Seminars in Immunopathology最新文献

{"title":"Immune biology of NSCLC revealed by single-cell technologies: implications for the development of biomarkers in patients treated with immunotherapy.","authors":"J Wlosik,&nbsp;S Fattori,&nbsp;P Rochigneux,&nbsp;A Goncalves,&nbsp;D Olive,&nbsp;A S Chretien","doi":"10.1007/s00281-022-00973-1","DOIUrl":"https://doi.org/10.1007/s00281-022-00973-1","url":null,"abstract":"<p><p>First-line immunotherapy in non-small-cell lung cancer largely improved patients' survival. PD-L1 testing is required before immune checkpoint inhibitor initiation. However, this biomarker fails to accurately predict patients' response. On the other hand, immunotherapy exposes patients to immune-related toxicity, the mechanisms of which are still unclear. Hence, there is an unmet need to develop clinically approved predictive biomarkers to better select patients who will benefit the most from immune checkpoint inhibitors and improve risk management. Single-cell technologies provide unprecedented insight into the tumor and its microenvironment, leading to the discovery of immune cells involved in immune checkpoint inhibitor response or toxicity. In this review, we will underscore the potential of the single-cell approach to identify candidate biomarkers improving non-small-cell lung cancer patients' care.</p>","PeriodicalId":21704,"journal":{"name":"Seminars in Immunopathology","volume":"45 1","pages":"29-41"},"PeriodicalIF":9.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9974692/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9391272","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Learning cell identity in immunology, neuroscience, and cancer.","authors":"Stephanie Medina, Rebecca A Ihrie, Jonathan M Irish","doi":"10.1007/s00281-022-00976-y","DOIUrl":"10.1007/s00281-022-00976-y","url":null,"abstract":"<p><p>Suspension and imaging cytometry techniques that simultaneously measure hundreds of cellular features are powering a new era of cell biology and transforming our understanding of human tissues and tumors. However, a central challenge remains in learning the identities of unexpected or novel cell types. Cell identification rubrics that could assist trainees, whether human or machine, are not always rigorously defined, vary greatly by field, and differentially rely on cell intrinsic measurements, cell extrinsic tissue measurements, or external contextual information such as clinical outcomes. This challenge is especially acute in the context of tumors, where cells aberrantly express developmental programs that are normally time, location, or cell-type restricted. Well-established fields have contrasting practices for cell identity that have emerged from convention and convenience as much as design. For example, early immunology focused on identifying minimal sets of protein features that mark individual, functionally distinct cells. In neuroscience, features including morphology, development, and anatomical location were typical starting points for defining cell types. Both immunology and neuroscience now aim to link standardized measurements of protein or RNA to informative cell functions such as electrophysiology, connectivity, lineage potential, phospho-protein signaling, cell suppression, and tumor cell killing ability. The expansion of automated, machine-driven methods for learning cell identity has further created an urgent need for a harmonized framework for distinguishing cell identity across fields and technology platforms. Here, we compare practices in the fields of immunology and neuroscience, highlight concepts from each that might work well in the other, and propose ways to implement these ideas to study neural and immune cell interactions in brain tumors and associated model systems.</p>","PeriodicalId":21704,"journal":{"name":"Seminars in Immunopathology","volume":"45 1","pages":"3-16"},"PeriodicalIF":7.9,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9762661/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9455397","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Towards multiomic analysis of oral mucosal pathologies.","authors":"Jakob Einhaus, Xiaoyuan Han, Dorien Feyaerts, John Sunwoo, Brice Gaudilliere, Somayeh H Ahmad, Nima Aghaeepour, Karl Bruckman, David Ojcius, Christian M Schürch, Dyani K Gaudilliere","doi":"10.1007/s00281-022-00982-0","DOIUrl":"10.1007/s00281-022-00982-0","url":null,"abstract":"<p><p>Oral mucosal pathologies comprise an array of diseases with worldwide prevalence and medical relevance. Affecting a confined space with crucial physiological and social functions, oral pathologies can be mutilating and drastically reduce quality of life. Despite their relevance, treatment for these diseases is often far from curative and remains vastly understudied. While multiple factors are involved in the pathogenesis of oral mucosal pathologies, the host's immune system plays a major role in the development, maintenance, and resolution of these diseases. Consequently, a precise understanding of immunological mechanisms implicated in oral mucosal pathologies is critical (1) to identify accurate, mechanistic biomarkers of clinical outcomes; (2) to develop targeted immunotherapeutic strategies; and (3) to individualize prevention and treatment approaches. Here, we review key elements of the immune system's role in oral mucosal pathologies that hold promise to overcome limitations in current diagnostic and therapeutic approaches. We emphasize recent and ongoing multiomic and single-cell approaches that enable an integrative view of these pathophysiological processes and thereby provide unifying and clinically relevant biological signatures.</p>","PeriodicalId":21704,"journal":{"name":"Seminars in Immunopathology","volume":"45 1","pages":"111-123"},"PeriodicalIF":7.9,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9974703/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9098633","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Highly multiplexed spatial profiling with CODEX: bioinformatic analysis and application in human disease.","authors":"Wilson Kuswanto,&nbsp;Garry Nolan,&nbsp;Guolan Lu","doi":"10.1007/s00281-022-00974-0","DOIUrl":"https://doi.org/10.1007/s00281-022-00974-0","url":null,"abstract":"<p><p>Multiplexed imaging, which enables spatial localization of proteins and RNA to cells within tissues, complements existing multi-omic technologies and has deepened our understanding of health and disease. CODEX, a multiplexed single-cell imaging technology, utilizes a microfluidics system that incorporates DNA barcoded antibodies to visualize 50 + cellular markers at the single-cell level. Here, we discuss the latest applications of CODEX to studies of cancer, autoimmunity, and infection as well as current bioinformatics approaches for analysis of multiplexed imaging data from preprocessing to cell segmentation and marker quantification to spatial analysis techniques. We conclude with a commentary on the challenges and future developments for multiplexed spatial profiling.</p>","PeriodicalId":21704,"journal":{"name":"Seminars in Immunopathology","volume":"45 1","pages":"145-157"},"PeriodicalIF":9.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9684921/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9936615","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multiparameter single-cell proteomic technologies give new insights into the biology of ovarian tumors.","authors":"Ionut-Gabriel Funingana,&nbsp;Jacob S Bedia,&nbsp;Ying-Wen Huang,&nbsp;Antonio Delgado Gonzalez,&nbsp;Kenyi Donoso,&nbsp;Veronica D Gonzalez,&nbsp;James D Brenton,&nbsp;Alan Ashworth,&nbsp;Wendy J Fantl","doi":"10.1007/s00281-022-00979-9","DOIUrl":"https://doi.org/10.1007/s00281-022-00979-9","url":null,"abstract":"<p><p>High-grade serous ovarian cancer (HGSOC) is the most lethal gynecological malignancy. Its diagnosis at advanced stage compounded with its excessive genomic and cellular heterogeneity make curative treatment challenging. Two critical therapeutic challenges to overcome are carboplatin resistance and lack of response to immunotherapy. Carboplatin resistance results from diverse cell autonomous mechanisms which operate in different combinations within and across tumors. The lack of response to immunotherapy is highly likely to be related to an immunosuppressive HGSOC tumor microenvironment which overrides any clinical benefit. Results from a number of studies, mainly using transcriptomics, indicate that the immune tumor microenvironment (iTME) plays a role in carboplatin response. However, in patients receiving treatment, the exact mechanistic details are unclear. During the past decade, multiplex single-cell proteomic technologies have come to the forefront of biomedical research. Mass cytometry or cytometry by time-of-flight, measures up to 60 parameters in single cells that are in suspension. Multiplex cellular imaging technologies allow simultaneous measurement of up to 60 proteins in single cells with spatial resolution and interrogation of cell-cell interactions. This review suggests that functional interplay between cell autonomous responses to carboplatin and the HGSOC immune tumor microenvironment could be clarified through the application of multiplex single-cell proteomic technologies. We conclude that for better clinical care, multiplex single-cell proteomic technologies could be an integral component of multimodal biomarker development that also includes genomics and radiomics. Collection of matched samples from patients before and on treatment will be critical to the success of these efforts.</p>","PeriodicalId":21704,"journal":{"name":"Seminars in Immunopathology","volume":"45 1","pages":"43-59"},"PeriodicalIF":9.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9974728/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9789357","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-cell technologies uncover intra-tumor heterogeneity in childhood cancers.","authors":"Yu-Chen Lo,&nbsp;Yuxuan Liu,&nbsp;Marte Kammersgaard,&nbsp;Abhishek Koladiya,&nbsp;Timothy J Keyes,&nbsp;Kara L Davis","doi":"10.1007/s00281-022-00981-1","DOIUrl":"https://doi.org/10.1007/s00281-022-00981-1","url":null,"abstract":"<p><p>Childhood cancer is the second leading cause of death in children aged 1 to 14. Although survival rates have vastly improved over the past 40 years, cancer resistance and relapse remain a significant challenge. Advances in single-cell technologies enable dissection of tumors to unprecedented resolution. This facilitates unraveling the heterogeneity of childhood cancers to identify cell subtypes that are prone to treatment resistance. The rapid accumulation of single-cell data from different modalities necessitates the development of novel computational approaches for processing, visualizing, and analyzing single-cell data. Here, we review single-cell approaches utilized or under development in the context of childhood cancers. We review computational methods for analyzing single-cell data and discuss best practices for their application. Finally, we review the impact of several studies of childhood tumors analyzed with these approaches and future directions to implement single-cell studies into translational cancer research in pediatric oncology.</p>","PeriodicalId":21704,"journal":{"name":"Seminars in Immunopathology","volume":"45 1","pages":"61-69"},"PeriodicalIF":9.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10830508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Revisiting transplant immunology through the lens of single-cell technologies.","authors":"Arianna Barbetta, Brittany Rocque, Deepika Sarode, Johanna Ascher Bartlett, Juliet Emamaullee","doi":"10.1007/s00281-022-00958-0","DOIUrl":"10.1007/s00281-022-00958-0","url":null,"abstract":"<p><p>Solid organ transplantation (SOT) is the standard of care for end-stage organ disease. The most frequent complication of SOT involves allograft rejection, which may occur via T cell- and/or antibody-mediated mechanisms. Diagnosis of rejection in the clinical setting requires an invasive biopsy as there are currently no reliable biomarkers to detect rejection episodes. Likewise, it is virtually impossible to identify patients who exhibit operational tolerance and may be candidates for reduced or complete withdrawal of immunosuppression. Emerging single-cell technologies, including cytometry by time-of-flight (CyTOF), imaging mass cytometry, and single-cell RNA sequencing, represent a new opportunity for deep characterization of pathogenic immune populations involved in both allograft rejection and tolerance in clinical samples. These techniques enable examination of both individual cellular phenotypes and cell-to-cell interactions, ultimately providing new insights into the complex pathophysiology of allograft rejection. However, working with these large, highly dimensional datasets requires expertise in advanced data processing and analysis using computational biology techniques. Machine learning algorithms represent an optimal strategy to analyze and create predictive models using these complex datasets and will likely be essential for future clinical application of patient level results based on single-cell data. Herein, we review the existing literature on single-cell techniques in the context of SOT.</p>","PeriodicalId":21704,"journal":{"name":"Seminars in Immunopathology","volume":"45 1","pages":"91-109"},"PeriodicalIF":7.9,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9386203/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9233634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-cell high-dimensional imaging mass cytometry: one step beyond in oncology.","authors":"Yaël Glasson,&nbsp;Laure-Agnès Chépeaux,&nbsp;Anne-Sophie Dumé,&nbsp;Virginie Lafont,&nbsp;Julien Faget,&nbsp;Nathalie Bonnefoy,&nbsp;Henri-Alexandre Michaud","doi":"10.1007/s00281-022-00978-w","DOIUrl":"https://doi.org/10.1007/s00281-022-00978-w","url":null,"abstract":"<p><p>Solid tumors have a dynamic ecosystem in which malignant and non-malignant (endothelial, stromal, and immune) cell types constantly interact. Importantly, the abundance, localization, and functional orientation of each cell component within the tumor microenvironment vary significantly over time and in response to treatment. Such intratumoral heterogeneity influences the tumor course and its sensitivity to treatments. Recently, high-dimensional imaging mass cytometry (IMC) has been developed to explore the tumor ecosystem at the single-cell level. In the last years, several studies demonstrated that IMC is a powerful tool to decipher the tumor complexity. In this review, we summarize the potential of this technology and how it may be useful for cancer research (from preclinical to clinical studies).</p>","PeriodicalId":21704,"journal":{"name":"Seminars in Immunopathology","volume":"45 1","pages":"17-28"},"PeriodicalIF":9.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9812013/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9081607","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-cell RNA-seq methods to interrogate virus-host interactions.","authors":"Kalani Ratnasiri, Aaron J Wilk, Madeline J Lee, Purvesh Khatri, Catherine A Blish","doi":"10.1007/s00281-022-00972-2","DOIUrl":"10.1007/s00281-022-00972-2","url":null,"abstract":"<p><p>The twenty-first century has seen the emergence of many epidemic and pandemic viruses, with the most recent being the SARS-CoV-2-driven COVID-19 pandemic. As obligate intracellular parasites, viruses rely on host cells to replicate and produce progeny, resulting in complex virus and host dynamics during an infection. Single-cell RNA sequencing (scRNA-seq), by enabling broad and simultaneous profiling of both host and virus transcripts, represents a powerful technology to unravel the delicate balance between host and virus. In this review, we summarize technological and methodological advances in scRNA-seq and their applications to antiviral immunity. We highlight key scRNA-seq applications that have enabled the understanding of viral genomic and host response heterogeneity, differential responses of infected versus bystander cells, and intercellular communication networks. We expect further development of scRNA-seq technologies and analytical methods, combined with measurements of additional multi-omic modalities and increased availability of publicly accessible scRNA-seq datasets, to enable a better understanding of viral pathogenesis and enhance the development of antiviral therapeutics strategies.</p>","PeriodicalId":21704,"journal":{"name":"Seminars in Immunopathology","volume":"45 1","pages":"71-89"},"PeriodicalIF":7.9,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9684776/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9730561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Neuroimaging is the new \"spatial omic\": multi-omic approaches to neuro-inflammation and immuno-thrombosis in acute ischemic stroke.","authors":"Benjamin Maïer, Amy S Tsai, Jakob F Einhaus, Jean-Philippe Desilles, Benoît Ho-Tin-Noé, Benjamin Gory, Marina Sirota, Richard Leigh, Robin Lemmens, Gregory Albers, Jean-Marc Olivot, Mikael Mazighi, Brice Gaudillière","doi":"10.1007/s00281-023-00984-6","DOIUrl":"10.1007/s00281-023-00984-6","url":null,"abstract":"<p><p>Ischemic stroke (IS) is the leading cause of acquired disability and the second leading cause of dementia and mortality. Current treatments for IS are primarily focused on revascularization of the occluded artery. However, only 10% of patients are eligible for revascularization and 50% of revascularized patients remain disabled at 3 months. Accumulating evidence highlight the prognostic significance of the neuro- and thrombo-inflammatory response after IS. However, several randomized trials of promising immunosuppressive or immunomodulatory drugs failed to show positive results. Insufficient understanding of inter-patient variability in the cellular, functional, and spatial organization of the inflammatory response to IS likely contributed to the failure to translate preclinical findings into successful clinical trials. The inflammatory response to IS involves complex interactions between neuronal, glial, and immune cell subsets across multiple immunological compartments, including the blood-brain barrier, the meningeal lymphatic vessels, the choroid plexus, and the skull bone marrow. Here, we review the neuro- and thrombo-inflammatory responses to IS. We discuss how clinical imaging and single-cell omic technologies have refined our understanding of the spatial organization of pathobiological processes driving clinical outcomes in patients with an IS. We also introduce recent developments in machine learning statistical methods for the integration of multi-omic data (biological and radiological) to identify patient-specific inflammatory states predictive of IS clinical outcomes.</p>","PeriodicalId":21704,"journal":{"name":"Seminars in Immunopathology","volume":"45 1","pages":"125-143"},"PeriodicalIF":9.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10026385/pdf/nihms-1882345.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9141535","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}