1
|
Ramirez A, Orcutt-Jahns BT, Pascoe S, Abraham A, Remigio B, Thomas N, Meyer AS. Integrative, high-resolution analysis of single cells across experimental conditions with PARAFAC2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.29.605698. [PMID: 39131377 PMCID: PMC11312543 DOI: 10.1101/2024.07.29.605698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Effective tools for exploration and analysis are needed to extract insights from large-scale single-cell measurement data. However, current techniques for handling single-cell studies performed across experimental conditions (e.g., samples, perturbations, or patients) require restrictive assumptions, lack flexibility, or do not adequately deconvolute condition-to-condition variation from cell-to-cell variation. Here, we report that the tensor decomposition method PARAFAC2 (Pf2) enables the dimensionality reduction of single-cell data across conditions. We demonstrate these benefits across two distinct contexts of single-cell RNA-sequencing (scRNA-seq) experiments of peripheral immune cells: pharmacologic drug perturbations and systemic lupus erythematosus (SLE) patient samples. By isolating relevant gene modules across cells and conditions, Pf2 enables straightforward associations of gene variation patterns across specific patients or perturbations while connecting each coordinated change to certain cells without pre-defining cell types. The theoretical grounding of Pf2 suggests a unified framework for many modeling tasks associated with single-cell data. Thus, Pf2 provides an intuitive universal dimensionality reduction approach for multi-sample single-cell studies across diverse biological contexts.
Collapse
Affiliation(s)
- Andrew Ramirez
- Department of Bioengineering, University of California, Los Angeles (UCLA), CA, USA
| | | | - Sean Pascoe
- Department of Bioengineering, University of California, Los Angeles (UCLA), CA, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Armaan Abraham
- Department of Bioengineering, University of California, Los Angeles (UCLA), CA, USA
| | | | | | - Aaron S. Meyer
- Department of Bioengineering, University of California, Los Angeles (UCLA), CA, USA
- Jonsson Comprehensive Cancer Center, UCLA, CA, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, CA, USA
| |
Collapse
|
2
|
Monti M, Ferrari G, Gazzurelli L, Bugatti M, Facchetti F, Vermi W. Plasmacytoid dendritic cells at the forefront of anti-cancer immunity: rewiring strategies for tumor microenvironment remodeling. J Exp Clin Cancer Res 2024; 43:196. [PMID: 39020402 PMCID: PMC11253500 DOI: 10.1186/s13046-024-03121-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 07/08/2024] [Indexed: 07/19/2024] Open
Abstract
Plasmacytoid dendritic cells (pDCs) are multifaceted immune cells executing various innate immunological functions. Their first line of defence consists in type I interferons (I-IFN) production upon nucleic acids sensing through endosomal Toll-like receptor (TLR) 7- and 9-dependent signalling pathways. Type I IFNs are a class of proinflammatory cytokines that have context-dependent functions on cancer immunosurveillance and immunoediting. In the last few years, different studies have reported that pDCs are also able to sense cytosolic DNA through cGAS-STING (stimulator of interferon genes) pathway eliciting a potent I-IFN production independently of TLR7/9. Human pDCs are also endowed with direct effector functions via the upregulation of TRAIL and production of granzyme B, the latter modulated by cytokines abundant in cancer tissues. pDCs have been detected in a wide variety of human malignant neoplasms, including virus-associated cancers, recruited by chemotactic stimuli. Although the role of pDCs in cancer immune surveillance is still uncompletely understood, their spontaneous activation has been rarely documented; moreover, their presence in the tumor microenvironment (TME) has been associated with a tolerogenic phenotype induced by immunosuppressive cytokines or oncometabolites. Currently tested treatment options can lead to pDCs activation and disruption of the immunosuppressive TME, providing a relevant clinical benefit. On the contrary, the antibody-drug conjugates targeting BDCA-2 on immunosuppressive tumor-associated pDCs (TA-pDCs) could be proposed as novel immunomodulatory therapies to achieve disease control in patients with advance stage hematologic malignancies or solid tumors. This Review integrate recent evidence on the biology of pDCs and their pharmacological modulation, suggesting their relevant role at the forefront of cancer immunity.
Collapse
Affiliation(s)
- Matilde Monti
- Department of Molecular and Translational Medicine, Section of Pathology, University of Brescia, P.Le Spedali Civili 1, 25123, Brescia, Italy
| | - Giorgia Ferrari
- Department of Molecular and Translational Medicine, Section of Pathology, University of Brescia, P.Le Spedali Civili 1, 25123, Brescia, Italy
| | - Luisa Gazzurelli
- Department of Molecular and Translational Medicine, Section of Pathology, University of Brescia, P.Le Spedali Civili 1, 25123, Brescia, Italy
| | - Mattia Bugatti
- Department of Molecular and Translational Medicine, Section of Pathology, University of Brescia, P.Le Spedali Civili 1, 25123, Brescia, Italy
| | - Fabio Facchetti
- Department of Molecular and Translational Medicine, Section of Pathology, University of Brescia, P.Le Spedali Civili 1, 25123, Brescia, Italy
| | - William Vermi
- Department of Molecular and Translational Medicine, Section of Pathology, University of Brescia, P.Le Spedali Civili 1, 25123, Brescia, Italy.
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA.
| |
Collapse
|
3
|
Yang K, Li S, Ding Y, Meng X, Zhang C, Sun X. Effect of smoking-related features and 731 immune cell phenotypes on esophageal cancer: a two-sample and mediated Mendelian randomized study. Front Immunol 2024; 15:1336817. [PMID: 38601154 PMCID: PMC11004242 DOI: 10.3389/fimmu.2024.1336817] [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: 11/11/2023] [Accepted: 03/18/2024] [Indexed: 04/12/2024] Open
Abstract
Introduction Numerous observational studies have indicated that smoking is a substantial risk factor for esophageal cancer. However, there is a shortage of research that delves into the specific causal relationship and potential mediators between the two. Our study aims to validate the correlation between smoking-related traits and esophageal cancer while exploring the possible mediating effects of immune factors. Methods Initially, we conducted bidirectional univariate Mendelian Randomization (MR) analyses to forecast the causal effects linking smoking-related traits and esophageal cancer. Subsequently, we employed a two-step MR analysis to scrutinize immune cell phenotypes that could mediate these effects. Finally, the coefficient product method was employed to determine the precise mediating impact. Additionally, we have refined our sensitivity analysis to ensure the reliability of the outcomes. Results After analysis, Smoking status: Never had a significant negative association with the incidence of esophageal cancer (inverse-variance weighted (IVW) method, p=1.82e-05, OR=0.10, 95%CI=0.04~0.29). Ever smoked (IVW, p=1.49e-02, OR=4.31, 95%CI=1.33~13.94) and Current tobacco smoking (IVW, p=1.49e-02, OR=4.31, 95%CI=1.33~13.94) showed the promoting effect on the pathogenesis of esophageal cancer. Through further examination, researchers discovered 21 immune cell phenotypes that have a causal relationship with esophageal cancer. After careful screening, two immune cell phenotypes were found to have potential mediating effects. In particular, it was observed that in the case of the preventive effect of Smoking status: Never on esophageal cancer, the absolute count of CD62L plasmacytoid dendritic cells mediated a reduction of 4.21%, while the mediating effect of CD27 in CD20-CD38-B cells was -4.12%. In addition, sensitivity analyses did not reveal significant heterogeneity or level pleiotropy. Conclusion The study provides new evidence for the causal relationship between smoking-related features and esophageal cancer and proposes immune factors with potential mediating effects. However, this finding needs to be further demonstrated by more extensive clinical studies.
Collapse
Affiliation(s)
| | | | | | | | | | - Xiujing Sun
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| |
Collapse
|
4
|
Monti M, Ferrari G, Grosso V, Missale F, Bugatti M, Cancila V, Zini S, Segala A, La Via L, Consoli F, Orlandi M, Valerio A, Tripodo C, Rossato M, Vermi W. Impaired activation of plasmacytoid dendritic cells via toll-like receptor 7/9 and STING is mediated by melanoma-derived immunosuppressive cytokines and metabolic drift. Front Immunol 2024; 14:1227648. [PMID: 38239354 PMCID: PMC10795195 DOI: 10.3389/fimmu.2023.1227648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 12/04/2023] [Indexed: 01/22/2024] Open
Abstract
Introduction Plasmacytoid dendritic cells (pDCs) infiltrate a large set of human cancers. Interferon alpha (IFN-α) produced by pDCs induces growth arrest and apoptosis in tumor cells and modulates innate and adaptive immune cells involved in anti-cancer immunity. Moreover, effector molecules exert tumor cell killing. However, the activation state and clinical relevance of pDCs infiltration in cancer is still largely controversial. In Primary Cutaneous Melanoma (PCM), pDCs density decreases over disease progression and collapses in metastatic melanoma (MM). Moreover, the residual circulating pDC compartment is defective in IFN-α production. Methods The activation of tumor-associated pDCs was evaluated by in silico and microscopic analysis. The expression of human myxovirus resistant protein 1 (MxA), as surrogate of IFN-α production, and proximity ligation assay (PLA) to test dsDNA-cGAS activation were performed on human melanoma biopsies. Moreover, IFN-α and CXCL10 production by in vitro stimulated (i.e. with R848, CpG-A, ADU-S100) pDCs exposed to melanoma cell lines supernatants (SN-mel) was tested by intracellular flow cytometry and ELISA. We also performed a bulk RNA-sequencing on SN-mel-exposed pDCs, resting or stimulated with R848. Glycolytic rate assay was performed on SN-mel-exposed pDCs using the Seahorse XFe24 Extracellular Flux Analyzer. Results Based on a set of microscopic, functional and in silico analyses, we demonstrated that the melanoma milieu directly impairs IFN-α and CXCL10 production by pDCs via TLR-7/9 and cGAS-STING signaling pathways. Melanoma-derived immunosuppressive cytokines and a metabolic drift represent relevant mechanisms enforcing pDC-mediated melanoma escape. Discussion These findings propose a new window of intervention for novel immunotherapy approaches to amplify the antitumor innate immune response in cutaneous melanoma (CM).
Collapse
Affiliation(s)
- Matilde Monti
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Giorgia Ferrari
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Valentina Grosso
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Francesco Missale
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
- Department of Head & Neck Oncology & Surgery Otorhinolaryngology, Nederlands Kanker Instituut, Amsterdam, Netherlands
| | - Mattia Bugatti
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Valeria Cancila
- Tumor Immunology Unit, Department of Health Sciences, University of Palermo, Palermo, Italy
| | - Stefania Zini
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Agnese Segala
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Luca La Via
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Francesca Consoli
- Oncology Unit, Azienda Socio Sanitaria Territoriale (ASST) Spedali Civili di Brescia, Brescia, Italy
| | - Matteo Orlandi
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Alessandra Valerio
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Claudio Tripodo
- Tumor Immunology Unit, Department of Health Sciences, University of Palermo, Palermo, Italy
- IFOM ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
| | - Marzia Rossato
- Department of Biotechnology, University of Verona, Verona, Italy
| | - William Vermi
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, United States
| |
Collapse
|
5
|
Sosa Cuevas E, Saas P, Aspord C. Dendritic Cell Subsets in Melanoma: Pathophysiology, Clinical Prognosis and Therapeutic Exploitation. Cancers (Basel) 2023; 15:cancers15082206. [PMID: 37190135 DOI: 10.3390/cancers15082206] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/31/2023] [Accepted: 04/06/2023] [Indexed: 05/17/2023] Open
Abstract
Evasion from immunity is a hallmark of cancer development. Dendritic cells (DCs) are strategic immune cells shaping anti-tumor immune responses, but tumor cells exploit DC versatility to subvert their functions. Unveiling the puzzling role of DCs in the control of tumor development and mechanisms of tumor-induced DC hijacking is critical to optimize current therapies and to design future efficient immunotherapies for melanoma. Dendritic cells, crucially positioned at the center of anti-tumor immunity, represent attractive targets to develop new therapeutic approaches. Harnessing the potencies of each DC subset to trigger appropriate immune responses while avoiding their subversion is a challenging yet promising step to achieve tumor immune control. This review focuses on advances regarding the diversity of DC subsets, their pathophysiology and impact on clinical outcome in melanoma patients. We provide insights into the regulation mechanisms of DCs by the tumor, and overview DC-based therapeutic developments for melanoma. Further insights into DCs' diversity, features, networking, regulation and shaping by the tumor microenvironment will allow designing novel effective cancer therapies. The DCs deserve to be positioned in the current melanoma immunotherapeutic landscape. Recent discoveries strongly motivate exploitation of the exceptional potential of DCs to drive robust anti-tumor immunity, offering promising tracks for clinical successes.
Collapse
Affiliation(s)
- Eleonora Sosa Cuevas
- EFS AuRA, R&D Laboratory, 38000 Grenoble, France
- Inserm U 1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team: Epigenetics, Immunity, Metabolism, Cell Signaling and Cancer, Université Grenoble Alpes, 38000 Grenoble, France
| | - Philippe Saas
- EFS AuRA, R&D Laboratory, 38000 Grenoble, France
- Inserm U 1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team: Epigenetics, Immunity, Metabolism, Cell Signaling and Cancer, Université Grenoble Alpes, 38000 Grenoble, France
| | - Caroline Aspord
- EFS AuRA, R&D Laboratory, 38000 Grenoble, France
- Inserm U 1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team: Epigenetics, Immunity, Metabolism, Cell Signaling and Cancer, Université Grenoble Alpes, 38000 Grenoble, France
| |
Collapse
|
6
|
Plasmacytoid Dendritic Cells as a Novel Cell-Based Cancer Immunotherapy. Int J Mol Sci 2022; 23:ijms231911397. [PMID: 36232698 PMCID: PMC9570010 DOI: 10.3390/ijms231911397] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 12/15/2022] Open
Abstract
Plasmacytoid dendritic cells (pDCs) are multifaceted immune cells with a wide range of innate and adaptive immunological functions. They constitute the first line of defence against multiple viral infections and have also been reported to actively participate in antitumor immune responses. The clinical implication of the presence of pDCs in the tumor microenvironment (TME) is still ambiguous, but it is clear that pDCs possess the ability to modulate tumor-specific T cell responses and direct cytotoxic functions. Therapeutic strategies designed to exploit these qualities of pDCs to boost tumor-specific immune responses could represent an attractive alternative compared to conventional therapeutic approaches in the future, and promising antitumor effects have already been reported in phase I/II clinical trials. Here, we review the many roles of pDCs in cancer and present current advances in developing pDC-based immunotherapeutic approaches for treating cancer.
Collapse
|
7
|
Zhou B, Lawrence T, Liang Y. The Role of Plasmacytoid Dendritic Cells in Cancers. Front Immunol 2021; 12:749190. [PMID: 34737750 PMCID: PMC8560733 DOI: 10.3389/fimmu.2021.749190] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/05/2021] [Indexed: 11/13/2022] Open
Abstract
Plasmacytoid dendritic cells (pDCs) are a special subtype of dendritic cells with the morphology of plasma cells. pDCs produce massive amounts of type I interferon (IFN-I), which was originally found to play an extremely pivotal role in antiviral immunity. Interestingly, accumulated evidence indicates that pDCs can also play an important role in tumorigenesis. In the human body, most of the IFN-α is secreted by activated pDCs mediated by toll-like receptor (TLR) stimulation. In many types of cancer, tumors are infiltrated by a large number of pDCs, however, these pDCs exhibit no response to TLR stimulation, and reduced or absent IFN-α production. In addition, tumor-infiltrating pDCs promote recruitment of regulatory T cells (Tregs) into the tumor microenvironment, leading to immunosuppression and promoting tumor growth. In this review, we discuss recent insights into the development of pDCs and their roles in a variety of malignancies, with special emphasis on the basic mechanisms.
Collapse
Affiliation(s)
- Binhui Zhou
- Laboratory of Mouse Genetics, Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Henan, China.,Laboratory of Genetic Regulators in the Immune System, Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Henan, China
| | - Toby Lawrence
- Henan Key Laboratory of Immunology and Targeted Therapy, School of Laboratory Medicine, Xinxiang Medical University, Henan, China.,Centre for Inflammation Biology and Cancer Immunology, King's College London, London, United Kingdom
| | - Yinming Liang
- Laboratory of Mouse Genetics, Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Henan, China.,Laboratory of Genetic Regulators in the Immune System, Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Henan, China.,Henan Key Laboratory of Immunology and Targeted Therapy, School of Laboratory Medicine, Xinxiang Medical University, Henan, China
| |
Collapse
|
8
|
Lorenzi L, Lonardi S, Vairo D, Bernardelli A, Tomaselli M, Bugatti M, Licini S, Arisi M, Cerroni L, Tucci A, Vermi W, Giliani SC, Facchetti F. E-Cadherin Expression and Blunted Interferon Response in Blastic Plasmacytoid Dendritic Cell Neoplasm. Am J Surg Pathol 2021; 45:1428-1438. [PMID: 34081040 PMCID: PMC8428867 DOI: 10.1097/pas.0000000000001747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is an aggressive neoplasm derived from plasmacytoid dendritic cells (pDCs). In this study, we investigated by immunohistochemical analysis the expression of E-cadherin (EC) on pDCs in reactive lymph nodes and tonsils, bone marrow, and in BPDCN. We compared the expression of EC in BPDCN to that in leukemia cutis (LC) and cutaneous lupus erythematosus (CLE), the latter typically featuring pDC activation. In BPDCN, we also assessed the immunomodulatory activity of malignant pDCs through the expression of several type I interferon (IFN-I) signaling effectors and downstream targets, PD-L1/CD274, and determined the extent of tumor infiltration by CD8-expressing T cells. In reactive lymph nodes and tonsils, pDCs expressed EC, whereas no reactivity was observed in bone marrow pDCs. BPDCN showed EC expression in the malignant pDCs in the vast majority of cutaneous (31/33 cases, 94%), nodal, and spleen localizations (3/3 cases, 100%), whereas it was more variable in the bone marrow (5/13, 38,5%), where tumor cells expressed EC similarly to the skin counterpart in 4 cases and differently in other 4. Notably, EC was undetectable in LC (n=30) and in juxta-epidermal pDCs in CLE (n=31). Contrary to CLE showing robust expression of IFN-I-induced proteins MX1 and ISG5 in 20/23 cases (87%), and STAT1 phosphorylation, BPDCN biopsies showed inconsistent levels of these proteins in most cases (85%). Expression of IFN-I-induced genes, IFI27, IFIT1, ISG15, RSAD2, and SIGLEC1, was also significantly (P<0.05) lower in BPDCN as compared with CLE. In BPDCN, a significantly blunted IFN-I response correlated with a poor CD8+T-cell infiltration and the lack of PD-L1/CD274 expression by the tumor cells. This study identifies EC as a novel pDC marker of diagnostic relevance in BPDCN. The results propose a scenario whereby malignant pDCs through EC-driven signaling promote the blunting of IFN-I signaling and, thereby, the establishment of a poorly immunogenic tumor microenvironment.
Collapse
Affiliation(s)
- Luisa Lorenzi
- Department of Molecular and Translational Medicine, Section of Pathology
- Pathology Unit, ASST Spedali Civili di Brescia
| | - Silvia Lonardi
- Department of Molecular and Translational Medicine, Section of Pathology
- Pathology Unit, ASST Spedali Civili di Brescia
| | - Donatella Vairo
- Department of Molecular and Translational Medicine, A. Nocivelli Institute of Molecular Medicine, University of Brescia and Section of Medical Genetics, Spedali Civili
| | - Andrea Bernardelli
- Department of Molecular and Translational Medicine, Section of Pathology
| | | | - Mattia Bugatti
- Department of Molecular and Translational Medicine, Section of Pathology
- Pathology Unit, ASST Spedali Civili di Brescia
| | - Sara Licini
- Pathology Unit, ASST Spedali Civili di Brescia
| | - Mariachiara Arisi
- Department of Clinical and Experimental Sciences, Section of Dermatology, University of Brescia
| | - Lorenzo Cerroni
- Department of Dermatology, Medical University of Graz, Graz, Austria
| | - Alessandra Tucci
- Haematology Unit, ASST Spedali Civili di Brescia, Brescia, Italy
| | - William Vermi
- Department of Molecular and Translational Medicine, Section of Pathology
- Pathology Unit, ASST Spedali Civili di Brescia
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO
| | - Silvia Clara Giliani
- Department of Molecular and Translational Medicine, A. Nocivelli Institute of Molecular Medicine, University of Brescia and Section of Medical Genetics, Spedali Civili
| | - Fabio Facchetti
- Department of Molecular and Translational Medicine, Section of Pathology
- Pathology Unit, ASST Spedali Civili di Brescia
| |
Collapse
|
9
|
Lonardi S, Missale F, Calza S, Bugatti M, Vescovi R, Debora B, Uppaluri R, Egloff AM, Mattavelli D, Lombardi D, Benerini Gatta L, Marini O, Tamassia N, Gardiman E, Cassatella MA, Scapini P, Nicolai P, Vermi W. Tumor-associated neutrophils (TANs) in human carcinoma-draining lymph nodes: a novel TAN compartment. Clin Transl Immunology 2021; 10:e1252. [PMID: 33643653 PMCID: PMC7886597 DOI: 10.1002/cti2.1252] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/04/2020] [Accepted: 01/19/2021] [Indexed: 12/21/2022] Open
Abstract
Objectives The role of tumor‐associated neutrophils (TANs) in the nodal spread of cancer cells remains unexplored. The present study evaluates the occurrence and clinical significance of human nodal TANs. Methods The relevance, derivation, phenotype and interactions of nodal TANs were explored via a large immunohistochemical analysis of carcinoma‐draining lymph nodes, and their clinical significance was evaluated on a retrospective cohort of oral squamous cell carcinomas (OSCC). The tumor‐promoting function of nodal TAN was probed in the OSCC TCGA dataset combining TAN and epithelial‐to‐mesenchymal transition (EMT) signatures. Results The pan‐carcinoma screening identified a consistent infiltration (59%) of CD66b+ TANs in tumor‐draining lymph nodes (TDLNs). Microscopic findings, including the occurrence of intra‐lymphatic conjugates of TANs and cancer cells, indicate that TANs migrate through lymphatic vessels. In vitro experiments revealed that OSCC cell lines sustain neutrophil viability and activation via release of GM‐CSF. Moreover, by retrospective analysis, a high CD66b+ TAN density in M‐TDLNs of OSCC (n = 182 patients) predicted a worse prognosis. The analysis of the OSCC‐TCGA dataset unveiled that the expression of a set of neutrophil‐specific genes in the primary tumor (PT) is highly associated with an EMT signature, which predicts nodal spread. Accordingly, in the PT of OSCC cases, CD66b+TANs co‐localised with PDPN+S100A9− EMT‐switched tumor cells in areas of lymphangiogenesis. The pro‐EMT signature is lacking in peripheral blood neutrophils from OSCC patients, suggesting tissue skewing of TANs. Conclusion Our findings are consistent with a novel pro‐tumoral TAN compartment that may promote nodal spread via EMT, through the lymphatics.
Collapse
Affiliation(s)
- Silvia Lonardi
- Section of Pathology Department of Molecular and Translational Medicine University of Brescia Brescia Italy.,ASST- Spedali Civili di Brescia Brescia Italy
| | - Francesco Missale
- Unit of Otorhinolaryngology - Head and Neck Surgery Department of Surgical Specialties Radiological Sciences, and Public Health University of Brescia Brescia Italy.,IRCCS Ospedale Policlinico San Martino Unit of Otorhinolaryngology, Head and Neck Surgery Department of Surgical and Diagnostic Integrated Sciences University of Genoa Genoa Italy
| | - Stefano Calza
- Unit of Biostatistics Department of Molecular and Translational Medicine University of Brescia Brescia Italy.,Department of Medical Epidemiology and Biostatistics Karolinska Institutet Stockholm Sweden.,Big&Open Data Innovation Laboratory University of Brescia Brescia Italy
| | - Mattia Bugatti
- Section of Pathology Department of Molecular and Translational Medicine University of Brescia Brescia Italy.,ASST- Spedali Civili di Brescia Brescia Italy
| | - Raffaella Vescovi
- Section of Pathology Department of Molecular and Translational Medicine University of Brescia Brescia Italy
| | - Bresciani Debora
- Section of Pathology Department of Molecular and Translational Medicine University of Brescia Brescia Italy.,ASST- Spedali Civili di Brescia Brescia Italy
| | - Ravindra Uppaluri
- Department of Surgery/Otolaryngology Brigham and Women's Hospital and Dana-Farber Cancer Institute and Harvard Medical School Boston MA USA
| | - Ann Marie Egloff
- Department of Surgery/Otolaryngology Brigham and Women's Hospital and Dana-Farber Cancer Institute and Harvard Medical School Boston MA USA
| | - Davide Mattavelli
- Unit of Otorhinolaryngology - Head and Neck Surgery Department of Surgical Specialties Radiological Sciences, and Public Health University of Brescia Brescia Italy
| | - Davide Lombardi
- ASST- Spedali Civili di Brescia Brescia Italy.,Unit of Otorhinolaryngology - Head and Neck Surgery Department of Surgical Specialties Radiological Sciences, and Public Health University of Brescia Brescia Italy
| | - Luisa Benerini Gatta
- Section of Pathology Department of Molecular and Translational Medicine University of Brescia Brescia Italy.,ASST- Spedali Civili di Brescia Brescia Italy
| | - Olivia Marini
- Section of General Pathology Department of Medicine University of Verona Verona Italy
| | - Nicola Tamassia
- Section of General Pathology Department of Medicine University of Verona Verona Italy
| | - Elisa Gardiman
- Section of General Pathology Department of Medicine University of Verona Verona Italy
| | - Marco A Cassatella
- Section of General Pathology Department of Medicine University of Verona Verona Italy
| | - Patrizia Scapini
- Section of General Pathology Department of Medicine University of Verona Verona Italy
| | - Piero Nicolai
- ASST- Spedali Civili di Brescia Brescia Italy.,Unit of Otorhinolaryngology - Head and Neck Surgery Department of Surgical Specialties Radiological Sciences, and Public Health University of Brescia Brescia Italy
| | - William Vermi
- Section of Pathology Department of Molecular and Translational Medicine University of Brescia Brescia Italy.,ASST- Spedali Civili di Brescia Brescia Italy.,Department of Pathology and Immunology Washington University Saint Louis MO USA
| |
Collapse
|
10
|
Vera J, Lischer C, Nenov M, Nikolov S, Lai X, Eberhardt M. Mathematical Modelling in Biomedicine: A Primer for the Curious and the Skeptic. Int J Mol Sci 2021; 22:E547. [PMID: 33430432 PMCID: PMC7826848 DOI: 10.3390/ijms22020547] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/21/2020] [Accepted: 12/28/2020] [Indexed: 12/11/2022] Open
Abstract
In most disciplines of natural sciences and engineering, mathematical and computational modelling are mainstay methods which are usefulness beyond doubt. These disciplines would not have reached today's level of sophistication without an intensive use of mathematical and computational models together with quantitative data. This approach has not been followed in much of molecular biology and biomedicine, however, where qualitative descriptions are accepted as a satisfactory replacement for mathematical rigor and the use of computational models is seen by many as a fringe practice rather than as a powerful scientific method. This position disregards mathematical thinking as having contributed key discoveries in biology for more than a century, e.g., in the connection between genes, inheritance, and evolution or in the mechanisms of enzymatic catalysis. Here, we discuss the role of computational modelling in the arsenal of modern scientific methods in biomedicine. We list frequent misconceptions about mathematical modelling found among biomedical experimentalists and suggest some good practices that can help bridge the cognitive gap between modelers and experimental researchers in biomedicine. This manuscript was written with two readers in mind. Firstly, it is intended for mathematical modelers with a background in physics, mathematics, or engineering who want to jump into biomedicine. We provide them with ideas to motivate the use of mathematical modelling when discussing with experimental partners. Secondly, this is a text for biomedical researchers intrigued with utilizing mathematical modelling to investigate the pathophysiology of human diseases to improve their diagnostics and treatment.
Collapse
Affiliation(s)
- Julio Vera
- Laboratory of Systems Tumor Immunology, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, 91054 Erlangen, Germany; (C.L.); (X.L.); (M.E.)
| | - Christopher Lischer
- Laboratory of Systems Tumor Immunology, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, 91054 Erlangen, Germany; (C.L.); (X.L.); (M.E.)
| | - Momchil Nenov
- Institute of Mechanics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., bl. 4, 1113 Sofia, Bulgaria; (M.N.); (S.N.)
| | - Svetoslav Nikolov
- Institute of Mechanics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., bl. 4, 1113 Sofia, Bulgaria; (M.N.); (S.N.)
| | - Xin Lai
- Laboratory of Systems Tumor Immunology, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, 91054 Erlangen, Germany; (C.L.); (X.L.); (M.E.)
| | - Martin Eberhardt
- Laboratory of Systems Tumor Immunology, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, 91054 Erlangen, Germany; (C.L.); (X.L.); (M.E.)
| |
Collapse
|
11
|
Grossi I, Radeghieri A, Paolini L, Porrini V, Pilotto A, Padovani A, Marengoni A, Barbon A, Bellucci A, Pizzi M, Salvi A, De Petro G. MicroRNA‑34a‑5p expression in the plasma and in its extracellular vesicle fractions in subjects with Parkinson's disease: An exploratory study. Int J Mol Med 2020; 47:533-546. [PMID: 33416118 PMCID: PMC7797475 DOI: 10.3892/ijmm.2020.4806] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/09/2020] [Indexed: 02/07/2023] Open
Abstract
Parkinson's disease (PD) is an important disabling age-related disorder and is the second most common neuro-degenerative disease. Currently, no established molecular biomarkers exist for the early diagnosis of PD. Circulating microRNAs (miRNAs), either vesicle-free or encapsulated in extracellular vesicles (EVs), have emerged as potential blood-based biomarkers also for neurodegenerative diseases. In this exploratory study, we focused on miR-34a-5p because of its well-documented involvement in neurobiology. To explore a differential profile of circulating miR-34a-5p in PD, PD patients and age-matched control subjects were enrolled. Serial ultracentrifugation steps and density gradient were used to separate EV subpopulations from plasma according to their different sedimentation properties (Large, Medium, Small EVs). Characterization of EV types was performed using western blotting and atomic force microscopy (AFM); purity from protein contaminants was checked with the colorimetric nanoplasmonic assay. Circulating miR-34a-5p levels were evaluated using qPCR in plasma and in each EV type. miR-34a-5p was significantly up-regulated in small EVs devoid of exogenous protein contaminants (pure SEVs) from PD patients and ROC analysis indicated a good diagnostic performance in discriminating patients from controls (AUC=0.74, P<0.05). Moreover, miR-34a-5p levels in pure SEVs were associated with disease duration, Hoehn and Yahr and Beck Depression Inventory scores. These results under-line the necessity to examine the miRNA content of each EV subpopulation to identify miRNA candidates with potential diagnostic value and lay the basis for future studies to validate the overexpression of circulating miR-34a-5p in PD via the use of pure SEVs.
Collapse
Affiliation(s)
- Ilaria Grossi
- Department of Molecular and Translational Medicine, University of Brescia, I‑25123 Brescia, Italy
| | - Annalisa Radeghieri
- Department of Molecular and Translational Medicine, University of Brescia, I‑25123 Brescia, Italy
| | - Lucia Paolini
- Department of Molecular and Translational Medicine, University of Brescia, I‑25123 Brescia, Italy
| | - Vanessa Porrini
- Department of Molecular and Translational Medicine, University of Brescia, I‑25123 Brescia, Italy
| | - Andrea Pilotto
- Neurology Unit, Department of Clinical and Experimental Sciences, University of Brescia, I‑25123 Brescia, Italy
| | - Alessandro Padovani
- Neurology Unit, Department of Clinical and Experimental Sciences, University of Brescia, I‑25123 Brescia, Italy
| | - Alessandra Marengoni
- General Medicine and Geriatrics Unit, Department of Clinical and Experimental Sciences, University of Brescia, I‑25123 Brescia, Italy
| | - Alessandro Barbon
- Department of Molecular and Translational Medicine, University of Brescia, I‑25123 Brescia, Italy
| | - Arianna Bellucci
- Department of Molecular and Translational Medicine, University of Brescia, I‑25123 Brescia, Italy
| | - Marina Pizzi
- Department of Molecular and Translational Medicine, University of Brescia, I‑25123 Brescia, Italy
| | - Alessandro Salvi
- Department of Molecular and Translational Medicine, University of Brescia, I‑25123 Brescia, Italy
| | - Giuseppina De Petro
- Department of Molecular and Translational Medicine, University of Brescia, I‑25123 Brescia, Italy
| |
Collapse
|
12
|
Monti M, Vescovi R, Consoli F, Farina D, Moratto D, Berruti A, Specchia C, Vermi W. Plasmacytoid Dendritic Cell Impairment in Metastatic Melanoma by Lactic Acidosis. Cancers (Basel) 2020; 12:cancers12082085. [PMID: 32731406 PMCID: PMC7463681 DOI: 10.3390/cancers12082085] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/20/2020] [Accepted: 07/24/2020] [Indexed: 12/19/2022] Open
Abstract
The introduction of targeted therapies and immunotherapies has significantly improved the outcome of metastatic melanoma (MM) patients. These approaches rely on immune functions for their anti-melanoma response. Plasmacytoid dendritic cells (pDCs) exhibit anti-tumor function by production of effector molecules, type I interferons (I-IFNs), and cytokines. Tissue and blood pDCs result compromised in MM, although these findings are still partially conflicting. This study reports that blood pDCs were dramatically depleted in MM, particularly in patients with high lactate dehydrogenase (LDH) and high tumor burden; the reduced pDC frequency was associated with poor overall survival. Circulating pDCs resulted also in significant impairment in interferon alpha (IFN-α) and C-X-C motif chemokine 10 (CXCL10) production in response to toll-like receptor (TLR)-7/8 agonists; on the contrary, the response to TLR-9 agonist remained intact. In the BRAFV600+ subgroup, no recovery of pDC frequency could be obtained by BRAF and MEK inhibitors (BRAFi; MEKi), whereas their function was partially rescued. Mechanistically, in vitro exposure to lactic acidosis impaired both pDC viability and function. In conclusion, pDCs from MM patients were found to be severely impaired, with a potential role for lactic acidosis. Short-term responses to treatments were not associated with pDC recovery, suggesting long-lasting effects on their compartment.
Collapse
Affiliation(s)
- Matilde Monti
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (M.M.); (R.V.); (C.S.)
| | - Raffaella Vescovi
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (M.M.); (R.V.); (C.S.)
| | - Francesca Consoli
- Oncology Unit, ASST Spedali Civili di Brescia, 25123 Brescia, Italy; (F.C.); (A.B.)
| | - Davide Farina
- Radiology Unit, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia, 25123 Brescia, Italy;
| | - Daniele Moratto
- Laboratory of Genetic Disorders of Childhood, Angelo Nocivelli Institute for Molecular Medicine, ASST Spedali Civili di Brescia, 25123 Brescia, Italy;
| | - Alfredo Berruti
- Oncology Unit, ASST Spedali Civili di Brescia, 25123 Brescia, Italy; (F.C.); (A.B.)
| | - Claudia Specchia
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (M.M.); (R.V.); (C.S.)
| | - William Vermi
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (M.M.); (R.V.); (C.S.)
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63101, USA
- Correspondence: ; Tel.: +39-030-399-8425
| |
Collapse
|
13
|
Ridolfi A, Brucale M, Montis C, Caselli L, Paolini L, Borup A, Boysen AT, Loria F, van Herwijnen MJC, Kleinjan M, Nejsum P, Zarovni N, Wauben MHM, Berti D, Bergese P, Valle F. AFM-Based High-Throughput Nanomechanical Screening of Single Extracellular Vesicles. Anal Chem 2020; 92:10274-10282. [DOI: 10.1021/acs.analchem.9b05716] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Andrea Ridolfi
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Via della Lastruccia 3, 50019 Firenze, Italy
- Consiglio Nazionale delle Ricerche, Istituto per lo Studio dei Materiali Nanostrutturati, Via P. Gobetti 101, 40129 Bologna, Italy
- Dipartimento di Chimica “Ugo Schiff”, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Firenze, Italy
| | - Marco Brucale
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Via della Lastruccia 3, 50019 Firenze, Italy
- Consiglio Nazionale delle Ricerche, Istituto per lo Studio dei Materiali Nanostrutturati, Via P. Gobetti 101, 40129 Bologna, Italy
| | - Costanza Montis
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Via della Lastruccia 3, 50019 Firenze, Italy
- Dipartimento di Chimica “Ugo Schiff”, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Firenze, Italy
| | - Lucrezia Caselli
- Dipartimento di Chimica “Ugo Schiff”, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Firenze, Italy
| | - Lucia Paolini
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Via della Lastruccia 3, 50019 Firenze, Italy
- Dipartimento di Medicina Molecolare e Traslazionale, Università degli Studi di Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Anne Borup
- Department of Clinical Medicine, Faculty of Health, Aarhus University, P. Juul-Jensens Boulevard 45, 8200 Aarhus, Denmark
| | - Anders T. Boysen
- Department of Clinical Medicine, Faculty of Health, Aarhus University, P. Juul-Jensens Boulevard 45, 8200 Aarhus, Denmark
| | - Francesca Loria
- HansaBiomed Life Sciences, Mäealuse 2/1, 12618 Tallinn, Estonia
| | - Martijn J. C. van Herwijnen
- Department of Biochemistry & Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, The Netherlands
| | - Marije Kleinjan
- Department of Biochemistry & Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, The Netherlands
| | - Peter Nejsum
- Department of Clinical Medicine, Faculty of Health, Aarhus University, P. Juul-Jensens Boulevard 45, 8200 Aarhus, Denmark
| | - Natasa Zarovni
- HansaBiomed Life Sciences, Mäealuse 2/1, 12618 Tallinn, Estonia
| | - Marca H. M. Wauben
- Department of Biochemistry & Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, The Netherlands
| | - Debora Berti
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Via della Lastruccia 3, 50019 Firenze, Italy
- Dipartimento di Chimica “Ugo Schiff”, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Firenze, Italy
| | - Paolo Bergese
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Via della Lastruccia 3, 50019 Firenze, Italy
- Dipartimento di Medicina Molecolare e Traslazionale, Università degli Studi di Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Francesco Valle
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Via della Lastruccia 3, 50019 Firenze, Italy
- Consiglio Nazionale delle Ricerche, Istituto per lo Studio dei Materiali Nanostrutturati, Via P. Gobetti 101, 40129 Bologna, Italy
| |
Collapse
|
14
|
Montis C, Salvatore A, Valle F, Paolini L, Carlà F, Bergese P, Berti D. Biogenic supported lipid bilayers as a tool to investigate nano-bio interfaces. J Colloid Interface Sci 2020; 570:340-349. [DOI: 10.1016/j.jcis.2020.03.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/03/2020] [Accepted: 03/04/2020] [Indexed: 12/14/2022]
|
15
|
Lai X, Hao W, Friedman A. TNF-α inhibitor reduces drug-resistance to anti-PD-1: A mathematical model. PLoS One 2020; 15:e0231499. [PMID: 32310956 PMCID: PMC7170257 DOI: 10.1371/journal.pone.0231499] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/24/2020] [Indexed: 01/05/2023] Open
Abstract
Drug resistance is a primary obstacle in cancer treatment. In many patients who at first respond well to treatment, relapse occurs later on. Various mechanisms have been explored to explain drug resistance in specific cancers and for specific drugs. In this paper, we consider resistance to anti-PD-1, a drug that enhances the activity of anti-cancer T cells. Based on results in experimental melanoma, it is shown, by a mathematical model, that resistances to anti-PD-1 can be significantly reduced by combining it with anti-TNF-α. The model is used to simulate the efficacy of the combined therapy with different range of doses, different initial tumor volume, and different schedules. In particular, it is shown that under a course of treatment with 3-week cycles where each drug is injected in the first day of either week 1 or week 2, injecting anti-TNF-α one week after anti-PD-1 is the most effective schedule in reducing tumor volume.
Collapse
Affiliation(s)
- Xiulan Lai
- Institute for Mathematical Sciences, Renmin University of China, Beijing, P. R. China
| | - Wenrui Hao
- Department of Mathematics, Pennsylvania State University, State College, PA, United States of America
| | - Avner Friedman
- Mathematical Bioscience Institute & Department of Mathematics, Ohio State University, Columbus, OH, United States of America
| |
Collapse
|
16
|
Busatto S, Zendrini A, Radeghieri A, Paolini L, Romano M, Presta M, Bergese P. The nanostructured secretome. Biomater Sci 2020; 8:39-63. [PMID: 31799977 DOI: 10.1039/c9bm01007f] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The term secretome, which traditionally strictly refers to single proteins, should be expanded to also include the great variety of nanoparticles secreted by cells (secNPs) into the extracellular space, which ranges from high-density lipoproteins of a few nanometers to extracellular vesicles and fat globules of hundreds of nanometers. Widening the definition is urged by the ever-increasing understanding of the role of secNPs as regulators/mediators of key physiological and pathological processes, which also puts them in the running as breakthrough cell-free therapeutics and diagnostics. "Made by cells for cells", secNPs are envisioned as a sweeping paradigm shift in nanomedicine, promising to overcome the limitations of synthetic nanoparticles by unsurpassed circulation and targeting abilities, precision and sustainability. From a longer/wider perspective, advanced manipulation would possibly make secNPs available as building blocks for future "biogenic" nanotechnology. However, the current knowledge is fragmented and sectorial (the majority of the studies being focused on a specific biological and/or medical aspect of a given secNP class or subclass), the understanding of the nanoscale and interfacial properties is limited and the development of bioprocesses and regulatory initiatives is in the early days. We believe that new multidisciplinary competencies and synergistic efforts need to be attracted and augmented to move forward. This review will contribute to the effort by attempting for the first time to rationally gather and elaborate secNPs and their traits into a unique concise framework - from biogenesis to colloidal properties, engineering and clinical translation - disclosing the overall view and easing comparative analysis and future exploitation.
Collapse
Affiliation(s)
- S Busatto
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy.
| | | | | | | | | | | | | |
Collapse
|
17
|
Paolini L, Federici S, Consoli G, Arceri D, Radeghieri A, Alessandri I, Bergese P. Fourier-transform Infrared (FT-IR) spectroscopy fingerprints subpopulations of extracellular vesicles of different sizes and cellular origin. J Extracell Vesicles 2020; 9:1741174. [PMID: 32341767 PMCID: PMC7170381 DOI: 10.1080/20013078.2020.1741174] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 02/20/2020] [Accepted: 02/28/2020] [Indexed: 12/13/2022] Open
Abstract
Identification of extracellular vesicle (EV) subpopulations remains an open challenge. To date, the common strategy is based on searching and probing set of molecular components and physical properties intended to be univocally characteristics of the target subpopulation. Pitfalls include the risk to opt for an unsuitable marker set - which may either not represent the subpopulation or also cover other unintended subpopulations - and the need to use different characterization techniques and equipment. This approach focused on specific markers may result inadequate to routinely deal with EV subpopulations that have an intrinsic high level of heterogeneity. In this paper, we show that Fourier-transform Infrared (FT-IR) spectroscopy can provide a collective fingerprint of EV subpopulations in one single experiment. FT-IR measurements were performed on large (LEVs, ~600 nm), medium (MEVs, ~200 nm) and small (SEVs ~60 nm) EVs enriched from two different cell lines medium: murine prostate cancer (TRAMP-C2) and skin melanoma (B16). Spectral regions between 3100-2800 cm-1 and 1880-900 cm-1, corresponding to functional groups mainly ascribed to lipid and protein contributions, were acquired and processed by Principal Component Analysis (PCA). LEVs, MEVs and SEVs were separately grouped for both the considered cell lines. Moreover, subpopulations of the same size but from different sources were assigned (with different degrees of accuracy) to two different groups. These findings demonstrate that FT-IR has the potential to quickly fingerprint EV subpopulations as a whole, suggesting an appealing complement/alternative for their characterization and grading, extendable to healthy and pathological EVs and fully artificial nanovesicles.
Collapse
Affiliation(s)
- Lucia Paolini
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
- Consorzio Sistemi a Grande Interfase (CSGI), Department of Chemistry, University of Florence, Sesto Fiorentino (FI), Italy
| | - Stefania Federici
- Department of Mechanical and Industrial Engineering, University of Brescia, Brescia, Italy
- Consorzio Interuniversitario Nazionale per la Scienza e la Tecnologia dei Materiali (INSTM), Florence, Italy
| | - Giovanni Consoli
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Diletta Arceri
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Annalisa Radeghieri
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
- Consorzio Sistemi a Grande Interfase (CSGI), Department of Chemistry, University of Florence, Sesto Fiorentino (FI), Italy
| | - Ivano Alessandri
- Consorzio Interuniversitario Nazionale per la Scienza e la Tecnologia dei Materiali (INSTM), Florence, Italy
- Department of Information Engineering, University of Brescia, Brescia, Italy
- National Institute of Optics, National Research Council of Italy (CNR-INO), Unit of Brescia, Italy
| | - Paolo Bergese
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
- Consorzio Sistemi a Grande Interfase (CSGI), Department of Chemistry, University of Florence, Sesto Fiorentino (FI), Italy
- Consorzio Interuniversitario Nazionale per la Scienza e la Tecnologia dei Materiali (INSTM), Florence, Italy
- Institute for Biomedical Research and Innovation, National Research Council of Italy, Palermo, Italy
| |
Collapse
|
18
|
Monti M, Consoli F, Vescovi R, Bugatti M, Vermi W. Human Plasmacytoid Dendritic Cells and Cutaneous Melanoma. Cells 2020; 9:E417. [PMID: 32054102 PMCID: PMC7072514 DOI: 10.3390/cells9020417] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 12/12/2022] Open
Abstract
The prognosis of metastatic melanoma (MM) patients has remained poor for a long time. However, the recent introduction of effective target therapies (BRAF and MEK inhibitors for BRAFV600-mutated MM) and immunotherapies (anti-CTLA-4 and anti-PD-1) has significantly improved the survival of MM patients. Notably, all these responses are highly dependent on the fitness of the host immune system, including the innate compartment. Among immune cells involved in cancer immunity, properly activated plasmacytoid dendritic cells (pDCs) exert an important role, bridging the innate and adaptive immune responses and directly eliminating cancer cells. A distinctive feature of pDCs is the production of high amount of type I Interferon (I-IFN), through the Toll-like receptor (TLR) 7 and 9 signaling pathway activation. However, published data indicate that melanoma-associated escape mechanisms are in place to hijack pDC functions. We have recently reported that pDC recruitment is recurrent in the early phases of melanoma, but the entire pDC compartment collapses over melanoma progression. Here, we summarize recent advances on pDC biology and function within the context of melanoma immunity.
Collapse
Affiliation(s)
- Matilde Monti
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (M.M.); (R.V.); (M.B.)
| | - Francesca Consoli
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, Medical Oncology, University of Brescia at ASST-Spedali Civili, 25123 Brescia, Italy;
| | - Raffaella Vescovi
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (M.M.); (R.V.); (M.B.)
| | - Mattia Bugatti
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (M.M.); (R.V.); (M.B.)
| | - William Vermi
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (M.M.); (R.V.); (M.B.)
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| |
Collapse
|
19
|
Friedman A, Siewe N. Overcoming Drug Resistance to BRAF Inhibitor. Bull Math Biol 2020; 82:8. [PMID: 31933021 DOI: 10.1007/s11538-019-00691-0] [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: 07/29/2019] [Accepted: 12/20/2019] [Indexed: 11/25/2022]
Abstract
One of the most frequently found mutations in human melanomas is in the B-raf gene, making its protein BRAF a key target for therapy. However, in patients treated with BRAF inhibitor (BRAFi), although the response is very good at first, relapse occurs within 6 months, on the average. In order to overcome this drug resistance to BRAFi, various combinations of BRAFi with other drugs have been explored, and some are being applied clinically, such as a combination of BRAF and MEK inhibitors. Experimental data for melanoma in mice show that under continuous treatment with BRAFi, the pro-cancer MDSCs and chemokine CCL2 initially decrease but eventually increase to above their original level, while the anticancer T cells continuously decrease. In this paper, we develop a mathematical model that explains these experimental results. The model is used to explore the efficacy of combinations of BRAFi with anti-CCL2, anti-PD-1 and anti-CTLA-4, with the aim of eliminating or reducing drug resistance to BRAFi.
Collapse
Affiliation(s)
- Avner Friedman
- Mathematical Biosciences Institute & Department of Mathematics, The Ohio State University, Columbus, OH, USA
| | - Nourridine Siewe
- Department of Mathematics, The University of British Columbia Okanagan, Kelowna, BC, Canada.
| |
Collapse
|
20
|
Salvi A, Vezzoli M, Busatto S, Paolini L, Faranda T, Abeni E, Caracausi M, Antonaros F, Piovesan A, Locatelli C, Cocchi G, Alvisi G, De Petro G, Ricotta D, Bergese P, Radeghieri A. Analysis of a nanoparticle‑enriched fraction of plasma reveals miRNA candidates for Down syndrome pathogenesis. Int J Mol Med 2019; 43:2303-2318. [PMID: 31017260 PMCID: PMC6488180 DOI: 10.3892/ijmm.2019.4158] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/20/2019] [Indexed: 12/12/2022] Open
Abstract
Down syndrome (DS) is caused by the presence of part or all of a third copy of chromosome 21. DS is associated with several phenotypes, including intellectual disability, congenital heart disease, childhood leukemia and immune defects. Specific microRNAs (miRNAs/miR) have been described to be associated with DS, although none of them so far have been unequivocally linked to the pathology. The present study focuses to the best of our knowledge for the first time on the miRNAs contained in nanosized RNA carriers circulating in the blood. Fractions enriched in nanosized RNA-carriers were separated from the plasma of young participants with DS and their non-trisomic siblings and miRNAs were extracted. A microarray-based analysis on a small cohort of samples led to the identification of the three most abundant miRNAs, namely miR-16-5p, miR-99b-5p and miR-144-3p. These miRNAs were then profiled for 15 pairs of DS and non-trisomic sibling couples by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Results identified a clear differential expression trend of these miRNAs in DS with respect to their non-trisomic siblings and gene ontology analysis pointed to their potential role in a number of typical DS features, including 'nervous system development', 'neuronal cell body' and certain forms of 'leukemia'. Finally, these expression levels were associated with certain typical quantitative and qualitative clinical features of DS. These results contribute to the efforts in defining the DS-associated pathogenic mechanisms and emphasize the importance of properly stratifying the miRNA fluid vehicles in order to probe biomolecules that are otherwise hidden and/or not accessible to (standard) analysis.
Collapse
Affiliation(s)
- Alessandro Salvi
- Department of Molecular and Translational Medicine, University of Brescia, I‑25123 Brescia, Italy
| | - Marika Vezzoli
- Unit of Biostatistics, Department of Molecular and Translational Medicine, University of Brescia, I‑25123 Brescia, Italy
| | - Sara Busatto
- Department of Molecular and Translational Medicine, University of Brescia, I‑25123 Brescia, Italy
| | - Lucia Paolini
- Department of Molecular and Translational Medicine, University of Brescia, I‑25123 Brescia, Italy
| | - Teresa Faranda
- Department of Molecular and Translational Medicine, University of Brescia, I‑25123 Brescia, Italy
| | - Edoardo Abeni
- Department of Molecular and Translational Medicine, University of Brescia, I‑25123 Brescia, Italy
| | - Maria Caracausi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, I‑40138 Bologna, Italy
| | - Francesca Antonaros
- CSGI, Research Center for Colloids and Nanoscience, Sesto Fiorentino, I‑50019 Florence, Italy
| | - Allison Piovesan
- CSGI, Research Center for Colloids and Nanoscience, Sesto Fiorentino, I‑50019 Florence, Italy
| | - Chiara Locatelli
- Neonatology Unit, St. Orsola‑Malpighi Polyclinic, I‑40138 Bologna, Italy
| | - Guido Cocchi
- Neonatology Unit, St. Orsola‑Malpighi Polyclinic, I‑40138 Bologna, Italy
| | - Gualtiero Alvisi
- Department of Molecular Medicine, University of Padua, I‑35121 Padua, Italy
| | - Giuseppina De Petro
- Department of Molecular and Translational Medicine, University of Brescia, I‑25123 Brescia, Italy
| | - Doris Ricotta
- Department of Molecular and Translational Medicine, University of Brescia, I‑25123 Brescia, Italy
| | - Paolo Bergese
- Department of Molecular and Translational Medicine, University of Brescia, I‑25123 Brescia, Italy
| | - Annalisa Radeghieri
- Department of Molecular and Translational Medicine, University of Brescia, I‑25123 Brescia, Italy
| |
Collapse
|
21
|
Correction: Collapse of the Plasmacytoid Dendritic Cell Compartment in Advanced Cutaneous Melanomas by Components of the Tumor Cell Secretome. Cancer Immunol Res 2019; 7:693. [PMID: 30936090 DOI: 10.1158/2326-6066.cir-19-0108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
22
|
Ling Z, Shao L, Liu X, Cheng Y, Yan C, Mei Y, Ji F, Liu X. Regulatory T Cells and Plasmacytoid Dendritic Cells Within the Tumor Microenvironment in Gastric Cancer Are Correlated With Gastric Microbiota Dysbiosis: A Preliminary Study. Front Immunol 2019; 10:533. [PMID: 30936882 PMCID: PMC6433099 DOI: 10.3389/fimmu.2019.00533] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 02/27/2019] [Indexed: 12/26/2022] Open
Abstract
Substantial evidence indicates that gastric microbiota dysbiosis, immune system dysfunction especially immune escape are critical for gastric cancer (GC) occurrence and progression. As two important elements of tumor microenvironment (TME), the relationship between gastric microbiota and tumor-immune microenvironment is still unclear. Our present study aimed to explore the correlation between gastric mucosal microbiota in different microhabitats and its corresponding gastric immunosuppressive cells such as regulatory T cells (Tregs) and plasmacytoid dendritic cells (pDCs) in the TME. A cohort of 64 GC patients without preoperative chemotherapy was enrolled retrospectively, and 60 normal, 61 peritumoral and 59 tumoral tissues were obtained for gastric mucosal microbiota analysis and immunohistochemistry analysis. From different microhabitats, BDCA2+pDCs and Foxp3+Tregs were observed positively correlated, and increased in tumoral and peritumoral tissues compared to normal ones. The diversity, composition and function of gastric mucosal microbiota also changed more significantly in tumoral tissues than those in normal and peritumoral ones. With pearson's correlation analysis, we found that several non-abundant genera such as Stenotrophomonas and Selenomonas were positively correlated with BDCA2+pDCs and Foxp3+Tregs, respectively, while Comamonas and Gaiella were negatively correlated with BDCA2+pDCs and Foxp3+ Tregs, respectively. The increased BDCA2+pDCs and Foxp3+Tregs might be modulated by gastric mucosal microbiota, both participated in the immunosuppression microenvironment of GC, which might provide evidence to establish new strategies in antitumor therapy targeting on gastric microbiota.
Collapse
Affiliation(s)
- Zongxin Ling
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University Hangzhou, China
| | - Li Shao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University Hangzhou, China
| | - Xia Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University Hangzhou, China
| | - Yiwen Cheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University Hangzhou, China
| | - Chongxian Yan
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University Hangzhou, China
| | - Ying Mei
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University Hangzhou, China
| | - Feng Ji
- Department of Gastroenterology, The First Affiliated Hospital, School of Medicine, Zhejiang University Hangzhou, China
| | - Xiaosun Liu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University Hangzhou, China
| |
Collapse
|