immune-related adverse events of checkpoint blockade therapy in cancer. NATURE CANCER 2023; 4:844-859. [PMID: 37308678 DOI: 10.1038/s43018-023-00572-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 05/05/2023] [Indexed: 06/14/2023]
Abstract
Immune-related adverse events (irAEs) induced by checkpoint inhibitors involve a multitude of different risk factors. Here, to interrogate the multifaceted underlying mechanisms, we compiled germline exomes and blood transcriptomes with clinical data, before and after checkpoint inhibitor treatment, from 672 patients with cancer. Overall, irAE samples showed a substantially lower contribution of neutrophils in terms of baseline and on-therapy cell counts and gene expression markers related to neutrophil function. Allelic variation of HLA-B correlated with overall irAE risk. Analysis of germline coding variants identified a nonsense mutation in an immunoglobulin superfamily protein, TMEM162. In our cohort and the Cancer Genome Atlas (TCGA) data, TMEM162 alteration was associated with higher peripheral and tumor-infiltrating B cell counts and suppression of regulatory T cells in response to therapy. We developed machine learning models for irAE prediction, validated using additional data from 169 patients. Our results provide valuable insights into risk factors of irAE and their clinical utility.
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Affiliation(s)
- Changhwan Sung
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, Republic of Korea
- Department of Nuclear Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jinhyeon An
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Soohyeon Lee
- Division of Oncology-Hematology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jaesoon Park
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Kang Seon Lee
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Il-Hwan Kim
- Department of Oncology, Haeundae Paik Hospital, Cancer Center, Inje University College of Medicine, Busan, Republic of Korea
| | - Ji-Youn Han
- Center for Lung Cancer, National Cancer Center, Goyang, Republic of Korea
| | - Yeon Hee Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jee Hyun Kim
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea
| | - Eun Joo Kang
- Division of Oncology, Department of Internal Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Min Hee Hong
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Tae-Yong Kim
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jae Cheol Lee
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jae Lyun Lee
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Shinkyo Yoon
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Chang-Min Choi
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Dae Ho Lee
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Changhoon Yoo
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sang-We Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jae Ho Jeong
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Seyoung Seo
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sun Young Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sun-Young Kong
- Targeted Therapy Branch, Research Institute, National Cancer Center, Goyang, Republic of Korea
- Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Republic of Korea
- Department of Laboratory Medicine, Hospital, National Cancer Center, Goyang, Republic of Korea
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea.
- Penta Medix Co., Ltd., Seongnam, Republic of Korea.
| | - Sook Ryun Park
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
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Solis-Leal A, Boby N, Mallick S, Cheng Y, Wu F, De La Torre G, Dufour J, Alvarez X, Shivanna V, Liu Y, Fennessey CM, Lifson JD, Li Q, Keele BF, Ling B. Lymphoid tissues contribute to viral clonotypes present in plasma at early post-ATI in SIV-infected rhesus macaques. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.30.542512. [PMID: 37398418 PMCID: PMC10312542 DOI: 10.1101/2023.05.30.542512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The rebound-competent viral reservoir (RCVR), comprised of virus that is able to persist during antiretroviral therapy (ART) and mediate reactivation of systemic viral replication and rebound viremia after antiretroviral therapy interruption (ATI), remains the biggest obstacle to the eradication of HIV infection. A better understanding of the cellular and tissue origins and the dynamics of viral populations that initiate rebound upon ATI could help develop targeted therapeutic strategies for reducing the RCVR. In this study, barcoded SIVmac239M was used to infect rhesus macaques to enable monitoring of viral barcode clonotypes contributing to virus detectable in plasma after ATI. Blood, lymphoid tissues (LTs, spleen, mesenteric and inguinal lymph nodes), and non-lymphoid tissues (NLTs, colon, ileum, lung, liver, and brain) were analyzed using viral barcode sequencing, intact proviral DNA assay, single-cell RNA sequencing, and combined CODEX/RNAscope/ in situ hybridization. Four of seven animals had viral barcodes detectable by deep sequencing of plasma at necropsy although plasma viral RNA remained < 22 copies/mL. Among the tissues studied, mesenteric and inguinal lymph nodes, and spleen contained viral barcodes detected in plasma, and trended to have higher cell-associated viral loads, higher intact provirus levels, and greater diversity of viral barcodes. CD4+ T cells were the main cell type harboring viral RNA (vRNA) after ATI. Further, T cell zones in LTs showed higher vRNA levels than B cell zones for most animals. These findings are consistent with LTs contributing to virus present in plasma early after ATI. One Sentence Summary The reemerging of SIV clonotypes at early post-ATI are likely from the secondary lymphoid tissues.
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45
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Caserta S, Genovese C, Cicero N, Gangemi S, Allegra A. The Anti-Cancer Effect of Cinnamon Aqueous Extract: A Focus on Hematological Malignancies. Life (Basel) 2023; 13:life13051176. [PMID: 37240821 DOI: 10.3390/life13051176] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/10/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Cinnamon is an evergreen and tropical plant of the family Lauraceae, growing particularly in Sri Lanka, whose aqueous extract has been tested in different studies to evaluate its possible use as an anti-cancer compound. Both in vitro and in vivo experiments seem to confirm that it acts on various cellular pathways, contributing to down-regulating the activity of molecules that stimulate the proliferation and survival of cells such as the transcription factors NF-KB and AP-1, COX-2, dihydrofolate reductase and pro-angiogenic substances such as VEGF, while up-regulating the function of immune cells against tumors, such as cytotoxic CD8+ T cells. In hematological malignancies, aqueous cinnamon extract has been studied in order to understand if it is possible to count on its help, alone or in combination with traditional drugs such as doxorubicin, to treat patients. The aim of our work is to investigate results from in vitro and in vivo studies about the possible anti-cancer effect of aqueous cinnamon extract in hematological malignancies and the different pathways involved in its action. The possibility of using cinnamon extract in clinical practice is discussed; even if its use could appear very interesting, more studies are necessary to clear the real potentiality of this substance in cancer.
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Affiliation(s)
- Santino Caserta
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood "Gaetano Barresi", University of Messina, Via Consolare Valeria, 98125 Messina, Italy
| | - Claudia Genovese
- National Research Council, Institute for Agricultural and Forest Systems in the Mediterranean, Via Empedocle 58, 95128 Catania, Italy
| | - Nicola Cicero
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences, University of Messina, Via Consolare Valeria, 98125 Messina, Italy
| | - Sebastiano Gangemi
- Allergy and Clinical Immunology Unit, Department of Clinical and Experimental Medicine, University of Messina, Via Consolare Valeria, 98125 Messina, Italy
| | - Alessandro Allegra
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood "Gaetano Barresi", University of Messina, Via Consolare Valeria, 98125 Messina, Italy
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Hao Y, Miraghazadeh B, Chand R, Davies AR, Cardinez C, Kwong K, Downes MB, Sweet RA, Cañete PF, D'Orsogna LJ, Fulcher DA, Choo S, Yip D, Peters G, Yip S, Witney MJ, Nekrasov M, Feng ZP, Tscharke DC, Vinuesa CG, Cook MC. CTLA4 protects against maladaptive cytotoxicity during the differentiation of effector and follicular CD4 + T cells. Cell Mol Immunol 2023:10.1038/s41423-023-01027-8. [PMID: 37161048 PMCID: PMC10166697 DOI: 10.1038/s41423-023-01027-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/11/2023] [Indexed: 05/11/2023] Open
Abstract
As chronic antigenic stimulation from infection and autoimmunity is a feature of primary antibody deficiency (PAD), analysis of affected patients could yield insights into T-cell differentiation and explain how environmental exposures modify clinical phenotypes conferred by single-gene defects. CD57 marks dysfunctional T cells that have differentiated after antigenic stimulation. Indeed, while circulating CD57+ CD4+ T cells are normally rare, we found that they are increased in patients with PAD and markedly increased with CTLA4 haploinsufficiency or blockade. We performed single-cell RNA-seq analysis of matched CD57+ CD4+ T cells from blood and tonsil samples. Circulating CD57+ CD4+ T cells (CD4cyt) exhibited a cytotoxic transcriptome similar to that of CD8+ effector cells, could kill B cells, and inhibited B-cell responses. CTLA4 restrained the formation of CD4cyt. While CD57 also marked an abundant subset of follicular helper T cells, which is consistent with their antigen-driven differentiation, this subset had a pre-exhaustion transcriptomic signature marked by TCF7, TOX, and ID3 expression and constitutive expression of CTLA4 and did not become cytotoxic even after CTLA4 inhibition. Thus, CD57+ CD4+ T-cell cytotoxicity and exhaustion phenotypes are compartmentalised between blood and germinal centers. CTLA4 is a key modifier of CD4+ T-cell cytotoxicity, and the pathological CD4cyt phenotype is accentuated by infection.
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Affiliation(s)
- Yuwei Hao
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Bahar Miraghazadeh
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Rochna Chand
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Ainsley R Davies
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Chelisa Cardinez
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Kristy Kwong
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Morgan B Downes
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Rebecca A Sweet
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Pablo F Cañete
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Lloyd J D'Orsogna
- Department of Immunology, Fiona Stanley Hospital, Perth, WA, Australia
| | - David A Fulcher
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Sharon Choo
- Department of Immunology, The Royal Children's Hospital, Melbourne, VIC, Australia
| | - Desmond Yip
- Department of Medical Oncology, The Canberra Hospital, Canberra, ACT, Australia
- ANU Medical School, The Australian National University, Canberra, ACT, Australia
| | - Geoffrey Peters
- Department of Medical Oncology, The Canberra Hospital, Canberra, ACT, Australia
- ANU Medical School, The Australian National University, Canberra, ACT, Australia
| | - Sonia Yip
- NHMRC Clinical Trials Unit, The University of Sydney, Sydney, NSW, Australia
| | - Matthew J Witney
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Maxim Nekrasov
- The ACRF Biomolecular Resource Facility, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Zhi-Ping Feng
- ANU Bioinformatics Consultancy, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - David C Tscharke
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Carola G Vinuesa
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Matthew C Cook
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia.
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.
- ANU Medical School, The Australian National University, Canberra, ACT, Australia.
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom.
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Phan JM, Layton ED, Yu KK, Aguilar MS, Golez I, Franko NM, Logue JK, Rodda LB, Howard CA, Pepper M, Gale M, Chu HY, Seshadri C. Cytotoxic T Cells Targeting Spike Glycoprotein Are Associated with Hybrid Immunity to SARS-CoV-2. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:1236-1246. [PMID: 36961450 PMCID: PMC10121904 DOI: 10.4049/jimmunol.2200815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/22/2023] [Indexed: 03/25/2023]
Abstract
mRNA vaccination of individuals with prior SARS-CoV-2 infection provides superior protection against breakthrough infections with variants of concern compared with vaccination in the absence of prior infection. However, the immune mechanisms by which this hybrid immunity is generated and maintained are unknown. Whereas genetic variation in spike glycoprotein effectively subverts neutralizing Abs, spike-specific T cells are generally maintained against SARS-CoV-2 variants. Thus, we comprehensively profiled human T cell responses against the S1 and S2 domains of spike glycoprotein in a cohort of SARS-CoV-2-naive (n = 13) or -convalescent (n = 17) individuals who received two-dose mRNA vaccine series and were matched by age, sex, and vaccine type. Using flow cytometry, we observed that the overall functional breadth of CD4 T cells and polyfunctional Th1 responses was similar between the two groups. However, polyfunctional cytotoxic CD4 T cell responses against both S1 and S2 domains trended higher among convalescent subjects. Multimodal single-cell RNA sequencing revealed diverse functional programs in spike-specific CD4 and CD8 T cells in both groups. However, convalescent individuals displayed enhanced cytotoxic and antiviral CD8 T cell responses to both S1 and S2 in the absence of cytokine production. Taken together, our data suggest that cytotoxic CD4 and CD8 T cells targeting spike glycoprotein may partially account for hybrid immunity and protection against breakthrough infections with SARS-CoV-2.
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Affiliation(s)
- Jolie M. Phan
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Erik D. Layton
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Krystle K.Q. Yu
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Melissa S. Aguilar
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Inah Golez
- Department of Immunology, Center for Innate Immunity and Immune Disease, and Washington National Primate Research Center, University of Washington School of Medicine, Seattle, Washington, USA
| | - Nicholas M. Franko
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Jennifer K. Logue
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Lauren B. Rodda
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Christian A. Howard
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Marion Pepper
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Michael Gale
- Department of Immunology, Center for Innate Immunity and Immune Disease, and Washington National Primate Research Center, University of Washington School of Medicine, Seattle, Washington, USA
| | - Helen Y. Chu
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Chetan Seshadri
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
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Yip F, Lai B, Yang D. Role of Coxsackievirus B3-Induced Immune Responses in the Transition from Myocarditis to Dilated Cardiomyopathy and Heart Failure. Int J Mol Sci 2023; 24:ijms24097717. [PMID: 37175422 PMCID: PMC10178405 DOI: 10.3390/ijms24097717] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/16/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
Dilated cardiomyopathy (DCM) is a cardiac disease marked by the stretching and thinning of the heart muscle and impaired left ventricular contractile function. While most patients do not develop significant cardiac diseases from myocarditis, disparate immune responses can affect pathological outcomes, including DCM progression. These altered immune responses, which may be caused by genetic variance, can prolong cytotoxicity, induce direct cleavage of host protein, or encourage atypical wound healing responses that result in tissue scarring and impaired mechanical and electrical heart function. However, it is unclear which alterations within host immune profiles are crucial to dictating the outcomes of myocarditis. Coxsackievirus B3 (CVB3) is a well-studied virus that has been identified as a causal agent of myocarditis in various models, along with other viruses such as adenovirus, parvovirus B19, and SARS-CoV-2. This paper takes CVB3 as a pathogenic example to review the recent advances in understanding virus-induced immune responses and differential gene expression that regulates iron, lipid, and glucose metabolic remodeling, the severity of cardiac tissue damage, and the development of DCM and heart failure.
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Affiliation(s)
- Fione Yip
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
- The Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC V6Z 1Y6, Canada
| | - Brian Lai
- The Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC V6Z 1Y6, Canada
| | - Decheng Yang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
- The Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC V6Z 1Y6, Canada
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49
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Guo M, Abd-Rabbo D, Bertol B, Carew M, Lukhele S, Snell LM, Xu W, Boukhaled GM, Elsaesser H, Halaby MJ, Hirano N, McGaha TL, Brooks DG. Molecular, metabolic and functional CD4 T cell paralysis impedes tumor control. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.15.536946. [PMID: 37131587 PMCID: PMC10153152 DOI: 10.1101/2023.04.15.536946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
CD4 T cells are important effectors of anti-tumor immunity, yet the regulation of CD4 tumor-specific T (T TS ) cells during cancer development is still unclear. We demonstrate that CD4 T TS cells are initially primed in the tumor draining lymph node and begin to divide following tumor initiation. Distinct from CD8 T TS cells and previously defined exhaustion programs, CD4 T TS cell proliferation is rapidly frozen in place and differentiation stunted by a functional interplay of T regulatory cells and both intrinsic and extrinsic CTLA4 signaling. Together these mechanisms paralyze CD4 T TS cell differentiation, redirecting metabolic and cytokine production circuits, and reducing CD4 T TS cell accumulation in the tumor. Paralysis is actively maintained throughout cancer progression and CD4 T TS cells rapidly resume proliferation and functional differentiation when both suppressive reactions are alleviated. Strikingly, Treg depletion alone reciprocally induced CD4 T TS cells to themselves become tumor-specific Tregs, whereas CTLA4 blockade alone failed to promote T helper differentiation. Overcoming their paralysis established long-term tumor control, demonstrating a novel immune evasion mechanism that specifically cripples CD4 T TS cells to favor tumor progression.
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50
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Sharma M, Niu L, Zhang X, Huang S. Comparative transcriptomes reveal pro-survival and cytotoxic programs of mucosal-associated invariant T cells upon Bacillus Calmette-Guérin stimulation. Front Cell Infect Microbiol 2023; 13:1134119. [PMID: 37091679 PMCID: PMC10116416 DOI: 10.3389/fcimb.2023.1134119] [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: 12/29/2022] [Accepted: 03/15/2023] [Indexed: 04/08/2023] Open
Abstract
Mucosal-associated invariant T (MAIT) cells are protective against tuberculous and non-tuberculous mycobacterial infections with poorly understood mechanisms. Despite an innate-like nature, MAIT cell responses remain heterogeneous in bacterial infections. To comprehensively characterize MAIT activation programs responding to different bacteria, we stimulated MAIT cells with E. coli to compare with Bacillus Calmette-Guérin (BCG), which remains the only licensed vaccine and a feasible tool for investigating anti-mycobacterial immunity in humans. Upon sequencing mRNA from the activated and inactivated CD8+ MAIT cells, results demonstrated the altered MAIT cell gene profiles by each bacterium with upregulated expression of activation markers, transcription factors, cytokines, and cytolytic mediators crucial in anti-mycobacterial responses. Compared with E. coli, BCG altered more MAIT cell genes to enhance cell survival and cytolysis. Flow cytometry analyses similarly displayed a more upregulated protein expression of B-cell lymphoma 2 and T-box transcription factor Eomesodermin in BCG compared to E.coli stimulations. Thus, the transcriptomic program and protein expression of MAIT cells together displayed enhanced pro-survival and cytotoxic programs in response to BCG stimulation, supporting BCG induces cell-mediated effector responses of MAIT cells to fight mycobacterial infections.
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Affiliation(s)
| | | | | | - Shouxiong Huang
- Department of Environmental and Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH, United States
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