Human Molecular Genomics
The main goal of the Human Molecular Genomics Group is to understand the role of non-coding mutations and structural variants as the cause of human disease. We aim to understand the pleiotropic effects of mutations and structural variants during embryogenesis and investigate their influence on the 3D architecture of the genome. In order to achieve this goal, we are applying the latest high-throughput technologies during mouse embryonic development including single cell analysis, chromosome conformation capture techniques and massively parallel reporter assays
Single-cell human genetics: Pleiotropic effects of mutations and structural variants during embryonic development at single cell resolution
We are applying single cell RNA and single cell ATAC sequencing to mouse embryos harboring mutations and structural variants of patients with congenital disease. For the first time, this enables the single cell analysis of whole mouse embryos and thus allows the investigation of the pleiotropic effects of mutations and structural variants at the single cell level in a complex organism. Different organs and cell subpopulations react completely differently to mutations and show very specific cellular phenotypes. These analyses are of enormous interest for human genetics as genotype-phenotype correlations are extremely difficult to understand since the severity of genetic disorders can differ even in individuals with mutations in the same gene.
Structural variants in congenital malformations and their influence on the 3D architecture of the genome
Deletions, duplications and inversions can alter the cis-regulatory 3D architecture of the non-coding genome by altering the positions of TADs and boundaries, leading to misregulation of genes and congenital malformation. We have previously shown that these position effects of non-coding DNA with up to 56% are an important mutational mechanism in congenital limb malformations. Using whole genome sequencing, we are investigating further clinical cohorts including brain malformations and patients with developmental delay on non-coding variants. Functional follow up studies are performed in mouse models.
High throughput analysis methods for the evaluation of non-coding variants from whole genome sequencing data
With the introduction of NGS technologies and Whole Genome Sequencing in clinical practice, the number of genetic variants increases exponentially and about 60-100 de novo variants are detected per family. The sheer number of the variants makes traditional functional analyses impossible. Therefore, we are applying massively parallel reporter assays (MPRAs) for the simultaneous investigation of thousands of non-coding variants in vitro and in vivo. These data have a direct impact on clinical genetics, as the medical interpretation of variants of variants uncertain (or unknown) significance is currently one of the central challenges of human genetics.
Smajic S, Prada-Medna CA, Landoulsi Z, Dietrich C, Jarazo J, Henck J, Balachandran S, Pachchek S, Morris CM, Anthony P, Timmermann B, Sauer S, Schwamborn JC, May P, Grunewald A, Spielmann M. Single-cell sequencing of the human midbrain reveals glial activation and a neuronal state specific to Parkinson's disease Brain 2021 Dec 17;awab446.
Srivatsan SR, Regier MC, Barkan E, Franks JM, Packer JS, Grosjean P, Duran M, Saxton S, Ladd JJ, Spielmann M, Lois C, Lampe PD, Shendure J, Stevens KR, Trapnell C. Embryo-scale, single-cell spatial transcriptomics. Science 2021 Jul 2;373(6550):111-117
Socha M, Sowińska-Seidler A, Melo US, Kragesteen BK, Franke M, Heinrich V, Schöpflin R, Nagel I, Gruchy N, Mundlos S, Sreenivasan VKA, López C, Vingron M, Bukowska-Olech E, Spielmann M*, Jamsheer A*. Position effects at the FGF8 locus are associated with femoral hypoplasia. Am J Hum Genet. 2021 108(9):1725-1734. doi:10.1016/j.ajhg.2021.08.001 *corresponding authors
Allou L, Balzano S, Magg A, Quinodoz M, Royer-Bertrand B, Schöpflin R, Chan WL, Speck-Martins CE, Carvalho DR, Farage L, Lourenço CM, Albuquerque R, Rajagopal S, Nampoothiri S, Campos-Xavier B, Chiesa C, Niel-Bütschi F, Wittler L, Timmermann B, Spielmann M, Robson MI, Ringel A, Heinrich V, Cova G, Andrey G, Prada-Medina CA, Pescini-Gobert R, Unger S, Bonafé L, Grote P, Rivolta C, Mundlos S, Superti-Furga A. Non-coding deletions identify Maenli lncRNA as a limb-specific En1 regulator Nature 2021 Apr;592(7852):93-98
Cao J, O'Day DR, Pliner HA, Kingsley PD, Deng M, Daza RM, Zager MA, Aldinger KA, Blecher-Gonen R, Zhang F, Spielmann M, Palis J, Doherty D, Steemers FJ, Glass IA, Trapnell C, Shendure J A human cell atlas of fetal gene expression
Science. 2020 Nov 13;370(6518):eaba7721. DOI: 10.1126/science.aba7721
Melo US, Schöpflin R, Acuna-Hidalgo R, Mensah MA, Fischer-Zirnsak B, Holtgrewe M, Klever MK, Türkmen S, Heinrich V, Pluym ID, Matoso E, Bernardo de Sousa S, Louro P, Hülsemann W, Cohen M, Dufke A, Latos-Bieleńska A, Vingron M, Kalscheuer V, Quintero-Rivera F, Spielmann M*, Mundlos S*. Hi-C Identifies Complex Genomic Rearrangements and TAD-Shuffling in Developmental Diseases. Am J Hum Genet 2020 DOI *corresponding author Selected as “Best of AJHG 2020"
Cao J*, Spielmann M*, Qiu X, Huang X, Ibrahim DM, Hill AJ, Zhang F, Mundlos S, Christiansen L, Steemers FJ, Trapnell C & Shendure J. The single-cell transcriptional landscape of mammalian organogenesis. Nature 2019 Feb 20. DOI *equal contribution
Kragesteen BK*, Spielmann M*, Paliou C, Heinrich V, Schöpflin R, Esposito A, Annunziatella C, Bianco S, Chiariello AM, Jerković I, Harabula I, Guckelberger P, Pechstein M, Wittler L, Chan WL, Franke M, Lupiáñez DG, Kraft K, Timmermann B, Vingron M, Visel A, Nicodemi M, Mundlos S, Andrey G. Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis. Nat Genet. 2018 Oct;50(10):1463-1473. Epub 2018 Sep 27. DOI *equal contribution
Spielmann M, Lupiáñez DG, Mundlos S. Structural variation in the 3D genome. Nat Rev Genet. 2018 Jul;19(7):453-467. Review. DOI
Flöttmann R, Kragesteen BK, Geuer S, Socha M, Allou L, Sowińska-Seidler A, Bosquillon de Jarcy L, Wagner J, Jamsheer A, Oehl-Jaschkowitz B, Wittler L, de Silva D, Kurth I, Maya I, Santos-Simarro F, Hülsemann W, Klopocki E, Mountford R, Fryer A, Borck G, Horn D, Lapunzina P, Wilson M, Mascrez B, Duboule D, Mundlos S, Spielmann M. Noncoding copy-number variations are associated with congenital limb malformation.
Genet Med. 2018 Jun;20(6):599-607. Epub 2017 Oct 12. DOI
Spielmann M, Kakar N, Tayebi N, Leettola C, Nürnberg G, Sowada N, Lupiáñez DG, Harabula I, Flöttmann R, Horn D, Chan WL, Wittler L, Yilmaz R, Altmüller J, Thiele H, van Bokhoven H, Schwartz CE, Nürnberg P, Bowie JU, Ahmad J, Kubisch C, Mundlos S, Borck G. Exome sequencing and CRISPR/Cas genome editing identify mutations of ZAK as a cause of limb defects in humans and mice. Genome Res. 2016 Feb;26(2):183-91. DOI
Lupiáñez DG, Kraft K, Heinrich V, Krawitz P, Brancati F, Klopocki E, Horn D, Kayserili H, Opitz JM, Laxova R, Santos-Simarro F, Gilbert-Dussardier B, Wittler L, Borschiwer M, Haas SA, Osterwalder M, Franke M, Timmermann B, Hecht J, Spielmann M, Visel A, Mundlos S. Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell2015 161(5):1012-1025. doi:10.1016/j.cell.2015.04.004
Spielmann M, Brancati F, Krawitz PM, Robinson PN, Ibrahim DM, Franke M, Hecht J, Lohan S, Dathe K, Nardone A, Landi A, Wittler L, Timmermann B, Chan D, Mennen U, Klopocki E, Mundlos S. Homeotic Arm-to-Leg Transformation Associated with Genomic Rearrangements at the PITX1 Locus. Am J Hum Genet. 2012 Oct 5;91(4):629-35. doi: 10.1016/j.ajhg.2012.08.014. Selected as “Best of AJHG 2012 and 2013”