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Li Y, Cai Y, Ji L, Wang B, Shi D, Li X. Machine learning and bioinformatics analysis of diagnostic biomarkers associated with the occurrence and development of lung adenocarcinoma. PeerJ 2024; 12:e17746. [PMID: 39071134 PMCID: PMC11276766 DOI: 10.7717/peerj.17746] [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] [Received: 03/28/2024] [Accepted: 06/24/2024] [Indexed: 07/30/2024] Open
Abstract
Objective Lung adenocarcinoma poses a major global health challenge and is a leading cause of cancer-related deaths worldwide. This study is a review of three molecular biomarkers screened by machine learning that are not only important in the occurrence and progression of lung adenocarcinoma but also have the potential to serve as biomarkers for clinical diagnosis, prognosis evaluation and treatment guidance. Methods Differentially expressed genes (DEGs) were identified using comprehensive GSE1987 and GSE18842 gene expression databases. A comprehensive bioinformatics analysis of these DEGs was conducted to explore enriched functions and pathways, relative expression levels, and interaction networks. Random Forest and LASSO regression analysis techniques were used to identify the three most significant target genes. The TCGA database and quantitative polymerase chain reaction (qPCR) experiments were used to verify the expression levels and receiver operating characteristic (ROC) curves of these three target genes. Furthermore, immune invasiveness, pan-cancer, and mRNA-miRNA interaction network analyses were performed. Results Eighty-nine genes showed increased expression and 190 genes showed decreased expression. Notably, the upregulated DEGs were predominantly associated with organelle fission and nuclear division, whereas the downregulated DEGs were mainly associated with genitourinary system development and cell-substrate adhesion. The construction of the DEG protein-protein interaction network revealed 32 and 19 hub genes with the highest moderate values among the upregulated and downregulated genes, respectively. Using random forest and LASSO regression analyses, the hub genes were employed to identify three most significant target genes.TCGA database and qPCR experiments were used to verify the expression levels and ROC curves of these three target genes, and immunoinvasive analysis, pan-cancer analysis and mRNA-miRNA interaction network analysis were performed. Conclusion Three target genes identified by machine learning: BUB1B, CENPF, and PLK1 play key roles in LUAD development of lung adenocarcinoma.
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Affiliation(s)
- Yong Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Huzhou University, The First People’s Hospital of Huzhou City, Zhejiang Province, China
- School of Medical Technology and Information Engineering, Zhejiang University of Traditional Chinese Medicine, Zhejiang Province, China
| | - Yunxiang Cai
- Department of Clinical Laboratory, The First Affiliated Hospital of Huzhou University, The First People’s Hospital of Huzhou City, Zhejiang Province, China
| | - Longfei Ji
- Department of Clinical Laboratory, The First Affiliated Hospital of Huzhou University, The First People’s Hospital of Huzhou City, Zhejiang Province, China
| | - Binyu Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Huzhou University, The First People’s Hospital of Huzhou City, Zhejiang Province, China
| | - Danfei Shi
- Department of Pathology, The First Affiliated Hospital of Huzhou University, The First People’s Hospital of Huzhou City, Zhejiang Province, China
| | - Xinmin Li
- Department of Clinical Laboratory, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
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2
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Gupta S, Agrawal A. Dendritic cells in inborn errors of immunity. Front Immunol 2023; 14:1080129. [PMID: 36756122 PMCID: PMC9899832 DOI: 10.3389/fimmu.2023.1080129] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/06/2023] [Indexed: 01/24/2023] Open
Abstract
Dendritic cells (DCs) are crucial cells for initiating and maintaining immune response. They play critical role in homeostasis, inflammation, and autoimmunity. A number of molecules regulate their functions including synapse formation, migration, immunity, and induction of tolerance. A number of IEI are characterized by mutations in genes encoding several of these molecules resulting in immunodeficiency, inflammation, and autoimmunity in IEI. Currently, there are 465 Inborn errors of immunity (IEI) that have been grouped in 10 different categories. However, comprehensive studies of DCs have been reported in only few IEI. Here we have reviewed biology of DCs in IEI classified according to recently published IUIS classification. We have reviewed DCs in selected IEI in each group category and discussed in depth changes in DCs where significant data are available regarding role of DCs in clinical and immunological manifestations. These include severe immunodeficiency diseases, antibody deficiencies, combined immunodeficiency with associated and syndromic features, especially disorders of synapse formation, and disorders of immune regulation.
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Affiliation(s)
- Sudhir Gupta
- Division of Basic and Clinical Immunology, University of California, Irvine, CA, United States
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3
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Morreale A, Dotta L, Vairo D, Bazzana T, Lougaris V, Soresina A, Plebani A, Giliani SC, Porta F, Matteelli A, Redaelli De Zinis LO, Badolato R. When a Nontuberculous Mycobacterial Infection Reveals an Error of Immunity: A Single Center's Experience. Pediatr Infect Dis J 2022; 41:427-429. [PMID: 35086117 DOI: 10.1097/inf.0000000000003461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We present an algorithm that may be applied in case of a diagnosis of pediatric nontuberculous mycobacterial disease to identify the patients who may require an immunologic assessment to discover a possible underlying immune system defect predisposing to their nontuberculous mycobacterial infections.
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Affiliation(s)
- Alessia Morreale
- From the Department of Pediatrics, ASST Spedali Civili of Brescia, University of Brescia
| | - Laura Dotta
- Department of Pediatrics, Institute for Molecular Medicine A. Nocivelli, ASST Spedali Civili of Brescia
| | - Donatella Vairo
- Department of Molecular and Translational Medicine, Institute for Molecular Medicine A. Nocivelli, University of Brescia
| | - Tullia Bazzana
- Department of Pediatric Otorhinolaryngology, ASST Spedali Civili of Brescia
| | - Vassilios Lougaris
- Department of Pediatrics, Institute for Molecular Medicine A. Nocivelli, Department of Clinical and Experimental Sciences, University of Brescia and ASST Spedali Civili of Brescia
| | | | - Alessandro Plebani
- Department of Pediatrics, Institute for Molecular Medicine A. Nocivelli, Department of Clinical and Experimental Sciences, University of Brescia and ASST Spedali Civili of Brescia
| | - Silvia Clara Giliani
- Institute for Molecular Medicine A. Nocivelli, Department of Pathology, Laboratory of Genetic Disorders of Childhood, Department of Molecular and Translational Medicine, University of Brescia, ASST Spedali Civili of Brescia
| | - Fulvio Porta
- Department of Pediatric Onco-Hematology and BMT, ASST Spedali Civili of Brescia
| | - Alberto Matteelli
- Department of Infectious and Tropical Diseases, WHO Collaborating Centre for TB/human immunodeficiency virus and TB Elimination, University of Brescia and ASST Spedali Civili of Brescia
| | - Luca Oscar Redaelli De Zinis
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, Section of Head and Neck Surgery, University of Brescia, Pediatric Otorhinolaryngology Head Neck Surgery Division, Children Hospital, ASST Spedali Civili of Brescia, Brescia, Italy
| | - Raffaele Badolato
- Department of Pediatrics, Institute for Molecular Medicine A. Nocivelli, Department of Clinical and Experimental Sciences, University of Brescia and ASST Spedali Civili of Brescia
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4
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Exploring Potential COPD Immunosuppression Pathways Causing Increased Susceptibility for MAC Infections among COPD Patients. Clin Pract 2021; 11:619-630. [PMID: 34563006 PMCID: PMC8482292 DOI: 10.3390/clinpract11030077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 08/31/2021] [Accepted: 09/07/2021] [Indexed: 11/17/2022] Open
Abstract
Although there has been a drastic decline in the cases of Tuberculosis in the United States, the prevalence of infections caused by Mycobacterium avium Complex (MAC) has steadily increased in the past decades. Mycobacterium avium (M. avium) is one of the most abundant microorganisms in the MAC species. The mycobacterium genus is divided into two major groups: tuberculosis causing mycobacteria and non-tuberculous mycobacteria. MAC is most prominent among the non-tuberculous mycobacteria. MAC is an opportunistic pathogen that is present in soil, water, and droplets in the air. MAC infections can result in respiratory disease and can disseminate in affected patients. MAC infections are especially prevalent in patients with preexisting respiratory conditions such as Chronic Obstructive Pulmonary Disease (COPD). COPD is one of the most common lung conditions in the world with the primary cause being smoking in developed countries. COPD involves chronic inflammation of lung tissue resulting in increased susceptibility to infection. There is a lack of research regarding the pathophysiology that leads COPD patients to be susceptible to MAC infection. Our review paper therefore aims to investigate how the pathogenicity of MAC bacteria and immune decline seen in COPD patients leads to a greater susceptibility to MAC infection among COPD patients.
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Tsumura M, Miki M, Mizoguchi Y, Hirata O, Nishimura S, Tamaura M, Kagawa R, Hayakawa S, Kobayashi M, Okada S. Enhanced osteoclastogenesis in patients with MSMD due to impaired response to IFN-γ. J Allergy Clin Immunol 2021; 149:252-261.e6. [PMID: 34176646 DOI: 10.1016/j.jaci.2021.05.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 05/06/2021] [Accepted: 05/11/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Patients with Mendelian susceptibility to mycobacterial disease (MSMD) experience recurrent and/or persistent infectious diseases associated with poorly virulent mycobacteria. Multifocal osteomyelitis is among the representative manifestations of MSMD. The frequency of multifocal osteomyelitis is especially high in patients with MSMD etiologies that impair cellular response to IFN-γ, such as IFN-γR1, IFN-γR2, or STAT1 deficiency. OBJECTIVES This study sought to characterize the mechanism underlying multifocal osteomyelitis in MSMD. METHODS GM colonies prepared from bone marrow mononuclear cells from patients with autosomal dominant (AD) IFN-γR1 deficiency, AD STAT1 deficiency, or STAT1 gain of function (GOF) and from healthy controls were differentiated into osteoclasts in the presence or absence of IFN-γ. The inhibitory effect of IFN-γ on osteoclastogenesis was investigated by quantitative PCR, immunoblotting, tartrate-resistant acid phosphatase staining, and pit formation assays. RESULTS Increased osteoclast numbers were identified by examining the histopathology of osteomyelitis in patients with AD IFN-γR1 deficiency or AD STAT1 deficiency. In the presence of receptor activator of nuclear factor kappa-B ligand and M-CSF, GM colonies from patients with AD IFN-γR1 deficiency, AD STAT1 deficiency, or STAT1 GOF differentiated into osteoclasts, similar to GM colonies from healthy volunteers. IFN-γ concentration-dependent inhibition of osteoclast formation was impaired in GM colonies from patients with AD IFN-γR1 deficiency or AD STAT1 deficiency, whereas it was enhanced in GM colonies from patients with STAT1 GOF. CONCLUSIONS Osteoclast differentiation is increased in AD IFN-γR1 deficiency and AD STAT1 deficiency due to an impaired response to IFN-γ, leading to excessive osteoclast proliferation and, by inference, increased bone resorption in infected foci, which may underlie multifocal osteomyelitis.
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Affiliation(s)
- Miyuki Tsumura
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical Sciences, Hiroshima, Japan
| | - Mizuka Miki
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical Sciences, Hiroshima, Japan; Department of Pediatrics, Hiroshima Red Cross Hospital and Atomic-bomb Survivors Hospital, Hiroshima, Japan
| | - Yoko Mizoguchi
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical Sciences, Hiroshima, Japan
| | - Osamu Hirata
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical Sciences, Hiroshima, Japan; Hidamari Children Clinic, Hiroshima, Japan
| | - Shiho Nishimura
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical Sciences, Hiroshima, Japan; Department of Pediatrics, Hiroshima City Hiroshima Citizens Hospital, Hiroshima, Japan
| | - Moe Tamaura
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical Sciences, Hiroshima, Japan; Department of Pediatrics, Hiroshima-Nishi Medical Center, Hiroshima, Japan
| | - Reiko Kagawa
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical Sciences, Hiroshima, Japan
| | - Seiichi Hayakawa
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical Sciences, Hiroshima, Japan
| | - Masao Kobayashi
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical Sciences, Hiroshima, Japan; Japanese Red Cross, Chugoku-Shikoku Block Blood Center, Hiroshima, Japan
| | - Satoshi Okada
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical Sciences, Hiroshima, Japan.
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Caldarale F, Giacomelli M, Garrafa E, Tamassia N, Morreale A, Poli P, Timpano S, Baresi G, Zunica F, Cattalini M, Moratto D, Chiarini M, Cannizzo ES, Marchetti G, Cassatella MA, Taddio A, Tommasini A, Badolato R. Plasmacytoid Dendritic Cells Depletion and Elevation of IFN-γ Dependent Chemokines CXCL9 and CXCL10 in Children With Multisystem Inflammatory Syndrome. Front Immunol 2021; 12:654587. [PMID: 33841438 PMCID: PMC8033149 DOI: 10.3389/fimmu.2021.654587] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 03/03/2021] [Indexed: 12/22/2022] Open
Abstract
Background SARS-CoV-2 occurs in the majority of children as COVID-19, without symptoms or with a paucisymptomatic respiratory syndrome, but a small proportion of children develop the systemic Multi Inflammatory Syndrome (MIS-C), characterized by persistent fever and systemic hyperinflammation, with some clinical features resembling Kawasaki Disease (KD). Objective With this study we aimed to shed new light on the pathogenesis of these two SARS-CoV-2-related clinical manifestations. Methods We investigated lymphocyte and dendritic cells subsets, chemokine/cytokine profiles and evaluated the neutrophil activity mediators, myeloperoxidase (MPO), and reactive oxygen species (ROS), in 10 children with COVID-19 and 9 with MIS-C at the time of hospital admission. Results Patients with MIS-C showed higher plasma levels of C reactive protein (CRP), MPO, IL-6, and of the pro-inflammatory chemokines CXCL8 and CCL2 than COVID-19 children. In addition, they displayed higher levels of the chemokines CXCL9 and CXCL10, mainly induced by IFN-γ. By contrast, we detected IFN-α in plasma of children with COVID-19, but not in patients with MIS-C. This observation was consistent with the increase of ISG15 and IFIT1 mRNAs in cells of COVID-19 patients, while ISG15 and IFIT1 mRNA were detected in MIS-C at levels comparable to healthy controls. Moreover, quantification of the number of plasmacytoid dendritic cells (pDCs), which constitute the main source of IFN-α, showed profound depletion of this subset in MIS-C, but not in COVID-19. Conclusions Our results show a pattern of immune response which is suggestive of type I interferon activation in COVID-19 children, probably related to a recent interaction with the virus, while in MIS-C the immune response is characterized by elevation of the inflammatory cytokines/chemokines IL-6, CCL2, and CXCL8 and of the chemokines CXCL9 and CXL10, which are markers of an active Th1 type immune response. We believe that these immunological events, together with neutrophil activation, might be crucial in inducing the multisystem and cardiovascular damage observed in MIS-C.
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Affiliation(s)
- Francesca Caldarale
- Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
- ”Angelo Nocivelli” Institute of Molecular Medicine, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Mauro Giacomelli
- Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
- ”Angelo Nocivelli” Institute of Molecular Medicine, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Emirena Garrafa
- Department of Molecular and translational Medicin and Clinical Chemistry Laboratory ASST Spedali Civili, Brescia, Italy
| | - Nicola Tamassia
- Section of General Pathology, Department of Medicine, University of Verona, Verona, Italy
| | - Alessia Morreale
- Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
- ”Angelo Nocivelli” Institute of Molecular Medicine, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Piercarlo Poli
- Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
- ”Angelo Nocivelli” Institute of Molecular Medicine, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Silviana Timpano
- Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
- ”Angelo Nocivelli” Institute of Molecular Medicine, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Giulia Baresi
- Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
- ”Angelo Nocivelli” Institute of Molecular Medicine, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Fiammetta Zunica
- Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
- ”Angelo Nocivelli” Institute of Molecular Medicine, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Marco Cattalini
- Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
- ”Angelo Nocivelli” Institute of Molecular Medicine, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Daniele Moratto
- Flow Cytometry & Clinical Chemistry Laboratory, ASST Spedali Civili, Brescia, Italy
| | - Marco Chiarini
- Flow Cytometry & Clinical Chemistry Laboratory, ASST Spedali Civili, Brescia, Italy
| | - Elvira Stefania Cannizzo
- Clinic of Infectious Diseases, Department of Health Sciences, ASST Santi Paolo e Carlo, University of Milan, Milan, Italy
| | - Giulia Marchetti
- Clinic of Infectious Diseases, Department of Health Sciences, ASST Santi Paolo e Carlo, University of Milan, Milan, Italy
| | | | - Andrea Taddio
- Pediatric Department, IRCCS Burlo Garofolo, Trieste, Italy
| | | | - Raffaele Badolato
- Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
- ”Angelo Nocivelli” Institute of Molecular Medicine, University of Brescia, ASST Spedali Civili, Brescia, Italy
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