Laboratory of Genomics


 

Head:
Luiza Handschuh, Ph.D.

 

 


Staff:
Jan Podkowiński, Ph.D.,

Marcin Radom, D.Eng.,

Aleksandra Świercz, D.Eng.,

Paweł Wojciechowski,D.Eng.,

Agnieszka Żmieńko, Ph.D.

 


 

Laboratory of Genomics affiliated to Department of Molecular and Systems Biology

 

Key words:

genomics, microarrays, next generation sequencing, gene expression analysis, computational biology

 

Research offer:

Owing to the development facilities and many years of experience, we can offer support in genomic research, from microarrays through next generation sequencing to quantitative PCR-based analysis of selected genes/transcripts.

 

Equipment:

  1. Genome Analyzer IIx sequencing system (Illumina)
  2. QX200 Droplet Digital PCR (ddPCR™) System (BioRad)
  3. Rotor-Gene Q real-time PCR cycler (Qiagen)
  4. 2100 Bioanalyzer (Agilent)
  5. NanoPrint LM60 microarray printer (Telechem)
  6. SpotArray24 microarray printer (PerkinElmer)
  7. HS 4800 Pro microarray hybridization station (Tecan)
  8. Axon 4200AL microarray scanner (Molecular Devices)
  9. ScanArray Express microarray scanner (PerkinElmer)
  10. DNA CL E508 G Crosslinker (Uvitec)
  11. Bioruptor NextGen sonication system (Diagenode)
  12. Nanodrop 2000 spectrophotometer (Thermo Scientific)
  13. Qubit Fluorometer (Invitrogen)
  14. Thermocyclers (Techne, BioRad)
  15. Quantum St4 system for gel documentation (Fisher Biotec)

 

Scientific profile:

The major part of our activities is designing and application of genomic tools to solve various biological problems. We determine expression profiles of protein-coding genes and regulatory RNAs, analyze genome sequences of plants, animals and humans. We focus on basic research, however, we are also implicated in research and development projects in the field of biomedicine and plant biotechnology. Additionally, we are engaged in teaching and popularization of science, organizing workshops for children and teenagers, e.g. during The Nights of Scientists or Poznan Festivals of Science and Art.

 

Current research activity

  • Studies on acute myeloid leukemia in adults – transcriptome and genome level – in collaboration with Poznan University of Medical Sciences
  • Ancient DNA analysis in human populations – in collaboration with Adam Mickiewicz University in Poznan, Faculty of History and Faculty of Biology
  • Studies of gene expression and signal transduction pathway changes induced by erythropoietin, cisplatin and paclitaxel  in human ovarian cancer cell lines with different levels of drug resistance – in collaboration with Military Institute of Medicine, Warsaw
  • Screening for genes regulated by PUMILIO and MAELSTROM RNA-binding proteins in human seminoma – in collaboration with the Institute of Human Genetics PAS, Poznan

 

Most important research achievements:

  • Identification of differentially expressed genes in acute myeloid leukemia
  • Determination of differentially expressed genes associated with the development of drug resistance in human ovarian cancer cell lines
  • Identification of transcripts regulated by PUMILIO and MAELSTROM RNA-binding proteins in human seminoma
  • Identification and comparative analysis of short non-coding RNAs (piRNAs, miRNAs and tRFs) in Sus scrofa gonads
  • Development of NPM1 mutation detection method in acute myeloid leukemia samples (NPM1mut+assay)
  • Development of a new strategy of exome enrichment validation assay (MTTE, Multipoint Test for Targeted-enrichment Efficiency)
  • Elaboration of procedures for selection of optimal data normalization method in reference to microarray and next generation sequencing data
  • Design and application of microarrays dedicated to the studies of: Tc-1 transposones in fish genomes; transcriptional activity of chloroplast genomes; expression changes of selected genes in the development of acute myeloid leukemia

 

Actual research projects:

  • Dynasty and population of the Piast state in view of the integrated historical, anthropological and genomic studies, National Science Center Poland SYMFONIA grant, 2014/12/W/NZ2/00466, 2014 – 2019, leader: prof. Marek Figlerowicz, Institute of Bioorganic Chemistry PAS, Poznan
  • Do erythropoietin signal transduction pathways cross with the signal transduction pathways induced by cisplatin and paclitaxel in human ovarian cancer cells? The Ministry of Science and Higher Education Poland grant, N N401 532740, 2010 – 2016, leader:  dr J. Szenajch, Military Institute of Medicine, Warsaw
  • Global PUMILIO regulation of mRNAs and role of MAELSTROM, a nuage component and a cancer testis marker, in human seminoma, National Science Center Poland OPUS grant, 2013/09/B/NZ1/01878, 2013-2017, Institute of Human Genetics PAS, Poznan, leader: prof. Jadwiga Jaruzelska
  • Identification of circular RNAs and protein factors involved in their biogenesis in a model plant, Arabidopsis thaliana, National Science Center Poland SONATA grant, 2014/15/D/NZ2/02305, 2015 – 2018, leader: dr Anna Philips, Institute of Bioorganic Chemistry PAS, Poznan

 

Selected publications:

Philips A, Stolarek I, Kuczkowska B, Juras A, Handschuh L, Piontek J, Kozlowski P, Figlerowicz M. Comprehensive analysis of microorganisms accompanying human archaeological remains, Gigascience. 2017 Jun 13. doi: 10.1093/gigascience/gix044.

Budny B, Szczepanek-Parulska E, Zemojtel T, Szaflarski W, Rydzanicz M, Wesoly J, Handschuh L, Wolinski K, Piatek K, Niedziela M, Ziemnicka K, Figlerowicz M, Zabel M, Ruchala M. Mutations in proteasome-related genes are associated with thyroid hemiagenesis, Endocrine 2017, 56(2):279-285.

Samelak-Czajka A, Marszalek-Zenczak M, Marcinkowska-Swojak M, Kozlowski P, Figlerowicz M, Zmienko A. MLPA-Based Analysis of Copy Number Variation in Plant Populations, Front Plant Sci. 2017, 8:222.

Marcinkowska-Swojak M, Handschuh L, Wojciechowski P, Goralski M, Tomaszewski K, Kazmierczak M, Lewandowski K, Komarnicki M, Blazewicz J, Figlerowicz M, Kozlowski P. Simultaneous detection of mutations and copy number variation of NPM1 in the acute myeloid leukemia using multiplex ligation-dependent probe amplification, Mutation Research 2016, 786:14-26.

Klonowska K, Handschuh L, Swiercz A, Figlerowicz M, Kozlowski P. MTTE: an innovative strategy for the evaluation of targeted/exome enrichment efficiency, Oncotarget. 2016, 7:67266-67276.

Klonowska K, Czubak K, Wojciechowska M, Handschuh L, Zmienko A, Figlerowicz M, Dams-Kozlowska H, Kozlowski P. Oncogenomic portals for the visualization and analysis of genome-wide cancer data. Oncotarget. 2016, 7:176-92.

Zmienko A, Samelak-Czajka A, Kozlowski P, Szymanska M, Figlerowicz M. Arabidopsis thaliana population analysis reveals high plasticity of the genomic region spanning MSH2, AT3G18530 and AT3G18535 genes and provides evidence for NAHR-driven recurrent CNV events occurring in this location. BMC Genomics, 2016, 17(1):893.

Goralski M., Sobieszczanska P., Obrepalska-Steplowska A., Swiercz A., Zmienko A., Figlerowicz M., A gene expression microarray for Nicotiana benthamiana based on de novo transcriptome sequence assembly, Plant Methods, 2016, 12:28.

Hojka-Osinska A, Budzko L, Zmienko A, Rybarczyk A, Maillard P, Budkowska A, Figlerowicz M, Jackowiak P. RNA-Seq-based analysis of differential gene expression associated with hepatitis C virus infection in a cell culture. Acta Biochim Pol., 2016, 63(4):789-798.

Zmienko A, Goralski M, Samelak-Czajka A, Sobieszczuk-Nowicka E, Figlerowicz M. Time course transcriptional profiling of senescing barley leaves. Genom Data, 2015, 4:78-81.

Klonowska K, Ratajska M, Czubak K, Kuzniacka A, Brozek I, Koczkowska M, Sniadecki M, Debniak J, Wydra D, Balut M, Stukan M, Zmienko A, Nowakowska B, Irminger-Finger I, Limon J, Kozlowski P. Analysis of large mutations in BARD1 in patients with breast and/or ovarian cancer: the Polish population as an example, Sci Rep. 2015, 5:10424.

Zmienko A, Samelak-Czajka A, Goralski M, Sobieszczuk-Nowicka E, Kozlowski P, Figlerowicz M. Selection of reference genes for qPCR- and ddPCR-based analyses of gene expression in Senescing Barley leaves. PLoS One. 2015, 10(2):e0118226.

Zyprych-Walczak J, Szabelska A, Handschuh L, Górczak K, Klamecka K, Figlerowicz M, Siatkowski I. The Impact of Normalization Methods on RNA-Seq Data Analysis. Biomed Res Int. 2015, 2015:621690.

Janus P, Stokowy T, Jaksik R, Szoltysek K, Handschuh L, Podkowinski J, Widlak W, Kimmel M, Widlak P. Cross talk between cytokine and hyperthermia-induced pathways: identification of different subsets of NF-κB-dependent genes regulated by TNFα and heat shock. Mol Genet Genomics. 2015, 290:1979-90.

Gurda D, Handschuh L, Kotkowiak W, Jakubowski H. Homocysteine thiolactone and N-homocysteinylated protein induce pro-atherogenic changes in gene expression in human vascular endothelial cells. Amino Acids. 2015, 47:1319-39.

Korfanty J, Stokowy T, Widlak P, Gogler-Piglowska A, Handschuh L, Podkowiński J, Vydra N, Naumowicz A, Toma-Jonik A, Widlak W. Crosstalk between HSF1 and HSF2 during the heat shock response in mouse testes. Int J Biochem Cell Biol. 2014, 57:76-83.

Kowalczykiewicz D, Świercz A, Handschuh L, Leśniak K, Figlerowicz M, Wrzesinski J. Characterization of Sus scrofa small non-coding RNAs present in both female and male gonads. PLoS One. 2014, 9:e113249.

Santoni D, Swiercz A, Zmieńko A, Kasprzak M, Blazewicz M, Bertolazzi P, Felici G. An integrated approach (CLuster Analysis Integration Method) to combine expression data and protein-protein interaction networks in agrigenomics: application on Arabidopsis thaliana. OMICS. 2014, 18:155-65.

Kaźmierczak M, Luczak M, Lewandowski K, Handschuh L, Czyż A, Jarmuż M, Gniot M, Michalak M, Figlerowicz M, Komarnicki M. Esterase D and gamma 1 actin level might predict results of induction therapy in patients with acute myeloid leukemia without and with maturation. Med Oncol. 2013, 30:725.

Uszczyńska B, Zyprych-Walczak J, Handschuh L, Szabelska A, Kaźmierczak M, Woronowicz W, Kozłowski P, Sikorski MM, Komarnicki M, Siatkowski I, Figlerowicz M. Analysis of boutique arrays: a universal method for the selection of the optimal data normalization procedure. Int J Mol Med. 2013, 32:668-84.

Luczak M, Kaźmierczak M, Handschuh L, Lewandowski K, Komarnicki M, Figlerowicz M. Comparative proteome analysis of acute myeloid leukemia with and without maturation. J Proteomics. 2012, 75:5734-48.