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Wang X, Zhang T, Zheng B, Lu Y, Liang Y, Xu G, Zhao L, Tao Y, Song Q, You H, Hu H, Li X, Sun K, Li T, Zhang Z, Wang J, Lan X, Pan D, Fu YX, Yue B, Zheng H. Lymphotoxin-β promotes breast cancer bone metastasis colonization and osteolytic outgrowth. Nat Cell Biol 2024:10.1038/s41556-024-01478-9. [PMID: 39147874 DOI: 10.1038/s41556-024-01478-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 07/11/2024] [Indexed: 08/17/2024]
Abstract
Bone metastasis is a lethal consequence of breast cancer. Here we used single-cell transcriptomics to investigate the molecular mechanisms underlying bone metastasis colonization-the rate-limiting step in the metastatic cascade. We identified that lymphotoxin-β (LTβ) is highly expressed in tumour cells within the bone microenvironment and this expression is associated with poor bone metastasis-free survival. LTβ promotes tumour cell colonization and outgrowth in multiple breast cancer models. Mechanistically, tumour-derived LTβ activates osteoblasts through nuclear factor-κB2 signalling to secrete CCL2/5, which facilitates tumour cell adhesion to osteoblasts and accelerates osteoclastogenesis, leading to bone metastasis progression. Blocking LTβ signalling with a decoy receptor significantly suppressed bone metastasis in vivo, whereas clinical sample analysis revealed significantly higher LTβ expression in bone metastases than in primary tumours. Our findings highlight LTβ as a bone niche-induced factor that promotes tumour cell colonization and osteolytic outgrowth and underscore its potential as a therapeutic target for patients with bone metastatic disease.
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Affiliation(s)
- Xuxiang Wang
- Center for Cancer Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Tengjiang Zhang
- Center for Cancer Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Bingxin Zheng
- Department of Orthopedic Oncology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Youxue Lu
- Center for Cancer Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Yong Liang
- Center for Cancer Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Guoyuan Xu
- Center for Cancer Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Luyang Zhao
- Center for Cancer Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Yuwei Tao
- Center for Cancer Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Qianhui Song
- Center for Cancer Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Huiwen You
- Center for Cancer Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Haitian Hu
- Center for Cancer Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Xuan Li
- Center for Cancer Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Keyong Sun
- Center for Cancer Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Tianqi Li
- School of Life Sciences and Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
| | - Zian Zhang
- Department of Joint Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jianbin Wang
- School of Life Sciences and Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
| | - Xun Lan
- State Key Laboratory of Molecular Oncology and Center for Cancer Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Deng Pan
- State Key Laboratory of Molecular Oncology and Center for Cancer Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Yang-Xin Fu
- State Key Laboratory of Molecular Oncology and Center for Cancer Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Bin Yue
- Department of Orthopedic Oncology, The Affiliated Hospital of Qingdao University, Qingdao, China.
| | - Hanqiu Zheng
- State Key Laboratory of Molecular Oncology and Center for Cancer Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, China.
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, China.
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Deka A, Kumar N, Basu S, Chawla M, Bhattacharya N, Ali SA, Bhawna, Madan U, Kumar S, Das B, Sengupta D, Awasthi A, Basak S. Non-canonical NF-κB signaling limits the tolerogenic β-catenin-Raldh2 axis in gut dendritic cells to exacerbate intestinal pathologies. EMBO J 2024:10.1038/s44318-024-00182-6. [PMID: 39060515 DOI: 10.1038/s44318-024-00182-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 07/12/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Dendritic cell (DC) dysfunction is known to exacerbate intestinal pathologies, but the mechanisms compromising DC-mediated immune regulation in this context remain unclear. Here, we show that intestinal dendritic cells from a mouse model of experimental colitis exhibit significant levels of noncanonical NF-κB signaling, which activates the RelB:p52 heterodimer. Genetic inactivation of this pathway in DCs alleviates intestinal pathologies in mice suffering from colitis. Deficiency of RelB:p52 diminishes transcription of Axin1, a critical component of the β-catenin destruction complex, reinforcing β-catenin-dependent expression of Raldh2, which imparts tolerogenic DC attributes by promoting retinoic acid synthesis. DC-specific impairment of noncanonical NF-κB signaling leads to increased colonic numbers of Tregs and IgA+ B cells, which promote luminal IgA production and foster eubiosis. Experimentally introduced β-catenin haploinsufficiency in DCs with deficient noncanonical NF-κB signaling moderates Raldh2 activity, reinstating colitogenic sensitivity in mice. Finally, inflammatory bowel-disease patients also display a deleterious noncanonical NF-κB signaling signature in intestinal DCs. In sum, we establish how noncanonical NF-κB signaling in dendritic cells can subvert retinoic acid synthesis to fuel intestinal inflammation.
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Affiliation(s)
- Alvina Deka
- Systems Immunology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Naveen Kumar
- Systems Immunology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Swapnava Basu
- Systems Immunology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Meenakshi Chawla
- Systems Immunology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Namrata Bhattacharya
- Indraprastha Institute of Information Technology Delhi, New Delhi, India
- Australian Prostate Cancer Research Centre-Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Sk Asif Ali
- Systems Immunology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Bhawna
- Systems Immunology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Upasna Madan
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Shakti Kumar
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Bhabatosh Das
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Debarka Sengupta
- Indraprastha Institute of Information Technology Delhi, New Delhi, India
| | - Amit Awasthi
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Soumen Basak
- Systems Immunology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Pierre N, Huynh-Thu VA, Baiwir D, Vieujean S, Bequet E, Reenaers C, Van Kemseke C, Salée C, Massot C, Fléron M, Mazzucchelli G, Trzpiot L, Eppe G, De Pauw E, Louis E, Meuwis MA. Serum proteome signatures associated with ileal and colonic ulcers in Crohn's disease. J Proteomics 2024; 302:105199. [PMID: 38763457 DOI: 10.1016/j.jprot.2024.105199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/06/2024] [Accepted: 05/15/2024] [Indexed: 05/21/2024]
Abstract
At a clinical level, ileal and colonic Crohn's disease (CD) are considered as separate entities. These subphenotypes need to be better supported by biological data to develop personalised medicine in CD. To this end, we combined different technologies (proximity extension assay, selected reaction monitoring, and high-sensitivity turbidimetric immunoassay (hsCRP)) to measure 207 immune-related serum proteins in CD patients presenting no endoscopic lesions (endoscopic remission) (n = 23), isolated ileal ulcers (n = 17), or isolated colonic ulcers (n = 16). We showed that isolated ileal ulcers and isolated colonic ulcers were specifically associated with 6 and 18 serum proteins, respectively: (high level: JUN, CNTNAP2; low level: FCRL6, LTA, CLEC4A, NTF4); (high level: hsCRP, IL6, APCS, CFB, MBL2, IL7, IL17A, CCL19, CXCL10, CSF3, IL10, CLEC4G, MMP12, VEGFA; low level: CLEC3B, GSN, TNFSF12, TPSAB1). Isolated ileal ulcers and isolated colonic ulcers were detected by hsCRP with an area under the receiver operating characteristics curve of 0.64 (p-value = 0.07) and 0.77 (p-value = 0.001), respectively. We highlighted distinct serum proteome profiles associated with ileal and colonic ulcers in CD, this finding might support the development of therapeutics and biomarkers tailored to disease location. SIGNIFICANCE: Although ileal and colonic Crohn's disease present important clinical differences (eg, progression, response to treatment and reliability of biomarkers), these two entities are managed with the same therapeutic strategy. The biological specificities of ileal and colonic Crohn's disease need to be better characterised to develop more personalised approaches. The present study used robust technologies (selected reaction monitoring, proximity extension assays and turbidimetric immunoassay) to quantify precisely 207 serum immune-related proteins in three groups of Crohn's disease patients presenting: 1) no endoscopic lesions (endoscopic remission) (n = 23); 2) isolated ileal ulcers (n = 17); 3) isolated colonic ulcers (n = 16). We found distinct serum proteome signatures associated with ileal and colonic ulcers. Our findings could foster the development of biomarkers and treatments tailored to Crohn's disease location.
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Affiliation(s)
- Nicolas Pierre
- Laboratory of Translational Gastroenterology, GIGA-institute, University of Liege, Liege, Belgium.
| | - Vân Anh Huynh-Thu
- Department of Electrical Engineering and Computer Science, University of Liege, Liege, Belgium
| | | | - Sophie Vieujean
- Laboratory of Translational Gastroenterology, GIGA-institute, University of Liege, Liege, Belgium; Hepato-Gastroenterology and Digestive Oncology Department, Liege University Hospital, Liege, Belgium
| | - Emeline Bequet
- Laboratory of Translational Gastroenterology, GIGA-institute, University of Liege, Liege, Belgium; Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Liege University Hospital, Liege, Belgium
| | - Catherine Reenaers
- Hepato-Gastroenterology and Digestive Oncology Department, Liege University Hospital, Liege, Belgium
| | - Catherine Van Kemseke
- Hepato-Gastroenterology and Digestive Oncology Department, Liege University Hospital, Liege, Belgium
| | - Catherine Salée
- Laboratory of Translational Gastroenterology, GIGA-institute, University of Liege, Liege, Belgium
| | - Charlotte Massot
- Laboratory of Translational Gastroenterology, GIGA-institute, University of Liege, Liege, Belgium
| | | | - Gabriel Mazzucchelli
- Laboratory of Mass Spectrometry, MolSys Research Unit, University of Liege, Liege, Belgium
| | - Lisette Trzpiot
- Laboratory of Mass Spectrometry, MolSys Research Unit, University of Liege, Liege, Belgium
| | - Gauthier Eppe
- Laboratory of Mass Spectrometry, MolSys Research Unit, University of Liege, Liege, Belgium
| | - Edwin De Pauw
- Laboratory of Mass Spectrometry, MolSys Research Unit, University of Liege, Liege, Belgium
| | - Edouard Louis
- Laboratory of Translational Gastroenterology, GIGA-institute, University of Liege, Liege, Belgium; Hepato-Gastroenterology and Digestive Oncology Department, Liege University Hospital, Liege, Belgium
| | - Marie-Alice Meuwis
- Laboratory of Translational Gastroenterology, GIGA-institute, University of Liege, Liege, Belgium; Hepato-Gastroenterology and Digestive Oncology Department, Liege University Hospital, Liege, Belgium
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Yuan DY, McKeague ML, Raghu VK, Schoen RE, Finn OJ, Benos PV. Cellular and transcriptional profiles of peripheral blood mononuclear cells pre-vaccination predict immune response to preventative MUC1 vaccine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.598031. [PMID: 38948837 PMCID: PMC11212910 DOI: 10.1101/2024.06.14.598031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
A single arm trial (NCT007773097) and a double-blind, placebo controlled randomized trial ( NCT02134925 ) were conducted in individuals with a history of advanced colonic adenoma to test the safety and immunogenicity of the MUC1 tumor antigen vaccine and its potential to prevent new adenomas. These were the first two trials of a non-viral cancer vaccine administered in the absence of cancer. The vaccine was safe and strongly immunogenic in 43% (NCT007773097) and 25% ( NCT02134925 ) of participants. The lack of response in a significant number of participants suggested, for the first time, that even in a premalignant setting, the immune system may have already been exposed to some level of suppression previously reported only in cancer. Single-cell RNA-sequencing (scRNA-seq) on banked pre-vaccination peripheral blood mononuclear cells (PBMCs) from 16 immune responders and 16 non-responders identified specific cell types, genes, and pathways of a productive vaccine response. Responders had a significantly higher percentage of CD4+ naive T cells pre-vaccination, but a significantly lower percentage of CD8+ T effector memory (TEM) cells and CD16+ monocytes. Differential gene expression (DGE) and transcription factor inference analysis showed a higher level of expression of T cell activation genes, such as Fos and Jun, in CD4+ naive T cells, and pathway analysis showed enriched signaling activity in responders. Furthermore, Bayesian network analysis suggested that these genes were mechanistically connected to response. Our analyses identified several immune mechanisms and candidate biomarkers to be further validated as predictors of immune responses to a preventative cancer vaccine that could facilitate selection of individuals likely to benefit from a vaccine or be used to improve vaccine responses.
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Sankaran DG, Zhu H, Maymi VI, Forlastro IM, Jiang Y, Laniewski N, Scheible KM, Rudd BD, Grimson AW. Gene Regulatory Programs that Specify Age-Related Differences during Thymocyte Development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.599011. [PMID: 38948840 PMCID: PMC11212896 DOI: 10.1101/2024.06.14.599011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
T cell development is fundamental to immune system establishment, yet how this development changes with age remains poorly understood. Here, we construct a transcriptional and epigenetic atlas of T cell developmental programs in neonatal and adult mice, revealing the ontogeny of divergent gene regulatory programs and their link to age-related differences in phenotype and function. Specifically, we identify a gene module that diverges with age from the earliest stages of genesis and includes programs that govern effector response and cell cycle regulation. Moreover, we reveal that neonates possess more accessible chromatin during early thymocyte development, likely establishing poised gene expression programs that manifest later in thymocyte development. Finally, we leverage this atlas, employing a CRISPR-based perturbation approach coupled with single-cell RNA sequencing as a readout to uncover a conserved transcriptional regulator, Zbtb20, that contributes to age-dependent differences in T cell development. Altogether, our study defines transcriptional and epigenetic programs that regulate age-specific differences in T cell development.
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Fang X, Lan G, Lin Y, Xie Z, Zhong Y, Luo S, Xiao X, Luo L, Zhang Y, Li H, Wu H. Inflammation due to ocular surface homeostasis imbalance caused by pterygia: tear lymphotoxin-alpha study and a literature review. J Ophthalmic Inflamm Infect 2024; 14:28. [PMID: 38874736 PMCID: PMC11178703 DOI: 10.1186/s12348-024-00413-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 06/10/2024] [Indexed: 06/15/2024] Open
Abstract
OBJECTIVE To estimate the pterygium ocular surface state, and compare with healthy eyes and dry eyes. To investigate the inflammation due to pterygia growth by tear Lymphotoxin-alpha (LT α) test. DESIGN Prospective, single-center study. PARTICIPANTS 400 patients, divided into 100 pterygium group, 100 mild dry eye group, 100 moderate dry eye group, and 100 age-and sex-matched normal controls. METHODS The non-invasive break-up time (NIBUT), tear meniscus height (TMH) test, corneal fluorescein staining (CFS), meibomian gland loss score (MGs), and lipid layer thickness (LLT) were evaluated in all patients. Pterygium status and ocular status in the pterygium group were collected. The tear LT α test was conducted in the pterygium patients group. RESULT Pterygium can affect the ocular surface, leading to decreased tear film stability. The TMH, NIBUT, CFS, MGs, and lipid layer thickness can provide insights into this phenomenon. The presence of pterygium can change the structure and condition of the ocular surface. Tear LT α testing shows an abnormal decrease in LT α levels in pterygium patients. This indicates an immune-inflammation microenvironment that causes tissue repair deficiency. CONCLUSION The dry eye triggered by the growth of pterygium may originate from the tear film instability due to pterygia. As an inflammatory index, LT α in the development of pterygium and the aggravation of dry eye patients can indicate that the ocular surface is in different inflammatory states. Future tear testing in LT α may be a potential indicator to assess the inflammatory status of the dry eye.
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Affiliation(s)
- Xie Fang
- Xiamen Eye Center and Eye Institute of Xiamen University, Xiamen, China
- Xiamen Clinical Research Center for Eye Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Ophthalmology, Xiamen, Fujian, China
- Fujian Key Laboratory of Corneal & Ocular Surface Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Corneal & Ocular Surface Diseases, Xiamen, Fujian, China
- Translational Medicine Institute of Xiamen Eye Center of Xiamen University, Xiamen, Fujian, China
| | - Guoli Lan
- Xiamen Eye Center and Eye Institute of Xiamen University, Xiamen, China
- Xiamen Clinical Research Center for Eye Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Ophthalmology, Xiamen, Fujian, China
- Fujian Key Laboratory of Corneal & Ocular Surface Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Corneal & Ocular Surface Diseases, Xiamen, Fujian, China
- Translational Medicine Institute of Xiamen Eye Center of Xiamen University, Xiamen, Fujian, China
| | - Yuan Lin
- Xiamen Eye Center and Eye Institute of Xiamen University, Xiamen, China.
- Xiamen Clinical Research Center for Eye Diseases, Xiamen, Fujian, China.
- Xiamen Key Laboratory of Ophthalmology, Xiamen, Fujian, China.
- Fujian Key Laboratory of Corneal & Ocular Surface Diseases, Xiamen, Fujian, China.
- Xiamen Key Laboratory of Corneal & Ocular Surface Diseases, Xiamen, Fujian, China.
- Translational Medicine Institute of Xiamen Eye Center of Xiamen University, Xiamen, Fujian, China.
| | - Zhiwen Xie
- Xiamen Eye Center and Eye Institute of Xiamen University, Xiamen, China
- Xiamen Clinical Research Center for Eye Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Ophthalmology, Xiamen, Fujian, China
- Fujian Key Laboratory of Corneal & Ocular Surface Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Corneal & Ocular Surface Diseases, Xiamen, Fujian, China
- Translational Medicine Institute of Xiamen Eye Center of Xiamen University, Xiamen, Fujian, China
| | - Yanlin Zhong
- Xiamen Eye Center and Eye Institute of Xiamen University, Xiamen, China
- Xiamen Clinical Research Center for Eye Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Ophthalmology, Xiamen, Fujian, China
- Fujian Key Laboratory of Corneal & Ocular Surface Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Corneal & Ocular Surface Diseases, Xiamen, Fujian, China
- Translational Medicine Institute of Xiamen Eye Center of Xiamen University, Xiamen, Fujian, China
| | - Shunrong Luo
- Xiamen Eye Center and Eye Institute of Xiamen University, Xiamen, China
- Xiamen Clinical Research Center for Eye Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Ophthalmology, Xiamen, Fujian, China
- Fujian Key Laboratory of Corneal & Ocular Surface Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Corneal & Ocular Surface Diseases, Xiamen, Fujian, China
- Translational Medicine Institute of Xiamen Eye Center of Xiamen University, Xiamen, Fujian, China
| | - Xianwen Xiao
- Xiamen Eye Center and Eye Institute of Xiamen University, Xiamen, China
- Xiamen Clinical Research Center for Eye Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Ophthalmology, Xiamen, Fujian, China
- Fujian Key Laboratory of Corneal & Ocular Surface Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Corneal & Ocular Surface Diseases, Xiamen, Fujian, China
- Translational Medicine Institute of Xiamen Eye Center of Xiamen University, Xiamen, Fujian, China
| | - Lianghuan Luo
- Xiamen Eye Center and Eye Institute of Xiamen University, Xiamen, China
- Xiamen Clinical Research Center for Eye Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Ophthalmology, Xiamen, Fujian, China
- Fujian Key Laboratory of Corneal & Ocular Surface Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Corneal & Ocular Surface Diseases, Xiamen, Fujian, China
- Translational Medicine Institute of Xiamen Eye Center of Xiamen University, Xiamen, Fujian, China
| | - Yiqiu Zhang
- Xiamen Eye Center and Eye Institute of Xiamen University, Xiamen, China
- Xiamen Clinical Research Center for Eye Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Ophthalmology, Xiamen, Fujian, China
- Fujian Key Laboratory of Corneal & Ocular Surface Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Corneal & Ocular Surface Diseases, Xiamen, Fujian, China
- Translational Medicine Institute of Xiamen Eye Center of Xiamen University, Xiamen, Fujian, China
| | - Hanqiao Li
- Xiamen Eye Center and Eye Institute of Xiamen University, Xiamen, China
- Xiamen Clinical Research Center for Eye Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Ophthalmology, Xiamen, Fujian, China
- Fujian Key Laboratory of Corneal & Ocular Surface Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Corneal & Ocular Surface Diseases, Xiamen, Fujian, China
- Translational Medicine Institute of Xiamen Eye Center of Xiamen University, Xiamen, Fujian, China
| | - Huping Wu
- Xiamen Eye Center and Eye Institute of Xiamen University, Xiamen, China.
- Xiamen Clinical Research Center for Eye Diseases, Xiamen, Fujian, China.
- Xiamen Key Laboratory of Ophthalmology, Xiamen, Fujian, China.
- Fujian Key Laboratory of Corneal & Ocular Surface Diseases, Xiamen, Fujian, China.
- Xiamen Key Laboratory of Corneal & Ocular Surface Diseases, Xiamen, Fujian, China.
- Translational Medicine Institute of Xiamen Eye Center of Xiamen University, Xiamen, Fujian, China.
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Chen Q, Muñoz AR, Korchagina AA, Shou Y, Vallecer J, Todd AW, Shein SA, Tumanov AV, Koroleva E. LTβR-RelB signaling in intestinal epithelial cells protects from chemotherapy-induced mucosal damage. Front Immunol 2024; 15:1388496. [PMID: 38873613 PMCID: PMC11169669 DOI: 10.3389/fimmu.2024.1388496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 05/01/2024] [Indexed: 06/15/2024] Open
Abstract
The intricate immune mechanisms governing mucosal healing following intestinal damage induced by cytotoxic drugs remain poorly understood. The goal of this study was to investigate the role of lymphotoxin beta receptor (LTβR) signaling in chemotherapy-induced intestinal damage. LTβR deficient mice exhibited heightened body weight loss, exacerbated intestinal pathology, increased proinflammatory cytokine expression, reduced IL-22 expression, and proliferation of intestinal epithelial cells following methotrexate (MTX) treatment. Furthermore, LTβR-/-IL-22-/- mice succumbed to MTX treatment, suggesting that LTβR- and IL-22- dependent pathways jointly promote mucosal repair. Although both LTβR ligands LIGHT and LTβ were upregulated in the intestine early after MTX treatment, LIGHT-/- mice, but not LTβ-/- mice, displayed exacerbated disease. Further, we revealed the critical role of T cells in mucosal repair as T cell-deficient mice failed to upregulate intestinal LIGHT expression and exhibited increased body weight loss and intestinal pathology. Analysis of mice with conditional inactivation of LTβR revealed that LTβR signaling in intestinal epithelial cells, but not in Lgr5+ intestinal stem cells, macrophages or dendritic cells was critical for mucosal repair. Furthermore, inactivation of the non-canonical NF-kB pathway member RelB in intestinal epithelial cells promoted MTX-induced disease. Based on these results, we propose a model wherein LIGHT produced by T cells activates LTβR-RelB signaling in intestinal epithelial cells to facilitate mucosal repair following chemotherapy treatment.
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Affiliation(s)
- Qiangxing Chen
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
- Department of Gastroenterology, Second Xiangya Hospital, and Research Center of Digestive Disease, Central South University, Changsha, Hunan, China
| | - Amanda R. Muñoz
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Anna A. Korchagina
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Yajun Shou
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
- Department of Gastroenterology, Second Xiangya Hospital, and Research Center of Digestive Disease, Central South University, Changsha, Hunan, China
| | - Jensine Vallecer
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Austin W. Todd
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Sergey A. Shein
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Alexei V. Tumanov
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Ekaterina Koroleva
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
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Harris JR, Zoccoli-Rodriguez V, Delaney MS, Cruz TN, Gaudette BT, Wilmore JR. Gut commensals require Peyer's patches to induce protective systemic IgA responses. RESEARCH SQUARE 2024:rs.3.rs-4220532. [PMID: 38798510 PMCID: PMC11118714 DOI: 10.21203/rs.3.rs-4220532/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Gut educated IgA secreting plasma cells that disseminate beyond the mucosa and into systemic tissues have been described as providing beneficial effects from disease in several contexts. Several bacteria have been implicated in the induction of systemic IgA, however the mechanisms that result in differential levels of induction by each bacterial species are still unknown. Here we show, the commensal bacteria, Bacteroides fragilis (Bf), is an efficient inducer of systemic IgA responses. The ability of Bf to induce the production of bone marrow IgA plasma cells and high levels of serum IgA relied on high levels of gut colonization in a dose-dependent manner. Colonization induced Bf-specific IgA responses were severely diminished in the absence of Peyer's patches, but not the murine cecal patch. Colonization of mice with Bf, a natural human commensal, resulted in few changes within the microbiome and the host transcriptional profile in the gut, suggesting a commensal relationship with the host. Bf colonization did benefit the mice by inducing systemic IgA that led to increased protection in a bowel perforation model resulting in lower peritoneal abscess formation. These findings demonstrate a critical role for bacterial colonization and Peyer's patches in the induction of robust systemic IgA responses that confer protection from bacterial dissemination outside of the gut.
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Affiliation(s)
- Joshua R. Harris
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY
| | | | - Mara S. Delaney
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY
| | - Tania N. Cruz
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY
| | - Brian T. Gaudette
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH
| | - Joel R. Wilmore
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY
- Sepsis Interdisciplinary Research Center, SUNY Upstate Medical University, Syracuse, NY
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9
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Ranek JS, Stallaert W, Milner JJ, Redick M, Wolff SC, Beltran AS, Stanley N, Purvis JE. DELVE: feature selection for preserving biological trajectories in single-cell data. Nat Commun 2024; 15:2765. [PMID: 38553455 PMCID: PMC10980758 DOI: 10.1038/s41467-024-46773-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 03/07/2024] [Indexed: 04/02/2024] Open
Abstract
Single-cell technologies can measure the expression of thousands of molecular features in individual cells undergoing dynamic biological processes. While examining cells along a computationally-ordered pseudotime trajectory can reveal how changes in gene or protein expression impact cell fate, identifying such dynamic features is challenging due to the inherent noise in single-cell data. Here, we present DELVE, an unsupervised feature selection method for identifying a representative subset of molecular features which robustly recapitulate cellular trajectories. In contrast to previous work, DELVE uses a bottom-up approach to mitigate the effects of confounding sources of variation, and instead models cell states from dynamic gene or protein modules based on core regulatory complexes. Using simulations, single-cell RNA sequencing, and iterative immunofluorescence imaging data in the context of cell cycle and cellular differentiation, we demonstrate how DELVE selects features that better define cell-types and cell-type transitions. DELVE is available as an open-source python package: https://github.com/jranek/delve .
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Affiliation(s)
- Jolene S Ranek
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wayne Stallaert
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - J Justin Milner
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Margaret Redick
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Samuel C Wolff
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Adriana S Beltran
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Human Pluripotent Cell Core, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Natalie Stanley
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Jeremy E Purvis
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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10
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Randolph G, Erlich E, Czepielewski R, Field R, Dunning T, Saleh L, Hoofnagle M, Tumanov A, Guilak F, Brestoff J. Distinct roles for LTalpha3 and LTalpha1beta2 produced by B cells contribute to their multi-faceted impact on ileitis. RESEARCH SQUARE 2024:rs.3.rs-3962916. [PMID: 38464070 PMCID: PMC10925464 DOI: 10.21203/rs.3.rs-3962916/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
B lymphocytes may facilitate chronic inflammation through antibody production or secretion of cytokines, including lymphotoxin (LT)-a 1 b 2 associated with development of lymphoid tissue. Tertiary lymphoid structures (TLS) characterize human and murine ileitis by suppressing outflow from the ileum. Here, we show that B cell-derived secretory IgA protected against ileal inflammation, whereas B cell-derived LTa guarded against ileitis-associated loss of body mass. We initially hypothesized this protection resulted from formation of TLS that suppressed lymphatic outflow and thereby restrained systemic spread of inflammatory signals, but B cell-selective deletion of LTb did not exacerbate weight loss, despite eliminating TLS. Instead, weight loss driven by the cachectic cytokine TNF was exacerbated when LTa 3 , another ligand for TNF receptors, was selectively neutralized. Thus, B cells' multi-faceted impact on ileitis includes generating secretory IgA, expressing LTa 1 b 2 to drive formation of TLS, and producing LTa 3 for protecting against weight loss in the presence of TNF.
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11
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Cummings MJ, Bakamutumaho B, Lutwama JJ, Owor N, Che X, Astorkia M, Postler TS, Kayiwa J, Kiconco J, Muwanga M, Nsereko C, Rwamutwe E, Nayiga I, Kyebambe S, Haumba M, Bosa HK, Ocom F, Watyaba B, Kikaire B, Tomoiaga AS, Kisaka S, Kiwanuka N, Lipkin WI, O'Donnell MR. COVID-19 immune signatures in Uganda persist in HIV co-infection and diverge by pandemic phase. Nat Commun 2024; 15:1475. [PMID: 38368384 PMCID: PMC10874401 DOI: 10.1038/s41467-024-45204-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 01/17/2024] [Indexed: 02/19/2024] Open
Abstract
Little is known about the pathobiology of SARS-CoV-2 infection in sub-Saharan Africa, where severe COVID-19 fatality rates are among the highest in the world and the immunological landscape is unique. In a prospective cohort study of 306 adults encompassing the entire clinical spectrum of SARS-CoV-2 infection in Uganda, we profile the peripheral blood proteome and transcriptome to characterize the immunopathology of COVID-19 across multiple phases of the pandemic. Beyond the prognostic importance of myeloid cell-driven immune activation and lymphopenia, we show that multifaceted impairment of host protein synthesis and redox imbalance define core biological signatures of severe COVID-19, with central roles for IL-7, IL-15, and lymphotoxin-α in COVID-19 respiratory failure. While prognostic signatures are generally consistent in SARS-CoV-2/HIV-coinfection, type I interferon responses uniquely scale with COVID-19 severity in persons living with HIV. Throughout the pandemic, COVID-19 severity peaked during phases dominated by A.23/A.23.1 and Delta B.1.617.2/AY variants. Independent of clinical severity, Delta phase COVID-19 is distinguished by exaggerated pro-inflammatory myeloid cell and inflammasome activation, NK and CD8+ T cell depletion, and impaired host protein synthesis. Combining these analyses with a contemporary Ugandan cohort of adults hospitalized with influenza and other severe acute respiratory infections, we show that activation of epidermal and platelet-derived growth factor pathways are distinct features of COVID-19, deepening translational understanding of mechanisms potentially underlying SARS-CoV-2-associated pulmonary fibrosis. Collectively, our findings provide biological rationale for use of broad and targeted immunotherapies for severe COVID-19 in sub-Saharan Africa, illustrate the relevance of local viral and host factors to SARS-CoV-2 immunopathology, and highlight underemphasized yet therapeutically exploitable immune pathways driving COVID-19 severity.
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Affiliation(s)
- Matthew J Cummings
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA.
| | - Barnabas Bakamutumaho
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Julius J Lutwama
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Nicholas Owor
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Xiaoyu Che
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Maider Astorkia
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Thomas S Postler
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - John Kayiwa
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Jocelyn Kiconco
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | | | | | | | - Irene Nayiga
- Entebbe Regional Referral Hospital, Entebbe, Uganda
| | | | - Mercy Haumba
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Henry Kyobe Bosa
- Uganda Peoples' Defence Forces, Kampala, Uganda
- Ministry of Health, Kampala, Uganda
| | | | - Benjamin Watyaba
- European and Developing Countries Clinical Trials Partnership-Eastern Africa Consortium for Clinical Research, Uganda Virus Research Institute, Entebbe, Uganda
| | - Bernard Kikaire
- European and Developing Countries Clinical Trials Partnership-Eastern Africa Consortium for Clinical Research, Uganda Virus Research Institute, Entebbe, Uganda
- Department of Pediatrics, Makerere University College of Health Sciences, Kampala, Uganda
| | - Alin S Tomoiaga
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Accounting, Business Analytics, Computer Information Systems, and Law, Manhattan College, New York, NY, USA
| | - Stevens Kisaka
- Department of Epidemiology and Biostatistics, Makerere University School of Public Health, Kampala, Uganda
- Institute of Tropical and Infectious Diseases, University of Nairobi, Nairobi, Kenya
| | - Noah Kiwanuka
- Department of Epidemiology and Biostatistics, Makerere University School of Public Health, Kampala, Uganda
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Max R O'Donnell
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
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12
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Lan G, Fang X, Zhong Y, Luo S, Xiao X, Xie Z, Luo L, Zhang Y, Li H, Lin Y, Wu H. Evaluation of lymphotoxin-alpha in pterygium and diagnostic value in active and inactive pterygium states. Sci Rep 2024; 14:1866. [PMID: 38253817 PMCID: PMC10803762 DOI: 10.1038/s41598-024-52382-z] [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: 10/11/2023] [Accepted: 01/18/2024] [Indexed: 01/24/2024] Open
Abstract
To explore the correlation between tear LT-a, pterygium status, and dry eye indicators. We established a diagnostic model to evaluate active pterygium. A retrospective study was conducted between June 2021 and June 2023 on 172 patients, comprising 108 men and 64 women. The study analyzed LT-a and various ocular parameters in all participants. The data was collected using Excel software and analyzed using SPSS 25.0 statistical software and Medcalc. We made a nomogram diagnostic model to different diagnosed the state of pterygium. This study found that pterygium has progressive eye surface damage during the active state. There was no significant difference in dry eye indicators between the two groups. However, the concentration of LT-a in the active group was significantly lower than that in the inactive group (P < 0.001). We observed that increased pterygium grade corresponded to a worse ocular surface condition. In addition, LT-a was significantly positively correlated with disease duration, but negatively correlated with age, pterygium size, active pterygium state, and LLT value. The optimal intercept value for evaluating active pterygium in Lt-a was ≤ 0.49 dg/ml. We screened three variables for evaluating active pterygium through Single and Multiple regression analysis: LT-a grading, pterygium size, and congestion score. Finally, we made a reliable diagnostic nomogram model. Pterygium development triggers immune inflammation. Our model based on LT-a identifies active pterygium for personalized treatment options and new research directions.
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Affiliation(s)
- Guoli Lan
- Xiamen Eye Center and Eye Institute of Xiamen University, Xiamen, China
- Xiamen Clinical Research Center for Eye Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Ophthalmology, Xiamen, Fujian, China
- Fujian Key Laboratory of Corneal and Ocular Surface Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Corneal and Ocular Surface Diseases, Xiamen, Fujian, China
- Translational Medicine Institute of Xiamen Eye Center of Xiamen University, Xiamen, Fujian, China
| | - Xie Fang
- Xiamen Eye Center and Eye Institute of Xiamen University, Xiamen, China
- Xiamen Clinical Research Center for Eye Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Ophthalmology, Xiamen, Fujian, China
- Fujian Key Laboratory of Corneal and Ocular Surface Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Corneal and Ocular Surface Diseases, Xiamen, Fujian, China
- Translational Medicine Institute of Xiamen Eye Center of Xiamen University, Xiamen, Fujian, China
| | - Yanlin Zhong
- Xiamen Eye Center and Eye Institute of Xiamen University, Xiamen, China
- Xiamen Clinical Research Center for Eye Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Ophthalmology, Xiamen, Fujian, China
- Fujian Key Laboratory of Corneal and Ocular Surface Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Corneal and Ocular Surface Diseases, Xiamen, Fujian, China
- Translational Medicine Institute of Xiamen Eye Center of Xiamen University, Xiamen, Fujian, China
| | - Shunrong Luo
- Xiamen Eye Center and Eye Institute of Xiamen University, Xiamen, China
- Xiamen Clinical Research Center for Eye Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Ophthalmology, Xiamen, Fujian, China
- Fujian Key Laboratory of Corneal and Ocular Surface Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Corneal and Ocular Surface Diseases, Xiamen, Fujian, China
- Translational Medicine Institute of Xiamen Eye Center of Xiamen University, Xiamen, Fujian, China
| | - Xianwen Xiao
- Xiamen Eye Center and Eye Institute of Xiamen University, Xiamen, China
- Xiamen Clinical Research Center for Eye Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Ophthalmology, Xiamen, Fujian, China
- Fujian Key Laboratory of Corneal and Ocular Surface Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Corneal and Ocular Surface Diseases, Xiamen, Fujian, China
- Translational Medicine Institute of Xiamen Eye Center of Xiamen University, Xiamen, Fujian, China
| | - Zhiwen Xie
- Xiamen Eye Center and Eye Institute of Xiamen University, Xiamen, China
- Xiamen Clinical Research Center for Eye Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Ophthalmology, Xiamen, Fujian, China
- Fujian Key Laboratory of Corneal and Ocular Surface Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Corneal and Ocular Surface Diseases, Xiamen, Fujian, China
- Translational Medicine Institute of Xiamen Eye Center of Xiamen University, Xiamen, Fujian, China
| | - Lianghuan Luo
- Xiamen Eye Center and Eye Institute of Xiamen University, Xiamen, China
- Xiamen Clinical Research Center for Eye Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Ophthalmology, Xiamen, Fujian, China
- Fujian Key Laboratory of Corneal and Ocular Surface Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Corneal and Ocular Surface Diseases, Xiamen, Fujian, China
- Translational Medicine Institute of Xiamen Eye Center of Xiamen University, Xiamen, Fujian, China
| | - Yiqiu Zhang
- Xiamen Eye Center and Eye Institute of Xiamen University, Xiamen, China
- Xiamen Clinical Research Center for Eye Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Ophthalmology, Xiamen, Fujian, China
- Fujian Key Laboratory of Corneal and Ocular Surface Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Corneal and Ocular Surface Diseases, Xiamen, Fujian, China
- Translational Medicine Institute of Xiamen Eye Center of Xiamen University, Xiamen, Fujian, China
| | - Hanqiao Li
- Xiamen Eye Center and Eye Institute of Xiamen University, Xiamen, China
- Xiamen Clinical Research Center for Eye Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Ophthalmology, Xiamen, Fujian, China
- Fujian Key Laboratory of Corneal and Ocular Surface Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Corneal and Ocular Surface Diseases, Xiamen, Fujian, China
- Translational Medicine Institute of Xiamen Eye Center of Xiamen University, Xiamen, Fujian, China
| | - Yuan Lin
- Xiamen Eye Center and Eye Institute of Xiamen University, Xiamen, China.
- Xiamen Clinical Research Center for Eye Diseases, Xiamen, Fujian, China.
- Xiamen Key Laboratory of Ophthalmology, Xiamen, Fujian, China.
- Fujian Key Laboratory of Corneal and Ocular Surface Diseases, Xiamen, Fujian, China.
- Xiamen Key Laboratory of Corneal and Ocular Surface Diseases, Xiamen, Fujian, China.
- Translational Medicine Institute of Xiamen Eye Center of Xiamen University, Xiamen, Fujian, China.
| | - Huping Wu
- Xiamen Eye Center and Eye Institute of Xiamen University, Xiamen, China.
- Xiamen Clinical Research Center for Eye Diseases, Xiamen, Fujian, China.
- Xiamen Key Laboratory of Ophthalmology, Xiamen, Fujian, China.
- Fujian Key Laboratory of Corneal and Ocular Surface Diseases, Xiamen, Fujian, China.
- Xiamen Key Laboratory of Corneal and Ocular Surface Diseases, Xiamen, Fujian, China.
- Translational Medicine Institute of Xiamen Eye Center of Xiamen University, Xiamen, Fujian, China.
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13
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Bishu S. Nurturing the Gut, Moms with IBD and Their Babies. J Crohns Colitis 2023; 17:1705-1706. [PMID: 37749070 PMCID: PMC10673811 DOI: 10.1093/ecco-jcc/jjad139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Affiliation(s)
- Shrinivas Bishu
- Crohn’s and Colitis Center, University of Michigan, Ann Arbor, MI, USA
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14
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Wang M, Rajkumar S, Lai Y, Liu X, He J, Ishikawa T, Nallapothula D, Singh RR. Tertiary lymphoid structures as local perpetuators of organ-specific immune injury: implication for lupus nephritis. Front Immunol 2023; 14:1204777. [PMID: 38022566 PMCID: PMC10644380 DOI: 10.3389/fimmu.2023.1204777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
In response to inflammatory stimuli in conditions such as autoimmune disorders, infections and cancers, immune cells organize in nonlymphoid tissues, which resemble secondary lymphoid organs. Such immune cell clusters are called tertiary lymphoid structures (TLS). Here, we describe the potential role of TLS in the pathogenesis of autoimmune disease, focusing on lupus nephritis, a condition that incurs major morbidity and mortality. In the kidneys of patients and animals with lupus nephritis, the presence of immune cell aggregates with similar cell composition, structure, and gene signature as lymph nodes and of lymphoid tissue-inducer and -organizer cells, along with evidence of communication between stromal and immune cells are indicative of the formation of TLS. TLS formation in kidneys affected by lupus may be instigated by local increases in lymphorganogenic chemokines such as CXCL13, and in molecules associated with leukocyte migration and vascularization. Importantly, the presence of TLS in kidneys is associated with severe tubulointerstitial inflammation, higher disease activity and chronicity indices, and poor response to treatment in patients with lupus nephritis. TLS may contribute to the pathogenesis of lupus nephritis by increasing local IFN-I production, facilitating the recruitment and supporting survival of autoreactive B cells, maintaining local production of systemic autoantibodies such as anti-dsDNA and anti-Sm/RNP autoantibodies, and initiating epitope spreading to local autoantigens. Resolution of TLS, along with improvement in lupus, by treating animals with soluble BAFF receptor, docosahexaenoic acid, complement inhibitor C4BP(β-), S1P1 receptor modulator Cenerimod, dexamethasone, and anti-CXCL13 further emphasizes a role of TLS in the pathogenesis of lupus. However, the mechanisms underlying TLS formation and their roles in the pathogenesis of lupus nephritis are not fully comprehended. Furthermore, the lack of non-invasive methods to visualize/quantify TLS in kidneys is also a major hurdle; however, recent success in visualizing TLS in lupus-prone mice by photon emission computed tomography provides hope for early detection and manipulation of TLS.
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Affiliation(s)
- Meiying Wang
- Department of Rheumatology and Immunology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
- Peking University Shenzhen Hosiptal, Shenzhen, China
- Autoimmunity and Tolerance Laboratory, Division of Rheumatology, Department of Medicine, David Geffen School of Medicine at University of California Los Angeles (UCLA), Los Angeles, CA, United States
| | - Snehin Rajkumar
- Autoimmunity and Tolerance Laboratory, Division of Rheumatology, Department of Medicine, David Geffen School of Medicine at University of California Los Angeles (UCLA), Los Angeles, CA, United States
| | - Yupeng Lai
- Department of Rheumatology and Immunology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Xingjiao Liu
- Department of Rheumatology and Immunology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Jing He
- Department of Rheumatology and Immunology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
- Department of Nephrology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Tatsuya Ishikawa
- Autoimmunity and Tolerance Laboratory, Division of Rheumatology, Department of Medicine, David Geffen School of Medicine at University of California Los Angeles (UCLA), Los Angeles, CA, United States
| | - Dhiraj Nallapothula
- Autoimmunity and Tolerance Laboratory, Division of Rheumatology, Department of Medicine, David Geffen School of Medicine at University of California Los Angeles (UCLA), Los Angeles, CA, United States
| | - Ram Raj Singh
- Autoimmunity and Tolerance Laboratory, Division of Rheumatology, Department of Medicine, David Geffen School of Medicine at University of California Los Angeles (UCLA), Los Angeles, CA, United States
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
- Molecular Toxicology Interdepartmental Program, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
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15
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Bogdanov IV, Streltsova MA, Kovalenko EI, Sapozhnikov AM, Panteleev PV, Ovchinnikova TV. Epithelial-Immune Cell Crosstalk Determines the Activation of Immune Cells In Vitro by the Human Cathelicidin LL-37 at Low Physiological Concentrations. Biomolecules 2023; 13:1316. [PMID: 37759716 PMCID: PMC10526274 DOI: 10.3390/biom13091316] [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: 07/25/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
The only human cathelicidin, LL-37, is a host defense antimicrobial peptide with antimicrobial activities against protozoans, fungi, Gram(+) and Gram(-) bacteria, and enveloped viruses. It has been shown in experiments in vitro that LL-37 is able to induce the production of various inflammatory and anti-inflammatory cytokines and chemokines by different human cell types. However, it remains an open question whether such cytokine induction is physiologically relevant, as LL-37 exhibited its immunomodulatory properties at concentrations that are much higher (>20 μg/mL) than those observed in non-inflamed tissues (1-5 μg/mL). In the current study, we assessed the permeability of LL-37 across the Caco-2 polarized monolayer and showed that this peptide could pass through the Caco-2 monolayer with low efficiency, which predetermined its low absorption in the gut. We showed that LL-37 at low physiological concentrations (<5 μg/mL) was not able to directly activate monocytes. However, in the presence of polarized epithelial monolayers, LL-37 is able to activate monocytes through the MAPK/ERK signaling pathway and induce the production of cytokines, as assessed by a multiplex assay at the protein level. We have demonstrated that LL-37 is able to fulfill its immunomodulatory action in vivo in non-inflamed tissues at low physiological concentrations. In the present work, we revealed a key role of epithelial-immune cell crosstalk in the implementation of immunomodulatory functions of the human cathelicidin LL-37, which might shed light on its physiological action in vivo.
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Affiliation(s)
- Ivan V. Bogdanov
- M.M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (M.A.S.); (E.I.K.); (A.M.S.); (P.V.P.); (T.V.O.)
| | - Maria A. Streltsova
- M.M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (M.A.S.); (E.I.K.); (A.M.S.); (P.V.P.); (T.V.O.)
| | - Elena I. Kovalenko
- M.M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (M.A.S.); (E.I.K.); (A.M.S.); (P.V.P.); (T.V.O.)
| | - Alexander M. Sapozhnikov
- M.M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (M.A.S.); (E.I.K.); (A.M.S.); (P.V.P.); (T.V.O.)
| | - Pavel V. Panteleev
- M.M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (M.A.S.); (E.I.K.); (A.M.S.); (P.V.P.); (T.V.O.)
| | - Tatiana V. Ovchinnikova
- M.M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (M.A.S.); (E.I.K.); (A.M.S.); (P.V.P.); (T.V.O.)
- Department of Biotechnology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
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16
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Ranek JS, Stallaert W, Milner J, Stanley N, Purvis JE. Feature selection for preserving biological trajectories in single-cell data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.540043. [PMID: 37214963 PMCID: PMC10197710 DOI: 10.1101/2023.05.09.540043] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Single-cell technologies can readily measure the expression of thousands of molecular features from individual cells undergoing dynamic biological processes, such as cellular differentiation, immune response, and disease progression. While examining cells along a computationally ordered pseudotime offers the potential to study how subtle changes in gene or protein expression impact cell fate decision-making, identifying characteristic features that drive continuous biological processes remains difficult to detect from unenriched and noisy single-cell data. Given that all profiled sources of feature variation contribute to the cell-to-cell distances that define an inferred cellular trajectory, including confounding sources of biological variation (e.g. cell cycle or metabolic state) or noisy and irrelevant features (e.g. measurements with low signal-to-noise ratio) can mask the underlying trajectory of study and hinder inference. Here, we present DELVE (dynamic selection of locally covarying features), an unsupervised feature selection method for identifying a representative subset of dynamically-expressed molecular features that recapitulates cellular trajectories. In contrast to previous work, DELVE uses a bottom-up approach to mitigate the effect of unwanted sources of variation confounding inference, and instead models cell states from dynamic feature modules that constitute core regulatory complexes. Using simulations, single-cell RNA sequencing data, and iterative immunofluorescence imaging data in the context of the cell cycle and cellular differentiation, we demonstrate that DELVE selects features that more accurately characterize cell populations and improve the recovery of cell type transitions. This feature selection framework provides an alternative approach for improving trajectory inference and uncovering co-variation amongst features along a biological trajectory. DELVE is implemented as an open-source python package and is publicly available at: https://github.com/jranek/delve.
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Affiliation(s)
- Jolene S. Ranek
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wayne Stallaert
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Justin Milner
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Natalie Stanley
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeremy E. Purvis
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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17
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Alladina J, Smith NP, Kooistra T, Slowikowski K, Kernin IJ, Deguine J, Keen HL, Manakongtreecheep K, Tantivit J, Rahimi RA, Sheng SL, Nguyen ND, Haring AM, Giacona FL, Hariri LP, Xavier RJ, Luster AD, Villani AC, Cho JL, Medoff BD. A human model of asthma exacerbation reveals transcriptional programs and cell circuits specific to allergic asthma. Sci Immunol 2023; 8:eabq6352. [PMID: 37146132 PMCID: PMC10440046 DOI: 10.1126/sciimmunol.abq6352] [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: 04/22/2022] [Accepted: 04/13/2023] [Indexed: 05/07/2023]
Abstract
Asthma is a chronic disease most commonly associated with allergy and type 2 inflammation. However, the mechanisms that link airway inflammation to the structural changes that define asthma are incompletely understood. Using a human model of allergen-induced asthma exacerbation, we compared the lower airway mucosa in allergic asthmatics and allergic non-asthmatic controls using single-cell RNA sequencing. In response to allergen, the asthmatic airway epithelium was highly dynamic and up-regulated genes involved in matrix degradation, mucus metaplasia, and glycolysis while failing to induce injury-repair and antioxidant pathways observed in controls. IL9-expressing pathogenic TH2 cells were specific to asthmatic airways and were only observed after allergen challenge. Additionally, conventional type 2 dendritic cells (DC2 that express CD1C) and CCR2-expressing monocyte-derived cells (MCs) were uniquely enriched in asthmatics after allergen, with up-regulation of genes that sustain type 2 inflammation and promote pathologic airway remodeling. In contrast, allergic controls were enriched for macrophage-like MCs that up-regulated tissue repair programs after allergen challenge, suggesting that these populations may protect against asthmatic airway remodeling. Cellular interaction analyses revealed a TH2-mononuclear phagocyte-basal cell interactome unique to asthmatics. These pathogenic cellular circuits were characterized by type 2 programming of immune and structural cells and additional pathways that may sustain and amplify type 2 signals, including TNF family signaling, altered cellular metabolism, failure to engage antioxidant responses, and loss of growth factor signaling. Our findings therefore suggest that pathogenic effector circuits and the absence of proresolution programs drive structural airway disease in response to type 2 inflammation.
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Affiliation(s)
- Jehan Alladina
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Neal P. Smith
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Tristan Kooistra
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Kamil Slowikowski
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Isabela J. Kernin
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Jacques Deguine
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Henry L. Keen
- Iowa Institute of Human Genetics, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Kasidet Manakongtreecheep
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Jessica Tantivit
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Rod A. Rahimi
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Susan L. Sheng
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Nhan D. Nguyen
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Alexis M. Haring
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Francesca L. Giacona
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Lida P. Hariri
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Ramnik J. Xavier
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Andrew D. Luster
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Alexandra-Chloé Villani
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Josalyn L. Cho
- Division of Pulmonary, Critical Care and Occupational Medicine, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Benjamin D. Medoff
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
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18
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Wu T, Womersley HJ, Wang JR, Scolnick J, Cheow LF. Time-resolved assessment of single-cell protein secretion by sequencing. Nat Methods 2023; 20:723-734. [PMID: 37037998 DOI: 10.1038/s41592-023-01841-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 03/06/2023] [Indexed: 04/12/2023]
Abstract
Secreted proteins play critical roles in cellular communication. Methods enabling concurrent measurement of cellular protein secretion, phenotypes and transcriptomes are still unavailable. Here we describe time-resolved assessment of protein secretion from single cells by sequencing (TRAPS-seq). Released proteins are trapped onto the cell surface and probed by oligonucleotide-barcoded antibodies before being simultaneously sequenced with transcriptomes in single cells. We demonstrate that TRAPS-seq helps unravel the phenotypic and transcriptional determinants of the secretion of pleiotropic TH1 cytokines (IFNγ, IL-2 and TNF) in activated T cells. In addition, we show that TRAPS-seq can be used to track the secretion of multiple cytokines over time, uncovering unique molecular signatures that govern the dynamics of single-cell cytokine secretions. Our results revealed that early central memory T cells with CD45RA expression (TCMRA) are important in both the production and maintenance of polyfunctional cytokines. TRAPS-seq presents a unique tool for seamless integration of secretomics measurements with multi-omics profiling in single cells.
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Affiliation(s)
- Tongjin Wu
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
| | - Howard John Womersley
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
| | | | - Jonathan Scolnick
- Singleron Biotechnologies Pte. Ltd., Singapore, Singapore
- Healthy Longevity Translational Research Program, Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Lih Feng Cheow
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore.
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore.
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19
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Alhelf M, Shoaib RMS, Elsaid A, Bastawy N, Elbeltagy NS, Salem ET, Refaat S, Abuelnadar EH. Prognostic significance of the genetic variant of lymphotoxin alpha (p.Thr60Asn) in egyptian patients with advanced hepatocellular carcinoma. Mol Biol Rep 2023; 50:4317-4327. [PMID: 36929286 PMCID: PMC10147750 DOI: 10.1007/s11033-023-08281-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 01/13/2023] [Indexed: 03/18/2023]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide in terms of mortality, and susceptibility is attributed to genetic, lifestyle, and environmental factors. Lymphotoxin alpha (LTA) has a crucial role in communicating the lymphocytes with stromal cells and provoking cytotoxic effects on the cancer cells. There are no reports on the contribution of the LTA (c.179 C>A; p.Thr60Asn; rs1041981) gene polymorphism to HCC susceptibility. The main aim of this study is to investigate the association of LTA (c.179 C>A; p.Thr60Asn; rs1041981) variant with the HCC risk in the Egyptian population. METHODS This case-control study included 317 participants (111 HCC patients, and 206 healthy controls). The LTA (c.179 C>A; p.Thr60Asn; rs1041981) polymorphism was assessed by tetra-primer amplification refractory mutation system polymerase chain reaction (T-ARMS-PCR) technique. RESULTS The frequencies of the dominant and recessive models (CA + AA; AA) of the LTA (c.179 C>A; p.Thr60Asn; rs1041981) variant were statistically significant among HCC patients in comparison to controls (p = 0.01; p = 0.007; respectively). The A-allele of LTA (c.179 C>A; p.Thr60Asn; rs1041981) variant was statistically significant in HCC patients in comparison to controls (p ˂ 0.001). CONCLUSION The LTA (c.179 C>A; p.Thr60Asn; rs1041981) polymorphism was independently associated with an increased risk for hepatocellular carcinoma in the Egyptian population.
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Affiliation(s)
- Maha Alhelf
- Biotechnology School, Nile University, Giza, Egypt.,Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Cairo University, Giza, Egypt
| | - Rasha M S Shoaib
- Food and Dairy Sciences and Technology Department, Faculty of Environmental Agricultural Sciences, Arish University, 45511, North Sinai, Egypt.
| | - Afaf Elsaid
- Genetics Unit, Mansoura University, Children Hospital, Mansoura, Egypt
| | - Nermeen Bastawy
- Medical Physiology Department, Faculty of Medicine, Cairo University, Giza, Egypt
| | - Nanis S Elbeltagy
- Department of Laboratories, Faculty of Medicine, Mansoura University, Children Hospital, Mansoura, Egypt
| | - Eman T Salem
- Department of Basic Science, Faculty of Physical Therapy, Horus University, Damietta, Egypt
| | - Sherif Refaat
- Oncology Center, Mansoura University, Mansoura, Egypt
| | - Eman H Abuelnadar
- Department of Laboratories, Faculty of Medicine, Mansoura University, Children Hospital, Mansoura, Egypt
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20
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Harris CS, Miaskowski CA, Conley YP, Hammer MJ, Dhruva AA, Levine JD, Olshen AB, Kober KM. Gastrointestinal Symptom Cluster is Associated With Epigenetic Regulation of Lymphotoxin Beta in Oncology Patients Receiving Chemotherapy. Biol Res Nurs 2023; 25:51-64. [PMID: 35929442 PMCID: PMC9900252 DOI: 10.1177/10998004221115863] [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: 12/14/2022]
Abstract
OBJECTIVES While the gastrointestinal symptom cluster (GISC) is common in patients receiving chemotherapy, limited information is available on its underlying mechanism(s). Emerging evidence suggests a role for inflammatory processes through the actions of the nuclear factor kappa B (NF-κB) signaling pathway. This study evaluated for associations between a GISC and levels of DNA methylation for genes within this pathway. METHODS Prior to their second or third cycle of chemotherapy, 1071 outpatients reported symptom occurrence using the Memorial Symptom Assessment Scale. A GISC was identified using exploratory factor analysis. Differential methylation analyses were performed in two independent samples using EPIC (n = 925) and 450K (n = 146) microarrays. Trans expression-associated CpG (eCpG) loci for 56 NF-κB signaling pathway genes were evaluated. Loci significance were assessed using an exploratory false discovery rate (FDR) of 25% for the EPIC sample. For the validation assessment using the 450K sample, significance was assessed at an unadjusted p-value of 0.05. RESULTS For the EPIC sample, the GISC was associated with increased expression of lymphotoxin beta (LTB) at one differentially methylated trans eCpG locus (cg03171795; FDR = 0.168). This association was not validated in the 450K sample. CONCLUSIONS This study is the first to identify an association between a GISC and epigenetic regulation of a gene that is involved in the initiation of gastrointestinal immune responses. Findings suggest that increased LTB expression by hypermethylation of a trans eCpG locus is involved in the occurrence of this cluster in patients receiving chemotherapy. LTB may be a potential therapeutic target for this common cluster.
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Affiliation(s)
| | - Christine A. Miaskowski
- School of Nursing, University of
California, San Francisco, CA, USA
- School of Medicine, University of
California, San Francisco, CA, USA
| | - Yvette P. Conley
- School of Nursing, University of
Pittsburgh, Pittsburgh, PA, USA
| | - Marilyn J. Hammer
- The Phyllis F. Cantor Center for
Research in Nursing and Patient Care Services, Dana-Farber Cancer
Institute, Boston, MA, USA
| | - Anand A. Dhruva
- School of Medicine, University of
California, San Francisco, CA, USA
| | - Jon D. Levine
- School of Medicine, University of
California, San Francisco, CA, USA
| | - Adam B. Olshen
- School of Medicine, University of
California, San Francisco, CA, USA
| | - Kord M. Kober
- School of Nursing, University of
California, San Francisco, CA, USA
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21
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Martín-Vañó S, Miralles-Abella A, Castaño P, Hurtado-Genovés G, Aguilar-Ballester M, Herrero-Cervera A, Vinué A, Martínez-Hervás S, González-Navarro H. Vascular smooth muscle cell phenotype is modulated by ligands of the lymphotoxin β receptor and the tumor necrosis factor receptor. CLINICA E INVESTIGACION EN ARTERIOSCLEROSIS : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE ARTERIOSCLEROSIS 2023; 35:1-11. [PMID: 35738949 DOI: 10.1016/j.arteri.2022.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/18/2022] [Accepted: 05/22/2022] [Indexed: 02/08/2023]
Abstract
OBJECTIVE Vascular smooth muscle cells (VSMCs) undergo a phenotypic-switching process during the generation of unstable atheroma plaques. In this investigation, the potential implication of the tumor necrosis factor superfamily (TNFSF) ligands, in the gene expression signature associated with VSMC plasticity was studied. MATERIAL AND METHODS Human aortic (ha)VSMCs were obtained commercially and treated with the cytokine TNFSF14, also called LIGHT, the lymphotoxin alpha (LTα), the heterotrimer LTα1β2 or with vehicle for 72h. The effect of the different treatments on gene expression was analyzed by quantitative PCR and included the study of genes associated with myofibroblast-like cell function, osteochondrogenesis, pluripotency, lymphorganogenesis and macrophage-like cell function. RESULTS HaVSMCs displayed a change in myofibroblast-like cell genes which consisted in reduced COL1A1 and TGFB1 mRNA levels when treated with LTα or LIGHT and with augmented MMP9 expression levels when treated with LTα. LTα and LIGHT treatments also diminished the expression of genes associated with osteochondrogenesis and pluripotency SOX9, CKIT, and KLF4. By contrary, all the above genes were no affected by the treatment with the trimer LTα1β2. In addition, haVSMC treatment with LTα, LTα1β2 and LIGHT altered lymphorganogenic cytokine gene expression which consisted of augmented CCL20 and CCL21 mRNA levels by LTα and a reduction in the gene expression of CCL21 and CXCL13 by LIGHT and LTα1β2 respectively. Neither, LTα or LIGHT or LTα1β2 treatments affected the expression of macrophage-like cell markers in haVSMC. CONCLUSIONS Altogether, indicates that the TNFSF ligands through their interconnected network of signaling, are important in the preservation of VSMC identity against the acquisition of a genetic expression signature compatible with functional cellular plasticity.
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Affiliation(s)
| | | | | | | | | | | | - Angela Vinué
- Institute of Health Research-INCLIVA, Valencia, Spain
| | - Sergio Martínez-Hervás
- Institute of Health Research-INCLIVA, Valencia, Spain; Endocrinology and Nutrition Department Clinic Hospital and Department of Medicine, University of Valencia, Valencia, Spain; CIBER de Diabetes y Enfermedades Metabólicas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
| | - Herminia González-Navarro
- Institute of Health Research-INCLIVA, Valencia, Spain; CIBER de Diabetes y Enfermedades Metabólicas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain; Biochemistry and Molecular Biology Department, Faculty of Medicine, University of Valencia, Valencia, Spain.
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22
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Jin L, Jiang BG, Yin Y, Guo J, Jiang JF, Qi X, Crispell G, Karim S, Cao WC, Lai R. Interference with LTβR signaling by tick saliva facilitates transmission of Lyme disease spirochetes. Proc Natl Acad Sci U S A 2022; 119:e2208274119. [PMID: 36383602 PMCID: PMC9704693 DOI: 10.1073/pnas.2208274119] [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: 05/13/2022] [Accepted: 10/04/2022] [Indexed: 11/17/2022] Open
Abstract
Lyme spirochetes have coevolved with ticks to optimize transmission to hosts using tick salivary molecules (TSMs) to counteract host defenses. TSMs modulate various molecular events at the tick-host interface. Lymphotoxin-beta receptor (LTβR) is a vital immune receptor and plays protective roles in host immunity against microbial infections. We found that Ltbr knockout mice were more susceptible to Lyme disease spirochetes, suggesting the involvement of LTβR signaling in tick-borne Borrelia infection. Further investigation showed that a 15-kDa TSM protein from Ixodes persulcatus (I. persulcatus salivary protein; IpSAP) functioned as an immunosuppressant to facilitate the transmission and infection of Lyme disease spirochetes. IpSAP directly interacts with LTβR to block its activation, thus inhibiting the downstream signaling and consequently suppressing immunity. IpSAP immunization provided mice with significant protection against I. persulcatus-mediated Borrelia garinii infection. Notably, the immunization showed considerable cross-protection against other Borrelia infections mediated by other ixodid ticks. One of the IpSAP homologs from other ixodid ticks showed similar effects on Lyme spirochete transmission. Together, our findings suggest that LTβR signaling plays an important role in blocking the transmission and pathogenesis of tick-borne Lyme disease spirochetes, and that IpSAP and its homologs are promising candidates for broad-spectrum vaccine development.
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Affiliation(s)
- Lin Jin
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Bao-Gui Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100101, China
| | - Yizhu Yin
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China
| | - Jingya Guo
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jia-Fu Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100101, China
| | - Xiaopeng Qi
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China
| | - Gary Crispell
- Cell and Molecular Biology, School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406
| | - Shahid Karim
- Cell and Molecular Biology, School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406
| | - Wu-Chun Cao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100101, China
| | - Ren Lai
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China
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23
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Liu SW, Sun F, Rong SJ, Wang T, Wang CY. Lymphotoxins Serve as a Novel Orchestrator in T1D Pathogenesis. Front Immunol 2022; 13:917577. [PMID: 35757751 PMCID: PMC9219589 DOI: 10.3389/fimmu.2022.917577] [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: 04/11/2022] [Accepted: 04/29/2022] [Indexed: 11/18/2022] Open
Abstract
Type 1 diabetes (T1D) stems from pancreatic β cell destruction by islet reactive immune cells. Similar as other autoimmune disorders, there is no curative remedy for T1D thus far. Chronic insulitis is the hallmark of T1D, which creates a local inflammatory microenvironment that impairs β cell function and ultimately leads to β cell death. Immune regulation shows promise in T1D treatment by providing a time window for β cell recovery. However, due to the complex nature of T1D pathogenesis, the therapeutic effect of immune regulation is often short-lasting and unsatisfying in monotherapies. Lymphotoxins (LTs) were first identified in 1960s as the lymphocyte-producing cytokine that can kill other cell types. As a biological cousin of tumor necrosis factor alpha (TNFα), LTs play unique roles in T1D development. Herein in this review, we summarized the advancements of LTs in T1D pathogenesis. We particularly highlighted their effect on the formation of peri-islet tertiary lymphoid organs (TLOs), and discussed their synergistic effect with other cytokines on β cell toxicity and autoimmune progression. Given the complex and dynamic crosstalk between immune cells and β cells in T1D setting, blockade of lymphotoxin signaling applied to the existing therapies could be an efficient approach to delay or even reverse the established T1D.
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Affiliation(s)
- Shi-Wei Liu
- Department of Endocrinology, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Fei Sun
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, National Health Commission (NHC) Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Shan-Jie Rong
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, National Health Commission (NHC) Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Ting Wang
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, National Health Commission (NHC) Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Cong-Yi Wang
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, National Health Commission (NHC) Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
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24
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Rosichini M, Catanoso M, Screpanti I, Felli MP, Locatelli F, Velardi E. Signaling Crosstalks Drive Generation and Regeneration of the Thymus. Front Immunol 2022; 13:920306. [PMID: 35734178 PMCID: PMC9207182 DOI: 10.3389/fimmu.2022.920306] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/17/2022] [Indexed: 12/19/2022] Open
Abstract
Optimal recovery of immune competence after periods of hematopoietic insults or stress is crucial to re-establish patient response to vaccines, pathogens and tumor antigens. This is particularly relevant for patients receiving high doses of chemotherapy or radiotherapy, who experience prolonged periods of lymphopenia, which can be associated with an increased risk of infections, malignant relapse, and adverse clinical outcome. While the thymus represents the primary organ responsible for the generation of a diverse pool of T cells, its function is profoundly impaired by a range of acute insults (including those caused by cytoreductive chemo/radiation therapy, infections and graft-versus-host disease) and by the chronic physiological deterioration associated with aging. Impaired thymic function increases the risk of infections and tumor antigen escape due to a restriction in T-cell receptor diversity and suboptimal immune response. Therapeutic approaches that can promote the renewal of the thymus have the potential to restore immune competence in patients. Previous work has documented the importance of the crosstalk between thymocytes and thymic epithelial cells in establishing correct architecture and function of thymic epithelium. This crosstalk is relevant not only during thymus organogenesis, but also to promote the recovery of its function after injuries. In this review, we will analyze the signals involved in the crosstalk between TECs and hematopoietic cells. We will focus in particular on how signals from T-cells can regulate TEC function and discuss the relevance of these pathways in restoring thymic function and T-cell immunity in experimental models, as well as in the clinical setting.
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Affiliation(s)
- Marco Rosichini
- Department of Pediatric Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Marialuigia Catanoso
- Department of Pediatric Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Isabella Screpanti
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Maria Pia Felli
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Franco Locatelli
- Department of Pediatric Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Department of Maternal and Child Health, Sapienza University of Rome, Rome, Italy
| | - Enrico Velardi
- Department of Pediatric Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- *Correspondence: Enrico Velardi,
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Intestinal fibroblastic reticular cell niches control innate lymphoid cell homeostasis and function. Nat Commun 2022; 13:2027. [PMID: 35440118 PMCID: PMC9018819 DOI: 10.1038/s41467-022-29734-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 03/21/2022] [Indexed: 11/30/2022] Open
Abstract
Innate lymphoid cells (ILCs) govern immune cell homeostasis in the intestine and protect the host against microbial pathogens. Various cell-intrinsic pathways have been identified that determine ILC development and differentiation. However, the cellular components that regulate ILC sustenance and function in the intestinal lamina propria are less known. Using single-cell transcriptomic analysis of lamina propria fibroblasts, we identify fibroblastic reticular cells (FRCs) that underpin cryptopatches (CPs) and isolated lymphoid follicles (ILFs). Genetic ablation of lymphotoxin-β receptor expression in Ccl19-expressing FRCs blocks the maturation of CPs into mature ILFs. Interactome analysis shows the major niche factors and processes underlying FRC-ILC crosstalk. In vivo validation confirms that a sustained lymphotoxin-driven feedforward loop of FRC activation including IL-7 generation is critical for the maintenance of functional ILC populations. In sum, our study indicates critical fibroblastic niches within the intestinal lamina propria that control ILC homeostasis and functionality and thereby secure protective gut immunity. Fibroblastic reticular cells (FRCs) support localisation of immune cells in secondary lymphoid tissues but less is known about the lamina propria. Here the authors use scRNA-seq and intestinal infection to characterise FRCs in the intestinal lamina propria and show specialised niches that foster innate lymphoid cells during homeostasis and infection.
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Prognostic role of TNF alpha, LT alpha, MDR1 and codon 72 Tp53 Gene polymorphisms on Multiple Myeloma Egyptian patients. Leuk Res 2022; 117:106854. [DOI: 10.1016/j.leukres.2022.106854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 04/12/2022] [Accepted: 04/25/2022] [Indexed: 11/18/2022]
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Liu Y, Zou L, Tang H, Li J, Liu H, Jiang X, Jiang B, Dong Z, Fu W. Single-Cell Sequencing of Immune Cells in Human Aortic Dissection Tissue Provides Insights Into Immune Cell Heterogeneity. Front Cardiovasc Med 2022; 9:791875. [PMID: 35433892 PMCID: PMC9008490 DOI: 10.3389/fcvm.2022.791875] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 03/14/2022] [Indexed: 11/25/2022] Open
Abstract
Background Inflammation plays an important role in the progression of sporadic aortic dissection (AD). Immune cells, especially macrophages, infiltrate the aorta and secrete inflammatory cytokines and matrix metalloproteinases to cause degradation of the extracellular matrix, thereby contributing to the pathogenesis of AD. However, the cellular heterogeneity within these immune cells has not been fully characterized. Methods We used single-cell RNA sequencing to profile the transcriptomes of all immune cells in AD tissue and normal aorta. Using magnetic-activated cell sorting gating on CD45, we obtained a higher resolution identification of the immune cell subsets in the aorta. Results We observed significant differences in the proportion of major immune cell subpopulations between AD and normal aorta tissues. Macrophages accounted for a higher percentage in the normal aorta, while the proportions of T cells, B cells and natural killer (NK) cells were all increased in AD tissues. Macrophage clusters that expanded in AD tissues originated primarily from circulating monocytes and expressed genes encoding proinflammatory cytokines and molecules involved in tissue repair. T and NK cells in AD tissues exhibited enhanced cytotoxic properties. A cluster of CD4+ T cells that had expanded in AD tissues was Th17-like and might contribute to the pathogenesis of AD. Cell–cell interaction analysis highlighted the increased communication between macrophages and T cells, which primarily regulated the costimulation of T cells. Conclusions Our study provides a comprehensive characterization of immune cells in the dissected aorta with an emphasis on the role of macrophages and T cells. The information from our study improves our understanding of immune mechanisms in AD formation and helps to identify additional useful targets for early diagnosis or therapy of AD.
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Affiliation(s)
- Yifan Liu
- Department of Vascular Surgery, Institute of Vascular Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Shanghai, China
| | - Lingwei Zou
- Department of Vascular Surgery, Institute of Vascular Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Shanghai, China
| | - Hanfei Tang
- Department of Vascular Surgery, Institute of Vascular Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Shanghai, China
| | - Jie Li
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Hao Liu
- Department of Vascular Surgery, Institute of Vascular Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Shanghai, China
| | - Xiaolang Jiang
- Department of Vascular Surgery, Institute of Vascular Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Shanghai, China
| | - Baohong Jiang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Weiguo Fu
| | - Zhihui Dong
- Department of Vascular Surgery, Institute of Vascular Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Shanghai, China
- Zhihui Dong
| | - Weiguo Fu
- Department of Vascular Surgery, Institute of Vascular Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Shanghai, China
- Baohong Jiang
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Kottom TJ, Carmona EM, Limper AH. Gene Expression in Lung Epithelial Cells Following Interaction with Pneumocystis carinii and its Specific Life Forms Yields Insights into Host Gene Responses to Infection. Microbiol Immunol 2022; 66:238-251. [PMID: 35229348 PMCID: PMC9090966 DOI: 10.1111/1348-0421.12972] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 02/01/2022] [Accepted: 02/22/2022] [Indexed: 11/29/2022]
Abstract
Pneumocystis spp. interacts with epithelial cells in the alveolar spaces of the lung. It is thought that the binding of Pneumocystis to host cell epithelium is needed for life cycle completion and proliferation. The effect of this interaction on lung epithelial cells have previously shown that the trophic form of this organism greatly inhibits p34 cdc2 activity, a serine/threonine kinase required for transition from G2 to M phase in the cell cycle. To gain further insight into the host response during Pneumocystis pneumonia (PCP), we used microarray technology to profile epithelial cell (A549) gene expression patterns following Pneumocystis carinii interaction. Furthermore, we isolated separate populations of cyst and trophic forms of P. carinii, which were then applied to the lung epithelial cells. Differential expression of genes involved in various cellular functions dependent on the specific P. carinii life form in contact with the A549 cell were identified. The reliability of our data was further confirmed by Northern blot analysis on a number of selected up or down regulated transcripts. The transcriptional response to P. carinii was dominated by cytokines, apoptotic, and anti-apoptotic related genes. These results reveal several previously unknown effects of P. carinii on the lung epithelial cell and provide insight into the complex interactions of host and pathogen. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Theodore J Kottom
- Thoracic Diseases Research Unit, Departments of Medicine and Biochemistry, Mayo Clinic College of Medicine, Rochester, Minnesota, 55905, USA
| | - Eva M Carmona
- Thoracic Diseases Research Unit, Departments of Medicine and Biochemistry, Mayo Clinic College of Medicine, Rochester, Minnesota, 55905, USA
| | - Andrew H Limper
- Thoracic Diseases Research Unit, Departments of Medicine and Biochemistry, Mayo Clinic College of Medicine, Rochester, Minnesota, 55905, USA
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Neonatal LTβR signaling is required for the accumulation of eosinophils in the inflamed adult mesenteric lymph node. Mucosal Immunol 2022; 15:418-427. [PMID: 35181738 DOI: 10.1038/s41385-022-00493-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 01/15/2022] [Accepted: 01/29/2022] [Indexed: 02/04/2023]
Abstract
Although eosinophils are important contributors to mucosal immune responses, mechanisms that regulate their accumulation in mucosal-associated lymphoid tissues remain ill-defined. Combining bone marrow chimeras and pharmacological inhibition approaches, here we find that lymphotoxin-beta receptor (LTβR) signaling during the neonatal period is required for the accumulation of eosinophils in the mesenteric lymph nodes (MLN) during an enteric viral infection in adult male and female mice. We demonstrate that MLN stromal cells express genes that are important for eosinophil migration and survival, such as Ccl-11 (eotaxin-1), Ccl7, Ccl9, and Cxcl2, and that expression of most of these genes is downregulated as a consequence of neonatal LTβR blockade. We also find that neonatal LTβR signaling is required for the generation of a rotavirus-specific IgA antibody response in the adult MLN, but eosinophils are dispensable for this response. Collectively, our studies reveal a role for neonatal LTβR signaling in regulating eosinophil numbers in the adult MLN.
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30
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Ko S, Lim J, Hong S. Functional characterization of a novel tumor necrosis factor gene (TNF-New) in rock bream (Oplegnathus fasciatus). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 127:104269. [PMID: 34600021 DOI: 10.1016/j.dci.2021.104269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/03/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
The novel tumor necrosis factor (TNF-New or TNFN) gene has been identified only in teleost such as zebrafish, medaka (Oryzias latipes), fugu (Takifugu rubripes), and rainbow trout (Oncorhynchus mykiss). In this study, a putative TNFN gene in rock bream (named RB-TNFN) was cloned and its functional expression in the immune system was analyzed. Although it was previously reported to share a high degree of homology with mammalian lymphotoxin (LT)-β, in silico analysis revealed that RB-TNFN differed slightly from mammalian LT-β in its genomic structure, phylogenetic relationship, and predicted protein tertiary structure, whereas the genomic location of TNFN (immediately behind TNF-α) was the same as that of LT-β. In healthy rock bream, RB-TNFN gene expression was the highest in the liver and the lowest in the head kidney. In vitro, it was significantly upregulated in head kidney cells following polyinosinic:polycytidylic acid, concanavalin A, phytohemagglutinin, or calcium ionophore (CI) stimulation and in spleen cells by lipopolysaccharide (LPS), CI, and rock bream iridovirus (RBIV). In vivo, it was upregulated in the spleen, liver, and gut on day 1 and in the blood on day 3 following LPS injection, and in the blood, head kidney, and liver following RBIV vaccination. Post-RBIV infection, the vaccinated group showed a significantly higher TNFN gene expression in the head kidney and blood than the unvaccinated group. Treatment with recombinant TNFN protein (RB-rTNFN) resulted in significantly upregulated interleukin-1β expression in the head kidney, spleen, blood, liver, and peritoneal cells. It also enhanced IL-8 gene expression in the head kidney, blood, and peritoneal cells, and interferon γ gene expression in the gut and gills on day 1. TNFN and cyclo-oxygenase-2 gene expression was upregulated in peritoneal cells on day 3. Flow cytometry analysis revealed a significant increase in the peritoneal lymphocyte population after the intraperitoneal (i.p.) injection of RB-rTNFN. These results suggest that RB-TNFN mediated innate and adaptive immunity in rock bream.
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Affiliation(s)
- Sungjae Ko
- Department of Marine Biotechnology, Gangneung-Wonju National University, Gangneung, South Korea
| | - Jongwon Lim
- Department of Marine Biotechnology, Gangneung-Wonju National University, Gangneung, South Korea
| | - Suhee Hong
- East Coast Research institute of Life Science, Gangneung-Wonju National University, South Korea.
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Chen ST, Park MD, Del Valle DM, Buckup M, Tabachnikova A, Simons NW, Mouskas K, Lee B, Geanon D, D’Souza D, Dawson T, Marvin R, Nie K, Thompson RC, Zhao Z, LeBerichel J, Chang C, Jamal H, Chaddha U, Mathews K, Acquah S, Brown SA, Reiss M, Harkin T, Feldmann M, Powell CA, Hook JL, Kim-Schulze S, Rahman AH, Brown BD, Beckmann ND, Gnjatic S, Kenigsberg E, Charney AW, Merad M. Shift of lung macrophage composition is associated with COVID-19 disease severity and recovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.01.11.475918. [PMID: 35043110 PMCID: PMC8764718 DOI: 10.1101/2022.01.11.475918] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Though it has been 2 years since the start of the Coronavirus Disease 19 (COVID-19) pandemic, COVID-19 continues to be a worldwide health crisis. Despite the development of preventive vaccines, very little progress has been made to identify curative therapies to treat COVID-19 and other inflammatory diseases which remain a major unmet need in medicine. Our study sought to identify drivers of disease severity and death to develop tailored immunotherapy strategies to halt disease progression. Here we assembled the Mount Sinai COVID-19 Biobank which was comprised of ~600 hospitalized patients followed longitudinally during the peak of the pandemic. Moderate disease and survival were associated with a stronger antigen (Ag) presentation and effector T cell signature, while severe disease and death were associated with an altered Ag presentation signature, increased numbers of circulating inflammatory, immature myeloid cells, and extrafollicular activated B cells associated with autoantibody formation. Strikingly, we found that in severe COVID-19 patients, lung tissue resident alveolar macrophages (AM) were not only severely depleted, but also had an altered Ag presentation signature, and were replaced by inflammatory monocytes and monocyte-derived macrophages (MoMΦ). Notably, the size of the AM pool correlated with recovery or death, while AM loss and functionality were restored in patients that recovered. These data therefore suggest that local and systemic myeloid cell dysregulation is a driver of COVID-19 severity and that modulation of AM numbers and functionality in the lung may be a viable therapeutic strategy for the treatment of critical lung inflammatory illnesses.
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Affiliation(s)
- Steven T. Chen
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Matthew D. Park
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Diane Marie Del Valle
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Mark Buckup
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alexandra Tabachnikova
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nicole W. Simons
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Konstantinos Mouskas
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Brian Lee
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Daniel Geanon
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Darwin D’Souza
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Travis Dawson
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Robert Marvin
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kai Nie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ryan C. Thompson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, 10029, USA
| | - Zhen Zhao
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jessica LeBerichel
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Christie Chang
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hajra Jamal
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Udit Chaddha
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kusum Mathews
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Samuel Acquah
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Stacey-Ann Brown
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Michelle Reiss
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Timothy Harkin
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Marc Feldmann
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK
| | - Charles A. Powell
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jaime L. Hook
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Seunghee Kim-Schulze
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Adeeb H. Rahman
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Immunai, New York, NY, USA
| | - Brian D. Brown
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, 10029, USA
| | | | - Noam D. Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, 10029, USA
| | - Sacha Gnjatic
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ephraim Kenigsberg
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, 10029, USA
| | - Alexander W. Charney
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Miriam Merad
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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Shi Y. PLAN B for immunotherapy: Promoting and leveraging anti-tumor B cell immunity. J Control Release 2021; 339:156-163. [PMID: 34563591 DOI: 10.1016/j.jconrel.2021.09.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/19/2021] [Accepted: 09/21/2021] [Indexed: 12/19/2022]
Abstract
Current immuno-oncology primarily focuses on adaptive cellular immunity mediated by T lymphocytes. The other important lymphocytes, B cells, are largely ignored in cancer immunotherapy. B cells are generally considered to be responsible for humoral immune response to viral and bacterial infections. The role of B cells in cancer immunity has long been under debate. Recently, increasing evidence from both preclinical and clinical research has shown that B cells can also induce potent anti-cancer immunity, via humoral and cellular immune responses. Yet it is unclear how to efficiently integrate B cell immunity in cancer immunotherapy. In the current perspective, anti-tumor immunity of B cells is discussed regarding antibody production, antigen presentation, cytokine release and contribution to intratumoral tertiary lymphoid structures. Afterwards, immunosuppressive regulatory phenotypes of B cells are summarized. Furthermore, strategies to activate and modulate B cells using nanomedicines and biomaterials are discussed. This article provides a unique perspective on "PLAN B" (promoting and leveraging anti-tumor B cell immunity) using nanomedicines and biomaterials for cancer immunotherapy. This is envisaged to form a new research direction with the potential to reach the next breakthrough in immunotherapy.
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Affiliation(s)
- Yang Shi
- Institute for Experimental Molecular Imaging, Uniklinik RWTH Aachen and Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Aachen 52074, Germany.
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33
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Alvarez-de Miranda FJ, Alonso-Sánchez I, Alcamí A, Hernaez B. TNF Decoy Receptors Encoded by Poxviruses. Pathogens 2021; 10:pathogens10081065. [PMID: 34451529 PMCID: PMC8401223 DOI: 10.3390/pathogens10081065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/29/2021] [Accepted: 08/18/2021] [Indexed: 12/16/2022] Open
Abstract
Tumour necrosis factor (TNF) is an inflammatory cytokine produced in response to viral infections that promotes the recruitment and activation of leukocytes to sites of infection. This TNF-based host response is essential to limit virus spreading, thus poxviruses have evolutionarily adopted diverse molecular mechanisms to counteract TNF antiviral action. These include the expression of poxvirus-encoded soluble receptors or proteins able to bind and neutralize TNF and other members of the TNF ligand superfamily, acting as decoy receptors. This article reviews in detail the various TNF decoy receptors identified to date in the genomes from different poxvirus species, with a special focus on their impact on poxvirus pathogenesis and their potential use as therapeutic molecules.
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Gershony LC, Belanger JM, Hytönen MK, Lohi H, Oberbauer AM. Whole Genome Sequencing Reveals Multiple Linked Genetic Variants on Canine Chromosome 12 Associated with Risk for Symmetrical Lupoid Onychodystrophy (SLO) in the Bearded Collie. Genes (Basel) 2021; 12:1265. [PMID: 34440439 PMCID: PMC8394396 DOI: 10.3390/genes12081265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/17/2021] [Accepted: 08/17/2021] [Indexed: 01/16/2023] Open
Abstract
In dogs, symmetrical lupoid onychodystrophy (SLO) results in nail loss and an abnormal regrowth of the claws. In Bearded Collies, an autoimmune nature has been suggested because certain dog leukocyte antigen (DLA) class II haplotypes are associated with the condition. A genome-wide association study of the Bearded Collie revealed two regions of association that conferred risk for disease: one on canine chromosome (CFA) 12 that encompasses the DLA genes, and one on CFA17. Case-control association was employed on whole genome sequencing data to uncover putative causative variants in SLO within the CFA12 and CFA17 associated regions. Genotype imputation was then employed to refine variants of interest. Although no SLO-associated protein-coding variants were identified on CFA17, multiple variants, many with predicted damaging effects, were identified within potential candidate genes on CFA12. Furthermore, many potentially damaging alleles were fully correlated with the presence of DLA class II risk haplotypes for SLO, suggesting that the variants may reflect DLA class II haplotype association with disease or vice versa. Strong linkage disequilibrium in the region precluded the ability to isolate and assess the individual or combined effect of variants on disease development. Nonetheless, all were predictive of risk for SLO and, with judicious assessment, their application in selective breeding may prove useful to reduce the incidence of SLO in the breed.
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Affiliation(s)
- Liza C. Gershony
- Department on Animal Science, University of California, Davis, CA 95616, USA; (L.C.G.); (J.M.B.)
| | - Janelle M. Belanger
- Department on Animal Science, University of California, Davis, CA 95616, USA; (L.C.G.); (J.M.B.)
| | - Marjo K. Hytönen
- Department of Medical and Clinical Genetics, University of Helsinki, 00014 Helsinki, Finland; (M.K.H.); (H.L.)
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland
- Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Hannes Lohi
- Department of Medical and Clinical Genetics, University of Helsinki, 00014 Helsinki, Finland; (M.K.H.); (H.L.)
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland
- Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Anita M. Oberbauer
- Department on Animal Science, University of California, Davis, CA 95616, USA; (L.C.G.); (J.M.B.)
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35
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Borelli A, Irla M. Lymphotoxin: from the physiology to the regeneration of the thymic function. Cell Death Differ 2021; 28:2305-2314. [PMID: 34290396 PMCID: PMC8329281 DOI: 10.1038/s41418-021-00834-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 01/31/2023] Open
Abstract
The members of the Tumor Necrosis Factor (TNF) superfamily, the ligand lymphotoxin α1β2 (LTα1β2) and its unique receptor lymphotoxin β receptor (LTβR), play a pivotal role in the establishment and regulation of the immune system by allowing a tight communication between lymphocytes and stromal cells. Recent advances using transgenic mice harboring a specific deletion of the Ltbr gene in distinct stromal cells have revealed important roles for LTβR signaling in the thymic function that ensures the generation of a diverse and self-tolerant T-cell repertoire. In this review, we summarize our current knowledge on this signaling axis in the thymic homing of lymphoid progenitors and peripheral antigen-presenting cells, the trafficking and egress of thymocytes, the differentiation of medullary thymic epithelial cells, and the establishment of central tolerance. We also highlight the importance of LTα1β2/LTβR axis in controlling the recovery of the thymic function after myeloablative conditioning regimen, opening novel perspectives in regenerative medicine.
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Affiliation(s)
- Alexia Borelli
- grid.417850.f0000 0004 0639 5277Aix-Marseille University, CNRS, INSERM, CIML, Centre d’Immunologie de Marseille-Luminy, Marseille, France
| | - Magali Irla
- grid.417850.f0000 0004 0639 5277Aix-Marseille University, CNRS, INSERM, CIML, Centre d’Immunologie de Marseille-Luminy, Marseille, France
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36
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Bieberich F, Vazquez-Lombardi R, Yermanos A, Ehling RA, Mason DM, Wagner B, Kapetanovic E, Di Roberto RB, Weber CR, Savic M, Rudolf F, Reddy ST. A Single-Cell Atlas of Lymphocyte Adaptive Immune Repertoires and Transcriptomes Reveals Age-Related Differences in Convalescent COVID-19 Patients. Front Immunol 2021; 12:701085. [PMID: 34322127 PMCID: PMC8312723 DOI: 10.3389/fimmu.2021.701085] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/24/2021] [Indexed: 01/23/2023] Open
Abstract
COVID-19 disease outcome is highly dependent on adaptive immunity from T and B lymphocytes, which play a critical role in the control, clearance and long-term protection against SARS-CoV-2. To date, there is limited knowledge on the composition of the T and B cell immune receptor repertoires [T cell receptors (TCRs) and B cell receptors (BCRs)] and transcriptomes in convalescent COVID-19 patients of different age groups. Here, we utilize single-cell sequencing (scSeq) of lymphocyte immune repertoires and transcriptomes to quantitatively profile the adaptive immune response in COVID-19 patients of varying age. We discovered highly expanded T and B cells in multiple patients, with the most expanded clonotypes coming from the effector CD8+ T cell population. Highly expanded CD8+ and CD4+ T cell clones show elevated markers of cytotoxicity (CD8: PRF1, GZMH, GNLY; CD4: GZMA), whereas clonally expanded B cells show markers of transition into the plasma cell state and activation across patients. By comparing young and old convalescent COVID-19 patients (mean ages = 31 and 66.8 years, respectively), we found that clonally expanded B cells in young patients were predominantly of the IgA isotype and their BCRs had incurred higher levels of somatic hypermutation than elderly patients. In conclusion, our scSeq analysis defines the adaptive immune repertoire and transcriptome in convalescent COVID-19 patients and shows important age-related differences implicated in immunity against SARS-CoV-2.
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Affiliation(s)
- Florian Bieberich
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Alexander Yermanos
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Institute of Microbiology and Immunology, Department of Biology, ETH Zurich, Zurich, Switzerland.,Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland.,Botnar Research Centre for Child Health, Basel, Switzerland
| | - Roy A Ehling
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Derek M Mason
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,deepCDR Biologics AG, Basel, Switzerland
| | - Bastian Wagner
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Edo Kapetanovic
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Cédric R Weber
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,deepCDR Biologics AG, Basel, Switzerland
| | - Miodrag Savic
- Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland.,Department of Surgery, Oral and Cranio-Maxillofacial Surgery, University Hospital Basel, Basel, Switzerland.,Department of Health, Economics and Health Directorate, Canton Basel-Landschaft, Switzerland
| | - Fabian Rudolf
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Botnar Research Centre for Child Health, Basel, Switzerland
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37
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Chawla M, Mukherjee T, Deka A, Chatterjee B, Sarkar UA, Singh AK, Kedia S, Lum J, Dhillon MK, Banoth B, Biswas SK, Ahuja V, Basak S. An epithelial Nfkb2 pathway exacerbates intestinal inflammation by supplementing latent RelA dimers to the canonical NF-κB module. Proc Natl Acad Sci U S A 2021; 118:e2024828118. [PMID: 34155144 PMCID: PMC8237674 DOI: 10.1073/pnas.2024828118] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Aberrant inflammation, such as that associated with inflammatory bowel disease (IBD), is fueled by the inordinate activity of RelA/NF-κB factors. As such, the canonical NF-κB module mediates controlled nuclear activation of RelA dimers from the latent cytoplasmic complexes. What provokes pathological RelA activity in the colitogenic gut remains unclear. The noncanonical NF-κB pathway typically promotes immune organogenesis involving Nfkb2 gene products. Because NF-κB pathways are intertwined, we asked whether noncanonical signaling aggravated inflammatory RelA activity. Our investigation revealed frequent engagement of the noncanonical pathway in human IBD. In a mouse model of experimental colitis, we established that Nfkb2-mediated regulations escalated the RelA-driven proinflammatory gene response in intestinal epithelial cells, exacerbating the infiltration of inflammatory cells and colon pathologies. Our mechanistic studies clarified that cell-autonomous Nfkb2 signaling supplemented latent NF-κB dimers, leading to a hyperactive canonical RelA response in the inflamed colon. In sum, the regulation of latent NF-κB dimers appears to link noncanonical Nfkb2 signaling to RelA-driven inflammatory pathologies and may provide for therapeutic targets.
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Affiliation(s)
- Meenakshi Chawla
- Systems Immunology Laboratory, National Institute of Immunology, New Delhi 110067, India
| | - Tapas Mukherjee
- Systems Immunology Laboratory, National Institute of Immunology, New Delhi 110067, India
| | - Alvina Deka
- Systems Immunology Laboratory, National Institute of Immunology, New Delhi 110067, India
| | - Budhaditya Chatterjee
- Systems Immunology Laboratory, National Institute of Immunology, New Delhi 110067, India
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Uday Aditya Sarkar
- Systems Immunology Laboratory, National Institute of Immunology, New Delhi 110067, India
| | - Amit K Singh
- Department of Gastroenterology, All India Institute of Medical Science, New Delhi 110029, India
| | - Saurabh Kedia
- Department of Gastroenterology, All India Institute of Medical Science, New Delhi 110029, India
| | - Josephine Lum
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore 138632
| | - Manprit Kaur Dhillon
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore 138632
| | - Balaji Banoth
- Systems Immunology Laboratory, National Institute of Immunology, New Delhi 110067, India
| | - Subhra K Biswas
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore 138632
| | - Vineet Ahuja
- Department of Gastroenterology, All India Institute of Medical Science, New Delhi 110029, India
| | - Soumen Basak
- Systems Immunology Laboratory, National Institute of Immunology, New Delhi 110067, India;
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38
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Filderman JN, Appleman M, Chelvanambi M, Taylor JL, Storkus WJ. STINGing the Tumor Microenvironment to Promote Therapeutic Tertiary Lymphoid Structure Development. Front Immunol 2021; 12:690105. [PMID: 34054879 PMCID: PMC8155498 DOI: 10.3389/fimmu.2021.690105] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 04/30/2021] [Indexed: 12/11/2022] Open
Abstract
Tertiary lymphoid structures (TLS), also known as ectopic lymphoid structures (ELS) or tertiary lymphoid organs (TLO), represent a unique subset of lymphoid tissues noted for their architectural similarity to lymph nodes, but which conditionally form in peripheral tissues in a milieu of sustained inflammation. TLS serve as regional sites for induction and expansion of the host B and T cell repertoires via an operational paradigm involving mature dendritic cells (DC) and specialized endothelial cells (i.e. high endothelial venules; HEV) in a process directed by TLS-associated cytokines and chemokines. Recent clinical correlations have been reported for the presence of TLS within tumor biopsies with overall patient survival and responsiveness to interventional immunotherapy. Hence, therapeutic strategies to conditionally reinforce TLS formation within the tumor microenvironment (TME) via the targeting of DC, vascular endothelial cells (VEC) and local cytokine/chemokine profiles are actively being developed and tested in translational tumor models and early phase clinical trials. In this regard, a subset of agents that promote tumor vascular normalization (VN) have been observed to coordinately support the development of a pro-inflammatory TME, maturation of DC and VEC, local production of TLS-inducing cytokines and chemokines, and therapeutic TLS formation. This mini-review will focus on STING agonists, which were originally developed as anti-angiogenic agents, but which have recently been shown to be effective in promoting VN and TLS formation within the therapeutic TME. Future application of these drugs in combination immunotherapy approaches for greater therapeutic efficacy is further discussed.
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Affiliation(s)
- Jessica N Filderman
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Mark Appleman
- Department of Dermatology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Manoj Chelvanambi
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Jennifer L Taylor
- Department of Dermatology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Walter J Storkus
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.,Department of Dermatology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.,Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.,Department of Bioengineering, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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39
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Hendriks A, Mnich ME, Clemente B, Cruz AR, Tavarini S, Bagnoli F, Soldaini E. Staphylococcus aureus-Specific Tissue-Resident Memory CD4 + T Cells Are Abundant in Healthy Human Skin. Front Immunol 2021; 12:642711. [PMID: 33796109 PMCID: PMC8008074 DOI: 10.3389/fimmu.2021.642711] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/18/2021] [Indexed: 12/12/2022] Open
Abstract
The skin is an immunocompetent tissue that harbors several kinds of immune cells and a plethora of commensal microbes constituting the skin microbiome. Staphylococcus aureus is a prominent skin pathogen that colonizes a large proportion of the human population. We currently have an incomplete understanding of the correlates of protection against S. aureus infection, however genetic and experimental evidence has shown that CD4+ T cells play a key role in orchestrating a protective anti-S. aureus immune response. A high S. aureus-specific memory CD4+ T cell response has been reported in the blood of healthy subjects. Since T cells are more abundant in the skin than in blood, we hypothesized that S. aureus-specific CD4+ T cells could be present in the skin of healthy individuals. Indeed, we observed proliferation of tissue-resident memory CD4+ T cells and production of IL-17A, IL-22, IFN-γ and TNF-β by cells isolated from abdominal skin explants in response to heat-killed S. aureus. Remarkably, these cytokines were produced also during an ex vivo epicutaneous S. aureus infection of human skin explants. These findings highlight the importance of tissue-resident memory CD4+ T cells present at barrier sites such as the skin, a primary entry site for S. aureus. Further phenotypical and functional characterization of these cells will ultimately aid in the development of novel vaccine strategies against this elusive pathogen.
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Affiliation(s)
- Astrid Hendriks
- GSK, Siena, Italy.,Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Malgorzata Ewa Mnich
- GSK, Siena, Italy.,Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | | | - Ana Rita Cruz
- GSK, Siena, Italy.,Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
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40
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Bi S, Liu R, He L, Li J, Gu J. Bioinformatics analysis of common key genes and pathways of intracranial, abdominal, and thoracic aneurysms. BMC Cardiovasc Disord 2021; 21:14. [PMID: 33407182 PMCID: PMC7788746 DOI: 10.1186/s12872-020-01838-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 12/18/2020] [Indexed: 02/08/2023] Open
Abstract
Background Aneurysm is a severe and fatal disease. This study aims to comprehensively identify the highly conservative co-expression modules and hub genes in the abdominal aortic aneurysm (AAA), thoracic aortic aneurysm (TAA) and intracranial aneurysm (ICA) and facilitate the discovery of pathogenesis for aneurysm. Methods GSE57691, GSE122897, and GSE5180 microarray datasets were downloaded from the Gene Expression Omnibus database. We selected highly conservative modules using weighted gene co‑expression network analysis before performing the Gene Ontology, Kyoto Encyclopedia of Genes and Genomes pathway and Reactome enrichment analysis. The protein–protein interaction (PPI) network and the miRNA-hub genes network were constructed. Furtherly, we validated the preservation of hub genes in three other datasets. Results Two modules with 193 genes and 159 genes were identified as well preserved in AAA, TAA, and ICA. The enrichment analysis identified that these genes were involved in several biological processes such as positive regulation of cytosolic calcium ion concentration, hemostasis, and regulation of secretion by cells. Ten highly connected PPI networks were constructed, and 55 hub genes were identified. In the miRNA-hub genes network, CCR7 was the most connected gene, followed by TNF and CXCR4. The most connected miRNAs were hsa-mir-26b-5p and hsa-mir-335-5p. The hub gene module was proved to be preserved in all three datasets. Conclusions Our study highlighted and validated two highly conservative co-expression modules and miRNA-hub genes network in three kinds of aneurysms, which may promote understanding of the aneurysm and provide potential therapeutic targets and biomarkers of aneurysm.
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Affiliation(s)
- Siwei Bi
- West China School of Medicine, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Ruiqi Liu
- Department of Burn and Plastic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Linfeng He
- West China School of Medicine, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Jingyi Li
- West China School of Medicine, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Jun Gu
- Department of Cardiovascular Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China.
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41
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Jasenosky LD, Nambu A, Tsytsykova AV, Ranjbar S, Haridas V, Kruidenier L, Tough DF, Goldfeld AE. Identification of a Distal Locus Enhancer Element That Controls Cell Type-Specific TNF and LTA Gene Expression in Human T Cells. THE JOURNAL OF IMMUNOLOGY 2020; 205:2479-2488. [PMID: 32978279 DOI: 10.4049/jimmunol.1901311] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 08/24/2020] [Indexed: 12/16/2022]
Abstract
The human TNF/LT locus genes TNF, LTA, and LTB are expressed in a cell type-specific manner. In this study, we show that a highly conserved NFAT binding site within the distal noncoding element hHS-8 coordinately controls TNF and LTA gene expression in human T cells. Upon activation of primary human CD4+ T cells, hHS-8 and the TNF and LTA promoters display increased H3K27 acetylation and nuclease sensitivity and coordinate induction of TNF, LTA, and hHS-8 enhancer RNA transcription occurs. Functional analyses using CRISPR/dead(d)Cas9 targeting of the hHS-8-NFAT site in the human T cell line CEM demonstrate significant reduction of TNF and LTA mRNA synthesis and of RNA polymerase II recruitment to their promoters. These studies elucidate how a distal element regulates the inducible cell type-specific gene expression program of the human TNF/LT locus and provide an approach for modulation of TNF and LTA transcription in human disease using CRISPR/dCas9.
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Affiliation(s)
- Luke D Jasenosky
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
| | - Aya Nambu
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
| | - Alla V Tsytsykova
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115.,Program in Hematology, Boston Children's Hospital, Boston, MA 02115
| | - Shahin Ranjbar
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
| | - Viraga Haridas
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
| | | | - David F Tough
- Adaptive Immunity Research Unit, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage SG1 2NY, United Kingdom
| | - Anne E Goldfeld
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115;
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42
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Zhang H, Madi A, Yosef N, Chihara N, Awasthi A, Pot C, Lambden C, Srivastava A, Burkett PR, Nyman J, Christian E, Etminan Y, Lee A, Stroh H, Xia J, Karwacz K, Thakore PI, Acharya N, Schnell A, Wang C, Apetoh L, Rozenblatt-Rosen O, Anderson AC, Regev A, Kuchroo VK. An IL-27-Driven Transcriptional Network Identifies Regulators of IL-10 Expression across T Helper Cell Subsets. Cell Rep 2020; 33:108433. [PMID: 33238123 PMCID: PMC7771052 DOI: 10.1016/j.celrep.2020.108433] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 07/14/2020] [Accepted: 11/04/2020] [Indexed: 12/16/2022] Open
Abstract
Interleukin-27 (IL-27) is an immunoregulatory cytokine that suppresses inflammation through multiple mechanisms, including induction of IL-10, but the transcriptional network mediating its diverse functions remains unclear. Combining temporal RNA profiling with computational algorithms, we predict 79 transcription factors induced by IL-27 in T cells. We validate 11 known and discover 5 positive (Cebpb, Fosl2, Tbx21, Hlx, and Atf3) and 2 negative (Irf9 and Irf8) Il10 regulators, generating an experimentally refined regulatory network for Il10. We report two central regulators, Prdm1 and Maf, that cooperatively drive the expression of signature genes induced by IL-27 in type 1 regulatory T cells, mediate IL-10 expression in all T helper cells, and determine the regulatory phenotype of colonic Foxp3+ regulatory T cells. Prdm1/Maf double-knockout mice develop spontaneous colitis, phenocopying ll10-deficient mice. Our work provides insights into IL-27-driven transcriptional networks and identifies two shared Il10 regulators that orchestrate immunoregulatory programs across T helper cell subsets. Zhang et al. construct a transcriptional network for IL-27-mediated Il10 production in CD4 T cells, characterize the function of 16 Il10 regulators, and uncover the role of two transcription factors, Prdm1 and Maf, in driving Il10 production in all T helper cells and in maintaining immune homeostasis in the colon.
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Affiliation(s)
- Huiyuan Zhang
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Asaf Madi
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA; Department of Pathology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Nir Yosef
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA; Department of Electrical Engineering and Computer Science and Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Norio Chihara
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA; Division of Neurology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Amit Awasthi
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA; Center for Human Microbial Ecology, Translational Health Science and Technology Institute(an autonomous institute of the Department of Biotechnology, Government of India), NCR Biotech Science Cluster, Faridabad, India
| | - Caroline Pot
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA; Laboratories of Neuroimmunology, Division of Neurology and Neuroscience Research Center, Department of Clinical Neurosciences, Lausanne University Hospital, Lausanne, Switzerland
| | - Conner Lambden
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Patrick R Burkett
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA; Biogen, 300 Binney St., Cambridge, MA, USA
| | - Jackson Nyman
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Elena Christian
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yasaman Etminan
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Annika Lee
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Helene Stroh
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Junrong Xia
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Katarzyna Karwacz
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA; Regeneron Pharmaceuticals, 777 Old Saw Mill River Road, Tarrytown, NY, USA
| | - Pratiksha I Thakore
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nandini Acharya
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Alexandra Schnell
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Chao Wang
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Lionel Apetoh
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA; INSERM, U1231, Dijon, France
| | | | - Ana C Anderson
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Department of Biology, Koch Institute and Ludwig Center, Massachusetts Institute of Technology, Cambridge, MA, USA; Genentech, 1 DNA Way, South San Francisco, CA, USA.
| | - Vijay K Kuchroo
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Caruso FP, Garofano L, D'Angelo F, Yu K, Tang F, Yuan J, Zhang J, Cerulo L, Pagnotta SM, Bedognetti D, Sims PA, Suvà M, Su XD, Lasorella A, Iavarone A, Ceccarelli M. A map of tumor-host interactions in glioma at single-cell resolution. Gigascience 2020; 9:giaa109. [PMID: 33155039 PMCID: PMC7645027 DOI: 10.1093/gigascience/giaa109] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 08/08/2020] [Accepted: 09/17/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Single-cell RNA sequencing is the reference technique for characterizing the heterogeneity of the tumor microenvironment. The composition of the various cell types making up the microenvironment can significantly affect the way in which the immune system activates cancer rejection mechanisms. Understanding the cross-talk signals between immune cells and cancer cells is of fundamental importance for the identification of immuno-oncology therapeutic targets. RESULTS We present a novel method, single-cell Tumor-Host Interaction tool (scTHI), to identify significantly activated ligand-receptor interactions across clusters of cells from single-cell RNA sequencing data. We apply our approach to uncover the ligand-receptor interactions in glioma using 6 publicly available human glioma datasets encompassing 57,060 gene expression profiles from 71 patients. By leveraging this large-scale collection we show that unexpected cross-talk partners are highly conserved across different datasets in the majority of the tumor samples. This suggests that shared cross-talk mechanisms exist in glioma. CONCLUSIONS Our results provide a complete map of the active tumor-host interaction pairs in glioma that can be therapeutically exploited to reduce the immunosuppressive action of the microenvironment in brain tumor.
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Affiliation(s)
- Francesca Pia Caruso
- Department of Electrical Engineering and Information Technology (DIETI), University of Naples “Federico II”, Via Claudio 21, 80128 Naples, Italy
- Bioinformatics Lab, BIOGEM, Via Camporeale, 83031 Ariano Irpino, Italy
| | - Luciano Garofano
- Department of Electrical Engineering and Information Technology (DIETI), University of Naples “Federico II”, Via Claudio 21, 80128 Naples, Italy
- Institute for Cancer Genetics, Columbia University, 1130 St Nicholas Ave, New York, NY 10032, USA
| | - Fulvio D'Angelo
- Bioinformatics Lab, BIOGEM, Via Camporeale, 83031 Ariano Irpino, Italy
- Institute for Cancer Genetics, Columbia University, 1130 St Nicholas Ave, New York, NY 10032, USA
| | - Kai Yu
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, 5 Yiheyuan Rd, Haidian District, 100871 Beijing, China
| | - Fuchou Tang
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, 5 Yiheyuan Rd, Haidian District, 100871 Beijing, China
| | - Jinzhou Yuan
- Department of Science and Technologies, Università degli Studi del Sannio, Via de Sanctis, 82100 Benevento, Italy
- Cancer Program, Sidra Medicine, Al Luqta Street, Zone 52, Education City, 26999, Doha Qatar
| | - Jing Zhang
- Institute for Cancer Genetics, Columbia University, 1130 St Nicholas Ave, New York, NY 10032, USA
| | - Luigi Cerulo
- Bioinformatics Lab, BIOGEM, Via Camporeale, 83031 Ariano Irpino, Italy
- Department of Science and Technologies, Università degli Studi del Sannio, Via de Sanctis, 82100 Benevento, Italy
| | - Stefano M Pagnotta
- Department of Science and Technologies, Università degli Studi del Sannio, Via de Sanctis, 82100 Benevento, Italy
| | - Davide Bedognetti
- Cancer Program, Sidra Medicine, Al Luqta Street, Zone 52, Education City, 26999, Doha Qatar
- Department of Internal Medicine and Medical Specialties (Di.M.I.), University of Genoa, Viale Benedetto XV 10, 16132 Genoa, Italy
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, 1130 St Nicholas Ave, New York , NY 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, 1130 St Nicholas Ave, New York, NY 10032, USA
| | - Mario Suvà
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, 55 Fruit St, Boston, MA 02114, USA
- Broad Institute of Harvard and MIT, 415 Main St, Cambridge, MA 02142, USA
| | - Xiao-Dong Su
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, 5 Yiheyuan Rd, Haidian District, 100871 Beijing, China
| | - Anna Lasorella
- Institute for Cancer Genetics, Columbia University, 1130 St Nicholas Ave, New York, NY 10032, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, 1130 St Nicholas Ave, New York , NY 10032 USA
| | - Antonio Iavarone
- Institute for Cancer Genetics, Columbia University, 1130 St Nicholas Ave, New York, NY 10032, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, 1130 St Nicholas Ave, New York , NY 10032 USA
- Department of Neurology, Columbia University Medical Center, 1130 St Nicholas Ave, New York, NY 10032, USA
| | - Michele Ceccarelli
- Department of Electrical Engineering and Information Technology (DIETI), University of Naples “Federico II”, Via Claudio 21, 80128 Naples, Italy
- Bioinformatics Lab, BIOGEM, Via Camporeale, 83031 Ariano Irpino, Italy
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Kempski J, Giannou AD, Riecken K, Zhao L, Steglich B, Lücke J, Garcia-Perez L, Karstens KF, Wöstemeier A, Nawrocki M, Pelczar P, Witkowski M, Nilsson S, Konczalla L, Shiri AM, Kempska J, Wahib R, Brockmann L, Huber P, Gnirck AC, Turner JE, Zazara DE, Arck PC, Stein A, Simon R, Daubmann A, Meiners J, Perez D, Strowig T, Koni P, Kruglov AA, Sauter G, Izbicki JR, Guse AH, Rösch T, Lohse AW, Flavell RA, Gagliani N, Huber S. IL22BP Mediates the Antitumor Effects of Lymphotoxin Against Colorectal Tumors in Mice and Humans. Gastroenterology 2020; 159:1417-1430.e3. [PMID: 32585307 PMCID: PMC7607422 DOI: 10.1053/j.gastro.2020.06.033] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 05/13/2020] [Accepted: 06/10/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS Unregulated activity of interleukin (IL) 22 promotes intestinal tumorigenesis in mice. IL22 binds the antagonist IL22 subunit alpha 2 (IL22RA2, also called IL22BP). We studied whether alterations in IL22BP contribute to colorectal carcinogenesis in humans and mice. METHODS We obtained tumor and nontumor tissues from patients with colorectal cancer (CRC) and measured levels of cytokines by quantitative polymerase chain reaction, flow cytometry, and immunohistochemistry. We measured levels of Il22bp messenger RNA in colon tissues from wild-type, Tnf-/-, Lta-/-, and Ltb-/- mice. Mice were given azoxymethane and dextran sodium sulfate to induce colitis and associated cancer or intracecal injections of MC38 tumor cells. Some mice were given inhibitors of lymphotoxin beta receptor (LTBR). Intestine tissues were analyzed by single-cell sequencing to identify cell sources of lymphotoxin. We performed immunohistochemistry analysis of colon tissue microarrays from patients with CRC (1475 tissue cores, contained tumor and nontumor tissues) and correlated levels of IL22BP with patient survival times. RESULTS Levels of IL22BP were decreased in human colorectal tumors, compared with nontumor tissues, and correlated with levels of lymphotoxin. LTBR signaling was required for expression of IL22BP in colon tissues of mice. Wild-type mice given LTBR inhibitors had an increased tumor burden in both models, but LTBR inhibitors did not increase tumor growth in Il22bp-/- mice. Lymphotoxin directly induced expression of IL22BP in cultured human monocyte-derived dendritic cells via activation of nuclear factor κB. Reduced levels of IL22BP in colorectal tumor tissues were associated with shorter survival times of patients with CRC. CONCLUSIONS Lymphotoxin signaling regulates expression of IL22BP in colon; levels of IL22BP are reduced in human colorectal tumors, associated with shorter survival times. LTBR signaling regulates expression of IL22BP in colon tumors in mice and cultured human dendritic cells. Patients with colorectal tumors that express low levels of IL22BP might benefit from treatment with an IL22 antagonist.
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Affiliation(s)
- Jan Kempski
- Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany,The Calcium Signaling Group, Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anastasios D. Giannou
- Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kristoffer Riecken
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lilan Zhao
- Department of General, Visceral, and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany,Department of General Thoracic Surgery, Fujian Provincial Hospital, Fujian Medical University, Fuzhou 350003, People’s Republic of China
| | - Babett Steglich
- Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jöran Lücke
- Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Laura Garcia-Perez
- Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Karl-Frederick Karstens
- Department of General, Visceral, and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna Wöstemeier
- Department of General, Visceral, and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mikolaj Nawrocki
- Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Penelope Pelczar
- Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mario Witkowski
- Institut für Mikrobiologie und Infektionsimmunologie, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Sven Nilsson
- II. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Leonie Konczalla
- Department of General, Visceral, and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ahmad Mustafa Shiri
- Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Joanna Kempska
- Department of Gynecology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ramez Wahib
- Department of General, Visceral, and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Leonie Brockmann
- Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Philipp Huber
- Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ann-Christin Gnirck
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jan-Eric Turner
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dimitra E. Zazara
- Laboratory for Experimental Feto-Maternal Medicine, Department of Obstetrics and Prenatal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Petra C. Arck
- Laboratory for Experimental Feto-Maternal Medicine, Department of Obstetrics and Prenatal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alexander Stein
- II. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anne Daubmann
- Department of Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jan Meiners
- Department of General, Visceral, and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Daniel Perez
- Department of General, Visceral, and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Till Strowig
- Helmholtz Center for Infection Research, Braunschweig, Germany
| | | | - Andrey A. Kruglov
- German Rheumatism Research Center, a Leibniz Institute, Berlin, Germany,Belozersky Institute of Physico-Chemical Biology and Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Guido Sauter
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jakob R. Izbicki
- Department of General, Visceral, and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andreas H. Guse
- The Calcium Signaling Group, Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Rösch
- Department of Interdisciplinary Endoscopy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ansgar W. Lohse
- Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Richard A. Flavell
- Department of Immunobiology, School of Medicine, Yale University, New Haven, Connecticut,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut
| | - Nicola Gagliani
- Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Department of General, Visceral, and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Samuel Huber
- Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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Król E, Noguera P, Shaw S, Costelloe E, Gajardo K, Valdenegro V, Bickerdike R, Douglas A, Martin SAM. Integration of Transcriptome, Gross Morphology and Histopathology in the Gill of Sea Farmed Atlantic Salmon ( Salmo salar): Lessons From Multi-Site Sampling. Front Genet 2020; 11:610. [PMID: 32636874 PMCID: PMC7316992 DOI: 10.3389/fgene.2020.00610] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 05/19/2020] [Indexed: 12/11/2022] Open
Abstract
The gill of teleost fish is a multifunctional organ involved in many physiological processes such as gas exchange, osmotic and ionic regulation, acid-base balance and excretion of nitrogenous waste. Due to its extensive interface with the environment, the gill plays a key role as a primary mucosal defense tissue against pathogens, as manifested by the presence of the gill-associated lymphoid tissue (GIALT). In recent years, the prevalence of multifactorial gill pathologies has increased significantly, causing substantial losses in Atlantic salmon aquaculture. The transition from healthy to unhealthy gill phenotypes and the progression of multifactorial gill pathologies, such as proliferative gill disease (PGD), proliferative gill inflammation (PGI) and complex gill disorder (CGD), are commonly characterized by epithelial hyperplasia, lamellar fusion and inflammation. Routine monitoring for PGD relies on visual inspection and non-invasive scoring of the gill tissue (gross morphology), coupled with histopathological examination of gill sections. To explore the underlying molecular events that are associated with the progression of PGD, we sampled Atlantic salmon from three different marine production sites in Scotland and examined the gill tissue at three different levels of organization: gross morphology with the use of PGD scores (macroscopic examination), whole transcriptome (gene expression by RNA-seq) and histopathology (microscopic examination). Our results strongly suggested that the changes in PGD scores of the gill tissue were not associated with the changes in gene expression or histopathology. In contrast, integration of the gill RNA-seq data with the gill histopathology enabled us to identify common gene expression patterns associated with multifactorial gill disease, independently from the origin of samples. We demonstrated that the gene expression patterns associated with multifactorial gill disease were dominated by two processes: a range of immune responses driven by pro-inflammatory cytokines and the events associated with tissue damage and repair, driven by caspases and angiogenin.
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Affiliation(s)
- Elżbieta Król
- School of Biological Sciences, Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Patricia Noguera
- Fish Health and Welfare, Marine Scotland Science, Aberdeen, United Kingdom
| | - Sophie Shaw
- Centre for Genome-Enabled Biology and Medicine, University of Aberdeen, Aberdeen, United Kingdom
| | - Eoin Costelloe
- School of Biological Sciences, Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | | | | | | | - Alex Douglas
- School of Biological Sciences, Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Samuel A. M. Martin
- School of Biological Sciences, Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
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46
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Heimroth RD, Casadei E, Salinas I. Molecular Drivers of Lymphocyte Organization in Vertebrate Mucosal Surfaces: Revisiting the TNF Superfamily Hypothesis. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2020; 204:2697-2711. [PMID: 32238457 PMCID: PMC7872792 DOI: 10.4049/jimmunol.1901059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 02/26/2020] [Indexed: 12/19/2022]
Abstract
The adaptive immune system of all jawed vertebrates relies on the presence of B and T cell lymphocytes that aggregate in specific body sites to form primary and secondary lymphoid structures. Secondary lymphoid organs include organized MALT (O-MALT) such as the tonsils and Peyer patches. O-MALT became progressively organized during vertebrate evolution, and the TNF superfamily of genes has been identified as essential for the formation and maintenance of O-MALT and other secondary and tertiary lymphoid structures in mammals. Yet, the molecular drivers of O-MALT structures found in ectotherms and birds remain essentially unknown. In this study, we provide evidence that TNFSFs, such as lymphotoxins, are likely not a universal mechanism to maintain O-MALT structures in adulthood of teleost fish, sarcopterygian fish, or birds. Although a role for TNFSF2 (TNF-α) cannot be ruled out, transcriptomics suggest that maintenance of O-MALT in nonmammalian vertebrates relies on expression of diverse genes with shared biological functions in neuronal signaling. Importantly, we identify that expression of many genes with olfactory function is a unique feature of mammalian Peyer patches but not the O-MALT of birds or ectotherms. These results provide a new view of O-MALT evolution in vertebrates and indicate that different genes with shared biological functions may have driven the formation of these lymphoid structures by a process of convergent evolution.
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Affiliation(s)
- Ryan D Heimroth
- Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM 87131; and
- Department of Biology, University of New Mexico, Albuquerque, NM 87131
| | - Elisa Casadei
- Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM 87131; and
- Department of Biology, University of New Mexico, Albuquerque, NM 87131
| | - Irene Salinas
- Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM 87131; and
- Department of Biology, University of New Mexico, Albuquerque, NM 87131
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Dalton B, Leppanen J, Campbell IC, Chung R, Breen G, Schmidt U, Himmerich H. A longitudinal analysis of cytokines in anorexia nervosa. Brain Behav Immun 2020; 85:88-95. [PMID: 31077775 DOI: 10.1016/j.bbi.2019.05.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/17/2019] [Accepted: 05/08/2019] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVE Inflammation has been proposed to have a pathophysiological role in anorexia nervosa (AN) and to contribute to the maintenance of the disorder. Longitudinal cytokine research in AN has focused on only a few pro-inflammatory cytokines. We assessed a broad range of cytokines over time in people undergoing specialised treatment for AN. METHOD We measured serum concentrations of 27 cytokines in people with AN (n = 23). Body mass index (BMI), eating disorder (ED) symptoms and general psychopathology were assessed and blood samples were collected within four weeks of the commencement of specialised ED treatment (baseline) and at 12- and 24-week follow-ups. RESULTS Both BMI and ED symptoms improved over the assessment period. Linear mixed models showed that log IL-6 decreased between baseline and week 12 assessments. By week 12, log IL-6 values were comparable to levels in healthy individuals. Log IL-7 increased from week 12 to week 24. DISCUSSION Initially elevated IL-6 serum concentrations appear to 'normalize' during the first 3-months of specialised treatment for AN and this co-occurs with improvements in ED symptoms. Therefore, IL-6 has the potential to be a state biomarker for AN.
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Affiliation(s)
- Bethan Dalton
- Section of Eating Disorders, Department of Psychological Medicine, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 8AF, UK.
| | - Jenni Leppanen
- Section of Eating Disorders, Department of Psychological Medicine, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 8AF, UK
| | - Iain C Campbell
- Section of Eating Disorders, Department of Psychological Medicine, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 8AF, UK
| | - Raymond Chung
- MRC Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 8AF, UK
| | - Gerome Breen
- MRC Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 8AF, UK; National Institute for Health Research Biomedical Research Centre for Mental Health, King's College London, UK
| | - Ulrike Schmidt
- Section of Eating Disorders, Department of Psychological Medicine, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 8AF, UK; South London and Maudsley NHS Foundation Trust, Bethlem Royal Hospital, Monks Orchard Road, Beckenham, Kent BR3 3BX, UK
| | - Hubertus Himmerich
- Section of Eating Disorders, Department of Psychological Medicine, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 8AF, UK; South London and Maudsley NHS Foundation Trust, Bethlem Royal Hospital, Monks Orchard Road, Beckenham, Kent BR3 3BX, UK
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Associations of lymphotoxin-a (LTA) rs909253 A/G gene polymorphism, plasma level and risk of ankylosing spondylitis in a Chinese Han population. Sci Rep 2020; 10:1412. [PMID: 31996699 PMCID: PMC6989688 DOI: 10.1038/s41598-020-57927-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 01/07/2020] [Indexed: 01/17/2023] Open
Abstract
Lymphotoxin-a (LTA) may be associated with the pathogenesis of inflammatory diseases. To assess the association of the LTA rs909253 A/G polymorphism with plasma level and risk of ankylosing spondylitis (AS) in a Chinese Han population. Genotyping and LTA plasma were tested by mass spectroscopy and enzyme-linked immunosorbent assay (ELISA), respectively. The results showed that the average plasma level of LTA in AS was significantly lower than in the controls (P = 0.000). Our results also indicated that LTA rs909253 A/G was associated with a decreased risk of AS (G vs. A: P = 0.014). Significant differences were also found between the rs909253 A/G genotype and down-regulated plasma level in AS patients, compared with controls. After stratification analysis, a decreased risk of AS was associated with the LTA rs909253 G allele (G vs. A) among female patients, younger patients (Yr. < 30), HLA-B27-positive patients. In addition, In conclusion, LTA rs909253 A/G genotype has a significant relationship with decreased susceptibility to AS.
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Hamzabegovic F, Goll JB, Hooper WF, Frey S, Gelber CE, Abate G. Flagellin adjuvanted F1/V subunit plague vaccine induces T cell and functional antibody responses with unique gene signatures. NPJ Vaccines 2020; 5:6. [PMID: 31993217 PMCID: PMC6978331 DOI: 10.1038/s41541-020-0156-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 12/30/2019] [Indexed: 12/13/2022] Open
Abstract
Yersinia pestis, the cause of plague, could be weaponized. Unfortunately, development of new vaccines is limited by lack of correlates of protection. We used pre- and post-vaccination sera and peripheral blood mononuclear cells from a flagellin adjuvanted F1/V vaccine trial to evaluate for protective markers. Here, we report for the first time in humans that inverse caspase-3 levels, which are measures of protective antibody, significantly increased by 29% and 75% on days 14 and 28 post-second vaccination, respectively. In addition, there were significant increases in T-cell responses on day 28 post-second vaccination. The strongest positive and negative correlations between protective antibody levels and gene expression signatures were identified for IFNG and ENSG00000225107 genes, respectively. Flagellin/F1/V subunit vaccine induced macrophage-protective antibody and significant CD4+ T-cell responses. Several genes associated with these responses were identified that could serve as potential correlates of protection.
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Affiliation(s)
- Fahreta Hamzabegovic
- Division of Infectious Diseases, Allergy and Immunology, Saint Louis University, Saint Louis, MO USA
| | | | | | - Sharon Frey
- Division of Infectious Diseases, Allergy and Immunology, Saint Louis University, Saint Louis, MO USA
| | | | - Getahun Abate
- Division of Infectious Diseases, Allergy and Immunology, Saint Louis University, Saint Louis, MO USA
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50
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Francipane MG, Han B, Lagasse E. Host Lymphotoxin-β Receptor Signaling Is Crucial for Angiogenesis of Metanephric Tissue Transplanted into Lymphoid Sites. THE AMERICAN JOURNAL OF PATHOLOGY 2020; 190:252-269. [PMID: 31585070 PMCID: PMC6943804 DOI: 10.1016/j.ajpath.2019.08.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 08/09/2019] [Accepted: 08/20/2019] [Indexed: 12/16/2022]
Abstract
The mouse lymph node (LN) can provide a niche to grow metanephric kidney to maturity. Here, we show that signaling through the lymphotoxin-β receptor (LTβR) is critical for kidney organogenesis both in the LN and the omentum. By transplanting kidney rudiments either in the LNs of mice undergoing LTβR antagonist treatment or in the omenta of Ltbr knockout (Ltbr-/-) mice, the host LTβR signals were found to be crucial for obtaining a well-vascularized kidney graft. Indeed, defective LTβR signaling correlated with decreased expression of endothelial and angiogenic markers in kidney grafts as well as structural alterations. Because the number of glomerular endothelial cells expressing the LTβR target nuclear factor κB-inducing kinase (NIK) decreased in the absence of a functional LTβR, it was speculated that an LTβR/NIK axis mediated the angiogenetic signals required for successful ectopic kidney organogenesis, given the established role of NIK in neovascularization. However, the transplantation of kidney rudiments in omenta of Nik-/- mice revealed that NIK is dispensable for ectopic kidney vascular integration and maturation. Finally, defective LTβR signaling impaired compensatory glomerular adaptation to renal mass reduction, indicating that kidney regeneration approaches, besides whole kidney reconstruction, might benefit from the presence of LTβR signals.
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Affiliation(s)
- Maria Giovanna Francipane
- McGowan Institute for Regenerative Medicine and Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania; Ri.MED Foundation, Palermo, Italy.
| | - Bing Han
- McGowan Institute for Regenerative Medicine and Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Eric Lagasse
- McGowan Institute for Regenerative Medicine and Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania.
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