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World of Genomics: Lithuania

Kira Newbon 1 August 2023

Original article by Shannon Gunn, updated by Kira Newbon in July 2023.

Sometimes referred to as the Land of Nature, for this week’s World of Genomics we head over to Lithuania. Over the past couple of decades, the Baltic States have transformed their economies, with increasing focus on technologies and science. Lithuania’s life sciences industry has gained significant momentum, particularly in the genomics and biotech sectors, attracting more and more international attention.

The Population of Lithuania

The Republic of Lithuania is a small European country located by the south-east coast of the Baltic Sea (Figure 1). The ancestors of modern Lithuanians were a people called the Balts who arrived in the area around 2,000 BC. In the 1230s, Lithuanian lands were united by a man named Mindaugas, who founded the Kingdom of Lithuania.

In September 1991, Lithuania finally regained independence from the former Soviet Union. Since the 1990s, Lithuania has experienced a gradual population decline. This has been linked with social issues such as income equality and high suicide rates.

Figure 1 | Map of Lithuania

Geographic and Demographic Information

Summary statistics

  • Land area: 65,300 km2 
  • Gross domestic product (GDP): 
    • Total: $70.33 billion (2022) 
    • Per capita: $24,826.80 (2022) 

Population statistics

  • Population size: 2,718,352 (2023) 
  • Birth rate: 9.837 per 1,000 (2023) 
  • Death rate: 14.430 per 1,000 (2023) 
  • Infant mortality rate: 3.522 per 1,000 (2023) 
  • Average life expectancy: 76.41 (2023) 
    • Male: 70 (2021) 
    • Female: 79 (2021) 
  • Ethnicity: 84.2% ethnic Lithuanians, 6.6% Poles, 5.8% Russians, 1.2% Belarusians, 0.5% Ukrainians (2011 Census) 

Healthcare System

Lithuania’s healthcare system has made great strides and is continually addressing old and emerging issues. Lithuania has a modern state healthcare system, which is funded by the government through a national health insurance scheme. The National Health Insurance Fund or VLK (Lithuanian: Valstybinė ligonių kasa) was established in 1993. Primary and secondary healthcare are delivered by local councils. Tertiary care is mostly provided by university hospitals. Private healthcare is rare for Lithuanians, with very few locals able to afford the cost. Private clinics for medical tourists are a growing industry in the country. The number of doctors per 1,000 people in Lithuania is larger than in most Western societies, and hospitals have high-tech equipment and adequate facilities to perform complex surgeries. 

While most services are free of charge in Lithuania, the system is plagued by corruption (although this is improving). In addition, out-of-pocket spending remains high, particularly for pharmaceuticals, which threatens healthcare access for vulnerable groups. The percentage of Lithuanians recording good health is only 43%. Lithuania also continues to fall behind other European countries in preventative healthcare, which has contributed to a higher mortality rate than the EU average. 

Healthcare priorities

Health outcomes in Lithuania remain among the worst in the EU. It also has one of the highest mortality rates from preventable and treatable causes in the EU. Cardiovascular diseases, oncological disorders and mental health conditions are the top three causes of the deaths in Lithuania. 

Analysis of the data of more than 50,000 Lithuanian patients (with an average age of 62 years) revealed that almost half of them had hypertension, and 62 percent had high cholesterol. Mortality from cardiovascular diseases in Lithuania is three times higher than in other EU countries.

Compared to other European countries, Lithuania’s cancer mortality rates remain among the highest. The incidence of cancer is increasing by 1% every year. Men most often have cancer of the prostate gland, lung and skin, while women are more likely to have skin tumours, breast and uterine cancers.

The morbidity rates in Lithuania compared to other countries of the EU are quite low, lower than the EU average. However, the mortality rate is higher. For many years, Lithuania has had the highest mortality rate from suicide in the EU. At 31.5 deaths per 100,000 population, it is almost three times higher than the EU average. The rate of suicide among men is extremely high, but women also have a relatively high rate, the second highest in the EU. Inpatient deaths from suicide among patients hospitalised with a mental disorder, as well as suicide rates one month and one year after hospitalisation, are also substantially higher than in neighbouring countries.

Lifestyle-related risk factors account for more than half of all deaths in Lithuania. Alcohol consumption is higher than in any other EU country. In 2014, it was reported that one in five adults smoked on a daily basis. In addition, in 2017, 17% of adults were recorded as being obese, a proportion also higher than the EU average. This situation led to the adoption of the National Health Strategy 2014-2025, which aims to reduce harmful alcohol consumption and smoking, and encourage intersectoral action to promote healthy diets and physical activity. 

Genomic Medicine Capabilities

Genetic testing in Lithuania is available at the main university hospital – the Centre for Medical Genetics – and several private laboratories. The Centre for Medical Genetics is a unit of Vilnius University Hospital Santara Clinics, providing comprehensive Level III genetic counselling services, clinical and laboratory examination of a wide range of inherited diseases and congenital malformations, general neonatal screening and treatment of rare disease patients. The Centre provides around 26,000 neonatal screenings and 10,000 consultations annually. The number of consultations and tests performed at the Medical Genetics Centre is increasing every year, and new methodologies for diagnosing hereditary diseases are being introduced.

Prenatal genetic diagnosis began in Lithuania in 1987. The Vilnius University Human Genetic Centre is the only institution in Lithuania where congenital foetal diseases are detected by invasive procedures for foetal chromosomal analysis and single-gene disorders.

Nationwide neonatal screening programmes for phenylketonuria (PKU) and congenital hypothyroidism (CH) have been in action since 1975 and 1993, respectively. All newborns are also screened for congenital adrenal hyperplasia and galactosemia (GAL).

The first genetic counselling clinic in Lithuania was founded in 1971 at Vilnius Republican Clinical Hospital. In 1986, it was reorganised as the Centre of Medical Genetics and then, in 1991, it was reorganised as Vilnius University Human Genetics Centre.

Notable Projects

Work by Lithuanian researchers established our early knowledge of CRISPR-Cas systems. Now, more recently, researchers in Lithuania are continuing to expand on these systems to improve gene editing technologies. Some examples of this work are indicated below:

  • CRISPR systems can function heterologously in other species: Professor Virginijus Šikšnys and colleagues cloned the entire CRISPR-Cas locus from Streptococcus thermophilus and expressed it in Escherichia coli, where they demonstrated that it could provide plasmid resistance. This suggested that CRISPR systems were self-contained units and verified that all of the required components of the Type II system were known (Sapranauskas et al., 2011).
  • Biochemical characterisation of Cas9-mediated cleavage: Prof. Šikšnys and his team purified Cas9 in complex with crRNA from the E. coli strain engineered to carry the S. thermophilus CRISPR locus and undertook a series of biochemical experiments to mechanistically characterise Cas9’s mode of action. They demonstrated that the system introduces in vitro double-strand breaks at specific sites in DNA containing a sequence complementary to crRNA. They saw that DNA cleavage was executed by Cas9, which uses two distinct active sites, RuvC and HNH, to generate site-specific nicks on opposite DNA strands (Gasiunas et al., 2012).
  • Miniature type V-F CRISPR-Cas nucleases enable targeted DNA modification in cells: Prof. Šikšnys and his team biochemically characterised two miniature type V-F Cas nucleases, SpCas12f1 and AsCas12f1, and showed that SpCas12f1 functions in both plant and human cells to produce targeted modifications with outcomes in plants being enhanced with short heat pulses. This discovery paves the way for the development of miniature Cas12f1-based genome editing tools. (Bigelyte et al., 2021).
  • Discovery of a new gene editing tool – TnpB protein: For the first time, a group of Vilnius University scientists showed that the TnpB protein, which is linked to mobile genetic elements called transposons, acts as an RNA-programmed nuclease that can cut DNA, i.e., TnpB acts as a ‘DNA scissor’ independent of CRISPR systems. These experiments not only suggested for the first time a possible new function of TnpB in transposition, but also experimentally confirmed the hypothesis that the TnpB protein associated with mobile genetic elements is the ancestor of ‘DNA scissors’. (Karvelis et al., 2021).

Other projects include the ANELGEMIA (Ancient and new alleles in Lithuanian’s genome: mutations, selection and adaptation) Project and the ongoing ADAPT (Adaptive genetic mechanisms: a comprehensive study of whole genome variation in the group of the Lithuanian Chernobyl catastrophe liquidators) Project.

Notable Organisations and Companies

  • The Life Sciences Centre of Vilnius University: Home to three academic branches that take part in joint activities: the Institutes of Biochemistry, Biotechnology and Biosciences. The Life Science Centre is a new and innovative centre possessing modern laboratory equipment and top-level scientific research services. The centre has strengthened research studies and technological advance in the fields of biochemistry, biotechnology, molecular biology, genetics, neurobiology, molecular medicine, next generation genome editing and epigenomics related areas.
  • National Public Health Surveillance Laboratory (NPHSL): Under the control of the Ministry of Health, the NPHSL was responsible for genomic sequencing of SARS-CoV-2 variants during the pandemic, leading testing and tracing efforts in Lithuania. 
  • Lithuanian University of Health Sciences: Founded in 2010, the University focuses entirely on health and life sciences. Research specialties include microbiology, oncology and genetics. 

Notable Individuals

  • Prof. Virginijus Šikšnys (1956-): A Lithuanian biochemist and Professor at Vilnius University. He is one of the pioneers in CRISPR-Cas technology, being the first to show that this system could be transferred from one bacterium to another.
  • Prof. Vaidutis Kucinskas (1947-): The pioneer of Lithuanian human genetics and a world-renowned scientist. He established the Human Genome Research Centre at the Institute of Biomedical Sciences of the Faculty of Medicine of Vilnius University and is the Chief Scientist and Head of this centre, conducting fundamental and clinical research in genome diversity and inherited diseases in Lithuania. Kucinskas is one of the most cited researchers in the Baltics.
  • Prof. Saulius Klimasauskas: A director and distinguished Professor at the Institute of Biotechnology, Life Sciences Centre of Vilnius University. He has been researching enzymes that are involved in the process of recording epigenetic information in human cells for several decades.
  • Aaron Klug (1926-2018): Born in Lithuania and later moved to the UK, Klug was winner of the 1982 Nobel Prize in Chemistry for combining x-ray crystallography with electron microscopy, to study complex structures of DNA and proteins. He studied the structure of transfer RNA and found zinc fingers as well as the neurofibrils in Alzheimer’s disease.

Future Genomics Landscape

Over the past decade, Lithuania has established itself within the fields of genomics and genome-editing. This has led to the development of innovative businesses and start-ups, which have further helped accelerate knowledge in these areas. Since the early work from the laboratory of Professor Šikšnys, there is now a lot of effort to find new gene editing tools as well as improve on existing ones.

Moving forward, there are several exciting projects in the pipeline including:

  • The development of new CRISPR-based molecular tools: The Department of Protein-DNA Interactions at Vilnius University and CasZyme are currently expanding the gene editing toolbox for CRISPR/Cas technology by searching for new nucleases.
  • CRISPR-Cas based COVID-19 diagnostic test: CasZyme and Vilnius University Santara Clinics teams are aiming to improve the quality of personal healthcare by developing a rapid and accurate CRISPR-Cas based diagnostic tool for the detection of SARS-CoV-2 virus and other infectious agents.
  • Novel approaches to epigenome profiling: The Department of Biological DNA Modification at Vilnius University aims to develop new experimental approaches to genome-wide profiling of DNA methylation for epigenome studies and improved diagnostics of pathogens, viruses and fungi. In addition, the establishment of the Partnership Institute between Vilnius University Life Sciences Center (VU LSC) and the European Molecular Biology Laboratory (EMBL), over a year ago, has already gained momentum. Five research groups have been established and a sixth is being recruited to initiate and develop new directions and technologies in genome editing research and applications, and to promote their application in collaboration with business.  
  • Whole-genome sequencing (WGS) study sheds light on genomic variation in Lithuanian families: A 2022 study conducted by Urnikyte and colleagues identified three potential pathogenic de novo variants that will be useful targets for future research. 

Lithuania’s strong academic research centres and institutions have formed the backbone of its life sciences industry. In recent years, expansion of its infrastructure has been instrumental in the growth of the biotech and life sciences industry, particularly in its capital. Several key Lithuanian geneticists have positioned Lithuania as a world leader in the genome editing.  

With continued growth, collaboration and building of expertise, Lithuania will continue to contribute to the development of molecular tools. Recent studies utilising WGS have identified several potential pathogenic genetic variants in Lithuanian populations which will likely drive further study and may push for a public genetic database to support further research. 

Thank you to Monika Paule (CEO and Co-founder, CasZyme), Enterprise Lithuania and Lithuanian Biotechnology Association for their support writing this piece.

References

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