1
|
Yi L, Guo X, Liu Y, Jirimutu, Wang Z. Single-cell 5' RNA sequencing of camelid peripheral B cells provides insights into cellular basis of heavy-chain antibody production. Comput Struct Biotechnol J 2024; 23:1705-1714. [PMID: 38689719 PMCID: PMC11059136 DOI: 10.1016/j.csbj.2024.04.041] [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: 01/19/2024] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
Camelids produce both conventional tetrameric antibodies (Abs) and dimeric heavy-chain antibodies (HCAbs). Although B cells that generate these two types of Abs exhibit distinct B cell receptors (BCRs), whether these two B cell populations differ in their phenotypes and developmental processes remains unclear. Here, we performed single-cell 5' RNA profiling of peripheral blood mononuclear cell samples from Bactrian camels before and after immunization. We characterized the functional subtypes and differentiation trajectories of circulating B cells in camels, and reconstructed single-cell BCR sequences. We found that in contrast to humans, the proportion of T-bet+ B cells was high among camelid peripheral B cells. Several marker genes of human B cell subtypes, including CD27 and IGHD, were expressed at low levels in the corresponding camel B cell subtypes. Camelid B cells expressing variable genes of HACbs (VHH) were widely present in various functional subtypes and showed highly overlapping differentiation trajectories with B cells expressing variable genes of conventional Abs (VH). After immunization, the transcriptional changes in VHH+ and VH+ B cells were largely consistent. Through structure modeling, we identified a variety of scaffold types among the reconstructed VHH sequences. Our study provides insights into the cellular context of HCAb production in camels and lays the foundation for developing single-B cell-based camelid single-domain Ab screening.
Collapse
Affiliation(s)
- Li Yi
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Xin Guo
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuexing Liu
- Guangzhou Laboratory, Guangzhou 510005, China
| | - Jirimutu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
- Inner Mongolia China-Kazakhstan Camel Research Institute, Alxa 750306, China
| | - Zhen Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| |
Collapse
|
2
|
Bai J, Kato A, Hulse KE, Wechsler JB, Gujar V, Poposki JA, Harmon R, Iwasaki N, Wang BF, Huang JH, Stevens WW, Conley DB, Welch KC, Kern RC, Peters AT, Eisenbarth SC, Schleimer RP, Tan BK. Increased autoreactivity and maturity of EBI2+ antibody-secreting cells from nasal polyps. JCI Insight 2024; 9:e177729. [PMID: 39253973 PMCID: PMC11385095 DOI: 10.1172/jci.insight.177729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 07/18/2024] [Indexed: 09/11/2024] Open
Abstract
Elevated numbers of antibody-secreting cells (ASCs) and anti-double-stranded DNA (anti-dsDNA) antibodies are found in nasal polyp (NP) tissue. The presence of anti-dsDNA IgG in tissue prospectively predicts recurrent NP but the characteristics of the source ASCs are unknown. Here, we investigated whether NP B cells expressing the extrafollicular marker EBI2 have increased propensity for autoantibody production and evaluated the molecular characteristics of NP ASCs. NPs showed increased frequencies of anti-dsDNA IgG and total IgG ASCs compared with tonsils, with more pronounced differences among EBI2+ cells. In NPs, EBI2+ cells were frequently double negative (IgD-CD27-) and ASCs. Single-cell RNA-Seq analysis of tonsils and NPs revealed substantial differences in B lineage composition, including differences in percentages of ASCs, germinal centers, proliferative cells, and non-ASCs. NPs exhibited higher expression of specific isotypes (IGHE, IGHA1, IGHA2, and IGHG4) and mature plasma genes, including SDC1 and XBP1, than tonsils. Gene Ontology biological processes indicated upregulated NF-κB and downregulated apoptosis pathways in NP ASCs. Together, these data indicate that NP EBI2+ ASCs secret increased total and anti-dsDNA IgG compared with those from tonsils and had molecular features of mature plasma cell differentiation.
Collapse
Affiliation(s)
| | - Atsushi Kato
- Department of Otolaryngology
- Division of Allergy and Immunology, Department of Medicine, and
| | - Kathryn E Hulse
- Division of Allergy and Immunology, Department of Medicine, and
| | - Joshua B Wechsler
- Departments of Pediatrics and Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Vikram Gujar
- Department of Anatomy and Cell Biology, Oklahoma State University, Tulsa, Oklahoma, USA
| | - Julie A Poposki
- Division of Allergy and Immunology, Department of Medicine, and
| | | | | | - Bao-Feng Wang
- Department of Otolaryngology-Head and Neck Surgery, Tongji Hospital, Wuhan, China
| | | | - Whitney W Stevens
- Department of Otolaryngology
- Division of Allergy and Immunology, Department of Medicine, and
| | | | | | | | - Anju T Peters
- Department of Otolaryngology
- Division of Allergy and Immunology, Department of Medicine, and
| | | | - Robert P Schleimer
- Department of Otolaryngology
- Division of Allergy and Immunology, Department of Medicine, and
| | - Bruce K Tan
- Department of Otolaryngology
- Division of Allergy and Immunology, Department of Medicine, and
| |
Collapse
|
3
|
Park J, Ke W, Kaage A, Feigin CY, Pritykin Y, Donia MS, Mallarino R. Marsupial immune protection is shaped by enhancer sharing and gene cluster duplication of cathelicidin antimicrobial peptides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.29.605640. [PMID: 39211247 PMCID: PMC11361154 DOI: 10.1101/2024.07.29.605640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Marsupial neonates are born with immature immune systems, making them vulnerable to pathogens. While neonates receive maternal protection, they can also independently combat pathogens, though the mechanisms remain unknown. Using the sugar glider (Petaurus breviceps) as a model, we investigated immunological defense strategies of marsupial neonates. Cathelicidins, a family of antimicrobial peptides expanded in the genomes of marsupials, are highly expressed in developing neutrophils. Sugar glider cathelicidins reside in two genomic clusters and their coordinated expression is achieved by enhancer sharing within clusters and long-range physical interactions between clusters. These cathelicidins modulate immune responses and have potent antimicrobial effects, sufficient to provide protection in a mouse model of sepsis. Lastly, cathelicidins have a complex evolutionary history, where marsupials and monotremes are the only tetrapods that retained two cathelicidin clusters. Thus, cathelicidins are critical mediators of marsupial immunity, and their evolution reflects the life history-specific immunological needs of these animals.
Collapse
|
4
|
Spencer J, Dionisi C. Immature B cell homing shapes human lymphoid tissue structure and function. J Exp Med 2024; 221:e20240085. [PMID: 39093311 PMCID: PMC11296955 DOI: 10.1084/jem.20240085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/18/2024] [Accepted: 07/23/2024] [Indexed: 08/04/2024] Open
Abstract
Shortly after the emergence of newly formed human B cells from bone marrow as transitional cells, they diverge along two developmental pathways that can be distinguished by the level of IgM they express and migratory biases. Here, we propose that differential tissue homing of immature B cell subsets contributes to human lymphoid tissue structure and function.
Collapse
Affiliation(s)
- Jo Spencer
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Chiara Dionisi
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, London, UK
| |
Collapse
|
5
|
Yang Y, Chen X, Pan J, Ning H, Zhang Y, Bo Y, Ren X, Li J, Qin S, Wang D, Chen MM, Zhang Z. Pan-cancer single-cell dissection reveals phenotypically distinct B cell subtypes. Cell 2024; 187:4790-4811.e22. [PMID: 39047727 DOI: 10.1016/j.cell.2024.06.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 04/25/2024] [Accepted: 06/26/2024] [Indexed: 07/27/2024]
Abstract
Characterizing the compositional and phenotypic characteristics of tumor-infiltrating B cells (TIBs) is important for advancing our understanding of their role in cancer development. Here, we establish a comprehensive resource of human B cells by integrating single-cell RNA sequencing data of B cells from 649 patients across 19 major cancer types. We demonstrate substantial heterogeneity in their total abundance and subtype composition and observe immunoglobulin G (IgG)-skewness of antibody-secreting cell isotypes. Moreover, we identify stress-response memory B cells and tumor-associated atypical B cells (TAABs), two tumor-enriched subpopulations with prognostic potential, shared in a pan-cancer manner. In particular, TAABs, characterized by a high clonal expansion level and proliferative capacity as well as by close interactions with activated CD4 T cells in tumors, are predictive of immunotherapy response. Our integrative resource depicts distinct clinically relevant TIB subsets, laying a foundation for further exploration of functional commonality and diversity of B cells in cancer.
Collapse
Affiliation(s)
- Yu Yang
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Xueyan Chen
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Jieying Pan
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Huiheng Ning
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yaojun Zhang
- State Key Laboratory of Oncology in South China, Department of Liver Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Yufei Bo
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Xianwen Ren
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Jiesheng Li
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Shishang Qin
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Dongfang Wang
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China.
| | - Min-Min Chen
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China.
| | - Zemin Zhang
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China.
| |
Collapse
|
6
|
Rodrigues KA, Zhang YJ, Aung A, Morgan DM, Maiorino L, Yousefpour P, Gibson G, Ozorowski G, Gregory JR, Amlashi P, Buckley M, Ward AB, Schief WR, Love JC, Irvine DJ. Vaccines combining slow delivery and follicle targeting of antigens increase germinal center B cell clonal diversity and clonal expansion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.19.608655. [PMID: 39229011 PMCID: PMC11370361 DOI: 10.1101/2024.08.19.608655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Vaccines incorporating slow delivery, multivalent antigen display, or immunomodulation through adjuvants have an important role to play in shaping the humoral immune response. Here we analyzed mechanisms of action of a clinically relevant combination adjuvant strategy, where phosphoserine (pSer)-tagged immunogens bound to aluminum hydroxide (alum) adjuvant (promoting prolonged antigen delivery to draining lymph nodes) are combined with a potent saponin nanoparticle adjuvant termed SMNP (which alters lymph flow and antigen entry into lymph nodes). When employed with a stabilized HIV Env trimer antigen in mice, this combined adjuvant approach promoted substantial enhancements in germinal center (GC) and antibody responses relative to either adjuvant alone. Using scRNA-seq and scBCR-seq, we found that the alum-pSer/SMNP combination both increased the diversity of GC B cell clones and increased GC B cell clonal expansion, coincident with increases in the expression of Myc and the proportion of S-phase GC B cells. To gain insight into the source of these changes in the GC response, we analyzed antigen biodistribution and structural integrity in draining lymph nodes and found that the combination adjuvant approach, but not alum-pSer delivery or SMNP alone, promoted accumulation of highly intact antigen on follicular dendritic cells, reflecting an integration of the slow antigen delivery and altered lymph node uptake effects of these two adjuvants. These results demonstrate how adjuvants with complementary mechanisms of action impacting vaccine biodistribution and kinetics can synergize to enhance humoral immunity.
Collapse
Affiliation(s)
- Kristen A Rodrigues
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
- Harvard-MIT Health Sciences and Technology Program, Institute for Medical Engineering and Science; Massachusetts Institute of Technology, Cambridge, MA 02139 USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
| | - Yiming J Zhang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
| | - Aereas Aung
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
| | - Duncan M Morgan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
- Department of Chemical Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
| | - Laura Maiorino
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
| | - Parisa Yousefpour
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
| | - Grace Gibson
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037 USA
| | - Gabriel Ozorowski
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037 USA
| | - Justin R Gregory
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
| | - Parastoo Amlashi
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
| | - Maureen Buckley
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
| | - Andrew B Ward
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037 USA
| | - William R Schief
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - J Christopher Love
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Department of Chemical Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
| | - Darrell J Irvine
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Materials Science and Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
- Howard Hughes Medical Institute; Chevy Chase, MD 20815 USA
| |
Collapse
|
7
|
Wiarda JE, Shircliff AL, Becker SR, Stasko JB, Sivasankaran SK, Ackermann MR, Loving CL. Conserved B cell signaling, activation, and differentiation in porcine jejunal and ileal Peyer's patches despite distinct immune landscapes. Mucosal Immunol 2024:S1933-0219(24)00086-2. [PMID: 39147277 DOI: 10.1016/j.mucimm.2024.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 08/01/2024] [Accepted: 08/08/2024] [Indexed: 08/17/2024]
Abstract
Peyer's patches (PPs) are B cell-rich sites of intestinal immune induction, yet PP-associated B cell signaling, activation, and differentiation are poorly defined. Single-cell and spatial transcriptomics were completed to study B cells from porcine jejunum and ileum containing PPs. Intestinal locations had distinct immune landscapes, including more follicular B cells in ileum and increased MHC-II-encoding gene expression in jejunal B cells. Despite distinct landscapes, conserved B cell dynamics were detected across intestinal locations, including B cell signaling to CD4+ macrophages that are putative phagocytic, cytotoxic, effector cells and deduced routes of B cell activation/differentiation, including resting B cells migrating into follicles to replicate/divide or differentiate into antibody-secreting cells residing in intestinal crypts. A six-biomarker panel recapitulated transcriptomics findings of B cell phenotypes, frequencies, and spatial locations via ex vivo and in situ staining. Findings convey conserved B cell dynamics across intestinal locations containing PPs, despite location-specific immune environments. Results establish a benchmark of B cell dynamics for understanding intestinal immune induction important to promoting gut/overall health.
Collapse
Affiliation(s)
- Jayne E Wiarda
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA; Oak Ridge Institute for Science and Education, Agricultural Research Service Participation Program, Oak Ridge, TN, USA
| | - Adrienne L Shircliff
- Microscopy Services Laboratory, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA
| | - Sage R Becker
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA; Oak Ridge Institute for Science and Education, Agricultural Research Service Participation Program, Oak Ridge, TN, USA; Immunobiology Graduate Program, Iowa State University, Ames, IA, USA
| | - Judith B Stasko
- Microscopy Services Laboratory, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA
| | - Sathesh K Sivasankaran
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA; Genome Informatics Facility, Iowa State University, Ames, IA, USA
| | - Mark R Ackermann
- Office of the Director, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA
| | - Crystal L Loving
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA.
| |
Collapse
|
8
|
Aguilar D, Zhu F, Millet A, Millet N, Germano P, Pisegna J, Akbari O, Doherty TA, Swidergall M, Jendzjowsky N. Sensory neurons regulate stimulus-dependent humoral immunity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.04.574231. [PMID: 38260709 PMCID: PMC10802321 DOI: 10.1101/2024.01.04.574231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Sensory neurons sense pathogenic infiltration, serving to inform immune coordination of host defense. However, sensory neuron-immune interactions have been predominantly shown to drive innate immune responses. Humoral memory, whether protective or destructive, is acquired early in life - as demonstrated by both early exposure to streptococci and allergic disease onset. Our study further defines the role of sensory neuron influence on humoral immunity in the lung. Using a murine model of Streptococcus pneumonia pre-exposure and infection and a model of allergic asthma, we show that sensory neurons are required for B-cell and plasma cell recruitment and antibody production. In response to S. pneumoniae, sensory neuron depletion resulted in a larger bacterial burden, reduced B-cell populations, IgG release and neutrophil stimulation. Conversely, sensory neuron depletion reduced B-cell populations, IgE and asthmatic characteristics during allergen-induced airway inflammation. The sensory neuron neuropeptide released within each model differed. With bacterial infection, vasoactive intestinal polypeptide (VIP) was preferentially released, whereas substance P was released in response to asthma. Administration of VIP into sensory neuron-depleted mice suppressed bacterial burden and increased IgG levels, while VIP1R deficiency increased susceptibility to bacterial infection. Sensory neuron-depleted mice treated with substance P increased IgE and asthma, while substance P genetic ablation resulted in blunted IgE, similar to sensory neuron-depleted asthmatic mice. These data demonstrate that the immunogen differentially stimulates sensory neurons to release specific neuropeptides which specifically target B-cells. Targeting sensory neurons may provide an alternate treatment pathway for diseases involved with insufficient and/or aggravated humoral immunity.
Collapse
|
9
|
Kim J, Yong SH, Jang G, Kim Y, Park R, Koh HH, Kim S, Oh CM, Lee SH. Spatial profiling of non-small cell lung cancer provides insights into tumorigenesis and immunotherapy response. Commun Biol 2024; 7:930. [PMID: 39095464 PMCID: PMC11297140 DOI: 10.1038/s42003-024-06568-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 07/05/2024] [Indexed: 08/04/2024] Open
Abstract
Lung cancer is the second most common cancer worldwide and a leading cause of cancer-related deaths. Despite advances in targeted therapy and immunotherapy, the prognosis remains unfavorable, especially in metastatic cases. This study aims to identify molecular changes in non-small cell lung cancer (NSCLC) patients based on their response to treatment. Using tumor and matched immune cell rich peritumoral tissues, we perform a retrospective, comprehensive spatial transcriptomic analysis of a proven malignant NSCLC sample treated with immune checkpoint inhibitor (ICI). In addition to T cells, other immune cell types, such as B cells and macrophages, were also activated in responders to ICI treatment. In particular, B cells and B cell-mediated immunity pathways are consistently found to be activated. Analysis of the histologic subgroup (lung squamous cell carcinoma, LUSC; lung adenocarcinoma, LUAD) of NSCLC also confirms activation of B cell mediated immunity. Analysis of B cell subtypes shows that B cell subtypes were more activated in immune cell-rich tissues near tumor tissue. Furthermore, increased expression of B cell immunity-related genes is associated with better prognosis. These findings provide insight into predicting ICI treatment responses and identifying appropriate candidates for immunotherapy in NSCLC patients.
Collapse
Affiliation(s)
- Joon Kim
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Korea
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seung Hyun Yong
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Gyuho Jang
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Korea
| | - Yumin Kim
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Korea
| | - Raekil Park
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Korea
| | - Hyun-Hee Koh
- Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sehui Kim
- Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Department of Pathology, Korea University Guro Hospital, Seoul, Republic of Korea.
| | - Chang-Myung Oh
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Korea.
| | - Sang Hoon Lee
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea.
| |
Collapse
|
10
|
Ramani M, Singh RK, Shrivastva S, Ribeyron L, Gupta SK, Roy A. A pre-B acute lymphoblastic leukemia cell line model reveals the mechanism of thalidomide therapy-related B-cell leukemogenesis. J Biol Chem 2024; 300:107578. [PMID: 39029626 PMCID: PMC11367411 DOI: 10.1016/j.jbc.2024.107578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 05/21/2024] [Accepted: 06/19/2024] [Indexed: 07/21/2024] Open
Abstract
Lenalidomide, a thalidomide derivative, is prescribed as maintenance therapy for multiple myeloma (MM). Patients with MM receiving lenalidomide were found to develop a distinct therapy-related B cell acute lymphoblastic leukemia (B-ALL). However, the molecular mechanism by which lenalidomide drives B-ALL is unknown. We show that thalidomide treatment of B cell lines increased CD34 expression and fibronectin adhesion. This resembled the effects of Ikzf1 loss of function mutations in B-ALL. IKZF1 is a transcription factor that can act as both a transcriptional activator and a repressor depending upon the target loci. In our experiments, thalidomide-induced degradation of IKZF1 increased the expression of its transcriptional repression targets Itga5 and CD34 explaining the increased adhesion and stemness. Strikingly, withdrawal of thalidomide lead to the mis-localization of IKZF1 to the cytoplasm. Moreover, chromatin immunoprecipitation data showed a long-term effect of thalidomide treatment on IKZF1 target loci. This included decreased chromatin occupancy at early B cell factor 1 (EBF1) and Spi1 (PU.1). Consequently, B-cell lineage specifying transcription factors including Pax5, Spi1 and EBF1 were downregulated even after 7 days of thalidomide withdrawal. Our study thus provides a molecular mechanism of thalidomide-induced B-ALL whereby thalidomide alters the chromatin occupancy of IKZF1 at key B-cell lineage transcription factors leading to a persistent block in B-cell differentiation.
Collapse
Affiliation(s)
- Malvika Ramani
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi, India
| | - Rishi Kant Singh
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi, India
| | - Saurabh Shrivastva
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi, India
| | - Louis Ribeyron
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi, India; Faculty of Sciences and Engineering, Sorbonne Université, Paris, France
| | | | - Anita Roy
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi, India.
| |
Collapse
|
11
|
Sun ED, Zhou OY, Hauptschein M, Rappoport N, Xu L, Navarro Negredo P, Liu L, Rando TA, Zou J, Brunet A. Spatiotemporal transcriptomic profiling and modeling of mouse brain at single-cell resolution reveals cell proximity effects of aging and rejuvenation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.16.603809. [PMID: 39071282 PMCID: PMC11275735 DOI: 10.1101/2024.07.16.603809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Old age is associated with a decline in cognitive function and an increase in neurodegenerative disease risk1. Brain aging is complex and accompanied by many cellular changes2-20. However, the influence that aged cells have on neighboring cells and how this contributes to tissue decline is unknown. More generally, the tools to systematically address this question in aging tissues have not yet been developed. Here, we generate spatiotemporal data at single-cell resolution for the mouse brain across lifespan, and we develop the first machine learning models based on spatial transcriptomics ('spatial aging clocks') to reveal cell proximity effects during brain aging and rejuvenation. We collect a single-cell spatial transcriptomics brain atlas of 4.2 million cells from 20 distinct ages and across two rejuvenating interventions-exercise and partial reprogramming. We identify spatial and cell type-specific transcriptomic fingerprints of aging, rejuvenation, and disease, including for rare cell types. Using spatial aging clocks and deep learning models, we find that T cells, which infiltrate the brain with age, have a striking pro-aging proximity effect on neighboring cells. Surprisingly, neural stem cells have a strong pro-rejuvenating effect on neighboring cells. By developing computational tools to identify mediators of these proximity effects, we find that pro-aging T cells trigger a local inflammatory response likely via interferon-γ whereas pro-rejuvenating neural stem cells impact the metabolism of neighboring cells possibly via growth factors (e.g. vascular endothelial growth factor) and extracellular vesicles, and we experimentally validate some of these predictions. These results suggest that rare cells can have a drastic influence on their neighbors and could be targeted to counter tissue aging. We anticipate that these spatial aging clocks will not only allow scalable assessment of the efficacy of interventions for aging and disease but also represent a new tool for studying cell-cell interactions in many spatial contexts.
Collapse
Affiliation(s)
- Eric D. Sun
- Department of Biomedical Data Science, Stanford University, CA, USA
- Department of Genetics, Stanford University, CA, USA
| | - Olivia Y. Zhou
- Department of Genetics, Stanford University, CA, USA
- Stanford Biophysics Program, Stanford University, CA, USA
- Stanford Medical Scientist Training Program, Stanford University, CA, USA
| | | | | | - Lucy Xu
- Department of Genetics, Stanford University, CA, USA
- Department of Biology, Stanford University, CA, USA
| | | | - Ling Liu
- Department of Neurology, Stanford University, CA, USA
- Department of Neurology, UCLA, Los Angeles, CA, USA
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Biology, UCLA, Los Angeles, CA, USA
| | - Thomas A. Rando
- Department of Neurology, Stanford University, CA, USA
- Department of Neurology, UCLA, Los Angeles, CA, USA
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Biology, UCLA, Los Angeles, CA, USA
| | - James Zou
- Department of Biomedical Data Science, Stanford University, CA, USA
- These authors contributed equally: James Zou, Anne Brunet
| | - Anne Brunet
- Department of Genetics, Stanford University, CA, USA
- Glenn Center for the Biology of Aging, Stanford University, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, CA, USA
- These authors contributed equally: James Zou, Anne Brunet
| |
Collapse
|
12
|
Perdrizet UG, Hill JE, Sobchishin L, Singh B, Fernando C, Bollinger TK, Misra V. Tissue and cellular tropism of Eptesicus fuscus gammaherpesvirus in big brown bats, potential role of pulmonary intravascular macrophages. Vet Pathol 2024; 61:550-561. [PMID: 38619093 PMCID: PMC11264566 DOI: 10.1177/03009858241244849] [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: 04/16/2024]
Abstract
Gammaherpesviruses (γHVs) are recognized as important pathogens in humans but their relationship with other animal hosts, especially wildlife species, is less well characterized. Our objectives were to examine natural Eptesicus fuscus gammaherpesvirus (EfHV) infections in their host, the big brown bat (Eptesicus fuscus), and determine whether infection is associated with disease. In tissue samples from 132 individual big brown bats, EfHV DNA was detected by polymerase chain reaction in 41 bats. Tissues from 59 of these cases, including 17 from bats with detectable EfHV genomes, were analyzed. An EfHV isolate was obtained from one of the cases, and electron micrographs and whole genome sequencing were used to confirm that this was a unique isolate of EfHV. Although several bats exhibited various lesions, we did not establish EfHV infection as a cause. Latent infection, defined as RNAScope probe binding to viral latency-associated nuclear antigen in the absence of viral envelope glycoprotein probe binding, was found within cells of the lymphoid tissues. These cells also had colocalization of the B-cell probe targeting CD20 mRNA. Probe binding for both latency-associated nuclear antigen and a viral glycoprotein was observed in individual cells dispersed throughout the alveolar capillaries of the lung, which had characteristics of pulmonary intravascular macrophages. Cells with a similar distribution in bat lungs expressed major histocompatibility class II, a marker for antigen presenting cells, and the existence of pulmonary intravascular macrophages in bats was confirmed with transmission electron microscopy. The importance of this cell type in γHVs infections warrants further investigation.
Collapse
Affiliation(s)
| | | | | | - Baljit Singh
- University of Saskatchewan, Saskatoon, SK, Canada
| | | | | | - Vikram Misra
- University of Saskatchewan, Saskatoon, SK, Canada
| |
Collapse
|
13
|
McAndrews KM, Mahadevan KK, Kalluri R. Mouse Models to Evaluate the Functional Role of the Tumor Microenvironment in Cancer Progression and Therapy Responses. Cold Spring Harb Perspect Med 2024; 14:a041411. [PMID: 38191175 PMCID: PMC11216184 DOI: 10.1101/cshperspect.a041411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
The tumor microenvironment (TME) is a complex ecosystem of both cellular and noncellular components that functions to impact the evolution of cancer. Various aspects of the TME have been targeted for the control of cancer; however, TME composition is dynamic, with the overall abundance of immune cells, endothelial cells (ECs), fibroblasts, and extracellular matrix (ECM) as well as subsets of TME components changing at different stages of progression and in response to therapy. To effectively treat cancer, an understanding of the functional role of the TME is needed. Genetically engineered mouse models have enabled comprehensive insight into the complex interactions within the TME ecosystem that regulate disease progression. Here, we review recent advances in mouse models that have been employed to understand how the TME regulates cancer initiation, progression, metastasis, and response to therapy.
Collapse
Affiliation(s)
- Kathleen M McAndrews
- Department of Cancer Biology, Metastasis Research Center, University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Krishnan K Mahadevan
- Department of Cancer Biology, Metastasis Research Center, University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Raghu Kalluri
- Department of Cancer Biology, Metastasis Research Center, University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
- Department of Bioengineering, Rice University, Houston, Texas 77251, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| |
Collapse
|
14
|
Huang D, Jiao X, Huang S, Liu J, Si H, Qi D, Pei X, Lu D, Wang Y, Li Z. Analysis of the heterogeneity and complexity of murine extraorbital lacrimal gland via single-cell RNA sequencing. Ocul Surf 2024; 34:60-95. [PMID: 38945476 DOI: 10.1016/j.jtos.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 06/22/2024] [Accepted: 06/26/2024] [Indexed: 07/02/2024]
Abstract
PURPOSE The lacrimal gland is essential for maintaining ocular surface health and avoiding external damage by secreting an aqueous layer of the tear film. However, a healthy lacrimal gland's inventory of cell types and heterogeneity remains understudied. METHODS Here, 10X Genome-based single-cell RNA sequencing was used to generate an unbiased classification of cellular diversity in the extraorbital lacrimal gland (ELG) of C57BL/6J mice. From 43,850 high-quality cells, we produced an atlas of cell heterogeneity and defined cell types using classic marker genes. The possible functions of these cells were analyzed through bioinformatics analysis. Additionally, the CellChat was employed for a preliminary analysis of the cell-cell communication network in the ELG. RESULTS Over 37 subclasses of cells were identified, including seven types of glandular epithelial cells, three types of fibroblasts, ten types of myeloid-derived immune cells, at least eleven types of lymphoid-derived immune cells, and five types of vascular-associated cell subsets. The cell-cell communication network analysis revealed that fibroblasts and immune cells play a pivotal role in the dense intercellular communication network within the mouse ELG. CONCLUSIONS This study provides a comprehensive transcriptome atlas and related database of the mouse ELG.
Collapse
Affiliation(s)
- Duliurui Huang
- Department of Ophthalmology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Xinwei Jiao
- Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, 450000, China
| | - Shenzhen Huang
- Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, 450000, China
| | - Jiangman Liu
- Department of Ophthalmology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Hongli Si
- Department of Ophthalmology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Di Qi
- Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, 450000, China
| | - Xiaoting Pei
- Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, 450000, China
| | - Dingli Lu
- Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, 450000, China
| | - Yimian Wang
- Division of Medicine, Faculty of Medical Sciences, University College London, Gower Street, London, WC1E 6BT, UK
| | - Zhijie Li
- Department of Ophthalmology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China; Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, 450000, China.
| |
Collapse
|
15
|
Xu J, Zhai J, Zhao J. Pathogenic roles of follicular helper T cells in IgG4-related disease and implications for potential therapy. Front Immunol 2024; 15:1413860. [PMID: 38911857 PMCID: PMC11190345 DOI: 10.3389/fimmu.2024.1413860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 05/27/2024] [Indexed: 06/25/2024] Open
Abstract
IgG4-related disease (IgG4-RD) is a recently described autoimmune disorder characterized by elevated serum IgG4 levels and tissue infiltration of IgG4+ plasma cells in multiple organ systems. Recent advancements have significantly enhanced our understanding of the pathological mechanism underlying this immune-mediated disease. T cell immunity plays a crucial role in the pathogenesis of IgG4-RD, and follicular helper T cells (Tfh) are particularly important in germinal center (GC) formation, plasmablast differentiation, and IgG4 class-switching. Apart from serum IgG4 concentrations, the expansion of circulating Tfh2 cells and plasmablasts may also serve as novel biomarkers for disease diagnosis and activity monitoring in IgG4-RD. Further exploration into the pathogenic roles of Tfh in IgG4-RD could potentially lead to identifying new therapeutic targets that offer more effective alternatives for treating this condition. In this review, we will focus on the current knowledge regarding the pathogenic roles Tfh cells play in IgG4-RD and outline potential therapeutic targets for future clinical intervention.
Collapse
Affiliation(s)
- Jingyi Xu
- Department of Rheumatology and Immunology, Peking University Third Hospital, Beijing, China
| | - Jiayu Zhai
- Department of Rheumatology and Immunology, Peking University Third Hospital, Beijing, China
- Center for Rare Disease, Peking University Third Hospital, Beijing, China
| | - Jinxia Zhao
- Department of Rheumatology and Immunology, Peking University Third Hospital, Beijing, China
- Center for Rare Disease, Peking University Third Hospital, Beijing, China
| |
Collapse
|
16
|
Islam R, Heyer J, Figura M, Wang X, Nie X, Nathaniel B, Indumathy S, Hartmann K, Pleuger C, Fijak M, Kliesch S, Dittmar F, Pilatz A, Wagenlehner F, Hedger M, Loveland B, Hotaling JH, Guo J, Loveland KL, Schuppe HC, Fietz D. T cells in testicular germ cell tumors: new evidence of fundamental contributions by rare subsets. Br J Cancer 2024; 130:1893-1903. [PMID: 38649788 PMCID: PMC11183042 DOI: 10.1038/s41416-024-02669-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 03/21/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Immune cell infiltration is heterogeneous but common in testicular germ cell tumors (TGCT) and pre-invasive germ cell neoplasia in situ (GCNIS). Tumor-infiltrating T cells including regulatory T (Treg) and follicular helper T (Tfh) cells are found in other cancer entities, but their contributions to TGCT are unknown. METHODS Human testis specimens from independent patient cohorts were analyzed using immunohistochemistry, flow cytometry and single-cell RNA sequencing (scRNA-seq) with special emphasis on delineating T cell subtypes. RESULTS Profound changes in immune cell composition within TGCT, shifting from macrophages in normal testes to T cells plus B and dendritic cells in TGCT, were documented. In most samples (96%), the CD4+ T cell frequency exceeded that of CD8+ cells, with decreasing numbers from central to peripheral tumor areas, and to tumor-free, contralateral testes. T cells including Treg and Tfh were most abundant in seminoma compared to mixed tumors and embryonal carcinoma. CONCLUSION Despite considerable heterogeneity between patients, T cell subtypes form a key part of the TGCT microenvironment. The novel finding of rare Treg and Tfh cells in human testis suggests their involvement in TGCT pathobiology, with implications for understanding tumor progression, to assess patients' prognosis, and as putative targets for personalized immunotherapy.
Collapse
Affiliation(s)
- Rashidul Islam
- Dept. of Veterinary Anatomy, Histology and Embryology, Justus Liebig University, Giessen, Germany
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
- Department of Developmental Pathology, Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - Jannis Heyer
- Dept. of Veterinary Anatomy, Histology and Embryology, Justus Liebig University, Giessen, Germany
- Dept. of Urology, Pediatric Urology and Andrology, Justus Liebig University, Giessen, Germany
| | - Miriam Figura
- Dept. of Veterinary Anatomy, Histology and Embryology, Justus Liebig University, Giessen, Germany
- Dept. of Urology, Pediatric Urology and Andrology, Justus Liebig University, Giessen, Germany
| | - Xiaoyan Wang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute of Stem Cell and Regenerative Medicine, Beijing, China
| | - Xichen Nie
- Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Benedict Nathaniel
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Sivanjah Indumathy
- Dept. of Veterinary Anatomy, Histology and Embryology, Justus Liebig University, Giessen, Germany
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Katja Hartmann
- Dept. of Veterinary Anatomy, Histology and Embryology, Justus Liebig University, Giessen, Germany
| | - Christiane Pleuger
- Hessian Centre of Reproductive Medicine, Justus-Liebig-University, Giessen, Germany
- Institute of Anatomy and Cell Biology, Justus Liebig University, Giessen, Germany
| | - Monika Fijak
- Hessian Centre of Reproductive Medicine, Justus-Liebig-University, Giessen, Germany
- Institute of Anatomy and Cell Biology, Justus Liebig University, Giessen, Germany
| | - Sabine Kliesch
- Centre of Reproductive Medicine and Andrology, University of Muenster, Muenster, Germany
| | - Florian Dittmar
- Dept. of Urology, Pediatric Urology and Andrology, Justus Liebig University, Giessen, Germany
| | - Adrian Pilatz
- Dept. of Urology, Pediatric Urology and Andrology, Justus Liebig University, Giessen, Germany
- Hessian Centre of Reproductive Medicine, Justus-Liebig-University, Giessen, Germany
| | - Florian Wagenlehner
- Dept. of Urology, Pediatric Urology and Andrology, Justus Liebig University, Giessen, Germany
- Hessian Centre of Reproductive Medicine, Justus-Liebig-University, Giessen, Germany
| | - Mark Hedger
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | | | - James H Hotaling
- Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Jingtao Guo
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute of Stem Cell and Regenerative Medicine, Beijing, China
- Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Kate L Loveland
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Hans-Christian Schuppe
- Dept. of Urology, Pediatric Urology and Andrology, Justus Liebig University, Giessen, Germany
- Hessian Centre of Reproductive Medicine, Justus-Liebig-University, Giessen, Germany
| | - Daniela Fietz
- Dept. of Veterinary Anatomy, Histology and Embryology, Justus Liebig University, Giessen, Germany.
- Hessian Centre of Reproductive Medicine, Justus-Liebig-University, Giessen, Germany.
| |
Collapse
|
17
|
Zhang Y, Fu Z, Zhang H, Lin K, Song J, Guo J, Zhang Q, Yuan G, Wang H, Fan M, Zhao Y, Sun R, Guo T, Jiang N, Qiu C, Zhang W, Ai J. Proteomic and Cellular Characterization of Omicron Breakthrough Infections and a Third Homologous or Heterologous Boosting Vaccination in a Longitudinal Cohort. Mol Cell Proteomics 2024; 23:100769. [PMID: 38641227 PMCID: PMC11154224 DOI: 10.1016/j.mcpro.2024.100769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 01/18/2024] [Accepted: 03/23/2024] [Indexed: 04/21/2024] Open
Abstract
The understanding of dynamic plasma proteome features in hybrid immunity and breakthrough infection is limited. A deeper understanding of the immune differences between heterologous and homologous immunization could assist in the future establishment of vaccination strategies. In this study, 40 participants who received a third dose of either a homologous BBIBP-CorV or a heterologous ZF2001 protein subunit vaccine following two doses of inactivated coronavirus disease 2019 vaccines and 12 patients with BA2.2 breakthrough infections were enrolled. Serum samples were collected at days 0, 28, and 180 following the boosting vaccination and breakthrough and then analyzed using neutralizing antibody tests and mass spectrometer-based proteomics. Mass cytometry of peripheral blood mononuclear cell samples was also performed in this cohort. The chemokine signaling pathway and humoral response markers (IgG2 and IgG3) associated with infection were found to be upregulated in breakthrough infections compared to vaccination-induced immunity. Elevated expression of IGKV, IGHV, IL-17 signaling, and the phagocytosis pathway, along with lower expression of FGL2, were correlated with higher antibody levels in the boosting vaccination groups. The MAPK signaling pathway and Fc gamma R-mediated phagocytosis were more enriched in the heterologous immunization groups than in the homologous immunization groups. Breakthrough infections can trigger more intensive inflammatory chemokine responses than vaccination. T-cell and innate immune activation have been shown to be closely related to enhanced antibody levels after vaccination and therefore might be potential targets for vaccine adjuvant design.
Collapse
Affiliation(s)
- Yi Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhangfan Fu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Haocheng Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ke Lin
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jieyu Song
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jingxin Guo
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qiran Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Guanmin Yuan
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hongyu Wang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Mingxiang Fan
- Tongji Medical School, Tongji University, Shanghai, China
| | - Yuanhan Zhao
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Rui Sun
- iMarker lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
| | - Tiannan Guo
- iMarker lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
| | - Ning Jiang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chao Qiu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenhong Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China; National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China; Shanghai huashen institute of microbes and infections, Shanghai, China.
| | - Jingwen Ai
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.
| |
Collapse
|
18
|
Yu L, Zhang Y, Li W, Mao J, Li Y, Wang H, Li C, Yang L, He W, Jia Y, Tang W, Zhou L, Zhang Z, Jia Y, Tang X, Zhao X, An Y. Fluoxetine Successfully Treats Intracranial Enterovirus E18 Infection in a Patient with CD79a Deficiency Arising from Segmental Uniparental Disomy of Chromosome 19. J Clin Immunol 2024; 44:137. [PMID: 38805163 DOI: 10.1007/s10875-024-01740-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 05/20/2024] [Indexed: 05/29/2024]
Abstract
The pre BCR complex plays a crucial role in B cell production, and its successful expression marks the B cell differentiation from the pro-B to pre-B. The CD79a and CD79b mutations, encoding Igα and Igβ respectively, have been identified as the cause of autosomal recessive agammaglobulinemia (ARA). Here, we present a case of a patient with a homozygous CD79a mutation, exhibiting recurrent respiratory infections, diarrhea, growth and development delay, unique facial abnormalities and microcephaly, as well as neurological symptoms including tethered spinal cord, sacral canal cyst, and chronic enteroviral E18 meningitis. Complete blockade of the early B cell development in the bone marrow of the patient results in the absence of peripheral circulating mature B cells. Whole exome sequencing revealed a Loss of Heterozygosity (LOH) of approximately 19.20Mb containing CD79a on chromosome 19 in the patient. This is the first case of a homozygous CD79a mutation caused by segmental uniparental diploid (UPD). Another key outcome of this study is the effective management of long-term chronic enteroviral meningitis using a combination of intravenous immunoglobulin (IVIG) and fluoxetine. This approach offers compelling evidence of fluoxetine's utility in treating enteroviral meningitis, particularly in immunocompromised patients.
Collapse
Affiliation(s)
- Lang Yu
- National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Yishi Zhang
- National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Wenhui Li
- National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
- Molecular Medicine Diagnostic and Testing Center, Chongqing Medical University, Chongqing, China
| | - Jinxiao Mao
- Department of Pharmacy, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Yulin Li
- National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Haoru Wang
- National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Neurodevelopment and Cognitive Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Department of Radiology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Chenlin Li
- National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Lu Yang
- National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Wenli He
- National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Yanjun Jia
- National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Wenjing Tang
- National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
- Department of Rheumatology & Immunology, Children's Hospital of Chongqing Medical University, No. 136, Zhongshan 2nd Road, Yuzhong District, Chongqing, 400014, China
| | - Lina Zhou
- National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Zhiyong Zhang
- National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
- Department of Rheumatology & Immunology, Children's Hospital of Chongqing Medical University, No. 136, Zhongshan 2nd Road, Yuzhong District, Chongqing, 400014, China
| | - Yuntao Jia
- National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Department of Pharmacy, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Xuemei Tang
- National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
- Department of Rheumatology & Immunology, Children's Hospital of Chongqing Medical University, No. 136, Zhongshan 2nd Road, Yuzhong District, Chongqing, 400014, China
| | - Xiaodong Zhao
- National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.
- Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China.
- Department of Rheumatology & Immunology, Children's Hospital of Chongqing Medical University, No. 136, Zhongshan 2nd Road, Yuzhong District, Chongqing, 400014, China.
| | - Yunfei An
- National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.
- Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China.
- Department of Rheumatology & Immunology, Children's Hospital of Chongqing Medical University, No. 136, Zhongshan 2nd Road, Yuzhong District, Chongqing, 400014, China.
| |
Collapse
|
19
|
Kessler S, Burke B, Andrieux G, Schinköthe J, Hamberger L, Kacza J, Zhan S, Reasoner C, Dutt TS, Kaukab Osman M, Henao-Tamayo M, Staniek J, Villena Ossa JF, Frank DT, Ma W, Ulrich R, Cathomen T, Boerries M, Rizzi M, Beer M, Schwemmle M, Reuther P, Schountz T, Ciminski K. Deciphering bat influenza H18N11 infection dynamics in male Jamaican fruit bats on a single-cell level. Nat Commun 2024; 15:4500. [PMID: 38802391 PMCID: PMC11130286 DOI: 10.1038/s41467-024-48934-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 05/17/2024] [Indexed: 05/29/2024] Open
Abstract
Jamaican fruit bats (Artibeus jamaicensis) naturally harbor a wide range of viruses of human relevance. These infections are typically mild in bats, suggesting unique features of their immune system. To better understand the immune response to viral infections in bats, we infected male Jamaican fruit bats with the bat-derived influenza A virus (IAV) H18N11. Using comparative single-cell RNA sequencing, we generated single-cell atlases of the Jamaican fruit bat intestine and mesentery. Gene expression profiling showed that H18N11 infection resulted in a moderate induction of interferon-stimulated genes and transcriptional activation of immune cells. H18N11 infection was predominant in various leukocytes, including macrophages, B cells, and NK/T cells. Confirming these findings, human leukocytes, particularly macrophages, were also susceptible to H18N11, highlighting the zoonotic potential of this bat-derived IAV. Our study provides insight into a natural virus-host relationship and thus serves as a fundamental resource for future in-depth characterization of bat immunology.
Collapse
Affiliation(s)
- Susanne Kessler
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bradly Burke
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Geoffroy Andrieux
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Jan Schinköthe
- Institute of Veterinary Pathology, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - Lea Hamberger
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Johannes Kacza
- BioImaging Core Facility, Faculty of Veterinary Medicine, University of Leipzig, Leipzig, Germany
| | - Shijun Zhan
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Clara Reasoner
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Taru S Dutt
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Maria Kaukab Osman
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Marcela Henao-Tamayo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Julian Staniek
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Department of Rheumatology and Clinical Immunology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg, Germany
| | - Jose Francisco Villena Ossa
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg, Germany
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany
| | - Dalit T Frank
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Wenjun Ma
- Department of Veterinary Pathobiology and Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| | - Reiner Ulrich
- Institute of Veterinary Pathology, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - Toni Cathomen
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg, Germany
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany
| | - Melanie Boerries
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner site Freiburg, a partnership between DKFZ and Medical Center - University of Freiburg, Freiburg, Germany
| | - Marta Rizzi
- Department of Rheumatology and Clinical Immunology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- Division of Clinical and Experimental Immunology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald, Insel Riems, Germany
| | - Martin Schwemmle
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Peter Reuther
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tony Schountz
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.
| | - Kevin Ciminski
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany.
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| |
Collapse
|
20
|
Li CC, Liu M, Lee HP, Wu W, Ma L. Heterogeneity in Liver Cancer Immune Microenvironment: Emerging Single-Cell and Spatial Perspectives. Semin Liver Dis 2024; 44:133-146. [PMID: 38788780 DOI: 10.1055/s-0044-1787152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Primary liver cancer is a solid malignancy with a high mortality rate. The success of immunotherapy has shown great promise in improving patient care and highlights a crucial need to understand the complexity of the liver tumor immune microenvironment (TIME). Recent advances in single-cell and spatial omics technologies, coupled with the development of systems biology approaches, are rapidly transforming the landscape of tumor immunology. Here we review the cellular landscape of liver TIME from single-cell and spatial perspectives. We also discuss the cellular interaction networks within the tumor cell community in regulating immune responses. We further highlight the challenges and opportunities with implications for biomarker discovery, patient stratification, and combination immunotherapies.
Collapse
Affiliation(s)
- Caiyi Cherry Li
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Meng Liu
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Hsin-Pei Lee
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Wenqi Wu
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Lichun Ma
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| |
Collapse
|
21
|
Cho H, Kwon HY, Kim Y, Kim K, Lee EJ, Kang NY, Chang YT. Development of a Mature B Lymphocyte Probe through Gating-Oriented Live-Cell Distinction (GOLD) and Selective Imaging of Topical Spleen. JACS AU 2024; 4:1450-1457. [PMID: 38665660 PMCID: PMC11040558 DOI: 10.1021/jacsau.4c00001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 04/28/2024]
Abstract
B lymphocytes play a pivotal role in the adaptive immune system by facilitating antibody production. Young B cell progenitors originate in the bone marrow and migrate to the spleen for antigen-dependent maturation, leading to the development of diverse B cell subtypes. Thus, tracking B cell trajectories through cell type distinction is essential for an appropriate checkpoint assessment. Despite its significance, monitoring specific B cell subclasses in live states has been hindered by a lack of suitable molecular tools. In this study, we introduce CDoB as the first mature B cell-selective probe, enabling real-time discrimination of three classified stages in B-cell development: progenitor, transitional, and mature B cells, through a single analysis using CyTOF. The selective mechanism of CDoB, elucidated as gating-oriented live-cell distinction (GOLD), targets SLC25A16, identified through systematic screening of SLC-CRISPRa and CRISPRi libraries. CDoB selectively brightens mature B cells in the mitochondrial area using SLC25A16 as the main gate, and the staining intensity correlates positively with the expression level of SLC25A16 along the B cell maturation continuum. In spleen tissues, CDoB demonstrates selective marking in mature B cell areas in live tissue status, representing the first performance achieved by a small-molecule fluorescent probe.
Collapse
Affiliation(s)
- Heewon Cho
- Department
of Chemistry, Pohang University of Science
and Technology (POSTECH), Pohang, Gyeongsangbuk-do 37673, Republic of Korea
| | - Haw-Young Kwon
- Department
of Chemistry, Pohang University of Science
and Technology (POSTECH), Pohang, Gyeongsangbuk-do 37673, Republic of Korea
- Center
for Self-Assembly and Complexity, Institute
for Basic Science (IBS), Pohang, Gyeongsangbuk-do 37673, Republic of Korea
| | - Youngsook Kim
- Endocrinology,
Institute of Endocrine Research, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Kyungwon Kim
- Endocrinology,
Institute of Endocrine Research, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Eun Jig Lee
- Endocrinology,
Institute of Endocrine Research, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Nam-Young Kang
- Department
of Convergence IT Engineering, Pohang University
of Science and Technology (POSTECH), Pohang, Gyeongsangbuk-do 37673, Republic of Korea
| | - Young-Tae Chang
- Department
of Chemistry, Pohang University of Science
and Technology (POSTECH), Pohang, Gyeongsangbuk-do 37673, Republic of Korea
- Center
for Self-Assembly and Complexity, Institute
for Basic Science (IBS), Pohang, Gyeongsangbuk-do 37673, Republic of Korea
| |
Collapse
|
22
|
Kassis G, Palshikar MG, Hilchey SP, Zand MS, Thakar J. Discrete-state models identify pathway specific B cell states across diseases and infections at single-cell resolution. J Theor Biol 2024; 583:111769. [PMID: 38423206 PMCID: PMC11046450 DOI: 10.1016/j.jtbi.2024.111769] [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: 05/28/2023] [Revised: 02/10/2024] [Accepted: 02/17/2024] [Indexed: 03/02/2024]
Abstract
Oxygen (O2) regulated pathways modulate B cell activation, migration and proliferation during infection, vaccination, and other diseases. Modeling these pathways in health and disease is critical to understand B cell states and ways to mediate them. To characterize B cells by their activation of O2 regulated pathways we develop pathway specific discrete state models using previously published single-cell RNA-sequencing (scRNA-seq) datasets from isolated B cells. Specifically, Single Cell Boolean Omics Network Invariant-Time Analysis (scBONITA) was used to infer logic gates for known pathway topologies. The simplest inferred set of logic gates that maximized the number of "OR" interactions between genes was used to simulate B cell networks involved in oxygen sensing until they reached steady network states (attractors). By focusing on the attractors that best represented sequenced cells, we identified genes critical in determining pathway specific cellular states that corresponded to diseased and healthy B cell phenotypes. Specifically, we investigate the transendothelial migration, regulation of actin cytoskeleton, HIF1A, and Citrate Cycle pathways. Our analysis revealed attractors that resembled the state of B cell exhaustion in HIV+ patients as well as attractors that promoted anerobic metabolism, angiogenesis, and tumorigenesis in breast cancer patients, which were eliminated after neoadjuvant chemotherapy (NACT). Finally, we investigated the attractors to which the Azimuth-annotated B cells mapped and found that attractors resembling B cells from HIV+ patients encompassed a significantly larger number of atypical memory B cells than HIV- attractors. Meanwhile, attractors resembling B cells from breast cancer patients post NACT encompassed a reduced number of atypical memory B cells compared to pre-NACT attractors.
Collapse
Affiliation(s)
- George Kassis
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, USA
| | - Mukta G Palshikar
- Biophysics, Structural, and Computational Biology Program, University of Rochester School of Medicine and Dentistry, Rochester, USA
| | - Shannon P Hilchey
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY, USA
| | - Martin S Zand
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY, USA
| | - Juilee Thakar
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, USA; Biophysics, Structural, and Computational Biology Program, University of Rochester School of Medicine and Dentistry, Rochester, USA; Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, USA; Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry, Rochester, USA.
| |
Collapse
|
23
|
Huang X, Li Y, Zhang J, Yan L, Zhao H, Ding L, Bhatara S, Yang X, Yoshimura S, Yang W, Karol SE, Inaba H, Mullighan C, Litzow M, Zhu X, Zhang Y, Stock W, Jain N, Jabbour E, Kornblau SM, Konopleva M, Pui CH, Paietta E, Evans W, Yu J, Yang JJ. Single-cell systems pharmacology identifies development-driven drug response and combination therapy in B cell acute lymphoblastic leukemia. Cancer Cell 2024; 42:552-567.e6. [PMID: 38593781 PMCID: PMC11008188 DOI: 10.1016/j.ccell.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 02/19/2024] [Accepted: 03/11/2024] [Indexed: 04/11/2024]
Abstract
Leukemia can arise at various stages of the hematopoietic differentiation hierarchy, but the impact of developmental arrest on drug sensitivity is unclear. Applying network-based analyses to single-cell transcriptomes of human B cells, we define genome-wide signaling circuitry for each B cell differentiation stage. Using this reference, we comprehensively map the developmental states of B cell acute lymphoblastic leukemia (B-ALL), revealing its strong correlation with sensitivity to asparaginase, a commonly used chemotherapeutic agent. Single-cell multi-omics analyses of primary B-ALL blasts reveal marked intra-leukemia heterogeneity in asparaginase response: resistance is linked to pre-pro-B-like cells, with sensitivity associated with the pro-B-like population. By targeting BCL2, a driver within the pre-pro-B-like cell signaling network, we find that venetoclax significantly potentiates asparaginase efficacy in vitro and in vivo. These findings demonstrate a single-cell systems pharmacology framework to predict effective combination therapies based on intra-leukemia heterogeneity in developmental state, with potentially broad applications beyond B-ALL.
Collapse
Affiliation(s)
- Xin Huang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, Anhui 230601, China
| | - Yizhen Li
- Division of Pharmaceutical Sciences, Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Hematology, Children's Hospital of Soochow University, Suzhou, Jiangsu 215003, China
| | - Jingliao Zhang
- Department of Pediatrics Blood Diseases Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Lei Yan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Huanbin Zhao
- Division of Pharmaceutical Sciences, Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Liang Ding
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Sheetal Bhatara
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xu Yang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Satoshi Yoshimura
- Division of Pharmaceutical Sciences, Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Wenjian Yang
- Division of Pharmaceutical Sciences, Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Seth E Karol
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hiroto Inaba
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Charles Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mark Litzow
- Division of Hematology, Mayo Clinic, Rochester, MN 55905, USA
| | - Xiaofan Zhu
- Department of Pediatrics Blood Diseases Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Yingchi Zhang
- Department of Pediatrics Blood Diseases Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Wendy Stock
- Department of Medicine Section of Hematology-Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Nitin Jain
- Department of Leukemia, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Elias Jabbour
- Department of Leukemia, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Steven M Kornblau
- Department of Leukemia, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Marina Konopleva
- Department of Oncology and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Elisabeth Paietta
- Cancer Center, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - William Evans
- Division of Pharmaceutical Sciences, Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jiyang Yu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Jun J Yang
- Division of Pharmaceutical Sciences, Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| |
Collapse
|
24
|
Koga R, Maehara T, Aoyagi R, Munemura R, Murakami Y, Doi A, Kono M, Yamamoto H, Niiro H, Kiyoshima T, Tanabe M, Nakano T, Matsukuma Y, Kawano M, Stone JH, Pillai S, Nakamura S, Kawano S. Granzyme K- and amphiregulin-expressing cytotoxic T cells and activated extrafollicular B cells are potential drivers of IgG4-related disease. J Allergy Clin Immunol 2024; 153:1095-1112. [PMID: 38092138 DOI: 10.1016/j.jaci.2023.11.916] [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: 09/05/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 01/06/2024]
Abstract
BACKGROUND IgG4-related disease (IgG4-RD), an example of a type I immune disease, is an immune-mediated fibrotic disorder characterized by dysregulated resolution of severe inflammation and wound healing. However, truly dominant or pathognomonic autoantibodies related to IgG4-RD are not identified. OBJECTIVE We sought to perform single-cell RNA sequencing and T-cell receptor and B-cell receptor sequencing to obtain a comprehensive, unbiased view of tissue-infiltrating T and B cells. METHODS We performed unbiased single-cell RNA-sequencing analysis for the transcriptome and T-cell receptor sequencing and B-cell receptor sequencing on sorted CD3+ T or CD19+ B cells from affected tissues of patients with IgG4-RD. We also conducted quantitative analyses of CD3+ T-cell and CD19+ B-cell subsets in 68 patients with IgG4-RD and 30 patients with Sjögren syndrome. RESULTS Almost all clonally expanded T cells in these lesions were either Granzyme K (GZMK)-expressing CD4+ cytotoxic T cells or GZMK+CD8+ T cells. These GZMK-expressing cytotoxic T cells also expressed amphiregulin and TGF-β but did not express immune checkpoints, and the tissue-infiltrating CD8+ T cells were phenotypically heterogeneous. MKI67+ B cells and IgD-CD27-CD11c-CXCR5- double-negative 3 B cells were clonally expanded and infiltrated affected tissue lesions. GZMK+CD4+ cytotoxic T cells colocalized with MKI67+ B cells in the extrafollicular area from affected tissue sites. CONCLUSIONS The above-mentioned cells likely participate in T-B collaborative events, suggesting possible avenues for targeted therapies. Our findings were validated using orthogonal approaches, including multicolor immunofluorescence and the use of comparator disease groups, to support the central role of cytotoxic CD4+ and CD8+ T cells expressing GZMK, amphiregulin, and TGF-β in the pathogenesis of inflammatory fibrotic disorders.
Collapse
Affiliation(s)
- Risako Koga
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Takashi Maehara
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan; Dento-craniofacial Development and Regeneration Research Center, Faculty of Dental Science, Kyushu University, Kyushu, Japan.
| | - Ryuichi Aoyagi
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Ryusuke Munemura
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Yuka Murakami
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | | | - Michihito Kono
- Department of Rheumatology, Endocrinology and Nephrology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Hidetaka Yamamoto
- Graduate School of Medicine, Dentistry & Pharmaceutical Science, Okayama University, Okayama, Japan
| | - Hiroaki Niiro
- Department of Medical Education, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tamotsu Kiyoshima
- Laboratory of Oral Pathology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Mika Tanabe
- Department of Ophthalmology, Graduate School of Medicine Sciences, Kyushu University, Fukuoka, Japan
| | - Toshiaki Nakano
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yuta Matsukuma
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Mitsuhiro Kawano
- Division of Rheumatology, Department of Internal Medicine, Kanazawa University Hospital, Kanazawa, Japan
| | - John H Stone
- Division of Rheumatology, Allergy, and Immunology, Harvard Medical School, Boston, Mass
| | - Shiv Pillai
- Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital, Harvard Medical School, Boston, Mass
| | - Seiji Nakamura
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Shintaro Kawano
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| |
Collapse
|
25
|
Lee H, Shin K, Lee Y, Lee S, Lee S, Lee E, Kim SW, Shin HY, Kim JH, Chung J, Kwon S. Identification of B cell subsets based on antigen receptor sequences using deep learning. Front Immunol 2024; 15:1342285. [PMID: 38576618 PMCID: PMC10991714 DOI: 10.3389/fimmu.2024.1342285] [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: 11/21/2023] [Accepted: 03/07/2024] [Indexed: 04/06/2024] Open
Abstract
B cell receptors (BCRs) denote antigen specificity, while corresponding cell subsets indicate B cell functionality. Since each B cell uniquely encodes this combination, physical isolation and subsequent processing of individual B cells become indispensable to identify both attributes. However, this approach accompanies high costs and inevitable information loss, hindering high-throughput investigation of B cell populations. Here, we present BCR-SORT, a deep learning model that predicts cell subsets from their corresponding BCR sequences by leveraging B cell activation and maturation signatures encoded within BCR sequences. Subsequently, BCR-SORT is demonstrated to improve reconstruction of BCR phylogenetic trees, and reproduce results consistent with those verified using physical isolation-based methods or prior knowledge. Notably, when applied to BCR sequences from COVID-19 vaccine recipients, it revealed inter-individual heterogeneity of evolutionary trajectories towards Omicron-binding memory B cells. Overall, BCR-SORT offers great potential to improve our understanding of B cell responses.
Collapse
Affiliation(s)
- Hyunho Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Kyoungseob Shin
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Yongju Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Soobin Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Seungyoun Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Eunjae Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seung Woo Kim
- Department of Neurology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ha Young Shin
- Department of Neurology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Hoon Kim
- Department of Dermatology and Cutaneous Biology Research Institute, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Republic of Korea
- Bio-MAX Institute, Seoul National University, Seoul, Republic of Korea
- Inter-University Semiconductor Research Center, Seoul National University, Seoul, Republic of Korea
| |
Collapse
|
26
|
Mani S, Garifallou J, Kim SJ, Simoni MK, Huh DD, Gordon SM, Mainigi M. Uterine macrophages and NK cells exhibit population and gene-level changes after implantation but maintain pro-invasive properties. Front Immunol 2024; 15:1364036. [PMID: 38566989 PMCID: PMC10985329 DOI: 10.3389/fimmu.2024.1364036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction Prior to pregnancy, hormonal changes lead to cellular adaptations in the endometrium allowing for embryo implantation. Critical for successful pregnancy establishment, innate immune cells constitute a significant proportion of uterine cells prior to arrival of the embryo and throughout the first trimester in humans and animal models. Abnormal uterine immune cell function during implantation is believed to play a role in multiple adverse pregnancy outcomes. Current work in humans has focused on uterine immune cells present after pregnancy establishment, and limited in vitro models exist to explore unique functions of these cells. Methods With single-cell RNA-sequencing (scRNAseq), we comprehensively compared the human uterine immune landscape of the endometrium during the window of implantation and the decidua during the first trimester of pregnancy. Results We uncovered global and cell-type-specific gene signatures for each timepoint. Immune cells in the endometrium prior to implantation expressed genes associated with immune metabolism, division, and activation. In contrast, we observed widespread interferon signaling during the first trimester of pregnancy. We also provide evidence of specific inflammatory pathways enriched in pre- and post-implantation macrophages and natural killer (NK) cells in the uterine lining. Using our novel implantation-on-a-chip (IOC) to model human implantation ex vivo, we demonstrate for the first time that uterine macrophages strongly promote invasion of extravillous trophoblasts (EVTs), a process essential for pregnancy establishment. Pre- and post-implantation uterine macrophages promoted EVT invasion to a similar degree as pre- and post-implantation NK cells on the IOC. Conclusions This work provides a foundation for further investigation of the individual roles of uterine immune cell subtypes present prior to embryo implantation and during early pregnancy, which will be critical for our understanding of pregnancy complications associated with abnormal trophoblast invasion and placentation.
Collapse
Affiliation(s)
- Sneha Mani
- Division of Reproductive Endocrinology and Infertility, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, United States
| | - James Garifallou
- Division of Neonatology, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Se-jeong Kim
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States
| | - Michael K. Simoni
- Division of Reproductive Endocrinology and Infertility, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, United States
| | - Dan Dongeun Huh
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States
- National Science Foundation (NSF) Science and Technology Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, United States
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Scott M. Gordon
- Division of Neonatology, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Pediatrics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, United States
| | - Monica Mainigi
- Division of Reproductive Endocrinology and Infertility, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, United States
| |
Collapse
|
27
|
Tangye SG, Mackie J, Pathmanandavel K, Ma CS. The trajectory of human B-cell function, immune deficiency, and allergy revealed by inborn errors of immunity. Immunol Rev 2024; 322:212-232. [PMID: 37983844 DOI: 10.1111/imr.13288] [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: 11/22/2023]
Abstract
The essential role of B cells is to produce protective immunoglobulins (Ig) that recognize, neutralize, and clear invading pathogens. This results from the integration of signals provided by pathogens or vaccines and the stimulatory microenvironment within sites of immune activation, such as secondary lymphoid tissues, that drive mature B cells to differentiate into memory B cells and antibody (Ab)-secreting plasma cells. In this context, B cells undergo several molecular events including Ig class switching and somatic hypermutation that results in the production of high-affinity Ag-specific Abs of different classes, enabling effective pathogen neutralization and long-lived humoral immunity. However, perturbations to these key signaling pathways underpin immune dyscrasias including immune deficiency and autoimmunity or allergy. Inborn errors of immunity that disrupt critical immune pathways have identified non-redundant requirements for eliciting and maintaining humoral immune memory but concomitantly prevent immune dysregulation. Here, we will discuss our studies on human B cells, and how our investigation of cytokine signaling in B cells have identified fundamental requirements for memory B-cell formation, Ab production as well as regulating Ig class switching in the context of protective versus allergic immune responses.
Collapse
Affiliation(s)
- Stuart G Tangye
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Joseph Mackie
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Karrnan Pathmanandavel
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Cindy S Ma
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| |
Collapse
|
28
|
Afzali AM, Nirschl L, Sie C, Pfaller M, Ulianov O, Hassler T, Federle C, Petrozziello E, Kalluri SR, Chen HH, Tyystjärvi S, Muschaweckh A, Lammens K, Delbridge C, Büttner A, Steiger K, Seyhan G, Ottersen OP, Öllinger R, Rad R, Jarosch S, Straub A, Mühlbauer A, Grassmann S, Hemmer B, Böttcher JP, Wagner I, Kreutzfeldt M, Merkler D, Pardàs IB, Schmidt Supprian M, Buchholz VR, Heink S, Busch DH, Klein L, Korn T. B cells orchestrate tolerance to the neuromyelitis optica autoantigen AQP4. Nature 2024; 627:407-415. [PMID: 38383779 PMCID: PMC10937377 DOI: 10.1038/s41586-024-07079-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 01/16/2024] [Indexed: 02/23/2024]
Abstract
Neuromyelitis optica is a paradigmatic autoimmune disease of the central nervous system, in which the water-channel protein AQP4 is the target antigen1. The immunopathology in neuromyelitis optica is largely driven by autoantibodies to AQP42. However, the T cell response that is required for the generation of these anti-AQP4 antibodies is not well understood. Here we show that B cells endogenously express AQP4 in response to activation with anti-CD40 and IL-21 and are able to present their endogenous AQP4 to T cells with an AQP4-specific T cell receptor (TCR). A population of thymic B cells emulates a CD40-stimulated B cell transcriptome, including AQP4 (in mice and humans), and efficiently purges the thymic TCR repertoire of AQP4-reactive clones. Genetic ablation of Aqp4 in B cells rescues AQP4-specific TCRs despite sufficient expression of AQP4 in medullary thymic epithelial cells, and B-cell-conditional AQP4-deficient mice are fully competent to raise AQP4-specific antibodies in productive germinal-centre responses. Thus, the negative selection of AQP4-specific thymocytes is dependent on the expression and presentation of AQP4 by thymic B cells. As AQP4 is expressed in B cells in a CD40-dependent (but not AIRE-dependent) manner, we propose that thymic B cells might tolerize against a group of germinal-centre-associated antigens, including disease-relevant autoantigens such as AQP4.
Collapse
Affiliation(s)
- Ali Maisam Afzali
- Institute for Experimental Neuroimmunology, Technical University of Munich School of Medicine and Health, Munich, Germany
- Department of Neurology, Technical University of Munich School of Medicine and Health, Munich, Germany
- Munich Cluster for Systems Neurology, Munich, Germany
| | - Lucy Nirschl
- Institute for Experimental Neuroimmunology, Technical University of Munich School of Medicine and Health, Munich, Germany
| | - Christopher Sie
- Institute for Experimental Neuroimmunology, Technical University of Munich School of Medicine and Health, Munich, Germany
| | - Monika Pfaller
- Institute for Experimental Neuroimmunology, Technical University of Munich School of Medicine and Health, Munich, Germany
| | - Oleksii Ulianov
- Institute for Experimental Neuroimmunology, Technical University of Munich School of Medicine and Health, Munich, Germany
| | - Tobias Hassler
- Biomedical Center (BMC), Institute for Immunology, Faculty of Medicine, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Christine Federle
- Biomedical Center (BMC), Institute for Immunology, Faculty of Medicine, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Elisabetta Petrozziello
- Biomedical Center (BMC), Institute for Immunology, Faculty of Medicine, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Sudhakar Reddy Kalluri
- Department of Neurology, Technical University of Munich School of Medicine and Health, Munich, Germany
| | - Hsin Hsiang Chen
- Institute for Experimental Neuroimmunology, Technical University of Munich School of Medicine and Health, Munich, Germany
| | - Sofia Tyystjärvi
- Institute for Experimental Neuroimmunology, Technical University of Munich School of Medicine and Health, Munich, Germany
| | - Andreas Muschaweckh
- Institute for Experimental Neuroimmunology, Technical University of Munich School of Medicine and Health, Munich, Germany
| | - Katja Lammens
- Department of Biochemistry at the Gene Center, Ludwig-Maximilians-University, Munich, Germany
| | - Claire Delbridge
- Institute of Pathology, Technical University of Munich School of Medicine and Health, Munich, Germany
- Department of Neuropathology, Institute of Pathology, Technical University of Munich School of Medicine and Health, Munich, Germany
| | - Andreas Büttner
- Institute of Forensic Medicine, Rostock University Medical Center, Rostock, Germany
| | - Katja Steiger
- Institute of Pathology, Technical University of Munich School of Medicine and Health, Munich, Germany
| | - Gönül Seyhan
- Institute for Experimental Hematology, TranslaTUM Cancer Center, Technical University of Munich School of Medicine and Health, Munich, Germany
| | - Ole Petter Ottersen
- Division of Anatomy, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics, TranslaTUM Cancer Center, Technical University of Munich School of Medicine and Health, Munich, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, TranslaTUM Cancer Center, Technical University of Munich School of Medicine and Health, Munich, Germany
| | - Sebastian Jarosch
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich School of Medicine and Health, Munich, Germany
| | - Adrian Straub
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich School of Medicine and Health, Munich, Germany
| | - Anton Mühlbauer
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich School of Medicine and Health, Munich, Germany
| | - Simon Grassmann
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bernhard Hemmer
- Department of Neurology, Technical University of Munich School of Medicine and Health, Munich, Germany
- Munich Cluster for Systems Neurology, Munich, Germany
| | - Jan P Böttcher
- Institute of Molecular Immunology, Technical University of Munich School of Medicine and Health, Munich, Germany
| | - Ingrid Wagner
- Department of Pathology and Immunology, Division of Clinical Pathology, Geneva Faculty of Medicine, Centre Médical Universitaire, Geneva, Switzerland
| | - Mario Kreutzfeldt
- Department of Pathology and Immunology, Division of Clinical Pathology, Geneva Faculty of Medicine, Centre Médical Universitaire, Geneva, Switzerland
| | - Doron Merkler
- Department of Pathology and Immunology, Division of Clinical Pathology, Geneva Faculty of Medicine, Centre Médical Universitaire, Geneva, Switzerland
| | | | - Marc Schmidt Supprian
- Institute for Experimental Hematology, TranslaTUM Cancer Center, Technical University of Munich School of Medicine and Health, Munich, Germany
| | - Veit R Buchholz
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich School of Medicine and Health, Munich, Germany
| | - Sylvia Heink
- Institute for Experimental Neuroimmunology, Technical University of Munich School of Medicine and Health, Munich, Germany
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich School of Medicine and Health, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Ludger Klein
- Biomedical Center (BMC), Institute for Immunology, Faculty of Medicine, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Thomas Korn
- Institute for Experimental Neuroimmunology, Technical University of Munich School of Medicine and Health, Munich, Germany.
- Department of Neurology, Technical University of Munich School of Medicine and Health, Munich, Germany.
- Munich Cluster for Systems Neurology, Munich, Germany.
| |
Collapse
|
29
|
Andresen AMS, Taylor RS, Grimholt U, Daniels RR, Sun J, Dobie R, Henderson NC, Martin SAM, Macqueen DJ, Fosse JH. Mapping the cellular landscape of Atlantic salmon head kidney by single cell and single nucleus transcriptomics. FISH & SHELLFISH IMMUNOLOGY 2024; 146:109357. [PMID: 38181891 DOI: 10.1016/j.fsi.2024.109357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/07/2024]
Abstract
Single-cell transcriptomics is the current gold standard for global gene expression profiling, not only in mammals and model species, but also in non-model fish species. This is a rapidly expanding field, creating a deeper understanding of tissue heterogeneity and the distinct functions of individual cells, making it possible to explore the complexities of immunology and gene expression on a highly resolved level. In this study, we compared two single cell transcriptomic approaches to investigate cellular heterogeneity within the head kidney of healthy farmed Atlantic salmon (Salmo salar). We compared 14,149 cell transcriptomes assayed by single cell RNA-seq (scRNA-seq) with 18,067 nuclei transcriptomes captured by single nucleus RNA-Seq (snRNA-seq). Both approaches detected eight major cell populations in common: granulocytes, heamatopoietic stem cells, erythrocytes, mononuclear phagocytes, thrombocytes, B cells, NK-like cells, and T cells. Four additional cell types, endothelial, epithelial, interrenal, and mesenchymal cells, were detected in the snRNA-seq dataset, but appeared to be lost during preparation of the single cell suspension submitted for scRNA-seq library generation. We identified additional heterogeneity and subpopulations within the B cells, T cells, and endothelial cells, and revealed developmental trajectories of heamatopoietic stem cells into differentiated granulocyte and mononuclear phagocyte populations. Gene expression profiles of B cell subtypes revealed distinct IgM and IgT-skewed resting B cell lineages and provided insights into the regulation of B cell lymphopoiesis. The analysis revealed eleven T cell sub-populations, displaying a level of T cell heterogeneity in salmon head kidney comparable to that observed in mammals, including distinct subsets of cd4/cd8-negative T cells, such as tcrγ positive, progenitor-like, and cytotoxic cells. Although snRNA-seq and scRNA-seq were both useful to resolve cell type-specific expression in the Atlantic salmon head kidney, the snRNA-seq pipeline was overall more robust in identifying several cell types and subpopulations. While scRNA-seq displayed higher levels of ribosomal and mitochondrial genes, snRNA-seq captured more transcription factor genes. However, only scRNA-seq-generated data was useful for cell trajectory inference within the myeloid lineage. In conclusion, this study systematically outlines the relative merits of scRNA-seq and snRNA-seq in Atlantic salmon, enhances understanding of teleost immune cell lineages, and provides a comprehensive list of markers for identifying major cell populations in the head kidney with significant immune relevance.
Collapse
Affiliation(s)
| | - Richard S Taylor
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Rose Ruiz Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Jianxuan Sun
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Ross Dobie
- Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, United Kingdom
| | - Neil C Henderson
- Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, United Kingdom; MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Samuel A M Martin
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Daniel J Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom.
| | | |
Collapse
|
30
|
Guo S, Mohan GS, Wang B, Li T, Daver N, Zhao Y, Reville PK, Hao D, Abbas HA. Paired single-B-cell transcriptomics and receptor sequencing reveal activation states and clonal signatures that characterize B cells in acute myeloid leukemia. J Immunother Cancer 2024; 12:e008318. [PMID: 38418394 PMCID: PMC10910691 DOI: 10.1136/jitc-2023-008318] [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] [Accepted: 01/23/2024] [Indexed: 03/01/2024] Open
Abstract
BACKGROUND Acute myeloid leukemia (AML) is associated with a dismal prognosis. Immune checkpoint blockade (ICB) to induce antitumor activity in AML patients has yielded mixed results. Despite the pivotal role of B cells in antitumor immunity, a comprehensive assessment of B lymphocytes within AML's immunological microenvironment along with their interaction with ICB remains rather constrained. METHODS We performed an extensive analysis that involved paired single-cell RNA and B-cell receptor (BCR) sequencing on 52 bone marrow aspirate samples. These samples included 6 from healthy bone marrow donors (normal), 24 from newly diagnosed AML patients (NewlyDx), and 22 from 8 relapsed or refractory AML patients (RelRef), who underwent assessment both before and after azacitidine/nivolumab treatment. RESULTS We delineated nine distinct subtypes of B cell lineage in the bone marrow. AML patients exhibited reduced nascent B cell subgroups but increased differentiated B cells compared with healthy controls. The limited diversity of BCR profiles and extensive somatic hypermutation indicated antigen-driven affinity maturation within the tumor microenvironment of RelRef patients. We established a strong connection between the activation or stress status of naïve and memory B cells, as indicated by AP-1 activity, and their differentiation state. Remarkably, atypical memory B cells functioned as specialized antigen-presenting cells closely interacting with AML malignant cells, correlating with AML stemness and worse clinical outcomes. In the AML microenvironment, plasma cells demonstrated advanced differentiation and heightened activity. Notably, the clinical response to ICB was associated with B cell clonal expansion and plasma cell function. CONCLUSIONS Our findings establish a comprehensive framework for profiling the phenotypic diversity of the B cell lineage in AML patients, while also assessing the implications of immunotherapy. This will serve as a valuable guide for future inquiries into AML treatment strategies.
Collapse
Affiliation(s)
- Shengnan Guo
- School of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang, China
| | - Gopi S Mohan
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Bofei Wang
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Tianhao Li
- School of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang, China
| | - Naval Daver
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yuting Zhao
- School of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang, China
| | - Patrick K Reville
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Dapeng Hao
- School of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang, China
| | - Hussein A Abbas
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| |
Collapse
|
31
|
Lee CM, Hwang Y, Jeong JW, Kim M, Lee J, Bae SJ, Ahn SG, Fang S. BRCA1 mutation promotes sprouting angiogenesis in inflammatory cancer-associated fibroblast of triple-negative breast cancer. Cell Death Discov 2024; 10:5. [PMID: 38182557 PMCID: PMC10770063 DOI: 10.1038/s41420-023-01768-5] [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: 10/25/2023] [Revised: 12/02/2023] [Accepted: 12/07/2023] [Indexed: 01/07/2024] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype with inferior outcomes owing to its low treatment response and high invasiveness. Based on abundant cancer-associated fibroblasts (CAFs) and frequent mutation of breast cancer-associated 1 (BRCA1) in TNBC, the characteristics of CAFs in TNBC patients with BRCA1 mutation compared to wild-type were investigated using single-cell analysis. Intriguingly, we observed that characteristics of inflammatory CAFs (iCAFs) were enriched in patients with BRCA1 mutation compared to the wild-type. iCAFs in patients with BRCA1 mutation exhibited outgoing signals to endothelial cells (ECs) clusters, including chemokine (C-X-C motif) ligand (CXCL) and vascular endothelial growth factor (VEGF). During CXCL signaling, the atypical chemokine receptor 1 (ACKR1) mainly interacts with CXCL family members in tumor endothelial cells (TECs). ACKR1-high TECs also showed high expression levels of angiogenesis-related genes, such as ANGPT2, MMP1, and SELE, which might lead to EC migration. Furthermore, iCAFs showed VEGF signals for FLT1 and KDR in TECs, which showed high co-expression with tip cell marker genes, including ZEB1 and MAFF, involved in sprouting angiogenesis. Moreover, BRCA1 mutation patients with relatively abundant iCAFs and tip cell gene expression exhibited a limited response to neoadjuvant chemotherapy, including cisplatin and bevacizumab. Importantly, our study observed the intricate link between iCAFs-mediated angiogenesis and chemoresistance in TNBC with BRCA1 mutation.
Collapse
Affiliation(s)
- Chae Min Lee
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
- Department of Biomedical Sciences, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Yeseong Hwang
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
- Department of Biomedical Sciences, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Jae Woong Jeong
- Department of Medicine, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Minki Kim
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
- Department of Biomedical Sciences, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Janghee Lee
- Department of Surgery, Sacred Heart Hospital, Hallym University, Dongtan, 18450, Republic of Korea
- Department of Medicine, Yonsei University Graduate School, Seoul, 03722, Republic of Korea
| | - Soong June Bae
- Department of Surgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 06273, Republic of Korea
- Institute for Breast Cancer Precision Medicine, Yonsei University College of Medicine, Seoul, 06273, Republic of Korea
| | - Sung Gwe Ahn
- Department of Surgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 06273, Republic of Korea.
- Institute for Breast Cancer Precision Medicine, Yonsei University College of Medicine, Seoul, 06273, Republic of Korea.
| | - Sungsoon Fang
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
- Department of Biomedical Sciences, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
- Chronic Intractable Disease for Systems Medicine Research Center, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
- Severance Institute for Vascular and Metabolic Research, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
| |
Collapse
|
32
|
Chaudhary R, Khanna J, Rohilla M, Gupta S, Bansal S. Investigation of Pancreatic-beta Cells Role in the Biological Process of Ageing. Endocr Metab Immune Disord Drug Targets 2024; 24:348-362. [PMID: 37608675 DOI: 10.2174/1871530323666230822095932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/27/2023] [Accepted: 07/20/2023] [Indexed: 08/24/2023]
Abstract
BACKGROUND Cellular senescence is associated with the formation and progression of a range of illnesses, including ageing and metabolic disorders such as diabetes mellitus and pancreatic beta cell dysfunction. Ageing and reduced glucose tolerance are interconnected. Often, Diabetes is becoming more common, which is concerning since it raises the risk of a variety of age-dependent disorders such as cardiovascular disease, cancer, Parkinson's disease, stroke, and Alzheimer's disease. OBJECTIVES The objectives of this study are to find out the most recent research on how ageing affects the functions of pancreatic beta cells, beta cell mass, beta cell senescence, mitochondrial dysfunction, and hormonal imbalance. METHODS Various research and review manuscripts are gathered from various records such as Google Scholar, PubMed, Mendeley, Scopus, Science Open, the Directory of Open Access Journals, and the Education Resources Information Centre, using different terms like "Diabetes, cellular senescence, beta cells, ageing, insulin, glucose". RESULTS In this review, we research novel targets in order to discover new strategies to treat diabetes. Abnormal glucose homeostasis and type 2 diabetes mellitus in the elderly may aid in the development of novel medicines to delay or prevent diabetes onset, improve quality of life, and, finally, increase life duration. CONCLUSION Aging accelerates beta cell senescence by generating premature cell senescence, which is mostly mediated by high glucose levels. Despite higher plasma glucose levels, hepatic gluconeogenesis accelerates and adipose tissue lipolysis rises, resulting in an increase in free fatty acid levels in the blood and worsening insulin resistance throughout the body.
Collapse
Affiliation(s)
- Rishabh Chaudhary
- Department of Pharmacology, M. M. College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133206, India
| | - Janvi Khanna
- Department of Pharmacology, M. M. College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133206, India
| | - Manni Rohilla
- Department of Pharmacology, M. M. College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133206, India
- Department of Pharmacology, Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab, 140401, India
| | - Sumeet Gupta
- Department of Pharmacology, M. M. College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133206, India
| | - Seema Bansal
- Department of Pharmacology, M. M. College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133206, India
| |
Collapse
|
33
|
de Melo DB, Pereira RMR, Sini B, Levy D, Takayama L, Kokron CM, Berselli Marinho AK, Grecco O, Filho JEK, Barros MT. Bone Mineral Density is Related to CD4 + T Cell Counts and Muscle Mass is Associated with B Cells in Common Variable Immunodeficiency Patients. Endocr Metab Immune Disord Drug Targets 2024; 24:242-254. [PMID: 37608677 DOI: 10.2174/1871530323666230822100031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 06/11/2023] [Accepted: 07/12/2023] [Indexed: 08/24/2023]
Abstract
BACKGROUND Common variable immunodeficiency (CVID) is a primary immunodeficiency characterized by chronic/recurrent respiratory infections, bronchiectasis, autoimmunity, inflammatory, gastrointestinal diseases and malignancies associated with a chronic inflammatory state and increased risk of osteoporosis and muscle loss. AIM The aim of this study was to evaluate bone mineral density (BMD), body composition and their relationship with lymphocyte subpopulations in CVID patients. METHODS Dual-energy X-ray absorptiometry was performed to assess BMD, lean mass, and fat mass in CVID patients. Peripheral blood CD4+, CD8+, and CD19+ cells were measured using flow cytometry. RESULTS Thirty-three patients (37.3 ± 10.8 years old) were examined. Although only 11.8% of the individuals were malnourished (BMI <18.5 kg/m2), 27.7% of them had low skeletal muscle mass index (SMI), and 57.6% of them had low BMD. Patients with osteopenia/osteoporosis presented lower weight (p = 0.007), lean mass (p = 0.011), appendicular lean mass (p = 0.011), SMI (p = 0.017), and CD4+ count (p = 0.030). Regression models showed a positive association between CD4+ count and bone/muscle parameters, whereas CD19+ B cell count was only associated with muscle variables. Analysis of ROC curves indicated a cutoff value of CD4+ count (657 cells/mm3; AUC: 0.71, 95% CI 0.52-0.90) which was related to low BMD. Weight (p = 0.004), lean mass (p = 0.027), appendicular lean mass (p = 0.022), SMI (p = 0.029), total bone mineral content (p = 0.005), lumbar (p = 0.005), femoral neck (p = 0.035), and total hip BMD (p<0.001) were found to be lower in patients with CD4+ count below the cutoff. CONCLUSION CVID patients presented with low BMD, which was associated with CD4+ count. Moreover, low muscle parameters were correlated with B cell count.
Collapse
Affiliation(s)
- Daniel Barreto de Melo
- Clinical Immunology and Allergy Division, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | | | - Bruno Sini
- Clinical Immunology and Allergy Division, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Débora Levy
- Laboratory of Histo-compatibility and Cellular Immunity - LIM19, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Lilian Takayama
- Rheumatology Division, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Cristina Maria Kokron
- Clinical Immunology and Allergy Division, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | | | - Octavio Grecco
- Clinical Immunology and Allergy Division, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Jorge Elias Kalil Filho
- Clinical Immunology and Allergy Division, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Myrthes Toledo Barros
- Clinical Immunology and Allergy Division, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| |
Collapse
|
34
|
Ning K, Shi C, Chi YY, Zhou YF, Zheng W, Duan Y, Tong W, Xie Q, Xiang H. Portulaca oleracea L. polysaccharide alleviates dextran sulfate sodium-induced ulcerative colitis by regulating intestinal homeostasis. Int J Biol Macromol 2024; 256:128375. [PMID: 38000581 DOI: 10.1016/j.ijbiomac.2023.128375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 11/26/2023]
Abstract
Portulaca oleracea L. (purslane) is a vegetable that contains a variety of active compounds with nutritional properties and has the potential to treat ulcerative colitis (UC). However, the mechanisms underlying the effects of Portulaca oleracea L. polysaccharide (POP) in alleviating UC remain unclear. In this study, we prepared an aqueous extract of purslane and separated a fraction with molecular weight >10 kDa using membrane separation. This fraction was used to isolate POP. The effect of POP on gut microbiota and colon transcriptome in dextran sulfate sodium-induced UC model mice was evaluated. POP treatment reduced inflammation and oxidative stress imbalance in UC mice. In addition, POP improved the intestinal barrier and regulated intestinal homeostasis. Importantly, POP was found to regulate gut microbiota, maintain the levels of retinol and short-chain fatty acids in the gut, promote the proliferation and differentiation of B cells in the colon, and increase the expression of immunoglobulin A. These results provide novel insights into the role of POP in regulating intestinal homeostasis, which should guide further development of POP as a functional food.
Collapse
Affiliation(s)
- Ke Ning
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, PR China
| | - Chao Shi
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, PR China
| | - Yan-Yu Chi
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, PR China
| | - Yong-Fei Zhou
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, PR China
| | - Weiwei Zheng
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, PR China
| | - Yameng Duan
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, PR China
| | - Weiwei Tong
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, PR China
| | - Qiuhong Xie
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, PR China; Institute of Changbai Mountain Resource and Health, Jilin University, Fusong 134504, PR China.
| | - Hongyu Xiang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, PR China; Institute of Changbai Mountain Resource and Health, Jilin University, Fusong 134504, PR China.
| |
Collapse
|
35
|
Hu T, Allam M, Cai S, Henderson W, Yueh B, Garipcan A, Ievlev AV, Afkarian M, Beyaz S, Coskun AF. Single-cell spatial metabolomics with cell-type specific protein profiling for tissue systems biology. Nat Commun 2023; 14:8260. [PMID: 38086839 PMCID: PMC10716522 DOI: 10.1038/s41467-023-43917-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Metabolic reprogramming in cancer and immune cells occurs to support their increasing energy needs in biological tissues. Here we propose Single Cell Spatially resolved Metabolic (scSpaMet) framework for joint protein-metabolite profiling of single immune and cancer cells in male human tissues by incorporating untargeted spatial metabolomics and targeted multiplexed protein imaging in a single pipeline. We utilized the scSpaMet to profile cell types and spatial metabolomic maps of 19507, 31156, and 8215 single cells in human lung cancer, tonsil, and endometrium tissues, respectively. The scSpaMet analysis revealed cell type-dependent metabolite profiles and local metabolite competition of neighboring single cells in human tissues. Deep learning-based joint embedding revealed unique metabolite states within cell types. Trajectory inference showed metabolic patterns along cell differentiation paths. Here we show scSpaMet's ability to quantify and visualize the cell-type specific and spatially resolved metabolic-protein mapping as an emerging tool for systems-level understanding of tissue biology.
Collapse
Affiliation(s)
- Thomas Hu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Mayar Allam
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Shuangyi Cai
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Walter Henderson
- Institute for Electronics and Nanotechnology, Georgia Institute of Technology, Atlanta, GA, USA
| | - Brian Yueh
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Anton V Ievlev
- Oak Ridge National Laboratory, Center for Nanophase Materials Sciences, Oak Ridge, TN, USA
| | - Maryam Afkarian
- Division of Nephrology, Department of Internal Medicine, University of California, Davis, CA, USA
| | - Semir Beyaz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Ahmet F Coskun
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, GA, USA.
- Winship Cancer Institute, Emory University, Atlanta, GA, USA.
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA.
| |
Collapse
|
36
|
Hsieh CH, Lee J, Sung HH, Huang YF, Ding YS, Li CY, Yen CL, Hsu CK, Yu CK, Hsieh HY, Hughes MW, Chen PC, Shieh CC. Novel SLC5A6 mutations lead to B lymphocyte maturation defects with metabolic abnormality rescuable by biotin replenishment. Clin Immunol 2023; 257:109855. [PMID: 38036278 DOI: 10.1016/j.clim.2023.109855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/27/2023] [Accepted: 11/21/2023] [Indexed: 12/02/2023]
Abstract
We characterized a family diagnosed with immunodeficiency disease presenting with low immunoglobulin levels and skin dyskeratosis. Exome sequencing revealed compound heterozygous missense variants in SLC5A6, the gene encoding a cellular sodium-dependent multivitamin transporter (SMVT) responsible for transporting vitamins, including biotin (vitamin B7). We showed that the biotin deficiency was caused by the SLC5A6 variants resulting in defective B cell differentiation and antibody deficiency. Altered cellular metabolic profiles, including aberrant mitochondrial respiration and reliance on glycolysis, may underlie the failure in plasma cell maturation. Replenishment of biotin improved plasma cell maturation and recovered the antibody producing activity in the patient and in a CRISPR-Cas9 gene-edited mouse model bearing a patient-specific SLC5A6 variant. Our results demonstrate the critical role of metabolic reprogramming in the maturation of plasma cells and nominate SLC5A6 as a causative gene for immunodeficiency that may be treated by biotin replenishment.
Collapse
Affiliation(s)
- Chu-Han Hsieh
- Institute of Clinical Medicine, College of Medicine, National Cheng-Kung University, Tainan, Taiwan
| | - Ju Lee
- Department of Pediatrics, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Hsiang-Hsuan Sung
- National Laboratory Animal Center, National Applied Research Laboratory, Taipei, Taiwan
| | - Ya-Fang Huang
- National Laboratory Animal Center, National Applied Reasearch Laboratories, Tainan, Taiwan
| | - Yu-Sian Ding
- National Laboratory Animal Center, National Applied Reasearch Laboratories, Tainan, Taiwan
| | - Chia-Yi Li
- Institute of Clinical Medicine, College of Medicine, National Cheng-Kung University, Tainan, Taiwan
| | - Chia-Liang Yen
- Institute of Clinical Medicine, College of Medicine, National Cheng-Kung University, Tainan, Taiwan
| | - Chao-Kai Hsu
- Institute of Clinical Medicine, College of Medicine, National Cheng-Kung University, Tainan, Taiwan; International Research Center for Wound Repair and Regeneration, National Cheng Kung University, Tainan, Taiwan
| | - Chun-Keung Yu
- National Laboratory Animal Center, National Applied Research Laboratory, Taipei, Taiwan; Department of Microbiology and Immunology, Center of Infectious Disease and Signaling Research, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hsin-Ying Hsieh
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
| | - Michael Warren Hughes
- Institute of Clinical Medicine, College of Medicine, National Cheng-Kung University, Tainan, Taiwan; International Research Center for Wound Repair and Regeneration, National Cheng Kung University, Tainan, Taiwan
| | - Peng-Chieh Chen
- Institute of Clinical Medicine, College of Medicine, National Cheng-Kung University, Tainan, Taiwan; Research Center of Clinical Medicine, College of Medicine, National Cheng Kung University Hospital, National Cheng-Kung University, Tainan, Taiwan.
| | - Chi-Chang Shieh
- Institute of Clinical Medicine, College of Medicine, National Cheng-Kung University, Tainan, Taiwan; Research Center of Clinical Medicine, College of Medicine, National Cheng Kung University Hospital, National Cheng-Kung University, Tainan, Taiwan; Department of Pediatrics, National Cheng Kung University Hospital, Tainan, Taiwan.
| |
Collapse
|
37
|
Kim CW, Joo SY, Kim B, Kim JY, Jang S, Tzeng SJ, Lee SJ, Kim M, Kim I. Single cell transcriptome analyses reveal the roles of B cells in fructose-induced hypertension. Front Immunol 2023; 14:1279439. [PMID: 38045685 PMCID: PMC10691591 DOI: 10.3389/fimmu.2023.1279439] [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: 08/18/2023] [Accepted: 10/31/2023] [Indexed: 12/05/2023] Open
Abstract
Rationale While the immune system plays a crucial role in the development of hypertension, the specific contributions of distinct immune cell populations remain incompletely understood. The emergence of single-cell RNA-sequencing (scRNA-seq) technology enables us to analyze the transcriptomes of individual immune cells and to assess the significance of each immune cell type in hypertension development. Objective We aimed to investigate the hypothesis that B cells play a crucial role in the development of fructose-induced hypertension. Methods and Results Eight-week-old Dahl salt-sensitive (SS) male rats were divided into two groups and given either tap water (TW) or a 20% fructose solution (HFS) for 4 weeks. Systolic blood pressure was measured using the tail-cuff method. ScRNA-seq analysis was performed on lamina propria cells (LPs) and peripheral blood mononuclear cells (PBMCs) obtained from SS rats subjected to either TW or HFS. The HFS treatment induced hypertension in the SS rats. The analysis revealed 27 clusters in LPs and 28 clusters in PBMCs, allowing for the identification and characterization of various immune cell types within each cluster. Specifically, B cells and follicular helper T (Tfh) cells were prominent in LPs, while B cells and M1 macrophages dominated PBMCs in the HFS group. Moreover, the HFS treatment triggered an increase in the number of B cells in both LPs and PBMCs, accompanied by activation of the interferon pathway. Conclusions The significant involvement of B cells in intestinal and PBMC responses indicates their pivotal contribution to the development of hypertension. This finding suggests that targeting B cells could be a potential strategy to mitigate high blood pressure in fructose-induced hypertension. Moreover, the simultaneous increase in follicular B cells and Tfh cells in LPs, along with the upregulation of interferon pathway genes in B cells, underscores a potential autoimmune factor contributing to the pathogenesis of fructose-induced hypertension in the intestine.
Collapse
Affiliation(s)
- Cheong-Wun Kim
- Department of Pharmacology, BK21 Plus Kyungpook National University (KNU) Biomedical Convergence Program, Cardiovascular Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Sung Yong Joo
- Department of Animal Science, Pusan National University, Miryang, Republic of Korea
| | - Boa Kim
- Cardiovascular Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Jee Young Kim
- Department of Pharmacology, BK21 Plus Kyungpook National University (KNU) Biomedical Convergence Program, Cardiovascular Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Sungmin Jang
- Department of Pharmacology, BK21 Plus Kyungpook National University (KNU) Biomedical Convergence Program, Cardiovascular Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Shiang-Jong Tzeng
- Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Sang Jin Lee
- Division of Rheumatology, Cardiovascular Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Myunghoo Kim
- Department of Animal Science, Pusan National University, Miryang, Republic of Korea
| | - Inkyeom Kim
- Department of Pharmacology, BK21 Plus Kyungpook National University (KNU) Biomedical Convergence Program, Cardiovascular Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| |
Collapse
|
38
|
Leuschner G, Semenova A, Mayr CH, Kapellos TS, Ansari M, Seeliger B, Frankenberger M, Kneidinger N, Hatz RA, Hilgendorff A, Prasse A, Behr J, Mann M, Schiller HB. Mass spectrometry-based autoimmune profiling reveals predictive autoantigens in idiopathic pulmonary fibrosis. iScience 2023; 26:108345. [PMID: 38026226 PMCID: PMC10661358 DOI: 10.1016/j.isci.2023.108345] [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: 07/05/2023] [Revised: 09/13/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Autoimmunity plays a role in certain types of lung fibrosis, notably connective tissue disease-associated interstitial lung disease (CTD-ILD). In idiopathic pulmonary fibrosis (IPF), an incurable and fatal lung disease, diagnosis typically requires clinical exclusion of autoimmunity. However, autoantibodies of unknown significance have been detected in IPF patients. We conducted computational analysis of B cell transcriptomes in published transcriptomics datasets and developed a proteomic Differential Antigen Capture (DAC) assay that captures plasma antibodies followed by affinity purification of lung proteins coupled to mass spectrometry. We analyzed antibody capture in two independent cohorts of IPF and CTL-ILD patients over two disease progression time points. Our findings revealed significant upregulation of specific immunoglobulins with V-segment bias in IPF across multiple cohorts. We identified a predictive autoimmune signature linked to reduced transplant-free survival in IPF, persisting over time. Notably, autoantibodies against thrombospondin-1 were associated with decreased survival, suggesting their potential as predictive biomarkers.
Collapse
Affiliation(s)
- Gabriela Leuschner
- Institute of Lung Health and Immunity, Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
- Department of Internal Medicine V, Ludwig-Maximilian University Munich, CPC-M bioArchive, Munich, Asklepios Clinics, Gauting, Germany
| | - Anna Semenova
- Institute of Lung Health and Immunity, Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Christoph H. Mayr
- Institute of Lung Health and Immunity, Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Theodore S. Kapellos
- Institute of Lung Health and Immunity, Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Meshal Ansari
- Institute of Lung Health and Immunity, Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Benjamin Seeliger
- Department of Pneumology, Hannover Medical School, Member of the German Center for Lung Research (DZL), Hannover, Germany
| | - Marion Frankenberger
- Institute of Lung Health and Immunity, Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
- Department of Internal Medicine V, Ludwig-Maximilian University Munich, CPC-M bioArchive, Munich, Asklepios Clinics, Gauting, Germany
| | - Nikolaus Kneidinger
- Department of Internal Medicine V, Ludwig-Maximilian University Munich, CPC-M bioArchive, Munich, Asklepios Clinics, Gauting, Germany
| | - Rudolf A. Hatz
- Center for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich (LMU), Munich, and Asklepios Medical Center, Member of the German Center for Lung Research (DZL), Gauting, Germany
| | - Anne Hilgendorff
- Institute of Lung Health and Immunity, Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
- Center for Comprehensive Developmental Care (CDeCLMU), Hospital of the Ludwig-Maximilians University (LMU), Member of the German Center for Lung Research (DZL), CPC-M bioArchive, Munich, Germany
| | - Antje Prasse
- Department of Pneumology, Hannover Medical School, Member of the German Center for Lung Research (DZL), Hannover, Germany
| | - Jürgen Behr
- Department of Internal Medicine V, Ludwig-Maximilian University Munich, CPC-M bioArchive, Munich, Asklepios Clinics, Gauting, Germany
| | - Matthias Mann
- Max Planck Institute of Biochemistry, Department of Proteomics and Signal Transduction, Martinsried, Germany
| | - Herbert B. Schiller
- Institute of Lung Health and Immunity, Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
- Institute of Experimental Pneumology, LMU University Hospital, Ludwig-Maximilians University, Munich, Germany
| |
Collapse
|
39
|
Sinton MC, Chandrasegaran PRG, Capewell P, Cooper A, Girard A, Ogunsola J, Perona-Wright G, M Ngoyi D, Kuispond N, Bucheton B, Camara M, Kajimura S, Bénézech C, Mabbott NA, MacLeod A, Quintana JF. IL-17 signalling is critical for controlling subcutaneous adipose tissue dynamics and parasite burden during chronic murine Trypanosoma brucei infection. Nat Commun 2023; 14:7070. [PMID: 37923768 PMCID: PMC10624677 DOI: 10.1038/s41467-023-42918-8] [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: 05/26/2023] [Accepted: 10/25/2023] [Indexed: 11/06/2023] Open
Abstract
In the skin, Trypanosoma brucei colonises the subcutaneous white adipose tissue, and is proposed to be competent for forward transmission. The interaction between parasites, adipose tissue, and the local immune system is likely to drive the adipose tissue wasting and weight loss observed in cattle and humans infected with T. brucei. However, mechanistically, events leading to subcutaneous white adipose tissue wasting are not fully understood. Here, using several complementary approaches, including mass cytometry by time of flight, bulk and single cell transcriptomics, and in vivo genetic models, we show that T. brucei infection drives local expansion of several IL-17A-producing cells in the murine WAT, including TH17 and Vγ6+ cells. We also show that global IL-17 deficiency, or deletion of the adipocyte IL-17 receptor protect from infection-induced WAT wasting and weight loss. Unexpectedly, we find that abrogation of adipocyte IL-17 signalling results in a significant accumulation of Dpp4+ Pi16+ interstitial preadipocytes and increased extravascular parasites in the WAT, highlighting a critical role for IL-17 signalling in controlling preadipocyte fate, subcutaneous WAT dynamics, and local parasite burden. Taken together, our study highlights the central role of adipocyte IL-17 signalling in controlling WAT responses to infection, suggesting that adipocytes are critical coordinators of tissue dynamics and immune responses to T. brucei infection.
Collapse
Affiliation(s)
- Matthew C Sinton
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK.
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK.
- Division of Cardiovascular Science, University of Manchester, Manchester, UK.
| | - Praveena R G Chandrasegaran
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Paul Capewell
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Anneli Cooper
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Alex Girard
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - John Ogunsola
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Georgia Perona-Wright
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | - Dieudonné M Ngoyi
- Department of Parasitology, National Institute of Biomedical Research, Kinshasa, Democratic Republic of Congo
- Member of TrypanoGEN, Kinshasa, Democratic Republic of Congo
| | - Nono Kuispond
- Department of Parasitology, National Institute of Biomedical Research, Kinshasa, Democratic Republic of Congo
- Member of TrypanoGEN, Kinshasa, Democratic Republic of Congo
| | - Bruno Bucheton
- Member of TrypanoGEN, Kinshasa, Democratic Republic of Congo
- Institut de Recherche pour le Développement, Unité Mixte de Recherche IRD-CIRAD 177, Campus International de Baillarguet, Montpellier, France
| | - Mamadou Camara
- Member of TrypanoGEN, Kinshasa, Democratic Republic of Congo
- Programme National de Lutte contre la Trypanosomiase Humaine Africaine, Ministère de la Santé, Conakry, Guinea
| | - Shingo Kajimura
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Cécile Bénézech
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, EH16 4TJ, Scotland, UK
| | - Neil A Mabbott
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Annette MacLeod
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
- Member of TrypanoGEN, Kinshasa, Democratic Republic of Congo
| | - Juan F Quintana
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK.
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK.
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UK.
- Division of Immunology, Immunity to Infection and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.
| |
Collapse
|
40
|
Hou P, Luo Y, Wu N. TCL1A+ B cells predict prognosis in triple-negative breast cancer through integrative analysis of single-cell and bulk transcriptomic data. Open Life Sci 2023; 18:20220707. [PMID: 37791059 PMCID: PMC10543705 DOI: 10.1515/biol-2022-0707] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/18/2023] [Accepted: 08/02/2023] [Indexed: 10/05/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive subtype with limited treatment options and high mortality rates. It remains a prevailing clinical need to distinguish whether the patient can benefit from therapy, such as chemotherapy. By integrating single-cell and global transcriptome data, we have for the first time identified TCL1A+ B cell functions that are prognostically relevant in TNBC. This finding broadens the perspective of traditional tumor-infiltrating lymphocytes in predicting survival, especially the potential value of B cells in TNBC. Single-cell RNA-seq data from five TNBC patients were collected to identify the association between immune cell populations and clinical outcomes. Functional analysis was according to gene set enrichment analysis using pathways from MsigDB. Subsequently, the gene signature of TCL1A+ B cells based on differential expression genes of TCL1A+ B cells versus other immune cells was used to explore the correlation with tumor microenvironment (TME) and construct a prognostic signature using a non-parametric and unsupervised method. We identified TCL1A+ B cells as a cluster of B cells associated with clinical outcomes in TNBC. Functional analysis demonstrated its function in B cell activation and regulation of immune response. The highly enriched TCL1A+ B cell population was found to be associated with a thermal TME with anti-tumor effects. A high abundance of TCL1A+ B cell population is positively correlated with a favorable therapeutic outcome, as indicated by longer overall survival. The present study suggests that TCL1A+ B cells play a key role in the treatment and prognostic prediction of TNBC, although further studies are needed to validate our findings. Moreover, the integration of transcriptome data at various resolutions provides a viable approach for the discovery of novel prognostic markers.
Collapse
Affiliation(s)
- Peifeng Hou
- Department of Oncology, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, China
- Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou, Fujian, 350000, China
- Fujian Medical University Stem Cell Research Institute, Fuzhou, Fujian, 350000, China
| | - Yang Luo
- Department of Oncology, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, China
| | - Ningzi Wu
- Department of Oncology, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, China
| |
Collapse
|
41
|
Lende SSF, Barnkob NM, Hansen RW, Bansia H, Vestergaard M, Rothemejer FH, Worsaae A, Brown D, Pedersen ML, Rahimic AHF, Juhl AK, Gjetting T, Østergaard L, Georges AD, Vuillard LM, Schleimann MH, Koefoed K, Tolstrup M. Discovery of neutralizing SARS-CoV-2 antibodies enriched in a unique antigen specific B cell cluster. PLoS One 2023; 18:e0291131. [PMID: 37729215 PMCID: PMC10511142 DOI: 10.1371/journal.pone.0291131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 08/22/2023] [Indexed: 09/22/2023] Open
Abstract
Despite development of effective SARS-CoV-2 vaccines, a sub-group of vaccine non-responders depends on therapeutic antibodies or small-molecule drugs in cases of severe disease. However, perpetual viral evolution has required continuous efficacy monitoring as well as exploration of new therapeutic antibodies, to circumvent resistance mutations arising in the viral population. We performed SARS-CoV-2-specific B cell sorting and subsequent single-cell sequencing on material from 15 SARS-CoV-2 convalescent participants. Through screening of 455 monoclonal antibodies for SARS-CoV-2 variant binding and virus neutralization, we identified a cluster of activated B cells highly enriched for SARS-CoV-2 neutralizing antibodies. Epitope binning and Cryo-EM structure analysis identified the majority of neutralizing antibodies having epitopes overlapping with the ACE2 receptor binding motif (class 1 binders). Extensive functional antibody characterization identified two potent neutralizing antibodies, one retaining SARS-CoV-1 neutralizing capability, while both bind major common variants of concern and display prophylactic efficacy in vivo. The transcriptomic signature of activated B cells harboring broadly binding neutralizing antibodies with therapeutic potential identified here, may be a guide in future efforts of rapid therapeutic antibody discovery.
Collapse
Affiliation(s)
- Stine Sofie Frank Lende
- Department of Infectious Diseases, Aarhus University Hospital, Skejby, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | | | | | - Harsh Bansia
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, United States of America
| | | | - Frederik Holm Rothemejer
- Department of Infectious Diseases, Aarhus University Hospital, Skejby, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | | | - Deijona Brown
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, United States of America
| | - Maria Lange Pedersen
- Department of Infectious Diseases, Aarhus University Hospital, Skejby, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | | | - Anna Karina Juhl
- Department of Infectious Diseases, Aarhus University Hospital, Skejby, Denmark
| | - Torben Gjetting
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, United States of America
- Antibody Technology, Novo Nordisk A/S, Måløv, Denmark
| | - Lars Østergaard
- Department of Infectious Diseases, Aarhus University Hospital, Skejby, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Amédée Des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, United States of America
- Department of Chemistry and Biochemistry, City College of New York, New York, NY, United States of America
- PhD Programs in Biochemistry, and Chemistry, Graduate Center, City University of New York, New York, NY, United States of America
| | | | | | | | - Martin Tolstrup
- Department of Infectious Diseases, Aarhus University Hospital, Skejby, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| |
Collapse
|
42
|
Hung CY, Hsiao SH, Huang CG, Chang CS, Chen GY, Huang YL, Dutta A, Huang CT. Relatively preserved functional immune capacity with standard COVID-19 vaccine regimen in people living with HIV. Front Immunol 2023; 14:1204314. [PMID: 37731482 PMCID: PMC10507403 DOI: 10.3389/fimmu.2023.1204314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 08/14/2023] [Indexed: 09/22/2023] Open
Abstract
Introduction People living with HIV (PLWH) are at a higher risk of severe disease with SARS-CoV-2 virus infection. COVID-19 vaccines are effective in most PLWH. However, suboptimal immune responses to the standard two-shot regimen are a concern, especially for those with moderate to severe immunodeficiency. An additional dose is recommended as part of the extended primary series in Taiwan. Herein, we study the efficacy of this additional shot in PLWH with mild immunodeficiency compared to that in healthy non-HIV people. Methods In total, 72 PLWH that were asymptomatic or with mild immunodeficiency (CD4 counts ≥200/mm3) and suppressed virology, and 362 healthcare workers of our hospital were enrolled. None of the participants had a history of SARS-CoV-2 infection. They received mRNA-1273 and ChAdOx1 vaccines. Anti-SARS-CoV-2 neutralizing and anti-Spike IgG antibodies, and SARS-CoV-2-specific T cell responses were evaluated. Results The standard two-shot regimen elicited lower responses in PLWH than the healthcare workers without HIV infection, although the difference was statistically insignificant. They had comparable levels of neutralizing and anti-Spike antibodies and comparable effector CD4+ and CD8+ T cell responses. The third shot boosted the SARS-CoV-2 immunity significantly more with better antibody responses and higher IFN-γ and IL-2 responses of the CD4+ and CD8+ T cells in PLWH compared to those without HIV. Upon in vitro stimulation with extracted Wuhan strain SARS-CoV-2 proteins, CD8+ T cells from PLWH after 3 shots had more durable effector responses than the non-HIV controls with extended time of stimulation. Conclusion This subtle difference between PLWH and non-HIV people implied immune exhaustion with two shots in non-HIV people. Slightly compromised immunity in PLWH indeed preserved the functional capacity for further response to the third shot or natural infection.
Collapse
Affiliation(s)
- Chen-Yiu Hung
- Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Sung-Han Hsiao
- Division of Infectious Diseases, Department of Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chung-Guei Huang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chia-Shiang Chang
- Division of Infectious Diseases, Department of Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Guan-Yan Chen
- Division of Infectious Diseases, Department of Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yu-Lin Huang
- Division of Infectious Diseases, Department of Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Avijit Dutta
- Division of Infectious Diseases, Department of Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ching-Tai Huang
- Division of Infectious Diseases, Department of Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Infectious Diseases, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| |
Collapse
|
43
|
Korzhenevich J, Janowska I, van der Burg M, Rizzi M. Human and mouse early B cell development: So similar but so different. Immunol Lett 2023; 261:1-12. [PMID: 37442242 DOI: 10.1016/j.imlet.2023.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/09/2023] [Accepted: 07/10/2023] [Indexed: 07/15/2023]
Abstract
Early B cell development in the bone marrow ensures the replenishment of the peripheral B cell pool. Immature B cells continuously develop from hematopoietic stem cells, in a process guided by an intricate network of transcription factors as well as chemokine and cytokine signals. Humans and mice possess somewhat similar regulatory mechanisms of B lymphopoiesis. The continuous discovery of monogenetic defects that impact early B cell development in humans substantiates the similarities and differences with B cell development in mice. These differences become relevant when targeted therapeutic approaches are used in patients; therefore, predicting potential immunological adverse events is crucial. In this review, we have provided a phenotypical classification of human and murine early progenitors and B cell stages, based on surface and intracellular protein expression. Further, we have critically compared the role of key transcription factors (Ikaros, E2A, EBF1, PAX5, and Aiolos) and chemo- or cytokine signals (FLT3, c-kit, IL-7R, and CXCR4) during homeostatic and aberrant B lymphopoiesis in both humans and mice.
Collapse
Affiliation(s)
- Jakov Korzhenevich
- Division of Clinical and Experimental Immunology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, 1090, Vienna, Austria
| | - Iga Janowska
- Department of Rheumatology and Clinical Immunology, Freiburg University Medical Center, University of Freiburg, 79106, Freiburg, Germany
| | - Mirjam van der Burg
- Department of Pediatrics, Laboratory for Pediatric Immunology, Willem-Alexander Children's Hospital, Leiden University Medical Center, 2333, ZA Leiden, The Netherlands
| | - Marta Rizzi
- Division of Clinical and Experimental Immunology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, 1090, Vienna, Austria; Department of Rheumatology and Clinical Immunology, Freiburg University Medical Center, University of Freiburg, 79106, Freiburg, Germany; Center for Chronic Immunodeficiency, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany.
| |
Collapse
|
44
|
Lewis JE, Hergott CB. The Immunophenotypic Profile of Healthy Human Bone Marrow. Clin Lab Med 2023; 43:323-332. [PMID: 37481314 DOI: 10.1016/j.cll.2023.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
Flow cytometry enables multiparametric characterization of hematopoietic cell immunophenotype. Deviations from normal immunophenotypic patterns comprise a cardinal feature of many hematopoietic neoplasms, underscoring the ongoing essentiality of flow cytometry as a diagnostic tool. However, understanding of aberrant hematopoiesis requires an equal understanding of normal hematopoiesis as a comparator. In this review, we outline key features of healthy adult hematopoiesis and lineage specification as illuminated by flow cytometry and provide diagrams illustrating what a diagnostician may observe in flow cytometric plots. These features provide a profile of baseline hematopoiesis, to which clinical samples with suspected neoplasia may be compared.
Collapse
Affiliation(s)
- Joshua E Lewis
- Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA; Harvard Medical School, 25 Shattuck St, Boston, MA 02115, USA
| | - Christopher B Hergott
- Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA; Harvard Medical School, 25 Shattuck St, Boston, MA 02115, USA.
| |
Collapse
|
45
|
Elizaldi SR, Hawes CE, Verma A, Dinasarapu AR, Lakshmanappa YS, Schlegel BT, Rajasundaram D, Li J, Durbin-Johnson BP, Ma ZM, Beckman D, Ott S, Lifson J, Morrison JH, Iyer SS. CCR7+ CD4 T Cell Immunosurveillance Disrupted in Chronic SIV-Induced Neuroinflammation in Rhesus Brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.28.555037. [PMID: 37693567 PMCID: PMC10491118 DOI: 10.1101/2023.08.28.555037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
CD4 T cells survey and maintain immune homeostasis in the brain, yet their differentiation states and functional capabilities remain unclear. Our approach, combining single-cell transcriptomic analysis, ATAC-seq, spatial transcriptomics, and flow cytometry, revealed a distinct subset of CCR7+ CD4 T cells resembling lymph node central memory (T CM ) cells. We observed chromatin accessibility at the CCR7, CD28, and BCL-6 loci, defining molecular features of T CM . Brain CCR7+ CD4 T cells exhibited recall proliferation and interleukin-2 production ex vivo, showcasing their functional competence. We identified the skull bone marrow as a local niche for these cells alongside other CNS border tissues. Sequestering T CM cells in lymph nodes using FTY720 led to reduced CCR7+ CD4 T cell frequencies in the cerebrospinal fluid, accompanied by increased monocyte levels and soluble markers indicating immune activation. In macaques chronically infected with SIVCL57 and experiencing viral rebound due to cessation of antiretroviral therapy, a decrease in brain CCR7+ CD4 T cells was observed, along with increased microglial activation and initiation of neurodegenerative pathways. Our findings highlight a role for CCR7+ CD4 T cells in CNS immune surveillance and their decline during chronic SIV-induced neuroinflammation highlights their responsiveness to neuroinflammatory processes. GRAPHICAL ABSTRACT In Brief Utilizing single-cell and spatial transcriptomics on adult rhesus brain, we uncover a unique CCR7+ CD4 T cell subset resembling central memory T cells (T CM ) within brain and border tissues, including skull bone marrow. Our findings show decreased frequencies of this subset during SIV- induced chronic neuroinflammation, emphasizing responsiveness of CCR7+ CD4 T cells to CNS disruptions. Highlights CCR7+ CD4 T cells survey border and parenchymal CNS compartments during homeostasis; reduced presence of CCR7+ CD4 T cells in cerebrospinal fluid leads to immune activation, implying a role in neuroimmune homeostasis. CNS CCR7+ CD4 T cells exhibit phenotypic and functional features of central memory T cells (T CM ) including production of interleukin 2 and the capacity for rapid recall proliferation. Furthermore, CCR7+ CD4 T cells reside in the skull bone marrow. CCR7+ CD4 T cells are markedly decreased within the brain parenchyma during chronic viral neuroinflammation.
Collapse
|
46
|
Nayak P, Mukund K, Subramaniam S. The Janus face of proliferating plasmablasts in dengue and COVID-19 infections. Front Immunol 2023; 14:1068424. [PMID: 37638019 PMCID: PMC10450630 DOI: 10.3389/fimmu.2023.1068424] [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: 10/12/2022] [Accepted: 07/20/2023] [Indexed: 08/29/2023] Open
Abstract
Introduction B cells play an integral role in the immune response to both dengue fever and COVID-19. Prior scRNAseq analyses of peripheral plasmablasts in COVID-19 have revealed a heterogeneous population with distinct cell subsets associated with proliferation; prior studies in patients with dengue fever have likewise shown the presence of proliferative pre-plasmablasts in the circulation. These findings may have implications for disease severity. In this study, we sought to gain a mechanistic understanding of the intracellular processes in naive and memory B cells that are associated with and may lead to an expanded proliferative plasmablast population in the circulation. Methods We analyzed age-controlled (pediatric and adult), peripheral blood mononuclear cell scRNAseq datasets from patients infected with either dengue (primary or secondary) or COVID-19 (non-severe or severe) from previously published studies. Our preliminary analysis showed that pediatric patients with dengue and adults with COVID-19 had an expanded proliferative plasmablast (p-PB) population. By contrast, neither the adults with dengue nor the children with COVID-19 in our dataset had p-PBs. We used this distinctive preliminary signature to guide our analyses design and expanded our analyses to naive and memory B cells. Results In age/disease conditions with and without p-PBs, we found differences in cell sensing and activation, including via the B cell receptor and downstream signal transduction. Likewise, inflammation was mediated differently: relative to groups without p-PBs, those with p-PBs had increased expression of interferon response and S100 genes (particularly severe COVID-19). Furthermore, several transcription factors at the nexus of activation, inflammation, and cell fate decisions were expressed differently in groups with and without p-PBs. Discussion We used dengue and COVID-19 infections in adult and pediatric patients (focusing on naive B, memory B, and plasmablast cells) as a model to better understand the mechanisms that may give rise to p-PB populations in the circulation. Our results indicate that a more pro-inflammatory state in naive and memory B cells correlated with - and could influence the generation of- proliferating plasmablasts. Further exploration of these mechanisms will have implications for immune memory, vaccine development, and post-viral autoimmune syndromes.
Collapse
Affiliation(s)
- Priya Nayak
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
| | - Kavitha Mukund
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
| | - Shankar Subramaniam
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, United States
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, United States
| |
Collapse
|
47
|
Fan H, Wang F, Zeng A, Murison A, Tomczak K, Hao D, Jelloul FZ, Wang B, Barrodia P, Liang S, Chen K, Wang L, Zhao Z, Rai K, Jain AK, Dick J, Daver N, Futreal A, Abbas HA. Single-cell chromatin accessibility profiling of acute myeloid leukemia reveals heterogeneous lineage composition upon therapy-resistance. Commun Biol 2023; 6:765. [PMID: 37479893 PMCID: PMC10362028 DOI: 10.1038/s42003-023-05120-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 07/07/2023] [Indexed: 07/23/2023] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease characterized by high rate of therapy resistance. Since the cell of origin can impact response to therapy, it is crucial to understand the lineage composition of AML cells at time of therapy resistance. Here we leverage single-cell chromatin accessibility profiling of 22 AML bone marrow aspirates from eight patients at time of therapy resistance and following subsequent therapy to characterize their lineage landscape. Our findings reveal a complex lineage architecture of therapy-resistant AML cells that are primed for stem and progenitor lineages and spanning quiescent, activated and late stem cell/progenitor states. Remarkably, therapy-resistant AML cells are also composed of cells primed for differentiated myeloid, erythroid and even lymphoid lineages. The heterogeneous lineage composition persists following subsequent therapy, with early progenitor-driven features marking unfavorable prognosis in The Cancer Genome Atlas AML cohort. Pseudotime analysis further confirms the vast degree of heterogeneity driven by the dynamic changes in chromatin accessibility. Our findings suggest that therapy-resistant AML cells are characterized not only by stem and progenitor states, but also by a continuum of differentiated cellular lineages. The heterogeneity in lineages likely contributes to their therapy resistance by harboring different degrees of lineage-specific susceptibilities to therapy.
Collapse
Affiliation(s)
- Huihui Fan
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Feng Wang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andy Zeng
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Alex Murison
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Katarzyna Tomczak
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dapeng Hao
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fatima Zahra Jelloul
- Department of Hematopathology, University of Texas M D Anderson Cancer Center, Houston, TX, USA
| | - Bofei Wang
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Praveen Barrodia
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shaoheng Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Linghua Wang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Kunal Rai
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Abhinav K Jain
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John Dick
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Naval Daver
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andy Futreal
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hussein A Abbas
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| |
Collapse
|
48
|
Guldenpfennig C, Teixeiro E, Daniels M. NF-kB's contribution to B cell fate decisions. Front Immunol 2023; 14:1214095. [PMID: 37533858 PMCID: PMC10391175 DOI: 10.3389/fimmu.2023.1214095] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/03/2023] [Indexed: 08/04/2023] Open
Abstract
NF-κB signaling is essential to an effective innate and adaptive immune response. Many immune-specific functional and developmental outcomes depend in large on NF-κB. The formidable task of sorting out the mechanisms behind the regulation and outcome of NF-κB signaling remains an important area of immunology research. Here we briefly discuss the role of NF-κB in regulating cell fate decisions at various times in the path of B cell development, activation, and the generation of long-term humoral immunity.
Collapse
Affiliation(s)
- Caitlyn Guldenpfennig
- Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States
- NextGen Precision Health, University of Missouri, Columbia, MO, United States
| | - Emma Teixeiro
- Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States
- NextGen Precision Health, University of Missouri, Columbia, MO, United States
| | - Mark Daniels
- Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States
- NextGen Precision Health, University of Missouri, Columbia, MO, United States
| |
Collapse
|
49
|
Nicholas CA, Smith MJ. Application of single-cell RNA sequencing methods to develop B cell targeted treatments for autoimmunity. Front Immunol 2023; 14:1103690. [PMID: 37520578 PMCID: PMC10382068 DOI: 10.3389/fimmu.2023.1103690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 06/29/2023] [Indexed: 08/01/2023] Open
Abstract
The COVID-19 pandemic coincided with several transformative advances in single-cell analysis. These new methods along with decades of research and trials with antibody therapeutics and RNA based technologies allowed for highly effective vaccines and treatments to be produced at astonishing speeds. While these tools were initially focused on models of infection, they also show promise in an autoimmune setting. Self-reactive B cells play important roles as antigen-presenting cells and cytokine and autoantibody producers for many autoimmune diseases. Yet, current therapies to target autoreactive B cells deplete all B cells irrespective of their pathogenicity. Development of self-reactive B cell targeting therapies that would spare non-pathogenic B cells are needed to treat disease while allowing effective immune responses to other ailments. Single-cell RNA sequencing (scRNA-seq) approaches will aid in identification of the pathogenic self-reactive B cells operative in autoimmunity and help with development of more favorable precision targeted therapies.
Collapse
Affiliation(s)
- Catherine A. Nicholas
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, United States
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, United States
| | - Mia J. Smith
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, United States
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| |
Collapse
|
50
|
Patel AJ, Khan N, Richter A, Naidu B, Drayson MT, Middleton GW. Deep immune B and plasma cell repertoire in non-small cell lung cancer. Front Immunol 2023; 14:1198665. [PMID: 37398676 PMCID: PMC10311499 DOI: 10.3389/fimmu.2023.1198665] [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: 04/01/2023] [Accepted: 06/01/2023] [Indexed: 07/04/2023] Open
Abstract
Introduction B cells, which have long been thought to be minor players in the development of anti-tumor responses, have been implicated as key players in lung cancer pathogenesis and response to checkpoint blockade in patients with lung cancer. Enrichment of late-stage plasma and memory cells in the tumor microenvironment has been shown in lung cancer, with the plasma cell repertoire existing on a functional spectrum with suppressive phenotypes correlating with outcome. B cell dynamics may be influenced by the inflammatory microenvironment observed in smokers and between LUAD and LUSC. Methods Here, we show through high-dimensional deep phenotyping using mass cytometry (CyTOF), next generation RNA sequencing and multispectral immunofluorescence imaging (VECTRA Polaris) that key differences exist in the B cell repertoire between tumor and circulation in paired specimens from lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC). Results In addition to the current literature, this study provides insight into the in-depth description of the B cell contexture in Non-Small Cell Lung Cancer (NSCLC) with reference to broad clinico-pathological parameters based on our analysis of 56 patients. Our findings reinforce the phenomenon of B-cell trafficking from distant circulatory compartments into the tumour microenvironment (TME). The circulatory repertoire shows a predilection toward plasma and memory phenotypes in LUAD however no major differences exist between LUAD and LUSC at the level of the TME. B cell repertoire, amongst other factors, may be influenced by the inflammatory burden in the TME and circulation, that is, smokers and non-smokers. We have further clearly demonstrated that the plasma cell repertoire exists on a functional spectrum in lung cancer, and that the suppressive regulatory arm of this axis may play a significant role in determining postoperative outcomes as well as following checkpoint blockade. This will require further long-term functional correlation. Conclusion B and Plasma cell repertoire is very diverse and heterogeneous across different tissue compartments in lung cancer. Smoking status associates with key differences in the immune milieu and the consequent inflammatory microenvironment is likely responsible for the functional and phenotypic spectrum we have seen in the plasma cell and B cell repertoire in this condition.
Collapse
Affiliation(s)
- Akshay J. Patel
- Institute of Immunology and Immunotherapy (III), College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Naeem Khan
- Institute of Immunology and Immunotherapy (III), College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Alex Richter
- Institute of Immunology and Immunotherapy (III), College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Babu Naidu
- Institute of Inflammation and Ageing (IIA), College of Medical Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Mark T. Drayson
- Institute of Immunology and Immunotherapy (III), College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Gary W. Middleton
- Institute of Immunology and Immunotherapy (III), College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| |
Collapse
|