Principal investigators

Stefan Coassin, Florian Kronenberg

Other GenEpi Investigators involved

Team members

  • Patricia Döttelmayer (Biomedical Scientist)
  • Gertraud Erhart (Biomedical Scientist)
  • Rebecca Grüneis (PhD student)
  • Silvia Di Maio (PhD student)
  • Monika Summerer (PostDoc)
  • Peter Zöscher (MSc Student)

Aims

We are interested in identifying genetic variants that regulate the LPA gene and determine Lp(a) phenotypes in families and populations.

To this extend we apply several genomic technologies and develop together with the Genepi Informatics Group dedicated bioinformatic analysis approaches to screen individuals and families with peculiar Lp(a) phenotypes for causative mutations.

Ongoing Projects

  1. Functional investigation of the effects of the frequent Lp(a)-lowering mutation 4925G>A in the KIV-2 region (FWF Grant P 31458 to S.C.)
  2. Generation of a fully Lp(a)-phenotyped and genotyped collection of mRNA samples from human liver tissue (FWF Grant P 31458 to S.C.)
  3. Investigation of family pedigrees and population samples with notable or discordant Lp(a) phenotypes. (Supported by the Lipoprotein(a) Center And Research InstitutE [Lp(a)CARE])
  4. Development of a dedicated, highly specific exome sequencing pipeline for LPA mutation screening in families (AAS Research grant 2018 to S.C., ongoing)

Supported by

Lipoprotein(a)

Lipoprotein(a) [Lp(a)] concentrations in plasma represent one of the most important genetically determined cardiovascular risk factors in the general population. About 25% of the population presents Lp(a) concentrations that put them at up to three times increased cardiovascular risk. More than 90% of the Lp(a) variance are determined by the LPA gene, which codes for the apolipoprotein(a) [apo(a)] protein.

The LPA gene presents several peculiarities and differs strongly from most other human genes. It consists of ten so-called “kringle IV domains” (type 1 to 10, partially with additional subtypes), one “kringle V” domain and an inactive protease domain. All regions are highy homologous to each other as well as to plasminogen, a pseudogene nearby (LPAL2) and several regions on other chromosomes. This precludes mutation screening using common sequencing technologies.

Additionally, the kringle IV type 2 (KIV-2) domain is encoded by a 5,500 bp large copy number variation that can be present in one to more than 40 nearly identifical repeats. Up to 70% of the coding sequence of the LPA gene are located within the KIV-2 repeat region and are thus missed when using standard sequencing techniques. Therefore most of the genetic variability in this clinically very relevant gene is commonly missed and several genetic variants affecting Lp(a) concentrations might still hide in this region.

Technologies available in our lab for genetic analysis of Lipoprotein(a)

  • Lp(a) quantification by ELISA.
  • Apo(a) phenotyping by Western blot.
  • Genotyping of the LPA KIV-2 copy number and haplotyping of mutations by pulsed field gel electrophoresis (PFGE).
  • Ultra-deep targeted and whole exome next generation sequencing.
  • Oxford Nanopore Technologies long read sequencing.
  • Allele-specific qPCR, droplet digital PCR and castPCR for high throughput genotyping of variants located inside the KIV-2 region.
  • TaqMan qPCR for high throughput genotyping of variants located outside the KIV-2 region.
  • PCR for KIV-2 copy number determination (estimates the sum of KIV-2 repeats on DNA level).
  • Quantitative qPCR.
  • HepG2 cell lines stably transfected with apo(a) cDNA.
  • Functional assays and cloning techniques.

Why searching for mutations in the LPA gene?

On average, small (“low molecular weight”) isoforms are associated with high Lp(a) concentrations and high molecular isoforms are associated with low Lp(a) concentrations. However, the relationship between Lp(a) concentration and isoform size is far from being simple. Alleles of the same size are associated with a >200-fold Lp(a) range between two unrelated individuals. The genetic variants responsible for this are largely unknown, but are likely located in the LPA gene locus. Since the KIV-2 repeat encompasses up to 70% of the LPA gene, many of these variants might likely be hidden in the KIV-2 region.

Our group recently produced the largest survey of genetic variation in the KIV-2 region, finding hundreds of variants. In this figure each line represents a variant in the KIV-2 region and the height gives the number of carriers. Some positions were variable in every individual we looked at (Coassin et al, EHJ 38, 2017).

Some variants in the KIV-2 region can have large effects on the Lp(a) concentrations. In the figure left-hand, the 4925G>A variant (carriers shown in red) is associated with an up to 30 mg/dL decrease in Lp(a) concentrations (double the median in the general population) compared to non-carriers (“wt”). This effect is most pronounced in the smaller Lp(a) isoforms, which are those which present otherwise the largest cardiovascular risk (Coassin et al, EHJ 38, 2017) .

Updates

April 2020

Finally published: our methylome-wide association study for Lp(a) concentrations (PI Claudia Lamina) with linkage disequilibrium structures in LPA giving a lot of surprises. Read in Pubmed

April 2020

Rebecca will give her first progress seminar for the Innsbruck Genetics, Epigenetics and Genomics PhD School on April 30th 2020. Has been a year with lots of work, indeed…

March 2020

After a great year Peter now leaves the lab to write up his thesis. Great work and looking forward to read it!

May 2019

Welcome in the team to Rebecca

May 2019

Stefan presented our recent survey on the complete genetic variability in the KIV-2 region (Coassin et al, JLR 60, 2019) and the effects of the LPA KIV-2 R21X null allele in 11,000 individuals at the EAS 2019 in Maastricht.

April & May 2019

Silvia Di Maio presented her master thesis work on the effects of the LPA KIV-2 R21X null allele in 11,000 individuals at the Austrian Atherosclerosis Society meeting 2019 and at the Grainau Workshop on Genetic Epidemiology 2019.

April & May 2019

Silvia Di Maio presented her master thesis work on the effects of the LPA KIV-2 R21X null allele in 11,000 individuals at the Austrian Atherosclerosis Society meeting 2019 and at the Grainau Workshop on Genetic Epidemiology 2019.

April 2019

Welcome in the team to Monika

March 2019

Welcome in the team to Peter

Collaborators

  1. Manuel Maglione and the team of the University Hospital for Visceral, Transplant and Thoracic Surgery (Head: Univ. Prof. Dietmar Öfner-Velano)
  2. Gilles Lambert, DéTROI INSERM U1188, Université de la Réunion
  3. Alexander Hüttenhofer, Institute of RNomics, MUI
  4. Lukas A. Huber, Institute of Cell Biology, MUI
  5. Austrian Drug Screening Institute (ADSI)

Previous projects

  1. 2015-2018: Mapping of the variability in the LPA KIV-2 region. PubMed
  2. 2015-2017: Generation of standards for automated large scale validation of NGS sequencing analysis pipelines for LPA (DACH Award 2015 to S.C.). PubMed
  3. 2015-2017: Development of a third generation long range sequencing approach to LPA and specifically the LPA cDNA (MUI-START 2015-07 to S.C) PubMed
  4. 2015-2016: Oxford Nanopore Technologies Early Access Program to the MinION Nanopore sequencing device: Application of Nanopore sequencing to the LPA gene (S.C.)

Former team members

  • Paul Bicher (BSc thesis, 2015)
  • Johanna Schachtl-Riess (BSc thesis, 2015)
  • Jamie Lee Losso (BSc thesis, 2016)
  • Verena Sturmlehner (BSc thesis, 2019)