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Whole-exome sequencing identifies rare genetic variations in German families with pulmonary sarcoidosis

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Abstract

Genome-wide and candidate gene studies for pulmonary sarcoidosis have highlighted several candidate variants among different populations. However, the genetic basis of functional rare variants in sarcoidosis still needs to be explored. To identify functional rare variants in sarcoidosis, we sequenced exomes of 22 sarcoidosis cases from six families. Variants were prioritized using linkage and high-penetrance approaches, and filtered to identify novel and rare variants. Functional networking and pathway analysis of identified variants was performed using gene ontology based gene–phenotype, gene–gene, and protein–protein interactions. The linkage (n = 1007–7640) and high-penetrance (n = 11,432) prioritized variants were filtered to select variants with (a) reported allele frequency < 5% in databases (1.2–3.4%) or (b) novel (0.7–2.3%). Further selection based on functional properties and validation revealed a panel of 40 functional rare variants (33 from linkage region, 6 highly penetrant and 1 shared by both approaches). Functional network analysis implicated these gene variants in immune responses, such as regulation of pro-inflammatory cytokines including production of IFN-γ and anti-inflammatory cytokine IL-10, leukocyte proliferation, bacterial defence, and vesicle-mediated transport. The KEGG pathway analysis indicated inflammatory bowel disease as most relevant. This study highlights the subsets of functional rare gene variants involved in pulmonary sarcoidosis, such as, regulations of calcium ions, G-protein-coupled receptor, and immune system including retinoic acid binding. The implicated mechanisms in etiopathogenesis of familial sarcoidosis thus include Wnt signalling, inflammation mediated by chemokine and cytokine signalling and cadherin signalling pathways.

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Abbreviations

ANNOVAR:

Annotate variation

DAVID:

Database for annotation visualization and integrated discovery

dbSNP:

NCBI single nucleotide polymorphism database

EASE score:

Expression analysis systemic explorer score

GeneMANIA:

Gene multiple association network integration algorithm

GO:

Gene ontology

LRR:

Leucine-rich repeats

PANTHER:

Protein annotation through evolutionary relationship

PPI:

Protein–protein interactions

STRING:

Search tool for the retrieval of interacting genes/proteins

WES:

Whole-exome sequencing

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Acknowledgements

The authors thank Prof. Manfred Schürmann, Institute of Human Genetics, University of Lübeck, for his involvement in the study subject characterisation; Dr. Kumari Neelam, Punjab Agricultural University, Ludhiana, for her helpful suggestions in the manuscript; and to the Sequencing and Genotyping Core Facilities at IKMB for the technical support. The authors were supported by the DFG Cluster of Excellence “Inflammation at Interfaces”, the Deutsche Forschungsgemeinschaft (DFG) Grant EXC 306 (present responsible person: prof. D. Ellinghaus); DFG “Systematic identification and modelling of rare and common genetic risk factors for sarcoidosis” Grant FI 1935/1-1; and the Grants NV18-05-00134, IGA_LF_2018_015 (Czech Republic).

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Authors and Affiliations

  1. Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany

    Amit Kishore, Britt-Sabina Petersen, Marcel Nutsua, Andre Franke, Annegret Fischer & Stefan Schreiber

  2. Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic

    Amit Kishore & Martin Petrek

  3. Department of Pneumology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany

    Joachim Müller-Quernheim

  4. Clinic of Internal Medicine I, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany

    Stefan Schreiber

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  1. Amit Kishore
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Correspondence to Stefan Schreiber or Martin Petrek.

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Kishore, A., Petersen, BS., Nutsua, M. et al. Whole-exome sequencing identifies rare genetic variations in German families with pulmonary sarcoidosis. Hum Genet 137, 705–716 (2018). https://doi.org/10.1007/s00439-018-1915-y

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