AG Schäfer „Molecular Genetics of Oral Inflammatory Diseases"

Area of research

Genome-wide association studies (GWAS) and exome sequencing offer a hypothesis-free and very systematic approach to identify genetic variants in the genetic information (DNA) that contribute to an increased disease risk.
A GWAS compares the frequency of millions of DNA sequence differences between thousands of patients and healthy controls. These comparisons are used, for example, to identify particular variants of genetic information that are more common in patient groups than in groups of healthy people. These DNA sequence differences provide information about the genes involved in the disease as well as disease-related molecular processes.
With exome sequencing, the individual DNA sequences of all protein-coding sections within the genome of patients with a particularly severe clinical picture, as well as their healthy siblings and parents, are determined. A comparative sequence analysis can then be used to find changes in the DNA sequences that are the cause of the disease.

Current project

Whole Exome Sequencing of Patients with Early-Onset Severe Periodontitis
Principal investigator: Dr. rer. nat. Gesa Richter
Funding: DFG
Cooperation partner: Dr. Sandra Freitag-Wolf, UKSH Kiel, IMIS

Selected publications

• Richter GM, Wagner G, Reichenmiller K, Staufenbiel I, Martins O, Löscher BS, Holtgrewe M, Jepsen S, Dommisch H, Schaefer AS. Exome Sequencing of 5 Families with Severe Early-Onset Periodontitis. J Dent Res. 2022 Feb;101(2):151-157. doi: 10.1177/00220345211029266. PMID: 34515563
• Richter GM, Kruppa J, Keceli HG, Ataman-Duruel ET, Graetz C, Pischon N, Wagner G, Rendenbach C, Jockel-Schneider Y, Martins O, Bruckmann C, Staufenbiel I, Franke A, Nohutcu RM, Jepsen S, Dommisch H, Schaefer AS. Epigenetic adaptations of the masticatory mucosa to periodontal inflammation. Clin Epigenetics. 2021 Nov 3;13(1):203. doi: 10.1186/s13148-021-01190-7.PMID: 34732256
• Richter GM, Kruppa J, Munz M, Wiehe R, Häsler R, Franke A, Martins O, Jockel-Schneider Y, Bruckmann C, Dommisch H, Schaefer AS. A combined epigenome- and transcriptome-wide association study of the oral masticatory mucosa assigns CYP1B1 a central role for epithelial health in smokers. Clin Epigenetics. 2019 Jul 22;11(1):105. doi: 10.1186/s13148-019-0697-y.PMID: 31331382 
• Munz M, Willenborg C, Richter GM, Jockel-Schneider Y, Graetz C, Staufenbiel I, Wellmann J, Berger K, Krone B, Hoffmann P, van der Velde N, Uitterlinden AG, de Groot LCPGM, Sawalha AH, Direskeneli H, Saruhan-Direskeneli G, Guzeldemir-Akcakanat E, Keceli HG, Laudes M, Noack B, Teumer A, Holtfreter B, Kocher T, Eickholz P, Meyle J, Doerfer C, Bruckmann C, Lieb W, Franke A, Schreiber S, Nohutcu RM, Erdmann J, Loos BG, Jepsen S, Dommisch H, Schaefer AS. A genome-wide association study identifies nucleotide variants at SIGLEC5 and DEFA1A3 as risk loci for periodontitis. Hum Mol Genet. 2018 Mar 1;27(5):941-942. doi: 10.1093/hmg/ddy015.PMID: 29346566
   

Area of research

Periodontitis is a common inflammatory disease of the periodontium and the sixth most common disease worldwide. The individual differences in the clinical picture are to a very large extent due to the genetic variability between different individuals and the specific biological consequences of the respective genetic variants. In their entirety, these genetic variants form the genetic architecture and influence and shape the various disease manifestations. We conducted a series of genome-wide association studies, which allowed us to identify various regions in the genome associated with periodontitis. Some of these regions and nucleotide polymorphisms are also associated with other complex diseases (e.g. myocardial infarction, hypertension, bone mineral densitiy) and thus indicate pleiotropic effects.
We suspect that within these regions there are genetic variants that affect the activity of genes relevant to oral health. We want to identify these putative causal genetic variants and elucidate their molecular biological effects. For example, this can be influencing the binding sites of transcription factors or the expression of other regulatory molecules such as non-protein-coding RNAs (miRNAs, lncRNAs). 
For this purpose, we use methods such as Massively Parallel Reporter Assays (MPRAs), which allow to examine the associated alleles of tens of thousands of sequences (Candidate Regulatory Sequences) for their regulatory function. Furthermore, we determine the target genes of the regulatory variants by CRISPR-dCas9 gene activation and inhibition. The identified causal variants, as well as the molecules that bind to them, also represent potential molecular targets for new drugs.

Research assistants

Weiwei Shi
Jiahui Song
Luyang Zhang

Current project

Decoding pleiotropic causal genetic risk variants of periodontitis using massively parallel reporter 
Funding: DFG
Cooperation partner: Prof. Dr. Martin Kircher, AG Regulatory Genomics, Institut für Humangenetik, UKSH – Campus Lübeck

Selected publications

• RSPO4 is a potential risk gene of stages III-IV, grade C periodontitis through effects on innate immune response and oral barrier integrity. Chopra A, Song J, Weiner J 3rd, Keceli HG, Dincer PR, Cruz R, Carracedo A, Blanco J, Dommisch H, Schaefer AS. J Clin Periodontol. 2022 Dec 12. doi: 10.1111/jcpe.13758. PMID: 36507580
• Case-only design identifies interactions of genetic risk variants at SIGLEC5 and PLG with the lncRNA CTD-2353F22.1 implying the importance of periodontal wound healing for disease aetiology. Müller R, Freitag-Wolf S, Weiner J 3rd, Chopra A, Top T, Dommisch H, Schaefer AS. J Clin Periodontol. 2023 Jan;50(1):90-101. doi: 10.1111/jcpe.13712. Epub 2022 Aug 15.PMID: 36129033
• Periodontitis Risk Variants at SIGLEC5 Impair ERG and MAFB Binding. Mueller R, Chopra A, Dommisch H, Schaefer AS. J Dent Res. 2022 May;101(5):551-558. doi: 10.1177/00220345211049984. PMID: 34852650
• BACH1 Binding Links the Genetic Risk for Severe Periodontitis with ST8SIA1. Chopra A, Mueller R, Weiner J 3rd, Rosowski J, Dommisch H, Grohmann E, Schaefer AS.J Dent Res. 2022 Jan;101(1):93-101. doi:10.1177/00220345211017510..PMID: 34160287

Area of research

Periodontitis is a common inflammatory disease of the oral cavity in which 11% of the population develop severe clinical pictures. Oral inflammation leads to bleeding gums and loss of connective tissue and alveolar bone with subsequent tooth loss. Periodontitis is characterized in particular by an increased diversity of the oral microflora in the inflamed periodontal pockets. The identification of specific pathogens with a causal influence on the oral immune response and inflammation is of particular clinical importance. To date, these are largely unknown. One of the characteristics is the high prevalence of the protozoan Entamoeba ginigvalis. We were able to show that this protozoan is able to enter the oral mucosa, move there, phagocytose the host cells and contribute to tissue destruction and inflammation. We are currently investigating the defense mechanisms of the human host against Entamoeba gingivalis. 
Periodontitis can also contribute to an increased risk of cardiovascular disease. Oral microorganisms or their components are suspected to be the possible cause of this connection. During the course of oral inflammation, these microorganisms enter the bloodstream and can trigger inflammatory reactions in the vessels. To test this hypothesis, two population-representative cohorts were established as part of the NAKO Health Study with the aim of identifying factors that influence onset and progression of cardiovascular disease and periodontitis. In the PAROCARD and MikroZahn projects, medical information, saliva, and supra- and subgingival plaque samples are available for determining the oral microbiota. With these samples, we identify the individual oral microbiome by metagenome sequencing in 1,200 periodontitis patients with or without cardiovascular diseases. This allows the determination of individual frequencies of individual microbial species in the healthy and inflamed oral cavity in patients with periodontitis and with or without cardiovascular diseases, as well as microbial virulence factors at the genetic information level.
These findings may contribute to a better understanding of putative causal factors that explain the increased relative risk of cardiovascular disease in the context of oral inflammation. 

Current projects

Characterization of host-parasite interactions between the oral mucosa and the protozoan Entamoeba gingivalis that drive tissue invasion, destruction and microbial dysbiosis
Principal investigator: Still determined
Funding: DFG

Identification of oral microbial signatures in periodontitis and their relationship to cardiovascular disease
Research assistant: pending
Funding: DFG
Cooperation project with

• Dr. Ghazal Aarabi, Universitätsklinikum Hamburg-Eppendorf, Zentrum für Zahn-, Mund- und Kieferheilkunde, Poliklinik für Parodontologie, Präventive Zahnmedizin
• Dr. Katrin Hertrampf, Universitätsklinikum Schleswig-Holstein, Klinik für Mund-, Kiefer- und Gesichtschirurgie

Selected publications

• Host prediction for disease-associated gastrointestinal cressdnaviruses. Kinsella CM, Deijs M, Becker C, Broekhuizen P, van Gool T, Bart A, Schaefer AS, van der Hoek L. Virus Evol. 2022 Sep 16;8(2):veac087. doi: 10.1093/ve/veac087. eCollection 2022.PMID: 36325032
• Entamoeba gingivalis Causes Oral Inflammation and Tissue Destruction. Bao X, Wiehe R, Dommisch H, Schaefer AS. J Dent Res. 2020 May;99(5):561-567. doi: 10.1177/0022034520901738. Epub 2020 Feb 5.PMID: 32023135
• Entamoeba gingivalis Exerts Severe Pathogenic Effects on the Oral Mucosa. Bao X, Weiner J 3rd, Meckes O, Dommisch H, Schaefer AS. J Dent Res. 2021 Jul;100(7):771-776. doi: 10.1177/00220345211004498. Epub 2021 Apr 1.PMID: 33792418