1
|
Gilchrist JJ, Fang H, Danielli S, Tomkova M, Nassiri I, Ng E, Tong O, Taylor C, Muldoon D, Cohen LRZ, Al-Mossawi H, Lau E, Neville M, Schuster-Boeckler B, Knight JC, Fairfax BP. Characterization of the genetic determinants of context-specific DNA methylation in primary monocytes. CELL GENOMICS 2024; 4:100541. [PMID: 38663408 PMCID: PMC11099345 DOI: 10.1016/j.xgen.2024.100541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 11/24/2023] [Accepted: 03/27/2024] [Indexed: 05/12/2024]
Abstract
To better understand inter-individual variation in sensitivity of DNA methylation (DNAm) to immune activity, we characterized effects of inflammatory stimuli on primary monocyte DNAm (n = 190). We find that monocyte DNAm is site-dependently sensitive to lipopolysaccharide (LPS), with LPS-induced demethylation occurring following hydroxymethylation. We identify 7,359 high-confidence immune-modulated CpGs (imCpGs) that differ in genomic localization and transcription factor usage according to whether they represent a gain or loss in DNAm. Demethylated imCpGs are profoundly enriched for enhancers and colocalize to genes enriched for disease associations, especially cancer. DNAm is age associated, and we find that 24-h LPS exposure triggers approximately 6 months of gain in epigenetic age, directly linking epigenetic aging with innate immune activity. By integrating LPS-induced changes in DNAm with genetic variation, we identify 234 imCpGs under local genetic control. Exploring shared causal loci between LPS-induced DNAm responses and human disease traits highlights examples of disease-associated loci that modulate imCpG formation.
Collapse
Affiliation(s)
- James J Gilchrist
- Department of Paediatrics, University of Oxford, Oxford OX3 9DU, UK; MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Hai Fang
- Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Sara Danielli
- Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Marketa Tomkova
- Ludwig Cancer Research Oxford, University of Oxford, Oxford OX3 7DQ, UK
| | - Isar Nassiri
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Esther Ng
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | - Orion Tong
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Chelsea Taylor
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Dylan Muldoon
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Lea R Z Cohen
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Hussein Al-Mossawi
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | - Evelyn Lau
- Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Matt Neville
- Oxford Centre for Diabetes, Endocrinology, and Metabolism, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LE, UK
| | | | - Julian C Knight
- Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Benjamin P Fairfax
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Department of Oncology, University of Oxford, Oxford OX3 9DS, UK.
| |
Collapse
|
2
|
Zhang L, Nishi H, Kinoshita K. Multi-Omics Profiling Reveals Phenotypic and Functional Heterogeneity of Neutrophils in COVID-19. Int J Mol Sci 2024; 25:3841. [PMID: 38612651 PMCID: PMC11011481 DOI: 10.3390/ijms25073841] [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: 03/12/2024] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Accumulating evidence has revealed unexpected phenotypic heterogeneity and diverse functions of neutrophils in several diseases. Coronavirus disease (COVID-19) can alter the leukocyte phenotype based on disease severity, including neutrophil activation in severe cases. However, the plasticity of neutrophil phenotypes and their relative impact on COVID-19 pathogenesis has not been well addressed. This study aimed to identify and validate the heterogeneity of neutrophils in COVID-19 and evaluate the functions of each subpopulation. We analyzed public single-cell RNA-seq, bulk RNA-seq, and proteome data from healthy donors and patients with COVID-19 to investigate neutrophil subpopulations and their response to disease pathogenesis. We identified eight neutrophil subtypes: pro-neutrophil, pre-neutrophil, immature neutrophil, and five mature neutrophil subpopulations. The subtypes exhibited distinct features, including diverse activation signatures and multiple enriched pathways. The pro-neutrophil subtype was associated with severe and fatal disease, while the pre-neutrophil subtype was particularly abundant in mild/moderate disease. One of the mature neutrophil subtypes showed consistently large fractions in patients with different disease severity. Bulk RNA-seq dataset analyses using a cellular deconvolution approach validated the relative abundances of neutrophil subtypes and the expansion of pro-neutrophils in severe COVID-19 patients. Cell-cell communication analysis revealed representative ligand-receptor interactions among the identified neutrophil subtypes. Further investigation into transcription factors and differential protein abundance revealed the regulatory network differences between healthy donors and patients with severe COVID-19. Overall, we demonstrated the complex interactions among heterogeneous neutrophil subtypes and other blood cell types during COVID-19 disease. Our work has great value in terms of both clinical and public health as it furthers our understanding of the phenotypic and functional heterogeneity of neutrophils and other cell populations in multiple diseases.
Collapse
Affiliation(s)
- Lin Zhang
- Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Miyagi, Japan
- Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, Sendai 980-8579, Miyagi, Japan
| | - Hafumi Nishi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Miyagi, Japan
- Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, Sendai 980-8579, Miyagi, Japan
- Faculty of Core Research, Ochanomizu University, Tokyo 112-8610, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Miyagi, Japan
- Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, Sendai 980-8579, Miyagi, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai 980-8573, Miyagi, Japan
- Department of In Silico Analyses, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai 980-8575, Miyagi, Japan
| |
Collapse
|
3
|
Blanton LV, San Roman AK, Wood G, Buscetta A, Banks N, Skaletsky H, Godfrey AK, Pham TT, Hughes JF, Brown LG, Kruszka P, Lin AE, Kastner DL, Muenke M, Page DC. Stable and robust Xi and Y transcriptomes drive cell-type-specific autosomal and Xa responses in vivo and in vitro in four human cell types. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585578. [PMID: 38562807 PMCID: PMC10983990 DOI: 10.1101/2024.03.18.585578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Recent in vitro studies of human sex chromosome aneuploidy showed that the Xi ("inactive" X) and Y chromosomes broadly modulate autosomal and Xa ("active" X) gene expression in two cell types. We tested these findings in vivo in two additional cell types. Using linear modeling in CD4+ T cells and monocytes from individuals with one to three X chromosomes and zero to two Y chromosomes, we identified 82 sex-chromosomal and 344 autosomal genes whose expression changed significantly with Xi and/or Y dosage in vivo . Changes in sex-chromosomal expression were remarkably constant in vivo and in vitro across all four cell types examined. In contrast, autosomal responses to Xi and/or Y dosage were largely cell-type-specific, with up to 2.6-fold more variation than sex-chromosomal responses. Targets of the X- and Y-encoded transcription factors ZFX and ZFY accounted for a significant fraction of these autosomal responses both in vivo and in vitro . We conclude that the human Xi and Y transcriptomes are surprisingly robust and stable across the four cell types examined, yet they modulate autosomal and Xa genes - and cell function - in a cell-type-specific fashion. These emerging principles offer a foundation for exploring the wide-ranging regulatory roles of the sex chromosomes across the human body.
Collapse
|
4
|
Vochteloo M, Deelen P, Vink B, Tsai EA, Runz H, Andreu-Sánchez S, Fu J, Zhernakova A, Westra HJ, Franke L. PICALO: principal interaction component analysis for the identification of discrete technical, cell-type, and environmental factors that mediate eQTLs. Genome Biol 2024; 25:29. [PMID: 38254182 PMCID: PMC10802033 DOI: 10.1186/s13059-023-03151-0] [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: 12/22/2022] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Expression quantitative trait loci (eQTL) offer insights into the regulatory mechanisms of trait-associated variants, but their effects often rely on contexts that are unknown or unmeasured. We introduce PICALO, a method for hidden variable inference of eQTL contexts. PICALO identifies and disentangles technical from biological context in heterogeneous blood and brain bulk eQTL datasets. These contexts are biologically informative and reproducible, outperforming cell counts or expression-based principal components. Furthermore, we show that RNA quality and cell type proportions interact with thousands of eQTLs. Knowledge of hidden eQTL contexts may aid in the inference of functional mechanisms underlying disease variants.
Collapse
Affiliation(s)
- Martijn Vochteloo
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Patrick Deelen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Britt Vink
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Institute for Life Science & Technology, Hanze University of Applied Sciences, Groningen, The Netherlands
| | - Ellen A Tsai
- Translational Sciences, Research and Development, Biogen, Cambridge, MA, USA
| | - Heiko Runz
- Translational Sciences, Research and Development, Biogen, Cambridge, MA, USA
| | - Sergio Andreu-Sánchez
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jingyuan Fu
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Harm-Jan Westra
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
| |
Collapse
|
5
|
Shafqat A, Khan JA, Alkachem AY, Sabur H, Alkattan K, Yaqinuddin A, Sing GK. How Neutrophils Shape the Immune Response: Reassessing Their Multifaceted Role in Health and Disease. Int J Mol Sci 2023; 24:17583. [PMID: 38139412 PMCID: PMC10744338 DOI: 10.3390/ijms242417583] [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: 11/19/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
Neutrophils are the most abundant of the circulating immune cells and are the first to be recruited to sites of inflammation. Neutrophils are a heterogeneous group of immune cells from which are derived extracellular traps (NETs), reactive oxygen species, cytokines, chemokines, immunomodulatory factors, and alarmins that regulate the recruitment and phenotypes of neutrophils, macrophages, dendritic cells, T cells, and B cells. In addition, cytokine-stimulated neutrophils can express class II major histocompatibility complex and the internal machinery necessary for successful antigen presentation to memory CD4+ T cells. This may be relevant in the context of vaccine memory. Neutrophils thus emerge as orchestrators of immune responses that play a key role in determining the outcome of infections, vaccine efficacy, and chronic diseases like autoimmunity and cancer. This review aims to provide a synthesis of current evidence as regards the role of these functions of neutrophils in homeostasis and disease.
Collapse
Affiliation(s)
- Areez Shafqat
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia (K.A.); (A.Y.); (G.K.S.)
| | | | | | | | | | | | | |
Collapse
|
6
|
Ng JWY, Felix JF, Olson DM. A novel approach to risk exposure and epigenetics-the use of multidimensional context to gain insights into the early origins of cardiometabolic and neurocognitive health. BMC Med 2023; 21:466. [PMID: 38012757 PMCID: PMC10683259 DOI: 10.1186/s12916-023-03168-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 11/09/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Each mother-child dyad represents a unique combination of genetic and environmental factors. This constellation of variables impacts the expression of countless genes. Numerous studies have uncovered changes in DNA methylation (DNAm), a form of epigenetic regulation, in offspring related to maternal risk factors. How these changes work together to link maternal-child risks to childhood cardiometabolic and neurocognitive traits remains unknown. This question is a key research priority as such traits predispose to future non-communicable diseases (NCDs). We propose viewing risk and the genome through a multidimensional lens to identify common DNAm patterns shared among diverse risk profiles. METHODS We identified multifactorial Maternal Risk Profiles (MRPs) generated from population-based data (n = 15,454, Avon Longitudinal Study of Parents and Children (ALSPAC)). Using cord blood HumanMethylation450 BeadChip data, we identified genome-wide patterns of DNAm that co-vary with these MRPs. We tested the prospective relation of these DNAm patterns (n = 914) to future outcomes using decision tree analysis. We then tested the reproducibility of these patterns in (1) DNAm data at age 7 and 17 years within the same cohort (n = 973 and 974, respectively) and (2) cord DNAm in an independent cohort, the Generation R Study (n = 686). RESULTS We identified twenty MRP-related DNAm patterns at birth in ALSPAC. Four were prospectively related to cardiometabolic and/or neurocognitive childhood outcomes. These patterns were replicated in DNAm data from blood collected at later ages. Three of these patterns were externally validated in cord DNAm data in Generation R. Compared to previous literature, DNAm patterns exhibited novel spatial distribution across the genome that intersects with chromatin functional and tissue-specific signatures. CONCLUSIONS To our knowledge, we are the first to leverage multifactorial population-wide data to detect patterns of variability in DNAm. This context-based approach decreases biases stemming from overreliance on specific samples or variables. We discovered molecular patterns demonstrating prospective and replicable relations to complex traits. Moreover, results suggest that patterns harbour a genome-wide organisation specific to chromatin regulation and target tissues. These preliminary findings warrant further investigation to better reflect the reality of human context in molecular studies of NCDs.
Collapse
Affiliation(s)
- Jane W Y Ng
- Department of Pediatrics, Cummings School of Medicine, University of Calgary, 28 Oki Drive NW, Calgary, AB, T3B 6A8, Canada
| | - Janine F Felix
- The Generation F Study Group, Erasmus MC University Medical Center Rotterdam, Postbus, 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - David M Olson
- Departments of Obstetrics and Gynecology, Physiology, and Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, 220 HMRC, Edmonton, AB, T6G2S2, Canada.
| |
Collapse
|
7
|
Magoulopoulou A, Salas SM, Tiklová K, Samuelsson ER, Hilscher MM, Nilsson M. Padlock Probe-Based Targeted In Situ Sequencing: Overview of Methods and Applications. Annu Rev Genomics Hum Genet 2023; 24:133-150. [PMID: 37018847 DOI: 10.1146/annurev-genom-102722-092013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Elucidating spatiotemporal changes in gene expression has been an essential goal in studies of health, development, and disease. In the emerging field of spatially resolved transcriptomics, gene expression profiles are acquired with the tissue architecture maintained, sometimes at cellular resolution. This has allowed for the development of spatial cell atlases, studies of cell-cell interactions, and in situ cell typing. In this review, we focus on padlock probe-based in situ sequencing, which is a targeted spatially resolved transcriptomic method. We summarize recent methodological and computational tool developments and discuss key applications. We also discuss compatibility with other methods and integration with multiomic platforms for future applications.
Collapse
Affiliation(s)
- Anastasia Magoulopoulou
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden; , , , , ,
| | - Sergio Marco Salas
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden; , , , , ,
| | - Katarína Tiklová
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden; , , , , ,
| | - Erik Reinhold Samuelsson
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden; , , , , ,
| | - Markus M Hilscher
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden; , , , , ,
| | - Mats Nilsson
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden; , , , , ,
| |
Collapse
|
8
|
Conley HE, Sheats MK. Targeting Neutrophil β 2-Integrins: A Review of Relevant Resources, Tools, and Methods. Biomolecules 2023; 13:892. [PMID: 37371473 DOI: 10.3390/biom13060892] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/15/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Neutrophils are important innate immune cells that respond during inflammation and infection. These migratory cells utilize β2-integrin cell surface receptors to move out of the vasculature into inflamed tissues and to perform various anti-inflammatory responses. Although critical for fighting off infection, neutrophil responses can also become dysregulated and contribute to disease pathophysiology. In order to limit neutrophil-mediated damage, investigators have focused on β2-integrins as potential therapeutic targets, but so far these strategies have failed in clinical trials. As the field continues to move forward, a better understanding of β2-integrin function and signaling will aid the design of future therapeutics. Here, we provide a detailed review of resources, tools, experimental methods, and in vivo models that have been and will continue to be utilized to investigate the vitally important cell surface receptors, neutrophil β2-integrins.
Collapse
Affiliation(s)
- Haleigh E Conley
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27607, USA
| | - M Katie Sheats
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27607, USA
| |
Collapse
|
9
|
Herrera-Uribe J, Lim KS, Byrne KA, Daharsh L, Liu H, Corbett RJ, Marco G, Schroyen M, Koltes JE, Loving CL, Tuggle CK. Integrative profiling of gene expression and chromatin accessibility elucidates specific transcriptional networks in porcine neutrophils. Front Genet 2023; 14:1107462. [PMID: 37287538 PMCID: PMC10242145 DOI: 10.3389/fgene.2023.1107462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 04/27/2023] [Indexed: 06/09/2023] Open
Abstract
Neutrophils are vital components of the immune system for limiting the invasion and proliferation of pathogens in the body. Surprisingly, the functional annotation of porcine neutrophils is still limited. The transcriptomic and epigenetic assessment of porcine neutrophils from healthy pigs was performed by bulk RNA sequencing and transposase accessible chromatin sequencing (ATAC-seq). First, we sequenced and compared the transcriptome of porcine neutrophils with eight other immune cell transcriptomes to identify a neutrophil-enriched gene list within a detected neutrophil co-expression module. Second, we used ATAC-seq analysis to report for the first time the genome-wide chromatin accessible regions of porcine neutrophils. A combined analysis using both transcriptomic and chromatin accessibility data further defined the neutrophil co-expression network controlled by transcription factors likely important for neutrophil lineage commitment and function. We identified chromatin accessible regions around promoters of neutrophil-specific genes that were predicted to be bound by neutrophil-specific transcription factors. Additionally, published DNA methylation data from porcine immune cells including neutrophils were used to link low DNA methylation patterns to accessible chromatin regions and genes with highly enriched expression in porcine neutrophils. In summary, our data provides the first integrative analysis of the accessible chromatin regions and transcriptional status of porcine neutrophils, contributing to the Functional Annotation of Animal Genomes (FAANG) project, and demonstrates the utility of chromatin accessible regions to identify and enrich our understanding of transcriptional networks in a cell type such as neutrophils.
Collapse
Affiliation(s)
- Juber Herrera-Uribe
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Kyu-Sang Lim
- Department of Animal Science, Iowa State University, Ames, IA, United States
- Department of Animal Resource Science, Kongju National University, Yesan, Republic of Korea
| | - Kristen A. Byrne
- USDA-Agriculture Research Service, National Animal Disease Center, Food Safety and Enteric Pathogens Research Unit, Ames, IA, United States
| | - Lance Daharsh
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Haibo Liu
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Ryan J. Corbett
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Gianna Marco
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Martine Schroyen
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - James E. Koltes
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Crystal L. Loving
- USDA-Agriculture Research Service, National Animal Disease Center, Food Safety and Enteric Pathogens Research Unit, Ames, IA, United States
| | | |
Collapse
|
10
|
Powell J, Talenti A, Fisch A, Hemmink JD, Paxton E, Toye P, Santos I, Ferreira BR, Connelley TK, Morrison LJ, Prendergast JGD. Profiling the immune epigenome across global cattle breeds. Genome Biol 2023; 24:127. [PMID: 37218021 DOI: 10.1186/s13059-023-02964-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 05/08/2023] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Understanding the variation between well and poorly adapted cattle breeds to local environments and pathogens is essential for breeding cattle with improved climate and disease-resistant phenotypes. Although considerable progress has been made towards identifying genetic differences between breeds, variation at the epigenetic and chromatin levels remains poorly characterized. Here, we generate, sequence and analyse over 150 libraries at base-pair resolution to explore the dynamics of DNA methylation and chromatin accessibility of the bovine immune system across three distinct cattle lineages. RESULTS We find extensive epigenetic divergence between the taurine and indicine cattle breeds across immune cell types, which is linked to the levels of local DNA sequence divergence between the two cattle sub-species. The unique cell type profiles enable the deconvolution of complex cellular mixtures using digital cytometry approaches. Finally, we show distinct sub-categories of CpG islands based on their chromatin and methylation profiles that discriminate between classes of distal and gene proximal islands linked to discrete transcriptional states. CONCLUSIONS Our study provides a comprehensive resource of DNA methylation, chromatin accessibility and RNA expression profiles of three diverse cattle populations. The findings have important implications, from understanding how genetic editing across breeds, and consequently regulatory backgrounds, may have distinct impacts to designing effective cattle epigenome-wide association studies in non-European breeds.
Collapse
Affiliation(s)
- Jessica Powell
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK.
| | - Andrea Talenti
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK
| | - Andressa Fisch
- Ribeirão Preto College of Nursing, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Johanneke D Hemmink
- Centre for Tropical Livestock Genetics and Health, Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK
- The International Livestock Research Institute, PO Box 30709, Nairobi, 00100, Kenya
| | - Edith Paxton
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK
| | - Philip Toye
- The International Livestock Research Institute, PO Box 30709, Nairobi, 00100, Kenya
- Centre for Tropical Livestock Genetics and Health, ILRI Kenya, PO Box 30709, Nairobi, 00100, Kenya
| | - Isabel Santos
- Ribeirão Preto College of Nursing, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Beatriz R Ferreira
- Ribeirão Preto College of Nursing, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Tim K Connelley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK
- Centre for Tropical Livestock Genetics and Health, Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK
| | - Liam J Morrison
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK.
- Centre for Tropical Livestock Genetics and Health, Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK.
| | - James G D Prendergast
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK.
- Centre for Tropical Livestock Genetics and Health, Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK.
| |
Collapse
|
11
|
Palomino-Segura M, Sicilia J, Ballesteros I, Hidalgo A. Strategies of neutrophil diversification. Nat Immunol 2023; 24:575-584. [PMID: 36959290 PMCID: PMC10139675 DOI: 10.1038/s41590-023-01452-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/03/2023] [Indexed: 03/25/2023]
Abstract
Neutrophils are formidable defenders. Their vast numbers, constant production, high cytotoxicity and capacity to produce extracellular traps, underlie their ability to efficiently protect in a microorganism-rich world. However, neutrophils are much more than immune sentinels, as evidenced by the expanding repertoire of functions discovered in the context of tissue homeostasis, regeneration or chronic pathologies. In this Perspective, we discuss general functional features of the neutrophil compartment that may be relevant in most, if not all, physiological scenarios in which they participate, including specialization in naïve tissues, transcriptional noise in the bloodstream as a potential strategy for diversification and functional bias in inflammatory sites. We intentionally present the reader with more questions than answers and propose models and approaches that we hope will shed new light onto the biology of these fascinating cells and spark new directions of research.
Collapse
Affiliation(s)
- Miguel Palomino-Segura
- Area of Cell & Developmental Biology, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain.
- Immunophysiology Research Group, Instituto Universitario de Investigación Biosanitaria de Extremadura (INUBE) and Department of Physiology, Faculty of Sciences, University of Extremadura, Badajoz, Spain.
| | - Jon Sicilia
- Area of Cell & Developmental Biology, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - Iván Ballesteros
- Area of Cell & Developmental Biology, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - Andrés Hidalgo
- Area of Cell & Developmental Biology, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain.
- Vascular Biology and Therapeutics Program and Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
| |
Collapse
|
12
|
Komal S, Han SN, Cui LG, Zhai MM, Zhou YJ, Wang P, Shakeel M, Zhang LR. Epigenetic Regulation of Macrophage Polarization in Cardiovascular Diseases. Pharmaceuticals (Basel) 2023; 16:141. [PMID: 37259293 PMCID: PMC9963081 DOI: 10.3390/ph16020141] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 08/17/2023] Open
Abstract
Cardiovascular diseases (CVDs) are the leading cause of hospitalization and death worldwide, especially in developing countries. The increased prevalence rate and mortality due to CVDs, despite the development of several approaches for prevention and treatment, are alarming trends in global health. Chronic inflammation and macrophage infiltration are key regulators of the initiation and progression of CVDs. Recent data suggest that epigenetic modifications, such as DNA methylation, posttranslational histone modifications, and RNA modifications, regulate cell development, DNA damage repair, apoptosis, immunity, calcium signaling, and aging in cardiomyocytes; and are involved in macrophage polarization and contribute significantly to cardiac disease development. Cardiac macrophages not only trigger damaging inflammatory responses during atherosclerotic plaque formation, myocardial injury, and heart failure but are also involved in tissue repair, remodeling, and regeneration. In this review, we summarize the key epigenetic modifications that influence macrophage polarization and contribute to the pathophysiology of CVDs, and highlight their potential for the development of advanced epigenetic therapies.
Collapse
Affiliation(s)
- Sumra Komal
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Sheng-Na Han
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Liu-Gen Cui
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Miao-Miao Zhai
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yue-Jiao Zhou
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Pei Wang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Muhammad Shakeel
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Li-Rong Zhang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| |
Collapse
|
13
|
Xie M, Hao Y, Feng L, Wang T, Yao M, Li H, Ma D, Feng J. Neutrophil Heterogeneity and its Roles in the Inflammatory Network after Ischemic Stroke. Curr Neuropharmacol 2023; 21:621-650. [PMID: 35794770 PMCID: PMC10207908 DOI: 10.2174/1570159x20666220706115957] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/19/2022] [Accepted: 06/13/2022] [Indexed: 11/22/2022] Open
Abstract
As the first peripheral immune cells to enter the brain after ischemic stroke, neutrophils are important participants in stroke-related neuroinflammation. Neutrophils are quickly mobilized from the periphery in response to a stroke episode and cross the blood-brain barrier to reach the ischemic brain parenchyma. This process involves the mobilization and activation of neutrophils from peripheral immune organs (including the bone marrow and spleen), their chemotaxis in the peripheral blood, and their infiltration into the brain parenchyma (including disruption of the blood-brain barrier, inflammatory effects on brain tissue, and interactions with other immune cell types). In the past, it was believed that neutrophils aggravated brain injuries through the massive release of proteases, reactive oxygen species, pro-inflammatory factors, and extracellular structures known as neutrophil extracellular traps (NETs). With the failure of early clinical trials targeting neutrophils and uncovering their underlying heterogeneity, our view of their role in ischemic stroke has become more complex and multifaceted. As neutrophils can be divided into N1 and N2 phenotypes in tumors, neutrophils have also been found to have similar phenotypes after ischemic stroke, and play different roles in the development and prognosis of ischemic stroke. N1 neutrophils are dominant during the acute phase of stroke (within three days) and are responsible for the damage to neural structures via the aforementioned mechanisms. However, the proportion of N2 neutrophils gradually increases in later phases, and this has a beneficial effect through the release of anti-inflammatory factors and other neuroprotective mediators. Moreover, the N1 and N2 phenotypes are highly plastic and can be transformed into each other under certain conditions. The pronounced differences in their function and their high degree of plasticity make these neutrophil subpopulations promising targets for the treatment of ischemic stroke.
Collapse
Affiliation(s)
- Meizhen Xie
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Xinmin, Changchun, Jilin Province 130021, China
| | - Yulei Hao
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Xinmin, Changchun, Jilin Province 130021, China
| | - Liangshu Feng
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Xinmin, Changchun, Jilin Province 130021, China
| | - Tian Wang
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Xinmin, Changchun, Jilin Province 130021, China
| | - Mengyue Yao
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Xinmin, Changchun, Jilin Province 130021, China
| | - Hui Li
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Xinmin, Changchun, Jilin Province 130021, China
| | - Di Ma
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Xinmin, Changchun, Jilin Province 130021, China
| | - Jiachun Feng
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Xinmin, Changchun, Jilin Province 130021, China
| |
Collapse
|
14
|
Saddiki H, Colicino E, Lesseur C. Assessing Differential Variability of High-Throughput DNA Methylation Data. Curr Environ Health Rep 2022; 9:625-630. [PMID: 36040576 DOI: 10.1007/s40572-022-00374-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2022] [Indexed: 01/31/2023]
Abstract
PURPOSE OF REVIEW DNA methylation (DNAm) is essential to human development and plays an important role as a biomarker due to its susceptibility to environmental exposures. This article reviews the current state of statistical methods developed for differential variability analysis focusing on DNAm data. RECENT FINDINGS With the advent of high-throughput technologies allowing for highly reliable and cost-effective measurements of DNAm, many epigenome studies have analyzed DNAm levels to uncover biological mechanisms underlying past environmental exposures and subsequent health outcomes. These studies typically focused on detecting sites or regions which differ in their mean DNAm levels among exposure groups. However, more recent studies highlighted the importance of identifying differentially variable sites or regions as biologically relevant features. Currently, the analysis of differentially variable DNAm sites has not yet gained widespread adoption in environmental studies; yet, it is important to examine the effects of environmental exposures on inter-individual epigenetic variability. In this article, we describe six of the most widely used statistical approaches for analyzing differential variability of DNAm levels and provide a discussion of their advantages and current limitations.
Collapse
Affiliation(s)
- Hachem Saddiki
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elena Colicino
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Corina Lesseur
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| |
Collapse
|
15
|
Gudgeon J, Marín-Rubio JL, Trost M. The role of macrophage scavenger receptor 1 (MSR1) in inflammatory disorders and cancer. Front Immunol 2022; 13:1012002. [PMID: 36325338 PMCID: PMC9618966 DOI: 10.3389/fimmu.2022.1012002] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/28/2022] [Indexed: 08/27/2023] Open
Abstract
Macrophage scavenger receptor 1 (MSR1), also named CD204, holds key inflammatory roles in multiple pathophysiologic processes. Present primarily on the surface of various types of macrophage, this receptor variably affects processes such as atherosclerosis, innate and adaptive immunity, lung and liver disease, and more recently, cancer. As highlighted throughout this review, the role of MSR1 is often dichotomous, being either host protective or detrimental to the pathogenesis of disease. We will discuss the role of MSR1 in health and disease with a focus on the molecular mechanisms influencing MSR1 expression, how altered expression affects disease process and macrophage function, the limited cell signalling pathways discovered thus far, the emerging role of MSR1 in tumour associated macrophages as well as the therapeutic potential of targeting MSR1.
Collapse
Affiliation(s)
| | - José Luis Marín-Rubio
- Laboratory for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Matthias Trost
- Laboratory for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| |
Collapse
|
16
|
Predicting Immunotherapy Outcomes in Older Patients with Solid Tumors Using the LIPI Score. Cancers (Basel) 2022; 14:cancers14205078. [PMID: 36291861 PMCID: PMC9600023 DOI: 10.3390/cancers14205078] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/21/2022] [Accepted: 10/07/2022] [Indexed: 11/21/2022] Open
Abstract
Immunotherapy with immune checkpoint blockers (ICB) represents a valid therapeutic option in older patients for several solid cancer types. However, most of the data concerning efficacy and adverse events of ICB available are derived from younger and fitter patients. Reliable biomarkers are needed to better select the population that will benefit from ICB especially in older patients who may be at a higher risk of developing immune-related adverse events (irAEs) with a greater impact on their quality of life. The Lung Immune Prognostic Index (LIPI) is a score that combines pretreatment dNLR (neutrophils/[leukocytes − neutrophils]) and lactate dehydrogenase (LDH) and is correlated with outcomes in patients treated with ICB in non-small-cell lung cancer. We aimed to assess the impact of LIPI in ICB outcomes in a dedicated cohort of older patients. The primary objective was to study the prognostic role of LIPI score in patients aged 70 years or above in a real-life population treated with anti-programmed death-(ligand)1 (anti PD-(L)1). dNLR and LDH were collected in a prospective cohort of patients aged 70 years or above treated with PD-(L)1 inhibitors with metastatic disease between June 2014 and October 2017 at Gustave Roussy. LIPI categorizes the population into three different prognostic groups: good (dNLR ≤ 3 and LDH ≤ ULN—upper normal limit), intermediate (dNLR > 3 or LDH > ULN), and poor (dNLR > 3 and LDH > ULN). Anti PD-(L)1 benefit was analyzed according to overall survival (OS), progression free survival (PFS), and overall response rate (ORR) using RECIST v1.1. criteria. In the 191 older patients treated, most of them (95%) were ICB-naïve, and 160 (84%) had an ECOG performance status of 0−1 with a median age at ICB treatment of 77 (range, 70−93). The most common tumor types were melanoma (66%) and non-small-cell lung cancer (15%). The median follow-up duration was 18.8 months (95% CI 14.7−24.2). LIPI classified the population into three different groups: 38 (23%) patients had a good LIPI score, 84 (51%) had an intermediate LIPI score, and 43 (26%) had a poor LIPI score. The median OS was 20.7 months [95% CI, 12.6−not reached] compared to 11.2 months [95% CI, 8.41−22.2] and 4.7 months [95% CI, 2.2−11.3] in patients with a good, intermediate, and poor LIPI score, respectively (p = 0.0003). The median PFS was 9.2 months [95% CI, 6.2−18.1] in the good LIPI group, 7.2 months [95% CI, 5.4−13] in the intermediate LIPI group, and 3.9 months [95% CI, 2.3−8.2] in the poor LIPI group (p = 0.09). The rate of early death (OS < 3 months) was 37% in the poor LIPI group compared to 5% in the good LIPI group (<0.001). Poor LIPI score was associated with a poorer outcome in older patients treated with anti PD-(L)1. LIPI is a simple and accessible worldwide tool that can serve as a prognostic factor and can be useful for stratification benefit from ICB.
Collapse
|
17
|
Wiencke JK, Molinaro AM, Warrier G, Rice T, Clarke J, Taylor JW, Wrensch M, Hansen H, McCoy L, Tang E, Tamaki SJ, Tamaki CM, Nissen E, Bracci P, Salas LA, Koestler DC, Christensen BC, Zhang Z, Kelsey KT. DNA methylation as a pharmacodynamic marker of glucocorticoid response and glioma survival. Nat Commun 2022; 13:5505. [PMID: 36127421 PMCID: PMC9486797 DOI: 10.1038/s41467-022-33215-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/08/2022] [Indexed: 12/15/2022] Open
Abstract
Assessing individual responses to glucocorticoid drug therapies that compromise immune status and affect survival outcomes in neuro-oncology is a great challenge. Here we introduce a blood-based neutrophil dexamethasone methylation index (NDMI) that provides a measure of the epigenetic response of subjects to dexamethasone. This marker outperforms conventional approaches based on leukocyte composition as a marker of glucocorticoid response. The NDMI is associated with low CD4 T cells and the accumulation of monocytic myeloid-derived suppressor cells and also serves as prognostic factor in glioma survival. In a non-glioma population, the NDMI increases with a history of prednisone use. Therefore, it may also be informative in other conditions where glucocorticoids are employed. We conclude that DNA methylation remodeling within the peripheral immune compartment is a rich source of clinically relevant markers of glucocorticoid response.
Collapse
Affiliation(s)
- J K Wiencke
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.
| | - Annette M Molinaro
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Gayathri Warrier
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Terri Rice
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Jennifer Clarke
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Jennie W Taylor
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Margaret Wrensch
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Helen Hansen
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Lucie McCoy
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Emily Tang
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Stan J Tamaki
- Parnassus Flow Cytometry CoLab, University of California San Francisco, San Francisco, CA, USA
| | - Courtney M Tamaki
- Parnassus Flow Cytometry CoLab, University of California San Francisco, San Francisco, CA, USA
| | - Emily Nissen
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, USA
| | - Paige Bracci
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA
| | - Devin C Koestler
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA
- Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA
- Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA
| | - Ze Zhang
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, Providence, RI, USA
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| |
Collapse
|
18
|
Qin Y, Livingston DH, Spolarics Z. INTERACTIONS BETWEEN BIOLOGICAL SEX AND THE X-LINKED VARIANT IRAK1 HAPLOTYPE IN MODULATING CLINICAL OUTCOME AND CELLULAR PHENOTYPES AFTER TRAUMA. Shock 2022; 58:179-188. [PMID: 35953456 DOI: 10.1097/shk.0000000000001966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
ABSTRACT Sex-related outcome differences in trauma remain controversial. The mechanisms causing sex-biased outcomes are likely to have hormonal and genetic components, in which X-linked genetic polymorphisms may play distinct roles because of X-linked inheritance, hemizygosity in males, and X chromosome mosaicism in females. The study aimed to elucidate the contribution of biological sex and the common X-linked IRAK1 haplotype to posttrauma clinical complications, inflammatory cytokine and chemokine production, and polymorphonuclear cell and monocyte activation. Postinjury clinical outcome was tested in 1507 trauma patients (1,110 males, 397 females) after stratification by sex or the variant IRAK1 haplotype. Males showed a three- to fivefold greater frequency of posttrauma sepsis, but similar mortality compared to females. Stratification by the variant IRAK1 haplotype revealed increased pneumonia and urinary tract infection in Wild type (WT) versus variant IRAK1 males, whereas increased respiratory failures in variant versus WT females. Cytokine/chemokine profiles were tested in whole blood from a subset of patients (n = 81) and healthy controls (n = 51), which indicated sex-related differences in ex vivo lipopolysaccharide responsiveness manifesting in a 1.5- to 2-fold increased production rate of tumor necrosis factor α, interleukin-1β (IL-1β), IL-10, Macrophage Inflammatory Protein-1 Alpha, and MIP1β in WT male compared to WT female trauma patients. Variant IRAK1 decreased IL-6, IL-8, and interferon gamma-induced protein 10 production in male trauma subjects compared to WT, whereas cytokine/chemokine responses were similar in variant IRAK1 and WT female trauma subjects. Trauma-induced and lipopolysaccharide-stimulated polymorphonuclear cell and monocyte activation determined by using a set of cluster of differentiation markers and flow cytometry were not influenced by sex or variant IRAK1. These findings suggest that variant IRAK1 is a potential contributor to sex-based outcome differences, but its immunomodulatory impacts are modulated by biological sex.
Collapse
Affiliation(s)
- Yong Qin
- Department of Surgery, Rutgers-New Jersey Medical School, Newark, New Jersey
| | | | | |
Collapse
|
19
|
Morinaga T, Iwatsuki M, Yamashita K, Matsumoto C, Harada K, Kurashige J, Iwagami S, Baba Y, Yoshida N, Komohara Y, Baba H. Evaluation of HLA-E Expression Combined with Natural Killer Cell Status as a Prognostic Factor for Advanced Gastric Cancer. Ann Surg Oncol 2022; 29:4951-4960. [PMID: 35412205 DOI: 10.1245/s10434-022-11665-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 03/07/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND The NKG2A/HLA-E pathway functions as an immune checkpoint with potential for inhibition using therapeutic antibodies. Through this pathway, immune cells lose activity, which allows cancers to progress. We aimed to determine whether HLA-E expression combined with NK cell status serves as a prognostic biomarker for gastric cancer (GC). METHODS We enrolled patients (n = 232) with advanced GC who underwent curative gastrectomy. Immunohistochemical analyses of global HLA-E expression, and the expression of CD56 and CD3 to identify NK cells were performed. Survival analysis was performed to evaluate the significance of HLA-E expression and NK status. RESULTS Patients with HLA-E-positive was 104 (41.3%) and had significantly worse prognosis of relapse-free survival (RFS) compared with those with HLA-E-negative. Moreover, patients with NK Low status had worse prognoses for RFS compared with those with NK High status. Statistical analysis of RFS demonstrated that HLA-E expression was a significant independent factor for poor prognosis (HR 1.57, 95% CI 1.04-2.36, P = 0.031). Furthermore, HLA-E-positive patients with low NK low status experienced the shortest RFS, particularly those in the upper GC group. CONCLUSIONS HLA-E served as a prognostic factor after curative resection of GC, and HLA-E expression combined with NK status served as a sensitive prognostic biomarker for advanced GC.
Collapse
Affiliation(s)
- Takeshi Morinaga
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Masaaki Iwatsuki
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan.
| | - Kohei Yamashita
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Chihiro Matsumoto
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Kazuto Harada
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Junji Kurashige
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Shiro Iwagami
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yoshifumi Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Naoya Yoshida
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yoshihiro Komohara
- Department of Cell Pathology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Hideo Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| |
Collapse
|
20
|
Breeze CE. Cell Type-Specific Signal Analysis in Epigenome-Wide Association Studies. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2432:57-71. [PMID: 35505207 DOI: 10.1007/978-1-0716-1994-0_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Hundreds of epigenome-wide association studies (EWAS) have been performed, successfully identifying replicated epigenomic signals in processes such as aging and smoking. Despite this progress, it remains a major challenge in EWAS to detect both cell type-specific and cell type confounding effects impacting study results. One way to identify these effects is through eFORGE (experimentally derived Functional element Overlap analysis of ReGions from EWAS), a published tool that uses 815 datasets from large-scale mapping studies to detect enriched tissues, cell types, and genomic regions. Here, I show that eFORGE analysis can be extended to EWAS differentially variable positions (DVPs), identifying target cell types and tissues. In addition, I also show that eFORGE tissue-specific enrichment can be detected for sites below EWAS significance threshold. I develop on these and other analysis examples, extending our knowledge of eFORGE cell type- and tissue-specific enrichment results for different EWAS.
Collapse
Affiliation(s)
- Charles E Breeze
- Altius Institute for Biomedical Sciences, Seattle, WA, USA.
- UCL Cancer Institute, University College London, London, UK.
| |
Collapse
|
21
|
Coxiella burnetii Virulent Phase I and avirulent Phase II Variants Differentially Manipulate Autophagy pathway in Neutrophils. Infect Immun 2022; 90:e0053421. [PMID: 35100012 DOI: 10.1128/iai.00534-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Coxiella burnetii is an obligate intracellular gram-negative bacterium that causes Q fever in humans. Virulent C. burnetii Nine Mile Phase I (NMI) strain causes disease in animal models, while avirulent NM phase II (NMII) strain does not. In this study, we found that NMI infection induces severe splenomegaly and bacterial burden in the spleen in BALB/c mice, while NMII infection does not. Compared to NMII-infected mice, a significantly higher number of CD11b+Ly6g+ neutrophils accumulated in the liver, lung and spleen of NMI-infected mice. Thus, neutrophil accumulation correlates with NMI and NMII infection induced inflammatory response. In vitro studies also demonstrated that although NMII exhibited a higher infection rate than NMI in mouse bone-marrow neutrophils (BMNs), NMI-infected BMNs survive longer than NMII-infected BMNs. These results suggest that the differential interactions of NMI and NMII with neutrophils may be related to their ability to cause disease in animals. To understand the molecular mechanism underlying the differential interactions of NMI and NMII with neutrophils, the global transcriptomic gene expressions were compared between NMI- and NMII-infected-BMNs by RNA-seq analysis. Interestingly, several genes involved in autophagy related pathways, particularly the membrane-trafficking and lipid metabolism are upregulated in NMII-infected BMNs but downregulated in NMI-infected BMNs. Immunofluorescence and immunoblot analysis indicate that compared to NMI-infected BMNs, vacuoles in NMII-infected-BMNs exhibit increased autophagic flux along with phosphatidylserine translocation in cell membrane. Similar to neutrophils, NMII activated LC3-mediated autophagy in human macrophage. These findings suggest that NMI and NMII's differential manipulation of autophagy may relate to their pathogenesis.
Collapse
|
22
|
Pancaldi V. Chromatin Network Analyses: Towards Structure-Function Relationships in Epigenomics. FRONTIERS IN BIOINFORMATICS 2021; 1:742216. [PMID: 36303769 PMCID: PMC9581029 DOI: 10.3389/fbinf.2021.742216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/04/2021] [Indexed: 01/16/2023] Open
Abstract
Recent technological advances have allowed us to map chromatin conformation and uncover the genome’s spatial organization of the genome inside the nucleus. These experiments have revealed the complexities of genome folding, characterized by the presence of loops and domains at different scales, which can change across development and in different cell types. There is strong evidence for a relationship between the topological properties of chromatin contacts and cellular phenotype. Chromatin can be represented as a network, in which genomic fragments are the nodes and connections represent experimentally observed spatial proximity of two genomically distant regions in a specific cell type or biological condition. With this approach we can consider a variety of chromatin features in association with the 3D structure, investigating how nuclear chromatin organization can be related to gene regulation, replication, malignancy, phenotypic variability and plasticity. We briefly review the results obtained on genome architecture through network theoretic approaches. As previously observed in protein-protein interaction networks and many types of non-biological networks, external conditions could shape network topology through a yet unidentified structure-function relationship. Similar to scientists studying the brain, we are confronted with a duality between a spatially embedded network of physical contacts, a related network of correlation in the dynamics of network nodes and, finally, an abstract definition of function of this network, related to phenotype. We summarise major developments in the study of networks in other fields, which we think can suggest a path towards better understanding how 3D genome configuration can impact biological function and adaptation to the environment.
Collapse
Affiliation(s)
- Vera Pancaldi
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (Inserm) U1037, Centre National de la Recherche Scientifique (CNRS) U5071, Université Paul Sabatier, Toulouse, France
- Barcelona Supercomputing Center, Barcelona, Spain
- *Correspondence: Vera Pancaldi,
| |
Collapse
|
23
|
Costello KR, Leung A, Trac C, Lee M, Basam M, Pospisilik JA, Schones DE. Sequence features of retrotransposons allow for epigenetic variability. eLife 2021; 10:71104. [PMID: 34668484 PMCID: PMC8555987 DOI: 10.7554/elife.71104] [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: 06/09/2021] [Accepted: 10/20/2021] [Indexed: 12/12/2022] Open
Abstract
Transposable elements (TEs) are mobile genetic elements that make up a large fraction of mammalian genomes. While select TEs have been co-opted in host genomes to have function, the majority of these elements are epigenetically silenced by DNA methylation in somatic cells. However, some TEs in mice, including the Intracisternal A-particle (IAP) subfamily of retrotransposons, have been shown to display interindividual variation in DNA methylation. Recent work has revealed that IAP sequence differences and strain-specific KRAB zinc finger proteins (KZFPs) may influence the methylation state of these IAPs. However, the mechanisms underlying the establishment and maintenance of interindividual variability in DNA methylation still remain unclear. Here, we report that sequence content and genomic context influence the likelihood that IAPs become variably methylated. IAPs that differ from consensus IAP sequences have altered KZFP recruitment that can lead to decreased KAP1 recruitment when in proximity of constitutively expressed genes. These variably methylated loci have a high CpG density, similar to CpG islands, and can be bound by ZF-CxxC proteins, providing a potential mechanism to maintain this permissive chromatin environment and protect from DNA methylation. These observations indicate that variably methylated IAPs escape silencing through both attenuation of KZFP binding and recognition by ZF-CxxC proteins to maintain a hypomethylated state.
Collapse
Affiliation(s)
- Kevin R Costello
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, Duarte, United States.,Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, United States
| | - Amy Leung
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, Duarte, United States
| | - Candi Trac
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, Duarte, United States
| | - Michael Lee
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, Duarte, United States.,Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, United States
| | - Mudaser Basam
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, Duarte, United States
| | | | - Dustin E Schones
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, Duarte, United States.,Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, United States
| |
Collapse
|
24
|
Current Understanding of the Neutrophil Transcriptome in Health and Disease. Cells 2021; 10:cells10092406. [PMID: 34572056 PMCID: PMC8469435 DOI: 10.3390/cells10092406] [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: 07/09/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 12/23/2022] Open
Abstract
Neutrophils are key cells of the innate immune system. It is now understood that this leukocyte population is diverse in both the basal composition and functional plasticity. Underlying this plasticity is a post-translational framework for rapidly achieving early activation states, but also a transcriptional capacity that is becoming increasingly recognized by immunologists. Growing interest in the contribution of neutrophils to health and disease has resulted in more efforts to describe their transcriptional activity. Whilst initial efforts focused predominantly on understanding the existing biology, investigations with advanced methods such as single cell RNA sequencing to understand interactions of the entire immune system are revealing higher flexibility in neutrophil transcription than previously thought possible and multiple transition states. It is now apparent that neutrophils utilise many forms of RNA in the regulation of their function. This review collates current knowledge on the nuclei structure and gene expression activity of human neutrophils across homeostasis and disease, before highlighting knowledge gaps that are research priority areas.
Collapse
|
25
|
Chen C, Huang T, Zhai X, Ma Y, Xie L, Lu B, Zhang Y, Li Y, Chen Z, Yin J, Li P. Targeting neutrophils as a novel therapeutic strategy after stroke. J Cereb Blood Flow Metab 2021; 41:2150-2161. [PMID: 33691513 PMCID: PMC8393299 DOI: 10.1177/0271678x211000137] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Stroke is followed by an intricate immune interaction involving the engagement of multiple immune cells, including neutrophils. As one of the first responders recruited to the brain, the crucial roles of neutrophils in the ischemic brain damage are receiving increasing attention in recent years. Notably, neutrophils are not homogenous, and yet there is still a lack of full knowledge about the extent and impact of neutrophil heterogeneity. The biological understanding of the neutrophil response to both innate and pathological conditions is rapidly evolving as single-cell-RNA sequencing uncovers overall neutrophil profiling across maturation and differentiation contexts. In this review, we scrutinize the latest research that points to the multifaceted role of neutrophils in different conditions and summarize the regulatory signals that may determine neutrophil diversity. In addition, we list several potential targets or therapeutic strategies targeting neutrophils to limit brain damage following ischemic stroke.
Collapse
Affiliation(s)
- Chen Chen
- Department of Anesthesiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tingting Huang
- Department of Anesthesiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaozhu Zhai
- Department of Anesthesiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yezhi Ma
- Department of Anesthesiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lv Xie
- Department of Anesthesiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bingwei Lu
- Department of Anesthesiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yueman Zhang
- Department of Anesthesiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Li
- Department of Anesthesiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zengai Chen
- Department of Radiology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiemin Yin
- Department of Anesthesiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Peiying Li
- Department of Anesthesiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
26
|
|
27
|
Silva-Gomes R, Mapelli SN, Boutet MA, Mattiola I, Sironi M, Grizzi F, Colombo F, Supino D, Carnevale S, Pasqualini F, Stravalaci M, Porte R, Gianatti A, Pitzalis C, Locati M, Oliveira MJ, Bottazzi B, Mantovani A. Differential expression and regulation of MS4A family members in myeloid cells in physiological and pathological conditions. J Leukoc Biol 2021; 111:817-836. [PMID: 34346525 PMCID: PMC9290968 DOI: 10.1002/jlb.2a0421-200r] [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] [Indexed: 12/22/2022] Open
Abstract
The MS4A gene family encodes 18 tetraspanin-like proteins, most of which with unknown function. MS4A1 (CD20), MS4A2 (FcεRIβ), MS4A3 (HTm4), and MS4A4A play important roles in immunity, whereas expression and function of other members of the family are unknown. The present investigation was designed to obtain an expression fingerprint of MS4A family members, using bioinformatics analysis of public databases, RT-PCR, and protein analysis when possible. MS4A3, MS4A4A, MS4A4E, MS4A6A, MS4A7, and MS4A14 were expressed by myeloid cells. MS4A6A and MS4A14 were expressed in circulating monocytes and decreased during monocyte-to-Mϕ differentiation in parallel with an increase in MS4A4A expression. Analysis of gene expression regulation revealed a strong induction of MS4A4A, MS4A6A, MS4A7, and MS4A4E by glucocorticoid hormones. Consistently with in vitro findings, MS4A4A and MS4A7 were expressed in tissue Mϕs from COVID-19 and rheumatoid arthritis patients. Interestingly, MS4A3, selectively expressed in myeloid precursors, was found to be a marker of immature circulating neutrophils, a cellular population associated to COVID-19 severe disease. The results reported here show that members of the MS4A family are differentially expressed and regulated during myelomonocytic differentiation, and call for assessment of their functional role and value as therapeutic targets.
Collapse
Affiliation(s)
- Rita Silva-Gomes
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy.,IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy.,ICBAS-Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde and Instituto Nacional de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
| | | | - Marie-Astrid Boutet
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute and Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.,Regenerative Medicine and Skeleton, RMeS, Inserm UMR 1229, Oniris, CHU Nantes, Université de Nantes, Nantes, France
| | - Irene Mattiola
- Laboratory of Innate Immunity, Department of Microbiology, Infectious Diseases and Immunology, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany.,Mucosal and Developmental Immunology, Berlin, Germany
| | - Marina Sironi
- IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Fabio Grizzi
- IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | | | - Domenico Supino
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
| | - Silvia Carnevale
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
| | - Fabio Pasqualini
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
| | | | - Rémi Porte
- IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy.,Infinity, Université Toulouse, CNRS, Inserm, UPS, Toulouse, France
| | - Andrea Gianatti
- Unit of Pathology, Azienda Ospedaliera Socio Sanitaria Territoriale Papa Giovanni XXIII, Bergamo, Italy
| | - Constantino Pitzalis
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute and Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Massimo Locati
- IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy.,Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy
| | - Maria José Oliveira
- ICBAS-Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde and Instituto Nacional de Engenharia Biomédica, Universidade do Porto, Porto, Portugal.,Department of Pathology and Oncology, Faculty of Medicine, University of Porto, Porto, Portugal
| | | | - Alberto Mantovani
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy.,IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy.,Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute and Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| |
Collapse
|
28
|
Turati VA, Guerra-Assunção JA, Potter NE, Gupta R, Ecker S, Daneviciute A, Tarabichi M, Webster AP, Ding C, May G, James C, Brown J, Conde L, Russell LJ, Ancliff P, Inglott S, Cazzaniga G, Biondi A, Hall GW, Lynch M, Hubank M, Macaulay I, Beck S, Van Loo P, Jacobsen SE, Greaves M, Herrero J, Enver T. Chemotherapy induces canalization of cell state in childhood B-cell precursor acute lymphoblastic leukemia. NATURE CANCER 2021; 2:835-852. [PMID: 34734190 PMCID: PMC7611923 DOI: 10.1038/s43018-021-00219-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 05/11/2021] [Indexed: 05/01/2023]
Abstract
Comparison of intratumor genetic heterogeneity in cancer at diagnosis and relapse suggests that chemotherapy induces bottleneck selection of subclonal genotypes. However, evolutionary events subsequent to chemotherapy could also explain changes in clonal dominance seen at relapse. We, therefore, investigated the mechanisms of selection in childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL) during induction chemotherapy where maximal cytoreduction occurs. To distinguish stochastic versus deterministic events, individual leukemias were transplanted into multiple xenografts and chemotherapy administered. Analyses of the immediate post-treatment leukemic residuum at single-cell resolution revealed that chemotherapy has little impact on genetic heterogeneity. Rather, it acts on extensive, previously unappreciated, transcriptional and epigenetic heterogeneity in BCP-ALL, dramatically reducing the spectrum of cell states represented, leaving a genetically polyclonal but phenotypically uniform population with hallmark signatures relating to developmental stage, cell cycle and metabolism. Hence, canalization of cell state accounts for a significant component of bottleneck selection during induction chemotherapy.
Collapse
Affiliation(s)
| | | | | | - Rajeev Gupta
- UCL Cancer Institute, University College London, United Kingdom
| | - Simone Ecker
- UCL Cancer Institute, University College London, United Kingdom
| | | | | | - Amy P. Webster
- UCL Cancer Institute, University College London, United Kingdom
| | - Chuling Ding
- UCL Cancer Institute, University College London, United Kingdom
| | - Gillian May
- UCL Cancer Institute, University College London, United Kingdom
| | - Chela James
- UCL Cancer Institute, University College London, United Kingdom
| | - John Brown
- UCL Cancer Institute, University College London, United Kingdom
| | - Lucia Conde
- UCL Cancer Institute, University College London, United Kingdom
| | - Lisa J. Russell
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, UK
| | - Phil Ancliff
- Great Ormond Street Hospital, London, United Kingdom
| | - Sarah Inglott
- Great Ormond Street Hospital, London, United Kingdom
| | - Giovanni Cazzaniga
- Centro Ricerca M. Tettamanti, University of Milano Bicocca, Monza, Italy
| | - Andrea Biondi
- University of Milano-Bicocca, Department of Pediatrics, Fondazione MBBM/Ospedale San Gerardo, Monza, Italy
| | | | - Mark Lynch
- Fluidigm Corporation, San Francisco, CA, USA
| | - Mike Hubank
- Institute of Cancer Research, Sutton, United Kingdom
- Royal Marsden Hospital, Sutton, United Kingdom
| | | | - Stephan Beck
- UCL Cancer Institute, University College London, United Kingdom
| | | | - Sten E. Jacobsen
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
- Center for Hematology and Regenerative Medicine, Department of Medicine and Department of Cell and Molecular Biology, Karolinska Institutet and Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Mel Greaves
- Institute of Cancer Research, Sutton, United Kingdom
| | - Javier Herrero
- UCL Cancer Institute, University College London, United Kingdom
| | - Tariq Enver
- UCL Cancer Institute, University College London, United Kingdom
| |
Collapse
|
29
|
Farquhar KS, Rasouli Koohi S, Charlebois DA. Does transcriptional heterogeneity facilitate the development of genetic drug resistance? Bioessays 2021; 43:e2100043. [PMID: 34160842 DOI: 10.1002/bies.202100043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/30/2021] [Accepted: 06/07/2021] [Indexed: 12/24/2022]
Abstract
Non-genetic forms of antimicrobial (drug) resistance can result from cell-to-cell variability that is not encoded in the genetic material. Data from recent studies also suggest that non-genetic mechanisms can facilitate the development of genetic drug resistance. We speculate on how the interplay between non-genetic and genetic mechanisms may affect microbial adaptation and evolution during drug treatment. We argue that cellular heterogeneity arising from fluctuations in gene expression, epigenetic modifications, as well as genetic changes contribute to drug resistance at different timescales, and that the interplay between these mechanisms enhance pathogen resistance. Accordingly, developing a better understanding of the role of non-genetic mechanisms in drug resistance and how they interact with genetic mechanisms will enhance our ability to combat antimicrobial resistance. Also see the video abstract here: https://youtu.be/aefGpdh-bgU.
Collapse
Affiliation(s)
| | - Samira Rasouli Koohi
- Department of Physics, University of Alberta, Edmonton, Alberta, T6G-2E1, Canada
| | - Daniel A Charlebois
- Department of Physics, University of Alberta, Edmonton, Alberta, T6G-2E1, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| |
Collapse
|
30
|
Ram-Mohan N, Thair SA, Litzenburger UM, Cogill S, Andini N, Yang X, Chang HY, Yang S. Profiling chromatin accessibility responses in human neutrophils with sensitive pathogen detection. Life Sci Alliance 2021; 4:4/8/e202000976. [PMID: 34145026 PMCID: PMC8321655 DOI: 10.26508/lsa.202000976] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 12/13/2022] Open
Abstract
ATAC-seq reveals unique neutrophil chromatin architecture changes in response to different stimuli before transcriptional activation, possibly regulating downstream gene expression. Sepsis, sequela of bloodstream infections and dysregulated host responses, is a leading cause of death globally. Neutrophils tightly regulate responses to pathogens to prevent organ damage. Profiling early host epigenetic responses in neutrophils may aid in disease recognition. We performed assay for transposase-accessible chromatin (ATAC)-seq of human neutrophils challenged with six toll-like receptor ligands and two organisms; and RNA-seq after Escherichia coli exposure for 1 and 4 h along with ATAC-seq. ATAC-seq of neutrophils facilitates detection of pathogen DNA. In addition, despite similarities in genomic distribution of differential chromatin changes across challenges, only a fraction overlaps between the challenges. Ligands depict shared signatures, but majority are unique in position, function, and challenge. Epigenomic changes are plastic, only ∼120 are shared by E. coli challenges over time, resulting in varied differential genes and associated processes. We identify three classes of gene regulation, chromatin access changes in the promoter; changes in the promoter and distal enhancers; and controlling expression through changes solely in distal enhancers. These and transcription factor footprinting reveal timely and challenge specific mechanisms of transcriptional regulation in neutrophils.
Collapse
Affiliation(s)
- Nikhil Ram-Mohan
- Department of Emergency Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Simone A Thair
- Department of Emergency Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Steven Cogill
- Department of Emergency Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Nadya Andini
- Department of Emergency Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Xi Yang
- Department of Emergency Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Samuel Yang
- Department of Emergency Medicine, Stanford University School of Medicine, Stanford, CA, USA
| |
Collapse
|
31
|
Watt S, Vasquez L, Walter K, Mann AL, Kundu K, Chen L, Sims Y, Ecker S, Burden F, Farrow S, Farr B, Iotchkova V, Elding H, Mead D, Tardaguila M, Ponstingl H, Richardson D, Datta A, Flicek P, Clarke L, Downes K, Pastinen T, Fraser P, Frontini M, Javierre BM, Spivakov M, Soranzo N. Genetic perturbation of PU.1 binding and chromatin looping at neutrophil enhancers associates with autoimmune disease. Nat Commun 2021; 12:2298. [PMID: 33863903 PMCID: PMC8052402 DOI: 10.1038/s41467-021-22548-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 03/17/2021] [Indexed: 02/06/2023] Open
Abstract
Neutrophils play fundamental roles in innate immune response, shape adaptive immunity, and are a potentially causal cell type underpinning genetic associations with immune system traits and diseases. Here, we profile the binding of myeloid master regulator PU.1 in primary neutrophils across nearly a hundred volunteers. We show that variants associated with differential PU.1 binding underlie genetically-driven differences in cell count and susceptibility to autoimmune and inflammatory diseases. We integrate these results with other multi-individual genomic readouts, revealing coordinated effects of PU.1 binding variants on the local chromatin state, enhancer-promoter contacts and downstream gene expression, and providing a functional interpretation for 27 genes underlying immune traits. Collectively, these results demonstrate the functional role of PU.1 and its target enhancers in neutrophil transcriptional control and immune disease susceptibility.
Collapse
Affiliation(s)
- Stephen Watt
- Human Genetics, Wellcome Sanger Institute, Genome Campus, Hinxton, UK
| | - Louella Vasquez
- Human Genetics, Wellcome Sanger Institute, Genome Campus, Hinxton, UK
| | - Klaudia Walter
- Human Genetics, Wellcome Sanger Institute, Genome Campus, Hinxton, UK
| | - Alice L Mann
- Human Genetics, Wellcome Sanger Institute, Genome Campus, Hinxton, UK
| | - Kousik Kundu
- Human Genetics, Wellcome Sanger Institute, Genome Campus, Hinxton, UK
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Lu Chen
- Human Genetics, Wellcome Sanger Institute, Genome Campus, Hinxton, UK
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Laboratory Medicine, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Ying Sims
- Human Genetics, Wellcome Sanger Institute, Genome Campus, Hinxton, UK
| | | | - Frances Burden
- Department of Haematology, University of Cambridge, Cambridge, UK
- National Health Service Blood and Transplant (NHSBT), Cambridge, UK
| | - Samantha Farrow
- Department of Haematology, University of Cambridge, Cambridge, UK
- National Health Service Blood and Transplant (NHSBT), Cambridge, UK
| | - Ben Farr
- Human Genetics, Wellcome Sanger Institute, Genome Campus, Hinxton, UK
| | - Valentina Iotchkova
- Human Genetics, Wellcome Sanger Institute, Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, UK
| | - Heather Elding
- Human Genetics, Wellcome Sanger Institute, Genome Campus, Hinxton, UK
| | - Daniel Mead
- Human Genetics, Wellcome Sanger Institute, Genome Campus, Hinxton, UK
| | - Manuel Tardaguila
- Human Genetics, Wellcome Sanger Institute, Genome Campus, Hinxton, UK
| | - Hannes Ponstingl
- Human Genetics, Wellcome Sanger Institute, Genome Campus, Hinxton, UK
| | - David Richardson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Avik Datta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge, UK
- National Health Service Blood and Transplant (NHSBT), Cambridge, UK
| | - Tomi Pastinen
- Center for Pediatric Genomic Medicine, Children's Mercy, Kansas City, MO, USA
| | - Peter Fraser
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Mattia Frontini
- Department of Haematology, University of Cambridge, Cambridge, UK
- National Health Service Blood and Transplant (NHSBT), Cambridge, UK
- British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge, UK
- Institute of Biomedical & Clinical Science, College of Medicine and Health, University of Exeter Medical School, RILD Building, Exeter, UK
| | - Biola-Maria Javierre
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK.
- Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Spain.
| | - Mikhail Spivakov
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK.
- Functional Gene Control Group, MRC London Institute of Medical Sciences (LMS), London, UK.
- Institute of Clinical Sciences, Imperial College Faculty of Medicine, London, UK.
| | - Nicole Soranzo
- Human Genetics, Wellcome Sanger Institute, Genome Campus, Hinxton, UK.
- School of Clinical Medicine, University of Cambridge, Cambridge, UK.
| |
Collapse
|
32
|
Zeming KK, Lu R, Woo KL, Sun G, Quek KY, Cheow LF, Chen CH, Han J, Lim SL. Multiplexed Single-Cell Leukocyte Enzymatic Secretion Profiling from Whole Blood Reveals Patient-Specific Immune Signature. Anal Chem 2021; 93:4374-4382. [PMID: 33600165 DOI: 10.1021/acs.analchem.0c03512] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enzymatic secretion of immune cells (leukocytes) plays a dominant role in host immune responses to a myriad of biological triggers, including infections, cancers, and cardiovascular diseases. Current tools to probe these leukocytes inadequately profile these vital biomarkers; the need for sample preprocessing steps of cell lysis, labeling, washing, and pipetting inevitably triggers the cells, changes its basal state, and dilutes the individual cell secretion in bulk assays. Using a fully integrated system for multiplexed profiling of native immune single-cell enzyme secretion from 50 μL of undiluted blood, we eliminate sample handling. With a total analysis time of 60 min, the integrated platform performs six tasks of leukocyte extraction, cell washing, fluorescent enzyme substrate mixing, single-cell droplet making, droplet incubation, and real-time readout for leukocyte secretion profiling of neutrophil elastase, granzyme B, and metalloproteinase. We calibrated the device, optimized the protocols, and tested the leukocyte secretion of acute heart failure (AHF) patients at admission and predischarge. This paper highlights the presence of single-cell enzymatic immune phenotypes independent of CD marker labeling, which could potentially elucidate the innate immune response states. We found that patients recovering from AHF showed a corresponding reduction in immune-cell enzymatic secretion levels and donor-specific enzymatic signatures were observed, which suggests patient-to-patient heterogeneous immune response. This platform presents opportunities to elucidate the complexities of the immune response from a single drop of blood and bridge the current technological, biological, and medical gap in understanding immune response and biological triggers.
Collapse
Affiliation(s)
- Kerwin Kwek Zeming
- Critical Analytics for Manufacturing of Personalised Medicine, Singapore-MIT Alliance for Research and Technology, 1 Create Way, Enterprise Wing #04-13/14, 138602 Singapore
| | - Ri Lu
- Critical Analytics for Manufacturing of Personalised Medicine, Singapore-MIT Alliance for Research and Technology, 1 Create Way, Enterprise Wing #04-13/14, 138602 Singapore.,Graduate School for Integrative Sciences and Engineering, National University of Singapore, University Hall, Tan Chin Tuan Wing Level 04, #04-02, 21 Lower Kent Ridge Road, 119077 Singapore
| | - Kai Lee Woo
- Department of Cardiology, National University Heart Center, 1E Kent Ridge Road, 119228, Singapore
| | - Guoyun Sun
- Graduate School for Integrative Sciences and Engineering, National University of Singapore, University Hall, Tan Chin Tuan Wing Level 04, #04-02, 21 Lower Kent Ridge Road, 119077 Singapore
| | - Kai Yun Quek
- Critical Analytics for Manufacturing of Personalised Medicine, Singapore-MIT Alliance for Research and Technology, 1 Create Way, Enterprise Wing #04-13/14, 138602 Singapore
| | - Lih Feng Cheow
- Critical Analytics for Manufacturing of Personalised Medicine, Singapore-MIT Alliance for Research and Technology, 1 Create Way, Enterprise Wing #04-13/14, 138602 Singapore.,Graduate School for Integrative Sciences and Engineering, National University of Singapore, University Hall, Tan Chin Tuan Wing Level 04, #04-02, 21 Lower Kent Ridge Road, 119077 Singapore.,Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 117583 Singapore
| | - Chia-Hung Chen
- Department of Biomedical Engineering, College of Engineering, City University of Hong Kong, YEUNG-B5121A, Hong Kong
| | - Jongyoon Han
- Critical Analytics for Manufacturing of Personalised Medicine, Singapore-MIT Alliance for Research and Technology, 1 Create Way, Enterprise Wing #04-13/14, 138602 Singapore.,Department of Electrical Engineering, Massachusetts Institute of Technology, 50 Vassar Street, Cambridge, Massachusetts 02142, United States.,Department of Biological Engineering, Massachusetts Institute of Technology, 21 Ames Street, #56-651, Cambridge, Massachusetts 02142, United States
| | - Shir Lynn Lim
- Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, 117597 Singapore.,Department of Cardiology, National University Heart Center, 1E Kent Ridge Road, 119228, Singapore
| |
Collapse
|
33
|
Chang YL, Rossetti M, Gjertson DW, Rubbi L, Thompson M, Montoya DJ, Morselli M, Ruffin F, Hoffmann A, Pellegrini M, Fowler VG, Yeaman MR, Reed EF. Human DNA methylation signatures differentiate persistent from resolving MRSA bacteremia. Proc Natl Acad Sci U S A 2021; 118:e2000663118. [PMID: 33649198 PMCID: PMC7958259 DOI: 10.1073/pnas.2000663118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 12/21/2020] [Indexed: 12/26/2022] Open
Abstract
Persistent methicillin-resistant Staphylococcus aureus (MRSA) bacteremia is life threatening and occurs in up to 30% of MRSA bacteremia cases despite appropriate antimicrobial therapy. Isolates of MRSA that cause antibiotic-persistent methicillin-resistant S. aureus bacteremia (APMB) typically have in vitro antibiotic susceptibilities equivalent to those causing antibiotic-resolving methicillin-resistant S. aureus bacteremia (ARMB). Thus, persistence reflects host-pathogen interactions occurring uniquely in context of antibiotic therapy in vivo. However, host factors and mechanisms involved in APMB remain unclear. We compared DNA methylomes in circulating immune cells from patients experiencing APMB vs. ARMB. Overall, methylation signatures diverged in the distinct patient cohorts. Differentially methylated sites intensified proximate to transcription factor binding sites, primarily in enhancer regions. In APMB patients, significant hypomethylation was observed in binding sites for CCAAT enhancer binding protein-β (C/EBPβ) and signal transducer/activator of transcription 1 (STAT1). In contrast, hypomethylation in ARMB patients localized to glucocorticoid receptor and histone acetyltransferase p300 binding sites. These distinct methylation signatures were enriched in neutrophils and achieved a mean area under the curve of 0.85 when used to predict APMB using a classification model. These findings validated by targeted bisulfite sequencing (TBS-seq) differentiate epigenotypes in patients experiencing APMB vs. ARMB and suggest a risk stratification strategy for antibiotic persistence in patients treated for MRSA bacteremia.
Collapse
Affiliation(s)
- Yu-Ling Chang
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Maura Rossetti
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - David W Gjertson
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA 90095
| | - Liudmilla Rubbi
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Michael Thompson
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, CA 90095
| | | | - Marco Morselli
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Felicia Ruffin
- Division of Infectious Diseases, Duke University, Durham, NC 27710
| | - Alexander Hoffmann
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA 90095
| | - Matteo Pellegrini
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Vance G Fowler
- Division of Infectious Diseases, Duke University, Durham, NC 27710
| | - Michael R Yeaman
- Division of Molecular Medicine, Harbor-University of California, Los Angeles Medical Center, Torrance, CA 90502
- Division of Infectious Diseases, Harbor-University of California, Los Angeles Medical Center, Torrance, CA 90502
- Lundquist Institute for Biomedical Innovation at Harbor-University of California, Los Angeles Medical Center, Torrance, CA 90502
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Elaine F Reed
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095;
| |
Collapse
|
34
|
Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation. Nat Commun 2021; 12:651. [PMID: 33510161 PMCID: PMC7844026 DOI: 10.1038/s41467-020-20849-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023] Open
Abstract
To investigate the three-dimensional (3D) genome architecture across normal B cell differentiation and in neoplastic cells from different subtypes of chronic lymphocytic leukemia and mantle cell lymphoma patients, here we integrate in situ Hi-C and nine additional omics layers. Beyond conventional active (A) and inactive (B) compartments, we uncover a highly-dynamic intermediate compartment enriched in poised and polycomb-repressed chromatin. During B cell development, 28% of the compartments change, mostly involving a widespread chromatin activation from naive to germinal center B cells and a reversal to the naive state upon further maturation into memory B cells. B cell neoplasms are characterized by both entity and subtype-specific alterations in 3D genome organization, including large chromatin blocks spanning key disease-specific genes. This study indicates that 3D genome interactions are extensively modulated during normal B cell differentiation and that the genome of B cell neoplasias acquires a tumor-specific 3D genome architecture.
Collapse
|
35
|
Ye J, Stefan-Lifshitz M, Tomer Y. Genetic and environmental factors regulate the type 1 diabetes gene CTSH via differential DNA methylation. J Biol Chem 2021; 296:100774. [PMID: 33992646 PMCID: PMC8191311 DOI: 10.1016/j.jbc.2021.100774] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 05/05/2021] [Accepted: 05/12/2021] [Indexed: 12/13/2022] Open
Abstract
Cathepsin H (CTSH) is a type 1 diabetes (T1D) risk gene; large-scale genetic and epidemiological studies found that T1D genetic risk correlates with high CTSH expression, rapid decline of beta-cell function, and early onset T1D. Counterintuitively, transcriptional downregulation of CTSH by proinflammatory cytokines has been shown to promote beta-cell apoptosis. Here, we potentially explain these observed contrasting effects, describing a new mechanism where proinflammatory cytokines and T1D genetic risk variants regulate CTSH transcription via differential DNA methylation. We show that, in human islets, CTSH downregulation by the proinflammatory cytokine cocktail interleukin 1β + tumor necrosis factor α + interferon γ was coupled with DNA hypermethylation in an open chromatin region in CTSH intron 1. A luciferase assay in human embryonic kidney 293 cells revealed that methylation of three key cytosine-phosphate-guanine dinucleotide (CpG) residues in intron 1 was responsible for the reduction of promoter activity. We further found that cytokine-induced intron 1 hypermethylation is caused by lowered Tet1/3 activities, suggesting that attenuated active demethylation lowered CTSH transcription. Importantly, individuals who carry the T1D risk variant showed lower methylation variability at the intron 1 CpG residues, presumably making them less sensitive to cytokines, whereas individuals who carry the protective variant showed higher methylation variability, presumably making them more sensitive to cytokines and implying differential responses to environment between the two patient populations. These findings suggest that genetic and environmental influences on a T1D locus are mediated by differential variability and mean of DNA methylation.
Collapse
Affiliation(s)
- Jody Ye
- Division of Endocrinology, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA.
| | - Mihaela Stefan-Lifshitz
- Division of Endocrinology, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Yaron Tomer
- Division of Endocrinology, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| |
Collapse
|
36
|
Quaas A, Pamuk A, Klein S, Quantius J, Rehkaemper J, Barutcu AG, Rueschoff J, Zander T, Gebauer F, Hillmer A, Buettner R, Schroeder W, Bruns CJ, Löser H, Schoemig-Markiefka B, Alakus H. Sex-specific prognostic effect of CD66b-positive tumor-infiltrating neutrophils (TANs) in gastric and esophageal adenocarcinoma. Gastric Cancer 2021; 24:1213-1226. [PMID: 34009535 PMCID: PMC8502159 DOI: 10.1007/s10120-021-01197-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/08/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Tumor-associated neutrophils (TANs) have recently been identified as a relevant component of the tumor microenvironment (TME) in solid tumors. Within the TME TANs mediate either tumor-promoting or tumor-inhibiting activities. So far, their prognostic relevance remains to be determined. This study aims to evaluate the prognostic relevance of TANs in different molecular subtypes of gastric and esophageal adenocarcinoma. METHODS We analyzed a total of 1118 Caucasian patients divided into gastric adenocarcinoma (n = 458) and esophageal adenocarcinoma cohort (n = 660) of primarily resected and neoadjuvant-treated individuals. The amount of CD66b + TANs in the tumor stroma was determined using quantitative image analysis and correlated to both molecular, as well as clinical data. RESULTS An accumulation of TANs in the tumor stroma of gastric carcinomas was associated to a significant favorable prognosis (p = 0.026). A subgroup analysis showed that this effect was primarily related to the molecular chromosomal instable subtype (CIN) of gastric carcinomas (p = 0.010). This was only observed in female patients (p = 0.014) but not in male patients (p = 0.315). The same sex-specific effect could be confirmed in adenocarcinomas of the esophagus (p = 0.027), as well as in female individuals after receiving neoadjuvant therapy (p = 0.034). CONCLUSIONS Together, we show a sex-specific prognostic effect of TANs in gastric cancer within a Caucasian cohort. For the first time, we showed that this sex-specific prognostic effect of TANs can also be seen in esophageal cancer.
Collapse
Affiliation(s)
- Alexander Quaas
- grid.411097.a0000 0000 8852 305XInstitute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Aylin Pamuk
- grid.411097.a0000 0000 8852 305XDepartment of General, Visceral, Cancer and Transplantation Surgery, University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
| | - Sebastian Klein
- grid.411097.a0000 0000 8852 305XInstitute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Jennifer Quantius
- grid.411097.a0000 0000 8852 305XInstitute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Jan Rehkaemper
- grid.411097.a0000 0000 8852 305XInstitute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Atakan G. Barutcu
- grid.411097.a0000 0000 8852 305XDepartment of General, Visceral, Cancer and Transplantation Surgery, University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
| | - Josef Rueschoff
- Institute of Pathology, Nordhessen and Targos Molecular Pathology GmbH, Kassel, Germany
| | - Thomas Zander
- grid.6190.e0000 0000 8580 3777Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Gastrointestinal Cancer Group Cologne GCGC, University of Cologne, Cologne, Germany
| | - Florian Gebauer
- grid.411097.a0000 0000 8852 305XDepartment of General, Visceral, Cancer and Transplantation Surgery, University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
| | - Axel Hillmer
- grid.411097.a0000 0000 8852 305XInstitute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Reinhard Buettner
- grid.411097.a0000 0000 8852 305XInstitute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Wolfgang Schroeder
- grid.411097.a0000 0000 8852 305XDepartment of General, Visceral, Cancer and Transplantation Surgery, University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
| | - Christiane J. Bruns
- grid.411097.a0000 0000 8852 305XDepartment of General, Visceral, Cancer and Transplantation Surgery, University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
| | - Heike Löser
- grid.411097.a0000 0000 8852 305XInstitute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Birgid Schoemig-Markiefka
- grid.411097.a0000 0000 8852 305XInstitute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Hakan Alakus
- grid.411097.a0000 0000 8852 305XDepartment of General, Visceral, Cancer and Transplantation Surgery, University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
| |
Collapse
|
37
|
Moorlag SJCFM, Rodriguez-Rosales YA, Gillard J, Fanucchi S, Theunissen K, Novakovic B, de Bont CM, Negishi Y, Fok ET, Kalafati L, Verginis P, Mourits VP, Koeken VACM, de Bree LCJ, Pruijn GJM, Fenwick C, van Crevel R, Joosten LAB, Joosten I, Koenen H, Mhlanga MM, Diavatopoulos DA, Chavakis T, Netea MG. BCG Vaccination Induces Long-Term Functional Reprogramming of Human Neutrophils. Cell Rep 2020; 33:108387. [PMID: 33207187 PMCID: PMC7672522 DOI: 10.1016/j.celrep.2020.108387] [Citation(s) in RCA: 135] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 07/16/2020] [Accepted: 10/23/2020] [Indexed: 12/31/2022] Open
Abstract
The tuberculosis vaccine bacillus Calmette-Guérin (BCG) protects against some heterologous infections, probably via induction of non-specific innate immune memory in monocytes and natural killer (NK) cells, a process known as trained immunity. Recent studies have revealed that the induction of trained immunity is associated with a bias toward granulopoiesis in bone marrow hematopoietic progenitor cells, but it is unknown whether BCG vaccination also leads to functional reprogramming of mature neutrophils. Here, we show that BCG vaccination of healthy humans induces long-lasting changes in neutrophil phenotype, characterized by increased expression of activation markers and antimicrobial function. The enhanced function of human neutrophils persists for at least 3 months after vaccination and is associated with genome-wide epigenetic modifications in trimethylation at histone 3 lysine 4. Functional reprogramming of neutrophils by the induction of trained immunity might offer novel therapeutic strategies in clinical conditions that could benefit from modulation of neutrophil effector function.
Collapse
Affiliation(s)
- Simone J C F M Moorlag
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Yessica Alina Rodriguez-Rosales
- Department of Laboratory Medicine, Laboratory of Medical Immunology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Joshua Gillard
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands; Radboud Center for Infectious Diseases, Radboudumc, Nijmegen, the Netherlands
| | - Stephanie Fanucchi
- Division of Chemical, Systems & Synthetic Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Institute of Infectious Disease & Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Kate Theunissen
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Boris Novakovic
- Epigenetics, Murdoch Children's Research Institute, Royal Children's Hospital, and Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Cynthia M de Bont
- Department of Biomolecular Chemistry, Institute for Molecules and Materials (IMM), Radboud University, Nijmegen, the Netherlands
| | - Yutaka Negishi
- Epigenomics & Single Cell Biophysics Group, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, the Netherlands; Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ezio T Fok
- Epigenomics & Single Cell Biophysics Group, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, the Netherlands; Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lydia Kalafati
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany; Laboratory of Immune Regulation and Tolerance, Autoimmunity and Inflammation, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece
| | - Panayotis Verginis
- Laboratory of Immune Regulation and Tolerance, Autoimmunity and Inflammation, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece
| | - Vera P Mourits
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Valerie A C M Koeken
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine (CiiM) & TWINCORE, joint ventures between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - L Charlotte J de Bree
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Research Center for Vitamins and Vaccines, Bandim Health Project, Statens Serum Institut, Copenhagen, Denmark; Odense Patient Data Explorative Network, University of Southern Denmark/Odense University Hospital, Odense, Denmark
| | - Ger J M Pruijn
- Department of Biomolecular Chemistry, Institute for Molecules and Materials (IMM), Radboud University, Nijmegen, the Netherlands
| | - Craig Fenwick
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Reinout van Crevel
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Irma Joosten
- Department of Laboratory Medicine, Laboratory of Medical Immunology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Hans Koenen
- Department of Laboratory Medicine, Laboratory of Medical Immunology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Musa M Mhlanga
- Epigenomics & Single Cell Biophysics Group, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, the Netherlands; Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Dimitri A Diavatopoulos
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands; Radboud Center for Infectious Diseases, Radboudumc, Nijmegen, the Netherlands
| | - Triantafyllos Chavakis
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany.
| |
Collapse
|
38
|
Fair BJ, Blake LE, Sarkar A, Pavlovic BJ, Cuevas C, Gilad Y. Gene expression variability in human and chimpanzee populations share common determinants. eLife 2020; 9:59929. [PMID: 33084571 PMCID: PMC7644215 DOI: 10.7554/elife.59929] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/20/2020] [Indexed: 12/20/2022] Open
Abstract
Inter-individual variation in gene expression has been shown to be heritable and is often associated with differences in disease susceptibility between individuals. Many studies focused on mapping associations between genetic and gene regulatory variation, yet much less attention has been paid to the evolutionary processes that shape the observed differences in gene regulation between individuals in humans or any other primate. To begin addressing this gap, we performed a comparative analysis of gene expression variability and expression quantitative trait loci (eQTLs) in humans and chimpanzees, using gene expression data from primary heart samples. We found that expression variability in both species is often determined by non-genetic sources, such as cell-type heterogeneity. However, we also provide evidence that inter-individual variation in gene regulation can be genetically controlled, and that the degree of such variability is generally conserved in humans and chimpanzees. In particular, we found a significant overlap of orthologous genes associated with eQTLs in both species. We conclude that gene expression variability in humans and chimpanzees often evolves under similar evolutionary pressures.
Collapse
Affiliation(s)
| | - Lauren E Blake
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Abhishek Sarkar
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Bryan J Pavlovic
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, United States
| | - Claudia Cuevas
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Yoav Gilad
- Department of Medicine, University of Chicago, Chicago, United States.,Department of Human Genetics, University of Chicago, Chicago, United States
| |
Collapse
|
39
|
Beecroft SJ, Lamont PJ, Edwards S, Goullée H, Davis MR, Laing NG, Ravenscroft G. The Impact of Next-Generation Sequencing on the Diagnosis, Treatment, and Prevention of Hereditary Neuromuscular Disorders. Mol Diagn Ther 2020; 24:641-652. [PMID: 32997275 DOI: 10.1007/s40291-020-00495-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2020] [Indexed: 12/13/2022]
Abstract
The impact of high-throughput sequencing in genetic neuromuscular disorders cannot be overstated. The ability to rapidly and affordably sequence multiple genes simultaneously has enabled a second golden age of Mendelian disease gene discovery, with flow-on impacts for rapid genetic diagnosis, evidence-based treatment, tailored therapy development, carrier-screening, and prevention of disease recurrence in families. However, there are likely many more neuromuscular disease genes and mechanisms to be discovered. Many patients and families remain without a molecular diagnosis following targeted panel sequencing, clinical exome sequencing, or even genome sequencing. Here we review how massively parallel, or next-generation, sequencing has changed the field of genetic neuromuscular disorders, and anticipate future benefits of recent technological innovations such as RNA-seq implementation and detection of tandem repeat expansions from short-read sequencing.
Collapse
Affiliation(s)
- Sarah J Beecroft
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, 6 Verdun St, Nedlands, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | | | - Samantha Edwards
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, 6 Verdun St, Nedlands, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | - Hayley Goullée
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, 6 Verdun St, Nedlands, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | - Mark R Davis
- Neurogenetic Unit, Department of Diagnostic Genomics, PP Block, QEII Medical Centre, Nedlands, WA, Australia
| | - Nigel G Laing
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, 6 Verdun St, Nedlands, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia.,Neurogenetic Clinic, Royal Perth Hospital, Perth, Australia
| | - Gianina Ravenscroft
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, 6 Verdun St, Nedlands, WA, 6009, Australia. .,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia.
| |
Collapse
|
40
|
Wu M, Ma M, Tan Z, Zheng H, Liu X. Neutrophil: A New Player in Metastatic Cancers. Front Immunol 2020; 11:565165. [PMID: 33101283 PMCID: PMC7546851 DOI: 10.3389/fimmu.2020.565165] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/12/2020] [Indexed: 12/11/2022] Open
Abstract
The interaction between cancer cells and immune cells is important for the cancer development. However, much attention has been given to T cells and macrophages. Being the most abundant leukocytes in the blood, the functions of neutrophils in cancer have been underdetermined. They have long been considered an “audience” in the development of cancer. However, emerging evidence indicate that neutrophils are a heterogeneous population with plasticity, and subpopulation of neutrophils (such as low density neutrophils, polymorphonuclear-myeloid-derived suppressor cells) are actively involved in cancer growth and metastasis. Here, we review the current understanding of the role of neutrophils in cancer development, with a specific focus on their pro-metastatic functions. We also discuss the potential and challenges of neutrophils as therapeutic targets. A better understanding the role of neutrophils in cancer will discover new mechanisms of metastasis and develop new immunotherapies by targeting neutrophils.
Collapse
Affiliation(s)
- Mengyue Wu
- Department of Pathophysiology, Anhui Medical University, Hefei, China
| | - Mutian Ma
- Department of Pathophysiology, Anhui Medical University, Hefei, China
| | - Zhenya Tan
- Department of Pathophysiology, Anhui Medical University, Hefei, China
| | - Hong Zheng
- Department of Pathophysiology, Anhui Medical University, Hefei, China
| | - Xia Liu
- Department of Toxicology and Cancer Biology, Markey Cancer Center, College of Medicine, University of Kentucky, Lexington, KY, United States
| |
Collapse
|
41
|
Oertelt-Prigione S, Mariman E. The impact of sex differences on genomic research. Int J Biochem Cell Biol 2020; 124:105774. [PMID: 32470538 DOI: 10.1016/j.biocel.2020.105774] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 05/15/2020] [Accepted: 05/22/2020] [Indexed: 01/23/2023]
Abstract
Sex and gender differences affect all dimensions of human health ranging from the biological basis of disease to therapeutic access, choice and response. Genomics research has long ignored the role of sex differences as potential modulators and the concept is gaining more attention only recently. In the present review we summarize the current knowledge of the impact of sex differences on genomic and epigenomic research, the potential interaction of genomics and gender and the role of these differences in disease etiopathogenesis. Sex differences can emerge from differences in the sex chromosomes themselves, from their interaction with the genome and from the influence of hormones on genomic processes. The impact of these processes on the incidence of autoimmune and oncologic disease is well documented. The growing field of systems biology, which aims at integrating information from different networks of the human body, could also greatly benefit from this approach. In the present review we summarize the current knowledge and provide recommendations for the future performance of sex-sensitive genomics research.
Collapse
Affiliation(s)
- Sabine Oertelt-Prigione
- Department of Primary and Community Care, Radboud Institute of Health Sciences, Radboudumc, Nijmegen, The Netherlands; Institute of Legal and Forensic Medicine, Charité - Universitätsmedizin, Berlin, Germany.
| | - Edwin Mariman
- Department of Human Biology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
| |
Collapse
|
42
|
Yang X, Ma Z, Zhang Y, Wu J, Huang J, Zhao W, Mo F, Lin Z, Xu Y, Zhou Z, Chen S. Anti-tumor immune response varies among individuals: A gene expression profiling of mouse melanoma. Int Immunopharmacol 2020; 80:106211. [PMID: 31972424 DOI: 10.1016/j.intimp.2020.106211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/30/2019] [Accepted: 01/08/2020] [Indexed: 12/24/2022]
Abstract
Melanoma is amongst the most aggressive malignant tumors. The purpose of this study is to detect the tumor microenvironment systematically using multi-omics analyses and to propose strategies for precision medicine. Multiple factors of tumor microenvironment contribute to the drug resistance and immune surveillance failure. Here we analyzed genome mutations and characterized the immune state of tumor microenvironments in mouse melanoma by whole exome sequencing (WES) and RNA sequencing (RNA-Seq) approaches. Somatic mutation analysis revealed 35.1% novel mutations in mouse tumors when compared with B16F10 cell line, provided a basis for multi-site sequencing for accurate neoantigen selection. Mutation cluster, gene expression comparison, and gene ontology (GO) analyses by R packages proved DNA repair damage, inflammation, slower cell division, and metabolic change in tumor microenvironment. Further analyses of T-cell receptor (TCR) sequences, immune signaling pathway activation, tumor infiltrated immune cells and chemokine expression revealed extensive difference of antitumor immune response among individuals. Our study revealed the characteristics of tumor microenvironment with mouse melanoma model, suggested the need of comprehensive genome mutations and personal immune state analyses for cancer precision medicine.
Collapse
Affiliation(s)
- Xiaoyue Yang
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Zhiming Ma
- Hangzhou Neoantigen Bio-Tech Ltd. Co., 688 Road Binan, Hangzhou 310051, China
| | - Ying Zhang
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Jingcheng Wu
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China; College of Computer Science and Technology, Zhejiang University, Hangzhou 310027, China
| | - Jin Huang
- Department of Medicine, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Wenyi Zhao
- College of Computer Science and Technology, Zhejiang University, Hangzhou 310027, China; Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Fan Mo
- Hangzhou Neoantigen Bio-Tech Ltd. Co., 688 Road Binan, Hangzhou 310051, China; Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, V6H 3Z6, Canada
| | - Zhiwei Lin
- Hangzhou Neoantigen Bio-Tech Ltd. Co., 688 Road Binan, Hangzhou 310051, China
| | - Yingchun Xu
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Zhan Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China.
| | - Shuqing Chen
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China.
| |
Collapse
|
43
|
Abstract
Structured models of ontogenic, phenotypic and functional diversity have been instrumental for a renewed understanding of the biology of immune cells, such as macrophages and lymphoid cells. However, there are no established models that can be used to define the diversity of neutrophils, the most abundant myeloid cells. This lack of an established model is largely due to the uniquely short lives of neutrophils, a consequence of their inability to divide once terminally differentiated, which has been perceived as a roadblock to functional diversity. This perception is rapidly evolving as multiple phenotypic and functional variants of neutrophils have been found, both in homeostatic and disease conditions. In this Opinion article, we present an overview of neutrophil heterogeneity and discuss possible mechanisms of diversification, including genomic regulation. We suggest that neutrophil heterogeneity is an important feature of immune pathophysiology, such that co-option of the mechanisms of diversification by cancer or other disorders contributes to disease progression.
Collapse
|
44
|
McMinn PH, Hind LE, Huttenlocher A, Beebe DJ. Neutrophil trafficking on-a-chip: an in vitro, organotypic model for investigating neutrophil priming, extravasation, and migration with spatiotemporal control. LAB ON A CHIP 2019; 19:3697-3705. [PMID: 31576879 PMCID: PMC7045365 DOI: 10.1039/c9lc00562e] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Neutrophil trafficking is essential for a strong and productive immune response to infection and injury. During acute inflammation, signals from resident immune cells, fibroblasts, and the endothelium help to prime, attract, and activate circulating neutrophils at sites of inflammation. Due to current limitations with in vitro and animal models, our understanding of these events is incomplete. In this paper, we describe a microfluidic technology which incorporates a lumen-based vascular component with a high degree of spatiotemporal control to facilitate the study of neutrophil trafficking using primary human cells. The improved spatiotemporal control allows functional selection of neutrophils based on their migratory capacity. We use this technology to investigate neutrophil-endothelial interactions and find that these interactions are necessary for robust neutrophil chemotaxis to interleukin-8 (IL-8) and priming of the neutrophils. In agreement with previous studies, we observed that transendothelial migration (TEM) is required for neutrophils to enter a primed phenotypic state. TEM neutrophils not only produce a significantly higher amount of reactive oxygen species (ROS) when treated with PMA, but also upregulate genes involved in ROS production (CYBB, NCF1, NFKB1, NFKBIA), cell adhesion (CEACAM-8, ITGAM), and chemokine receptors (CXCR2, TNFRSF1A). These results suggest that neutrophil-endothelial interactions are crucial to neutrophil chemotaxis and ROS generation.
Collapse
Affiliation(s)
- Patrick H McMinn
- Department of Biomedical Engineering, University of Wisconsin - Madison, 1451 Engineering Dr., Madison, WI 53706, USA and University of Wisconsin Carbone Cancer Center, Wisconsin Institutes for Medical Research, 1111 Highland Ave., Madison, WI 53705, USA
| | - Laurel E Hind
- Department of Medical Microbiology and Immunology, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Anna Huttenlocher
- Department of Medical Microbiology and Immunology, University of Wisconsin - Madison, Madison, WI 53706, USA and Department of Pediatrics, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - David J Beebe
- Department of Biomedical Engineering, University of Wisconsin - Madison, 1451 Engineering Dr., Madison, WI 53706, USA and University of Wisconsin Carbone Cancer Center, Wisconsin Institutes for Medical Research, 1111 Highland Ave., Madison, WI 53705, USA and Department of Pathology and Laboratory Medicine, University of Wisconsin - Madison, Madison, WI 53706, USA
| |
Collapse
|
45
|
Skendros P, Papagoras C, Mitroulis I, Ritis K. Autoinflammation: Lessons from the study of familial Mediterranean fever. J Autoimmun 2019; 104:102305. [PMID: 31337526 DOI: 10.1016/j.jaut.2019.102305] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 07/14/2019] [Indexed: 12/16/2022]
Abstract
Autoinflammatory disorders represent a heterogeneous group of systemic inflammatory diseases caused by genetic or acquired defects in key components of the innate immunity. Familial Mediterranean fever (FMF) is the most common among the other clinical phenotypes of the rare hereditary periodic fevers (HPFs) syndromes. FMF is associated with mutations in the MEFV gene encoding pyrin and is characterized by recurrent, often stress-provoked attacks of fever and serositis, but sometimes also by chronic subclinical inflammation. FMF is prevalent in Greece and other countries of the eastern Mediterranean region. Over the last 17 years, our group has focused on FMF as a model suitable for the research on innate immunity and particularly the role of neutrophils. Therefore, the study of Greek patients with FMF has yielded lessons across several levels: the epidemiology of the disease in Greece, the spectrum of its clinical manifestations and potential overlaps with other idiopathic inflammatory conditions, the demonstration of its rather complex and heterogeneous genetic background and the suggestion of a novel mechanism involved in the crosstalk between environmental stress and inflammation. Mechanistically, during FMF attack, neutrophils release chromatin structures called neutrophil extracellular traps (NETs), which are decorated with bioactive IL-1β. REDD1 (regulated in development and DNA damage responses 1), that encodes a stress-related mTOR repressor, has been found to be the most significantly upregulated gene in neutrophils during disease attacks. Upon adrenergic stress, REDD1-induced autophagy triggers a pyrin-driven IL-1β maturation, and the release of IL-1β-bearing NETs. Consequently, not only the mode of action of IL-1β-targeting therapies is explained, but also new treatment prospects emerge with the evaluation of old or the design of new drugs targeting autophagy-induced NETosis. Information gained from FMF studies may subsequently be applied in more complex but still relevant inflammatory conditions, such as adult-onset Still's disease, gout, ulcerative colitis and Behçet's disease.
Collapse
Affiliation(s)
- Panagiotis Skendros
- First Department of Internal Medicine and Laboratory of Molecular Hematology, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
| | - Charalampos Papagoras
- First Department of Internal Medicine and Laboratory of Molecular Hematology, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
| | - Ioannis Mitroulis
- First Department of Internal Medicine and Laboratory of Molecular Hematology, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
| | - Konstantinos Ritis
- First Department of Internal Medicine and Laboratory of Molecular Hematology, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece.
| |
Collapse
|
46
|
Khramtsova EA, Davis LK, Stranger BE. The role of sex in the genomics of human complex traits. Nat Rev Genet 2019; 20:173-190. [PMID: 30581192 DOI: 10.1038/s41576-018-0083-1] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nearly all human complex traits and disease phenotypes exhibit some degree of sex differences, including differences in prevalence, age of onset, severity or disease progression. Until recently, the underlying genetic mechanisms of such sex differences have been largely unexplored. Advances in genomic technologies and analytical approaches are now enabling a deeper investigation into the effect of sex on human health traits. In this Review, we discuss recent insights into the genetic models and mechanisms that lead to sex differences in complex traits. This knowledge is critical for developing deeper insight into the fundamental biology of sex differences and disease processes, thus facilitating precision medicine.
Collapse
Affiliation(s)
- Ekaterina A Khramtsova
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA.,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Lea K Davis
- Division of Medical Genetics, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA. .,Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Barbara E Stranger
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA. .,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA. .,Center for Data Intensive Science, University of Chicago, Chicago, IL, USA.
| |
Collapse
|
47
|
X-Linked IRAK1 Polymorphism is Associated with Sex-Related Differences in Polymorphonuclear Granulocyte and Monocyte Activation and Response Variabilities. Shock 2019; 53:434-441. [PMID: 31306349 DOI: 10.1097/shk.0000000000001404] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Common X-linked genetic polymorphisms are expected to alter cellular responses affecting males and females differently through sex-linked inheritance pattern as well as X chromosome (ChrX) mosaicism and associated ChrX skewing, which is unique to females. We tested this hypothesis in ex vivo lipopolysaccharide and phorbol ester-stimulated polymorphonuclear granulocytes (PMNs) and monocytes from healthy volunteers (n = 51). Observations were analyzed after stratification by sex alone or the presence of variant IRAK1 haplotype a common X-linked polymorphism with previously demonstrated major clinical impacts. Upon cell activation, CD11b, CD45, CD66b, CD63, and CD14 expression was markedly and similarly elevated in healthy males and females. By contrast, PMN and monocyte activation measured by CD11b, CD66b, and CD63 was increased in variant-IRAK1 subjects as compared with WT. Stratification by IRAK1 genotype and sex showed similar cell activation effect on variant-IRAK1 subjects and an intermediate degree of cell activation in heterozygous mosaic females. The increased membrane expression of these proteins in variant-IRAK1 subjects was associated with similar or increased intersubject but uniformly decreased intrasubject cell response variabilities as compared with WT. We also tested white blood cell ChrX skewing in the healthy cohort as well as in a sample of female trauma patients (n = 201). ChrX inactivation ratios were similar in IRAK1 WT, variant, and heterozygous healthy subjects. Trauma patients showed a trend of blunted ChrX skewing at admission in homozygous variant-IRAK1 and heterozygous mosaic-IRAK1 female subjects as compared with WT. Trauma-induced de novo ChrX skewing was also depressed in variant-IRAK1 and mosaic-IRAK1 female trauma patients as compared with WT. Our study indicates that augmented PMN and monocyte activation in variant-IRAK1 subjects is accompanied by decreased intrasubject cellular variability and blunted de novo ChrX skewing in response to trauma. A more pronounced cell activation of PMNs and monocytes accompanied by decreased response variabilities in variant-IRAK1 subjects may be a contributing mechanism affecting the course of sepsis and trauma and may also impact sex-based outcome differences due to its X-linked inheritance pattern and high prevalence.
Collapse
|
48
|
Bonaventura A, Montecucco F, Dallegri F, Carbone F, Lüscher TF, Camici GG, Liberale L. Novel findings in neutrophil biology and their impact on cardiovascular disease. Cardiovasc Res 2019; 115:1266-1285. [DOI: 10.1093/cvr/cvz084] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
Affiliation(s)
- Aldo Bonaventura
- First Clinic of Internal Medicine, Department of Internal Medicine, University of Genoa, 6 viale Benedetto XV, Genoa, Italy
- Division of Cardiology, Department of Internal Medicine, Pauley Heart Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Fabrizio Montecucco
- First Clinic of Internal Medicine, Department of Internal Medicine and Centre of Excellence for Biomedical Research (CEBR), University of Genoa, 6 viale Benedetto XV, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino Genoa – Italian Cardiovascular Network, 10 Largo Benzi, Genoa, Italy
| | - Franco Dallegri
- First Clinic of Internal Medicine, Department of Internal Medicine, University of Genoa, 6 viale Benedetto XV, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino Genoa – Italian Cardiovascular Network, 10 Largo Benzi, Genoa, Italy
| | - Federico Carbone
- First Clinic of Internal Medicine, Department of Internal Medicine, University of Genoa, 6 viale Benedetto XV, Genoa, Italy
| | - Thomas F Lüscher
- Center for Molecular Cardiology, University of Zürich, Wagistrasse 12, Schlieren, Switzerland
- Heart Division, Royal Brompton and Harefield Hospitals and Imperial College, London, UK
| | - Giovanni G Camici
- Center for Molecular Cardiology, University of Zürich, Wagistrasse 12, Schlieren, Switzerland
- University Heart Center, University Hospital Zürich, Rämistrasse 100, Zürich, Switzerland
- Department of Research and Education, University Hospital Zürich, Rämistrasse 100, Zürich, Switzerland
| | - Luca Liberale
- First Clinic of Internal Medicine, Department of Internal Medicine, University of Genoa, 6 viale Benedetto XV, Genoa, Italy
- Center for Molecular Cardiology, University of Zürich, Wagistrasse 12, Schlieren, Switzerland
| |
Collapse
|
49
|
Rungelrath V, Kobayashi SD, DeLeo FR. Neutrophils in innate immunity and systems biology-level approaches. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2019; 12:e1458. [PMID: 31218817 DOI: 10.1002/wsbm.1458] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/22/2019] [Accepted: 05/23/2019] [Indexed: 12/14/2022]
Abstract
The innate immune system is the first line of host defense against invading microorganisms. Polymorphonuclear leukocytes (PMNs or neutrophils) are the most abundant leukocyte in humans and essential to the innate immune response against invading pathogens. Compared to the acquired immune response, which requires time to develop and is dependent on previous interaction with specific microbes, the ability of neutrophils to kill microorganisms is immediate, nonspecific, and not dependent on previous exposure to microorganisms. Historically, studies of PMN-pathogen interaction focused on the events leading to killing of microorganisms, such as recruitment/chemotaxis, transmigration, phagocytosis, and activation, whereas postphagocytosis sequelae were infrequently considered. In addition, it was widely accepted that human neutrophils possessed limited capacity for new gene transcription and thus, relatively little biosynthetic capacity. This notion has changed dramatically within the past 20 years. Further, there is now more effort directed to understand the events occurring in PMNs after killing of microbes. Herein, we give an updated review of the systems biology-level approaches that have been used to gain an enhanced view of the role of neutrophils during host-pathogen interaction and neutrophil-mediated diseases. We anticipate that these and future systems-level studies will continue to provide information important for understanding, treatment, and control of diseases caused by pathogenic microorganisms. This article is categorized under: Physiology > Organismal Responses to Environment Physiology > Mammalian Physiology in Health and Disease Biological Mechanisms > Cell Fates.
Collapse
Affiliation(s)
- Viktoria Rungelrath
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana
| | - Scott D Kobayashi
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana
| | - Frank R DeLeo
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana
| |
Collapse
|
50
|
CRISPR/Cas9 guided genome and epigenome engineering and its therapeutic applications in immune mediated diseases. Semin Cell Dev Biol 2019; 96:32-43. [PMID: 31112800 DOI: 10.1016/j.semcdb.2019.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 12/21/2022]
Abstract
Recent developments in the nucleic acid editing technologies have provided a powerful tool to precisely engineer the genome and epigenome for studying many aspects of immune cell differentiation and development as well as several immune mediated diseases (IMDs) including autoimmunity and cancer. Here, we discuss the recent technological achievements of the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-based RNA-guided genome and epigenome editing toolkit and provide an insight into how CRISPR/Cas9 (CRISPR Associated Protein 9) toolbox could be used to examine genetic and epigenetic mechanisms underlying IMDs. In addition, we will review the progress in CRISPR/Cas9-based genome-wide genome and epigenome screens in various cell types including immune cells. Finally, we will discuss the potential of CRISPR/Cas9 in defining the molecular function of disease associated SNPs overlapping gene regulatory elements.
Collapse
|