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Liharska L, Charney A. Transcriptomics : Approaches to Quantifying Gene Expression and Their Application to Studying the Human Brain. Curr Top Behav Neurosci 2024. [PMID: 38972894 DOI: 10.1007/7854_2024_466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
To date, the field of transcriptomics has been characterized by rapid methods development and technological advancement, with new technologies continuously rendering older ones obsolete.This chapter traces the evolution of approaches to quantifying gene expression and provides an overall view of the current state of the field of transcriptomics, its applications to the study of the human brain, and its place in the broader emerging multiomics landscape.
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Affiliation(s)
- Lora Liharska
- Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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2
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Chakroborty NK, Leboulle, Einspanier R, Menzel R. Behavioral and genetic correlates of heterogeneity in learning performance in individual honeybees, Apis mellifera. PLoS One 2024; 19:e0304563. [PMID: 38865313 PMCID: PMC11168654 DOI: 10.1371/journal.pone.0304563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 05/13/2024] [Indexed: 06/14/2024] Open
Abstract
Learning an olfactory discrimination task leads to heterogeneous results in honeybees with some bees performing very well and others at low rates. Here we investigated this behavioral heterogeneity and asked whether it was associated with particular gene expression patterns in the bee's brain. Bees were individually conditioned using a sequential conditioning protocol involving several phases of olfactory learning and retention tests. A cumulative score was used to differentiate the tested bees into high and low performers. The rate of CS+ odor learning was found to correlate most strongly with a cumulative performance score extracted from all learning and retention tests. Microarray analysis of gene expression in the mushroom body area of the brains of these bees identified a number of differentially expressed genes between high and low performers. These genes are associated with diverse biological functions, such as neurotransmission, memory formation, cargo trafficking and development.
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Affiliation(s)
- Neloy Kumar Chakroborty
- Institute Biology, Neurobiology, Freie Universität Berlin, Königin Luisestr, Berlin, Germany
| | - Leboulle
- Institute Biology, Neurobiology, Freie Universität Berlin, Königin Luisestr, Berlin, Germany
| | - Ralf Einspanier
- Department of Veterinary Medicine, Institute of Veterinary Biochemistry, Freie Universität Berlin, Oertzenweg, Berlin, Germany
| | - Randolf Menzel
- Institute Biology, Neurobiology, Freie Universität Berlin, Königin Luisestr, Berlin, Germany
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3
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Yang R, Kong W, Liu K, Wen G, Yu Y. Exploring Imaging Genetic Markers of Alzheimer's Disease Based on a Novel Nonlinear Correlation Analysis Algorithm. J Mol Neurosci 2024; 74:35. [PMID: 38568443 DOI: 10.1007/s12031-024-02190-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/16/2024] [Indexed: 04/05/2024]
Abstract
Alzheimer's disease (AD) is an irreversible neurological disorder characterized by insidious onset. Identifying potential markers in its emergence and progression is crucial for early diagnosis and treatment. Imaging genetics typically merges genetic variables with multiple imaging parameters, employing various association analysis algorithms to investigate the links between pathological phenotypes and genetic variations, and to unearth molecular-level insights from brain images. However, most existing imaging genetics algorithms based on sparse learning assume a linear relationship between genetic factors and brain functions, limiting their ability to discern complex nonlinear correlation patterns and resulting in reduced accuracy. To address these issues, we propose a novel nonlinear imaging genetic association analysis method, Deep Self-Reconstruction-based Adaptive Sparse Multi-view Deep Generalized Canonical Correlation Analysis (DSR-AdaSMDGCCA). This approach facilitates joint learning of the nonlinear relationships between pathological phenotypes and genetic variations by integrating three different types of data: structural magnetic resonance imaging (sMRI), single-nucleotide polymorphism (SNP), and gene expression data. By incorporating nonlinear transformations in DGCCA, our model effectively uncovers nonlinear associations across multiple data types. Additionally, the DSR algorithm clusters samples with identical labels, incorporating label information into the nonlinear feature extraction process and thus enhancing the performance of association analysis. The application of the DSR-AdaSMDGCCA algorithm on real data sets identified several AD risk regions (such as the hippocampus, parahippocampus, and fusiform gyrus) and risk genes (including VSIG4, NEDD4L, and PINK1), achieving maximum classification accuracy with the fewest selected features compared to baseline algorithms. Molecular biology enrichment analysis revealed that the pathways enriched by these top genes are intimately linked to AD progression, affirming that our algorithm not only improves correlation analysis performance but also identifies biologically significant markers.
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Affiliation(s)
- Renbo Yang
- College of Information Engineering, Shanghai Maritime University, 1550 Haigang Ave, Shanghai, 201306, People's Republic of China
| | - Wei Kong
- College of Information Engineering, Shanghai Maritime University, 1550 Haigang Ave, Shanghai, 201306, People's Republic of China.
| | - Kun Liu
- College of Information Engineering, Shanghai Maritime University, 1550 Haigang Ave, Shanghai, 201306, People's Republic of China
| | - Gen Wen
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Yaling Yu
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
- Institute of Microsurgery on Extremities, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
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4
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Zhang C, Dai Z, Ferrier T, Orduña L, Santiago A, Peris A, Wong DCJ, Kappel C, Savoi S, Loyola R, Amato A, Kozak B, Li M, Liang A, Carrasco D, Meyer-Regueiro C, Espinoza C, Hilbert G, Figueroa-Balderas R, Cantu D, Arroyo-Garcia R, Arce-Johnson P, Claudel P, Errandonea D, Rodríguez-Concepción M, Duchêne E, Huang SSC, Castellarin SD, Tornielli GB, Barrieu F, Matus JT. MYB24 orchestrates terpene and flavonol metabolism as light responses to anthocyanin depletion in variegated grape berries. THE PLANT CELL 2023; 35:4238-4265. [PMID: 37648264 PMCID: PMC10689149 DOI: 10.1093/plcell/koad228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 08/13/2023] [Accepted: 08/30/2023] [Indexed: 09/01/2023]
Abstract
Variegation is a rare type of mosaicism not fully studied in plants, especially fruits. We examined red and white sections of grape (Vitis vinifera cv. 'Béquignol') variegated berries and found that accumulation of products from branches of the phenylpropanoid and isoprenoid pathways showed an opposite tendency. Light-responsive flavonol and monoterpene levels increased in anthocyanin-depleted areas in correlation with increasing MYB24 expression. Cistrome analysis suggested that MYB24 binds to the promoters of 22 terpene synthase (TPS) genes, as well as 32 photosynthesis/light-related genes, including carotenoid pathway members, the flavonol regulator HY5 HOMOLOGUE (HYH), and other radiation response genes. Indeed, TPS35, TPS09, the carotenoid isomerase gene CRTISO2, and HYH were activated in the presence of MYB24 and MYC2. We suggest that MYB24 modulates ultraviolet and high-intensity visible light stress responses that include terpene and flavonol synthesis and potentially affects carotenoids. The MYB24 regulatory network is developmentally triggered after the onset of berry ripening, while the absence of anthocyanin sunscreens accelerates its activation, likely in a dose-dependent manner due to increased radiation exposure. Anthocyanins and flavonols in variegated berry skins act as effective sunscreens but for different wavelength ranges. The expression patterns of stress marker genes in red and white sections of 'Béquignol' berries strongly suggest that MYB24 promotes light stress amelioration but only partly succeeds during late ripening.
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Affiliation(s)
- Chen Zhang
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna 46980, Valencia, Spain
| | - Zhanwu Dai
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Thilia Ferrier
- EGFV, Bordeaux Sciences Agro, University of Bordeaux, INRAE, ISVV, 210 Chemin de Leysotte, 33140 Villenave d'Ornon, France
| | - Luis Orduña
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna 46980, Valencia, Spain
| | - Antonio Santiago
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna 46980, Valencia, Spain
| | - Arnau Peris
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna 46980, Valencia, Spain
| | - Darren C J Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam-Golm 14476, Germany
| | - Stefania Savoi
- Department of Agricultural, Forest and Food Sciences, University of Turin, Turin 10124, Italy
| | - Rodrigo Loyola
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Alessandra Amato
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Bartosz Kozak
- Wine Research Centre, University of British Columbia, Vancouver, British Columbia V1V 1V7, Canada
| | - Miaomiao Li
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Akun Liang
- Departamento de Física Aplicada-ICMUV-MALTA Consolider Team, Universitat de València, Burjassot 46100, Valencia, Spain
| | - David Carrasco
- Centre for Plant Biotechnology and Genomics (CBGP), Universidad Politécnica de Madrid-INIA, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Carlos Meyer-Regueiro
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Carmen Espinoza
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago 8380453, Chile
| | - Ghislaine Hilbert
- EGFV, Bordeaux Sciences Agro, University of Bordeaux, INRAE, ISVV, 210 Chemin de Leysotte, 33140 Villenave d'Ornon, France
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - Rosa Arroyo-Garcia
- Centre for Plant Biotechnology and Genomics (CBGP), Universidad Politécnica de Madrid-INIA, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Patricio Arce-Johnson
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería Universidad Autónoma deChile
| | | | - Daniel Errandonea
- Departamento de Física Aplicada-ICMUV-MALTA Consolider Team, Universitat de València, Burjassot 46100, Valencia, Spain
| | - Manuel Rodríguez-Concepción
- Institute for Plant Molecular and Cell Biology (IBMCP), CSIC-Universitat Politècnica de València, Valencia 46022, Spain
| | - Eric Duchêne
- SVQV, University of Strasbourg, INRAE, Colmar 68000, France
| | - Shao-shan Carol Huang
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Simone Diego Castellarin
- Wine Research Centre, University of British Columbia, Vancouver, British Columbia V1V 1V7, Canada
| | | | - Francois Barrieu
- EGFV, Bordeaux Sciences Agro, University of Bordeaux, INRAE, ISVV, 210 Chemin de Leysotte, 33140 Villenave d'Ornon, France
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna 46980, Valencia, Spain
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5
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Maglov J, Feng MY, Lin D, Barkhouse K, Alexander A, Grbic M, Zhurov V, Grbic V, Tudzarova S. A link between energy metabolism and plant host adaptation states in the two-spotted spider mite, Tetranychus urticae (Koch). Sci Rep 2023; 13:19343. [PMID: 37935795 PMCID: PMC10630510 DOI: 10.1038/s41598-023-46589-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023] Open
Abstract
Energy metabolism is a highly conserved process that balances generation of cellular energy and maintenance of redox homeostasis. It consists of five interconnected pathways: glycolysis, tricarboxylic acid cycle, pentose phosphate, trans-sulfuration, and NAD+ biosynthesis pathways. Environmental stress rewires cellular energy metabolism. Type-2 diabetes is a well-studied energy metabolism rewiring state in human pancreatic β-cells where glucose metabolism is uncoupled from insulin secretion. The two-spotted spider mite, Tetranychus urticae (Koch), exhibits a remarkable ability to adapt to environmental stress. Upon transfer to unfavourable plant hosts, mites experience extreme xenobiotic stress that dramatically affects their survivorship and fecundity. However, within 25 generations, mites adapt to the xenobiotic stress and restore their fitness. Mites' ability to withstand long-term xenobiotic stress raises a question of their energy metabolism states during host adaptation. Here, we compared the transcriptional responses of five energy metabolism pathways between host-adapted and non-adapted mites while using responses in human pancreatic islet donors to model these pathways under stress. We found that non-adapted mites and human pancreatic β-cells responded in a similar manner to host plant transfer and diabetogenic stress respectively, where redox homeostasis maintenance was favoured over energy generation. Remarkably, we found that upon host-adaptation, mite energy metabolic states were restored to normal. These findings suggest that genes involved in energy metabolism can serve as molecular markers for mite host-adaptation.
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Affiliation(s)
- Jorden Maglov
- Department of Biology, The University of Western Ontario, London, N6A 5B7, Canada
| | - Min Yi Feng
- Department of Biology, The University of Western Ontario, London, N6A 5B7, Canada
| | - Dorothy Lin
- Department of Biology, The University of Western Ontario, London, N6A 5B7, Canada
| | - Kennedy Barkhouse
- Department of Biology, The University of Western Ontario, London, N6A 5B7, Canada
| | - Anton Alexander
- Department of Biology, The University of Western Ontario, London, N6A 5B7, Canada
| | - Miodrag Grbic
- Department of Biology, The University of Western Ontario, London, N6A 5B7, Canada
| | - Vladimir Zhurov
- Department of Biology, The University of Western Ontario, London, N6A 5B7, Canada.
| | - Vojislava Grbic
- Department of Biology, The University of Western Ontario, London, N6A 5B7, Canada.
| | - Slavica Tudzarova
- Larry L. Hillblom Islet Research Center, University of California, Los Angeles, CA, 90095, USA.
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6
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Wang X, Wang Z, Guo Z, Wang Z, Chen F, Wang Z. Exploring the Role of Different Cell-Death-Related Genes in Sepsis Diagnosis Using a Machine Learning Algorithm. Int J Mol Sci 2023; 24:14720. [PMID: 37834169 PMCID: PMC10572834 DOI: 10.3390/ijms241914720] [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: 07/31/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
Sepsis, a disease caused by severe infection, has a high mortality rate. At present, there is a lack of reliable algorithmic models for biomarker mining and diagnostic model construction for sepsis. Programmed cell death (PCD) has been shown to play a vital role in disease occurrence and progression, and different PCD-related genes have the potential to be targeted for the treatment of sepsis. In this paper, we analyzed PCD-related genes in sepsis. Implicated PCD processes include apoptosis, necroptosis, ferroptosis, pyroptosis, netotic cell death, entotic cell death, lysosome-dependent cell death, parthanatos, autophagy-dependent cell death, oxeiptosis, and alkaliptosis. We screened for diagnostic-related genes and constructed models for diagnosing sepsis using multiple machine-learning models. In addition, the immune landscape of sepsis was analyzed based on the diagnosis-related genes that were obtained. In this paper, 10 diagnosis-related genes were screened for using machine learning algorithms, and diagnostic models were constructed. The diagnostic model was validated in the internal and external test sets, and the Area Under Curve (AUC) reached 0.7951 in the internal test set and 0.9627 in the external test set. Furthermore, we verified the diagnostic gene via a qPCR experiment. The diagnostic-related genes and diagnostic genes obtained in this paper can be utilized as a reference for clinical sepsis diagnosis. The results of this study can act as a reference for the clinical diagnosis of sepsis and for target discovery for potential therapeutic drugs.
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Affiliation(s)
- Xuesong Wang
- School of Clinical Medicine, Tsinghua University, Beijing 100190, China; (X.W.); (Z.W.); (Z.W.); (F.C.)
- Beijing Tsinghua Changgung Hospital, Tsinghua University, Beijing 100084, China;
| | - Ziyi Wang
- School of Clinical Medicine, Tsinghua University, Beijing 100190, China; (X.W.); (Z.W.); (Z.W.); (F.C.)
| | - Zhe Guo
- Beijing Tsinghua Changgung Hospital, Tsinghua University, Beijing 100084, China;
| | - Ziwen Wang
- School of Clinical Medicine, Tsinghua University, Beijing 100190, China; (X.W.); (Z.W.); (Z.W.); (F.C.)
| | - Feng Chen
- School of Clinical Medicine, Tsinghua University, Beijing 100190, China; (X.W.); (Z.W.); (Z.W.); (F.C.)
| | - Zhong Wang
- School of Clinical Medicine, Tsinghua University, Beijing 100190, China; (X.W.); (Z.W.); (Z.W.); (F.C.)
- Beijing Tsinghua Changgung Hospital, Tsinghua University, Beijing 100084, China;
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7
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Steinberg C, Gaudreault N, Papadakis AI, Henry C, Champagne J, Philippon F, O’Hara G, Blier L, Plourde B, Nault I, Roy K, Sarrazin JF, Spatz A, Bossé Y. Leucocyte-derived micro-RNAs as candidate biomarkers in Brugada syndrome. Europace 2023; 25:euad145. [PMID: 37314195 PMCID: PMC10265963 DOI: 10.1093/europace/euad145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/02/2023] [Indexed: 06/15/2023] Open
Abstract
AIMS Risk stratification for sudden cardiac death in patients with Brugada syndrome remains a major challenge. Contemporary risk prediction models have only modest predictive value. The aim of this study was to assess the role of micro-RNAs from peripheral blood as candidate biomarkers in Brugada syndrome. METHODS AND RESULTS In this prospective study, Brugada patients and unaffected control individuals were enrolled for analysis of leucocyte-derived microRNAs (miRNAs) levels. Expression levels of 798 different circulating miRNAs were analysed on the NanoString® nCounter platform. All results were cross-validated by using a quantitative polymerase chain reaction. Micro-RNA expression levels of Brugada patients were compared with clinical data. A total of 21 definite Brugada patients (38% with a history of ventricular arrhythmia or cardiac arrest) and 30 unaffected control individuals were included in the study. Micro-RNA analysis showed a distinct expression profile in Brugada patients with 42 differentially expressed markers (38 up-regulated, 4 down-regulated miRNAs). The symptom status of Brugada patients was associated with a distinct miRNA signature. Micro-RNAs 145-5p and 585-3p were significantly up-regulated in symptomatic Brugada patients (P = 0.04). Incorporating miRNAs 145-5p and 585-3p into a multivariable model demonstrated significantly increased symptom prediction (area under the curve = 0.96; 95% confidence interval: 0.88-1.00). CONCLUSION Brugada patients display a distinct miRNA expression profile compared with unaffected control individuals. There is also evidence that certain miRNAs (miR-145-5p and miR-585-3p) are associated with the symptom status of Brugada patients. The results suggest the principal utility of leucocyte-derived miRNAs as prognostic biomarkers for Brugada syndrome.
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Affiliation(s)
- Christian Steinberg
- Institut universitaire de cardiologie et pneumologie de Québec, Université Laval, 2725, Chemin Ste-Foy, Quebec City, Canada G1V 4G5
| | - Nathalie Gaudreault
- Institut universitaire de cardiologie et pneumologie de Québec, Université Laval, 2725, Chemin Ste-Foy, Quebec City, Canada G1V 4G5
| | - Andreas I Papadakis
- Lady Davis Institute for Medical Research, Montreal Jewish Hospital, McGill University, Montreal, Canada
| | - Cyndi Henry
- Institut universitaire de cardiologie et pneumologie de Québec, Université Laval, 2725, Chemin Ste-Foy, Quebec City, Canada G1V 4G5
| | - Jean Champagne
- Institut universitaire de cardiologie et pneumologie de Québec, Université Laval, 2725, Chemin Ste-Foy, Quebec City, Canada G1V 4G5
| | - François Philippon
- Institut universitaire de cardiologie et pneumologie de Québec, Université Laval, 2725, Chemin Ste-Foy, Quebec City, Canada G1V 4G5
| | - Gilles O’Hara
- Institut universitaire de cardiologie et pneumologie de Québec, Université Laval, 2725, Chemin Ste-Foy, Quebec City, Canada G1V 4G5
| | - Louis Blier
- Institut universitaire de cardiologie et pneumologie de Québec, Université Laval, 2725, Chemin Ste-Foy, Quebec City, Canada G1V 4G5
| | - Benoit Plourde
- Institut universitaire de cardiologie et pneumologie de Québec, Université Laval, 2725, Chemin Ste-Foy, Quebec City, Canada G1V 4G5
| | - Isabelle Nault
- Institut universitaire de cardiologie et pneumologie de Québec, Université Laval, 2725, Chemin Ste-Foy, Quebec City, Canada G1V 4G5
| | - Karine Roy
- Institut universitaire de cardiologie et pneumologie de Québec, Université Laval, 2725, Chemin Ste-Foy, Quebec City, Canada G1V 4G5
| | - Jean-François Sarrazin
- Institut universitaire de cardiologie et pneumologie de Québec, Université Laval, 2725, Chemin Ste-Foy, Quebec City, Canada G1V 4G5
| | - Alan Spatz
- Lady Davis Institute for Medical Research, Montreal Jewish Hospital, McGill University, Montreal, Canada
| | - Yohan Bossé
- Institut universitaire de cardiologie et pneumologie de Québec, Université Laval, 2725, Chemin Ste-Foy, Quebec City, Canada G1V 4G5
- Department of Molecular Medicine, Laval University, Quebec City, Canada
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8
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Aryankalayil MJ, Bylicky MA, Martello S, Chopra S, Sproull M, May JM, Shankardass A, MacMillan L, Vanpouille-Box C, Eke I, Scott KMK, Dalo J, Coleman CN. Microarray analysis of hub genes, non-coding RNAs and pathways in lung after whole body irradiation in a mouse model. Int J Radiat Biol 2023; 99:1702-1715. [PMID: 37212632 PMCID: PMC10615684 DOI: 10.1080/09553002.2023.2214205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/05/2023] [Indexed: 05/23/2023]
Abstract
PURPOSE Previous research has highlighted the impact of radiation damage, with cancer patients developing acute disorders including radiation induced pneumonitis or chronic disorders including pulmonary fibrosis months after radiation therapy ends. We sought to discover biomarkers that predict these injuries and develop treatments that mitigate this damage and improve quality of life. MATERIALS AND METHODS Six- to eight-week-old female C57BL/6 mice received 1, 2, 4, 8, 12 Gy or sham whole body irradiation. Animals were euthanized 48 h post exposure and lungs removed, snap frozen and underwent RNA isolation. Microarray analysis was performed to determine dysregulation of messenger RNA (mRNA), microRNA (miRNA), and long non-coding RNA (lncRNA) after radiation injury. RESULTS We observed sustained dysregulation of specific RNA markers including: mRNAs, lncRNAs, and miRNAs across all doses. We also identified significantly upregulated genes that can indicate high dose exposure, including Cpt1c, Pdk4, Gdf15, and Eda2r, which are markers of senescence and fibrosis. Only three miRNAs were significantly dysregulated across all radiation doses: miRNA-142-3p and miRNA-142-5p were downregulated and miRNA-34a-5p was upregulated. IPA analysis predicted inhibition of several molecular pathways with increasing doses of radiation, including: T cell development, Quantity of leukocytes, Quantity of lymphocytes, and Cell viability. CONCLUSIONS These RNA biomarkers might be highly relevant in the development of treatments and in predicting normal tissue injury in patients undergoing radiation treatment. We are conducting further experiments in our laboratory, which includes a human lung-on-a-chip model, to develop a decision tree model using RNA biomarkers.
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Affiliation(s)
- Molykutty J Aryankalayil
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michelle A Bylicky
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shannon Martello
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sunita Chopra
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mary Sproull
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jared M May
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Aman Shankardass
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Iris Eke
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kevin M K Scott
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Juan Dalo
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - C Norman Coleman
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Radiation Research Program, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
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9
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Fajarda O, Almeida JR, Duarte-Pereira S, Silva RM, Oliveira JL. Methodology to identify a gene expression signature by merging microarray datasets. Comput Biol Med 2023; 159:106867. [PMID: 37060770 DOI: 10.1016/j.compbiomed.2023.106867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/01/2023] [Accepted: 03/30/2023] [Indexed: 04/17/2023]
Abstract
A vast number of microarray datasets have been produced as a way to identify differentially expressed genes and gene expression signatures. A better understanding of these biological processes can help in the diagnosis and prognosis of diseases, as well as in the therapeutic response to drugs. However, most of the available datasets are composed of a reduced number of samples, leading to low statistical, predictive and generalization power. One way to overcome this problem is by merging several microarray datasets into a single dataset, which is typically a challenging task. Statistical methods or supervised machine learning algorithms are usually used to determine gene expression signatures. Nevertheless, statistical methods require an arbitrary threshold to be defined, and supervised machine learning methods can be ineffective when applied to high-dimensional datasets like microarrays. We propose a methodology to identify gene expression signatures by merging microarray datasets. This methodology uses statistical methods to obtain several sets of differentially expressed genes and uses supervised machine learning algorithms to select the gene expression signature. This methodology was validated using two distinct research applications: one using heart failure and the other using autism spectrum disorder microarray datasets. For the first, we obtained a gene expression signature composed of 117 genes, with a classification accuracy of approximately 98%. For the second use case, we obtained a gene expression signature composed of 79 genes, with a classification accuracy of approximately 82%. This methodology was implemented in R language and is available, under the MIT licence, at https://github.com/bioinformatics-ua/MicroGES.
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Affiliation(s)
- Olga Fajarda
- DETI/IEETA, LASI, University of Aveiro, Aveiro, Portugal.
| | - João Rafael Almeida
- DETI/IEETA, LASI, University of Aveiro, Aveiro, Portugal; Department of Computation, University of A Coruña, A Coruña, Spain.
| | - Sara Duarte-Pereira
- DETI/IEETA, LASI, University of Aveiro, Aveiro, Portugal; Department of Medical Sciences and iBiMED-Institute of Biomedicine, University of Aveiro, Aveiro, Portugal.
| | - Raquel M Silva
- Universidade Católica Portuguesa, Faculty of Dental Medicine (FMD), Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal.
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10
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Agarwal A, Kansal V, Farooqi H, Singh VK, Prasad R. Differentially deregulated microRNAs contribute to ultraviolet radiation-induced photocarcinogenesis through immunomodulation: An-analysis of microRNAs expression profiling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.24.529976. [PMID: 36909651 PMCID: PMC10002698 DOI: 10.1101/2023.02.24.529976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
MicroRNAs (miRNAs) are short non-coding RNA molecules (18-25 nucleotides) that regulate several fundamental biological processes. Emerging evidence has shown more than 1500 miRNAs functions in the cell cycle, proliferation, apoptosis, oxidative stress, immune response, DNA damage, and epigenetics alterations. miRNAs are bidirectionally in nature and act as a tumor suppressor and as an oncogene through crosstalk between tumor cells and immune cells. Although the roles of miRNAs in several cancers are well studied, little is known about ultraviolet B (UVB) radiation-induced skin cancer. Here, we performed a comprehensive screening of 1281 miRNAs in tumor tissues and compared their expression with normal skin. Our results demonstrate that the expression levels of 587 miRNAs were altered in tumor tissues compared to their expression in normal skin. The expression of 337 miRNAs was upregulated from 1.5-12 folds, while the expression of 250 miRNAs was downregulated up to 1.5-10 folds in tumors. Further, intraperitoneal injection of a mimic of down-regulated miR-15b (30nM) and an inhibitor of upregulated miR-133a (20nM) protect UVB-induced suppression of contact hypersensitivity (CHS) response. In conclusion, we identified a network of altered miRNAs in tumors that can serve as prognostic biomarkers and therapeutic targets to manage photocarcinogenesis effectively.
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Affiliation(s)
- Anshu Agarwal
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, AL-35294, USA
- Deptartment of Zoology, Agra Collage, Agra-282001, India
- Department of Biotechnology, Hamdard University, New Delhi-110062, India
| | - Vikash Kansal
- Department of Otolaryngology, Emory University, Atlanta, GA 30322, USA
| | - Humaira Farooqi
- Department of Biotechnology, Hamdard University, New Delhi-110062, India
| | | | - Ram Prasad
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, AL-35294, USA
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11
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Overnight Corticosterone and Gene Expression in Mouse Hippocampus: Time Course during Resting Period. Int J Mol Sci 2023; 24:ijms24032828. [PMID: 36769150 PMCID: PMC9917930 DOI: 10.3390/ijms24032828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 02/05/2023] Open
Abstract
The aim of the experiment was to test the effect of an elevated level of glucocorticoids on the mouse hippocampal transcriptome after 12 h of treatment with corticosterone that was administered during an active phase of the circadian cycle. Additionally, we also tested the circadian changes in gene expression and the decay time of transcriptomic response to corticosterone. Gene expression was analyzed using microarrays. Obtained results show that transcriptomic responses to glucocorticoids are heterogeneous in terms of the decay time with some genes displaying persistent changes in expression during 9 h of rest. We have also found a considerable overlap between genes regulated by corticosterone and genes implicated previously in stress response. The examples of such genes are Acer2, Agt, Apod, Aqp4, Etnppl, Fabp7, Fam107a, Fjx1, Fmo2, Galnt15, Gjc2, Heph, Hes5, Htra1, Jdp2, Kif5a, Lfng, Lrg1, Mgp, Mt1, Pglyrp1, Pla2g3, Plin4, Pllp, Ptgds, Ptn, Slc2a1, Slco1c1, Sult1a1, Thbd and Txnip. This indicates that the applied model is a useful tool for the investigation of mechanisms underlying the stress response.
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12
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Wang Y, Schughart K, Pelaia TM, Chew T, Kim K, Karvunidis T, Knippenberg B, Teoh S, Phu AL, Short KR, Iredell J, Thevarajan I, Audsley J, Macdonald S, Burcham J, Tang B, McLean A, Shojaei M. Pathway and Network Analyses Identify Growth Factor Signaling and MMP9 as Potential Mediators of Mitochondrial Dysfunction in Severe COVID-19. Int J Mol Sci 2023; 24:ijms24032524. [PMID: 36768847 PMCID: PMC9917147 DOI: 10.3390/ijms24032524] [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: 12/15/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/31/2023] Open
Abstract
Patients with preexisting metabolic disorders such as diabetes are at a higher risk of developing severe coronavirus disease 2019 (COVID-19). Mitochondrion, the very organelle that controls cellular metabolism, holds the key to understanding disease progression at the cellular level. Our current study aimed to understand how cellular metabolism contributes to COVID-19 outcomes. Metacore pathway enrichment analyses on differentially expressed genes (encoded by both mitochondrial and nuclear deoxyribonucleic acid (DNA)) involved in cellular metabolism, regulation of mitochondrial respiration and organization, and apoptosis, was performed on RNA sequencing (RNASeq) data from blood samples collected from healthy controls and patients with mild/moderate or severe COVID-19. Genes from the enriched pathways were analyzed by network analysis to uncover interactions among them and up- or downstream genes within each pathway. Compared to the mild/moderate COVID-19, the upregulation of a myriad of growth factor and cell cycle signaling pathways, with concomitant downregulation of interferon signaling pathways, were observed in the severe group. Matrix metallopeptidase 9 (MMP9) was found in five of the top 10 upregulated pathways, indicating its potential as therapeutic target against COVID-19. In summary, our data demonstrates aberrant activation of endocrine signaling in severe COVID-19, and its implication in immune and metabolic dysfunction.
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Affiliation(s)
- Ya Wang
- Department of Intensive Care Medicine, Nepean Hospital, Kingswood, NSW 2747, Australia
- Centre for Immunology and Allergy Research, The Westmead Institute for Medical Research, Sydney, NSW 2145, Australia
- Faculty of Medicine and Health, Sydney Medical School Nepean, Nepean Hospital, The University of Sydney, Kingswood, NSW 2747, Australia
| | - Klaus Schughart
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Institute of Virology Münster, University of Münster, 48149 Münster, Germany
| | - Tiana Maria Pelaia
- Department of Intensive Care Medicine, Nepean Hospital, Kingswood, NSW 2747, Australia
| | - Tracy Chew
- Sydney Informatics Hub, Core Research Facilities, The University of Sydney, Sydney NSW 2006, Australia
| | - Karan Kim
- Centre for Immunology and Allergy Research, The Westmead Institute for Medical Research, Sydney, NSW 2145, Australia
| | - Thomas Karvunidis
- Medical ICU, 1st Department of Internal Medicine, Charles University and Teaching Hospital Pilsen, 323 00 Plzeň, Czech Republic
| | - Ben Knippenberg
- Department of Microbiology, St. George Hospital, Sydney, NSW 2217, Australia
| | - Sally Teoh
- Department of Intensive Care Medicine, Nepean Hospital, Kingswood, NSW 2747, Australia
| | - Amy L. Phu
- Research and Education Network, Western Sydney Local Health District, Westmead Hospital, CNR Darcy and Hawkesbury Roads, Sydney, NSW 2145, Australia
- Faculty of Medicine and Health, Sydney Medical School Westmead, Westmead Hospital, The University of Sydney, Sydney, NSW 2145, Australia
| | - Kirsty R. Short
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jonathan Iredell
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Sydney, NSW 2145, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, NSW 2145, Australia
- Westmead Hospital, Western Sydney Local Health District, Sydney, NSW 2145, Australia
- Sydney Institute for Infectious Disease, The University of Sydney, Sydney, NSW 2145, Australia
| | - Irani Thevarajan
- Victorian Infectious Disease Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3050, Australia
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Jennifer Audsley
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Stephen Macdonald
- Centre for Clinical Research in Emergency Medicine, Harry Perkins Institute of Medical Research, Royal Perth Hospital, Perth, WA 6000, Australia
- Medical School, University of Western Australia, Perth, WA 6009, Australia
- Emergency Department, Royal Perth Hospital, Perth, WA 6000, Australia
| | - Jonathon Burcham
- Centre for Clinical Research in Emergency Medicine, Royal Perth Bentley Group, Perth, WA 6000, Australia
| | | | - Benjamin Tang
- Department of Intensive Care Medicine, Nepean Hospital, Kingswood, NSW 2747, Australia
- Centre for Immunology and Allergy Research, The Westmead Institute for Medical Research, Sydney, NSW 2145, Australia
| | - Anthony McLean
- Department of Intensive Care Medicine, Nepean Hospital, Kingswood, NSW 2747, Australia
- Faculty of Medicine and Health, Sydney Medical School Nepean, Nepean Hospital, The University of Sydney, Kingswood, NSW 2747, Australia
- Correspondence: (A.M.); (M.S.)
| | - Maryam Shojaei
- Department of Intensive Care Medicine, Nepean Hospital, Kingswood, NSW 2747, Australia
- Centre for Immunology and Allergy Research, The Westmead Institute for Medical Research, Sydney, NSW 2145, Australia
- Faculty of Medicine and Health, Sydney Medical School Nepean, Nepean Hospital, The University of Sydney, Kingswood, NSW 2747, Australia
- Correspondence: (A.M.); (M.S.)
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13
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Wang Y, Schughart K, Pelaia TM, Chew T, Kim K, Karvunidis T, Knippenberg B, Teoh S, Phu AL, Short KR, Iredell J, Thevarajan I, Audsley J, Macdonald S, Burcham J, McLean A, Tang B, Shojaei M. Blood transcriptome responses in patients correlate with severity of COVID-19 disease. Front Immunol 2023; 13:1043219. [PMID: 36741372 PMCID: PMC9896980 DOI: 10.3389/fimmu.2022.1043219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 12/19/2022] [Indexed: 01/24/2023] Open
Abstract
Background Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Infected individuals display a wide spectrum of disease severity, as defined by the World Health Organization (WHO). One of the main factors underlying this heterogeneity is the host immune response, with severe COVID-19 often associated with a hyperinflammatory state. Aim Our current study aimed to pinpoint the specific genes and pathways underlying differences in the disease spectrum and outcomes observed, through in-depth analyses of whole blood transcriptomics in a large cohort of COVID-19 participants. Results All WHO severity levels were well represented and mild and severe disease displaying distinct gene expression profiles. WHO severity levels 1-4 were grouped as mild disease, and signatures from these participants were different from those with WHO severity levels 6-9 classified as severe disease. Severity level 5 (moderate cases) presented a unique transitional gene signature between severity levels 2-4 (mild/moderate) and 6-9 (severe) and hence might represent the turning point for better or worse disease outcome. Gene expression changes are very distinct when comparing mild/moderate or severe cases to healthy controls. In particular, we demonstrated the hallmark down-regulation of adaptive immune response pathways and activation of neutrophil pathways in severe compared to mild/moderate cases, as well as activation of blood coagulation pathways. Conclusions Our data revealed discrete gene signatures associated with mild, moderate, and severe COVID-19 identifying valuable candidates for future biomarker discovery.
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Affiliation(s)
- Ya Wang
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia,Centre for Immunology and Allergy Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia,Faculty of Medicine and Health, Sydney Medical School Nepean, Nepean Hospital, University of Sydney, Penrith, NSW, Australia,*Correspondence: Ya Wang,
| | - Klaus Schughart
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States,Institute of Molecular Virology, University of Münster, Münster, Germany
| | - Tiana Maria Pelaia
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia
| | - Tracy Chew
- Sydney Informatics Hub, Core Research Facilities, The University of Sydney, Sydney, NSW, Australia
| | - Karan Kim
- Centre for Immunology and Allergy Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Thomas Karvunidis
- Medical ICU, 1 Department of Internal Medicine, Charles University and Teaching Hospital, Pilsen, Czechia
| | - Ben Knippenberg
- Department of Microbiology. St George Hospital, Kogarah, NSW, Australia
| | - Sally Teoh
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia
| | - Amy L. Phu
- Research and Education Network, Western Sydney Local Health District, Westmead Hospital, NSW, Westmead, Australia,Faculty of Medicine and Health, Sydney Medical School Westmead, Westmead Hospital, University of Sydney, NSW, Westmead, Australia
| | - Kirsty R. Short
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jonathan Iredell
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Westmead, NSW, Australia,Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia,Westmead Hospital, Western Sydney Local Health District, Westmead, NSW, Australia,Sydney Institute for Infectious Disease, The University of Sydney, Sydney, NSW, Australia
| | - Irani Thevarajan
- Victorian Infectious Disease Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia,Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jennifer Audsley
- Victorian Infectious Disease Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia,Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Stephen Macdonald
- Centre for Clinical Research in Emergency Medicine, Harry Perkins Institute of Medical Research, Royal Perth Hospital, Perth, WA, Australia,Medical School, University of Western Australia, Perth, WA, Australia,Emergency Department, Royal Perth Hospital, Perth, WA, Australia
| | - Jonathon Burcham
- Centre for Clinical Research in Emergency Medicine, Royal Perth Bentley Group, Perth, WA, Australia
| | - Anthony McLean
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia,Faculty of Medicine and Health, Sydney Medical School Nepean, Nepean Hospital, University of Sydney, Penrith, NSW, Australia
| | | | - Benjamin Tang
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia,Centre for Immunology and Allergy Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Maryam Shojaei
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia,Centre for Immunology and Allergy Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia,Faculty of Medicine and Health, Sydney Medical School Nepean, Nepean Hospital, University of Sydney, Penrith, NSW, Australia
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14
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Acharjee A, Ray A, Salkar A, Bihani S, Tuckley C, Shastri J, Agrawal S, Duttagupta S, Srivastava S. Humoral Immune Response Profile of COVID-19 Reveals Severity and Variant-Specific Epitopes: Lessons from SARS-CoV-2 Peptide Microarray. Viruses 2023; 15:248. [PMID: 36680289 PMCID: PMC9866125 DOI: 10.3390/v15010248] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/12/2023] [Accepted: 01/14/2023] [Indexed: 01/18/2023] Open
Abstract
The amaranthine scale of the COVID-19 pandemic and unpredictable disease severity is of grave concern. Serological diagnostic aids are an excellent choice for clinicians for rapid and easy prognosis of the disease. To this end, we studied the humoral immune response to SARS-CoV-2 infection to map immunogenic regions in the SARS-CoV-2 proteome at amino acid resolution using a high-density SARS-CoV-2 proteome peptide microarray. The microarray has 4932 overlapping peptides printed in duplicates spanning the entire SARS-CoV-2 proteome. We found 204 and 676 immunogenic peptides against IgA and IgG, corresponding to 137 and 412 IgA and IgG epitopes, respectively. Of these, 6 and 307 epitopes could discriminate between disease severity. The emergence of variants has added to the complexity of the disease. Using the mutation panel available, we could detect 5 and 10 immunogenic peptides against IgA and IgG with mutations belonging to SAR-CoV-2 variants. The study revealed severity-based epitopes that could be presented as potential prognostic serological markers. Further, the mutant epitope immunogenicity could indicate the putative use of these markers for diagnosing variants responsible for the infection.
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Affiliation(s)
- Arup Acharjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Arka Ray
- Centre for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Akanksha Salkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Surbhi Bihani
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Chaitanya Tuckley
- Centre for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai 400076, India
| | | | - Sachee Agrawal
- Kasturba Hospital for Infectious Diseases, Mumbai 400011, India
| | - Siddhartha Duttagupta
- Department of Electrical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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15
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Aryankalayil MJ, Bylicky MA, Martello S, Chopra S, Sproull M, May JM, Shankardass A, MacMillan L, Vanpouille-Box C, Dalo J, Scott KMK, Norman Coleman C. Microarray analysis identifies coding and non-coding RNA markers of liver injury in whole body irradiated mice. Sci Rep 2023; 13:200. [PMID: 36604457 PMCID: PMC9814510 DOI: 10.1038/s41598-022-26784-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023] Open
Abstract
Radiation injury from medical, accidental, or intentional sources can induce acute and long-term hepatic dysregulation, fibrosis, and cancer. This long-term hepatic dysregulation decreases quality of life and may lead to death. Our goal in this study is to determine acute changes in biological pathways and discover potential RNA biomarkers predictive of radiation injury. We performed whole transcriptome microarray analysis of mouse liver tissue (C57BL/6 J) 48 h after whole-body irradiation with 1, 2, 4, 8, and 12 Gray to identify significant expression changes in mRNAs, lncRNAs, and miRNAs, We also validated changes in specific RNAs through qRT-PCR. We used Ingenuity Pathway Analysis (IPA) to identify pathways associated with gene expression changes. We observed significant dysregulation of multiple mRNAs across all doses. In contrast, miRNA dysregulation was observed upwards of 2 Gray. The most significantly upregulated mRNAs function as tumor suppressors: Cdkn1a, Phlda3, and Eda2r. The most significantly downregulated mRNAs were involved in hemoglobin synthesis, inflammation, and mitochondrial function including multiple members of Hbb and Hba. The most significantly upregulated miRNA included: miR-34a-5p, miR-3102-5p, and miR-3960, while miR-342-3p, miR-142a-3p, and miR-223-3p were most significantly downregulated. IPA predicted activation of cell cycle checkpoint control pathways and inhibition of pathways relevant to inflammation and erythropoietin. Clarifying expression of mRNA, miRNA and lncRNA at a short time point (48 h) offers insight into potential biomarkers, including radiation markers shared across organs and animal models. This information, once validated in human models, can aid in development of bio-dosimetry biomarkers, and furthers our understanding of acute pathway dysregulation.
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Affiliation(s)
- Molykutty J. Aryankalayil
- grid.48336.3a0000 0004 1936 8075Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Drive, Room B3B406, Bethesda, MD 20892 USA
| | - Michelle A. Bylicky
- grid.48336.3a0000 0004 1936 8075Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Drive, Room B3B406, Bethesda, MD 20892 USA
| | - Shannon Martello
- grid.48336.3a0000 0004 1936 8075Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Drive, Room B3B406, Bethesda, MD 20892 USA
| | - Sunita Chopra
- grid.48336.3a0000 0004 1936 8075Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Drive, Room B3B406, Bethesda, MD 20892 USA
| | - Mary Sproull
- grid.48336.3a0000 0004 1936 8075Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Drive, Room B3B406, Bethesda, MD 20892 USA
| | - Jared M. May
- grid.48336.3a0000 0004 1936 8075Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Drive, Room B3B406, Bethesda, MD 20892 USA
| | - Aman Shankardass
- grid.48336.3a0000 0004 1936 8075Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Drive, Room B3B406, Bethesda, MD 20892 USA
| | - Laurel MacMillan
- grid.420517.50000 0004 0490 0428Gryphon Scientific, Takoma Park, MD 20912 USA
| | - Claire Vanpouille-Box
- grid.5386.8000000041936877XDepartment of Radiation Oncology, Weill Cornell Medicine, New York, NY 10065 USA
| | - Juan Dalo
- grid.48336.3a0000 0004 1936 8075Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Drive, Room B3B406, Bethesda, MD 20892 USA
| | - Kevin M. K. Scott
- grid.48336.3a0000 0004 1936 8075Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Drive, Room B3B406, Bethesda, MD 20892 USA
| | - C. Norman Coleman
- grid.48336.3a0000 0004 1936 8075Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Drive, Room B3B406, Bethesda, MD 20892 USA ,grid.48336.3a0000 0004 1936 8075Radiation Research Program, National Cancer Institute, National Institutes of Health, Rockville, MD 20850 USA
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16
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Alotaibi A, Gadekar VP, Gundla PS, Mandarthi S, Ravi S, Mallya D, Tungekar A, Lavanya BV, Bhagavath AK, Cordero MW, Pitkaniemi J, Seetharam RN, Bepari A, Hebbar P. A comprehensive analysis of mRNA expression profiles of Esophageal Squamous Cell Carcinoma reveals downregulation of Desmoglein 1 and crucial genomic targets. Cancer Biomark 2023; 38:465-487. [PMID: 38073377 DOI: 10.3233/cbm-230145] [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] [Indexed: 12/26/2023]
Abstract
AIM Esophageal Squamous Cell Carcinoma (ESCC) is a histological subtype of esophageal cancer that begins in the squamous cells in the esophagus. In only 19% of the ESCC-diagnosed patients, a five-year survival rate has been seen. This necessitates the identification of high-confidence biomarkers for early diagnosis, prognosis, and potential therapeutic targets for the mitigation of ESCC. METHOD We performed a meta-analysis of 10 mRNA datasets and identified consistently perturbed genes across the studies. Then, integrated with ESCC ATLAS to segregate 'core' genes to identify consequences of primary gene perturbation events leading to gene-gene interactions and dysregulated molecular signaling pathways. Further, by integrating with toxicogenomics data, inferences were drawn for gene interaction with environmental exposures, trace elements, chemical carcinogens, and drug chemicals. We also deduce the clinical outcomes of candidate genes based on survival analysis using the ESCC related dataset in The Cancer Genome Atlas. RESULT We identified 237 known and 18 novel perturbed candidate genes. Desmoglein 1 (DSG1) is one such gene that we found significantly downregulated (Fold Change =-1.89, p-value = 8.2e-06) in ESCC across six different datasets. Further, we identified 31 'core' genes (that either harbor genetic variants or are regulated by epigenetic modifications) and found regulating key biological pathways via adjoining genes in gene-gene interaction networks. Functional enrichment analysis showed dysregulated biological processes and pathways including "Extracellular matrix", "Collagen trimmer" and "HPV infection" are significantly overrepresented in our candidate genes. Based on the toxicogenomic inferences from Comparative Toxicogenomics Database we report the key genes that interacted with risk factors such as tobacco smoking, zinc, nitroso benzylmethylamine, and drug chemicals such as cisplatin, Fluorouracil, and Mitomycin in relation to ESCC. We also point to the STC2 gene that shows a high risk for mortality in ESCC patients. CONCLUSION We identified novel perturbed genes in relation to ESCC and explored their interaction network. DSG1 is one such gene, its association with microbiota and a clinical presentation seen commonly with ESCC hints that it is a good candidate for early diagnostic marker. Besides, in this study we highlight candidate genes and their molecular connections to risk factors, biological pathways, drug chemicals, and the survival probability of ESCC patients.
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Affiliation(s)
- Amal Alotaibi
- Basic Science Department, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
- Basic Science Department, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Veerendra P Gadekar
- Mbiomics LLC, Lewes DE, USA
- Basic Science Department, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | | | | | | | | | | | | | - Ashok Kumar Bhagavath
- Department of Cellular and Molecular Biology, University of Texas Health Science Center, Tyler, Texas, TX, USA
| | - MaryAnne Wong Cordero
- Basic Science Department, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Janne Pitkaniemi
- Finnish Cancer Registry, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Raviraja N Seetharam
- Manipal Center for Biotherapeutics Research, Manipal Academy of Higher Education, Manipal, India
| | - Asmatanzeem Bepari
- Basic Science Department, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Prashantha Hebbar
- Mbiomics LLC, Lewes DE, USA
- Manipal Center for Biotherapeutics Research, Manipal Academy of Higher Education, Manipal, India
- Meta Biosciences Pvt Ltd., Manipal - GOK Bioincubator, Advanced Research Center, Manipal, India
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17
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Fritsche K, Boccellato F, Schlaermann P, Koeppel M, Denecke C, Link A, Malfertheiner P, Gut I, Meyer TF, Berger H. DNA methylation in human gastric epithelial cells defines regional identity without restricting lineage plasticity. Clin Epigenetics 2022; 14:193. [PMID: 36585699 PMCID: PMC9801550 DOI: 10.1186/s13148-022-01406-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 12/13/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Epigenetic modifications in mammalian DNA are commonly manifested by DNA methylation. In the stomach, altered DNA methylation patterns have been observed following chronic Helicobacter pylori infections and in gastric cancer. In the context of epigenetic regulation, the regional nature of the stomach has been rarely considered in detail. RESULTS Here, we establish gastric mucosa derived primary cell cultures as a reliable source of native human epithelium. We describe the DNA methylation landscape across the phenotypically different regions of the healthy human stomach, i.e., antrum, corpus, fundus together with the corresponding transcriptomes. We show that stable regional DNA methylation differences translate to a limited extent into regulation of the transcriptomic phenotype, indicating a largely permissive epigenetic regulation. We identify a small number of transcription factors with novel region-specific activity and likely epigenetic impact in the stomach, including GATA4, IRX5, IRX2, PDX1 and CDX2. Detailed analysis of the Wnt pathway reveals differential regulation along the craniocaudal axis, which involves non-canonical Wnt signaling in determining cell fate in the proximal stomach. By extending our analysis to pre-neoplastic lesions and gastric cancers, we conclude that epigenetic dysregulation characterizes intestinal metaplasia as a founding basis for functional changes in gastric cancer. We present insights into the dynamics of DNA methylation across anatomical regions of the healthy stomach and patterns of its change in disease. Finally, our study provides a well-defined resource of regional stomach transcription and epigenetics.
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Affiliation(s)
- Kristin Fritsche
- grid.418159.00000 0004 0491 2699Department of Molecular Biology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117 Berlin, Germany
| | - Francesco Boccellato
- grid.418159.00000 0004 0491 2699Department of Molecular Biology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117 Berlin, Germany ,grid.4991.50000 0004 1936 8948Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Philipp Schlaermann
- grid.418159.00000 0004 0491 2699Department of Molecular Biology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117 Berlin, Germany
| | - Max Koeppel
- grid.418159.00000 0004 0491 2699Department of Molecular Biology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117 Berlin, Germany
| | - Christian Denecke
- grid.6363.00000 0001 2218 4662Center for Bariatric and Metabolic Surgery, Center of Innovative Surgery (ZIC), Department of Surgery, Campus Virchow Klinikum and Campus Mitte, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Alexander Link
- grid.5807.a0000 0001 1018 4307Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-Von-Guericke University Hospital, Magdeburg, Germany
| | - Peter Malfertheiner
- grid.5807.a0000 0001 1018 4307Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-Von-Guericke University Hospital, Magdeburg, Germany
| | - Ivo Gut
- grid.452341.50000 0004 8340 2354Centro Nacional de Análisis Genómico (CNAG-CRG), Barcelona, Spain
| | - Thomas F. Meyer
- grid.418159.00000 0004 0491 2699Department of Molecular Biology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117 Berlin, Germany ,grid.412468.d0000 0004 0646 2097Laboratory of Infection Oncology, Institute of Clinical Molecular Biology, Christian Albrecht University of Kiel and University Hospital Schleswig-Holstein – Campus Kiel, Rosalind-Franklin-Straße 12, 24105 Kiel, Germany
| | - Hilmar Berger
- grid.418159.00000 0004 0491 2699Department of Molecular Biology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117 Berlin, Germany ,grid.412468.d0000 0004 0646 2097Laboratory of Infection Oncology, Institute of Clinical Molecular Biology, Christian Albrecht University of Kiel and University Hospital Schleswig-Holstein – Campus Kiel, Rosalind-Franklin-Straße 12, 24105 Kiel, Germany
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Proaño-Pérez E, Serrano-Candelas E, Mancia C, Navinés-Ferrer A, Guerrero M, Martin M. SH3BP2 Silencing Increases miRNAs Targeting ETV1 and Microphthalmia-Associated Transcription Factor, Decreasing the Proliferation of Gastrointestinal Stromal Tumors. Cancers (Basel) 2022; 14:cancers14246198. [PMID: 36551682 PMCID: PMC9777313 DOI: 10.3390/cancers14246198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/05/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the gastrointestinal tract. Gain of function in receptor tyrosine kinases type III, KIT, or PDGFRA drives the majority of GIST. Previously, our group reported that silencing of the adaptor molecule SH3 Binding Protein 2 (SH3BP2) downregulated KIT and PDGFRA and microphthalmia-associated transcription factor (MITF) levels and reduced tumor growth. This study shows that SH3BP2 silencing also decreases levels of ETV1, a required factor for GIST growth. To dissect the SH3BP2 pathway in GIST cells, we performed a miRNA array in SH3BP2-silenced GIST cell lines. Among the most up-regulated miRNAs, we found miR-1246 and miR-5100 to be predicted to target MITF and ETV1. Overexpression of these miRNAs led to a decrease in MITF and ETV1 levels. In this context, cell viability and cell cycle progression were affected, and a reduction in BCL2 and CDK2 was observed. Interestingly, overexpression of MITF enhanced cell proliferation and significantly rescued the viability of miRNA-transduced cells. Altogether, the KIT-SH3BP2-MITF/ETV1 pathway deserves to be considered in GIST cell survival and proliferation.
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Affiliation(s)
- Elizabeth Proaño-Pérez
- Biochemistry and Molecular Biology Unit, Biomedicine Department, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
- Clinical and Experimental Respiratory Immunoallergy (IRCE), Institut d’Investigacions Biomediques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
- Faculty of Health Sciences, Technical University of Ambato, Ambato 180105, Ecuador
| | - Eva Serrano-Candelas
- Biochemistry and Molecular Biology Unit, Biomedicine Department, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
- Clinical and Experimental Respiratory Immunoallergy (IRCE), Institut d’Investigacions Biomediques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Cindy Mancia
- Biochemistry and Molecular Biology Unit, Biomedicine Department, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
| | - Arnau Navinés-Ferrer
- Biochemistry and Molecular Biology Unit, Biomedicine Department, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
- Clinical and Experimental Respiratory Immunoallergy (IRCE), Institut d’Investigacions Biomediques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Mario Guerrero
- Biochemistry and Molecular Biology Unit, Biomedicine Department, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
| | - Margarita Martin
- Biochemistry and Molecular Biology Unit, Biomedicine Department, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
- Clinical and Experimental Respiratory Immunoallergy (IRCE), Institut d’Investigacions Biomediques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
- Correspondence:
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19
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Bryan JG, Hoff PD. Smaller p-values in genomics studies using distilled auxiliary information. Biostatistics 2022; 24:193-208. [PMID: 34269373 DOI: 10.1093/biostatistics/kxaa053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 09/25/2020] [Accepted: 11/15/2020] [Indexed: 12/16/2022] Open
Abstract
Medical research institutions have generated massive amounts of biological data by genetically profiling hundreds of cancer cell lines. In parallel, academic biology labs have conducted genetic screens on small numbers of cancer cell lines under custom experimental conditions. In order to share information between these two approaches to scientific discovery, this article proposes a "frequentist assisted by Bayes" (FAB) procedure for hypothesis testing that allows auxiliary information from massive genomics datasets to increase the power of hypothesis tests in specialized studies. The exchange of information takes place through a novel probability model for multimodal genomics data, which distills auxiliary information pertaining to cancer cell lines and genes across a wide variety of experimental contexts. If the relevance of the auxiliary information to a given study is high, then the resulting FAB tests can be more powerful than the corresponding classical tests. If the relevance is low, then the FAB tests yield as many discoveries as the classical tests. Simulations and practical investigations demonstrate that the FAB testing procedure can increase the number of effects discovered in genomics studies while still maintaining strict control of type I error and false discovery rate.
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Affiliation(s)
- Jordan G Bryan
- Department of Statistical Science, Duke University, 415 Chapel Drive, Durham, NC 27708, USA
| | - Peter D Hoff
- Department of Statistical Science, Duke University, 415 Chapel Drive, Durham, NC 27708, USA
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20
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Mowoe MO, Garnett S, Lennard K, Talbot J, Townsend P, Jonas E, Blackburn JM. Pro-MAP: a robust pipeline for the pre-processing of single channel protein microarray data. BMC Bioinformatics 2022; 23:534. [PMID: 36494629 PMCID: PMC9733281 DOI: 10.1186/s12859-022-05095-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The central role of proteins in diseases has made them increasingly attractive as therapeutic targets and indicators of cellular processes. Protein microarrays are emerging as an important means of characterising protein activity. Their accurate downstream analysis to produce biologically significant conclusions is largely dependent on proper pre-processing of extracted signal intensities. However, existing computational tools are not specifically tailored to the nature of these data and lack unanimity. RESULTS Here, we present the single-channel Protein Microarray Analysis Pipeline, a tailored computational tool for analysis of single-channel protein microarrays enabling biomarker identification, implemented in R, and as an interactive web application. We compared four existing background correction and normalization methods as well as three array filtering techniques, applied to four real datasets with two microarray designs, extracted using two software programs. The normexp, cyclic loess, and array weighting methods were most effective for background correction, normalization, and filtering respectively. CONCLUSIONS Thus, here we provided a versatile and effective pre-processing and differential analysis workflow for single-channel protein microarray data in form of an R script and web application ( https://metaomics.uct.ac.za/shinyapps/Pro-MAP/ .) for those not well versed in the R programming language.
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Affiliation(s)
- Metoboroghene Oluwaseyi Mowoe
- grid.7836.a0000 0004 1937 1151Department of Integrated Biomedical Sciences, Division of Chemical and Systems Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Shaun Garnett
- grid.7836.a0000 0004 1937 1151Department of Integrated Biomedical Sciences, Division of Chemical and Systems Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Katherine Lennard
- grid.7836.a0000 0004 1937 1151Department of Integrated Biomedical Sciences, Division of Chemical and Systems Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jade Talbot
- grid.5379.80000000121662407Manchester Cancer Research Centre, Division of Cancer Science, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Paul Townsend
- grid.5475.30000 0004 0407 4824Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey UK
| | - Eduard Jonas
- grid.7836.a0000 0004 1937 1151Surgical Gastroenterology Unit, Division of General Surgery, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Jonathan Michael Blackburn
- grid.7836.a0000 0004 1937 1151Department of Integrated Biomedical Sciences, Division of Chemical and Systems Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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Jung SM, Baek IW, Park KS, Kim KJ. De novo molecular subtyping of salivary gland tissue in the context of Sjögren's syndrome heterogeneity. Clin Immunol 2022; 245:109171. [DOI: 10.1016/j.clim.2022.109171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 11/08/2022]
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22
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Hidayat AS, Lefebvre KA, MacDonald J, Bammler T, Aluru N. Symptomatic and asymptomatic domoic acid exposure in zebrafish (Danio rerio) revealed distinct non-overlapping gene expression patterns in the brain. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2022; 252:106310. [PMID: 36198224 PMCID: PMC9701550 DOI: 10.1016/j.aquatox.2022.106310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Domoic acid (DA) is a naturally produced neurotoxin synthesized by marine diatoms in the genus Pseudo-nitzschia. DA accumulates in filter-feeders such as shellfish, and can cause severe neurotoxicity when contaminated seafood is ingested, resulting in Amnesic Shellfish Poisoning (ASP) in humans. Overt clinical signs of neurotoxicity include seizures and disorientation. ASP is a significant public health concern, and though seafood regulations have effectively minimized the human risk of severe acute DA poisoning, the effects of exposure at asymptomatic levels are poorly understood. The objective of this study was to determine the effects of exposure to symptomatic and asymptomatic doses of DA on gene expression patterns in the zebrafish brain. We exposed adult zebrafish to either a symptomatic (1.1 ± 0.2 μg DA/g fish) or an asymptomatic (0.31 ± 0.03 µg DA/g fish) dose of DA by intracelomic injection and sampled at 24, 48 and 168 h post-injection. Transcriptional profiling was done using Agilent and Affymetrix microarrays. Our analysis revealed distinct, non-overlapping changes in gene expression between the two doses. We found that the majority of transcriptional changes were observed at 24 h post-injection with both doses. Interestingly, asymptomatic exposure produced more persistent transcriptional effects - in response to symptomatic dose exposure, we observed only one differentially expressed gene one week after exposure, compared to 26 in the asymptomatic dose at the same time (FDR <0.05). GO term analysis revealed that symptomatic DA exposure affected genes associated with peptidyl proline modification and retinoic acid metabolism. Asymptomatic exposure caused differential expression of genes that were associated with GO terms including circadian rhythms and visual system, and also the neuroactive ligand-receptor signaling KEGG pathway. Overall, these results suggest that transcriptional responses are specific to the DA dose and that asymptomatic exposure can cause long-term changes. Further studies are needed to characterize the potential downstream neurobehavioral impacts of DA exposure.
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Affiliation(s)
- Alia S Hidayat
- MIT-WHOI Joint Program in Oceanography/Applied Ocean Science & Engineering, Cambridge and Woods Hole, MA, USA; Biology Department and Woods Hole Center for Oceans and Human Health, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
| | - Kathi A Lefebvre
- Environmental and Fisheries Science Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA, USA
| | - James MacDonald
- Department of Environmental and Occupational Health, University of Washington, Seattle, WA, USA
| | - Theo Bammler
- Department of Environmental and Occupational Health, University of Washington, Seattle, WA, USA
| | - Neelakanteswar Aluru
- Biology Department and Woods Hole Center for Oceans and Human Health, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
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23
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Casanova NG, Reyes-Hernon V, Gregory T, Sun B, Bermudez T, Hufford MK, Oita RC, Camp SM, Hernandez-Molina G, Serrano JR, Sun X, Fimbres J, Mirsaeidi M, Sammani S, Bime C, Garcia JGN. Biochemical and genomic identification of novel biomarkers in progressive sarcoidosis: HBEGF, eNAMPT, and ANG-2. Front Med (Lausanne) 2022; 9:1012827. [PMID: 36388923 PMCID: PMC9640603 DOI: 10.3389/fmed.2022.1012827] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/07/2022] [Indexed: 11/29/2022] Open
Abstract
Background Progressive pulmonary fibrosis is a serious complication in subjects with sarcoidosis. The absence of reliable, non-invasive biomarkers that detect early progression exacerbates the difficulty in predicting sarcoidosis severity. To potentially address this unmet need, we evaluated a panel of markers for an association with sarcoidosis progression (HBEGF, NAMPT, IL1-RA, IL-6, IL-8, ANG-2). This panel encompasses proteins related to inflammation, vascular injury, cell proliferation, and fibroblast mitogenesis processes. Methods Plasma biomarker levels and biomarker protein expression in lung and lymph nodes tissues (immunohistochemical studies) from sarcoidosis subjects with limited disease and progressive (complicated) sarcoidosis were performed. Gene expression of the protein-coding genes included in this panel was analyzed using RNAseq in sarcoidosis granulomatous tissues from lung and lymph nodes. Results Except for IL-8, plasma levels of each biomarker—eNAMPT, IL-1RA, IL-6, ANG-2, and HBEGF—were significantly elevated in sarcoidosis subjects compared to controls. In addition, plasma levels of HBEGF were elevated in complicated sarcoidosis, while eNAMPT and ANG-2 were observed to serve as markers of lung fibrosis in a subgroup of complicated sarcoidosis. Genomic studies corroborated HBEGF and NAMPT among the top dysregulated genes and identified cytokine-related and fibrotic pathways in lung granulomatous tissues from sarcoidosis. Conclusion These findings suggest HBEGF, eNAMPT, and ANG-2 may serve as potential novel indicators of the clinical severity of sarcoidosis disease.
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Affiliation(s)
- Nancy G. Casanova
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
| | - Vivian Reyes-Hernon
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
| | - Taylor Gregory
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
| | - Belinda Sun
- Department of Pathology, University of Arizona Health Sciences, Tucson, AZ, United States
| | - Tadeo Bermudez
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
| | - Matthew K. Hufford
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
| | - Radu C. Oita
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
| | - Sara M. Camp
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
| | | | | | - Xiaoguang Sun
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
| | - Jocelyn Fimbres
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, México City, Mexico
| | - Mehdi Mirsaeidi
- Department of Medicine, College of Medicine, University of Florida, Jacksonville, FL, United States
| | - Saad Sammani
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
| | - Christian Bime
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
| | - Joe G. N. Garcia
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
- *Correspondence: Joe G. N. Garcia,
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Rau A, Passet B, Castille J, Daniel-Carlier N, Asset A, Lecardonnel J, Moroldo M, Jaffrézic F, Laloë D, Moazami-Goudarzi K, Vilotte JL. Potential genetic robustness of Prnp and Sprn double knockout mouse embryos towards ShRNA-lentiviral inoculation. Vet Res 2022; 53:54. [PMID: 35799279 PMCID: PMC9264527 DOI: 10.1186/s13567-022-01075-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 06/13/2022] [Indexed: 11/10/2022] Open
Abstract
The Shadoo and PrP prion protein family members are thought to be functionally related, but previous knockdown/knockout experiments in early mouse embryogenesis have provided seemingly contradictory results. In particular, Shadoo was found to be indispensable in the absence of PrP in knockdown analyses, but a double-knockout of the two had little phenotypic impact. We investigated this apparent discrepancy by comparing transcriptomes of WT, Prnp0/0 and Prnp0/0Sprn0/0 E6.5 mouse embryos following inoculation by Sprn- or Prnp-ShRNA lentiviral vectors. Our results suggest the possibility of genetic adaptation in Prnp0/0Sprn0/0 mice, thus providing a potential explanation for their previously observed resilience.
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Affiliation(s)
- Andrea Rau
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France. .,BioEcoAgro Joint Research Unit, INRAE, Université de Liège, Université de Lille, Université de Picardie Jules Verne, 80203, Péronne, France.
| | - Bruno Passet
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Johan Castille
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | | | - Alexandre Asset
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Jérome Lecardonnel
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Marco Moroldo
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Florence Jaffrézic
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Denis Laloë
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | | | - Jean-Luc Vilotte
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
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Efficacy, T cell activation and antibody responses in accelerated Plasmodium falciparum sporozoite chemoprophylaxis vaccine regimens. NPJ Vaccines 2022; 7:59. [PMID: 35641527 PMCID: PMC9156686 DOI: 10.1038/s41541-022-00473-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 03/18/2022] [Indexed: 11/08/2022] Open
Abstract
Repeated direct venous inoculation of Plasmodium falciparum sporozoites (PfSPZ) together with antimalarial chemoprophylaxis (PfSPZ-CVac) is the most potent way to induce sterile immunity against P. falciparum infection in malaria-naive volunteers. However, established schedules are complex and long. Here, we tested two accelerated three-dose schedules (28- and 10-day regimen) assessing efficacy by controlled human malaria infection (CHMI) against placebo, comparing vaccine-specific T cell and antibody responses by antigen-reactive T cell enrichment (ARTE) and protein microarray, respectively. Both regimens were similarly efficacious (67 and 63% vaccine efficacy) but different in the induction of vaccine-specific T cells and antibodies. The 10-day regimen resulted in higher numbers of antigen-specific CD4+ effector memory pro-inflammatory T cells and a broader antibody response compared with the 28-day regimen. Usually in nature, P. falciparum liver stage lasts about 6.5 days. The short vaccination-interval of the 10-day regimen prolongs the time of continuous exposure to liver-stage parasites, which may explain the stronger response. Besides dose and number of vaccinations, duration of liver-stage exposure is a factor to optimize PfSPZ-CVac immunogenicity.
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Chiang IT, Liu YC, Liu HS, Ali AAA, Chou SY, Hsu TI, Hsu FT. Regorafenib Reverses Temozolomide-Induced CXCL12/CXCR4 Signaling and Triggers Apoptosis Mechanism in Glioblastoma. Neurotherapeutics 2022; 19:616-634. [PMID: 35267171 PMCID: PMC9226247 DOI: 10.1007/s13311-022-01194-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2022] [Indexed: 12/13/2022] Open
Abstract
Temozolomide (TMZ) monotherapy is known to be insufficient for resistant/relapsed glioblastoma (GBM), thus seeking a sensitization agent for TMZ is necessary. It was found that regorafenib may improve the overall survival of relapsed GBM patients. We aimed to discover whether regorafenib can enhance the anti-GBM effects of TMZ, and elucidate underlying mechanism. Our analysis of The Cancer Genome Atlas database revealed that the increased expression of CXCR4 is linked to poor survival of GBM patients. Additionally, TMZ treatment may trigger CXCR4/CXCL12 axis of GBM. We used two GBM cell lines, two primary GBM cells, and animal model to identify underlying mechanism and treatment efficacy of regorafenib combined with TMZ by cytotoxicity, apoptosis, reporter gene and invasion/migration assays, chemokine array, Western blotting, MRI, microarray, and immunohistochemistry. We observed that the chemokine CXCL-12 and its receptor CXCR4 regulate the resistance to TMZ, whereas the inhibition of CXCL-12/CXCR4 signaling sensitizes GBM cells to TMZ. The TMZ-induced CXCL-12/CXCR4 signaling, phosphor-extracellular signal-regulated kinases 1 and 2 (ERK1/2) and nuclear factor kappa light chain enhancer of activated B cells (NF-κB), and NF-κB-related proteins can effectively diminish when combining with regorafenib. Regorafenib significantly enhanced the TMZ-induced extrinsic/intrinsic apoptotic pathways, and facilitated the suppression of invasion and migration potential in GBM. Orthotopic tumor experiments demonstrated tumor size reduction and prolonged survival in combination group even with half-dose of TMZ. Our findings provide promising evidence that regorafenib may sensitize GBM to TMZ treatment through inhibition of the CXCL12/CXCR4/ERK/NF-κB signaling.
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Affiliation(s)
- I-Tsang Chiang
- Department of Radiation Oncology, Chang Bing Show Chwan Memorial Hospital, Changhua, 505, Taiwan
- Department of Radiation Oncology, Show Chwan Memorial Hospital, Changhua, 500, Taiwan
- Department of Medical Imaging and Radiological Sciences, Central Taiwan University of Science and Technology, Taichung, 406, Taiwan
- Medical administrative center, Show Chwan Memorial Hospital, Changhua, 500, Taiwan
| | - Yu-Chang Liu
- Department of Radiation Oncology, Chang Bing Show Chwan Memorial Hospital, Changhua, 505, Taiwan
- Department of Radiation Oncology, Show Chwan Memorial Hospital, Changhua, 500, Taiwan
- Department of Medical Imaging and Radiological Sciences, Central Taiwan University of Science and Technology, Taichung, 406, Taiwan
| | - Hua-Shan Liu
- School of Biomedical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, 110, Taiwan
- International Ph.D. Program in Biomedical Engineering & Graduate Institute of Biomedical Optomechatronics, College of Biomedical Engineering, Taipei Medical University, Taipei, 110, Taiwan
| | - Ahmed Atef Ahmed Ali
- TMU Neuroscience Research Center - NeuroImage, College of Medicine, Taipei Medical University, Taipei, 110, Taiwan
| | - Szu-Yi Chou
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, 110, Taiwan
- Ph.D. Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University and National Health Research Institute, Taipei, 110, Taiwan
| | - Tsung-I Hsu
- Ph.D. Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University and National Health Research Institute, Taipei, 110, Taiwan
- Ph.D. Program in Medical Neuroscience, College of Medical Science and Technology, Taipei Medical University and National Health Research Institute, Taipei, 110, Taiwan
| | - Fei-Ting Hsu
- Department of Biological Science and Technology, China Medical University, Taichung, 404, Taiwan.
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Webb JP, Paiva AC, Rossoni L, Alstrom-Moore A, Springthorpe V, Vaud S, Yeh V, Minde DP, Langer S, Walker H, Hounslow A, Nielsen DR, Larson T, Lilley K, Stephens G, Thomas GH, Bonev BB, Kelly DJ, Conradie A, Green J. Multi-omic based production strain improvement (MOBpsi) for bio-manufacturing of toxic chemicals. Metab Eng 2022; 72:133-149. [DOI: 10.1016/j.ymben.2022.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/11/2022] [Accepted: 03/08/2022] [Indexed: 11/25/2022]
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Awan Z, Al-Rayes N, Khan Z, Al Mansouri M, Ibrahim H. Bima A, Almukadi H, Ibrahim Kutbi H, Jayasheela Shetty P, Ahmad Shaik N, Banaganapalli B. Identifying Significant Genes and Functionally Enriched Pathways in Familial Hypercholesterolemia Using Integrated Gene Co-Expression Network Analysis. Saudi J Biol Sci 2022; 29:3287-3299. [PMID: 35844366 PMCID: PMC9280244 DOI: 10.1016/j.sjbs.2022.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 12/20/2022] Open
Abstract
Familial hypercholesterolemia (FH) is a monogenic lipid disorder which promotes atherosclerosis and cardiovascular diseases. Owing to the lack of sufficient published information, this study aims to identify the potential genetic biomarkers for FH by studying the global gene expression profile of blood cells. The microarray expression data of FH patients and controls was analyzed by different computational biology methods like differential expression analysis, protein network mapping, hub gene identification, functional enrichment of biological pathways, and immune cell restriction analysis. Our results showed the dysregulated expression of 115 genes connected to lipid homeostasis, immune responses, cell adhesion molecules, canonical Wnt signaling, mucin type O-glycan biosynthesis pathways in FH patients. The findings from expanded protein interaction network construction with known FH genes and subsequent Gene Ontology (GO) annotations have also supported the above findings, in addition to identifying the involvement of dysregulated thyroid hormone and ErbB signaling pathways in FH patients. The genes like CSNK1A1, JAK3, PLCG2, RALA, and ZEB2 were found to be enriched under all GO annotation categories. The subsequent phenotype ontology results have revealed JAK3I, PLCG2, and ZEB2 as key hub genes contributing to the inflammation underlying cardiovascular and immune response related phenotypes. Immune cell restriction findings show that above three genes are highly expressed by T-follicular helper CD4+ T cells, naïve B cells, and monocytes, respectively. These findings not only provide a theoretical basis to understand the role of immune dysregulations underlying the atherosclerosis among FH patients but may also pave the way to develop genomic medicine for cardiovascular diseases.
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Hanoudi SN, Talwar H, Draghici S, Samavati L. Autoantibodies against cytoskeletons and lysosomal trafficking discriminate sarcoidosis from healthy controls, tuberculosis and lung cancers. MOLECULAR BIOMEDICINE 2022; 3:3. [PMID: 35048206 PMCID: PMC8770712 DOI: 10.1186/s43556-021-00064-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/30/2021] [Indexed: 11/16/2022] Open
Abstract
Sarcoidosis is a systemic granulomatous disease of unknown etiology. Hypergammaglobulinemia and the presence of autoantibodies in sarcoidosis suggest active humoral immunity to unknown antigen(s). We developed a complex cDNA library derived from tissues of sarcoidosis patients. Using a high throughput method, we constructed a microarray platform from this cDNA library containing large numbers of sarcoidosis clones. After selective biopanning, 1070 sarcoidosis-specifc clones were arrayed and immunoscreend with 152 sera from patients with sarcoidosis and other pulmonary diseases. To identify the sarcoidosis classifiers two statistical approaches were conducted: First, we identified significant biomarkers between sarcoidosis and healthy controls, and second identified markers comparing sarcoidosis to all other groups. At the threshold of an False Discovery Rate (FDR) < 0.01, we identified 14 clones in the first approach and 12 clones in the second approach discriminating sarcoidosis from other groups. We used the classifiers to build a naïve Bayes model on the training-set and validated it on an independent test-set. The first approach yielded an AUC of 0.947 using 14 significant clones with a sensitivity of 0.93 and specificity of 0.88, whereas the AUC of the second option was 0.92 with a sensitivity of 0.96 and specificity of 0.83. These results suggest robust classifier performance. Furthermore, we characterized the informative phage clones by sequencing and homology searches. Large numbers of classifier-clones were peptides involved in cellular trafficking and cytoskeletons. These results show that sarcoidosis is associated with a specific pattern of immunoreactivity that can discriminate it from other diseases.
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Affiliation(s)
| | - Harvinder Talwar
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Wayne State University School of Medicine, 3990 John R, 3 Hudson, Detroit, MI 48201 USA
| | - Sorin Draghici
- Department of Computer Science, Wayne State University, Detroit, MI 48202 USA
| | - Lobelia Samavati
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Wayne State University School of Medicine, 3990 John R, 3 Hudson, Detroit, MI 48201 USA
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 540 E. Canfield, Detroit, MI 48201 USA
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Dhar D, Kallapura G. Analysis of Microarray Data from Medulloblastoma Tissue Samples. Methods Mol Biol 2022; 2423:59-64. [PMID: 34978688 DOI: 10.1007/978-1-0716-1952-0_6] [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] [Indexed: 06/14/2023]
Abstract
As a laboratory tool, microarray is used to detect the expression of thousands of genes at the same time. Typically, microscope slides have DNA microarrays that are printed with thousands of tiny spots in specified positions. Each spot contains a known DNA sequence or gene. These slides are commonly referred to as gene chips or DNA chips. The DNA molecules printed to each slide serve as probes to detect gene expression, which is also known as the transcriptome or the set of messenger RNA (mRNA) transcripts expressed by a group of genes. The goal of this chapter is to discuss the steps involved computational analysis of data after the completion of a typical microarray experiment.
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Diverse Effect of Two Cytokinins, Kinetin and Benzyladenine, on Plant Development, Biotic Stress Tolerance, and Gene Expression. Life (Basel) 2021; 11:life11121404. [PMID: 34947935 PMCID: PMC8706806 DOI: 10.3390/life11121404] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/07/2021] [Accepted: 12/11/2021] [Indexed: 02/02/2023] Open
Abstract
The plant hormones cytokinins affect a various array of plant growth and development processes as well as responses to biotic and abiotic stresses. In this study, the opposite effect of two different cytokinins kinetin (N6-furfuryladenine) and benzyladenine (BA) on development and on the tolerance of Arabidopsis and tobacco plants to virus, bacteria, and fungi infection was reported. Treatments of Arabidopsis and tobacco seedlings with saturated solutions of BA inhibited plant progress, while treatments with saturated water solution of kinetin promoted plant development. Furthermore, BA pre-treatments strongly reduced the number of TMV (Tobacco mosaic virus) lesions on tobacco and the tissue damage caused by the incompatible Pseudomonas bacteria on Arabidopsis and tobacco leaves. Similarly, BA pre-treatment significantly reduced the necrotic disease symptoms of Botrytis cinerea infection. Kinetin pre-treatments had a much weaker or no protective effect on the damage caused by the above pathogens. Accordingly, Arabidopsis gene expression profiles after treatments also showed that the two cytokinins have different effects on several plant processes. The gene expression results supported the more robust effect of BA, which up and downregulated more than 2000 genes, while only 436 genes were influenced by kinetin treatment. It is noteworthy that BA and kinetin treatment changed gene expressions in the same direction only in a relatively few cases (73 upregulated and 70 downregulated genes), and even 28 genes were regulated into the opposite directions by BA and kinetin. Both treatments had a strong effect on auxin and gibberellin-related genes, but only BA had a significant effect on cytokinin-induced processes. While kinetin exclusively activated the flavonoid synthesis genes, BA affected more significantly protein synthesis, photosynthesis, and plant defence-related genes. In conclusion, BA solution had sometimes the opposite and generally a much stronger effect than kinetin solution not only on the development and on biotic stress tolerance of tobacco and Arabidopsis plants but also on the gene expressions. The stronger protective effect of BA to necrotic stresses is probably due to its stronger senescence inhibitory effect on plant tissues, as supported by the stronger chlorophyll retardation of the BA-treated leaves.
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Xu Z, Niu L, Taylor JA. The ENmix DNA methylation analysis pipeline for Illumina BeadChip and comparisons with seven other preprocessing pipelines. Clin Epigenetics 2021; 13:216. [PMID: 34886879 PMCID: PMC8662917 DOI: 10.1186/s13148-021-01207-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/30/2021] [Indexed: 11/12/2022] Open
Abstract
Background Illumina DNA methylation arrays are high-throughput platforms for cost-effective genome-wide profiling of individual CpGs. Experimental and technical factors introduce appreciable measurement variation, some of which can be mitigated by careful “preprocessing” of raw data. Methods Here we describe the ENmix preprocessing pipeline and compare it to a set of seven published alternative pipelines (ChAMP, Illumina, SWAN, Funnorm, Noob, wateRmelon, and RnBeads). We use two large sets of duplicate sample measurements with 450 K and EPIC arrays, along with mixtures of isogenic methylated and unmethylated cell line DNA to compare raw data and that preprocessed via different pipelines. Results Our evaluations show that the ENmix pipeline performs the best with significantly higher correlation and lower absolute difference between duplicate pairs, higher intraclass correlation coefficients (ICC) and smaller deviations from expected methylation level in mixture experiments. In addition to the pipeline function, ENmix software provides an integrated set of functions for reading in raw data files from mouse and human arrays, quality control, data preprocessing, visualization, detection of differentially methylated regions (DMRs), estimation of cell type proportions, and calculation of methylation age clocks. ENmix is computationally efficient, flexible and allows parallel computing. To facilitate further evaluations, we make all datasets and evaluation code publicly available. Conclusion Careful selection of robust data preprocessing methods is critical for DNA methylation array studies. ENmix outperformed other pipelines in our evaluations to minimize experimental variation and to improve data quality and study power. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01207-1.
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Affiliation(s)
- Zongli Xu
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, MD A3-05, 111 T.W. Alexander Drive, PO Box 12233, Research Triangle Park, NC, 27709, USA
| | - Liang Niu
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, MD A3-05, 111 T.W. Alexander Drive, PO Box 12233, Research Triangle Park, NC, 27709, USA.
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Kim SK, Jung SM, Park KS, Kim KJ. Integrative analysis of lung molecular signatures reveals key drivers of idiopathic pulmonary fibrosis. BMC Pulm Med 2021; 21:404. [PMID: 34876074 PMCID: PMC8650281 DOI: 10.1186/s12890-021-01749-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/16/2021] [Indexed: 11/10/2022] Open
Abstract
Background Idiopathic pulmonary fibrosis (IPF) is a devastating disease with a high clinical burden. The molecular signatures of IPF were analyzed to distinguish molecular subgroups and identify key driver genes and therapeutic targets. Methods Thirteen datasets of lung tissue transcriptomics including 585 IPF patients and 362 normal controls were obtained from the databases and subjected to filtration of differentially expressed genes (DEGs). A functional enrichment analysis, agglomerative hierarchical clustering, network-based key driver analysis, and diffusion scoring were performed, and the association of enriched pathways and clinical parameters was evaluated. Results A total of 2,967 upregulated DEGs was filtered during the comparison of gene expression profiles of lung tissues between IPF patients and healthy controls. The core molecular network of IPF featured p53 signaling pathway and cellular senescence. IPF patients were classified into two molecular subgroups (C1, C2) via unsupervised clustering. C1 was more enriched in the p53 signaling pathway and ciliated cells and presented a worse prognostic score, while C2 was more enriched for cellular senescence, profibrosing pathways, and alveolar epithelial cells. The p53 signaling pathway was closely correlated with a decline in forced vital capacity and carbon monoxide diffusion capacity and with the activation of cellular senescence. CDK1/2, CKDNA1A, CSNK1A1, HDAC1/2, FN1, VCAM1, and ITGA4 were the key regulators as evidence by high diffusion scores in the disease module. Currently available and investigational drugs showed differential diffusion scores in terms of their target molecules. Conclusions An integrative molecular analysis of IPF lungs identified two molecular subgroups with distinct pathobiological characteristics and clinical prognostic scores. Inhibition against CDKs or HDACs showed great promise for controlling lung fibrosis. This approach provided molecular insights to support the prediction of clinical outcomes and the selection of therapeutic targets in IPF patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12890-021-01749-3.
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Affiliation(s)
- Sung Kyoung Kim
- Division of Pulmonology, Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seung Min Jung
- Division of Rheumatology, Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Kyung-Su Park
- Division of Rheumatology, Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Ki-Jo Kim
- Division of Rheumatology, Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea. .,Division of Rheumatology, Department of Internal Medicine, St. Vincent's Hospital, The Catholic University of Korea, 93 Jungbu-daero, Paldal-gu, Suwon, Gyeonggi-do, 16247, Republic of Korea.
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Qin Y, Yi D, Chen X, Guan Y. Deep learning identifies erroneous microarray-based, gene-level conclusions in literature. NAR Genom Bioinform 2021; 3:lqab089. [PMID: 34617014 PMCID: PMC8489595 DOI: 10.1093/nargab/lqab089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 08/25/2021] [Accepted: 09/17/2021] [Indexed: 11/14/2022] Open
Abstract
More than 110 000 publications have used microarrays to decipher phenotype-associated genes, clinical biomarkers and gene functions. Microarrays rely on digital assaying the fluorescence signals of arrays. In this study, we retrospectively constructed raw images for 37 724 published microarray data, and developed deep learning algorithms to automatically detect systematic defects. We report that an alarming amount of 26.73% of the microarray-based studies are affected by serious imaging defects. By literature mining, we found that publications associated with these affected microarrays have reported disproportionately more biological discoveries on the genes in the contaminated areas compared to other genes. 28.82% of the gene-level conclusions reported in these publications were based on measurements falling into the contaminated area, indicating severe, systematic problems caused by such contaminations. We provided the identified published, problematic datasets, affected genes and the imputed arrays as well as software tools for scanning such contamination that will become essential to future studies to scrutinize and critically analyze microarray data.
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Affiliation(s)
- Yanan Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Daiyao Yi
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Xianghao Chen
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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White MG, Szczepaniak Sloane R, Witt RG, Reuben A, Gaudreau PO, Andrews MC, Feng N, Johnson S, Class CA, Bristow C, Wani K, Hudgens C, Nezi L, Manzo T, De Macedo MP, Hu J, Davis R, Jiang H, Prieto P, Burton E, Hwu P, Tawbi H, Gershenwald J, Lazar AJ, Tetzlaff MT, Overwijk W, Woodman SE, Cooper ZA, Marszalek JR, Davies MA, Heffernan TP, Wargo JA. Short-term treatment with multi-drug regimens combining BRAF/MEK-targeted therapy and immunotherapy results in durable responses in Braf-mutated melanoma. Oncoimmunology 2021; 10:1992880. [PMID: 34777916 PMCID: PMC8583008 DOI: 10.1080/2162402x.2021.1992880] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Targeted and immunotherapy regimens have revolutionized the treatment of advanced melanoma patients. Despite this, only a subset of patients respond durably. Recently, combination strategies of BRAF/MEK inhibitors with immune checkpoint inhibitor monotherapy (α-CTLA-4 or α-PD-1) have increased the rate of durable responses. Based on evidence from our group and others, these therapies appear synergistic, but at the cost of significant toxicity. We know from other treatment paradigms (e.g. hematologic malignancies) that combination strategies with multi-drug regimens (>4 drugs) are associated with more durable disease control. To better understand the mechanism of these improved outcomes, and to identify and prioritize new strategies for testing, we studied several multi-drug regimens combining BRAF/MEK targeted therapy and immunotherapy combinations in a Braf-mutant murine melanoma model (BrafV600E/Pten−/−). Short-term treatment with α-PD-1 and α-CTLA-4 monotherapies were relatively ineffective, while treatment with α-OX40 demonstrated some efficacy [17% of mice with no evidence of disease, (NED), at 60-days]. Outcomes were improved in the combined α-OX40/α-PD-1 group (42% NED). Short-term treatment with quadruplet therapy of immunotherapy doublets in combination with targeted therapy [dabrafenib and trametinib (DT)] was associated with excellent tumor control, with 100% of mice having NED after combined DT/α-CTLA-4/α-PD-1 or DT/α-OX40/α-PD-1. Notably, tumors from mice in these groups demonstrated a high proportion of effector memory T cells, and immunologic memory was maintained with tumor re-challenge. Together, these data provide important evidence regarding the potential utility of multi-drug therapy in treating advanced melanoma and suggest these models can be used to guide and prioritize combinatorial treatment strategies.
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Affiliation(s)
- Michael G White
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Russell G Witt
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexandre Reuben
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pierre Olivier Gaudreau
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Miles C Andrews
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia.,School of Cancer Medicine, La Trobe University, Heidelberg, Victoria, Australia
| | - Ningping Feng
- Translational Research to AdvanCe Therapeutics and Innovation in ONcology (TRACTION), University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sarah Johnson
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Caleb A Class
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher Bristow
- Translational Research to AdvanCe Therapeutics and Innovation in ONcology (TRACTION), University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Khalida Wani
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Courtney Hudgens
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Luigi Nezi
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Teresa Manzo
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Jianhua Hu
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Richard Davis
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hong Jiang
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Peter Prieto
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Elizabeth Burton
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hussein Tawbi
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jeffrey Gershenwald
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexander J Lazar
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael T Tetzlaff
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Willem Overwijk
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Oncology Research, Nektar Therapeutics, San Francisco, CA, USA
| | - Scott E Woodman
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zachary A Cooper
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Translational Sciences Oncology, MedImmune, Gaithersburg, MD, USA
| | - Joseph R Marszalek
- Translational Research to AdvanCe Therapeutics and Innovation in ONcology (TRACTION), University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael A Davies
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Timothy P Heffernan
- Translational Research to AdvanCe Therapeutics and Innovation in ONcology (TRACTION), University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer A Wargo
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Keyloun JW, Campbell R, Carney BC, Yang R, Miller SA, Detwiler L, Gautam A, Moffatt LT, Hammamieh R, Jett M, Shupp JW. Early Transcriptomic Response to Burn Injury: Severe Burns Are Associated With Immune Pathway Shutdown. J Burn Care Res 2021; 43:306-314. [PMID: 34791339 PMCID: PMC9890902 DOI: 10.1093/jbcr/irab217] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Burn injury induces a systemic hyperinflammatory response with detrimental side effects. Studies have described the biochemical changes induced by severe burns, but the transcriptome response is not well characterized. The goal of this work is to characterize the blood transcriptome after burn injury. Burn patients presenting to a regional center between 2012 and 2017 were prospectively enrolled. Blood was collected on admission and at predetermined time points (hours 2, 4, 8, 12, and 24). RNA was isolated and transcript levels were measured with a gene expression microarray. To identify differentially regulated genes (false-discovery rate ≤0.1) by burn injury severity, patients were grouped by TBSA above or below 20% and statistically enriched pathways were identified. Sixty-eight patients were analyzed, most patients were male with a median age of 41 (interquartile range, 30.5-58.5) years, and TBSA of 20% (11%-34%). Thirty-five patients had % TBSA injury ≥20%, and this group experienced greater mortality (26% vs 3%, P = .008). Comparative analysis of genes from patients with </≥20% TBSA revealed 1505, 613, 380, 63, 1357, and 954 differentially expressed genes at hours 0, 2, 4, 8, 12, and 24, respectively. Pathway analysis revealed an initial up-regulation in several immune/inflammatory pathways within the ≥20% TBSA groups followed by shutdown. Severe burn injury is associated with an early proinflammatory immune response followed by shutdown of these pathways. Examination of the immunoinflammatory response to burn injury through differential gene regulation and associated immune pathways by injury severity may identify mechanistic targets for future intervention.
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Affiliation(s)
| | | | - Bonnie C Carney
- Firefighters’ Burn and Surgical Research Laboratory, MedStar Health Research Institute, Washington, District of Columbia, USA,Department of Surgery, Georgetown University School of Medicine, Washington, District of Columbia, USA,Department of Biochemistry, Georgetown University School of Medicine, Washington, District of Columbia, USA
| | - Ruoting Yang
- Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Stacy-Ann Miller
- Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA,Oak Ridge Institute for Science and Education, Silver Spring, Maryland, USA
| | - Leanne Detwiler
- The Geneva Foundation, Silver Spring, Maryland, USA,Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Aarti Gautam
- Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Lauren T Moffatt
- Firefighters’ Burn and Surgical Research Laboratory, MedStar Health Research Institute, Washington, District of Columbia, USA,Department of Surgery, Georgetown University School of Medicine, Washington, District of Columbia, USA,Department of Biochemistry, Georgetown University School of Medicine, Washington, District of Columbia, USA
| | - Rasha Hammamieh
- Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Marti Jett
- Headquarters Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Jeffrey W Shupp
- Address correspondence to Jeffrey W. Shupp, MD, The Burn Center, 110 Irving Street, NW, Suite 3B-55, Washington, DC 20010, USA.
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Keir ME, Fuh F, Ichikawa R, Acres M, Hackney JA, Hulme G, Carey CD, Palmer J, Jones CJ, Long AK, Jiang J, Klabunde S, Mansfield JC, Looney CM, Faubion WA, Filby A, Kirby JA, McBride J, Lamb CA. Regulation and Role of αE Integrin and Gut Homing Integrins in Migration and Retention of Intestinal Lymphocytes during Inflammatory Bowel Disease. THE JOURNAL OF IMMUNOLOGY 2021; 207:2245-2254. [PMID: 34561227 PMCID: PMC8525869 DOI: 10.4049/jimmunol.2100220] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 08/25/2021] [Indexed: 02/06/2023]
Abstract
Adhesion molecules are upregulated in inflamed intestinal mucosa in IBD patients. Baseline β7 expression does not impact αE induction or gene expression in T cells. Phospho-SMAD3 is increased in inflamed mucosa in IBD.
Targeting interactions between α4β7 integrin and endothelial adhesion molecule MAdCAM-1 to inhibit lymphocyte migration to the gastrointestinal tract is an effective therapy in inflammatory bowel disease (IBD). Following lymphocyte entry into the mucosa, a subset of these cells expresses αEβ7 integrin, which is expressed on proinflammatory lymphocytes, to increase cell retention. The factors governing lymphocyte migration into the intestinal mucosa and αE integrin expression in healthy subjects and IBD patients remain incompletely understood. We evaluated changes in factors involved in lymphocyte migration and differentiation within tissues. Both ileal and colonic tissue from active IBD patients showed upregulation of ICAM-1, VCAM-1, and MAdCAM-1 at the gene and protein levels compared with healthy subjects and/or inactive IBD patients. β1 and β7 integrin expression on circulating lymphocytes was similar across groups. TGF-β1 treatment induced expression of αE on both β7+ and β7− T cells, suggesting that cells entering the mucosa independently of MAdCAM-1/α4β7 can become αEβ7+. ITGAE gene polymorphisms did not alter protein induction following TGF-β1 stimulation. Increased phospho-SMAD3, which is directly downstream of TGF-β, and increased TGF-β–responsive gene expression were observed in the colonic mucosa of IBD patients. Finally, in vitro stimulation experiments showed that baseline β7 expression had little effect on cytokine, chemokine, transcription factor, and effector molecule gene expression in αE+ and αE− T cells. These findings suggest cell migration to the gut mucosa may be altered in IBD and α4β7−, and α4β7+ T cells may upregulate αEβ7 in response to TGF-β once within the gut mucosa.
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Affiliation(s)
| | | | | | - Meghan Acres
- Translational and Clinical Research Institute, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.,Department of Histopathology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | | | - Gillian Hulme
- Flow Cytometry Core Facility and Innovation, Methodology and Application Research Theme, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Christopher D Carey
- Translational and Clinical Research Institute, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.,Department of Haematology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Jeremy Palmer
- Translational and Clinical Research Institute, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Claire J Jones
- Department of Histopathology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Anna K Long
- Department of Histopathology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | | | | | - John C Mansfield
- Translational and Clinical Research Institute, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.,Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom; and
| | | | | | - Andrew Filby
- Flow Cytometry Core Facility and Innovation, Methodology and Application Research Theme, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - John A Kirby
- Translational and Clinical Research Institute, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Christopher A Lamb
- Translational and Clinical Research Institute, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom;
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38
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Khayer N, Jalessi M, Jahanbakhshi A, Tabib Khooei A, Mirzaie M. Nkx3-1 and Fech genes might be switch genes involved in pituitary non-functioning adenoma invasiveness. Sci Rep 2021; 11:20943. [PMID: 34686726 PMCID: PMC8536755 DOI: 10.1038/s41598-021-00431-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
Non-functioning pituitary adenomas (NFPAs) are typical pituitary macroadenomas in adults associated with increased mortality and morbidity. Although pituitary adenomas are commonly considered slow-growing benign brain tumors, numerous of them possess an invasive nature. Such tumors destroy sella turcica and invade the adjacent tissues such as the cavernous sinus and sphenoid sinus. In these cases, the most critical obstacle for complete surgical removal is the high risk of damaging adjacent vital structures. Therefore, the development of novel therapeutic strategies for either early diagnosis through biomarkers or medical therapies to reduce the recurrence rate of NFPAs is imperative. Identification of gene interactions has paved the way for decoding complex molecular mechanisms, including disease-related pathways, and identifying the most momentous genes involved in a specific disease. Currently, our knowledge of the invasion of the pituitary adenoma at the molecular level is not sufficient. The current study aimed to identify critical biomarkers and biological pathways associated with invasiveness in the NFPAs using a three-way interaction model for the first time. In the current study, the Liquid association method was applied to capture the statistically significant triplets involved in NFPAs invasiveness. Subsequently, Random Forest analysis was applied to select the most important switch genes. Finally, gene set enrichment (GSE) and gene regulatory network (GRN) analyses were applied to trace the biological relevance of the statistically significant triplets. The results of this study suggest that "mRNA processing" and "spindle organization" biological processes are important in NFAPs invasiveness. Specifically, our results suggest Nkx3-1 and Fech as two switch genes in NFAPs invasiveness that may be potential biomarkers or target genes in this pathology.
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Affiliation(s)
- Nasibeh Khayer
- Skull Base Research Center, The Five Senses Health Institute, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Jalessi
- Skull Base Research Center, The Five Senses Health Institute, Iran University of Medical Sciences, Tehran, Iran.
- ENT and Head & Neck Research Center and Department, Hazrat Rasoul Hospital, Iran University of Medical Sciences, Tehran, Iran.
| | - Amin Jahanbakhshi
- Skull Base Research Center, The Five Senses Health Institute, Iran University of Medical Sciences, Tehran, Iran
- Neurology Department, Hazrat Rasoul Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Alireza Tabib Khooei
- Neurology Department, Hazrat Rasoul Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Mehdi Mirzaie
- Department of Applied Mathematics, Faculty of Mathematical Sciences, Tarbiat Modares University, Tehran, Iran.
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39
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Blanc V, Riordan JD, Soleymanjahi S, Nadeau JH, Nalbantoglu ILK, Xie Y, Molitor EA, Madison BB, Brunt EM, Mills JC, Rubin DC, Ng IO, Ha Y, Roberts LR, Davidson NO. Apobec1 complementation factor overexpression promotes hepatic steatosis, fibrosis, and hepatocellular cancer. J Clin Invest 2021; 131:138699. [PMID: 33445170 DOI: 10.1172/jci138699] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 09/10/2020] [Indexed: 12/11/2022] Open
Abstract
The RNA-binding protein Apobec1 complementation factor (A1CF) regulates posttranscriptional ApoB mRNA editing, but the range of RNA targets and the long-term effect of altered A1CF expression on liver function are unknown. Here we studied hepatocyte-specific A1cf-transgenic (A1cf+/Tg), A1cf+/Tg Apobec1-/-, and A1cf-/- mice fed chow or high-fat/high-fructose diets using RNA-Seq, RNA CLIP-Seq, and tissue microarrays from human hepatocellular cancer (HCC). A1cf+/Tg mice exhibited increased hepatic proliferation and steatosis, with increased lipogenic gene expression (Mogat1, Mogat2, Cidea, Cd36) associated with shifts in polysomal RNA distribution. Aged A1cf+/Tg mice developed spontaneous fibrosis, dysplasia, and HCC, and this development was accelerated on a high-fat/high-fructose diet and was independent of Apobec1. RNA-Seq revealed increased expression of mRNAs involved in oxidative stress (Gstm3, Gpx3, Cbr3), inflammatory response (Il19, Cxcl14, Tnfα, Ly6c), extracellular matrix organization (Mmp2, Col1a1, Col4a1), and proliferation (Kif20a, Mcm2, Mcm4, Mcm6), and a subset of mRNAs (including Sox4, Sox9, Cdh1) were identified in RNA CLIP-Seq. Increased A1CF expression in human HCC correlated with advanced fibrosis and with reduced survival in a subset with nonalcoholic fatty liver disease. In conclusion, we show that hepatic A1CF overexpression selectively alters polysomal distribution and mRNA expression, promoting lipogenic, proliferative, and inflammatory pathways leading to HCC.
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Affiliation(s)
- Valerie Blanc
- Division of Gastroenterology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jesse D Riordan
- Pacific Northwest Research Institute, Seattle, Washington, USA
| | - Saeed Soleymanjahi
- Division of Gastroenterology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Joseph H Nadeau
- Pacific Northwest Research Institute, Seattle, Washington, USA
| | - ILKe Nalbantoglu
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Yan Xie
- Division of Gastroenterology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Elizabeth A Molitor
- Division of Gastroenterology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Blair B Madison
- Division of Gastroenterology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Elizabeth M Brunt
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jason C Mills
- Division of Gastroenterology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Deborah C Rubin
- Division of Gastroenterology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Irene O Ng
- Department of Pathology and State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Yeonjung Ha
- Department of Medicine, Mayo Clinic College of Medicine and Science, Rochester, Minnesota, USA
| | - Lewis R Roberts
- Department of Medicine, Mayo Clinic College of Medicine and Science, Rochester, Minnesota, USA
| | - Nicholas O Davidson
- Division of Gastroenterology, Washington University School of Medicine, St. Louis, Missouri, USA
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40
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Nething DB, Sukul A, Mishler‐Elmore JW, Held MA. Posttranscriptional regulation of cellulose synthase genes by small RNAs derived from cellulose synthase antisense transcripts. PLANT DIRECT 2021; 5:e347. [PMID: 34557619 PMCID: PMC8447916 DOI: 10.1002/pld3.347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/14/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Transcriptional regulatory mechanisms governing plant cell wall biosynthesis are incomplete. Expression programs that activate wall biosynthesis are well understood, but mechanisms that control the attenuation of gene expression networks remain elusive. Previous work has shown that small RNAs (sRNAs) derived from the HvCESA6 (Hordeum vulgare, Hv) antisense transcripts are naturally produced and are capable of regulating aspects of wall biosynthesis. Here, we further test the hypothesis that CESA-derived sRNAs generated from CESA antisense transcripts are involved in the regulation of cellulose and broader cell wall biosynthesis. Antisense transcripts were detected for some but not all members of the CESA gene family in both barley and Brachypodium distachyon. Phylogenetic analysis indicates that antisense transcripts are detected for most primary cell wall CESA genes, suggesting a possible role in the transition from primary to secondary cell wall biosynthesis. Focusing on one antisense transcript, HvCESA1 shows dynamic expression throughout development, is correlated with corresponding sRNAs over the same period and is anticorrelated with HvCESA1 mRNA expression. To assess the broader impacts of CESA-derived sRNAs on the regulation of cell wall biosynthesis, transcript profiling was performed on barley tissues overexpressing CESA-derived sRNAs. Together, the data support the hypothesis that CESA antisense transcripts function through an RNA-induced silencing mechanism, to degrade cis transcripts, and may also trigger trans-acting silencing on related genes to alter the expression of cell wall gene networks.
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Affiliation(s)
| | - Abhijit Sukul
- Department of Chemistry and BiochemistryOhio UniversityAthensOHUSA
| | | | - Michael A. Held
- Department of Chemistry and BiochemistryOhio UniversityAthensOHUSA
- Molecular and Cellular Biology ProgramOhio UniversityAthensOHUSA
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41
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Aryankalayil MJ, Martello S, Bylicky MA, Chopra S, May JM, Shankardass A, MacMillan L, Sun L, Sanjak J, Vanpouille-Box C, Eke I, Coleman CN. Analysis of lncRNA-miRNA-mRNA expression pattern in heart tissue after total body radiation in a mouse model. J Transl Med 2021; 19:336. [PMID: 34364390 PMCID: PMC8349067 DOI: 10.1186/s12967-021-02998-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 07/23/2021] [Indexed: 12/14/2022] Open
Abstract
Background Radiation therapy is integral to effective thoracic cancer treatments, but its application is limited by sensitivity of critical organs such as the heart. The impacts of acute radiation-induced damage and its chronic effects on normal heart cells are highly relevant in radiotherapy with increasing lifespans of patients. Biomarkers for normal tissue damage after radiation exposure, whether accidental or therapeutic, are being studied as indicators of both acute and delayed effects. Recent research has highlighted the potential importance of RNAs, including messenger RNAs (mRNAs), microRNAs (miRNAs), and long non-coding RNAs (lncRNAs) as biomarkers to assess radiation damage. Understanding changes in mRNA and non-coding RNA expression will elucidate biological pathway changes after radiation. Methods To identify significant expression changes in mRNAs, lncRNAs, and miRNAs, we performed whole transcriptome microarray analysis of mouse heart tissue at 48 h after whole-body irradiation with 1, 2, 4, 8, and 12 Gray (Gy). We also validated changes in specific lncRNAs through RT-qPCR. Ingenuity Pathway Analysis (IPA) was used to identify pathways associated with gene expression changes. Results We observed sustained increases in lncRNAs and mRNAs, across all doses of radiation. Alas2, Aplnr, and Cxc3r1 were the most significantly downregulated mRNAs across all doses. Among the significantly upregulated mRNAs were cell-cycle arrest biomarkers Gdf15, Cdkn1a, and Ckap2. Additionally, IPA identified significant changes in gene expression relevant to senescence, apoptosis, hemoglobin synthesis, inflammation, and metabolism. LncRNAs Abhd11os, Pvt1, Trp53cor1, and Dino showed increased expression with increasing doses of radiation. We did not observe any miRNAs with sustained up- or downregulation across all doses, but miR-149-3p, miR-6538, miR-8101, miR-7118-5p, miR-211-3p, and miR-3960 were significantly upregulated after 12 Gy. Conclusions Radiation-induced RNA expression changes may be predictive of normal tissue toxicities and may indicate targetable pathways for radiation countermeasure development and improved radiotherapy treatment plans. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-02998-w.
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Affiliation(s)
- Molykutty J Aryankalayil
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Drive, Room B3B406, Bethesda, MD, 20892, USA.
| | - Shannon Martello
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Drive, Room B3B406, Bethesda, MD, 20892, USA
| | - Michelle A Bylicky
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Drive, Room B3B406, Bethesda, MD, 20892, USA
| | - Sunita Chopra
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Drive, Room B3B406, Bethesda, MD, 20892, USA
| | - Jared M May
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Drive, Room B3B406, Bethesda, MD, 20892, USA
| | - Aman Shankardass
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Drive, Room B3B406, Bethesda, MD, 20892, USA
| | | | - Landy Sun
- Gryphon Scientific, Takoma Park, MD, 20912, USA
| | | | | | - Iris Eke
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Drive, Room B3B406, Bethesda, MD, 20892, USA.,Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - C Norman Coleman
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Drive, Room B3B406, Bethesda, MD, 20892, USA.,Radiation Research Program, National Cancer Institute, National Institutes of Health, Rockville, MD, 20850, USA
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42
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Wu J, Fang X, Xia X. Identification of Key Genes and Pathways associated with Endometriosis by Weighted Gene Co-expression Network Analysis. Int J Med Sci 2021; 18:3425-3436. [PMID: 34522169 PMCID: PMC8436105 DOI: 10.7150/ijms.63541] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/26/2021] [Indexed: 12/22/2022] Open
Abstract
Background: Endometriosis is a common gynecological disorder with high rates of infertility and pelvic pain. However, its pathogenesis and diagnostic biomarkers remain unclear. This study aimed to elucidate potential hub genes and key pathways associated with endometriosis in ectopic endometrium (EC) and eutopic endometrium (EU). Material and Method: EC and EU-associated microarray datasets were obtained from the gene expression omnibus (GEO) database. Gene set enrichment analysis was performed to obtain further biological insight into the EU and EC-associated genes. Weighted gene co-expression network analysis (WGCNA) was performed to find clinically significant modules of highly-correlated genes. The hub genes that belong to both the weighted gene co-expression network and protein-protein interaction (PPI) network were identified using a Venn diagram. Results: We obtained EC and EU-associated microarray datasets GSE7305 and GSE120103. Genes in the EC were mainly enriched in the immune response and immune cell trafficking, and genes in the EU were mainly enriched in stress response and steroid hormone biosynthesis. PPI networks and weighted gene co-expression networks were constructed. An EC-associated blue module and an EU-associated magenta module were identified, and their function annotations revealed that hormone receptor signaling or inflammatory microenvironments may promote EU passing through the oviducts and migrating to the ovarian surfaces, and adhesion and immune correlated genes may induce the successful ectopic implantation of the endometrium (EC). Twelve hub genes in the EC and sixteen hub genes in the EU were recognized and further validated in independent datasets. Conclusion: Our study identified, for the first time, the hub genes and enrichment pathways in the EC and EU using WGCNA, which may provide a comprehensive understanding of the pathogenesis of endometriosis and have important clinical implications for the treatment and diagnosis of endometriosis.
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Affiliation(s)
- Jingni Wu
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
- Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California, Los Angeles, California 90095, United States
| | - Xiaoling Fang
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Xiaomeng Xia
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
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43
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Mohammadnejad A, Baumbach J, Li W, Lund J, Larsen MJ, Li S, Mengel-From J, Michel TM, Christiansen L, Christensen K, Hjelmborg J, Tan Q. Differential lncRNA expression profiling of cognitive function in middle and old aged monozygotic twins using generalized association analysis. J Psychiatr Res 2021; 140:197-204. [PMID: 34118637 DOI: 10.1016/j.jpsychires.2021.05.074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 05/18/2021] [Accepted: 05/29/2021] [Indexed: 12/14/2022]
Abstract
Cognitive impairment is the most prominent symptom in neurodegenerative disorders affecting quality of life and mortality. However, despite years of research, the molecular mechanism underlying the regulation of cognitive function and its impairment is poorly understood. This study aims to elucidate the role of long non-coding RNAs (lncRNAs) expression and lncRNA-mRNA interaction networks, by analyzing lncRNA expression in whole blood samples of 400 middle and old aged monozygotic twins in association with cognitive function using both linear models and a generalized correlation coefficient (GCC) to capture the diverse patterns of correlation. We detected 13 probes (p < 1e-03) displaying nonlinear and 7 probes (p < 1e-03) showing linear correlations. After combining the results, we identified 20 lncRNA probes with p < 1e-03. The top lncRNA probes were annotated to genes, along with the non-coding MALAT1, that play roles in neurodegenerative diseases. The top lncRNAs were linked to functional clusters including peptidyl-glycine modification, vascular smooth muscle cells, mitotic spindle organization and protein tyrosine phosphatase. In addition, mapping of the top significant lncRNAs to the lncRNA-mRNA interaction network detected significantly enriched biological pathways involving neuroactive ligand-receptor interaction, proteasome and chemokines. We show that GCC served as a complementary approach in detecting lncRNAs missed by the conventional linear models. A combination of GCC and linear models identified lncRNAs of diverse patterns of association enriched for GO biological and molecular functions meaningful in cognitive performance and cognitive decline. The novel lncRNA regulatory network further contributed to detect significant pathways implicated in cognition.
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Affiliation(s)
- Afsaneh Mohammadnejad
- Unit of Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Denmark.
| | - Jan Baumbach
- Computational Biomedicine, Department of Mathematics and Computer Science, University of Southern Denmark, Denmark; Chair of Computational Systems Biology, University of Hamburg, Hamburg, Germany.
| | - Weilong Li
- Unit of Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Denmark.
| | - Jesper Lund
- Unit of Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Denmark.
| | - Martin J Larsen
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Denmark; Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark.
| | - Shuxia Li
- Unit of Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Denmark.
| | - Jonas Mengel-From
- Unit of Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Denmark; Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Denmark.
| | - Tanja Maria Michel
- Department of Psychiatry, Department of Clinical Research, University of Southern Denmark, Odense, Denmark; Psychiatry in the Region of Southern Denmark, Odense University Hospital, Odense, Denmark; Brain Research - Inter-Disciplinary Guided Excellence, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.
| | - Lene Christiansen
- Unit of Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Denmark; Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.
| | - Kaare Christensen
- Unit of Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Denmark; Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Denmark.
| | - Jacob Hjelmborg
- Unit of Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Denmark.
| | - Qihua Tan
- Unit of Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Denmark; Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Denmark.
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McGregor R, Tay ML, Carlton LH, Hanson-Manful P, Raynes JM, Forsyth WO, Brewster DT, Middleditch MJ, Bennett J, Martin WJ, Wilson N, Atatoa Carr P, Baker MG, Moreland NJ. Mapping Autoantibodies in Children With Acute Rheumatic Fever. Front Immunol 2021; 12:702877. [PMID: 34335616 PMCID: PMC8320770 DOI: 10.3389/fimmu.2021.702877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/02/2021] [Indexed: 01/16/2023] Open
Abstract
Background Acute rheumatic fever (ARF) is a serious sequela of Group A Streptococcus (GAS) infection associated with significant global mortality. Pathogenesis remains poorly understood, with the current prevailing hypothesis based on molecular mimicry and the notion that antibodies generated in response to GAS infection cross-react with cardiac proteins such as myosin. Contemporary investigations of the broader autoantibody response in ARF are needed to both inform pathogenesis models and identify new biomarkers for the disease. Methods This study has utilised a multi-platform approach to profile circulating autoantibodies in ARF. Sera from patients with ARF, matched healthy controls and patients with uncomplicated GAS pharyngitis were initially analysed for autoreactivity using high content protein arrays (Protoarray, 9000 autoantigens), and further explored using a second protein array platform (HuProt Array, 16,000 autoantigens) and 2-D gel electrophoresis of heart tissue combined with mass spectrometry. Selected autoantigens were orthogonally validated using conventional immunoassays with sera from an ARF case-control study (n=79 cases and n=89 matched healthy controls) and a related study of GAS pharyngitis (n=39) conducted in New Zealand. Results Global analysis of the protein array data showed an increase in total autoantigen reactivity in ARF patients compared with controls, as well as marked heterogeneity in the autoantibody profiles between ARF patients. Autoantigens previously implicated in ARF pathogenesis, such as myosin and collagens were detected, as were novel candidates. Disease pathway analysis revealed several autoantigens within pathways linked to arthritic and myocardial disease. Orthogonal validation of three novel autoantigens (PTPN2, DMD and ANXA6) showed significant elevation of serum antibodies in ARF (p < 0.05), and further highlighted heterogeneity with patients reactive to different combinations of the three antigens. Conclusions The broad yet heterogenous elevation of autoantibodies observed suggests epitope spreading, and an expansion of the autoantibody repertoire, likely plays a key role in ARF pathogenesis and disease progression. Multiple autoantigens may be needed as diagnostic biomarkers to capture this heterogeneity.
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Affiliation(s)
- Reuben McGregor
- School of Medical Sciences, The University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - Mei Lin Tay
- School of Medical Sciences, The University of Auckland, Auckland, New Zealand
| | - Lauren H. Carlton
- School of Medical Sciences, The University of Auckland, Auckland, New Zealand
| | | | - Jeremy M. Raynes
- School of Medical Sciences, The University of Auckland, Auckland, New Zealand
| | - Wasan O. Forsyth
- School of Medical Sciences, The University of Auckland, Auckland, New Zealand
| | | | | | - Julie Bennett
- Department of Public Health, University of Otago, Wellington, New Zealand
| | - William John Martin
- Science for Technological Innovation Science Challenge, Callaghan Innovation, Wellington, New Zealand
| | - Nigel Wilson
- Starship Children’s Hospital, Auckland, New Zealand
| | - Polly Atatoa Carr
- Waikato District Health Board and Waikato University, Hamilton, New Zealand
| | - Michael G. Baker
- Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
- Department of Public Health, University of Otago, Wellington, New Zealand
| | - Nicole J. Moreland
- School of Medical Sciences, The University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
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Cox N, Crozet L, Holtman IR, Loyher PL, Lazarov T, White JB, Mass E, Stanley ER, Elemento O, Glass CK, Geissmann F. Diet-regulated production of PDGFcc by macrophages controls energy storage. Science 2021; 373:373/6550/eabe9383. [PMID: 34210853 DOI: 10.1126/science.abe9383] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 05/13/2021] [Indexed: 12/12/2022]
Abstract
The mechanisms by which macrophages regulate energy storage remain poorly understood. We identify in a genetic screen a platelet-derived growth factor (PDGF)/vascular endothelial growth factor (VEGF)-family ortholog, Pvf3, that is produced by macrophages and is required for lipid storage in fat-body cells of Drosophila larvae. Genetic and pharmacological experiments indicate that the mouse Pvf3 ortholog PDGFcc, produced by adipose tissue-resident macrophages, controls lipid storage in adipocytes in a leptin receptor- and C-C chemokine receptor type 2-independent manner. PDGFcc production is regulated by diet and acts in a paracrine manner to control lipid storage in adipose tissues of newborn and adult mice. At the organismal level upon PDGFcc blockade, excess lipids are redirected toward thermogenesis in brown fat. These data identify a macrophage-dependent mechanism, conducive to the design of pharmacological interventions, that controls energy storage in metazoans.
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Affiliation(s)
- Nehemiah Cox
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lucile Crozet
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Inge R Holtman
- Department of Cellular and Molecular Medicine, University of California, San Diego, CA, USA
| | - Pierre-Louis Loyher
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Tomi Lazarov
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Jessica B White
- Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Elvira Mass
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Developmental Biology of the Immune System, LIMES Institute, University of Bonn, 53115 Bonn, Germany
| | - E Richard Stanley
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA.,Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, CA, USA
| | - Frederic Geissmann
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. .,Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
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46
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Mohammadnejad A, Li W, Lund JB, Li S, Larsen MJ, Mengel-From J, Michel TM, Christiansen L, Christensen K, Hjelmborg J, Baumbach J, Tan Q. Global Gene Expression Profiling and Transcription Factor Network Analysis of Cognitive Aging in Monozygotic Twins. Front Genet 2021; 12:675587. [PMID: 34194475 PMCID: PMC8236849 DOI: 10.3389/fgene.2021.675587] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/26/2021] [Indexed: 12/15/2022] Open
Abstract
Cognitive aging is one of the major problems worldwide, especially as people get older. This study aimed to perform global gene expression profiling of cognitive function to identify associated genes and pathways and a novel transcriptional regulatory network analysis to identify important regulons. We performed single transcript analysis on 400 monozygotic twins using an assumption-free generalized correlation coefficient (GCC), linear mixed-effect model (LME) and kinship model and identified six probes (one significant at the standard FDR < 0.05 while the other results were suggestive with 0.18 ≤ FDR ≤ 0.28). We combined the GCC and linear model results to cover diverse patterns of relationships, and meaningful and novel genes like APOBEC3G, H6PD, SLC45A1, GRIN3B, and PDE4D were detected. Our exploratory study showed the downregulation of all these genes with increasing cognitive function or vice versa except the SLC45A1 gene, which was upregulated with increasing cognitive function. Linear models found only H6PD and SLC45A1, the other genes were captured by GCC. Significant functional pathways (FDR < 3.95e-10) such as focal adhesion, ribosome, cysteine and methionine metabolism, Huntington's disease, eukaryotic translation elongation, nervous system development, influenza infection, metabolism of RNA, and cell cycle were identified. A total of five regulons (FDR< 1.3e-4) were enriched in a transcriptional regulatory analysis in which CTCF and REST were activated and SP3, SRF, and XBP1 were repressed regulons. The genome-wide transcription analysis using both assumption-free GCC and linear models identified important genes and biological pathways implicated in cognitive performance, cognitive aging, and neurological diseases. Also, the regulatory network analysis revealed significant activated and repressed regulons on cognitive function.
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Affiliation(s)
- Afsaneh Mohammadnejad
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Weilong Li
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark.,Population Research Unit, Faculty of Social Sciences, University of Helsinki, Helsinki, Finland
| | - Jesper Beltoft Lund
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark.,Digital Health & Machine Learning Research Group, Hasso Plattner Institute for Digital Engineering, Potsdam, Germany
| | - Shuxia Li
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Martin J Larsen
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Jonas Mengel-From
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark.,Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Tanja Maria Michel
- Department of Psychiatry, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Psychiatry in the Region of Southern Denmark, Odense University Hospital, Odense, Denmark.,Brain Research-Inter-Disciplinary Guided Excellence, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Lene Christiansen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark.,Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Kaare Christensen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark.,Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Jacob Hjelmborg
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Jan Baumbach
- Computational Biomedicine, Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark.,Chair of Computational Systems Biology, University of Hamburg, Hamburg, Germany
| | - Qihua Tan
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark.,Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
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47
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Salilew-Wondim D, Tesfaye D, Rings F, Held-Hoelker E, Miskel D, Sirard MA, Tholen E, Schellander K, Hoelker M. The global gene expression outline of the bovine blastocyst: reflector of environmental conditions and predictor of developmental capacity. BMC Genomics 2021; 22:408. [PMID: 34082721 PMCID: PMC8176733 DOI: 10.1186/s12864-021-07693-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/14/2021] [Indexed: 12/22/2022] Open
Abstract
Background Morphological evaluation of embryos has been used to screen embryos for transfer. However, the repeatability and accuracy of this method remains low. Thus, evaluation of an embryo’s gene expression signature with respect to its developmental capacity could provide new opportunities for embryo selection. Since the gene expression outline of an embryo is considered as an aggregate of its intrinsic characteristics and culture conditions, we have compared transcriptome profiles of in vivo and in vitro derived blastocysts in relation to pregnancy outcome to unravel the discrete effects of developmental competence and environmental conditions on bovine embryo gene expression outlines. To understand whether the gene expression patterns could be associated with blastocyst developmental competency, the global transcriptome profile of in vivo (CVO) and in vitro (CVT) derived competent blastocysts that resulted in pregnancy was investigated relative to that of in vivo (NVO) and in vitro (NVT) derived blastocysts which did not establish initial pregnancy, respectively while to unravel the effects of culture condition on the transcriptome profile of embryos, the transcriptional activity of the CVO group was compared to the CVT group and the NVO group was compared to the NVT ones. Results A total of 700 differentially expressed genes (DEGs) were identified between CVO and NVO blastocysts. These gene transcripts represent constitutive regions, indel variants, 3′-UTR sequence variants and novel transcript regions. The majority (82%) of these DEGs, including gene clusters like ATP synthases, eukaryotic translation initiation factors, ribosomal proteins, mitochondrial ribosomal proteins, NADH dehydrogenase and cytochrome c oxidase subunits were enriched in the CVO group. These DEGs were involved in pathways associated with glycolysis/glycogenesis, citrate acid cycle, pyruvate metabolism and oxidative phosphorylation. Similarly, a total of 218 genes were differentially expressed between CVT and NVT groups. Of these, 89%, including TPT1, PDIA6, HSP90AA1 and CALM, were downregulated in the CVT group and those DEGs were overrepresented in pathways related to protein processing, endoplasmic reticulum, spliceasome, ubiquitone mediated proteolysis and steroid biosynthesis. On the other hand, although both the CVT and CVO blastocyst groups resulted in pregnancy, a total of 937 genes were differential expressed between the two groups. Compared to CVO embryos, the CVT ones exhibited downregulation of gene clusters including ribosomal proteins, mitochondrial ribosomal protein, eukaryotic translation initiation factors, ATP synthases, NADH dehydrogenase and cytochrome c oxidases. Nonetheless, downregulation of these genes could be associated with pre and postnatal abnormalities observed after transfer of in vitro embryos. Conclusion The present study provides a detailed inventory of differentially expressed gene signatures and pathways specifically reflective of the developmental environment and future developmental capacities of bovine embryos suggesting that transcriptome activity observed in blastocysts could be indicative of further pregnancy success but also adaptation to culture environment. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07693-0.
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Affiliation(s)
- Dessie Salilew-Wondim
- Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany
| | - Dawit Tesfaye
- Animal Reproduction and Biotechnology Laboratory, Department of Biomedical Sciences, Colorado State University, 3105 Rampart Rd, CO, 80521, Fort Collins, USA
| | - Franca Rings
- Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany
| | - Eva Held-Hoelker
- Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany
| | - Dennis Miskel
- Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany
| | - Marc-Andre Sirard
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle, Faculté des sciences de l'agriculture et de l'alimentation, INAF, Pavillon des services, Université Laval (Québec), G1V 0A6, Quebec City, Canada
| | - Ernst Tholen
- Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany
| | - Karl Schellander
- Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany
| | - Michael Hoelker
- Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany. .,Department of Animal Science, Biotechnology & Reproduction in farm animals, University of Goettingen, Burckhardtweg 2, 37077, Goettingen, Germany.
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48
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Bali KK, Gandla J, Rangel DR, Castaldi L, Mouritzen P, Agarwal N, Schmelz M, Heppenstall P, Kuner R. A genome-wide screen reveals microRNAs in peripheral sensory neurons driving painful diabetic neuropathy. Pain 2021; 162:1334-1351. [PMID: 33492037 DOI: 10.1097/j.pain.0000000000002159] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 11/23/2020] [Indexed: 12/25/2022]
Abstract
ABSTRACT Diabetes is a leading cause of peripheral neuropathy (diabetic peripheral neuropathy, DPN), and uncontrolled long-lasting hyperglycemia leads to severe complications. A major proportion of diabetics develop excruciating pain with a variable course. Mechanisms leading to painful DPN are not completely understood and treatment options limited. We hypothesized that epigenetic modulation at the level of microRNA (miRNA) expression triggered by metabolic imbalance and nerve damage regulates the course of pain development. We used clinically relevant preclinical models, genome-wide screening, in silico analyses, cellular assays, miRNA fluorescent in situ hybridization, in vivo molecular manipulations, and behavioral analyses in the current study. We identified miRNAs and their targets that critically impact on nociceptive hypersensitivity in painful DPN. Our analyses identify miR-33 and miR-380 expressed in nociceptive neurons as critical denominators of diabetic pain and miR-124-1 as a mediator of physiological nociception. Our comprehensive analyses on the putative mRNA targets for miR-33 or miR-124-1 identified a set of mRNAs that are regulated after miR-33 or miR-124-1 overexpression in dorsal root ganglia in vivo. Our results shed light on the regulation of DPN pathophysiology and implicate specific miRNAs as novel therapeutic targets for treating painful DPN.
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Affiliation(s)
- Kiran Kumar Bali
- Department of Molecular Pharmacology, Pharmacology Institute, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany . Dr. Bali is now with the Department of Experimental Pain Research, Mannheim Center for Translational Neuroscience (MCTN), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Jagadeesh Gandla
- Department of Molecular Pharmacology, Pharmacology Institute, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany . Dr. Bali is now with the Department of Experimental Pain Research, Mannheim Center for Translational Neuroscience (MCTN), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Daniel Rojas Rangel
- Department of Molecular Pharmacology, Pharmacology Institute, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany . Dr. Bali is now with the Department of Experimental Pain Research, Mannheim Center for Translational Neuroscience (MCTN), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | | | | | - Nitin Agarwal
- Department of Molecular Pharmacology, Pharmacology Institute, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany . Dr. Bali is now with the Department of Experimental Pain Research, Mannheim Center for Translational Neuroscience (MCTN), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Martin Schmelz
- Department of Experimental Pain Research, Mannheim Center for Translational Neuroscience (MCTN), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | | | - Rohini Kuner
- Department of Molecular Pharmacology, Pharmacology Institute, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany . Dr. Bali is now with the Department of Experimental Pain Research, Mannheim Center for Translational Neuroscience (MCTN), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
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49
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Mwai K, Kibinge N, Tuju J, Kamuyu G, Kimathi R, Mburu J, Chepsat E, Nyamako L, Chege T, Nkumama I, Kinyanjui S, Musenge E, Osier F. protGear: A protein microarray data pre-processing suite. Comput Struct Biotechnol J 2021; 19:2518-2525. [PMID: 34025940 PMCID: PMC8114118 DOI: 10.1016/j.csbj.2021.04.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 11/29/2022] Open
Abstract
Protein microarrays are versatile tools for high throughput study of the human proteome, but systematic and non-systematic sources of bias constrain optimal interpretation and the ultimate utility of the data. Published guidelines to limit technical variability whilst maintaining important biological variation favour DNA-based microarrays that often differ fundamentally in their experimental design. Rigorous tools to guide background correction, the quantification of within-sample variation, normalisation, and batch correction specifically for protein microarrays are limited, require extensive investigation and are not centrally accessible. Here, we develop a generic one-stop-shop pre-processing suite for protein microarrays that is compatible with data from the major protein microarray scanners. Our graphical and tabular interfaces facilitate a detailed inspection of data and are coupled with supporting guidelines that enable users to select the most appropriate algorithms to systematically address bias arising in customized experiments. The localization and distribution of background signal intensities determine the optimal correction strategy. A novel function overcomes the limitations in the interpretation of the coefficient of variation when signal intensities are at the lower end of the detection threshold. We demonstrate essential considerations in the experimental design and their impact on a range of algorithms for normalization and minimization of batch effects. Our user-friendly interactive web-based platform eliminates the need for prowess in programming. The open-source R interface includes illustrative examples, generates an auditable record, enables reproducibility, and can incorporate additional custom scripts through its online repository. This versatility will enhance its broad uptake in the infectious disease and vaccine development community.
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Affiliation(s)
- Kennedy Mwai
- Epidemiology and Biostatistics Division, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa.,Centre for Geographic Medicine Research (Coast), Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Nelson Kibinge
- Centre for Geographic Medicine Research (Coast), Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - James Tuju
- Centre for Geographic Medicine Research (Coast), Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya.,Department of Biotechnology and Biochemistry, Pwani University, Kilifi, Kenya
| | - Gathoni Kamuyu
- Centre for Geographic Medicine Research (Coast), Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Rinter Kimathi
- Centre for Geographic Medicine Research (Coast), Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - James Mburu
- Centre for Geographic Medicine Research (Coast), Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Emily Chepsat
- Centre for Geographic Medicine Research (Coast), Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Lydia Nyamako
- Centre for Geographic Medicine Research (Coast), Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Timothy Chege
- Centre for Geographic Medicine Research (Coast), Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Irene Nkumama
- Centre for Geographic Medicine Research (Coast), Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya.,Centre of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Samson Kinyanjui
- Centre for Geographic Medicine Research (Coast), Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya.,Department of Biotechnology and Biochemistry, Pwani University, Kilifi, Kenya.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Eustasius Musenge
- Epidemiology and Biostatistics Division, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Faith Osier
- Centre for Geographic Medicine Research (Coast), Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya.,Centre of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany.,Department of Biotechnology and Biochemistry, Pwani University, Kilifi, Kenya.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
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50
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McNamara KL, Caswell-Jin JL, Joshi R, Ma Z, Kotler E, Bean GR, Kriner M, Zhou Z, Hoang M, Beechem J, Zoeller J, Press MF, Slamon DJ, Hurvitz SA, Curtis C. Spatial proteomic characterization of HER2-positive breast tumors through neoadjuvant therapy predicts response. NATURE CANCER 2021; 2:400-413. [PMID: 34966897 PMCID: PMC8713949 DOI: 10.1038/s43018-021-00190-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The addition of HER2-targeted agents to neoadjuvant chemotherapy has dramatically improved pathological complete response (pCR) rates in early-stage, HER2-positive breast cancer. Nonetheless, up to 50% of patients have residual disease after treatment, while others are likely overtreated. Here, we performed multiplex spatial proteomic characterization of 122 samples from 57 HER2-positive breast tumors from the neoadjuvant TRIO-US B07 clinical trial sampled pre-treatment, after 14-21 d of HER2-targeted therapy and at surgery. We demonstrated that proteomic changes after a single cycle of HER2-targeted therapy aids the identification of tumors that ultimately undergo pCR, outperforming pre-treatment measures or transcriptomic changes. We further developed and validated a classifier that robustly predicted pCR using a single marker, CD45, measured on treatment, and showed that CD45-positive cell counts measured via conventional immunohistochemistry perform comparably. These results demonstrate robust biomarkers that can be used to enable the stratification of sensitive tumors early during neoadjuvant HER2-targeted therapy, with implications for tailoring subsequent therapy.
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Affiliation(s)
- Katherine L. McNamara
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jennifer L. Caswell-Jin
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rohan Joshi
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Zhicheng Ma
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Eran Kotler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Gregory R. Bean
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Zoey Zhou
- NanoString Technologies, Seattle, WA, USA
| | | | | | - Jason Zoeller
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Michael F. Press
- Department of Pathology Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Dennis J. Slamon
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Sara A. Hurvitz
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Christina Curtis
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Correspondence and requests for materials should be addressed to C.C.
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