Institute for Digestive Research
Head of the Institute
Full member of the Lithuanian Academy of Sciences
prof. habil. dr. Limas Kupčinskas
Phone. +370 37 32 65 08, +37068640575
The Institute for Digestive Research was founded by the decision of the Senate of the Lithuanian University of Health Sciences within the University Hospital Kaunas Clinics in 2011. The head of the institute is prof. habil. dr. Limas Kupčinskas, full member of the Lithuanian Academy of Sciences. The institute has three research laboratories: the Laboratory of Clinical and Molecular Gastroenterology (head - dr. Jurgita Skiecevičienė) and the Laboratory of Surgical Gastroenterology (head - prof. dr. Antanas Gulbinas), and Laboratory of Translational Bioinformatics (head - dr. Simonas Juzėnas).
Laboratory of Clinical and Molecular Gastroenterology
Head of the Laboratory
dr. Jurgita Skiecevičienė
Phone. (+370 37) 327236
It is the vision of the laboratory to create a systemic understanding of complex human gastrointestinal diseases (inflammatory bowel diseases, premalignant and malignant diseases of gastrointestinal tract) as well as rare monogenic gastrointestinal (Wilson’s disease, hereditary hemochromatosis) disorders by using genetic, epigenetic, and metagenomic technologies. This includes the validation of the resulting models on the molecular level (including animal models of the disease) and their translation into the human diagnostic or therapeutic experiments. Clinical research includes epidemiological and clinical aspects of digestive diseases.
The laboratory research staff include geneticists, molecular biologists, bioinformaticians and gastroenterologists. The researchers of the laboratory have published more than 140 research articles, including more than 60 papers in Clarivate Analytics Web of Science journals with impact factor (IF), among them Lancet (2016, IF-47.8), Nature (2012, IF-40.1), Nature Genetics (2016-2014, 2011-2009, IF-31.6), Gastroenterology (2013, 2011, 2005, IF-18.3), Gut (2018, 2013, 2006, IF-16.6), Nature Structural and Molecular Biology (2016, IF-13.3), Nucleic Acid Reserach (2017, IF-10.12), Inflammatory bowel diseases (2013, IF- 4.5), and others. The papers were more than 1600 times cited in Clarivate Analytics Web of Science journals (total h-index - 17).
Research projects of Laboratory of Clinical and Molecular Gastroenterology
Participation in projects:
- "Development of novel methods for gut mircobiome modification" (grant no. 09.3.3-LMT-K-712-01-0130), project leader: dr. J. Skiecevičienė, funding source: EU structural fund, duration: 2018-2021.
- "Multi-layer omics approach to gastric cancer: circulating biomarker profiling in the blood on genetic, epigenetic and microbiome levels (MULTIOMICS)" (grant no. 09.3.3-LMT-K-712-01-0130), project leader: dr. J. Skiecevičienė, funding source: EU structural fund, duration: 2018-2021.
- "IsomiR in the pathogenesis of colorectal cancer: from miRNome-wide bioinformatic analysis to their functional validation" (grant no. S-MIP-17-22), project leader: prof. G. Kiudelis, funding source: Research Council of Lithuania, duration: 2017-2020.
- "Gastric microbiome: twin study" (grant no. APP-2/2016), project leader: dr. J. Skiecevičienė, funding source: Research Council of Lithuania, duration: 2016-2019.
- "The aging gut: genetic and enteric nervous system alterations in intestinal diverticulosis" (grant no. SEN-06/2015), project leader: prof. A. Tamelis, funding souce: Research Council of Lithuania, duration: 2015-2018.
- “MicroRNA Profiling in Tissues and Primary Intestinal Epithelial Cells of Patients with Active and Inactive Ulcerative Colitis”, project leader: J. Skiecevičienė, funding source: European Crohn’s and Colitis Organisation (ECCO), duration: 2016-2017.
- "Volatile biomarkers for early detection and characterisation of gastric and colorectal neoplasms (VOLGACORE)" (grant no. EURONANOMED2-01/2014), project leader: prof. L. Kupčinskas, funding source: EURONANOMED2, duration: 2014-2017.
- "Functional role of miR20b, miR451, miR29c, miR125b in pathogenesis of gastric and colorectal cancer" (grant no. MIP-007/2014), project leader: prof. G. Kiudelis, funding source: Research Council of Lithuania, duration: 2014-2016.
- "MicroRNA profiling and functional analysis in gastrointestinal stromal tumors" (grant no. MIP-006/2014), project leader: J. Skiecevičienė and L. Kučinskas, funding source: Research Council of Lithuania, duration: 2014 – 2016.
- "Development and validation of gastric cancer associated autoantibody test for early gastric cancer detection" (Baltic States-Taiwan project, grant no. TAP LLT 04/2014), project leader: prof. L.V. Jonaitis, funding source: Research Council of Lithuania, duration: 2014-2016.
- "Micro-RNA as biomarkers for early diagnosis of premalignant and malignant diseases of gastrointestinal tract" (grant no. VP1-3.1-ŠMM-07-156), project leader: prof. L. Kupčinskas, funding source: EU structural fund, duration: 2011-2015.
- "Role of gut microbiota in pathogenesis of pediatric IBD" (grant no. MIP-11217), project leader: prof. G. Kiudelis, funding source: Research Council of Lithuania, duration: 2011-2013.
- "Analysis of H.pylori virulence and host response factors in the development of atrophic gastritis in Baltic States and Taiwan" (Baltic states-Taiwan project) project leader: prof. L. Kupčinskas, funding source: Ministry of Education and Science, duration: 2007-2010.
- "Prevalence of HFE-hemochromatosis mutations c.845G>A (p.C282Y), c.187C>G (p.H63D) and c.193A>T (p.S65C) in the Lithuanian population" (grant no. T-25/09), project leader: prof. J. Kondrackienė, funding source: Lithuanian State Science and Studies Foundation, duration 2009.
- "Molecular mechanism of bacteria recognition in colonic epithelial cells and its association with inflammatory bowel disease etiopathogenesis" (grant no.T-39/08), project leader: prof. G. Kiudelis, funding source: Lithuanian State Science and Studies Foundation, duration: 2008.
- "Serological detection of atrophic gastritis and its evolution following H.pylori eradication in areas with high prevalence of H.pylori infection" (Baltic states-Taiwan project), project leader: prof. L. Kupčinskas, funding source: Ministry of Education and Science, duration: 2005-2007.
Participation in consortia:
- International IBD Genetics Consortium, 2011-up to now.
- European ECCO-EpiCom IBD epidemiology East-West gradient project, 2010-2015.
- PANcreatic Disease ReseArch (PANDoRA) consortium, 2012-2016- up to now.
- Gastric Cancer Research (staR) consortium, 2016- up to now.
- H. pylori world genome project, 2016- up to now.
Publications of Laboratory of Clinical and Molecular Gastroenterology
- Cleynen I,..., Kupcinskas L, ..., International IBD Genetics Consortium (IIBDGC), et al. Inherited determinants of Crohn's disease and ulcerative colitis phenotypes: a genetic association study. Lancet. 2016 Jan 9;387(10014):156-67. (IF- 47.8)
- Jostins L, ..., Kupcinskas L, ..., Sventoraityte J, ..., International IBD Genetics Consortium (IIBDGC), et al. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature. 2012 Nov 1;491(7422):119-24. (IF- 40.1)
- Childs EJ, ..., Kupcinskas J, et al. Common variation at 2p13.3, 3q29, 7p13 and 17q25.1 associated with susceptibility to pancreatic cancer. Nat Genet. 2015 Aug;47(8):911-6. (IF- 31.6)
- Wolpin BM, ..., Kupcinskas J, et al. Genome-wide association study identifies multiple susceptibility loci for pancreatic cancer. Nat Genet. 2014 Sep;46(9):994-1000. (IF- 31.6)
- Anderson CA, ..., Kupcinskas L, Sventoraityte J, et al. Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. Nat Genet. 2011 Mar;43(3):246-52. (IF- 31.6)
- Franke A, ..., Sventoraityte J, Kupcinskas L, et al. Genome-wide association study for ulcerative colitis identifies risk loci at 7q22 and 22q13 (IL17REL). Nat Genet. 2010 Apr;42(4):292-4. (IF- 31.6)
- Ellinghaus D, ..., Skieceviciene J, ..., Kupcinskas L, et al. Association Between Variants of PRDM1 and NDP52 and Crohns Disease, Based on Exome Sequencing and Functional Studies. Gastroenterology. 2013 Aug;145(2):339-47. (IF- 18.3)
- Lepage P, ..., Zvirbliene A, ..., Kupcinskas L, et al. Twin Study Indicates Loss of Interaction Between Microbiota and Mucosa of Patients With Ulcerative Colitis. Gastroenterology. 2011 Jul;141(1):227-36. (IF- 18.3)
- Burisch J, Kiudelis G, Kupcinskas L, et al. Natural disease course of Crohn's disease during the first 5 years after diagnosis in a European population-based inception cohort: an Epi-IBD study. Gut. 2018 Jan 23. pii: gutjnl-2017-315568. (IF-16.6).
- Rehman A, ..., Skieceviciene J, ..., Kupcinskas L, et al. Geographical patterns of the standing and active human gut microbiome in health and IBD. Gut. 2016 Feb;65(2):238-48. (IF- 16.6)
- Burisch J, ..., Kupcinskas L, et al. East-West gradient in the incidence of inflammatory bowel disease in Europe: the ECCO-EpiCom inception cohort. Gut. 2014 Apr;63(4):588-97. (IF-16.6).
- Labrie V, ..., Žvirbliene A, ..., Kupčinskas L, et al. Lactase nonpersistence is directed by DNA-variation-dependent epigenetic aging. Nat Struct Mol Biol. 2016 Jun;23(6):566-73. (IF-13.3)
- Klein AP, ..., Kupcinskas J, et al. Genome-wide meta-analysis identifies five new susceptibility loci for pancreatic cancer. Nat Commun. 2018 Feb 8;9(1):556. (IF-12.1)
- Juzenas S, ..., Kupcinskas L, et al. A comprehensive, cell specific microRNA catalogue of human peripheral blood. Nucleic Acids Res. 2017 Sep 19;45(16):9290-9301. (IF-10.12)
- Gyvyte U, Juzenas S, Salteniene V, Kupcinskas J, ..., Steponaitiene R, ..., Kupcinskas L, Skieceviciene J. MiRNA profiling of gastrointestinal stromal tumors by next-generation sequencing. Oncotarget. 2017 Jun 6;8(23):37225-37238. (IF-5.2)
Laboratory of Surgical Gastroenterology
Head of the Laboratory
prof. Antanas Gulbinas
Phone. (+370 37) 32 69 83
The mission of the Laboratory includes investigation into the molecular mechanism (genetic, epigenetic, protein analysis) of the digestive system tumours and inflammatory pancreatic diseases. The staff includes experienced scientists with necessary skills for gene expression, protein analysis, and cell culture experiments.
Research projects of Laboratory of Surgical Gastroenterology
1) Lithuanian oncology research project “NAVIKAS”, 2005-2006
2) Computer modeling and evaluation of biological response to thermal effect of radiofrequency ablation, 2007-2009 (No. P-02/2007)
3) Investigation of pancreatic stelate cells activity and redox state, 2012-2014 (LIG 12/2012)
4) Genetic, epigenetic and energetic mechanisms of resistance to chemotherapy of pancreatic adenocarcinoma, VP1-3.1-ŠMM-07-K-02-062, 2013-2015
5) Optimizing the effectiveness of hyperthermic chemotherapy by modulation of heat shock proteins, energetic resources and adhesion in malignant cells, SEN01/2015, 2015-2018
Publications of Laboratory of Surgical Gastroenterology
Laboratory of Translational Bioinformatics
Head of the Laboratory
prof. dr. Limas Kupcinskas
In the age of big data, enormous amounts of information are being generated, not only from scientific research and high throughput devices, but also from clinical settings. The vision of the laboratory is to simplify and transform high dimensional molecular data, including next generation sequencing of human genomes, transcriptomes, and microbiomes with phenotypical, clinical and behavior data, into clinically applicable knowledge, i.e. identify disease biomarkers and to develop individual predictive models which could be used in precision medicine.
Our laboratory has researchers with bioinformatics expertise in analyzing large molecular datasets, especially generated by next-generation sequencing platforms, and in assembling and maintaining analytical pipelines and computational infrastructure, which enables the application of bioinformatics in their research areas.
2017 - Dr. S. Juzėnas Ist place winner in the contest LSMU „PhD Student 2017“.
2017 - PhD student G. Streleckienė was awarded for the best oral presentation by Scientific committee of Fit for the Future in Gastroenterology Meeting (Berlin, Germany).
2016 - The Kaunas City Scientist Award was awarded for achievements in the field of physical, biomedical, agricultural and technological sciences to prof. habil. dr. L. Kupčinskas.
2016 - assoc. prof. J. Kupčinskas was given the name of the most promising medical doctor in Kaunas city.
2016 - dr. J. Skiecevičienė IIIrd place winner in the contest LSMU „Junior Scientist 2016“.
2015 - dr. A. Jasukaitienė (Jakštaitė) was awared for the best paper by Federtion of european physiological society and the baltic phusiological society (FEPS)
2015 - Assoc. prof. J. Kupčinskas IInd place winner in the contest LSMU „Junior Scientist 2015“.
2014 - prof. A. Gulbinas was awarded for the best poster and oral presentations by the organizing committee of the 11th World Congress of the International Hepato-Pancreato-Biliary Association (IHPBA World Congress 2014).
2014 – dr. A. Jasukaitienė (Jakštaitė) was awarded with the National Scholar Award be the Scientific committee of United European Gastroenterology (UEG) Week.
2013 - dr. J. Skiecevičienė Ist place winner in the contest LSMU „Junior Scientist 2013“.
2012 - prof. habil. dr. L. Kupčinskas was selected as the most prominent scientist in the field of medicine from year 2002-2012 by the magazine "Veidas" in the project "Mini-Nobel 2012".
2011 - prof. habil. dr. L. Kupčinkas was awarded the Order of the Lithuanian Grand Duke Gediminas (Class 5)
2011 - dr. J. Skiecevičienė recieved the award for the best disertation in biomedical field from the the Lithuanian Young Scientists' Union.
2010 - prof. habil. dr. L. Kupčinskas received Lithuanian Science Award for the work "Digestive system diseases: the role of microflora and genetic factors in etiopathogenesis of diseases, new aspects of diagnosis and treatment", year 1996–2009.
2010 - dr. J. Skiecevičienė (Šventoraitytė) Ist place winner in the contest LSMU „PhD Student 2010“.
2009 - prof. habil. dr. L. Kupčinskas given the name of the honorary Lithuanian medical doctor and received a symbol of honor.
2008 - prof. habil. dr. L. Kupčinskas received award "The Tree of Life" from the Lithuanian Academy of Sciences, Ministry of Health and the Confederation of Industrialists for his scientific work in the field of medicine and natural sciences.