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Al Ali F, Marr AK, Tatari-Calderone Z, Alfaki M, Toufiq M, Roelands J, Syed Ahamed Kabeer B, Bedognetti D, Marr N, Garand M, Rinchai D, Chaussabel D. Organizing training workshops on gene literature retrieval, profiling, and visualization for early career researchers. F1000Res 2023; 10:275. [PMID: 37448622 PMCID: PMC10336363 DOI: 10.12688/f1000research.36395.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/20/2023] [Indexed: 07/15/2023] Open
Abstract
Early-career researchers must acquire the skills necessary to effectively search and extract information from biomedical literature. This ability is for instance crucial for evaluating the novelty of experimental results, and assessing potential publishing opportunities. Given the rapidly growing volume of publications in the field of biomedical research, new systematic approaches need to be devised and adopted for the retrieval and curation of literature relevant to a specific theme. In this context, we present a hands-on training curriculum aimed at retrieval, profiling, and visualization of literature associated with a given topic. The curriculum was implemented in a workshop in January 2021. Here we provide supporting material and step-by-step implementation guidelines with the ISG15 gene literature serving as an illustrative use case. Workshop participants can learn several skills, including: 1) building and troubleshoot PubMed queries in order to retrieve the literature associated with a gene of interest; 2) identifying key concepts relevant to given themes (such as cell types, diseases, and biological processes); 3) measuring the prevalence of these concepts in the gene literature; 4) extracting key information from relevant articles, and 5) developing a background section or summary on the basis of this information. Finally, trainees can learn to consolidate the structured information captured through this process for presentation via an interactive web application.
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Affiliation(s)
| | | | | | | | | | | | | | - Davide Bedognetti
- Research Branch, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, 16126, Italy
| | - Nico Marr
- Research Branch, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
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Pullikuth AK, Routh ED, Zimmerman KD, Chifman J, Chou JW, Soike MH, Jin G, Su J, Song Q, Black MA, Print C, Bedognetti D, Howard-McNatt M, O’Neill SS, Thomas A, Langefeld CD, Sigalov AB, Lu Y, Miller LD. Bulk and Single-Cell Profiling of Breast Tumors Identifies TREM-1 as a Dominant Immune Suppressive Marker Associated With Poor Outcomes. Front Oncol 2021; 11:734959. [PMID: 34956864 PMCID: PMC8692779 DOI: 10.3389/fonc.2021.734959] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
BackgroundTriggering receptor expressed on myeloid cells (TREM)-1 is a key mediator of innate immunity previously associated with the severity of inflammatory disorders, and more recently, the inferior survival of lung and liver cancer patients. Here, we investigated the prognostic impact and immunological correlates of TREM1 expression in breast tumors.MethodsBreast tumor microarray and RNAseq expression profiles (n=4,364 tumors) were analyzed for associations between gene expression, tumor immune subtypes, distant metastasis-free survival (DMFS) and clinical response to neoadjuvant chemotherapy (NAC). Single-cell (sc)RNAseq was performed using the 10X Genomics platform. Statistical associations were assessed by logistic regression, Cox regression, Kaplan-Meier analysis, Spearman correlation, Student’s t-test and Chi-square test.ResultsIn pre-treatment biopsies, TREM1 and known TREM-1 inducible cytokines (IL1B, IL8) were discovered by a statistical ranking procedure as top genes for which high expression was associated with reduced response to NAC, but only in the context of immunologically “hot” tumors otherwise associated with a high NAC response rate. In surgical specimens, TREM1 expression varied among tumor molecular subtypes, with highest expression in the more aggressive subtypes (Basal-like, HER2-E). High TREM1 significantly and reproducibly associated with inferior distant metastasis-free survival (DMFS), independent of conventional prognostic markers. Notably, the association between high TREM1 and inferior DMFS was most prominent in the subset of immunogenic tumors that exhibited the immunologically hot phenotype and otherwise associated with superior DMFS. Further observations from bulk and single-cell RNAseq analyses indicated that TREM1 expression was significantly enriched in polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs) and M2-like macrophages, and correlated with downstream transcriptional targets of TREM-1 (IL8, IL-1B, IL6, MCP-1, SPP1, IL1RN, INHBA) which have been previously associated with pro-tumorigenic and immunosuppressive functions.ConclusionsTogether, these findings indicate that increased TREM1 expression is prognostic of inferior breast cancer outcomes and may contribute to myeloid-mediated breast cancer progression and immune suppression.
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Affiliation(s)
- Ashok K. Pullikuth
- Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC, United States
| | - Eric D. Routh
- Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Kip D. Zimmerman
- Center for Precision Medicine, Wake Forest School of Medicine, Winston Salem, NC, United States
| | - Julia Chifman
- Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC, United States
- Department of Mathematics and Statistics, American University, Washington, DC, United States
| | - Jeff W. Chou
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston Salem, NC, United States
- The Comprehensive Cancer Center of Wake Forest University, Winston Salem, NC, United States
| | - Michael H. Soike
- Department of Radiation Oncology, University of Alabama-Birmingham, Birmingham, AL, United States
| | - Guangxu Jin
- Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC, United States
- The Comprehensive Cancer Center of Wake Forest University, Winston Salem, NC, United States
| | - Jing Su
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston Salem, NC, United States
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Qianqian Song
- Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC, United States
- Center for Cancer Genomics and Precision Oncology, Wake Forest School of Medicine, Winston Salem, NC, United States
| | - Michael A. Black
- Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand
| | - Cristin Print
- Department of Molecular Medicine and Pathology and Maurice Wilkins Institute, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Davide Bedognetti
- Cancer Program, Sidra Medicine, Doha, Qatar & Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Marissa Howard-McNatt
- Surgical Oncology Service, Department of Surgery, Wake Forest School of Medicine, Winston Salem, NC, United States
| | - Stacey S. O’Neill
- The Comprehensive Cancer Center of Wake Forest University, Winston Salem, NC, United States
- Department of Pathology, Wake Forest School of Medicine, Winston Salem, NC, United States
| | - Alexandra Thomas
- The Comprehensive Cancer Center of Wake Forest University, Winston Salem, NC, United States
- Section of Hematology and Oncology, Department of Internal Medicine, Wake Forest Baptist Medical Center, Winston Salem, NC, United States
| | - Carl D. Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston Salem, NC, United States
- The Comprehensive Cancer Center of Wake Forest University, Winston Salem, NC, United States
| | | | - Yong Lu
- The Comprehensive Cancer Center of Wake Forest University, Winston Salem, NC, United States
- Department of Microbiology & Immunology, Wake Forest School of Medicine, Winston Salem, NC, United States
| | - Lance D. Miller
- Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC, United States
- The Comprehensive Cancer Center of Wake Forest University, Winston Salem, NC, United States
- *Correspondence: Lance D. Miller,
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Nwosu IO, Piccolo SR. A systematic review of datasets that can help elucidate relationships among gene expression, race, and immunohistochemistry-defined subtypes in breast cancer. Cancer Biol Ther 2021; 22:417-429. [PMID: 34412551 DOI: 10.1080/15384047.2021.1953902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Scholarly requirements have led to a massive increase of transcriptomic data in the public domain, with millions of samples available for secondary research. We identified gene-expression datasets representing 10,214 breast-cancer patients in public databases. We focused on datasets that included patient metadata on race and/or immunohistochemistry (IHC) profiling of the ER, PR, and HER-2 proteins. This review provides a summary of these datasets and describes findings from 32 research articles associated with the datasets. These studies have helped to elucidate relationships between IHC, race, and/or treatment options, as well as relationships between IHC status and the breast-cancer intrinsic subtypes. We have also identified broad themes across the analysis methodologies used in these studies, including breast cancer subtyping, deriving predictive biomarkers, identifying differentially expressed genes, and optimizing data processing. Finally, we discuss limitations of prior work and recommend future directions for reusing these datasets in secondary analyses.
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Affiliation(s)
| | - Stephen R Piccolo
- Department of Biology, Brigham Young University, Provo, Utah, United States
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4
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Al Ali F, Marr AK, Tatari-Calderone Z, Alfaki M, Toufiq M, Roelands J, Syed Ahamed Kabeer B, Bedognetti D, Marr N, Garand M, Rinchai D, Chaussabel D. Organizing gene literature retrieval, profiling, and visualization training workshops for early career researchers. F1000Res 2021. [DOI: 10.12688/f1000research.36395.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Developing the skills needed to effectively search and extract information from biomedical literature is essential for early-career researchers. It is, for instance, on this basis that the novelty of experimental results, and therefore publishing opportunities, can be evaluated. Given the unprecedented volume of publications in the field of biomedical research, new systematic approaches need to be devised and adopted for the retrieval and curation of literature relevant to a specific theme. Here we describe a hands-on training curriculum aimed at retrieval, profiling, and visualization of literature associated with a given topic. This curriculum was implemented in a workshop in January 2021. We provide supporting material and step-by-step implementation guidelines with the ISG15 gene literature serving as an illustrative use case. Through participation in such a workshop, trainees can learn: 1) to build and troubleshoot PubMed queries in order to retrieve the literature associated with a gene of interest; 2) to identify key concepts relevant to given themes (such as cell types, diseases, and biological processes); 3) to measure the prevalence of these concepts in the gene literature; 4) to extract key information from relevant articles, and 5) to develop a background section or summary on the basis of this information. Finally, trainees can learn to consolidate the structured information captured through this process for presentation via an interactive web application.
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5
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Krijgsman D, Roelands J, Hendrickx W, Bedognetti D, Kuppen PJK. HLA-G: A New Immune Checkpoint in Cancer? Int J Mol Sci 2020; 21:ijms21124528. [PMID: 32630545 PMCID: PMC7350262 DOI: 10.3390/ijms21124528] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 12/15/2022] Open
Abstract
Human leukocyte antigen G (HLA-G), known as a central protein in providing immune tolerance to the fetus in pregnant women, is also studied for a possible role in tumor development. Many studies have claimed HLA-G as a new immune checkpoint in cancer. Therefore, HLA-G and its receptors might be targets for immune checkpoint blockade in cancer immunotherapy. In order to substantiate that HLA-G is indeed an immune checkpoint in cancer, two important questions need to be answered: (1) To what extent is HLA-G expressed in the tumor by cancer cells? and (2) What is the function of HLA-G in cancer immune evasion? In this review, we discuss these questions. We agree that HLA-G is a potentially new immune checkpoint in cancer, but additional evidence is required to show the extent of intra-tumor and inter-tumor expression. These studies should focus on tumor expression patterns of the seven different HLA-G isoforms and of the receptors for HLA-G. Furthermore, specific roles for the different HLA-G isoforms should be established.
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Affiliation(s)
- Daniëlle Krijgsman
- Department of Surgery, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands; (D.K.); (J.R.)
| | - Jessica Roelands
- Department of Surgery, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands; (D.K.); (J.R.)
- Cancer Research Department, Research Branch, Sidra Medicine, Doha P.O. Box 26999, Qatar; (W.H.); (D.B.)
| | - Wouter Hendrickx
- Cancer Research Department, Research Branch, Sidra Medicine, Doha P.O. Box 26999, Qatar; (W.H.); (D.B.)
| | - Davide Bedognetti
- Cancer Research Department, Research Branch, Sidra Medicine, Doha P.O. Box 26999, Qatar; (W.H.); (D.B.)
| | - Peter J. K. Kuppen
- Department of Surgery, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands; (D.K.); (J.R.)
- Correspondence: ; Tel.: +31-71-5264569
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Mirbagheri E, Ahmadi M, Salmanian S. Common data elements of breast cancer for research databases: A systematic review. J Family Med Prim Care 2020; 9:1296-1301. [PMID: 32509607 PMCID: PMC7266190 DOI: 10.4103/jfmpc.jfmpc_931_19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 11/05/2022] Open
Abstract
Background: Common Data Elements (CDEs) are data-metadata descriptors used to collect research study data. CDEs facilitate the collection, processing, and sharing of breast cancer data. This study intended to explore the CDEs of breast cancer for research databases and primary care systems. Methods: This study was conducted using systematic search and review. This systematic literature review covered PubMed, Scopus, Science Direct, SID, ISC, Web of Science, and Google Scholar search engine. It included studies in English language with accessible full-text from the beginning of 2007 to September 2019. Results: Reviewing 25 studies revealed that 52 percent of studies were carried out in the US and most studies were conducted between 2013 and 2015. The most domains for using CDEs were: Pathology Report and Registry. The CDEs of breast cancer for research databases were categorized into three categories namely clinical, research, and non-clinical and indicate the importance of these data elements. Most of the studies focused on creating and deploying clinical CDEs as physical examination, clinical history and pathology data. Conclusion: The integration of biomedical and clinical data relevant to breast cancer enhances the power of research variable analysis and statistical analysis, thereby facilitating improved knowledge of effective therapeutic interventions. Also CDEs used to collect, store, and retrieve patient data in various health setting such as primary care and research databases.
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Affiliation(s)
- Esmat Mirbagheri
- Department of Health Information Management, School of Health Management and Information Sciences, Tehran, Iran
| | - Maryam Ahmadi
- Department of Health Information Management, School of Management and Medical Information Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Soraya Salmanian
- Assistant Professor, Radiation Oncology, Oncophathology Research Center, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
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Sola-Penna M, Paixão LP, Branco JR, Ochioni AC, Albanese JM, Mundim DM, Baptista-de-Souza D, Figueiredo CP, Coelho WS, Marcondes MC, Zancan P. Serotonin activates glycolysis and mitochondria biogenesis in human breast cancer cells through activation of the Jak1/STAT3/ERK1/2 and adenylate cyclase/PKA, respectively. Br J Cancer 2020; 122:194-208. [PMID: 31819176 PMCID: PMC7052254 DOI: 10.1038/s41416-019-0640-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 10/01/2019] [Accepted: 10/28/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Although produced by several types of tumours, the role of serotonin on cancer biology is yet to be understood. METHODS The effects of serotonin (5-HT) on human breast cancer cells proliferation, signalling pathways and metabolic profile were evaluated by cytometry, western blotting, qPCR, enzymology and confocal microscopy. RESULTS Our results revealed that incubation of MCF-7 cells with 10 µM 5-HT increased cell growth rate by 28%, an effect that was prevented by the 5-HTR2A/C antagonist, ketanserin. Conversely, increasing concentrations of 5-HT promoted glucose consumption and lactate production by MCF-7 cells. We also showed that increased glucose metabolism is provoked by the upregulation of pyruvate kinase M2 (PKM2) isoform through 5-HTR2A/C-triggered activation of Jak1/STAT3 and ERK1/2 subcellular pathways. However, we noticed a decrease in the rate of produced lactate per consumed glucose as a function of the hormone concentration, suggesting a disruption of the Warburg effect. The latter effect is due to 5-HTR2A/C-dependent mitochondrial biogenesis and metabolism, which is triggered by adenylyl cyclase/PKA, enhancing the oxidation of lactate within these cells. CONCLUSIONS We showed that serotonin, through 5-HTR2A/C, interferes with breast cancer cells proliferation and metabolism by triggering two distinct signalling pathways: Jak1/STAT3 that boosts glycolysis through upregulation of PKM2, and adenylyl cyclase/PKA that enhances mitochondrial biogenesis.
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Affiliation(s)
- Mauro Sola-Penna
- Laboratório de Enzimologia e Controle do Metabolismo, Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Larissa P Paixão
- Laboratório de Oncobiologia Molecular, Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Jessica R Branco
- Laboratório de Oncobiologia Molecular, Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Alan C Ochioni
- Laboratório de Oncobiologia Molecular, Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Jamille M Albanese
- Laboratório de Oncobiologia Molecular, Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Davi M Mundim
- Laboratório de Oncobiologia Molecular, Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | | | - Claudia P Figueiredo
- Nucleo de Neurociências da Faculdade de Farmácia, Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Wagner S Coelho
- Laboratório de Enzimologia e Controle do Metabolismo, Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
- Universidade Estadual da Zona Oeste, 23070-200, Rio de Janeiro, RJ, Brazil
| | - Mariah C Marcondes
- Laboratório de Oncobiologia Molecular, Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
- Instituto Nacional de Câncer José Alencar Gomes da Silva, 20230-130, Rio de Janeiro, RJ, Brazil
| | - Patricia Zancan
- Laboratório de Oncobiologia Molecular, Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil.
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Abstract
Checkpoint inhibitor therapy (CIT) has revolutionized cancer treatment but it has also reached a standstill when an absent dialog between cancer and immune cells makes it irrelevant. This occurs with high prevalence in the context of "immune silent" and, even perhaps, "immune-excluded" tumors. The latter are characterized by T cells restricted to the periphery of cancer nests. Since in either case T cells do not come in direct contact with most cancer cells, CIT rests immaterial. Adoptive cell therapy (ACT), may also be affected by limited access to antigen-bearing cancer cells. While lack of immunogenicity intuitively explains the immune silent phenotype, immune exclusion is perplexing. The presence of T cells at the periphery suggests that chemo-attraction recruits them and an immunogenic stimulus promotes their persistence. However, what stops the T cells from infiltrating the tumors' nests and reaching the germinal center (GC)? Possibly, a concentric gradient of increased chemo-repulsion or decreased chemo-attraction demarcates an abrupt "do not trespass" warning. Various hypotheses suggest physical or functional barriers but no definitive consensus exists over the weight that each plays in human cancers. On one hand, it could be hypothesized that the intrinsic biology of cancer cells may degenerate from a "cancer stem cell" (CSC)-like phenotype in the GC toward a progressively more immunogenic phenotype prone to immunogenic cell death (ICD) at the periphery. On the other hand, the intrinsic biology of the cancer cells may not change but it is the disorderly architecture of the tumor microenvironment (TME) that alters in a centripetal direction cancer cell metabolism, both directly and indirectly, the function of surrounding stromal cells. In this chapter, we examine whether the paradoxical exclusion of T cells from tumors may serve as a model to understand the requirements for tumor immune infiltration and, correspondingly, we put forth strategies to restore the dialog between immune cells and cancer to enhance the effectiveness of immune oncology (IO) approaches.
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Affiliation(s)
- Sara I Pai
- Massachusetts General Hospital, Harvard University, Boston, MA, USA.
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9
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Roelands J, Garand M, Hinchcliff E, Ma Y, Shah P, Toufiq M, Alfaki M, Hendrickx W, Boughorbel S, Rinchai D, Jazaeri A, Bedognetti D, Chaussabel D. Long-Chain Acyl-CoA Synthetase 1 Role in Sepsis and Immunity: Perspectives From a Parallel Review of Public Transcriptome Datasets and of the Literature. Front Immunol 2019; 10:2410. [PMID: 31681299 PMCID: PMC6813721 DOI: 10.3389/fimmu.2019.02410] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 09/26/2019] [Indexed: 12/21/2022] Open
Abstract
A potential role for the long-chain acyl-CoA synthetase family member 1 (ACSL1) in the immunobiology of sepsis was explored during a hands-on training workshop. Participants first assessed the robustness of the potential gap in biomedical knowledge identified via an initial screen of public transcriptome data and of the literature associated with ACSL1. Increase in ACSL1 transcript abundance during sepsis was confirmed in several independent datasets. Querying the ACSL1 literature also confirmed the absence of reports associating ACSL1 with sepsis. Inferences drawn from both the literature (via indirect associations) and public transcriptome data (via correlation) point to the likely participation of ACSL1 and ACSL4, another family member, in inflammasome activation in neutrophils during sepsis. Furthermore, available clinical data indicate that levels of ACSL1 and ACSL4 induction was significantly higher in fatal cases of sepsis. This denotes potential translational relevance and is consistent with involvement in pathways driving potentially deleterious systemic inflammation. Finally, while ACSL1 expression was induced in blood in vitro by a wide range of pathogen-derived factors as well as TNF, induction of ACSL4 appeared restricted to flagellated bacteria and pathogen-derived TLR5 agonists and IFNG. Taken together, this joint review of public literature and omics data records points to two members of the acyl-CoA synthetase family potentially playing a role in inflammasome activation in neutrophils. Translational relevance of these observations in the context of sepsis and other inflammatory conditions remain to be investigated.
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Affiliation(s)
- Jessica Roelands
- Sidra Medicine, Doha, Qatar.,Department of Surgery, Leiden University Medical Center, Leiden, Netherlands
| | | | - Emily Hinchcliff
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ying Ma
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Parin Shah
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | | | | | | | | | | | - Amir Jazaeri
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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Huang SSY, Al Ali F, Boughorbel S, Toufiq M, Chaussabel D, Garand M. A curated collection of transcriptome datasets to investigate the molecular mechanisms of immunoglobulin E-mediated atopic diseases. Database (Oxford) 2019; 2019:baz066. [PMID: 31290545 PMCID: PMC6616200 DOI: 10.1093/database/baz066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 04/14/2019] [Accepted: 04/29/2019] [Indexed: 12/17/2022]
Abstract
Prevalence of allergies has reached ~20% of population in developed countries and sensitization rate to one or more allergens among school age children are approaching 50%. However, the combination of the complexity of atopic allergy susceptibility/development and environmental factors has made identification of gene biomarkers challenging. The amount of publicly accessible transcriptomic data presents an unprecedented opportunity for mechanistic discoveries and validation of complex disease signatures across studies. However, this necessitates structured methodologies and visual tools for the interpretation of results. Here, we present a curated collection of transcriptomic datasets relevant to immunoglobin E-mediated atopic diseases (ranging from allergies to primary immunodeficiencies). Thirty-three datasets from the Gene Expression Omnibus, encompassing 1860 transcriptome profiles, were made available on the Gene Expression Browser (GXB), an online and open-source web application that allows for the query, visualization and annotation of metadata. The thematic compositions, disease categories, sample number and platforms of the collection are described. Ranked gene lists and sample grouping are used to facilitate data visualization/interpretation and are available online via GXB (http://ige.gxbsidra.org/dm3/geneBrowser/list). Dataset validation using associated publications showed good concordance in GXB gene expression trend and fold-change.
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Affiliation(s)
| | - Fatima Al Ali
- Sidra Medicine, Al Gharrafa Street Ar-Rayyan, Doha, Qatar
| | | | | | | | - Mathieu Garand
- Sidra Medicine, Al Gharrafa Street Ar-Rayyan, Doha, Qatar
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Chaussabel D, Rinchai D. Using 'collective omics data' for biomedical research training. Immunology 2018; 155:18-23. [PMID: 29705995 DOI: 10.1111/imm.12944] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 04/11/2018] [Indexed: 12/13/2022] Open
Abstract
Systems-scale molecular profiling data accumulating in public repositories may constitute a useful resource for immunologists. It is for instance likely that information relevant to their chosen line of research be found among the more than 90,000 data series available in the NCBI Gene Expression Omnibus. Such 'collective omics data' may also be employed as source material for training purposes. This is the case when training curricula aim at the development of bioinformatics skills necessary for the analysis, interpretation or visualization of data generated on global scales. But 'collective omics data' may also be reused for training purposes to foster the development of the skills and 'mental habits' underpinning traditional reductionist science approaches. This review describes a small-scale initiative involving investigators, for the most part immunologists, having engaged in a range of training activities relying on 'collective omics data'.
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Bedognetti D, Roelands J, Decock J, Wang E, Hendrickx W. The MAPK hypothesis: immune-regulatory effects of MAPK-pathway genetic dysregulations and implications for breast cancer immunotherapy. Emerg Top Life Sci 2017; 1:429-445. [PMID: 33525803 PMCID: PMC7289005 DOI: 10.1042/etls20170142] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 11/08/2017] [Accepted: 11/13/2017] [Indexed: 12/12/2022]
Abstract
With the advent of checkpoint inhibition, immunotherapy has revolutionized the clinical management of several cancers, but has demonstrated limited efficacy in mammary carcinoma. Transcriptomic profiling of cancer samples defined distinct immunophenotypic categories characterized by different prognostic and predictive connotations. In breast cancer, genomic alterations leading to the dysregulation of mitogen-activated protein kinase (MAPK) pathways have been linked to an immune-silent phenotype associated with poor outcome and treatment resistance. These aberrations include mutations of MAP3K1 and MAP2K4, amplification of KRAS, BRAF, and RAF1, and truncations of NF1. Anticancer therapies targeting MAPK signaling by BRAF and MEK inhibitors have demonstrated clear immunologic effects. These off-target properties could be exploited to convert the immune-silent tumor phenotype into an immune-active one. Preclinical evidence supports that MAPK-pathway inhibition can dramatically increase the efficacy of immunotherapy. In this review, we provide a detailed overview of the immunomodulatory impact of MAPK-pathway blockade through BRAF and MEK inhibitions. While BRAF inhibition might be relevant in melanoma only, MEK inhibition is potentially applicable to a wide range of tumors. Context-dependent similarities and differences of MAPK modulation will be dissected, in light of the complexity of the MAPK pathways. Therapeutic strategies combining the favorable effects of MAPK-oriented interventions on the tumor microenvironment while maintaining T-cell function will be presented. Finally, we will discuss recent studies highlighting the rationale for the implementation of MAPK-interference approaches in combination with checkpoint inhibitors and immune agonists in breast cancer.
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Affiliation(s)
- Davide Bedognetti
- Tumor Biology, Immunology, and Therapy Section, Department of Immunology, Inflammation and Metabolism, Division of Translational Medicine, Research Branch, Sidra Medical and Research Center, Doha, Qatar
- College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Jessica Roelands
- Tumor Biology, Immunology, and Therapy Section, Department of Immunology, Inflammation and Metabolism, Division of Translational Medicine, Research Branch, Sidra Medical and Research Center, Doha, Qatar
| | - Julie Decock
- Cancer Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Ena Wang
- Division of Translational Medicine, Research Branch, Sidra Medical and Research Center, Doha, Qatar
| | - Wouter Hendrickx
- Tumor Biology, Immunology, and Therapy Section, Department of Immunology, Inflammation and Metabolism, Division of Translational Medicine, Research Branch, Sidra Medical and Research Center, Doha, Qatar
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