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Dai Y, Zhou J, Shi C. Inflammasome: structure, biological functions, and therapeutic targets. MedComm (Beijing) 2023; 4:e391. [PMID: 37817895 PMCID: PMC10560975 DOI: 10.1002/mco2.391] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 08/25/2023] [Accepted: 08/29/2023] [Indexed: 10/12/2023] Open
Abstract
Inflammasomes are a group of protein complex located in cytoplasm and assemble in response to a wide variety of pathogen-associated molecule patterns, damage-associated molecule patterns, and cellular stress. Generally, the activation of inflammasomes will lead to maturation of proinflammatory cytokines and pyroptotic cell death, both associated with inflammatory cascade amplification. A sensor protein, an adaptor, and a procaspase protein interact through their functional domains and compose one subunit of inflammasome complex. Under physiological conditions, inflammasome functions against pathogen infection and endogenous dangers including mtROS, mtDNA, and so on, while dysregulation of its activation can lead to unwanted results. In recent years, advances have been made to clarify the mechanisms of inflammasome activation, the structural details of them and their functions (negative/positive) in multiple disease models in both animal models and human. The wide range of the stimuli makes the function of inflammasome diverse and complex. Here, we review the structure, biological functions, and therapeutic targets of inflammasomes, while highlight NLRP3, NLRC4, and AIM2 inflammasomes, which are the most well studied. In conclusion, this review focuses on the activation process, biological functions, and structure of the most well-studied inflammasomes, summarizing and predicting approaches for disease treatment and prevention with inflammasome as a target. We aim to provide fresh insight into new solutions to the challenges in this field.
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Affiliation(s)
- Yali Dai
- Institute of Rocket Force MedicineState Key Laboratory of Trauma and Chemical PoisoningArmy Medical UniversityChongqingChina
| | - Jing Zhou
- Institute of Rocket Force MedicineState Key Laboratory of Trauma and Chemical PoisoningArmy Medical UniversityChongqingChina
- Institute of ImmunologyArmy Medical UniversityChongqingChina
| | - Chunmeng Shi
- Institute of Rocket Force MedicineState Key Laboratory of Trauma and Chemical PoisoningArmy Medical UniversityChongqingChina
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Egan MS, Zhang J, Shin S. Human and mouse NAIP/NLRC4 inflammasome responses to bacterial infection. Curr Opin Microbiol 2023; 73:102298. [PMID: 37058933 PMCID: PMC10225321 DOI: 10.1016/j.mib.2023.102298] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 02/15/2023] [Accepted: 02/22/2023] [Indexed: 04/16/2023]
Abstract
Intracellular immune complexes known as inflammasomes sense breaches of cytosolic sanctity. Inflammasomes promote downstream proinflammatory events, including interleukin-1 (IL-1) family cytokine release and pyroptotic cell death. The nucleotide-binding leucine-rich repeat family, apoptosis inhibitory protein/nucleotide-binding leucine-rich repeat family, caspase recruitment domain (CARD) domain-containing protein 4 (NAIP/NLRC4) inflammasome is involved in a range of pathogenic and protective inflammatory processes in mammalian hosts. In particular, the NAIP/NLRC4 inflammasome responds to flagellin and components of the virulence-associated type III secretion (T3SS) apparatus in the host cytosol, thereby allowing it to be a critical mediator of host defense during bacterial infection. Notable species- and cell type-specific differences exist in NAIP/NLRC4 inflammasome responses to bacterial pathogens. With a focus on Salmonella enterica serovar Typhimurium as a model pathogen, we review differences between murine and human NAIP/NLRC4 inflammasome responses. Differences in NAIP/NLRC4 inflammasome responses across species and cell types may have arisen in part due to evolutionary pressures.
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Affiliation(s)
- Marisa S Egan
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jenna Zhang
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Sunny Shin
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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de Lima JD, de Paula AGP, Yuasa BS, de Souza Smanioto CC, da Cruz Silva MC, Dos Santos PI, Prado KB, Winter Boldt AB, Braga TT. Genetic and Epigenetic Regulation of the Innate Immune Response to Gout. Immunol Invest 2023; 52:364-397. [PMID: 36745138 DOI: 10.1080/08820139.2023.2168554] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Gout is a disease caused by uric acid (UA) accumulation in the joints, causing inflammation. Two UA forms - monosodium urate (MSU) and soluble uric acid (sUA) have been shown to interact physically with inflammasomes, especially with the nod-like receptor (NLR) family pyrin domain containing 3 (NLRP3), albeit the role of the immune response to UA is poorly understood, given that asymptomatic hyperuricemia does also exist. Macrophage phagocytosis of UA activate NLRP3, lead to cytokines release, and ultimately, lead to chemoattract neutrophils and lymphocytes to the gout flare joint spot. Genetic variants of inflammasome genes and of genes encoding their molecular partners may influence hyperuricemia and gout susceptibility, while also influencing other comorbidities such as metabolic syndrome and cardiovascular diseases. In this review, we summarize the inflammatory responses in acute and chronic gout, specifically focusing on innate immune cell mechanisms and genetic and epigenetic characteristics of participating molecules. Unprecedently, a novel UA binding protein - the neuronal apoptosis inhibitor protein (NAIP) - is suggested as responsible for the asymptomatic hyperuricemia paradox.Abbreviation: β2-integrins: leukocyte-specific adhesion molecules; ABCG2: ATP-binding cassete family/breast cancer-resistant protein; ACR: American college of rheumatology; AIM2: absent in melanoma 2, type of pattern recognition receptor; ALPK1: alpha-protein kinase 1; ANGPTL2: angiopoietin-like protein 2; ASC: apoptosis-associated speck-like protein; BIR: baculovirus inhibitor of apoptosis protein repeat; BIRC1: baculovirus IAP repeat-containing protein 1; BIRC2: baculoviral IAP repeat-containing protein 2; C5a: complement anaphylatoxin; cAMP: cyclic adenosine monophosphate; CARD: caspase activation and recruitment domains; CARD8: caspase recruitment domain-containing protein 8; CASP1: caspase 1; CCL3: chemokine (C-C motif) ligand 3; CD14: cluster of differentiation 14; CD44: cluster of differentiation 44; Cg05102552: DNA-methylation site, usually cytosine followed by guanine nucleotides; contains arbitrary identification code; CIDEC: cell death-inducing DNA fragmentation factor-like effector family; CKD: chronic kidney disease; CNV: copy number variation; CPT1A: carnitine palmitoyl transferase - type 1a; CXCL1: chemokine (CXC motif) ligand 1; DAMPs: damage associated molecular patterns; DC: dendritic cells; DNMT(1): maintenance DNA methyltransferase; eQTL: expression quantitative trait loci; ERK1: extracellular signal-regulated kinase 1; ERK2: extracellular signal-regulated kinase 2; EULAR: European league against rheumatism; GMCSF: granulocyte-macrophage colony-stimulating factor; GWAS: global wide association studies; H3K27me3: tri-methylation at the 27th lysine residue of the histone h3 protein; H3K4me1: mono-methylation at the 4th lysine residue of the histone h3 protein; H3K4me3: tri-methylation at the 4th lysine residue of the histone h3 protein; HOTAIR: human gene located between hoxc11 and hoxc12 on chromosome 12; IκBα: cytoplasmatic protein/Nf-κb transcription inhibitor; IAP: inhibitory apoptosis protein; IFNγ: interferon gamma; IL-1β: interleukin 1 beta; IL-12: interleukin 12; IL-17: interleukin 17; IL18: interleukin 18; IL1R1: interleukin-1 receptor; IL-1Ra: interleukin-1 receptor antagonist; IL-22: interleukin 22; IL-23: interleukin 23; IL23R: interleukin 23 receptor; IL-33: interleukin 33; IL-6: interleukin 6; IMP: inosine monophosphate; INSIG1: insulin-induced gene 1; JNK1: c-jun n-terminal kinase 1; lncRNA: long non-coding ribonucleic acid; LRR: leucine-rich repeats; miR: mature non-coding microRNAs measuring from 20 to 24 nucleotides, animal origin; miR-1: miR followed by arbitrary identification code; miR-145: miR followed by arbitrary identification code; miR-146a: miR followed by arbitrary identification code, "a" stands for mir family; "a" family presents similar mir sequence to "b" family, but different precursors; miR-20b: miR followed by arbitrary identification code; "b" stands for mir family; "b" family presents similar mir sequence to "a" family, but different precursors; miR-221: miR - followed by arbitrary identification code; miR-221-5p: miR followed by arbitrary identification code; "5p" indicates different mature miRNAs generated from the 5' arm of the pre-miRNA hairpin; miR-223: miR followed by arbitrary identification code; miR-223-3p: mir followed by arbitrary identification code; "3p" indicates different mature miRNAs generated from the 3' arm of the pre-miRNA hairpin; miR-22-3p: miR followed by arbitrary identification code, "3p" indicates different mature miRNAs generated from the 3' arm of the pre-miRNA hairpin; MLKL: mixed lineage kinase domain-like pseudo kinase; MM2P: inductor of m2-macrophage polarization; MSU: monosodium urate; mTOR: mammalian target of rapamycin; MyD88: myeloid differentiation primary response 88; n-3-PUFAs: n-3-polyunsaturated fatty-acids; NACHT: acronym for NAIP (neuronal apoptosis inhibitor protein), C2TA (MHC class 2 transcription activator), HET-E (incompatibility locus protein from podospora anserina) and TP1 (telomerase-associated protein); NAIP: neuronal apoptosis inhibitory protein (human); Naip1: neuronal apoptosis inhibitory protein type 1 (murine); Naip5: neuronal apoptosis inhibitory protein type 5 (murine); Naip6: neuronal apoptosis inhibitory protein type 6 (murine); NBD: nucleotide-binding domain; Nek7: smallest NIMA-related kinase; NET: neutrophil extracellular traps; Nf-κB: nuclear factor kappa-light-chain-enhancer of activated b cells; NFIL3: nuclear-factor, interleukin 3 regulated protein; NIIMA: network of immunity in infection, malignancy, and autoimmunity; NLR: nod-like receptor; NLRA: nod-like receptor NLRA containing acidic domain; NLRB: nod-like receptor NLRA containing BIR domain; NLRC: nod-like receptor NLRA containing CARD domain; NLRC4: nod-like receptor family CARD domain containing 4; NLRP: nod-like receptor NLRA containing PYD domain; NLRP1: nucleotide-binding oligomerization domain, leucine-rich repeat, and pyrin domain containing 1; NLRP12: nucleotide-binding oligomerization domain, leucine-rich repeat, and pyrin domain containing 12; NLRP3: nod-like receptor family pyrin domain containing 3; NOD2: nucleotide-binding oligomerization domain; NRBP1: nuclear receptor-binding protein; Nrf2: nuclear factor erythroid 2-related factor 2; OR: odds ratio; P2X: group of membrane ion channels activated by the binding of extracellular; P2X7: p2x purinoceptor 7 gene; p38: member of the mitogen-activated protein kinase family; PAMPs: pathogen associated molecular patters; PBMC: peripheral blood mononuclear cells; PGGT1B: geranylgeranyl transferase type-1 subunit beta; PHGDH: phosphoglycerate dehydrogenase; PI3-K: phospho-inositol; PPARγ: peroxisome proliferator-activated receptor gamma; PPARGC1B: peroxisome proliferative activated receptor, gamma, coactivator 1 beta; PR3: proteinase 3 antigen; Pro-CASP1: inactive precursor of caspase 1; Pro-IL1β: inactive precursor of interleukin 1 beta; PRR: pattern recognition receptors; PYD: pyrin domain; RAPTOR: regulatory associated protein of mTOR complex 1; RAS: renin-angiotensin system; REDD1: regulated in DNA damage and development 1; ROS: reactive oxygen species; rs000*G: single nuclear polymorphism, "*G" is related to snp where replaced nucleotide is guanine, usually preceded by an id number; SLC2A9: solute carrier family 2, member 9; SLC7A11: solute carrier family 7, member 11; SMA: smooth muscular atrophy; Smac: second mitochondrial-derived activator of caspases; SNP: single nuclear polymorphism; Sp3: specificity protein 3; ST2: serum stimulation-2; STK11: serine/threonine kinase 11; sUA: soluble uric acid; Syk: spleen tyrosine kinase; TAK1: transforming growth factor beta activated kinase; Th1: type 1 helper T cells; Th17: type 17 helper T cells; Th2: type 2 helper T cells; Th22: type 22 helper T cells; TLR: tool-like receptor; TLR2: toll-like receptor 2; TLR4: toll-like receptor 4; TNFα: tumor necrosis factor alpha; TNFR1: tumor necrosis factor receptor 1; TNFR2: tumor necrosis factor receptor 2; UA: uric acid; UBAP1: ubiquitin associated protein; ULT: urate-lowering therapy; URAT1: urate transporter 1; VDAC1: voltage-dependent anion-selective channel 1.
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Affiliation(s)
- Jordana Dinorá de Lima
- Microbiology, Parasitology and Pathology Program, Universidade Federal do Parana (UFPR), Curitiba, Brazil
| | | | - Bruna Sadae Yuasa
- Microbiology, Parasitology and Pathology Program, Universidade Federal do Parana (UFPR), Curitiba, Brazil
| | | | - Maria Clara da Cruz Silva
- Microbiology, Parasitology and Pathology Program, Universidade Federal do Parana (UFPR), Curitiba, Brazil
| | | | - Karin Braun Prado
- Genetics Program, Universidade Federal do Parana (UFPR), Curitiba, Brazil
| | - Angelica Beate Winter Boldt
- Program of Internal Medicine, Universidade Federal do Parana (UFPR), Curitiba, Brazil
- Genetics Program, Universidade Federal do Parana (UFPR), Curitiba, Brazil
| | - Tárcio Teodoro Braga
- Microbiology, Parasitology and Pathology Program, Universidade Federal do Parana (UFPR), Curitiba, Brazil
- Biosciences and Biotechnology Program, Instituto Carlos Chagas (ICC), Fiocruz-Parana, Brazil
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Naseer N, Zhang J, Bauer R, Constant DA, Nice TJ, Brodsky IE, Rauch I, Shin S. Salmonella enterica Serovar Typhimurium Induces NAIP/NLRC4- and NLRP3/ASC-Independent, Caspase-4-Dependent Inflammasome Activation in Human Intestinal Epithelial Cells. Infect Immun 2022; 90:e0066321. [PMID: 35678562 PMCID: PMC9302179 DOI: 10.1128/iai.00663-21] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/23/2022] [Indexed: 01/09/2023] Open
Abstract
Salmonella enterica serovar Typhimurium is a Gram-negative pathogen that causes diseases ranging from gastroenteritis to systemic infection and sepsis. Salmonella uses type III secretion systems (T3SS) to inject effectors into host cells. While these effectors are necessary for bacterial invasion and intracellular survival, intracellular delivery of T3SS products also enables detection of translocated Salmonella ligands by cytosolic immune sensors. Some of these sensors form multimeric complexes called inflammasomes, which activate caspases that lead to interleukin-1 (IL-1) family cytokine release and pyroptosis. In particular, the Salmonella T3SS needle, inner rod, and flagellin proteins activate the NAIP/NLRC4 inflammasome in murine intestinal epithelial cells (IECs), which leads to restriction of bacterial replication and extrusion of infected IECs into the intestinal lumen, thereby preventing systemic dissemination of Salmonella. While these processes are quite well studied in mice, the role of the NAIP/NLRC4 inflammasome in human IECs remains unknown. Unexpectedly, we found the NAIP/NLRC4 inflammasome is dispensable for early inflammasome responses to Salmonella in both human IEC lines and enteroids. Additionally, NLRP3 and the adaptor protein ASC are not required for inflammasome activation in Caco-2 cells. Instead, we observed a necessity for caspase-4 and gasdermin D pore-forming activity in mediating inflammasome responses to Salmonella in Caco-2 cells. These findings suggest that unlike murine IECs, human IECs do not rely on NAIP/NLRC4 or NLRP3/ASC inflammasomes and instead primarily use caspase-4 to mediate inflammasome responses to Salmonella pathogenicity island 1 (SPI-1)-expressing Salmonella.
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Affiliation(s)
- Nawar Naseer
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Jenna Zhang
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Renate Bauer
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
- Department of Biosciences, Paris Lodron University of Salzburg, Salzburg, Austria
| | - David A. Constant
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Timothy J. Nice
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Igor E. Brodsky
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, USA
| | - Isabella Rauch
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Sunny Shin
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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Naseer N, Egan MS, Reyes Ruiz VM, Scott WP, Hunter EN, Demissie T, Rauch I, Brodsky IE, Shin S. Human NAIP/NLRC4 and NLRP3 inflammasomes detect Salmonella type III secretion system activities to restrict intracellular bacterial replication. PLoS Pathog 2022; 18:e1009718. [PMID: 35073381 PMCID: PMC8812861 DOI: 10.1371/journal.ppat.1009718] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 02/03/2022] [Accepted: 12/27/2021] [Indexed: 01/16/2023] Open
Abstract
Salmonella enterica serovar Typhimurium is a Gram-negative pathogen that uses two distinct type III secretion systems (T3SSs), termed Salmonella pathogenicity island (SPI)-1 and SPI-2, to deliver virulence factors into the host cell. The SPI-1 T3SS enables Salmonella to invade host cells, while the SPI-2 T3SS facilitates Salmonella's intracellular survival. In mice, a family of cytosolic immune sensors, including NAIP1, NAIP2, and NAIP5/6, recognizes the SPI-1 T3SS needle, inner rod, and flagellin proteins, respectively. Ligand recognition triggers assembly of the NAIP/NLRC4 inflammasome, which mediates caspase-1 activation, IL-1 family cytokine secretion, and pyroptosis of infected cells. In contrast to mice, humans encode a single NAIP that broadly recognizes all three ligands. The role of NAIP/NLRC4 or other inflammasomes during Salmonella infection of human macrophages is unclear. We find that although the NAIP/NLRC4 inflammasome is essential for detecting T3SS ligands in human macrophages, it is partially required for responses to infection, as Salmonella also activated the NLRP3 and CASP4/5 inflammasomes. Importantly, we demonstrate that combinatorial NAIP/NLRC4 and NLRP3 inflammasome activation restricts Salmonella replication in human macrophages. In contrast to SPI-1, the SPI-2 T3SS inner rod is not sensed by human or murine NAIPs, which is thought to allow Salmonella to evade host recognition and replicate intracellularly. Intriguingly, we find that human NAIP detects the SPI-2 T3SS needle protein. Critically, in the absence of both flagellin and the SPI-1 T3SS, the NAIP/NLRC4 inflammasome still controlled intracellular Salmonella burden. These findings reveal that recognition of Salmonella SPI-1 and SPI-2 T3SSs and engagement of both the NAIP/NLRC4 and NLRP3 inflammasomes control Salmonella infection in human macrophages.
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Affiliation(s)
- Nawar Naseer
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Marisa S. Egan
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Valeria M. Reyes Ruiz
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - William P. Scott
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon
| | - Emma N. Hunter
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Tabitha Demissie
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Isabella Rauch
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon
| | - Igor E. Brodsky
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania
| | - Sunny Shin
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- * E-mail:
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Zhang XO, Pratt H, Weng Z. Investigating the Potential Roles of SINEs in the Human Genome. Annu Rev Genomics Hum Genet 2021; 22:199-218. [PMID: 33792357 DOI: 10.1146/annurev-genom-111620-100736] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Short interspersed nuclear elements (SINEs) are nonautonomous retrotransposons that occupy approximately 13% of the human genome. They are transcribed by RNA polymerase III and can be retrotranscribed and inserted back into the genome with the help of other autonomous retroelements. Because they are preferentially located close to or within gene-rich regions, they can regulate gene expression by various mechanisms that act at both the DNA and the RNA levels. In this review, we summarize recent findings on the involvement of SINEs in different types of gene regulation and discuss the potential regulatory functions of SINEs that are in close proximity to genes, Pol III-transcribed SINE RNAs, and embedded SINE sequences within Pol II-transcribed genes in the human genome. These discoveries illustrate how the human genome has exapted some SINEs into functional regulatory elements.
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Affiliation(s)
- Xiao-Ou Zhang
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; .,Current affiliation: School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Henry Pratt
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA;
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA;
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Plaza-Díaz J, Álvarez-Mercado AI, Robles-Sánchez C, Navarro-Oliveros M, Morón-Calvente V, Toribio-Castelló S, Sáez-Lara MJ, MacKenzie A, Fontana L, Abadía-Molina F. NAIP expression increases in a rat model of liver mass restoration. J Mol Histol 2021; 52:113-123. [PMID: 33237375 DOI: 10.1007/s10735-020-09928-y] [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: 07/28/2020] [Accepted: 11/13/2020] [Indexed: 11/26/2022]
Abstract
The neuronal apoptosis inhibitory protein (NAIP) is a constituent of the NLRC4 inflammasome, which plays a key role in innate immunity, and an antiapoptotic protein. Recently, we reported the previously undescribed role of NAIP in cell division. The liver is one of the body's most actively regenerative organs. Given the novel mitotic role of NAIP, we examined its expression in hepatic mass restoration. The major liver lobe of Wistar rats was removed, and samples from both newly formed liver tissue, assessed by positive Ki67 immunostaining, and the remnant, intact liver lobes from hepatectomized rats were taken 3 and 7 days after surgery. Naip5 and Naip6 mRNA levels were significantly higher in regenerating hepatic tissue than in intact liver lobe tissue, and this increase was also observed at the protein level. Naip5 and Naip6 mRNA in situ hybridization showed that this increase occurred in the hepatic parenchyma. The histology of the regenerated liver tissue was normal, with the exception of a noticeable deficiency of hepatic lobule central veins. The results of this study suggest the involvement of NAIP in liver mass restoration following partial hepatectomy.
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Affiliation(s)
- Julio Plaza-Díaz
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071, Granada, Spain
- Institute of Nutrition and Food Technology "José Mataix", Biomedical Research Center, Avda. del Conocimiento S/N, Armilla, 18016, Granada, Spain
- Instituto de Investigación Biosanitaria Ibs.GRANADA, Avda. de Madrid 15, 18012, Granada, Spain
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - Ana I Álvarez-Mercado
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071, Granada, Spain
- Institute of Nutrition and Food Technology "José Mataix", Biomedical Research Center, Avda. del Conocimiento S/N, Armilla, 18016, Granada, Spain
- Instituto de Investigación Biosanitaria Ibs.GRANADA, Avda. de Madrid 15, 18012, Granada, Spain
| | - Cándido Robles-Sánchez
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071, Granada, Spain
- Institute of Nutrition and Food Technology "José Mataix", Biomedical Research Center, Avda. del Conocimiento S/N, Armilla, 18016, Granada, Spain
| | - Miguel Navarro-Oliveros
- Instituto de Investigación Biosanitaria Ibs.GRANADA, Avda. de Madrid 15, 18012, Granada, Spain
| | - Virginia Morón-Calvente
- Department of Diabetes. Immunology, Diabetes & Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA
| | - Sofía Toribio-Castelló
- IBSAL, IBMCC, University of Salamanca-CSIC, Cancer Research Center, 37007, Salamanca, Spain
| | - María José Sáez-Lara
- Institute of Nutrition and Food Technology "José Mataix", Biomedical Research Center, Avda. del Conocimiento S/N, Armilla, 18016, Granada, Spain
- Instituto de Investigación Biosanitaria Ibs.GRANADA, Avda. de Madrid 15, 18012, Granada, Spain
- Department of Biochemistry and Molecular Biology I, School of Sciences, University of Granada, 18071, Granada, Spain
| | - Alex MacKenzie
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
- Department of Pediatrics, University of Ottawa, Ottawa, ON, K1H 8L1, Canada
| | - Luis Fontana
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071, Granada, Spain
- Institute of Nutrition and Food Technology "José Mataix", Biomedical Research Center, Avda. del Conocimiento S/N, Armilla, 18016, Granada, Spain
- Instituto de Investigación Biosanitaria Ibs.GRANADA, Avda. de Madrid 15, 18012, Granada, Spain
| | - Francisco Abadía-Molina
- Institute of Nutrition and Food Technology "José Mataix", Biomedical Research Center, Avda. del Conocimiento S/N, Armilla, 18016, Granada, Spain.
- Department of Cell Biology, School of Sciences, University of Granada, 18071, Granada, Spain.
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Miao B, Fu S, Lyu C, Gontarz P, Wang T, Zhang B. Tissue-specific usage of transposable element-derived promoters in mouse development. Genome Biol 2020; 21:255. [PMID: 32988383 PMCID: PMC7520981 DOI: 10.1186/s13059-020-02164-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are a significant component of eukaryotic genomes and play essential roles in genome evolution. Mounting evidence indicates that TEs are highly transcribed in early embryo development and contribute to distinct biological functions and tissue morphology. RESULTS We examine the epigenetic dynamics of mouse TEs during the development of five tissues: intestine, liver, lung, stomach, and kidney. We found that TEs are associated with over 20% of open chromatin regions during development. Close to half of these accessible TEs are only activated in a single tissue and a specific developmental stage. Most accessible TEs are rodent-specific. Across these five tissues, 453 accessible TEs are found to create the transcription start sites of downstream genes in mouse, including 117 protein-coding genes and 144 lincRNA genes, 93.7% of which are mouse-specific. Species-specific TE-derived transcription start sites are found to drive the expression of tissue-specific genes and change their tissue-specific expression patterns during evolution. CONCLUSION Our results suggest that TE insertions increase the regulatory potential of the genome, and some TEs have been domesticated to become a crucial component of gene and regulate tissue-specific expression during mouse tissue development.
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Affiliation(s)
- Benpeng Miao
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63108, USA
- Department of Genetics, Edison Family Center for Genomic Sciences and Systems Biology, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Shuhua Fu
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Cheng Lyu
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Paul Gontarz
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Ting Wang
- Department of Genetics, Edison Family Center for Genomic Sciences and Systems Biology, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA.
| | - Bo Zhang
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63108, USA.
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9
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Schubert KA, Xu Y, Shao F, Auerbuch V. The Yersinia Type III Secretion System as a Tool for Studying Cytosolic Innate Immune Surveillance. Annu Rev Microbiol 2020; 74:221-245. [PMID: 32660389 DOI: 10.1146/annurev-micro-020518-120221] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microbial pathogens have evolved complex mechanisms to interface with host cells in order to evade host defenses and replicate. However, mammalian innate immune receptors detect the presence of molecules unique to the microbial world or sense the activity of virulence factors, activating antimicrobial and inflammatory pathways. We focus on how studies of the major virulence factor of one group of microbial pathogens, the type III secretion system (T3SS) of human pathogenic Yersinia, have shed light on these important innate immune responses. Yersinia are largely extracellular pathogens, yet they insert T3SS cargo into target host cells that modulate the activity of cytosolic innate immune receptors. This review covers both the host pathways that detect the Yersinia T3SS and the effector proteins used by Yersinia to manipulate innate immune signaling.
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Affiliation(s)
- Katherine Andrea Schubert
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, California 95064, USA;
| | - Yue Xu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Feng Shao
- National Institute of Biological Sciences, Beijing 102206, China
| | - Victoria Auerbuch
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, California 95064, USA;
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10
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An integrated Asian human SNV and indel benchmark established using multiple sequencing methods. Sci Rep 2020; 10:9821. [PMID: 32555294 PMCID: PMC7300012 DOI: 10.1038/s41598-020-66605-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 05/05/2020] [Indexed: 11/08/2022] Open
Abstract
Sequencing technologies have been rapidly developed recently, leading to the breakthrough of sequencing-based clinical diagnosis, but accurate and complete genome variation benchmark would be required for further assessment of precision medicine applications. Despite the human cell line of NA12878 has been successfully developed to be a variation benchmark, population-specific variation benchmark is still lacking. Here, we established an Asian human variation benchmark by constructing and sequencing a stabilized cell line of a Chinese Han volunteer. By using seven different sequencing strategies, we obtained ~3.88 Tb clean data from different laboratories, hoping to reach the point of high sequencing depth and accurate variation detection. Through the combination of variations identified from different sequencing strategies and different analysis pipelines, we identified 3.35 million SNVs and 348.65 thousand indels, which were well supported by our sequencing data and passed our strict quality control, thus should be high confidence variation benchmark. Besides, we also detected 5,913 high-quality SNVs which had 969 sites were novel and located in the high homologous regions supported by long-range information in both the co-barcoding single tube Long Fragment Read (stLFR) data and PacBio HiFi CCS data. Furthermore, by using the long reads data (stLFR and HiFi CCS), we were able to phase more than 99% heterozygous SNVs, which helps to improve the benchmark to be haplotype level. Our study provided comprehensive sequencing data as well as the integrated variation benchmark of an Asian derived cell line, which would be valuable for future sequencing-based clinical development.
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11
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Bauer R, Rauch I. The NAIP/NLRC4 inflammasome in infection and pathology. Mol Aspects Med 2020; 76:100863. [PMID: 32499055 DOI: 10.1016/j.mam.2020.100863] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/30/2020] [Indexed: 12/16/2022]
Abstract
In this review we give an overview of the NAIP/NLRC4 activation mechanism as well as the described roles of this inflammasome, with a focus on in vivo infection and pathology. After ligand recognition by NAIP sensor proteins the NAIP/NLRC4 inflammasome forms through oligomerization with the NLRC4 adaptor to activate Caspase-1. The activating ligands are intracellular bacterial flagellin or type-3 secretion system components, delivered by pathogens. In vivo experiments indicate a role in macrophages during lung, spleen and liver infection and systemic sepsis like conditions, as well as in intestinal epithelial cells. Upon NAIP/NLRC4 activation in the intestine, epithelial cell extrusion is triggered in addition to the canonical inflammasome outcomes of cytokine cleavage and pyroptosis. Human patients with auto-activating mutations in NLRC4 present with an autoinflammatory syndrome including enterocolitis. Although one of the better understood inflammasomes in terms of mechanism, tissue specific functions of NAIP/NLRC4 are only beginning to be understood.
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Affiliation(s)
- Renate Bauer
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, USA; Department of Biosciences, University of Salzburg, A-5020, Salzburg, Austria
| | - Isabella Rauch
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, USA.
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12
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Jung S, Venkatesh J, Kang MY, Kwon JK, Kang BC. A non-LTR retrotransposon activates anthocyanin biosynthesis by regulating a MYB transcription factor in Capsicum annuum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 287:110181. [PMID: 31481212 DOI: 10.1016/j.plantsci.2019.110181] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 06/24/2019] [Accepted: 06/28/2019] [Indexed: 05/20/2023]
Abstract
The flavonoid compound anthocyanin is an important plant metabolite with nutritional and aesthetic value as well as anti-oxidative capacity. MYB transcription factors are key regulators of anthocyanin biosynthesis in plants. In pepper (Capsicum annuum), the CaAn2 gene, encoding an R2R3 MYB transcription factor, regulates anthocyanin biosynthesis. However, no functional study or structural analysis of functional and dysfunctional CaAn2 alleles has been performed. Here, to elucidate the function of CaAn2, we generated transgenic Nicotiana benthamiana and Arabidopsis thaliana plants expressing CaAn2. All of the tissues in these plants were purple. Promoter analysis of CaAn2 in purple C. annuum 'KC00134' plants revealed the insertion of a non-long terminal repeat (LTR) retrotransposon designated Ca-nLTR-A. To determine the promoter activity and functional domain of Ca-nLTR-A, various constructs carrying different domains of Ca-nLTR-A fused with GUS were transformed into N. benthamiana. Promoter analysis showed that the 3' untranslated region (UTR) of the second open reading frame of Ca-nLTR-A is responsible for CaAn2 expression in 'KC00134'. Sequence analysis of Ca-nLTR-A identified transcription factor binding sites known to regulate anthocyanin biosynthesis. This study indicates that insertion of a non-LTR retrotransposon in the promoter may activate expression of CaAn2 by recruiting transcription factors at the 3' UTR and thus provides the first example of exaptation of a non-LTR retrotransposon into a new promoter in plants.
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Affiliation(s)
- Soyoung Jung
- Department of Plant Science, Plant Genomics & Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.
| | - Jelli Venkatesh
- Department of Plant Science, Plant Genomics & Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.
| | - Min-Young Kang
- Department of Plant Science, Plant Genomics & Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.
| | - Jin-Kyung Kwon
- Department of Plant Science, Plant Genomics & Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.
| | - Byoung-Cheorl Kang
- Department of Plant Science, Plant Genomics & Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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Broad detection of bacterial type III secretion system and flagellin proteins by the human NAIP/NLRC4 inflammasome. Proc Natl Acad Sci U S A 2017; 114:13242-13247. [PMID: 29180436 DOI: 10.1073/pnas.1710433114] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Inflammasomes are cytosolic multiprotein complexes that initiate host defense against bacterial pathogens by activating caspase-1-dependent cytokine secretion and cell death. In mice, specific nucleotide-binding domain, leucine-rich repeat-containing family, apoptosis inhibitory proteins (NAIPs) activate the nucleotide-binding domain, leucine-rich repeat-containing family, CARD domain-containing protein 4 (NLRC4) inflammasome upon sensing components of the type III secretion system (T3SS) and flagellar apparatus. NAIP1 recognizes the T3SS needle protein, NAIP2 recognizes the T3SS inner rod protein, and NAIP5 and NAIP6 recognize flagellin. In contrast, humans encode a single functional NAIP, raising the question of whether human NAIP senses one or multiple bacterial ligands. Previous studies found that human NAIP detects both flagellin and the T3SS needle protein and suggested that the ability to detect both ligands was achieved by multiple isoforms encoded by the single human NAIP gene. Here, we show that human NAIP also senses the Salmonella Typhimurium T3SS inner rod protein PrgJ and that T3SS inner rod proteins from multiple bacterial species are also detected. Furthermore, we show that a single human NAIP isoform is capable of sensing the T3SS inner rod, needle, and flagellin. Our findings indicate that, in contrast to murine NAIPs, promiscuous recognition of multiple bacterial ligands is conferred by a single human NAIP.
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Spinal muscular atrophy carriers with two SMN1 copies. Brain Dev 2017; 39:851-860. [PMID: 28676237 DOI: 10.1016/j.braindev.2017.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 06/13/2017] [Accepted: 06/13/2017] [Indexed: 11/21/2022]
Abstract
BACKGROUND Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder. Over 95% of SMA patients have homozygous deletions of the SMA-causative gene, SMN1. Thus, SMA carriers are usually diagnosed based on SMN1 copy number, with one copy indicating SMA carrier status. However, two SMN1 copies do not always exclude carrier status. In this study, we identified SMA carriers with two SMN1 copies. SUBJECTS AND METHODS From 33 families, 65 parents of genetically confirmed SMA patients were tested to determine SMA carrier status. Molecular genetic analyses, including multiplex ligation-dependent probe amplification (MLPA) assay, were performed using blood samples from family members. RESULTS Of the 65 parents, three parents from three families had two SMN1 copies. Accordingly, the frequency of carriers with two SMN1 copies was 4.6%. Two of these families were further studied. Patient 1 was homozygous for SMN1 deletion. Patient 1's mother had two SMN1 copies on one chromosome, with deletion of SMN1 on the other chromosome ([2+0] genotype). Patient 1 inherited SMN1-deleted chromosomes from both parents. Patient 2 was compound heterozygous for two SMN1 mutations: whole-gene deletion and intragenic missense mutation, c.826T>C (p.Tyr276His). Patient 2's father had two SMN1 copies with the same intragenic mutation in one copy ([1+1d] genotype, d intragenic mutation). Patient 2 inherited the chromosome with an SMN1 mutation from the father and SMN1-deleted chromosome from the mother. CONCLUSION SMA carriers with two SMN1 copies may be rare, but its possibility should be taken into consideration in carrier testing and counseling for SMA families or population-based carrier screening.
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Anwar SL, Wulaningsih W, Lehmann U. Transposable Elements in Human Cancer: Causes and Consequences of Deregulation. Int J Mol Sci 2017; 18:E974. [PMID: 28471386 PMCID: PMC5454887 DOI: 10.3390/ijms18050974] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 04/26/2017] [Accepted: 04/29/2017] [Indexed: 01/04/2023] Open
Abstract
Transposable elements (TEs) comprise nearly half of the human genome and play an essential role in the maintenance of genomic stability, chromosomal architecture, and transcriptional regulation. TEs are repetitive sequences consisting of RNA transposons, DNA transposons, and endogenous retroviruses that can invade the human genome with a substantial contribution in human evolution and genomic diversity. TEs are therefore firmly regulated from early embryonic development and during the entire course of human life by epigenetic mechanisms, in particular DNA methylation and histone modifications. The deregulation of TEs has been reported in some developmental diseases, as well as for different types of human cancers. To date, the role of TEs, the mechanisms underlying TE reactivation, and the interplay with DNA methylation in human cancers remain largely unexplained. We reviewed the loss of epigenetic regulation and subsequent genomic instability, chromosomal aberrations, transcriptional deregulation, oncogenic activation, and aberrations of non-coding RNAs as the potential mechanisms underlying TE deregulation in human cancers.
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Affiliation(s)
- Sumadi Lukman Anwar
- Division of Surgical Oncology, Department of Surgery Faculty of Medicine, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia.
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover 30625, Germany.
- PILAR (Philippine and Indonesian Scholar) Research and Education, 20 Station Road, Cambridge CB1 2JD, UK.
| | - Wahyu Wulaningsih
- PILAR (Philippine and Indonesian Scholar) Research and Education, 20 Station Road, Cambridge CB1 2JD, UK.
- MRC (Medical Research Council) Unit for Lifelong Health and Ageing, University College London, London WC1B 5JU, UK.
- Division of Haematology/Oncology, Faculty of Medicine Universitas Gadjah Mada, Yogyakarta 55281, Indonesia.
| | - Ulrich Lehmann
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover 30625, Germany.
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Structural variants caused by Alu insertions are associated with risks for many human diseases. Proc Natl Acad Sci U S A 2017; 114:E3984-E3992. [PMID: 28465436 DOI: 10.1073/pnas.1704117114] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Interspersed repeat sequences comprise much of our DNA, although their functional effects are poorly understood. The most commonly occurring repeat is the Alu short interspersed element. New Alu insertions occur in human populations, and have been responsible for several instances of genetic disease. In this study, we sought to determine if there are instances of polymorphic Alu insertion variants that function in a common variant, common disease paradigm. We cataloged 809 polymorphic Alu elements mapping to 1,159 loci implicated in disease risk by genome-wide association study (GWAS) (P < 10-8). We found that Alu insertion variants occur disproportionately at GWAS loci (P = 0.013). Moreover, we identified 44 of these Alu elements in linkage disequilibrium (r2 > 0.7) with the trait-associated SNP. This figure represents a >20-fold increase in the number of polymorphic Alu elements associated with human phenotypes. This work provides a broader perspective on how structural variants in repetitive DNAs may contribute to human disease.
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17
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Neuronal apoptosis inhibitory protein (NAIP) localizes to the cytokinetic machinery during cell division. Sci Rep 2017; 7:39981. [PMID: 28059125 PMCID: PMC5216396 DOI: 10.1038/srep39981] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 11/30/2016] [Indexed: 12/17/2022] Open
Abstract
The neuronal apoptosis inhibitory protein (NAIP) is a constituent of the inflammasome and a key component of the innate immune system. Here we use immunofluorescence to position NAIP within the cytokinetic apparatus, contiguous to chromosomal passenger complex (CPC), Centralspindlin, PRC1 and KIF4A. During metaphase, NAIP accumulates in the mitotic spindle poles and is shown in spindle microtubules; in anaphase NAIP is detected in the middle of the central spindle. At the end of cytokinesis, NAIP is localized in the outlying region of the stem body, the center of the intercellular bridge formed between daughter cells prior to cellular abscission. We also describe the sustained presence of NAIP mRNA and protein throughout the cell cycle with a significant increase observed in the G2/M phase. Consistent with a role for NAIP in cytokinesis, NAIP overexpression in HeLa cells promotes the acquisition of a multinuclear phenotype. Conversely, NAIP siRNA gene silencing results in an apoptotic lethal phenotype. Our confocal and super resolution stimulated-emission-depletion (STED) examination of mammalian cell cytokinesis demonstrate a potential new role for NAIP in addition to anti-apoptotic and innate immunology functions.
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18
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Noguchi Y, Onishi A, Nakamachi Y, Hayashi N, Harahap NIF, Rochmah MA, Shima A, Yanagisawa S, Morisada N, Nakagawa T, Iijima K, Kasagi S, Saegusa J, Kawano S, Shinohara M, Tairaku S, Saito T, Kubo Y, Saito K, Nishio H. Telomeric Region of the Spinal Muscular Atrophy Locus Is Susceptible to Structural Variations. Pediatr Neurol 2016; 58:83-9. [PMID: 27268759 DOI: 10.1016/j.pediatrneurol.2016.01.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 01/18/2016] [Accepted: 01/22/2016] [Indexed: 01/11/2023]
Abstract
BACKGROUND Most patients with spinal muscular atrophy lack the survival motor neuron 1 gene (SMN1) in the telomeric region of the spinal muscular atrophy locus on chromosome 5q13. On the other hand, the copy number of SMN2, a centromeric homolog of SMN1, is increased in many of these patients. This study aimed to clarify the mechanism underlying these structural variations. METHODS We determined the copy numbers of telomeric and centromeric genes in the spinal muscular atrophy locus of 86 patients and 22 control subjects using multiplex ligation-dependent probe amplification analysis. Then, we chose 74 patients lacking SMN1 exons 7 and 8, and compared their dataset with that of 22 control subjects retaining SMN1 exons 7 and 8. RESULTS The SMN2 copy number was shown to vary widely and to correlate with the disease severity of the patients. Interestingly, telomeric NAIP and telomeric GTF2H2 showed similar tendencies. We also noted positive correlations among the copy number of SMN2 and the telomeric genes of the spinal muscular atrophy locus. However, the copy numbers of centromeric NAIP and centromeric GTF2H2 were stable among the patients, with both approximating a value of two. CONCLUSION Our findings suggested that the telomeric region of the spinal muscular atrophy locus appears to be susceptible to structural variation, whereas the centromeric region is stable. Moreover, according to our results, new SMN2 copies may be generated in the telomeric region of the spinal muscular atrophy locus, supporting the SMN1-to-SMN2 gene conversion theory.
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Affiliation(s)
- Yoriko Noguchi
- Department of Clinical Laboratory, Kobe University Hospital, Kobe, Japan
| | - Akira Onishi
- Department of Rheumatology and Clinical Immunology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yuji Nakamachi
- Department of Clinical Laboratory, Kobe University Hospital, Kobe, Japan
| | - Nobuhide Hayashi
- Department of Clinical Laboratory, Kobe University Hospital, Kobe, Japan
| | - Nur Imma Fatimah Harahap
- Department of Community Medicine and Social Health Care, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Mawaddah Ar Rochmah
- Department of Community Medicine and Social Health Care, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Ai Shima
- Department of Community Medicine and Social Health Care, Kobe University Graduate School of Medicine, Kobe, Japan
| | | | - Naoya Morisada
- Department of Community Medicine and Social Health Care, Kobe University Graduate School of Medicine, Kobe, Japan; Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Taku Nakagawa
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Shimpei Kasagi
- Department of Clinical Laboratory, Kobe University Hospital, Kobe, Japan
| | - Jun Saegusa
- Department of Clinical Laboratory, Kobe University Hospital, Kobe, Japan; Department of Rheumatology and Clinical Immunology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Seiji Kawano
- Department of Medical Education, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Masakazu Shinohara
- Department of Community Medicine and Social Health Care, Kobe University Graduate School of Medicine, Kobe, Japan; The Integrated Center for Mass Spectrometry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Shinya Tairaku
- Department of Obstetrics and Gynecology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Toshio Saito
- Division of Child Neurology, Department of Neurology, National Hospital Organization Toneyama National Hospital, Toyonaka, Japan
| | - Yuji Kubo
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Kayoko Saito
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Hisahide Nishio
- Department of Community Medicine and Social Health Care, Kobe University Graduate School of Medicine, Kobe, Japan; Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan.
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Lennartsson A, Arner E, Fagiolini M, Saxena A, Andersson R, Takahashi H, Noro Y, Sng J, Sandelin A, Hensch TK, Carninci P. Remodeling of retrotransposon elements during epigenetic induction of adult visual cortical plasticity by HDAC inhibitors. Epigenetics Chromatin 2015; 8:55. [PMID: 26673794 PMCID: PMC4678690 DOI: 10.1186/s13072-015-0043-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/09/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The capacity for plasticity in the adult brain is limited by the anatomical traces laid down during early postnatal life. Removing certain molecular brakes, such as histone deacetylases (HDACs), has proven to be effective in recapitulating juvenile plasticity in the mature visual cortex (V1). We investigated the chromatin structure and transcriptional control by genome-wide sequencing of DNase I hypersensitive sites (DHSS) and cap analysis of gene expression (CAGE) libraries after HDAC inhibition by valproic acid (VPA) in adult V1. RESULTS We found that VPA reliably reactivates the critical period plasticity and induces a dramatic change of chromatin organization in V1 yielding significantly greater accessibility distant from promoters, including at enhancer regions. VPA also induces nucleosome eviction specifically from retrotransposon (in particular SINE) elements. The transiently accessible SINE elements overlap with transcription factor-binding sites of the Fox family. Mapping of transcription start site activity using CAGE revealed transcription of epigenetic and neural plasticity-regulating genes following VPA treatment, which may help to re-program the genomic landscape and reactivate plasticity in the adult cortex. CONCLUSIONS Treatment with HDAC inhibitors increases accessibility to enhancers and repetitive elements underlying brain-specific gene expression and reactivation of visual cortical plasticity.
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Affiliation(s)
- Andreas Lennartsson
- />Department of Biosciences and Nutrition, NOVUM, Karolinska Institutet, Stockholm, Sweden
- />Genome Science Lab, RIKEN, Hirosawa, Wako-shi, Saitama 351-0198 Japan
| | - Erik Arner
- />Division of Genomic Technologies, RIKEN Center for Life Science Technologies, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Michela Fagiolini
- />Lab for Neuronal Circuit Development, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198 Japan
- />F. M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | - Alka Saxena
- />Division of Genomic Technologies, RIKEN Center for Life Science Technologies, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Robin Andersson
- />Department of Biology and BRIC, The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Hazuki Takahashi
- />Division of Genomic Technologies, RIKEN Center for Life Science Technologies, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Yukihiko Noro
- />Division of Genomic Technologies, RIKEN Center for Life Science Technologies, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Judy Sng
- />Lab for Neuronal Circuit Development, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198 Japan
- />F. M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- />Department of Pharmacology, National University of Singapore, 10 Medical Drive 05-34, Singapore, Singapore
| | - Albin Sandelin
- />Department of Biology and BRIC, The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Takao K. Hensch
- />Lab for Neuronal Circuit Development, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198 Japan
- />F. M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- />Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, 52 Oxford Street, Cambridge, MA 02138 USA
| | - Piero Carninci
- />Division of Genomic Technologies, RIKEN Center for Life Science Technologies, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
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Babaian A, Romanish MT, Gagnier L, Kuo LY, Karimi MM, Steidl C, Mager DL. Onco-exaptation of an endogenous retroviral LTR drives IRF5 expression in Hodgkin lymphoma. Oncogene 2015; 35:2542-6. [DOI: 10.1038/onc.2015.308] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 05/21/2015] [Accepted: 07/13/2015] [Indexed: 12/11/2022]
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Abstract
Salmonellae invasion and intracellular replication within host cells result in a range of diseases, including gastroenteritis, bacteraemia, enteric fever and focal infections. In recent years, considerable progress has been made in our understanding of the molecular mechanisms that salmonellae use to alter host cell physiology; through the delivery of effector proteins with specific activities and through the modulation of defence and stress response pathways. In this Review, we summarize our current knowledge of the complex interplay between bacterial and host factors that leads to inflammation, disease and, in most cases, control of the infection by its animal hosts, with a particular focus on Salmonella enterica subsp. enterica serovar Typhimurium. We also highlight gaps in our knowledge of the contributions of salmonellae and the host to disease pathogenesis, and we suggest future avenues for further study.
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Affiliation(s)
- Doris L. LaRock
- Department of Microbiology, University of Washington, Seattle, WA 98195
| | - Anu Chaudhary
- Department of Microbiology, University of Washington, Seattle, WA 98195
| | - Samuel I. Miller
- Department of Microbiology, University of Washington, Seattle, WA 98195
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
- Department of Immunology, University of Washington, Seattle, WA 98195
- Department of Medicine, University of Washington, Seattle, WA 98195
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22
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Allam R, Maillard MH, Tardivel A, Chennupati V, Bega H, Yu CW, Velin D, Schneider P, Maslowski KM. Epithelial NAIPs protect against colonic tumorigenesis. ACTA ACUST UNITED AC 2015; 212:369-83. [PMID: 25732303 PMCID: PMC4354369 DOI: 10.1084/jem.20140474] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
NLR family apoptosis inhibitory proteins (NAIPs) belong to both the Nod-like receptor (NLR) and the inhibitor of apoptosis (IAP) families. NAIPs are known to form an inflammasome with NLRC4, but other in vivo functions remain unexplored. Using mice deficient for all NAIP paralogs (Naip1-6(Δ/Δ)), we show that NAIPs are key regulators of colorectal tumorigenesis. Naip1-6(Δ/Δ) mice developed increased colorectal tumors, in an epithelial-intrinsic manner, in a model of colitis-associated cancer. Increased tumorigenesis, however, was not driven by an exacerbated inflammatory response. Instead, Naip1-6(Δ/Δ) mice were protected from severe colitis and displayed increased antiapoptotic and proliferation-related gene expression. Naip1-6(Δ/Δ) mice also displayed increased tumorigenesis in an inflammation-independent model of colorectal cancer. Moreover, Naip1-6(Δ/Δ) mice, but not Nlrc4-null mice, displayed hyper-activation of STAT3 and failed to activate p53 18 h after carcinogen exposure. This suggests that NAIPs protect against tumor initiation in the colon by promoting the removal of carcinogen-elicited epithelium, likely in a NLRC4 inflammasome-independent manner. Collectively, we demonstrate a novel epithelial-intrinsic function of NAIPs in protecting the colonic epithelium against tumorigenesis.
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Affiliation(s)
- Ramanjaneyulu Allam
- Department of Biochemistry, Ludwig Center for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland Universitätsklinik für Hämatologie und Hämatologisches Zentrallabor, Inselspital/Universitätsspital, 3010 Bern, Switzerland
| | - Michel H Maillard
- Service of Gastroenterology and Hepatology, Department of Medicine, Lausanne University Hospital, 1015 Lausanne, Switzerland
| | - Aubry Tardivel
- Department of Biochemistry, Ludwig Center for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
| | - Vijaykumar Chennupati
- Department of Biochemistry, Ludwig Center for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
| | - Hristina Bega
- Service of Gastroenterology and Hepatology, Department of Medicine, Lausanne University Hospital, 1015 Lausanne, Switzerland
| | - Chi Wang Yu
- Department of Biochemistry, Ludwig Center for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
| | - Dominique Velin
- Service of Gastroenterology and Hepatology, Department of Medicine, Lausanne University Hospital, 1015 Lausanne, Switzerland
| | - Pascal Schneider
- Department of Biochemistry, Ludwig Center for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
| | - Kendle M Maslowski
- Department of Biochemistry, Ludwig Center for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
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Harvey H, Piskareva O, Creevey L, Alcock LC, Buckley PG, O'Sullivan MJ, Segura MF, Gallego S, Stallings RL, Bray IM. Modulation of chemotherapeutic drug resistance in neuroblastoma SK-N-AS cells by the neural apoptosis inhibitory protein and miR-520f. Int J Cancer 2014; 136:1579-88. [PMID: 25137037 DOI: 10.1002/ijc.29144] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 06/20/2014] [Accepted: 07/23/2014] [Indexed: 12/26/2022]
Abstract
The acquisition of multidrug resistance is a major impediment to the successful treatment of neuroblastoma, a clinically heterogeneous cancer accounting for ∼15% of all pediatric cancer deaths. The MYCN transcription factor, whose gene is amplified in ∼30% of high-risk neuroblastoma cases, influences drug resistance by regulating a cadre of genes, including those involved with drug efflux, however, other high-risk subtypes of neuroblastoma lacking MYCN amplification, such as those with chromosome 11q deletions, also acquire multidrug resistance. To elucidate additional mechanisms involved with drug resistance in non-MYCN amplified tumour cells, an SK-N-AS subline (SK-N-AsCis24) that is significantly resistant to cisplatin and cross resistant to etoposide was developed through a pulse-selection process. High resolution aCGH analysis of SK-N-AsCis24 revealed a focal gain on chromosome 5 containing the coding sequence for the neural apoptosis inhibitory protein (NAIP). Significant overexpression of NAIP mRNA and protein was documented, while experimental modulation of NAIP levels in both SK-N-AsCis24 and in parental SK-N-AS cells confirmed that NAIP was responsible for the drug resistant phenotype by apoptosis inhibition. Furthermore, a decrease in the NAIP targeting microRNA, miR-520f, was also demonstrated to be partially responsible for increased NAIP levels in SK-N-AsCis24. Interestingly, miR-520f levels were determined to be significantly lower in postchemotherapy treatment tumours relative to matched prechemotherapy samples, consistent with a role for this miRNA in the acquisition of drug resistance in vivo, potentially through decreased NAIP targeting. Our findings provide biological novel insight into neuroblastoma drug-resistance and have implications for future therapeutic research.
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Affiliation(s)
- Harry Harvey
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin 2, Ireland; National Children's Research Centre, Our Ladies Hospital for Sick Children, Dublin 12, Ireland
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24
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Tempel S, Talla E. Visual ModuleOrganizer: a graphical interface for the detection and comparative analysis of repeat DNA modules. Mob DNA 2014; 5:9. [PMID: 24678954 PMCID: PMC4022104 DOI: 10.1186/1759-8753-5-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 02/25/2014] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND DNA repeats, such as transposable elements, minisatellites and palindromic sequences, are abundant in sequences and have been shown to have significant and functional roles in the evolution of the host genomes. In a previous study, we introduced the concept of a repeat DNA module, a flexible motif present in at least two occurences in the sequences. This concept was embedded into ModuleOrganizer, a tool allowing the detection of repeat modules in a set of sequences. However, its implementation remains difficult for larger sequences. RESULTS Here we present Visual ModuleOrganizer, a Java graphical interface that enables a new and optimized version of the ModuleOrganizer tool. To implement this version, it was recoded in C++ with compressed suffix tree data structures. This leads to less memory usage (at least 120-fold decrease in average) and decreases by at least four the computation time during the module detection process in large sequences. Visual ModuleOrganizer interface allows users to easily choose ModuleOrganizer parameters and to graphically display the results. Moreover, Visual ModuleOrganizer dynamically handles graphical results through four main parameters: gene annotations, overlapping modules with known annotations, location of the module in a minimal number of sequences, and the minimal length of the modules. As a case study, the analysis of FoldBack4 sequences clearly demonstrated that our tools can be extended to comparative and evolutionary analyses of any repeat sequence elements in a set of genomic sequences. With the increasing number of sequences available in public databases, it is now possible to perform comparative analyses of repeated DNA modules in a graphic and friendly manner within a reasonable time period. AVAILABILITY Visual ModuleOrganizer interface and the new version of the ModuleOrganizer tool are freely available at: http://lcb.cnrs-mrs.fr/spip.php?rubrique313.
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Affiliation(s)
- Sebastien Tempel
- Aix-Marseille Université, CNRS, LCB, UMR 7283, 13009 Marseille, France
| | - Emmanuel Talla
- Aix-Marseille Université, CNRS, LCB, UMR 7283, 13009 Marseille, France
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25
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López-Yglesias AH, Zhao X, Quarles EK, Lai MA, VandenBos T, Strong RK, Smith KD. Flagellin induces antibody responses through a TLR5- and inflammasome-independent pathway. THE JOURNAL OF IMMUNOLOGY 2014; 192:1587-96. [PMID: 24442437 DOI: 10.4049/jimmunol.1301893] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Flagellin is a potent immunogen that activates the innate immune system via TLR5 and Naip5/6, and generates strong T and B cell responses. The adaptor protein MyD88 is critical for signaling by TLR5, as well as IL-1Rs and IL-18Rs, major downstream mediators of the Naip5/6 Nlrc4-inflammasome. In this study, we define roles of known flagellin receptors and MyD88 in Ab responses generated toward flagellin. We used mice genetically deficient in flagellin recognition pathways to characterize innate immune components that regulate isotype-specific Ab responses. Using purified flagellin from Salmonella, we dissected the contribution of innate flagellin recognition pathways to promote Ab responses toward flagellin and coadministered OVA in C57BL/6 mice. We demonstrate IgG2c responses toward flagellin were TLR5 and inflammasome dependent; IgG1 was the dominant isotype and partially TLR5 and inflammasome dependent. Our data indicate a substantial flagellin-specific IgG1 response was induced through a TLR5-, inflammasome-, and MyD88-independent pathway. IgA anti-FliC responses were TLR5 and MyD88 dependent and caspase-1 independent. Unlike C57BL/6 mice, flagellin-immunized A/J mice induced codominant IgG1 and IgG2a responses. Furthermore, MyD88-independent, flagellin-induced Ab responses were even more pronounced in A/J MyD88(-/-) mice, and IgA anti-FliC responses were suppressed by MyD88. Flagellin also worked as an adjuvant toward coadministered OVA, but it only promoted IgG1 anti-OVA responses. Our results demonstrate that a novel pathway for flagellin recognition contributes to Ab production. Characterization of this pathway will be useful for understanding immunity to flagellin and the rationale design of flagellin-based vaccines.
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26
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Nakamura H, Wang Y, Xue H, Romanish MT, Mager DL, Helgason CD, Wang Y. Genistein versus ICI 182, 780: an ally or enemy in metastatic progression of prostate cancer. Prostate 2013; 73:1747-60. [PMID: 24038102 DOI: 10.1002/pros.22712] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 06/20/2013] [Indexed: 11/09/2022]
Abstract
BACKGROUND Androgen signalling through the androgen receptor (AR) plays a critical role in prostate cancer (PCa) initiation and progression. Estrogen in synergy with androgen is essential for cell growth of the normal and malignant prostate. However, the exact role that estrogen and the estrogen receptor play in prostate carcinogenesis remains unclear. We have previously demonstrated the metastasis-promoting effect of an estrogen receptor beta (ERβ) agonist (genistein) in a patient-derived PCa xenograft model mimicking localized and metastatic disease. METHODS To test the hypothesis that the tumor-promoting activity of genistein was due to its estrogenic properties, we treated the xenograft-bearing mice with genistein and an anti-estrogen compound (ICI 182, 780) and compared the differential gene expression using microarrays. RESULTS Using a second xenograft model which was derived from another patient, we showed that genistein promoted disease progression in vivo and ICI 182, 780 inhibited metastatic spread. The microarray analysis revealed that the metallothionein (MT) gene family was differentially expressed in tumors treated by these compounds. Using qRT-PCR, the differences in expression levels were validated in the metastatic and non-metastatic LTL313 PCa xenograft tumor lines, both of which were originally derived from the same PCa patient. CONCLUSIONS Together our data provide evidence that genistein stimulates and ICI 182, 780 inhibits metastatic progression, suggesting that these effects may be mediated by ERβ signalling.
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Affiliation(s)
- Hisae Nakamura
- Experimental Therapeutics, BC Cancer Agency, Vancouver, British Columbia, Canada; Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada; The Vancouver Prostate Centre, Vancouver, British Columbia, Canada
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27
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Bryant CE, Monie TP. Mice, men and the relatives: cross-species studies underpin innate immunity. Open Biol 2013; 2:120015. [PMID: 22724060 PMCID: PMC3376732 DOI: 10.1098/rsob.120015] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 03/16/2012] [Indexed: 12/18/2022] Open
Abstract
The innate immune response is the first line of defence against infection. Germ-line-encoded receptors recognize conserved molecular motifs from both exogenous and endogenous sources. Receptor activation results in the initiation of a pro-inflammatory immune response that enables the resolution of infection. Understanding the inner workings of the innate immune system is a fundamental requirement in the search to understand the basis of health and disease. The development of new vaccinations, the treatment of pathogenic infection, the generation of therapies for chronic and auto-inflammatory disorders, and the ongoing battle against cancer, diabetes and atherosclerosis will all benefit from a greater understanding of innate immunity. The rate of knowledge acquisition in this area has been outstanding. It has been underpinned and driven by the use of model organisms. Information obtained from Drospohila melanogaster, knock-out and knock-in mice, and through the use of forward genetics has resulted in discoveries that have opened our eyes to the functionality and complexity of the innate immune system. With the current increase in genomic information, the range of innate immune receptors and pathways of other species available to study is rapidly increasing, and provides a rich resource to continue the development of innate immune research. Here, we address some of the highlights of cross-species study in the innate immune field and consider the benefits of widening the species-field further.
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Affiliation(s)
- Clare E Bryant
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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28
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de Souza FS, Franchini LF, Rubinstein M. Exaptation of transposable elements into novel cis-regulatory elements: is the evidence always strong? Mol Biol Evol 2013; 30:1239-51. [PMID: 23486611 PMCID: PMC3649676 DOI: 10.1093/molbev/mst045] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Transposable elements (TEs) are mobile genetic sequences that can jump around the genome from one location to another, behaving as genomic parasites. TEs have been particularly effective in colonizing mammalian genomes, and such heavy TE load is expected to have conditioned genome evolution. Indeed, studies conducted both at the gene and genome levels have uncovered TE insertions that seem to have been co-opted--or exapted--by providing transcription factor binding sites (TFBSs) that serve as promoters and enhancers, leading to the hypothesis that TE exaptation is a major factor in the evolution of gene regulation. Here, we critically review the evidence for exaptation of TE-derived sequences as TFBSs, promoters, enhancers, and silencers/insulators both at the gene and genome levels. We classify the functional impact attributed to TE insertions into four categories of increasing complexity and argue that so far very few studies have conclusively demonstrated exaptation of TEs as transcriptional regulatory regions. We also contend that many genome-wide studies dealing with TE exaptation in recent lineages of mammals are still inconclusive and that the hypothesis of rapid transcriptional regulatory rewiring mediated by TE mobilization must be taken with caution. Finally, we suggest experimental approaches that may help attributing higher-order functions to candidate exapted TEs.
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Affiliation(s)
- Flávio S.J. de Souza
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Lucía F. Franchini
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Marcelo Rubinstein
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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29
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Babatz TD, Burns KH. Functional impact of the human mobilome. Curr Opin Genet Dev 2013; 23:264-70. [PMID: 23523050 DOI: 10.1016/j.gde.2013.02.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 02/07/2013] [Accepted: 02/14/2013] [Indexed: 02/02/2023]
Abstract
The human genome is replete with interspersed repetitive sequences derived from the propagation of mobile DNA elements. Three families of human retrotransposons remain active today: LINE1, Alu, and SVA elements. Since 1988, de novo insertions at previously recognized disease loci have been shown to generate highly penetrant alleles in Mendelian disorders. Only recently has the extent of germline-transmitted retrotransposon insertion polymorphism (RIP) in human populations been fully realized. Also exciting are recent studies of somatic retrotransposition in human tissues and reports of tumor-specific insertions, suggesting roles in tissue heterogeneity and tumorigenesis. Here we discuss mobile elements in human disease with an emphasis on exciting developments from the last several years.
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Affiliation(s)
- Timothy D Babatz
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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30
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Mandal AK, Pandey R, Jha V, Mukerji M. Transcriptome-wide expansion of non-coding regulatory switches: evidence from co-occurrence of Alu exonization, antisense and editing. Nucleic Acids Res 2013; 41:2121-37. [PMID: 23303787 PMCID: PMC3575813 DOI: 10.1093/nar/gks1457] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 12/13/2012] [Accepted: 12/13/2012] [Indexed: 12/18/2022] Open
Abstract
Non-coding RNAs from transposable elements of human genome are gaining prominence in modulating transcriptome dynamics. Alu elements, as exonized, edited and antisense components within same transcripts could create novel regulatory switches in response to different transcriptional cues. We provide the first evidence for co-occurrences of these events at transcriptome-wide scale through integrative analysis of data sets across diverse experimental platforms and tissues. This involved the following: (i) positional anchoring of Alu exonization events in the UTRs and CDS of 4663 transcript isoforms from RefSeq mRNAs and (ii) mapping on to them A→I editing events inferred from ∼7 million ESTs from dbEST and antisense transcripts identified from virtual serial analysis of gene expression tags represented in Cancer Genome Anatomy Project next-generation sequencing data sets across 20 tissues. We observed significant enrichment of these events in the 3'UTR as well as positional preference within the embedded Alus. More than 300 genes had co-occurrence of all these events at the exon level and were significantly enriched in apoptosis and lysosomal processes. Further, we demonstrate functional evidence of such dynamic interactions between Alu-mediated events in a time series data from Integrated Personal Omics Profiling during recovery from a viral infection. Such 'single transcript-multiple fate' opportunity facilitated by Alu elements may modulate transcriptional response, especially during stress.
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Affiliation(s)
- Amit K. Mandal
- GN Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India and Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India
| | - Rajesh Pandey
- GN Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India and Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India
| | - Vineet Jha
- GN Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India and Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India
| | - Mitali Mukerji
- GN Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India and Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India
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von Moltke J, Ayres JS, Kofoed EM, Chavarría-Smith J, Vance RE. Recognition of bacteria by inflammasomes. Annu Rev Immunol 2012; 31:73-106. [PMID: 23215645 DOI: 10.1146/annurev-immunol-032712-095944] [Citation(s) in RCA: 322] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Inflammasomes are cytosolic multiprotein complexes that assemble in response to a variety of infectious and noxious insults. Inflammasomes play a critical role in the initiation of innate immune responses, primarily by serving as platforms for the activation of inflammatory caspase proteases. One such caspase, CASPASE-1 (CASP1), initiates innate immune responses by cleaving pro-IL-1β and pro-IL-18, leading to their activation and release. CASP1 and another inflammatory caspase termed CASP11 can also initiate a rapid and inflammatory form of cell death termed pyroptosis. Several distinct inflammasomes have been described, each of which contains a unique sensor protein of the NLR (nucleotide-binding domain, leucine-rich repeat-containing) superfamily or the PYHIN (PYRIN and HIN-200 domain-containing) superfamily. Here we describe the surprisingly diverse mechanisms by which NLR/PYHIN proteins sense bacteria and initiate innate immune responses. We conclude that inflammasomes represent a highly adaptable scaffold ideally suited for detecting and initiating rapid innate responses to diverse and rapidly evolving bacteria.
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Affiliation(s)
- Jakob von Moltke
- Department of Molecular & Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, California 94720, USA
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Beug ST, Cheung HH, LaCasse EC, Korneluk RG. Modulation of immune signalling by inhibitors of apoptosis. Trends Immunol 2012; 33:535-45. [PMID: 22836014 DOI: 10.1016/j.it.2012.06.004] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 06/08/2012] [Accepted: 06/21/2012] [Indexed: 12/17/2022]
Abstract
The inhibitor of apoptosis (IAP) genes are critical regulators of multiple pathways that control cell death, proliferation, and differentiation. Several members of the IAP family regulate innate and adaptive immunity through modulation of signal transduction pathways, cytokine production, and cell survival. The regulation of immunity by the IAPs is primarily mediated through the ubiquitin ligase function of cellular IAP (cIAP)1, cIAP2, and X-linked IAP (XIAP), the targets of which impact nuclear factor (NF)-κB and mitogen-activated protein kinase (MAPK) signalling pathways. In addition, neuronal apoptosis inhibitory protein (NAIP), cIAP1, and cIAP2 modulate innate immune responses through control of the inflammasome complex. This review examines the role of mammalian IAPs in regulating immunity and describes the implications of a new class of pan-IAP antagonists for the treatment of immune disorders.
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Affiliation(s)
- Shawn T Beug
- Apoptosis Research Centre, Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario K1H 8L1, Canada
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33
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Yao S, Ireland SJ, Bee A, Beesley C, Forootan SS, Dodson A, Dickinson T, Gerard P, Lian LY, Risk JM, Smith P, Malki MI, Ke Y, Cooper CS, Gosden C, Foster CS. Splice variant PRKC-ζ(-PrC) is a novel biomarker of human prostate cancer. Br J Cancer 2012; 107:388-99. [PMID: 22644296 PMCID: PMC3394965 DOI: 10.1038/bjc.2012.162] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 02/24/2012] [Accepted: 03/25/2012] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Previously, using gene-knockdown techniques together with genome expression array analysis, we showed the gene protein Kinase C (PKC)-zeta (PRKCZ) to mediate the malignant phenotype of human prostate cancer. However, according to NCBI, the gene has undergone several major iterations. Therefore, to understand the relationship between its structure and biological activities, we have analysed its expressed sequence in prostate cancer cell lines and tissues. METHODS Transcriptome-walking and targeted PCR were used to sequence the mRNA transcribed from PRKCZ. Hydropathy analysis was employed to analyse the hypothetical protein sequence subsequently translated and to identify an appropriate epitope to generate a specific monoclonal antibody. RESULTS A novel sequence was identified within the 3'-terminal domain of human PRKCZ that, in prostate cancer cell lines and tissues, is expressed during transcription and thereafter translated into protein (designated PKC-ζ(-PrC)) independent of conventional PKC-ζ(-a). The monoclonal antibody detected expression of this 96 kD protein only within malignant prostatic epithelium. INTERPRETATION Transcription and translation of this gene sequence, including previous intronic sequences, generates a novel specific biomarker of human prostate cancer. The presence of catalytic domains characteristic of classic PKC-β and atypical PKC-ι within PKC-ζ(-PrC) provides a potential mechanism for this PRKCZ variant to modulate the malignant prostatic phenotype out-with normal cell-regulatory control.
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Affiliation(s)
- S Yao
- Division of Pathology, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6th Floor, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - S J Ireland
- Division of Pathology, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6th Floor, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - A Bee
- Division of Pathology, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6th Floor, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - C Beesley
- Division of Pathology, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6th Floor, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - S S Forootan
- Division of Pathology, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6th Floor, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - A Dodson
- Division of Pathology, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6th Floor, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - T Dickinson
- Division of Pathology, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6th Floor, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - P Gerard
- Division of Pathology, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6th Floor, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - L-Y Lian
- School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - J M Risk
- School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - P Smith
- Division of Pathology, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6th Floor, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - M I Malki
- Division of Pathology, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6th Floor, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - Y Ke
- Division of Pathology, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6th Floor, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - C S Cooper
- University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - C Gosden
- Division of Pathology, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6th Floor, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - C S Foster
- Division of Pathology, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 6th Floor, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
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34
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Kofoed EM, Vance RE. NAIPs: building an innate immune barrier against bacterial pathogens. NAIPs function as sensors that initiate innate immunity by detection of bacterial proteins in the host cell cytosol. Bioessays 2012; 34:589-98. [PMID: 22513803 DOI: 10.1002/bies.201200013] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The innate immune system of mammals encodes several families of immune detector proteins that monitor the cytosol for signs of pathogen invasion. One important but poorly understood family of cytosolic immunosurveillance proteins is the NLR (nucleotide-binding domain, leucine-rich repeat containing) proteins. Recent work has demonstrated that one subfamily of NLRs, the NAIPs (NLR family, apoptosis inhibitory proteins), are activated by specific interaction with bacterial ligands, such as flagellin. NAIP activation leads to assembly of a large multiprotein complex called the inflammasome, which initiates innate immune responses by activation of the Caspase-1 protease. NAIPs therefore appear to detect pathogen molecules via a simple and direct receptor-ligand mechanism. Interestingly, other NLR family members appear to detect pathogens indirectly, perhaps by responding to host cell "stress" caused by the pathogen. Thus, the NLR family may have evolved surprisingly diverse mechanisms for detecting pathogens.
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Affiliation(s)
- Eric M Kofoed
- UC Berkeley-MCB, Life Sciences Addition, University of California-Berkeley, CA, USA.
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35
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Vizirianakis IS, Tezias SS, Amanatiadou EP, Tsiftsoglou AS. Possible interaction between B1 retrotransposon-containing sequences and β majorglobin gene transcriptional activation during MEL cell erythroid differentiation. Cell Biol Int 2012; 36:47-55. [DOI: 10.1042/cbi20110236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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Pandey R, Mandal AK, Jha V, Mukerji M. Heat shock factor binding in Alu repeats expands its involvement in stress through an antisense mechanism. Genome Biol 2011; 12:R117. [PMID: 22112862 PMCID: PMC3334603 DOI: 10.1186/gb-2011-12-11-r117] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 11/09/2011] [Accepted: 11/23/2011] [Indexed: 01/22/2023] Open
Abstract
Background Alu RNAs are present at elevated levels in stress conditions and, consequently, Alu repeats are increasingly being associated with the physiological stress response. Alu repeats are known to harbor transcription factor binding sites that modulate RNA pol II transcription and Alu RNAs act as transcriptional co-repressors through pol II binding in the promoter regions of heat shock responsive genes. An observation of a putative heat shock factor (HSF) binding site in Alu led us to explore whether, through HSF binding, these elements could further contribute to the heat shock response repertoire. Results Alu density was significantly enriched in transcripts that are down-regulated following heat shock recovery in HeLa cells. ChIP analysis confirmed HSF binding to a consensus motif exhibiting positional conservation across various Alu subfamilies, and reporter constructs demonstrated a sequence-specific two-fold induction of these sites in response to heat shock. These motifs were over-represented in the genic regions of down-regulated transcripts in antisense oriented Alus. Affymetrix Exon arrays detected antisense signals in a significant fraction of the down-regulated transcripts, 50% of which harbored HSF sites within 5 kb. siRNA knockdown of the selected antisense transcripts led to the over-expression, following heat shock, of their corresponding down-regulated transcripts. The antisense transcripts were significantly enriched in processes related to RNA pol III transcription and the TFIIIC complex. Conclusions We demonstrate a non-random presence of Alu repeats harboring HSF sites in heat shock responsive transcripts. This presence underlies an antisense-mediated mechanism that represents a novel component of Alu and HSF involvement in the heat shock response.
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Affiliation(s)
- Rajesh Pandey
- Genomics and Molecular Medicine, Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research (CSIR-IGIB), Delhi- India
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37
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Population variation in NAIP functional copy number confers increased cell death upon Legionella pneumophila infection. Hum Immunol 2011; 73:196-200. [PMID: 22067212 DOI: 10.1016/j.humimm.2011.10.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Revised: 08/30/2011] [Accepted: 10/03/2011] [Indexed: 12/22/2022]
Abstract
The NAIP gene encodes an intracellular innate immunity receptor that senses flagellin. The genomic region containing NAIP presents a complex genomic organization and includes various NAIP paralogs. Here, we assessed the degree of copy number variation of the complete NAIP gene (NAIPFull) in various human populations and studied the functional impact of such variation on host cell fate using Legionella pneumophila as an infection model. We determined that African populations have a NAIPFull duplication at a higher frequency than Europeans and Asians, with an increased transcription of the gene. In addition, we demonstrated that a higher amount of the NAIPFull protein dramatically increases cell death upon infection by L. pneumophila, a mechanism that may account for increased host resistance to infection. We postulate that the NAIPFull gene duplication might have been evolutionary maintained, or even selected for, because it may confer an advantage to the host against flagellated bacteria.
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38
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Pandey R, Mukerji M. From 'JUNK' to Just Unexplored Noncoding Knowledge: the case of transcribed Alus. Brief Funct Genomics 2011; 10:294-311. [DOI: 10.1093/bfgp/elr029] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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Macaulay EC, Weeks RJ, Andrews S, Morison IM. Hypomethylation of functional retrotransposon-derived genes in the human placenta. Mamm Genome 2011; 22:722-35. [PMID: 21874386 DOI: 10.1007/s00335-011-9355-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 07/29/2011] [Indexed: 11/25/2022]
Abstract
DNA hypomethylation is assumed to be a feature of the mammalian placenta; however, its role in regulating placental gene expression is not well defined. In this study, MeDIP and Sequenom MassARRAY were used to identify hypomethylated gene promoters in the human placenta. Among the genes identified, the hypomethylation of an alternative promoter for KCNH5 was found to be restricted to the placenta and chorion. Complete methylation of this promoter correlates with a silenced KCNH5 transcript in embryonic tissues, including the amnion. Unusually, this hypomethylated promoter and the alternative first exon are derived from a SINE (AluY) retrotransposon. Examination of additional retrotransposon-derived gene promoters in the placenta confirmed that retrotransposon hypomethylation permits the placenta-specific expression of these genes. Furthermore, the lineage-specific methylation displayed by KCNH5, INSL4, and ERVWE1 revealed that dichotomous methylation establishes differential retrotransposon silencing between the extra-embryonic and embryonic lineages. The hypomethylation of the retrotransposons that regulate these genes, each of which arose during recent primate evolution, is consistent with these genes having functional roles that are unique to the invasive haemochorial placentas of humans and recent primates.
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Affiliation(s)
- Erin C Macaulay
- Department of Pathology, Dunedin School of Medicine and National Research Centre for Growth and Development, University of Otago, New Zealand
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40
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Morrissy AS, Griffith M, Marra MA. Extensive relationship between antisense transcription and alternative splicing in the human genome. Genome Res 2011; 21:1203-12. [PMID: 21719572 DOI: 10.1101/gr.113431.110] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
To analyze the relationship between antisense transcription and alternative splicing, we developed a computational approach for the detection of antisense-correlated exon splicing events using Affymetrix exon array data. Our analysis of expression data from 176 lymphoblastoid cell lines revealed that the majority of expressed sense-antisense genes exhibited alternative splicing events that were correlated to the expression of the antisense gene. Most of these events occurred in areas of sense-antisense (SAS) gene overlap, which were significantly enriched in both exons and nucleosome occupancy levels relative to nonoverlapping regions of the same genes. Nucleosome occupancy was highly correlated with Pol II abundance across overlapping regions and with concomitant increases in local alternative exon usage. These results are consistent with an antisense transcription-mediated mechanism of splicing regulation in normal human cells. A comparison of the prevalence of antisense-correlated splicing events between individuals of Mormon versus African descent revealed population-specific events that may indicate the continued evolution of new SAS loci. Furthermore, the presence of antisense transcription was correlated to alternative splicing across multiple metazoan species, suggesting that it may be a conserved mechanism contributing to splicing regulation.
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Affiliation(s)
- A Sorana Morrissy
- British Columbia Cancer Agency, Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada
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41
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Oliver KR, Greene WK. Mobile DNA and the TE-Thrust hypothesis: supporting evidence from the primates. Mob DNA 2011; 2:8. [PMID: 21627776 PMCID: PMC3123540 DOI: 10.1186/1759-8753-2-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 05/31/2011] [Indexed: 02/07/2023] Open
Abstract
Transposable elements (TEs) are increasingly being recognized as powerful facilitators of evolution. We propose the TE-Thrust hypothesis to encompass TE-facilitated processes by which genomes self-engineer coding, regulatory, karyotypic or other genetic changes. Although TEs are occasionally harmful to some individuals, genomic dynamism caused by TEs can be very beneficial to lineages. This can result in differential survival and differential fecundity of lineages. Lineages with an abundant and suitable repertoire of TEs have enhanced evolutionary potential and, if all else is equal, tend to be fecund, resulting in species-rich adaptive radiations, and/or they tend to undergo major evolutionary transitions. Many other mechanisms of genomic change are also important in evolution, and whether the evolutionary potential of TE-Thrust is realized is heavily dependent on environmental and ecological factors. The large contribution of TEs to evolutionary innovation is particularly well documented in the primate lineage. In this paper, we review numerous cases of beneficial TE-caused modifications to the genomes of higher primates, which strongly support our TE-Thrust hypothesis.
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Affiliation(s)
- Keith R Oliver
- School of Biological Sciences and Biotechnology, Faculty of Science and Engineering, Murdoch University, Perth W. A. 6150, Australia
| | - Wayne K Greene
- School of Veterinary and Biomedical Sciences, Faculty of Health Sciences, Murdoch University, Perth W. A. 6150, Australia
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Zhang Y, Romanish MT, Mager DL. Distributions of transposable elements reveal hazardous zones in mammalian introns. PLoS Comput Biol 2011; 7:e1002046. [PMID: 21573203 PMCID: PMC3088655 DOI: 10.1371/journal.pcbi.1002046] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 03/25/2011] [Indexed: 11/20/2022] Open
Abstract
Comprising nearly half of the human and mouse genomes, transposable elements (TEs) are found within most genes. Although the vast majority of TEs in introns are fixed in the species and presumably exert no significant effects on the enclosing gene, some markedly perturb transcription and result in disease or a mutated phenotype. Factors determining the likelihood that an intronic TE will affect transcription are not clear. In this study, we examined intronic TE distributions in both human and mouse and found several factors that likely contribute to whether a particular TE can influence gene transcription. Specifically, we observed that TEs near exons are greatly underrepresented compared to random distributions, but the size of these “underrepresentation zones” differs between TE classes. Compared to elsewhere in introns, TEs within these zones are shorter on average and show stronger orientation biases. Moreover, TEs in extremely close proximity (<20 bp) to exons show a strong bias to be near splice-donor sites. Interestingly, disease-causing intronic TE insertions show the opposite distributional trends, and by examining expressed sequence tag (EST) databases, we found that the proportion of TEs contributing to chimeric TE-gene transcripts is significantly higher within their underrepresentation zones. In addition, an analysis of predicted splice sites within human long terminal repeat (LTR) elements showed a significantly lower total number and weaker strength for intronic LTRs near exons. Based on these factors, we selectively examined a list of polymorphic mouse LTR elements in introns and showed clear evidence of transcriptional disruption by LTR element insertions in the Trpc6 and Kcnh6 genes. Taken together, these studies lend insight into the potential selective forces that have shaped intronic TE distributions and enable identification of TEs most likely to exert transcriptional effects on genes. Sequences derived from transposable elements (TEs) are major constituents of mammalian genomes and are found within introns of most genes. While nearly all TEs within introns appear harmless, some de novo intronic TE insertions do disrupt gene transcription and splicing and cause disease. It is unclear why some intronic TEs perturb gene transcription whereas most do not. Here, we examined intronic TE distributions in both human and mouse genes to gain insight into which TEs may be more likely to affect transcription. We found evidence that TEs near exons are likely subject to strong negative selection but the size of the region under selection or “underrepresentation zone” differs for different TE classes. Strikingly, all reported human disease-causing intronic TE insertions fall within these underrepresentation zones, and the proportion of TEs contributing to chimeric TE-gene transcripts is significantly higher when TEs are located in these zones. We also examined insertionally polymorphic mouse TEs located within underrepresentation zones and found evidence of transcriptional disruption in two genes. Given the growing appreciation for ongoing activity of TEs in human, our results should be of value in prioritizing insertionally polymorphic TEs for study of their potential contributions to gene expression differences and phenotypic variability.
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Affiliation(s)
- Ying Zhang
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mark T. Romanish
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dixie L. Mager
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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Tempel S, Rousseau C, Tahi F, Nicolas J. ModuleOrganizer: detecting modules in families of transposable elements. BMC Bioinformatics 2010; 11:474. [PMID: 20860790 PMCID: PMC2955051 DOI: 10.1186/1471-2105-11-474] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Accepted: 09/22/2010] [Indexed: 12/20/2022] Open
Abstract
Background Most known eukaryotic genomes contain mobile copied elements called transposable elements. In some species, these elements account for the majority of the genome sequence. They have been subject to many mutations and other genomic events (copies, deletions, captures) during transposition. The identification of these transformations remains a difficult issue. The study of families of transposable elements is generally founded on a multiple alignment of their sequences, a critical step that is adapted to transposons containing mostly localized nucleotide mutations. Many transposons that have lost their protein-coding capacity have undergone more complex rearrangements, needing the development of more complex methods in order to characterize the architecture of sequence variations. Results In this study, we introduce the concept of a transposable element module, a flexible motif present in at least two sequences of a family of transposable elements and built on a succession of maximal repeats. The paper proposes an assembly method working on a set of exact maximal repeats of a set of sequences to create such modules. It results in a graphical view of sequences segmented into modules, a representation that allows a flexible analysis of the transformations that have occurred between them. We have chosen as a demonstration data set in depth analysis of the transposable element Foldback in Drosophila melanogaster. Comparison with multiple alignment methods shows that our method is more sensitive for highly variable sequences. The study of this family and the two other families AtREP21 and SIDER2 reveals new copies of very different sizes and various combinations of modules which show the potential of our method. Conclusions ModuleOrganizer is available on the Genouest bioinformatics center at http://moduleorganizer.genouest.org
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Affiliation(s)
- Sebastien Tempel
- IBISC, Tour Evry 2, 523 Place des Terrasses del'Agora, 91000 Evry, France
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