UNIVERSIDADE ESTADUAL DE CAMPINAS
FACULDADE DE ODONTOLOGIA DE PIRACICABA
MAYRA DE FARIA FRANÇA LEITE
METHYLATION-SENSITIVE HIGH RESOLUTION
MELTING (MS-HRM) ANALYSIS OF SOCS1, P16 AND TIMP2
GENES IN LPS-STIMULATED HUMAN GINGIVAL
FIBROBLASTS
ANÁLISE ESPECÍFICA DE METILAÇÃO POR MELTING
DE ALTA RESOLUÇÃO (MS-HRM) DOS GENES SOCS1, P16 E
TIMP2 EM FIBROBLASTOS GENGIVAIS HUMANOS
Piracicaba
2017
MAYRA DE FARIA FRANÇA LEITE
METHYLATION-SENSITIVE HIGH RESOLUTION
MELTING (MS-HRM) ANALYSIS OF SOCS1, P16 AND TIMP2
GENES IN LPS-STIMULATED HUMAN GINGIVAL
FIBROBLASTS
ANÁLISE ESPECÍFICA DE METILAÇÃO POR MELTING
DE ALTA RESOLUÇÃO (MS-HRM) DOS GENES SOCS1, P16 E
TIMP2 EM FIBROBLASTOS GENGIVAIS HUMANOS
ESTIMULADOS POR LPS
Dissertação apresentada à Faculdade de Odontologia de Piracicaba da Universidade Estadual de Campinas como parte dos requisitos exigidos para a obtenção do título de Mestra em Biologia Buco-Dental, na Área de Histologia e Embriologia
Dissertation presented to the Piracicaba Dental School of the University of Campinas in partial fulfillment of the requirements for the degree of Master in Dental Biology, in Histology and Embryology
Orientador: Profa. Dra. Ana Paula de Souza
Coorientador: Profa. Dra. Aline Cristiane Planello
ESTE EXEMPLAR CORRESPONDE ÀVERSÃO FINAL DA DISSERTAÇÃO DEFENDIDA PELA ALUNA MAYRA DE FARIA FRANÇA LEITE E ORIENTADA PELA PROFESSORA ANA PAULA DE SOUZA.
Piracicaba
2017
DEDICATÓRIA
Dedico este trabalho à minha avó Odila, ao meu avô Sérgio (in memorian)
e à minha mãe Márcia por serem os meus grandes exemplos de amor e profissionais
da área da Saúde.
AGRADECIMENTOS
A Deus e aos meus amados pais pela vida e por todo o amor recebido.
À Faculdade de Odontologia de Piracicaba da Universidade Estadual de
Campinas (FOP/UNICAMP).
À Profa. Dra. Ana Paula de Souza pela oportunidade de ingressar na
Pós-Graduação, pela sua orientação, pelos seus conhecimentos compartilhados, pelo seu
fundamental apoio e principalmente pela sua importância no meu crescimento pessoal
e profissional.
À minha coorientadora Aline Cristina Planello pela sua orientação, pelos
conhecimentos compartilhados e pela amizade.
Ao Prof. Dr. Sérgio Roberto Peres Line, o qual permitiu que eu pudesse
ingressar no universo da pesquisa durante a minha graduação, pelo apoio e amizade.
À CAPES pela Bolsa de Mestrado.
À FAPESP pelo financiamento do projeto de pesquisa.
A todos os Professores da Área de Histologia e Embriologia da
FOP/UNICAMP pelos conhecimentos compartilhados, pelo apoio e amizade.
Aos meus amigos de Departamento e Laboratório, em especial ao Gabriell
Borgato, pela enorme participação na realização do meu projeto de mestrado.
Aos meus irmãos Jaqueline e Rodrigo pelo amor, incentivo e apoio
incondicional.
Ao meu namorado Alan pelo amor, incentivo e apoio incondicional.
Aos meus amigos por todo apoio e carinho, em especial à minha amiga
Joyce.
RESUMO
Objetivo: O papel do lipopolissacarídeo bacteriano (LPS) para desencadear a
inflamação periodontal é bem conhecido. No entanto, o efeito do LPS na modulação
do estado de metilação do DNA não está completamente claro. Aqui, investigamos o
efeito do LPS de P. gingivalis no perfil de metilação da região reguladora dos genes
SOCS1, P16 e TIMP2 em fibroblastos gengivais humanos cultivados, a fim de avaliar
se o LPS pode alterar o estado de metilação desses genes. Material e Métodos: As
células de fibroblastos gengivais humanos imortalizadas foram cultivadas em meio
suplementado com LPS de P. gingivalis ou com o veículo do LPS de P. gingivalis
durante 12, 24 e 48 horas. A seguir, a viabilidade celular foi avaliada por teste de MTT.
O DNA genômico foi isolado e convertido por bissulfito de sódio. O estado de
metilação da região reguladora dos genes P16, SOCS1 e TIMP2 foi analisado por
PCR específica de metilação seguida por análise de melting de alta resolução
(MS-HRM). Resultados: Tanto fibroblastos estimulados por LPS quanto os fibroblastos
tratados apenas com o veículo do LPS não mostraram diferenças significativas na
região analisada dos genes P16, SOCS1 e TIMP2 durante os períodos de 12, 24 e 48
horas. Conclusão: Pequenos períodos de estimulação com LPS não foram suficientes
para promover alterações de metilação nas regiões analisadas dos genes SOCS1,
P16 e TIMP2 em fibroblastos. Relevância clínica: Compreender o papel das moléculas
derivadas de periodontopatógenos na promoção de alterações de metilação dentro da
região reguladora de genes-chaves associados à periodontite é importante para
aumentar o reconhecimento da área e pode abrir portas para o desenvolvimento de
novas terapias adjuvantes.
Palavras-chave: Epigenética, metilação do DNA, lipopolissacarídeo, LPS,
fibroblasto, MS-HRM
ABSTRACT
Objective: The role of bacterial lipopolysaccharide (LPS) to trigger periodontal
inflammation is well known. However, the effect of LPS in modulating the methylation
status of DNA is not completely clear. Here, we investigated the effect of P. gingivalis
LPS on the methylation profile of regulatory region of SOCS1, P16 and TIMP2 genes
in cultured human gingival fibroblast in order to assess whether LPS can alter the
methylation status of these genes. Material and Methods: Immortalized human gingival
fibroblast cells were cultured in medium supplemented with P. gingivalis LPS or P.
gingivalis LPS vehicle during 12, 24 and 48 hours. Following, cell viability was
assessed by MTT test. Genomic DNA was isolated and converted by sodium bisulfite.
The methylation status of the regulatory region of P16, SOCS1 and TIMP2 genes was
analyzed by methylation specific PCR followed by high resolution melting analysis
(MS-HRM). Results: Either fibroblast LPS-stimulated or fibroblast treated only with
vehicle did not show significant differences in the analyzed region of P16, SOCS1 and
TIMP2 genes during the periods of 12, 24 and 48 hours. Conclusion: Short periods of
LPS stimulation were not enough to promote methylation changes in the analyzed
regions of SOCS1, P16 and TIMP2 genes in fibroblasts. Clinical Relevance:
Understanding the role of molecules derived from periodontopathogens in promoting
methylation changes within regulatory region of key genes associated with
periodontitis is important to increase the area acknowledgment and can open doors to
the development of new adjuvant therapies.
Key words: Epigenetics, DNA methylation, lipopolysaccharide, LPS, fibroblast,
MS-HRM
SUMÁRIO
1 INTRODUÇÃO
10
2 ARTIGO: Methylation-Sensitive High Resolution Melting (MS-HRM)
Analysis of SOCS1, P16 And TIMP2 Genes In LPS-Stimulated
Human Gingival Fibroblasts
13
3 CONCLUSÃO
29
REFERÊNCIAS
30
10
1 INTRODUÇÃO
A periodontite (ou doença periodontal) é uma desordem inflamatória que
afeta os tecidos de suporte dos dentes (periodonto) e que da fase aguda torna-se
crônica. Está claro que o acúmulo de bactérias sobre a superfície da região cervical
dos dentes desencadeia a doença, porém seu agravamento e severidade são
dependentes de fatores como o hábito de fumar, a genética do hospedeiro e a
condição de saúde sistêmica.
A composição genética e epigenética do hospedeiro também podem
modular o prognóstico da doença periodontal. A epigenética pode ser definida como
mudanças no padrão de expressão do gene não envolvendo a sequência do DNA
(Larsson et al., 2015). A metilação do DNA e modificações em histonas são as duas
principais alterações epigenéticas em humanos (Takai et al., 2015). Essas alterações
podem contribuir para o desenvolvimento e manutenção de doenças inflamatórias,
doenças autoimunes e do câncer (Larsson et al., 2015). A metilação do DNA é um
mecanismo epigenético primário caracterizado pela adição de um grupo metil em
citosinas precedidas de guanina em regiões nomeadas ilhas CpG. As ilhas CpG
(CGIs) são pequenas sequências intercaladas de DNA que desviam significantemente
da média do padrão genômico por serem ricas em GC e são predominantemente
não-metiladas. As ilhas CpG evidentemente contém sítios de ínicio de transcrição (TSS),
os quais coincidem com a região promotora dos genes em ratos e humanos. As
características das sequências de DNA partilhadas adaptaram as CGIs para a função
de regiões promotoras, desestabilizando nucleossomos e atraindo proteínas que
criam um estado de cromatina transcricionalmente permissivo (Deaton e Bird, 2011).
A metilação do DNA está associada à várias mudanças na estrutura da
cromatina e ao recrutamento de proteínas para os sítios metilados. A metilação
geralmente leva à obstrução da região promotora, dificultando a transcrição gênica e
subsequentemente causando o silenciamento do gene (Rettori et al., 2013). A
metilação é mediada pelas enzimas da família das DNA metiltransferases (DNMTs),
sendo a função principal da DNMT1 a manutenção da metilação, metilando sítios
hemimetilados gerados durante a replicação do DNA, e as enzimas de novo DNMT3a
e DNMT3b são responsáveis pela metilação do DNA durante o desenvolvimento
embrionário (Abiko et al., 2014). Infecções bacterianas também induzem
11
modificações epigenéticas em células humanas, e a hipermetilação do DNA tem sido
implicada na doença periodontal em humanos (Larsson et al., 2015).
Patógenos
periodontais
são
fatores
ambientais
cruciais
no
desenvolvimento da doença periodontal. Uma bactéria que é frequentemente
detectada em bolsas periodontais é a Porphyromonas gingivalis. P. gingivalis é uma
bactéria anaeróbica, gram-negativa, que possui muitos fatores de virulência como
enzimas proteolíticas, fímbrias e lipopolissacarídeos (LPS) (Palm et. al., 2015). O LPS
é utilizado como uma toxina bacteriana para provocar respostas agudas em modelos
experimentais de infecção (Ding e Jin, 2014) (Johansson et al., 1996).
Fibroblastos gengivais são o tipo mais comum de células encontradas no
tecido gengival. Além de fornecerem uma estrutura tecidual, os fibroblastos também
demonstram responderem aos patógenos associados a padrões moleculares
(PAMPs) via, por exemplo, receptores ativados por proteases (PARs) e receptores do
tipo toll (TLRs), sendo o TLR2 e o TLR4 (Palm et al., 2015). Além de manter a
integridade do tecido gengival por meio da regulação do metabolismo do colágeno e
dos proteoglicanos, os fibroblastos gengivais produzem várias citocinas
pró-inflamatórias, como a interleucina-1 (IL-1), IL-6 e IL-8 em resposta à estimulação direta
e indireta com LPS (Tabeta et al., 2000). Fibroblastos do ligamento periodontal de
humanos estimulados por um longo período por LPS apresentaram hipermetilação de
genes da matriz extracelular, e as metilações ocorridas nas regiões promotoras dos
genes FANK1, COL4A1-A2, 12A1 e 15A1, LAMA5 e B1, MMP25, POMT1 e EMILIN3
estavam relacionadas com o baixo nível de expressão transcricional desses genes
(Takai et al., 2015).
O estudo da epigenética, especialmente a metilação do DNA, oferece um
enorme potencial para a identificação de marcadores biológicos que podem ser
utilizados no diagnóstico dos primeiros estágios de desenvolvimento do câncer, e para
uma avaliação mais precisa do risco individual de desenvolver doenças (Calmon et al,
2007). A proliferação celular é regulada em parte pelo produto proteico do gene
supressor de tumor P16 (Cody et al, 1999). Tipicamente, p16 induz a parada do ciclo
celular e impede a divisão celular através da inibição das quinases dependentes de
ciclina CDK4 e CDK6, bem como a fosforilação mediada por CDK do gene do
retinoblastoma (Conceição et al, 2015). O gene P16 foi um dos primeiros genes
12
investigados em câncer de cabeça e pescoço associado com a metilação do promotor
do gene, e é amplamente investigado em câncer oral (Ha e Califano, 2006).
As metaloproteinases da matriz (MMPs) são consideradas enzimas de
grande importância na destruição do tecido conjuntivo. Essas enzimas eventualmente
degradam o ligamento periodontal e as proteínas da matriz óssea. Inibidores teciduais
das metaloproteinases da matriz (TIMPs) são inibidores específicos das MMPs, e
desempenham um papel relevante no metabolismo da matriz extracelular periodontal
através do controle da atividade das MMPs (Kubota et al., 2008). O inibidor tecidual
de metaloproteinases-2 (TIMP2) é conhecido por antagonizar a atividade das
metaloproteinases da matriz e suprimir o crescimento tumoral, angiogênese, invasão
e metástases (Parashar e Capalash, 2012). Um desequilíbrio na interação MMP-TIMP
está implicado na etiologia da doença periodontal, onde a degradação da matriz
extracelular é uma característica principal (de Souza et al., 2005).
Muitas citocinas pró-inflamatórias desempenham papéis fundamentais na
iniciação de vias de sinalização intracelular específicas. Umas das mais importantes
cascatas de sinalização induzidas por citocinas é a via JAK/STAT (JAK (Janus kinase)
/ STAT (Signal Transducer e Activator of Transcription) (Andia et al., 2015). Os
supressores de sinalização de citocinas (SOCS) são uma família de proteínas
intracelulares que participam da regulação da resposta de células imunes ao estímulo
de várias citocinas pró-inflamatórias. SOCS1 é um potente inibidor de sinalização de
citocinas (Andia et al., 2015). A metilação do DNA é um importante mecanismo que
controla os níveis de transcrição do gene SOCS1. A Ilha CpG do gene SOCS1 invade
a região do primeiro e segundo éxon (De Souza et al., 2014). A hipermetilação do
gene SOCS1 é capaz de controlar a expressão de outros genes através da interação
enhancer/promotor, e este evento tem grande importância na patogênese da
inflamação crônica (Planello, 2014).
O presente estudo teve como objetivo analisar por MS-HRM (Methylation
Sensitive High Resolution Melting) a porcentagem da metilação dos genes P16,
SOCS1 e TIMP2 em cultura de fibroblastos gengivais humanos expostos ao LPS no
13
2 ARTIGO: METHYLATION-SENSITIVE HIGH RESOLUTION MELTING (MS-HRM)
ANALYSIS SOCS1, P16 AND TIMP2 GENES IN LPS-STIMULATED HUMAN
GINGIVAL FIBROBLASTS
Submetido ao periódico Clinical Oral Investigation (Anexo 1)
Mayra de Faria França Leite, Gabriell Borgatto, Aline Cristiane Planello, Ana Paula de
Souza.
Department of Morphology Division of Histology, Piracicaba Dental School - UNICAMP, Piracicaba-SP, Brazil
Corresponding author:
Ana Paula de Souza, PhD, Department of Morphology Piracicaba Dental School – UNICAMP
Limeira Avenue, 901, 13414-018, Piracicaba, SP, Brazil +55 (19) 21065381
apsfop@unicamp.br
Financial Support: This study was supported by Fundação de Amparo a Pesquisa do Estado de São Paulo (FAPESP 2015/24749-6). Mayra de Faria França Leite and Gabriell Borgatto was supported by Conselho Nacional de Pesquisa (CNPq). Aline Cristiane Planello was supported by Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP 2014/05867-5).
14
ABSTRACT
Objective: The role of bacterial lipopolysaccharide (LPS) in triggering periodontal inflammation is well known. However, the effect of LPS in modulating the methylation status of DNA is not completely clear. Here, we investigated the effect of P. gingivalis LPS on the methylation profile of regulatory region of SOCS1, P16 and TIMP2 genes in cultured human gingival fibroblast in order to assess whether LPS can alter the methylation status of these genes.
Material and Methods: Immortalized human gingival fibroblast cells were cultured in medium supplemented with P. gingivalis LPS or P. gingivalis LPS vehicle during 12, 24 and 48 hours. Following, cell viability was assessed by MTT test. Genomic DNA was isolated and converted by sodium bisulfite. The methylation status of the regulatory region of P16, SOCS1 and TIMP2 genes was analyzed by Methylation-Sensitive High Resolution Melting (MS-HRM).
Results: Neither fibroblast LPS-stimulated nor fibroblast treated only with vehicle showed significant differences in the analyzed region of P16, SOCS1 and TIMP2 genes during the periods of 12, 24 and 48 hours of treatment.
Conclusion: Short periods of LPS stimulation were not enough to promote methylation changes in the analyzed regions of SOCS1, P16 and TIMP2 genes in fibroblasts.
Clinical Relevance: Understanding the role of molecules derived from periodontopathogens in promoting methylation changes within regulatory region of key genes associated with periodontitis is important to increase the area acknowledgment - opening doors to the development of new adjuvant therapies.
15
INTRODUCTION
Periodontitis represents the most important oral disease of industrialized countries, responsible for teeth-lost in more than 20% of adult population [1]. It is an infection-associated inflammation disease induced by bacteria-derived molecules, such as lipopolysaccharide (LPS), that promotes the collagen type I breakdown and its solubilization from soft and hard periodontal tissues [2, 3].
In the last decades, explosion of studies have focused on the molecular basis of periodontitis in order to find the pathways that regulate the host tissues destruction. The understanding of how signal factors, cytokines, growth factors and transcriptional factors act during periodontitis have raised the knowledge of area. However, the investigation of factors directly associated with gene function is essential to clarify the real mechanisms.
Addressed to this topic, epigenetic emerges as the field committed to investigate the genome regulation. Epigenetic is the study of DNA/histone chemical changes inherited after mitotically and meiotically cell divisions that control chromatin structure and, consequently, gene functions [4,5]. Several proteins and enzymes take part in the molecular basis of epigenetics that involves histones modifications, noncoding RNAs and DNA methylation. Surely, DNA methylation does represent the most studied epigenetic change in the human genome that is carried out by DNA methyltransferases (DNMTs): the maintenance methyltransferase DNMT1 and de novo methyltransferases DNMT3A and DNMT3B. CpG enriched regions (named as CpG islands) are not randomly distributed around the whole genome and tends to be concentrated within regulatory regions such as gene promoters [6]. Ordinarily, CpG islands are found unmethylated but can become methylated during diseases, especially during tumor development and chronic inflammation.
We have reported that LPS can modify the transcription level of some chromatin modifying enzymes in human keratinocytes cells [7]. Adding, a few studies have shown that LPS-stimulated cells can answer differentially to epigenetic drugs [8] as well as extracellular matrix-related genes can become hypermethylated in human periodontal fibroblasts stimulated for a prolonged period with LPS derived from P. gingivalis [9].
Therefore, in the present paper we hypothesized whether LPS derived from P. gingivalis could be able to promote DNA methylation changes in the regulatory region of three genes that contain CpG islands and are implicated in different cell functions: SOCS1 a member of Suppressor Of Cytokine Signaling family that acts as classic negative feedback inhibitors of JAK/STAT pathway and is key physiological regulator of both innate and adaptive immunity [10]; P16 (also known as P16INK4a or CDKN2A) a tumor suppressor gene implicated in the prevention of several cancers, including oropharyngeal squamous cell carcinoma, cervical cancer, esophageal cancer [11], considered a key factor in controlling the G1 phase of cell
16
cycle; and TIMP2 (Tissue Inhibitor of Metalloproteinases-2) a member of TIMP family responsible for the physiological inhibition of matrix metalloproteinases (MMPs), whose imbalance can lead to connective tissue destruction [12]. Our analysis were carried on human gingival fibroblasts and MS-HRM assay was performed in order to quantify the percentage of DNA methylation in LPS-stimulated and non-stimulated cells.
MATERIAL AND METHODS
Materials
DMEM medium (Dulbecco’s Modified Eagle’s medium, Sigma Chemical Co.) was obtained from Cultilab (São Paulo, Brazil). Heat-inactivated fetal bovine serum (FBS) and trypsin/ ethylenediamine tetraacetic acid (EDTA) solution used in all experiments were purchased from LGC Biotecnologia (São Paulo, Brazil). The antibiotics (penicillin/streptomycin/) were purchased from GIBCO (Grand Island, NY, USA). Tissue culture multiwell plates were obtained from TPP® (Switzerland). P. gingivalis lipopolysaccharide (P. gingivalis LPS), extracted from P. gingivalis strain ATCC 3327, was obtained from InvivoGen (cat. code: tlrl-pglps, San Diego, CA, USA). For the viability analysis, a MTT assay was purchased from Invitrogen, Thermo Fisher Scientific. Quick-DNA Universal kit was obtained from Zymo Research. MethyISEQr Bisulfite Conversion kit was purchased from Life (Carlsbad, CA, USA). LightCycler®480 HRM Master Mix was purchased from Roche (Mannheim, Germany). EpiTect PCR Control DNA Set was obtained from Qiagen.
Cell Culture and LPS Treatment
Immortalized human gingival fibroblast cell line (HGF-1, ATCC® CRL-201) were cultured in DMEM medium supplemented with 10% FBS (fetal bovine serum) and 1% antibiotics in the humidified atmosphere (5% CO2) at 37oC with subculture every 3 days. At harvest, the cells were plated at a concentration of 1x105/mL and were exposed to P. gingivalis LPS at concentration of 1g/mL in serum re-supplemented with 10% FCS. The experiments were carried on at 12, 24 and 48 hours and after each 24 hour new amount of DMEM medium containing 10% FBS and LPS (1g/mL) was replaced. Culture treated with LPS vehicle (deionized water used to dilute LPS) was used as control. The experiment was performed in triplicate.
17
Viability Cell Assay
Cell viability was assessed by MTT reduction to formazan crystals by mitochondrial enzyme reductases using a MTT biochemical assay in 96-well plates. 1x105 cells/mL were seeded in wells and the assay was carried on in triplicate for each experimental time. MTT assay was performed following the manufacturer ́s protocol (Invitrogen). Finally, the multiwell plate was mixed until complete salt crystal dissolution and absorbance was measured in an ELISA reader (Molecular Devices, CA, USA) using the software VersaMax (test wavelength 570 nm, reference wavelength 630 nm).
DNA Extraction and Bisulfite Treatment
DNA was purified using Quick-DNA Universal kit, according to the manufacturer ́s protocol. After, 0.5 g of gDNA was bisulfite converted by MethyISEQr Bisulfite Conversion kit, following the manufacturer ́s protocol. The samples were short time storage at 04C and used for MS-HRM.
Methylation Sensitive High Resolution Melting (MS-HRM)
Real-time PCR followed by HRM was carried out in Light Cycler 480 II (Roche, Mannheim, Germany). The sequence of the primer set used is shown in Table 1. The reaction mixture consisted of 18 ng of bisulfite-converted DNA, 1x LightCycler®480 HRM Master Mix, 150 nM of each primer, 3 mM of MgCl+2 in a final volume of 20 μl. The reaction conditions were performed in a equal start for all genes at 95°C for 10 minutes, followed by specific cycles for each gene: P16 – 45 cycles at 95°C for 10 seconds, 64°C for 10 seconds, 72 °C for 10 seconds; TIMP2 – 45 cycles at 95°C for 10 seconds, 59°C for 05 seconds, 72 °C for 10 seconds; SOCS1 – 45 cycles at 95°C for 10 seconds, 55°C for 04 seconds, 72 °C for 10 seconds. MS-HRM analyses were performed at the temperature ramping and fluorescence acquisition settings recommended by the manufacturer, 1 minute at 95 °C, a hold at 70 °C for 1 minute to allow re-anneling of all PCR product, then the acquisition step started ramping from 70 °C to 95 °C, rising by 0,2 °C/s with 25 acquisitions per °C.
To estimate the methylation level of the samples, converted fully methylated and fully unmethylated DNA (EpiTect PCR Control DNA Set) were used to prepare dilution series as controls. The dilution series of relevant methylated DNA in a background of unmethylated DNA
18
were prepare in the concentration of 0%, 5%, 10%, 25%, 50% and 100% of methylation to build standards curves. PCR bias toward unmethylated DNA was reversed following the guideline published by Wojdacz (22). Standard curves and no template controls were included in each experimental run. As a negative control, genomic unconverted DNA was tested once with each primer. Initial assays were first run using 50% and 0% controls until the proportionality of amplification was achieved. MS-HRM data were normalized with the Light Cycler 480 II analysis software to compensate for varying starting fluorescence levels. The amplicon melting profile of each sample was compared to standard curves, and based on that, samples of each individual was classified into different methylation categories; 0-5, 6-10, 11- 25, 26-50 and 51-100%. The experiment was performed in triplicate.
RESULTS
MTT assay showed no effect of LPS on HGF cells viability at concentration of 1g/mL as well this LPS concentration did not alter the morphology of cells when we observed them by microscopy (Figure 1).
Following, human gingival fibroblasts were treated with P. gingivalis LPS in order to analyze the potential of this molecule derived from bacteria in promoting methylation changes in the regulatory region of P16, TIMP2 and SOCS1 genes. The assays were performed using MS-HRM approach in order to quantify methylation changes in those genes. Either exposure of HGF cells to LPS for 12h, 24h or for 48h did not promote significant differences in the methylation profile of the analyzed regions of these genes. The MS-HRM results of P16, TIMP2 and SOCS1 genes are shown in Figure 2, 3 and 4, respectively.
DISCUSSION
Cell functions such as activation, proliferation, and survival are differently controlled during chronic inflammation. It occurs not only due the number of new cascades of signal transduction pathways installed during inflammation, that activate different transcriptions factors that take part in the immune-inflammatory response, but also due the chromatin-remodeling that allows or prohibits the access of transcription factors to different regions of genome [13,14].
19
LPS is a component of the cell wall of gram-negative bacteria responsible for inducing expression of a range of pro-inflammatory cytokines such as TNF-α, IL-1β and IL-6 [15]. Injection of sub-lethal doses of LPS into animals demonstrated that a state of “LPS tolerance” was induced in the animals [16]. Interesting, while some genes became unable to answer to LPS-stimulation another group of genes entitled “non-tolerizable” escape from the suppressive effect of LPS tolerance [15]. Addressed to it, studies have demonstrated that gene promoters can be regulated in order to confer their tolerized status and apparently, the mechanism associated to it is chromatin-remodeling. Histone-modifications are found associated with LPS stimulation. Different histone marks are found as consequence of LPS stimulation and depending on if acute or whether prolonged (chronic) stimulation, these marks are different and induce an open or compacted chromatin status. For example, upon an acute LPS stimulation, H3K9 unmethylated is found in naïve human monocytes, while H3K9 dimethylation is observed in the same but tolerized cells [17, 18, 19].
In addition to histone modifications, DNA methylation is other epigenetic event able to regulate gene expression and confers gene tolerance to LPS. Unfortunately, DNA methylation was not widely investigated in acquire LPS-tolerance until moment, but is hypothesized that DNA methylation could be the final step in the tolerization process [15]. Recently, we published a study reporting that short period of LPS stimulation modulates gene expression of some enzymes implicate with epigenetic changes, such as DNA methyltransferases (DNMT1 and DNMT3A) [7].
P. gingivalis is a distinguished gram-negative periodontal pathogen able to lead consequences on host cells and LPS is a key bacteria-derived molecule that recognizes and binds to toll-like receptors TLR2 and TLR4 to trigger its effects [8]. In this study we challenged human gingival fibroblast cells with LPS derived from P. gingivalis in order to assess how short period of LPS-stimulation could modify the methylation profile of SOCS1, P16 and TIMP2 genes that are associated with different cell functions. Performing MS-HRM analysis, it is possible to verify percentages changes of methylation within DNA in a scale less than 1%.
SOCS family is composed by eight members that share similar structure. However, only SOCS1 and SOCS3 contain in the N-terminus sequence of 12-amino acids capable to inhibit the kinase activity of JAK2, due the presence of a pseudo-substrate for JAK2 in this additional region. Transcription of SOCS1 can be induced by cytokines that trigger JAK-STAT signaling pathway. Although gene promoter of SOCS1 shows motif to STAT-binding, the expression of SOCS1 leads the inhibition of JAK-STAT signaling via down-regulation of STAT activation due the blockage of kinase activity by the pseudo-substrate present in SOCS1. Reports have suggested that SOCS1 down-regulates the TLR signaling via LPS sensitivity
20
modulation. SOCS1-/- and INF-γ-/- mice showed an increased response to LPS when compared to only INF-γ-/- mice. Added, SOCS1-/- macrophages were hyper-responsive to LPS, indicating that SOCS1 can play a key role in the regulation of TLR via LPS signaling [20].
The analysis of SOCS1 genes did not shown any methylation changes in DNA when a short period of LPS-stimulation was assayed. Epigenetic changes in the intragenic region of SOCS1 have been frequently associated with chronic inflammation [21]. SOCS1 is a small gene that contains a CpG island (CGI) inside the promoter region that overlaps the first and second exons. This CGI is frequently observed hypermethylated in chronic disease as hepatitis and some types of cancer, taking part in the CGI methylator phenotype (CIMP) panel in colon cancer. Positive correlation between presence of methylation in regulatory region of SOCS1 and down-regulation of gene transcription is not always found. Recently, we published a paper showing that this same region of SOCS1 may act as an enhancer element over other genes of chromosome 16 in gingival tissue [21].
The tumor suppressor gene P16 (P16INK4a) plays a key role in cell cycle regulation by
decelerating cells progression from G1 phase to S phase. The protein is encoded by the CDKN2A locus that is located within human chromosome 9p21. This protein is a member of INK4 family of cyclin-dependent kinase inhibitors, mainly known to form a complex with CDK4 and CDK6 [23]. Although the mainly function of P16 is associated with tumor prevention, other different functions have been described for P16 in chronic inflammation. Proliferation of synovial fibroblasts is an ordinary event in rheumatoid arthritis trigged by molecules of inflammation. The intra-articular gene transfer of P16 was capable to inhibit synovial hyperplasia, immune-inflammatory cells infiltration, bone and cartilage joint destruction [24,25]. These findings are credit to the ability of P16 in inhibiting CDK4 and CDK6 that are responsible to release E2F transcription factors that allow cell-cycle progression [26]. P16 can also modulate the pro-inflammatory transcription factors NF-kB and AP-1 via its ankyrin motifs that bind c-jun [27] and NF-kB [28] and inhibit their activity. However, this P16 function is not available apparently in all cell types.
P16 gene is frequently mutated or deleted in a variety of cancer types as well as it can be silencing by hypermethylation. The P16 gene is found methylated in oral, esophageal and lung squamous cell carcinoma, in all of them the hypermethylation suppresses the mRNA transcription and, consequently, the protein expression [29]. In this study we tested the thesis of P16 gene becomes methylated in fibroblast as a consequence of LPS-stimulation. However, the results showed P16 completely unmethylated after LPS-stimulation for a short period.
TIMP-2 is one of a group of four members that compose the TIMP family, the natural tissue inhibitors of matrix metalloproteinases (MMPs). The inhibition is reached by the
N-21
terminal region of TIMP proteins that binds to the catalytic domain of MMPs. TIMP-2 specifically binds to MT1-MMP and this bi-molecular complex takes part in the process of pro-MMP2 activation [30]. Thus, TIMP-2 represents an inhibitor and activator of MMPs. Although TIMP-2 is secreted in the extracellular matrix, having well know functions outside cells, a number of reports have suggested a other functions to TIMP proteins since these proteins link to membrane receptors of different types of cells [31]. TIMP2 gene transcription is regulated epigenetically. CpG island that overlapping TIMP2 gene promoter is commonly seen hypermethylated in MCF-7 cells, silencing the gene transcription [31]. We did not detected methylation in the TIMP2 gene after LPS-stimulation. However, we emphasize the same could not be repeated whether other assay conditions would be performed such as LPS-stimulation for long period.
Previous study reported hypermethylation of extracellular matrix-related genes when fibroblasts were induced by LPS-stimulation for a prolonged period [9]. The LPS-stimulation period was basically the difference between our study and the other one. These results agree with the clinical findings in patients. Gingivitis is an acute inflammation that shows a set of clinical signs, microscopic and molecular features completely different from the set of findings that are seen in chronic periodontitis. Probably, the long-term exposure to LPS may promote epigenetic changes that are not detectable when we performed a short-term assay.
In conclusion, LPS stimulation did not promote methylation changes in the promoter region of SOCS1, P16 and TIMP2 genes when human gingival fibroblasts were stimulated for a short period. There is no guarantee the same would be found if others genome regions, others genes, others cell types or others assay-periods would be tested. Then, we have an “open sea” of hypothesis that must be still assayed in order to increase our knowledge about the effects of LPS in promoting epigenetic changes.
22
Table 1: Sequence of MS-HRM primers set, amplicons size and number of CpG sites
analyzed in the fragments.
Gene
Primer sequences (CpG sites
underlined and converted Cs as
capital Ts or As). (5'
→ 3').
Amplicon
CpGs between
the primers set
P16
F: ggagTTttcggTtgaTtggTtggTT
R: aAcaAcgcccgcacctcctcta
69bp
05
TIMP2
F: gTaTcggggagTagTtgTagg
R: cgctcgAcctcctActActAA
66bp
06
SOCS1
F: tcgcggTtgTTatTTaggtgaaag
R: cgaAcccgtAAAcaccttcctA
140bp
12
23
Figure 1. The figure represents the % of cells viability after HGF cells exposed to P.
gingivalis LPS (1
g/mL) for 12h, 24h and 48h or only vehicle (deionized water/control)
at the same periods of time. No significant differences were observed on the HGF cells
viability after the treatments (n=3/group).
Figure 2. MS-HRM assay of P16 gene. Different percentages of DNA methylation are
shown in different color in the curves. The percentages are obtained from the mix of
methylated and unmethylated control DNAs what allowed to build the assay calibration
curve. Samples are shown as strong blue color near to 0% (brown lines). The result
indicates that the promoter of P16 gene is completely unmethylated (0%) in control
and HGF cells after all periods of LPS treatment.
0 20 40 60 80 100 120 12h 24h 48h
% Cell Viability
Control LPS(1µg/mL) 0% 5% 10% 25% 50 and 100%24
Figure 3. MS-HRM assay of TIMP2 gene. Different percentages of DNA methylation
are shown in different color in the curves. The percentages are obtained from the mix
of methylated and unmethylated control DNAs what allowed to build the assay
calibration curve. Samples are shown as strong blue color near to 0% (blue lines). The
result indicates that the promoter of TIMP2 gene is completely unmethylated (0%) in
the control and HGF cells after all periods of LPS treatment.
Figure 4. MS-HRM assay of SOCS1 gene. Different percentages of DNA methylation
are shown in different color in the curves. The percentages are obtained from the mix
of methylated and unmethylated control DNAs what allowed to build the assay
calibration curve. Samples are shown as strong blue color near to 0% (red lines). The
result indicates that the promoter of SOCS1 gene is completely unmethylated in the
control and HGF cells after all periods of LPS treatment.
0% 5% 10% 25% 50% 100% 5% 25% 50% 100% 0% 10%
25
REFERENCES
1. Pihlstrom BL, Michalowicz BS, Johnson NW (2005). Periodontal diseases. Lancet 366:1809-1820.
2. Armitage GC (1995). Clinical evaluation of periodontal diseases. Periodontol 2000 7:39-53.
3. Scheres N, Laine ML, de Vries TJ, Everts V, van Winkelhoff AJ (2010). Gingival and periodontal ligament fibroblasts differ in their inflammatory response to viable Porphyromonas gingivalis. J Periodontol Res 45:262-270.
4. Bird AP (1986). CpG-rich islands and the function of DNA methylation. Nature 321: 209-213.
5. Bird A(2007). Perceptions of epigenetics. Nature 447, 396-398.
6. Jones PA(2012). Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet 13: 484-492.
7. de Camargo Pereira G, Guimarães GN, Planello AC, Santamaria MP, de Souza AP, Line SR, Marques MR (2013). Porphyromonas gingivalis LPS stimulation downregulates DNMT1, DNMT3a, and JMJD3 gene expression levels in human HaCaT keratinocytes. Clin Oral Investig 17: 1279-1285.
8. Shen J, Wu S, Guo W, Liang S, Li X, Yang X (2016). Epigenetic regulation of pro-inflammatory cytokine genes in lipopolysaccharide-stimulated peripheral blood mononuclear cells from broilers. Immunobiol 2985: 30370-30379.
9.Takai R, Uehara O, Harada F, Utsunomiya M, Chujo T, Yoshida K, Sato J, Nishimura M, Chiba I, Abiko Y (2016). DNA hypermethylation of extracellular matrix-related genes in human periodontal fibroblasts induced by stimulation for a prolonged period with lipopolysaccharide derived from Porphyromonas gingivalis. J Periodontal Res 51:508-517.
10. Starr R, Willson TA, Viney EM, Murray LJ, Rayner JR, Jenkins BJ, Gonda TJ, Alexander WS, Metcalf D, Nicola NA, Hilton DJ (1997). A family of cytokine-inducible inhibitors of signalling. Nature 387: 917–21.
26
11. Nobori T, Miura K, Wu DJ, Lois A, Takabayashi K, Carson DA (1994). Deletions of the cyclin-dependent kinase-4 inhibitor gene in multiple human cancers. Nature 368: 753–6.
12. Overall CM, Tam E, McQuibban GA, Morrison C, Wallon UM, Bigg HF, King AE, Roberts CR (2000). Domain interactions in the gelatinase A.TIMP-2.MT1-MMP activation complex. The ectodomain of the 44-kDa form of membrane type-1 matrix metalloproteinase does not modulate gelatinase A activation. J Biol Chem 275: 39497–506.
13. Natoli G (2009). Control of NF-kappaB-dependent transcriptional responses by chromatin organization. Cold Spring Harb Perspect Biol. 1:a000224.
14. Grabiec AM, Tak PP, Reedquist KA (2008). Targeting histone deacetylase activity in rheumatoid arthritis and asthma as prototypes of inflammatory disease: should we keep our HATs on? Arthritis Res Ther. 10:1-13.
15. Seeley JJ, Ghosh S (2016). Molecular mechanisms of innate memory and tolerance to LPS. J Leukoc Biol. 101: 1-11.
16. Beeson PB (1946). Development of tolerance to typhoid bacterial pyrogen and its abolition by reticulo-endothelial blockade. Proc Soc Exp Biol Med. 61:248-50.
17. El Gazzar M, Yoza BK, Hu JY, Cousart SL, McCall CE (2007). Epigenetic silencing of tumor necrosis factor alpha during endotoxin tolerance. J Biol Chem. 282:26857-64.
18. Chen X, El Gazzar M, Yoza BK, McCall CE (2009). The NF-kappaB factor RelB and histone H3 lysine methyltransferase G9a directly interact to generate epigenetic silencing in endotoxin tolerance. J Biol Chem. 284:27857-65.
19. Chan C, Li L, McCall CE, Yoza BK (2005). Endotoxin tolerance disrupts chromatin remodeling and NF-kappaB transactivation at the IL-1beta promoter. J Immunol. 175:461-8.
20. Zhang J, Li H, Yu JP, Wang SE, Ren XB (2012). Role of SOCS1 in tumor progression and therapeutic application. Int J Cancer. 130:1971-80.
21. Planello AC, Singhania R, Kron KJ, Bailey SD, Roulois D, Lupien M, Line SR, de Souza AP, De Carvalho DD (2016). Pre-neoplastic epigenetic disruption of transcriptional enhancers in chronic inflammation. Oncotarget. 7:15772-86.
27
22. Wojdacz TK, Dobrovic A, Hansen LL (2008). Methylation-sensitive high-resolution melting. Nat Prot. 3:1903-1908.
23. Cudejko C, Wouters K, Fuentes L, Hannou SA, Paquet C, Bantubungi K, Bouchaert E, Vanhoutte J, Fleury S, Remy P, Tailleux A, Chinetti-Gbaguidi G, Dombrowicz D, Staels B, Paumelle R (2011). p16INK4a deficiency promotes IL-4-induced polarization and inhibits proinflammatory signaling in macrophages. Blood. 118:2556-66.
24. Taniguchi K, Kohsaka H, Inoue N, Terada Y, Ito H, Hirokawa K, Miyasaka N (1999). Induction of the p16INK4a senescence gene as a new therapeutic strategy for the treatment of rheumatoid arthritis. Nat Med. 5:760-7.
25. Nasu K, Kohsaka H, Nonomura Y, Terada Y, Ito H, Hirokawa K, Miyasaka N (2000). Adenoviral transfer of cyclin-dependent kinase inhibitor genes suppresses collagen-induced arthritis in mice. J Immunol. 165:7246-52.
26. Murakami Y, Mizoguchi F, Saito T, Miyasaka N, Kohsaka H (2012). p16(INK4a) exerts an anti-inflammatory effect through accelerated IRAK1 degradation in macrophages. J Immunol. 189:5066-72.
27. Choi BY, Choi HS, Ko K, Cho YY, Zhu F, Kang BS, Ermakova SP, Ma WY, Bode AM, Dong Z (2005). The tumor suppressor p16(INK4a) prevents cell transformation through inhibition of c-Jun phosphorylation and AP-1 activity. Nat Struct Mol Biol. 12:699-707.
28. Wolff B, Naumann M (1999). INK4 cell cycle inhibitors direct transcriptional inactivation of NF-kappaB. Oncogene. 18:2663-6.
29. Terayama Y, Matsuura T, Ozaki K (2016). Lack of Correlation between Aberrant p16, RAR-β2, TIMP3, ERCC1, and BRCA1 Protein Expression and Promoter Methylation in Squamous Cell Carcinoma Accompanying Candida albicans-Induced Inflammation. PLoS One. 11:e0159090.
30. Chernov AV, Sounni NE, Remacle AG, Strongin AY (2009). Epigenetic control of the invasion-promoting MT1-MMP/MMP-2/TIMP-2 axis in cancer cells. J Biol Chem. 284:12727-34.
28
31. Bourboulia D, Stetler-Stevenson WG (2010). Matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs): Positive and negative regulators in tumor cell adhesion. Semin Cancer Biol. 20:161-8.
29
3 CONCLUSÃO
No presente estudo, nós concluímos que fibroblastos gengivais humanos
estimulados por LPS em um curto período não apresentaram alterações de metilação
nos promotores dos genes P16, TIMP2 e SOCS1. Outros períodos de ensaio devem
ser realizados a fim de verificar se o LPS promoverá alterações na metilação dos
promotores desses genes, ou em outras regiões desses genes. Portanto, temos
inúmeras hipóteses que ainda devem ser ensaiadas, a fim de aumentar o nosso
conhecimento sobre os efeitos do LPS na promoção de alterações epigenéticas.
30
REFERÊNCIAS
*Abiko Y, Uehara O, Fukumoto S, Ohta T. Epigenetics of oral infection and inflammatory
diseases – DNA methylation changes in infections and inflammation diseases. J Oral
Biosci. 2014 Nov.56(4)105-9.
Andia DC, Planello AC, Portinho D, da Silva RA, Salmon CR, Sallum EA, et al. DNA
methylation analysis of SOCS1, SOCS3, and LINE-1 in microdissected gingival tissue.
Clin Oral Investig. 2015 Dec;19(9):2337-44. doi: 10.1007/s00784-015-1460-1.
Calmon MF, Colombo J, Carvalho F, Souza FP, Filho JF, Fukuyama EE, et al.
Methylation profile of genes CDKN2A (p14 and p16), DAPK1, CDH1, and ADAM23 in
head and neck cancer. Cancer Genet Cytogenet. 2007 Feb;173(1):31-7.
Cody DT 2nd, Huang Y, Darby CJ, Johnson GK, Domann FE. Differential DNA
methylation of the p16 INK4A/CDKN2A promoter in human oral cancer cells and
normal human oral keratinocytes. Oral Oncol. 1999 Sep;35(5):516-22.
Conceição AL, Babeto E, Candido NM, Franco FC, de Campos Zuccari DA, Bonilha
JL, et al. Differential Expression of ADAM23, CDKN2A (P16), MMP14 and VIM
Associated with Giant Cell Tumor of Bone. J Cancer. 2015 May 23;6(7):593-603. doi:
10.7150/jca.11238.
Deaton AM, Bird A. CpG islands and the regulation of transcription. Genes Dev. 2011
May 15;25(10):1010-22. doi: 10.1101/gad.2037511.
De Souza AP, Planello AC, Marques MR, De Carvalho DD, Line SR. High-throughput
DNA analysis shows the importance of methylation in the control of imune inflammatory
gene transcription in chronic periodontitis. Clin Epigenetics. 2014 Aug 12;6(1):15. doi:
10.1186/1868-7083-6-15.
De Souza AP, Trevilatto PC, Scarel-Caminaga RM, de Brito RB Jr, Barros SP, Line
SR. Analysis of the MMP-9 (C-1562 T) and TIMP-2 (G-418C) gene promoter
polymorphisms in patients with chronic periodontitis. J Clin Periodontol. 2005
Feb;32(2):207-11.
* De acordo com as normas da UNICAMP/FOP, baseadas na padronização do International Committee of Medical Journal Editors - Vancouver Group. Abreviatura dos periódicos em conformidade com o PubMed.
31
Ding PH, Jin LJ. The role of lipopolysaccharide-binding protein in innate immunity: a
revisit and its relevance to oral/periodontal health. J Periodontal Res. 2014
Feb;49(1):1-9. doi: 10.1111/jre.12081.
Egger G, Liang G, Aparicio A, Jones PA. Epigenetics in human disease and prospects
for epigenetic therapy. Nature. 2004 May 27;429(6990):457-63. Ha PK, Califano JA.
Promoter methylation and inactivation of tumour-suppressor genes in oral squamous
cell carcinoma. Lancet Oncol. 2006 Jan;7(1):77-82.
Johansson A, Bergenholtz A, Holm SE. Strong cytotoxicity to human gingival
fibroblasts by Porphyromonas gingivalis ATCC 33277. J Periodontal Res. 1996
Oct;31(7):477-82.
Kubota T, Itagaki M, Hoshino C, Nagata M, Morozumi T, Kobayashi T, et al. Altered
gene expression levels of matrix metalloproteinases and their inhibitors in
periodontitis-affected
gingival
tissue.
J
Periodontol.
2008
Jan;79(1):166-73.
doi:
10.1902/jop.2008.070159 .
Larsson L, Castilho RM, Giannobile WV. Epigenetics and its role in periodontal
diseases: a state-of-the-art review. J Periodontol. 2015 Apr;86(4):556-68. doi:
10.1902/jop.2014.140559.
Palm E, Demirel I, Bengtsson T, Khalaf H. The role of toll-like and protease-activated
receptors in the expression of cytokines by gingival fibroblasts stimulated with the
periodontal pathogen Porphyromonas gingivalis. Cytokine. 2015 Dec;76(2):424-32.
doi: 10.1016/j.cyto.2015.08.263.
Parashar G, Capalash N. Expression of the TIMP2 gene is not regulated by promoter
hypermethylation in the Caski cell line. Oncol Lett. 2012 May;3(5):1079-1082.
Planello AC. Epigenetics Analysis of SOCS1 Gene and Its Association with Chronic
Periodontitis [tese]. Piracicaba: Faculdade de Odontologia de Piracicaba,
Universidade Estadual de Campinas; 2014.
Rettori MM, de Carvalho AC, Longo AL, de Oliveira CZ, Kowalski LP, Carvalho AL, et
al. TIMP3 and CCNA1 hypermethylation in HNSCC is associated with na increased
incidence of second primary tumors. J Transl Med. 2013 Dec 20;11:316. doi:
10.1186/1479-5876-11-316.
32
Tabeta K, Yamazaki K, Akashi S, Miyake K, Kumada H, Umemoto T, et al. Toll-like
receptors confer responsiveness to lipopolysaccharide from Porphyromonas gingivalis
in human gingival fibroblasts. Infect Immun. 2000 Jun;68(6):3731-5.
Takai R, Uehara O, Harada F, Utsunomiya M, Chujo T, Yoshida K, et al. DNA
hypermethylation of extracellular matrix-related genes in human periodontal fibroblasts
induced by stimulation for a prolonged period with lipopolysaccharide derived from
Porphyromonas gingivalis. J Periodontal Res. 2016 Aug;51(4):508-17. doi:
10.1111/jre.12330.
33
