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  1. Article ; Online: Prostate-specific membrane antigen (PSMA) as a potential target for molecular imaging and treatment in bone and soft tissue sarcomas.

    Kleiburg, Fleur / Heijmen, Linda / Gelderblom, Hans / Kielbasa, Szymon M / Bovée, Judith Vmg / De Geus-Oei, Lioe-Fee

    The British journal of radiology

    2023  Volume 96, Issue 1145, Page(s) 20220886

    Abstract: Bone and soft tissue sarcomas are a group of rare malignant tumours with major histological and anatomical varieties. In a metastatic setting, sarcomas have a poor prognosis due to limited response rates to chemotherapy. Radioligand therapy targeting ... ...

    Abstract Bone and soft tissue sarcomas are a group of rare malignant tumours with major histological and anatomical varieties. In a metastatic setting, sarcomas have a poor prognosis due to limited response rates to chemotherapy. Radioligand therapy targeting prostate-specific membrane antigen (PSMA) may offer a new perspective. PSMA is a type II transmembrane glycoprotein which is present in all prostatic tissue and overexpressed in prostate cancer. Despite the name, PSMA is not prostate-specific. PSMA expression is also found in a multitude of non-prostatic diseases including a subgroup of sarcomas, mostly in its neovascular endothelial cells. On PET/CT imaging, multiple sarcomas have also shown intense PSMA-tracer accumulation. PSMA expression and PSMA-tracer uptake seem to be highest in patients with aggressive and advanced sarcomas, who are also in highest need of new therapeutic options. Although these results provide a good rationale for the future use of PSMA-targeted radioligand therapy in a selection of sarcoma patients, more research is needed to gain insight into optimal patient selection methods, PSMA-targeting antibodies and tracers, administered doses of radioligand therapy, and their efficacy and tolerability. In this review, mRNA expression of the FOLH1 gene which encodes PSMA, PSMA immunohistochemistry, PSMA-targeted imaging and PSMA-targeted therapy in sarcomas will be discussed.
    MeSH term(s) Male ; Humans ; Positron Emission Tomography Computed Tomography/methods ; Endothelial Cells/metabolism ; Endothelial Cells/pathology ; Prostatic Neoplasms/diagnostic imaging ; Prostatic Neoplasms/radiotherapy ; Sarcoma/diagnostic imaging ; Sarcoma/radiotherapy ; Prostate-Specific Antigen/metabolism ; Molecular Imaging
    Chemical Substances Prostate-Specific Antigen (EC 3.4.21.77)
    Language English
    Publishing date 2023-03-03
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2982-8
    ISSN 1748-880X ; 0007-1285
    ISSN (online) 1748-880X
    ISSN 0007-1285
    DOI 10.1259/bjr.20220886
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: MDMX Regulates Transcriptional Activity of p53 and FOXO Proteins to Stimulate Proliferation of Melanoma Cells.

    Heijkants, Renier C / Teunisse, Amina F A S / de Jong, Danielle / Glinkina, Kseniya / Mei, Hailiang / Kielbasa, Szymon M / Szuhai, Karoly / Jochemsen, Aart G

    Cancers

    2022  Volume 14, Issue 18

    Abstract: The tumor suppressor protein p53 has an important role in cell-fate determination. In cancer cells, the activity of p53 is frequently repressed by high levels of MDMX and/or MDM2. MDM2 is a ubiquitin ligase whose activity results in ubiquitin- and ... ...

    Abstract The tumor suppressor protein p53 has an important role in cell-fate determination. In cancer cells, the activity of p53 is frequently repressed by high levels of MDMX and/or MDM2. MDM2 is a ubiquitin ligase whose activity results in ubiquitin- and proteasome-dependent p53 degradation, while MDMX inhibits p53-activated transcription by shielding the p53 transactivation domain. Interestingly, the oncogenic functions of MDMX appear to be more wide-spread than inhibition of p53. The present study aimed to elucidate the MDMX-controlled transcriptome. Therefore, we depleted MDMX with four distinct shRNAs from a high MDMX expressing uveal melanoma cell line and determined the effect on the transcriptome by RNAseq. Biological function analyses indicate the inhibition of the cell cycle regulatory genes and stimulation of cell death activating genes upon MDMX depletion. Although the inhibition of p53 activity clearly contributes to the transcription regulation controlled by MDMX, it appeared that the transcriptional regulation of multiple genes did not only rely on p53 expression. Analysis of gene regulatory networks indicated a role for Forkhead box (FOX) transcription factors. Depletion of FOXO proteins partly prevented the transcriptional changes upon MDMX depletion. Furthermore, depletion of FOXO proteins relatively diminished the growth inhibition upon MDMX knockdown, although the knockdown of the FOXO transcription factors also reduces cell growth. In conclusion, the p53-independent oncogenic functions of MDMX could be partially explained by its regulation of FOXO activity.
    Language English
    Publishing date 2022-09-15
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2527080-1
    ISSN 2072-6694
    ISSN 2072-6694
    DOI 10.3390/cancers14184482
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Low-input nucleus isolation and multiplexing with barcoded antibodies of mouse sympathetic ganglia for single-nucleus rna sequencing

    Ge, Yang / van Roon, Lieke / Chen, H. Sophia / Methorst, Ruben / Paton, Martin / DeRuiter, Marco C. / Kielbasa, Szymon M. / Jongbloed, Monique R. M.

    Journal of visualized experiments. 2022 Mar. 23, , no. 181

    2022  

    Abstract: The cardiac autonomic nervous system is crucial in controlling cardiac function, such as heart rate and cardiac contractility, and is divided into sympathetic and parasympathetic branches. Normally, there is a balance between these two branches to ... ...

    Abstract The cardiac autonomic nervous system is crucial in controlling cardiac function, such as heart rate and cardiac contractility, and is divided into sympathetic and parasympathetic branches. Normally, there is a balance between these two branches to maintain homeostasis. However, cardiac disease states such as myocardial infarction, heart failure, and hypertension can induce the remodeling of cells involved in cardiac innervation, which is associated with an adverse clinical outcome. Although there are vast amounts of data for the histological structure and function of the cardiac autonomic nervous system, its molecular biological architecture in health and disease is still enigmatic in many aspects. Novel technologies such as single-cell RNA sequencing (scRNA-seq) hold promise for the genetic characterization of tissues at single-cell resolution. However, the relatively large size of neurons may impede the standardized use of these techniques. Here, this protocol exploits droplet-based single-nucleus RNA sequencing (snRNA-seq), a method to characterize the biological architecture of cardiac sympathetic neurons in health and disease. A stepwise approach is demonstrated to perform snRNA-seq of the bilateral superior cervical (SCG) and stellate ganglia (StG) dissected from adult mice. This method enables long-term sample preservation, maintaining an adequate RNA quality when samples from multiple individuals/experiments cannot be collected all at once within a short period of time. Barcoding the nuclei with hashtag oligos (HTOs) enables demultiplexing and the trace-back of distinct ganglionic samples post sequencing. Subsequent analyses revealed successful nuclei capture of neuronal, satellite glial, and endothelial cells of the sympathetic ganglia, as validated by snRNA-seq. In summary, this protocol provides a stepwise approach for snRNA-seq of sympathetic extrinsic cardiac ganglia, a method that has the potential for broader application in studies of the innervation of other organs and tissues.
    Keywords RNA ; adults ; autonomic nervous system ; barcoding ; cardiac output ; heart failure ; heart rate ; histology ; homeostasis ; hypertension ; innervation ; mice ; myocardial infarction ; neurons ; satellites
    Language English
    Dates of publication 2022-0323
    Size p. e63397.
    Publishing place Journal of Visualized Experiments
    Document type Article
    ZDB-ID 2259946-0
    ISSN 1940-087X
    ISSN 1940-087X
    DOI 10.3791/63397
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: Acquisition of a glycosylated B-cell receptor drives follicular lymphoma toward a dark zone phenotype.

    van Bergen, Cornelis A M / Kloet, Susan L / Quinten, Edwin / Sepúlveda Yáñez, Julieta H / Menafra, Roberta / Griffioen, Marieke / Jansen, Patty M / Koning, Marvyn T / Knijnenburg, Jeroen / Navarrete, Marcelo A / Kiełbasa, Szymon M / Veelken, Hendrik

    Blood advances

    2023  Volume 7, Issue 19, Page(s) 5812–5816

    Language English
    Publishing date 2023-07-24
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2915908-8
    ISSN 2473-9537 ; 2473-9529
    ISSN (online) 2473-9537
    ISSN 2473-9529
    DOI 10.1182/bloodadvances.2023010725
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Low-input Nucleus Isolation and Multiplexing with Barcoded Antibodies of Mouse Sympathetic Ganglia for Single-nucleus RNA Sequencing.

    Ge, Yang / van Roon, Lieke / Chen, H Sophia / Methorst, Ruben / Paton, Martin / DeRuiter, Marco C / Kielbasa, Szymon M / Jongbloed, Monique R M

    Journal of visualized experiments : JoVE

    2022  , Issue 181

    Abstract: The cardiac autonomic nervous system is crucial in controlling cardiac function, such as heart rate and cardiac contractility, and is divided into sympathetic and parasympathetic branches. Normally, there is a balance between these two branches to ... ...

    Abstract The cardiac autonomic nervous system is crucial in controlling cardiac function, such as heart rate and cardiac contractility, and is divided into sympathetic and parasympathetic branches. Normally, there is a balance between these two branches to maintain homeostasis. However, cardiac disease states such as myocardial infarction, heart failure, and hypertension can induce the remodeling of cells involved in cardiac innervation, which is associated with an adverse clinical outcome. Although there are vast amounts of data for the histological structure and function of the cardiac autonomic nervous system, its molecular biological architecture in health and disease is still enigmatic in many aspects. Novel technologies such as single-cell RNA sequencing (scRNA-seq) hold promise for the genetic characterization of tissues at single-cell resolution. However, the relatively large size of neurons may impede the standardized use of these techniques. Here, this protocol exploits droplet-based single-nucleus RNA sequencing (snRNA-seq), a method to characterize the biological architecture of cardiac sympathetic neurons in health and disease. A stepwise approach is demonstrated to perform snRNA-seq of the bilateral superior cervical (SCG) and stellate ganglia (StG) dissected from adult mice. This method enables long-term sample preservation, maintaining an adequate RNA quality when samples from multiple individuals/experiments cannot be collected all at once within a short period of time. Barcoding the nuclei with hashtag oligos (HTOs) enables demultiplexing and the trace-back of distinct ganglionic samples post sequencing. Subsequent analyses revealed successful nuclei capture of neuronal, satellite glial, and endothelial cells of the sympathetic ganglia, as validated by snRNA-seq. In summary, this protocol provides a stepwise approach for snRNA-seq of sympathetic extrinsic cardiac ganglia, a method that has the potential for broader application in studies of the innervation of other organs and tissues.
    MeSH term(s) Animals ; Autonomic Nervous System ; Endothelial Cells ; Ganglia, Sympathetic ; Mice ; RNA, Small Nuclear ; Sequence Analysis, RNA/methods
    Chemical Substances RNA, Small Nuclear
    Language English
    Publishing date 2022-03-23
    Publishing country United States
    Document type Journal Article ; Video-Audio Media ; Research Support, Non-U.S. Gov't
    ZDB-ID 2259946-0
    ISSN 1940-087X ; 1940-087X
    ISSN (online) 1940-087X
    ISSN 1940-087X
    DOI 10.3791/63397
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Tumor-expressed microRNAs associated with venous thromboembolism in colorectal cancer.

    Anijs, Rayna J S / Laghmani, El Houari / Ünlü, Betül / Kiełbasa, Szymon M / Mei, Hailiang / Cannegieter, Suzanne C / Klok, Frederikus A / Kuppen, Peter J K / Versteeg, Henri H / Buijs, Jeroen T

    Research and practice in thrombosis and haemostasis

    2022  Volume 6, Issue 5, Page(s) e12749

    Abstract: Background: Colorectal cancer patients have an increased risk of developing venous thromboembolism (VTE), resulting in increased morbidity and mortality. Because the exact mechanism is yet unknown, risk prediction is still challenging; therefore, new ... ...

    Abstract Background: Colorectal cancer patients have an increased risk of developing venous thromboembolism (VTE), resulting in increased morbidity and mortality. Because the exact mechanism is yet unknown, risk prediction is still challenging; therefore, new biomarkers are needed. MicroRNAs (miRNAs) are small, relatively stable RNAs, that regulate a variety of cellular processes, and are easily measured in body fluids.
    Objective: The aim of this study was to identify novel tumor-expressed miRNAs associated with VTE.
    Methods: In a cohort of 418 colorectal cancer patients diagnosed between 2001 and 2015 at the Leiden University Medical Center, 23 patients (5.5%) developed VTE 1 year before or after cancer diagnosis. Based on availability of frozen tumor material, tumor cells of 17 patients with VTE and 18 patients without VTE were isolated using laser capture microdissection and subsequently analyzed on the Illumina sequencing platform NovaSeq600 using 150-bp paired-end sequencing. Cases and controls were matched on age, sex, tumor stage, and grade. Differential miRNA expression was analyzed using edgeR.
    Results: A total of 547 miRNAs were detected. Applying a 1.5-fold difference and false discovery rate of <0.1, 19 tumor-miRNAs were differentially regulated in VTE cases versus controls, with hsa-miR-3652, hsa-miR-92b-5p, and hsa-miR-10,394-5p as most significantly downregulated. Seven of the 19 identified miRNAs were predicted to regulate the gonadotropin-releasing hormone receptor pathway.
    Conclusion: We identified 19 differentially regulated tumor-expressed miRNAs in colorectal cancer-associated VTE, which may provide insights into the biological mechanism and in the future might have potential to serve as novel, predictive biomarkers.
    Language English
    Publishing date 2022-07-01
    Publishing country United States
    Document type Journal Article
    ISSN 2475-0379
    ISSN (online) 2475-0379
    DOI 10.1002/rth2.12749
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Book ; Online ; Thesis: Bioinformatics of eukaryotic gene regulation

    Kielbasa, Szymon M

    2006  

    Author's details von Szymon M. Kielbasa
    Language English
    Size Online-Ressource
    Document type Book ; Online ; Thesis
    Thesis / German Habilitation thesis Humboldt-Univ., Diss--Berlin, 2006
    Database Former special subject collection: coastal and deep sea fishing

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  8. Article ; Online: Statistical method for modeling sequencing data from different technologies in longitudinal studies with application to Huntington disease.

    Fuady, Angga M / van Roon-Mom, Willeke M C / Kiełbasa, Szymon M / Uh, Hae-Won / Houwing-Duistermaat, Jeanine J

    Biometrical journal. Biometrische Zeitschrift

    2020  Volume 63, Issue 4, Page(s) 745–760

    Abstract: Advancement of gene expression measurements in longitudinal studies enables the identification of genes associated with disease severity over time. However, problems arise when the technology used to measure gene expression differs between time points. ... ...

    Abstract Advancement of gene expression measurements in longitudinal studies enables the identification of genes associated with disease severity over time. However, problems arise when the technology used to measure gene expression differs between time points. Observed differences between the results obtained at different time points can be caused by technical differences. Modeling the two measurements jointly over time might provide insight into the causes of these different results. Our work is motivated by a study of gene expression data of blood samples from Huntington disease patients, which were obtained using two different sequencing technologies. At time point 1, DeepSAGE technology was used to measure the gene expression, with a subsample also measured using RNA-Seq technology. At time point 2, all samples were measured using RNA-Seq technology. Significant associations between gene expression measured by DeepSAGE and disease severity using data from the first time point could not be replicated by the RNA-Seq data from the second time point. We modeled the relationship between the two sequencing technologies using the data from the overlapping samples. We used linear mixed models with either DeepSAGE or RNA-Seq measurements as the dependent variable and disease severity as the independent variable. In conclusion, (1) for one out of 14 genes, the initial significant result could be replicated with both technologies using data from both time points; (2) statistical efficiency is lost due to disagreement between the two technologies, measurement error when predicting gene expressions, and the need to include additional parameters to account for possible differences.
    MeSH term(s) Gene Expression Profiling ; Humans ; Huntington Disease/genetics ; Longitudinal Studies ; Technology
    Language English
    Publishing date 2020-12-22
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 131640-0
    ISSN 1521-4036 ; 0323-3847 ; 0006-3452
    ISSN (online) 1521-4036
    ISSN 0323-3847 ; 0006-3452
    DOI 10.1002/bimj.201900235
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: The distinct transcriptomes of slow and fast adult muscles are delineated by noncoding RNAs.

    Raz, Vered / Riaz, Muhammad / Tatum, Zuotian / Kielbasa, Szymon M / 't Hoen, Peter A C

    FASEB journal : official publication of the Federation of American Societies for Experimental Biology

    2018  Volume 32, Issue 3, Page(s) 1579–1590

    Abstract: Adult muscles have a vast adaptation capacity, enabling function switches in response to altered conditions. During intensive physical activity, disease, or aging, adult skeletal muscles change and adjust their functions. The competence to adjust varies ... ...

    Abstract Adult muscles have a vast adaptation capacity, enabling function switches in response to altered conditions. During intensive physical activity, disease, or aging, adult skeletal muscles change and adjust their functions. The competence to adjust varies among muscles. Muscle-specific molecular mechanisms in healthy and normal conditions could designate changes in physiologic and pathologic conditions. We generated deep mRNA-sequencing data in adult fast and slow mouse muscles, and applying paired analysis, we identified that the muscle-specific signatures are composed of half of the muscle transcriptome. The fast muscles showed a more compact gene network that is concordant with homogenous myofiber typing, compared with the pattern in the slow muscle. The muscle-specific mRNA landscape did not correlate with alternative spicing, alternative polyadenylation, or the expression of muscle transcription factor gene networks. However, we found significant correlation between the differentially expressed noncoding RNAs, microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) and their target genes. More than 25% of the genes expressed in a muscle-specific fashion were found to be targets of muscle-specific miRNAs and lncRNAs. We suggest that muscle-specific miRNAs and lncRNAs contribute to the establishment of muscle-specific transcriptomes in adult muscles.-Raz, V., Riaz, M., Tatum, Z., Kielbasa, S. M., 't Hoen, P. A. C. The distinct transcriptomes of slow and fast adult muscles are delineated by noncoding RNAs.
    MeSH term(s) Animals ; Gene Regulatory Networks/physiology ; Male ; Mice ; MicroRNAs/biosynthesis ; MicroRNAs/genetics ; Muscle Fibers, Fast-Twitch/metabolism ; Muscle Fibers, Slow-Twitch/metabolism ; RNA, Long Noncoding/biosynthesis ; RNA, Long Noncoding/genetics ; RNA, Messenger/biosynthesis ; RNA, Messenger/genetics ; Transcriptome/physiology
    Chemical Substances MicroRNAs ; RNA, Long Noncoding ; RNA, Messenger
    Language English
    Publishing date 2018-01-03
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 639186-2
    ISSN 1530-6860 ; 0892-6638
    ISSN (online) 1530-6860
    ISSN 0892-6638
    DOI 10.1096/fj.201700861R
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Cancer-Associated Fibroblasts Are Key Determinants of Cancer Cell Invasion in the Earliest Stage of Colorectal Cancer.

    Dang, Hao / Harryvan, Tom J / Liao, Chen-Yi / Danen, Erik H J / Spalburg, Vienna N L N / Kielbasa, Szymon M / Mei, Hailiang / Goeman, Jelle J / de Jonge-Muller, Eveline S / Janson, Stefanus G T / van der Reijden, Johan J / Crobach, Stijn / Hardwick, James C H / Boonstra, Jurjen J / de Miranda, Noel F C C / Hawinkels, Lukas J A C

    Cellular and molecular gastroenterology and hepatology

    2023  Volume 16, Issue 1, Page(s) 107–131

    Abstract: Background & aims: Improving clinical management of early stage colorectal cancers (T1CRCs) requires a better understanding of their underlying biology. Accumulating evidence shows that cancer-associated fibroblasts (CAFs) are important determinants of ... ...

    Abstract Background & aims: Improving clinical management of early stage colorectal cancers (T1CRCs) requires a better understanding of their underlying biology. Accumulating evidence shows that cancer-associated fibroblasts (CAFs) are important determinants of tumor progression in advanced colorectal cancer (CRC), but their role in the initial stages of CRC tumorigenesis is unknown. Therefore, we investigated the contribution of T1CAFs to early CRC progression.
    Methods: Primary T1CAFs and patient-matched normal fibroblasts (NFs) were isolated from endoscopic biopsy specimens of histologically confirmed T1CRCs and normal mucosa, respectively. The impact of T1CAFs and NFs on tumor behavior was studied using 3-dimensional co-culture systems with primary T1CRC organoids and extracellular matrix (ECM) remodeling assays. Whole-transcriptome sequencing and gene silencing were used to pinpoint mediators of T1CAF functions.
    Results: In 3-dimensional multicellular cultures, matrix invasion of T1CRC organoids was induced by T1CAFs, but not by matched NFs. Enhanced T1CRC invasion was accompanied by T1CAF-induced ECM remodeling and up-regulation of CD44 in epithelial cells. RNA sequencing of 10 NF-T1CAF pairs revealed 404 differentially expressed genes, with significant enrichment for ECM-related pathways in T1CAFs. Cathepsin H, a cysteine-type protease that was specifically up-regulated in T1CAFs but not in fibroblasts from premalignant lesions or advanced CRCs, was identified as a key factor driving matrix remodeling by T1CAFs. Finally, we showed high abundance of cathepsin H-expressing T1CAFs at the invasive front of primary T1CRC sections.
    Conclusions: Already in the earliest stage of CRC, cancer cell invasion is promoted by CAFs via direct interactions with epithelial cancer cells and stage-specific, cathepsin H-dependent ECM remodeling. RNA sequencing data of the 10 NF-T1CAF pairs can be found under GEO accession number GSE200660.
    MeSH term(s) Humans ; Cancer-Associated Fibroblasts/metabolism ; Cathepsin H/metabolism ; Neoplasm Invasiveness/genetics ; Neoplasm Invasiveness/pathology ; Fibroblasts/metabolism ; Colorectal Neoplasms/pathology
    Chemical Substances Cathepsin H (EC 3.4.22.16)
    Language English
    Publishing date 2023-04-20
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2819778-1
    ISSN 2352-345X ; 2352-345X
    ISSN (online) 2352-345X
    ISSN 2352-345X
    DOI 10.1016/j.jcmgh.2023.04.004
    Database MEDical Literature Analysis and Retrieval System OnLINE

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