Lipoprotein(a) Genomics

We are interested in understanding how functional genetic variants in LPA contribute to the huge variance in lipoprotein(a) concentrations observed between individuals and across ancestries and identifying the causal mechanisms.

Lead

Stefan Coassin, PhD
Assistant Professor

+43 512 9003 70576
stefan.coassin@i-med.ac.at

Co-Lead

Florian Kronenberg, MD, MAE
Full Professor

+43 512 9003 70560
florian.kronenberg@i-med.ac.at
Sebastian Schönherr, Dr.
Senior Scientist

+43 512 9003 70579
sebastian.schoenherr@i-med.ac.at

Team

Stephan Amstler, BSc.
Master Student

+43 512 9003 70581
stephan.amstler@i-med.ac.at
Silvia Di Maio, Dott. mag.
PhD Student

+43 512 9003 70567
silvia.di-maio@i-med.ac.at

About

Genetic variation in the LPA gene explains up to 90% of lipoprotein(a) [Lp(a)] plasma concentrations in the population but the genetic mechanisms that govern the individual lipoprotein(a) concentrations are still poorly understood. We are interested in understanding how functional genetic variants in LPA create the huge variance in lipoprotein(a) concentrations that we observe between individuals and across ancestries. A major part of our work concerns also the investigation of mutations located in the KIV-2 repeat region of the LPA gene. This repetitive region can encompass up to 70% of the coding sequence of the gene, but due to its complex structure, it has not been accessible until recently. By combining the computational expertise of the institute in the detection of low-level mutations, molecular biology and genetics and our long-standing experience in Lp(a) research, we have developed a comprehensive genetic toolset capable of adressing many difficult aspects of Lp(a) genetics.

Figure 1: Genetic factors affecting Lp(a) concentration in plasma. Figure modified from Coassin and Kronenberg, Atherosclerosis 349:17–35, 2022 (https://doi.org/10.1016/j.atherosclerosis.2022.04.003) under CC-BY 4.0 license.
Figure 1: Genetic factors affecting Lp(a) concentration in plasma. Figure modified from Coassin and Kronenberg, Atherosclerosis 349:17–35, 2022 (https://doi.org/10.1016/j.atherosclerosis.2022.04.003) under CC-BY 4.0 license.

Genetic variability in the LPA KIV-2 region

We developed a sequencing approach capable to resolve the variability in the LPA KIV-2 region with high sensitivity and at scale. A screen of 123 individuals revealed an unprecedented level of genetic variability hidden in the KIV-2 region, finding about 500 new variants. Some KIV-2 variants strongly regulate Lp(a) concentrations beyond the effect of the LPA isoforms and are among the most important contributors to Lp(a) variance (e.g. KIV-2 4925G>A, KIV-2 4733G>A) (J Lipid Res 2019; Eur Heart J 2017; J Am Coll Cardiol 2021). Moreover, we showed recently that also the effects of some well-known LPA polymorphisms (SNPs, microsatellites) are in fact driven by variants hidden in the KIV-2 region (Genome Med 2020; Atherosclerosis 2022, J Lipid Res 2022). Multiple variants identified in the KIV-2 region and in the rest of the LPA gene are now being characterised by genetic and functional analyses to improve our understanding of the genetic architecture of Lp(a).

Figure 2: SNPs that are reported to modify Lp(a) concentrations, including multiple variants in the KIV-2 region. The exons are numbered according to the domain that they encode (1–10: KIV-1 to KIV-10, L. leader sequence, P. protease domain, 5’: 5′UTR, 3’: 3′ UTR). For orientation, three exons carry a superscript that reports the exon number in the genome sequence hg38. SNPs that have been associated with higher Lp(a) concentrations are shown above the gene structure. SNPs that have been associated with lower Lp(a) are shown below. SNPs that prevent protein production completely (null alleles) are underlined. Figure reproduced from Coassin and Kronenberg, Atherosclerosis 349:17–35, 2022 (https://doi.org/10.1016/j.atherosclerosis.2022.04.003) under CC-BY 4.0 license.
Figure 2: SNPs that are reported to modify Lp(a) concentrations, including multiple variants in the KIV-2 region. The exons are numbered according to the domain that they encode (1–10: KIV-1 to KIV-10, L. leader sequence, P. protease domain, 5’: 5′UTR, 3’: 3′ UTR). For orientation, three exons carry a superscript that reports the exon number in the genome sequence hg38. SNPs that have been associated with higher Lp(a) concentrations are shown above the gene structure. SNPs that have been associated with lower Lp(a) are shown below. SNPs that prevent protein production completely (null alleles) are underlined. Figure reproduced from Coassin and Kronenberg, Atherosclerosis 349:17–35, 2022 (https://doi.org/10.1016/j.atherosclerosis.2022.04.003) under CC-BY 4.0 license.

Nanopore sequencing

Nanopore sequencing is a new sequencing technology that allows sequencing DNA and RNA molecules by monitoring fluctuations in the ionic current while a DNA or RNA strand moves through a pore embedded in a bilayer. Unlike other technologies, Nanopore sequencing provides data in realtime, allows read lengths up to several megabases, reads directly the native target molecule, provides true single molecule data and keeps information about epigenetic modifications. Despite a still higher error rate than NGS, these advantages make it an appealing technology to target complex genes with structural variants and extensive homologies like the LPA gene. It also allows direct phasing of variants over long DNA segments, which is of special use in Lp(a) genetics. In our lab we explore applications of this technologies in Lp(a) genetics, but also beyond.

Other GenEpi investigators involved

Technologies available

Ongoing FWF-funded Projects

Earlier Team Members and Students

Key Publications

Coassin S, Kronenberg F: Lipoprotein(a) beyond the kringle IV repeat polymorphism: The complexity of genetic variation in the LPA gene. Atherosclerosis 349:17-35, 2022. PMID: 35606073

Grüneis R, Weissensteiner H, Lamina C, Schönherr S, Forer L, Di Maio S, Streiter G, Peters A, Gieger C, Kronenberg F, Coassin S: The kringle IV type 2 domain variant 4925G>A causes the elusive association signal of the LPA pentanucleotide repeat. J. Lipid Res. :100306, 2022. PMID: 36309064

Grüneis R, Lamina C, Di Maio S, Schönherr S, Zoescher P, Forer L, Streiter G, Peters A, Gieger C, Köttgen A, Kronenberg F, Coassin S: The effect of LPA Thr3888Pro on lipoprotein(a) and coronary artery disease is modified by the LPA KIV-2 variant 4925G>A. Atherosclerosis 349:151-159, 2022. PMID: 35534298

Schachtl-Riess JF, Kheirkhah A, Grüneis R, Di Maio S, Schoenherr S, Streiter G, Losso JL, Paulweber B, Eckardt KU, Köttgen A, Lamina C, Kronenberg F, Coassin S, GCKD Investigators: Frequent LPA KIV-2 variants lower lipoprotein(a) concentrations and protect against coronary artery disease. J. Am. Coll. Cardiol. 78:437-449, 2021. PMID: 34325833

Di Maio S, Grüneis R, Streiter G, Lamina C, Maglione M, Schoenherr S, Öfner D, Thorand B, Peters A, Eckardt KU, Köttgen A, Kronenberg F, Coassin S: Investigation of a nonsense mutation located in the complex KIV-2 copy number variation region of apolipoprotein(a) in 10,910 individuals. Genome Med. 12:74, 2020. PMID: 32825847

Coassin S, Schönherr S, Weissensteiner H, Erhart G, Forer L, Losso JL, Lamina C, Haun M, Utermann G, Paulweber B, Specht G, Kronenberg F: A comprehensive map of single-base polymorphisms in the hypervariable LPA kringle IV type 2 copy number variation region. J. Lipid Res. 60:186-199, 2019. PMID: 30413653

Coassin S, Erhart G, Weissensteiner H, Eca Guimarães de Araújo M, Lamina C, Schönherr S, Forer L, Haun M, Losso JL, Köttgen A, Schmidt K, Utermann G, Peters A, Gieger C, Strauch K, Finkenstedt A, Bale R, Zoller H, Paulweber B, Eckardt KU, Hüttenhofer A, Huber LA, Kronenberg F: A novel but frequent variant in LPA KIV-2 is associated with a pronounced Lp(a) and cardiovascular risk reduction. Eur. Heart J. 38:1823-1831, 2017. PMID: 28444229

Erhart G, Lamina C, Lehtimäki T, Marques-Vidal P, Kähönen M, Vollenweider P, Raitakari OT, Waeber G, Thorand B, Strauch K, Gieger C, Meitinger T, Peters A, Kronenberg F, Coassin S: Genetic factors explain a major fraction of the 50% lower lipoprotein(a) concentrations in Finns. Arterioscler. Thromb. Vasc. Biol. 38:1230-1241, 2018. PMID: 29567679