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  1. Article ; Online: RNA-seq library preparation for comprehensive transcriptome analysis in cancer cells: The impact of insert size.

    Jaksik, Roman / Drobna-Śledzińska, Monika / Dawidowska, Małgorzata

    Genomics

    2021  Volume 113, Issue 6, Page(s) 4149–4162

    Abstract: With long reads and high coverage, RNA-seq enables comprehensive transcriptome analysis of cancer cells, provided that optimal length of libraries (and their inserts) is assured, to avoid overlap of paired reads and consequent loss of sequencing data. We ...

    Abstract With long reads and high coverage, RNA-seq enables comprehensive transcriptome analysis of cancer cells, provided that optimal length of libraries (and their inserts) is assured, to avoid overlap of paired reads and consequent loss of sequencing data. We assessed TruSeq Stranded library preparation protocols (poly(A) enrichment-PA and rRNA depletion-RD) for the thoroughness of transcriptome analysis of a heterogeneous cancer, acute lymphoblastic leukemia. We applied 2x150PE sequencing, >150 M reads/sample on Illumina NovaSeq6000. We show that PA outperforms RD for the analysis of gene expression and structural aberrations. RD is more suitable for detection of various classes of RNAs, mutations or polymorphisms. We demonstrate that reduced RNA fragmentation time (generating longer inserts) positively affects detection of structural RNA changes, without introducing bias into gene expression analysis. We recommend this modification for all RNA-seq studies utilizing reads longer than 75 nt, aimed to go beyond gene expression analysis and to detect also structural changes.
    MeSH term(s) Gene Expression Profiling/methods ; Gene Library ; High-Throughput Nucleotide Sequencing/methods ; Neoplasms/genetics ; RNA, Messenger/metabolism ; RNA-Seq ; Sequence Analysis, RNA/methods ; Transcriptome
    Chemical Substances RNA, Messenger
    Language English
    Publishing date 2021-11-03
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 356334-0
    ISSN 1089-8646 ; 0888-7543
    ISSN (online) 1089-8646
    ISSN 0888-7543
    DOI 10.1016/j.ygeno.2021.10.018
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2367: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (2.OG)
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  2. Article: RNA-seq library preparation for comprehensive transcriptome analysis in cancer cells: The impact of insert size

    Jaksik, Roman / Drobna-Śledzińska, Monika / Dawidowska, Małgorzata

    Genomics. 2021 Nov., v. 113, no. 6

    2021  

    Abstract: With long reads and high coverage, RNA-seq enables comprehensive transcriptome analysis of cancer cells, provided that optimal length of libraries (and their inserts) is assured, to avoid overlap of paired reads and consequent loss of sequencing data. We ...

    Abstract With long reads and high coverage, RNA-seq enables comprehensive transcriptome analysis of cancer cells, provided that optimal length of libraries (and their inserts) is assured, to avoid overlap of paired reads and consequent loss of sequencing data. We assessed TruSeq Stranded library preparation protocols (poly(A) enrichment-PA and rRNA depletion-RD) for the thoroughness of transcriptome analysis of a heterogeneous cancer, acute lymphoblastic leukemia. We applied 2x150PE sequencing, >150 M reads/sample on Illumina NovaSeq6000. We show that PA outperforms RD for the analysis of gene expression and structural aberrations. RD is more suitable for detection of various classes of RNAs, mutations or polymorphisms. We demonstrate that reduced RNA fragmentation time (generating longer inserts) positively affects detection of structural RNA changes, without introducing bias into gene expression analysis. We recommend this modification for all RNA-seq studies utilizing reads longer than 75 nt, aimed to go beyond gene expression analysis and to detect also structural changes.
    Keywords gene expression ; genomics ; lymphocytic leukemia ; sequence analysis ; transcriptomics
    Language English
    Dates of publication 2021-11
    Size p. 4149-4162.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 356334-0
    ISSN 1089-8646 ; 0888-7543
    ISSN (online) 1089-8646
    ISSN 0888-7543
    DOI 10.1016/j.ygeno.2021.10.018
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2367: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  3. Article ; Online: DNA Methylation in T-Cell Acute Lymphoblastic Leukemia: In Search for Clinical and Biological Meaning.

    Maćkowska, Natalia / Drobna-Śledzińska, Monika / Witt, Michał / Dawidowska, Małgorzata

    International journal of molecular sciences

    2021  Volume 22, Issue 3

    Abstract: Distinct DNA methylation signatures, related to different prognosis, have been observed across many cancers, including T-cell acute lymphoblastic leukemia (T-ALL), an aggressive hematological neoplasm. By global methylation analysis, two major phenotypes ...

    Abstract Distinct DNA methylation signatures, related to different prognosis, have been observed across many cancers, including T-cell acute lymphoblastic leukemia (T-ALL), an aggressive hematological neoplasm. By global methylation analysis, two major phenotypes might be observed in T-ALL: hypermethylation related to better outcome and hypomethylation, which is a candidate marker of poor prognosis. Moreover, DNA methylation holds more than a clinical meaning. It reflects the replicative history of leukemic cells and most likely different mechanisms underlying leukemia development in these T-ALL subtypes. The elucidation of the mechanisms and aberrations specific to (epi-)genomic subtypes might pave the way towards predictive diagnostics and precision medicine in T-ALL. We present the current state of knowledge on the role of DNA methylation in T-ALL. We describe the involvement of DNA methylation in normal hematopoiesis and T-cell development, focusing on epigenetic aberrations contributing to this leukemia. We further review the research investigating distinct methylation phenotypes in T-ALL, related to different outcomes, pointing to the most recent research aimed to unravel the biological mechanisms behind differential methylation. We highlight how technological advancements facilitated broadening the perspective of the investigation into DNA methylation and how this has changed our understanding of the roles of this epigenetic modification in T-ALL.
    MeSH term(s) Cell Differentiation/genetics ; Cell Proliferation/genetics ; DNA Methylation ; Epigenesis, Genetic ; Gene Expression Regulation, Leukemic ; Hematopoiesis/genetics ; Humans ; Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/blood ; Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/genetics ; Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/mortality ; Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/pathology ; Prognosis ; T-Lymphocytes/pathology
    Language English
    Publishing date 2021-01-30
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms22031388
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: CRISPRi for specific inhibition of miRNA clusters and miRNAs with high sequence homology.

    Drobna-Śledzińska, Monika / Maćkowska-Maślak, Natalia / Jaksik, Roman / Dąbek, Paulina / Witt, Michał / Dawidowska, Małgorzata

    Scientific reports

    2022  Volume 12, Issue 1, Page(s) 6297

    Abstract: miRNAs form a class of noncoding RNAs, involved in post-transcriptional regulation of gene expression, broadly studied for their involvement in physiological and pathological context. Inhibition of mature miRNA transcripts, commonly used in miRNA loss-of- ...

    Abstract miRNAs form a class of noncoding RNAs, involved in post-transcriptional regulation of gene expression, broadly studied for their involvement in physiological and pathological context. Inhibition of mature miRNA transcripts, commonly used in miRNA loss-of-function experiments, may not be specific in case of miRNAs with high sequence homology, e.g. miRNAs from the same seed family. Phenotypic effects of miRNA repression might be biased by the repression of highly similar miRNAs. Another challenge is simultaneous inhibition of multiple miRNAs encoded within policistronic clusters, potentially co-regulating common biological processes. To elucidate roles of miRNA clusters and miRNAs with high sequence homology, it is of key importance to selectively repress only the miRNAs of interest. Targeting miRNAs on genomic level with CRISPR/dCas9-based methods is an attractive alternative to blocking mature miRNAs. Yet, so far no clear guidelines on the design of CRISPR inhibition (CRISPRi) experiments, specifically for miRNA repression, have been proposed. To address this need, here we propose a strategy for effective inhibition of miRNAs and miRNA clusters using CRISPRi. We provide clues on how to approach the challenges in using CRISPR/dCas in miRNA studies, which include prediction of miRNA transcription start sites (TSSs) and the design of single guide RNAs (sgRNAs). The strategy implements three TSS prediction online tools, dedicated specifically for miRNAs: miRStart, FANTOM 5 miRNA atlas, DIANA-miRGen, and CRISPOR tool for sgRNAs design; it includes testing and selection of optimal sgRNAs. We demonstrate that compared to siRNA/shRNA-based miRNA silencing, CRISPRi improves the repression specificity for miRNAs with highly similar sequence and contribute to higher uniformity of the effects of silencing the whole miRNA clusters. This strategy may be adapted for CRISPR-mediated activation (CRISPRa) of miRNA expression.
    MeSH term(s) Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; MicroRNAs/genetics ; MicroRNAs/metabolism ; RNA, Guide, CRISPR-Cas Systems/genetics ; RNA, Guide, CRISPR-Cas Systems/metabolism ; Sequence Homology ; Transcription Initiation Site
    Chemical Substances MicroRNAs ; RNA, Guide, CRISPR-Cas Systems
    Language English
    Publishing date 2022-04-15
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-022-10336-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Multiomics to investigate the mechanisms contributing to repression of PTPRC and SOCS2 in pediatric T-ALL: Focus on miR-363-3p and promoter methylation.

    Drobna-Śledzińska, Monika / Maćkowska-Maślak, Natalia / Jaksik, Roman / Kosmalska, Maria / Szarzyńska, Bronisława / Lejman, Monika / Sędek, Łukasz / Szczepański, Tomasz / Taghon, Tom / Van Vlierberghe, Pieter / Witt, Michał / Dawidowska, Małgorzata

    Genes, chromosomes & cancer

    2022  Volume 61, Issue 12, Page(s) 720–733

    Abstract: T-cell acute lymphoblastic leukemia (T-ALL) is a heterogeneous and aggressive malignancy arising from T-cell precursors. MiRNAs are implicated in negative regulation of gene expression and when aberrantly expressed contribute to various cancer types, ... ...

    Abstract T-cell acute lymphoblastic leukemia (T-ALL) is a heterogeneous and aggressive malignancy arising from T-cell precursors. MiRNAs are implicated in negative regulation of gene expression and when aberrantly expressed contribute to various cancer types, including T-ALL. Previously we demonstrated the oncogenic potential of miR-363-3p overexpression in a subgroup of T-ALL patients. Here, using combined proteomic and transcriptomic approaches, we show that miR-363-3p enhances cell growth of T-ALL in vitro via inhibition of PTPRC and SOCS2, which are implicated in repression of the JAK-STAT pathway. We propose that overexpression of miR-363-3p is a novel mechanism potentially contributing to overactivation of JAK-STAT pathway. Additionally, by combining the transcriptomic and methylation data of T-ALL patients, we show that promoter methylation may also contribute to downregulation of SOCS2 expression and thus potentially to JAK-STAT activation. In conclusion, we highlight aberrant miRNA expression and aberrant promoter methylation as mechanisms, alternative to mutations of JAK-STAT-related genes, which might lead to the upregulation of JAK-dependent signaling in T-ALL.
    MeSH term(s) Cell Line, Tumor ; Child ; Humans ; Janus Kinases/genetics ; Leukocyte Common Antigens/metabolism ; Methylation ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/genetics ; Proteomics ; STAT Transcription Factors/genetics ; STAT Transcription Factors/metabolism ; Signal Transduction ; Suppressor of Cytokine Signaling Proteins/genetics ; Suppressor of Cytokine Signaling Proteins/metabolism
    Chemical Substances MIRN363 microRNA, human ; MicroRNAs ; SOCS2 protein, human ; STAT Transcription Factors ; Suppressor of Cytokine Signaling Proteins ; Janus Kinases (EC 2.7.10.2) ; Leukocyte Common Antigens (EC 3.1.3.48) ; PTPRC protein, human (EC 3.1.3.48)
    Language English
    Publishing date 2022-07-18
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1018988-9
    ISSN 1098-2264 ; 1045-2257
    ISSN (online) 1098-2264
    ISSN 1045-2257
    DOI 10.1002/gcc.23085
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 2966: Show issues Location:
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    ab Jg. 2022: Lesesaal (EG)

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  6. Article ; Online: Small RNA-Seq Reveals Similar miRNA Transcriptome in Children and Young Adults with T-ALL and Indicates miR-143-3p as Novel Candidate Tumor Suppressor in This Leukemia.

    Dawidowska, Małgorzata / Maćkowska-Maślak, Natalia / Drobna-Śledzińska, Monika / Kosmalska, Maria / Jaksik, Roman / Szymczak, Donata / Jarmuż-Szymczak, Małgorzata / Sadowska-Klasa, Alicja / Wojtaszewska, Marzena / Sędek, Łukasz / Wróbel, Tomasz / Zaucha, Jan Maciej / Szczepański, Tomasz / Lewandowski, Krzysztof / Giebel, Sebastian / Witt, Michał

    International journal of molecular sciences

    2022  Volume 23, Issue 17

    Abstract: We aimed to identify miRNAs and pathways specifically deregulated in adolescent and young adult (AYA) T-ALL patients. Small RNA-seq showed no major differences between AYA and pediatric T-ALL, but it revealed downregulation of miR-143-3p in T-ALL ... ...

    Abstract We aimed to identify miRNAs and pathways specifically deregulated in adolescent and young adult (AYA) T-ALL patients. Small RNA-seq showed no major differences between AYA and pediatric T-ALL, but it revealed downregulation of miR-143-3p in T-ALL patients. Prediction algorithms identified several known and putative oncogenes targeted by this miRNA, including
    MeSH term(s) Adolescent ; Child ; Fibroblast Growth Factor 1/metabolism ; Gene Expression Regulation, Neoplastic ; Humans ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Phosphatidylinositol 3-Kinases/metabolism ; Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/genetics ; Proto-Oncogene Proteins p21(ras)/genetics ; RNA-Seq ; Transcriptome ; Young Adult
    Chemical Substances MIRN143 microRNA, human ; MicroRNAs ; Fibroblast Growth Factor 1 (104781-85-3) ; Proto-Oncogene Proteins p21(ras) (EC 3.6.5.2)
    Language English
    Publishing date 2022-09-04
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms231710117
    Database MEDical Literature Analysis and Retrieval System OnLINE

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