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xcore: an R package for inference of gene expression regulators [article]

Maciej Migdał, Cecilia Lanny Winata, Takahiro Arakawa, Satoshi Takizawa, Masaaki Furuno, Harukazu Suzuki, Erik Arner, Bogumil Kaczkowski
2022 bioRxiv   pre-print
Elucidating the Transcription Factors (TFs) that drive the gene expression changes in a given experiment is one of the most common questions asked by researchers. The existing methods rely on the predicted Transcription Factor Binding Site (TFBS) to model the changes in the motif activity. Such methods only work for TFs that have a motif and assume TF binding profile is the same in all cell types. Given the wealth of the ChIP-seq data available for a wide range of the TFs in various cell types,
more » ... we propose that the modeling can be done using ChiP-seq signatures directly, effectively skipping the motif finding and TFBS prediction steps. We present xcore, an R package that allows Transcription Factor activity modeling based on their ChiP-seq signatures and user's gene expression data. We also provide xcoredata a companion data package that provides a collection of preprocessed ChiP-seq signatures. We demonstrate that xcore leads to biologically relevant predictions using TGF-beta induced epithelial-mesenchymal transition and rinderpest infection time-course CAGE data as examples.
doi:10.1101/2022.02.23.481130 fatcat:c2sligzbujbqzoukikg6uczaqe

MicroRNA Expression Profiling of the Porcine Developing Brain

Agnieszka Podolska, Bogumil Kaczkowski, Peter Kamp Busk, Rolf Søkilde, Thomas Litman, Merete Fredholm, Susanna Cirera, Joel S. Bader
2011 PLoS ONE  
MicroRNAs are small, non-coding RNA molecules that regulate gene expression at the post-transcriptional level and play an important role in the control of developmental and physiological processes. In particular, the developing brain contains an impressive diversity of microRNAs. Most microRNA expression profiling studies have been performed in human or rodents and relatively limited knowledge exists in other mammalian species. The domestic pig is considered to be an excellent, alternate, large
more » ... mammal model for human-related neurological studies, due to its similarity in both brain development and the growth curve when compared to humans. Considering these similarities, studies examining microRNA expression during porcine brain development could potentially be used to predict the expression profile and role of microRNAs in the human brain. Methodology/Principal Findings: MicroRNA expression profiling by use of microRNA microarrays and qPCR was performed on the porcine developing brain. Our results show that microRNA expression is regulated in a developmentally stagespecific, as well as a tissue-specific manner. Numerous developmental stage or tissue-specific microRNAs including, miR-17, miR-18a, miR-29c, miR-106a, miR-135a and b, miR-221 and miR-222 were found by microarray analysis. Expression profiles of selected candidates were confirmed by qPCR. Conclusions/Significance: The differential expression of specific microRNAs in fetal versus postnatal samples suggests that they likely play an important role in the regulation of developmental and physiological processes during brain development. The data presented here supports the notion that microRNAs act as post-transcriptional switches which may regulate gene expression when required.
doi:10.1371/journal.pone.0014494 pmid:21253018 pmcid:PMC3017054 fatcat:hbax6unpw5bp5dhlbph5odkfqm

A Decade of Global mRNA and miRNA Profiling of HPV-Positive Cell Lines and Clinical Specimens

Bogumil Kaczkowski
2012 Open Virology Journal  
The study by Kaczkowski et al.  ...  The Open Virology Journal, 2012, Volume 6 Kaczkowski et al. # MicroRNAs are presented in the review.  ... 
doi:10.2174/1874357901206010216 pmid:23341857 pmcid:PMC3547333 fatcat:4umdpl55x5eefjzcu6wsnvthbe

Integrative analyses reveal novel strategies in HPV11,-16 and -45 early infection

Bogumil Kaczkowski, Maria Rossing, Ditte K. Andersen, Anita Dreher, Marya Morevati, Melissa A. Visser, Ole Winther, Finn Cilius Nielsen, Bodil Norrild
2012 Scientific Reports  
Bogumil Kaczkowski was supported by the Novo Nordisk Foundation. Technician Melissa A. Visser was supported by a grant from the Laege Sophus Carl Emil Friis and hustru Olga Friis' Foundation.  ... 
doi:10.1038/srep00515 pmid:22808421 pmcid:PMC3398386 fatcat:4k6nbmfwnveurl5y4jirbw5o24

Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers

Bogumil Kaczkowski, Yuji Tanaka, Hideya Kawaji, Albin Sandelin, Robin Andersson, Masayoshi Itoh, Timo Lassmann, Yoshihide Hayashizaki, Piero Carninci, Alistair R.R. Forrest
2015 Cancer Research  
Genes that are commonly deregulated in cancer are clinically attractive as candidate pandiagnostic markers and therapeutic targets. To globally identify such targets, we compared Cap Analysis of Gene Expression (CAGE) profiles from 225 different cancer cell lines and 339 corresponding primary cell samples to identify transcripts that are deregulated recurrently in a broad range of cancer types. Comparing RNA-seq data from 4,055 tumors and 563 normal tissues profiled in the TCGA and FANTOM5
more » ... ets, we identified a core transcript set with theranostic potential. Our analyses also revealed enhancer RNAs which are upregulated in cancer, defining promoters which overlap with repetitive elements (especially SINE/Alu and LTR/ERV1 elements) that are often upregulated in cancer. Lastly, we documented for the first time upregulation of multiple copies of the REP522 interspersed repeat in cancer. Overall, our genome-wide expression profiling approach identified a comprehensive set of candidate biomarkers with pancancer potential, and extended the perspective and pathogenic significance of repetitive elements which are frequently activated during cancer progression.
doi:10.1158/0008-5472.can-15-0484 pmid:26552699 fatcat:umjtkerw6zdjvjhhirtkpoa6bi

HemaExplorer: a database of mRNA expression profiles in normal and malignant haematopoiesis

Frederik Otzen Bagger, Nicolas Rapin, Kim Theilgaard-Mönch, Bogumil Kaczkowski, Lina A. Thoren, Johan Jendholm, Ole Winther, Bo T. Porse
2012 Nucleic Acids Research  
The HemaExplorer (http://servers.binf.ku.dk/hemaexplorer) is a curated database of processed mRNA Gene expression profiles (GEPs) that provides an easy display of gene expression in haematopoietic cells. HemaExplorer contains GEPs derived from mouse/human haematopoietic stem and progenitor cells as well as from more differentiated cell types. Moreover, data from distinct subtypes of human acute myeloid leukemia is included in the database allowing researchers to directly compare gene expression
more » ... of leukemic cells with those of their closest normal counterpart. Normalization and batch correction lead to full integrity of the data in the database. The HemaExplorer has comprehensive visualization interface that can make it useful as a daily tool for biologists and cancer researchers to assess the expression patterns of genes encountered in research or literature. HemaExplorer is relevant for all research within the fields of leukemia, immunology, cell differentiation and the biology of the haematopoietic system.
doi:10.1093/nar/gks1021 pmid:23143109 pmcid:PMC3531225 fatcat:y4lxxogmjjgevg2yhi2c5ggagi

JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states [article]

Lusy Handoko, Bogumil Kaczkowski, Chung-Chau Hon, Marina Lizio, Masatoshi Wakamori, Takayoshi Matsuda, Takuhiro Ito, Prashanti Jeyamohan, Yuko Sato, Kensaku Sakamoto, Shigeyuki Yokoyama, Hiroshi Kimura (+2 others)
2017 bioRxiv   pre-print
The bromodomain and extra-terminal domain (BET) proteins are promising drug targets for cancer and immune diseases. However, BET inhibition effects have been studied more in the context of bromodomain-containing protein 4 (BRD4) than BRD2, and the BET protein association to histone H4-hyperacetylated chromatin is not understood at the genome-wide level. Here, we report transcription start site (TSS)-resolution integrative analyses of ChIP-seq and transcriptome profiles in human non-small cell
more » ... ng cancer (NSCLC) cell line H23. We show that di-acetylation at K5 and K8 of histone H4 (H4K5acK8ac) co-localizes with H3K27ac and BRD2 in the majority of active enhancers and promoters, where BRD2 has a stronger association with H4K5acK8ac than H3K27ac. Interestingly, although BET inhibition by JQ1 led to complete reduction of BRD2 binding to chromatin, only local changes of H4K5acK8ac levels were observed. In addition, a remarkable number of BRD2-bound genes, including MYC and its downstream target genes, were transcriptionally upregulated upon JQ1 treatment. Using BRD2-enriched sites and transcriptional activity analysis, we identified candidate transcription factors potentially involved in the JQ1 response in BRD2-dependent and independent manner.
doi:10.1101/215442 fatcat:zdszz2ai3bgtlksjwhw3urkziy

Inducing Human Retinal Pigment Epithelium-like Cells from Somatic Tissue [article]

Ivo Ngundu Woogeng, Imad Abugessaisa, Akihiro Tachibana, Yoshiki Sahara, Chung-Chau Hon, Akira Hasegawa, Bogumil Kaczkowski, Noriko Sakai, Mitsuhiro Nishida, Haiming Hu, Hashimita Sanyal, Junki Sho (+8 others)
2020 bioRxiv   pre-print
Regenerative medicine relies on basic research to find safe and useful outcomes that are only practical when cost-effective. The human eyeball requires the retinal pigment epithelium (RPE) for support and maintenance that interfaces the neural retina and the choroid at large. Nearly 200 million people suffer from age-related macular degeneration (AMD), a blinding multifactor genetic disease among other retinal pathologies related to RPE degradation. Recently, autologous pluripotent stem
more » ... ived RPE cells were prohibitively expensive due to time, therefore we developed a new simplified cell reprogramming system. We stably induced RPE-like cells (iRPE) from human fibroblasts by conditional overexpression of broad plasticity and lineage-specific pioneering transcription factors. iRPE cells showed features of modern RPE benchmarks and significant in-vivo integration in transplanted chimeric hosts. Herein, we detail the iRPE system with comprehensive modern single-cell RNA (scRNA) sequencing profiling to interpret and characterize its best cells. We anticipate that our system may enable robust retinal cell induction for regenerative medicine research and affordable autologous human RPE tissue for cell therapy.
doi:10.1101/2020.07.27.215103 fatcat:pb5q5jvnwrefzclzkvj3bpjpzi

Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages

Sugata Roy, Sebastian Schmeier, Bogumil Kaczkowski, Erik Arner, Tanvir Alam, Mumin Ozturk, Ousman Tamgue, Suraj P. Parihar, Hideya Kawaji, Masayoshi Itoh, Timo Lassmann, Piero Carninci (+6 others)
2018 Scientific Reports  
Mycobacterium tuberculosis (Mtb) infection reveals complex and dynamic host-pathogen interactions, leading to host protection or pathogenesis. Using a unique transcriptome technology (CAGE), we investigated the promoter-based transcriptional landscape of IFNγ (M1) or IL-4/IL-13 (M2) stimulated macrophages during Mtb infection in a time-kinetic manner. Mtb infection widely and drastically altered macrophage-specific gene expression, which is far larger than that of M1 or M2 activations. Gene
more » ... logy enrichment analysis for Mtb-induced differentially expressed genes revealed various terms, related to host-protection and inflammation, enriched in up-regulated genes. On the other hand, terms related to dis-regulation of cellular functions were enriched in down-regulated genes. Differential expression analysis revealed known as well as novel transcription factor genes in Mtb infection, many of them significantly down-regulated. IFNγ or IL-4/IL-13 pre-stimulation induce additional differentially expressed genes in Mtb-infected macrophages. Cluster analysis uncovered significant numbers, prolonging their expressional changes. Furthermore, Mtb infection augmented cytokine-mediated M1 and M2 pre-activations. In addition, we identified unique transcriptional features of Mtb-mediated differentially expressed lncRNAs. In summary we provide a comprehensive in depth gene expression/ regulation profile in Mtb-infected macrophages, an important step forward for a better understanding of host-pathogen interaction dynamics in Mtb infection. Despite the availability of four anti-tubercular drugs and BCG vaccine against Mycobacterium tuberculosis (Mtb) infection, tuberculosis still remains one of the most deadly infectious diseases worldwide, claiming over 1.5 million lives globally 1 . It is estimated that one third of the world population is infected with Mtb, however only 5-10% of individuals develop the active tuberculosis disease 2 , whereas the rest remain latently infected during their life time. Therefore defining the immune correlates which leads to host protection or pathogenesis during tuberculosis infection, could lead to the development of new alternative drug treatments 3 . Macrophages regulate inflammation and immune responses to Mtb infection. However, Mtb modulates host immunity by residing and Published: xx xx xxxx OPEN www.nature.com/scientificreports/ 2 Scientific RepORTS | (2018) 8:6758 | multiplying within lung macrophages 4 . In response to IFNγ which is secreted by T helper 1 cells and natural killer cells, macrophages are polarized to classically activated macrophages (M1 Mph), leading to the secretion of pro-inflammatory mediators, release of reactive oxygen and nitrogen intermediates, inducing protective immune responses against Mtb infection 5,6 . IFNγ stimulation activates IFNγ receptors, Janus kinase, MHC class I and II, guanosine triphosphatases (GTPases), chemokine receptors Cxcl2, Cxcl3, Cxcl4, Cxcl5, immune regulatory transcription factors such as Irf1 7 , Irf8 8 , Batf2 9 , Stat1 10 , Nfκb 11 , Ap1 10 and many effectors molecules such as TNFα, IL-6, IL-12, TGFβ, IL-10 cytokines and Ccl2, Ccl3, Ccl4, RANTES (Ccl5) chemokines 7,12,13 . Furthermore IFNγ induces phagocyte oxidase and inducible nitric oxide synthase (Nos2) that control Mtb growth by their antimicrobial activities 14, 15 . Several studies showed a sharp increase of Th2 cytokines IL-4 and IL-13 which polarize macrophages to an alternative activation status (M2 Mph) [16] [17] [18] . During this alternative activation process M2 Mph induces Arginase 1 (Arg1) which is a checkpoint enzyme since it competes with Nos2 for the same substrate L-Arginine. By metabolizing L-Arginine, Arg1 reduces Nitric Oxide (NO) production, tryptophan degradation and T cell proliferation [19] [20] [21] . Consequently Mtb has developed a myriad of evasion strategies to escape killing within M1 polarized macrophages by interfering with the macrophage activation status. Once infection is established within macrophages, Mtb is able to down-regulate IL-12 expression in macrophages 22 and thereby reducing optimal Th1 differentiation and subsequent IFNγ production. Moreover, Mtb blocks the recruitment of NOS2 to the phagosomal membrane, possibly as a means of limiting its exposure to nitric oxide 23 . Once phagocytosed, Mtb employs its prime evasion strategy to interference with intracellular signaling events to establish persistence. Mtb inhibits phagolysosome fusion, thus allowing virulent mycobacteria to persist within an immature phagosomal compartment that shields from the microbicidal challenges activated by the host cell 24,25 . Therefore the interaction between Mtb and M1/M2 macrophage that leads to a drastic genetic or epigenetic level reprogramming is still an area that needs to be further investigated. Over the last few decades, transcriptional programming of Mtb-infected macrophages has been studied using oligonucleotide microarrays. Gene expression was analyzed from IFNγ-stimulated, live Mtb, heat-killed Mtb, polystyrene beads-stimulated primary macrophages obtained from wild-type, NOS2 −/− , Phox −/− and NOS2 −/− Phox −/− which shows that gene induction by Mtb mimicked or synergized with IFNγ-stimulated macrophages 4 . Mtb-infected macrophage-like THP-1 gene profiling using microarray demonstrated an interferon-related signature in transcriptional core response to Mtb infection 26 . Using 858 spot cytokine array from Mtb-infected human monocytes-derived macrophages gene profiling up to 7 days after infection with Mtb showed up-regulation of previously known cytokines 27 . Recently it was also demonstrated that the macrophage transcriptional responses changes depending on Mtb strain infection (CDC1551 expressed higher levels of stress response genes than HN878) 28 . A previous comparative study of gene expression profile of IFNγ or IL-4 stimulated macrophages using microarray showed a delayed and partially diminished response to Mtb in IL-4-stimulated macrophages. The result highlight that IL-4-stimulated alternative macrophages may supports intercellular persistence of Mtb 20 . Of note, large consortia such as ImmGen 29 and the Human Immunology Genome Project 30 have contributed immensely by discovering the steady state transcription programs of murine macrophages 31 and dendrite cells 32 . Recently the FANTOM5 consortium has generated a comprehensive promoter expression atlas using 953 human and 399 mouse samples 33 , including classical, intermediate, non-classical monocyte samples 34 , which demonstrated promoters for known and novel coding/non-coding transcripts and enhancer expression profile 35 . CAGE (Capped Analysis of Gene Expression) technology was used for this transcriptome analysis and samples were sequenced using single molecule Helicos sequencer (non-biased deepCAGE). The second phase of FANTOM5 further revealed that enhancers reach maximal transcriptional activity prior to promoters in differentiation and activation of mammalian cells 36 . Recently as a satellite study of FANTOM5 we redefined the transcriptional regulatory dynamics of classically and alternatively activated mouse macrophages by identifying novel motifs, TFs, coding and non-coding marker genes using deepCAGE 37 . Here we focused on the transcriptional landscape of MtbHN878-infected macrophages compared to classical (IFNγ stimulated, M1) and alternative (IL-4/IL-13 stimulated, M2) activation by high throughput transcriptome analysis method, deepCAGE. Further, pre-stimulation with IFNγ or IL-4/IL-13 in Mtb-infected macrophage transcriptome was compared with non-pre-stimulated Mtb-infected macrophages. DeepCAGE analysis allowed us to identify drastic transcriptional reprogramming in Mtb infection and in IFNγ or IL-4/IL-13 pre-stimulation in Mtb infected macrophages. Taken together our CAGE analysis identified novel TFs, non TF genes and lncRNAs therefore redefining the transcriptional landscape of Mtb-infected macrophages. The work is part of Functional Annotation of Mammalian Genome (FANTOM5) project. Data, genomic tools, and co-published manuscripts are summarized online at http://fantom.gsc.riken.jp/5/.
doi:10.1038/s41598-018-24509-6 pmid:29712924 pmcid:PMC5928056 fatcat:t63nf2t22bhgtcjkqjmydhbbtu

JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states

Lusy Handoko, Bogumil Kaczkowski, Chung-Chau Hon, Marina Lizio, Masatoshi Wakamori, Takayoshi Matsuda, Takuhiro Ito, Prashanti Jeyamohan, Yuko Sato, Kensaku Sakamoto, Shigeyuki Yokoyama, Hiroshi Kimura (+2 others)
2018 Epigenetics  
The bromodomain and extra-terminal domain (BET) proteins are promising drug targets for cancer and immune diseases. However, BET inhibition effects have been studied more in the context of bromodomain-containing protein 4 (BRD4) than BRD2, and the BET protein association to histone H4-hyperacetylated chromatin is not understood at the genome-wide level. Here, we report transcription start site (TSS)-resolution integrative analyses of ChIP-seq and transcriptome profiles in human non-small cell
more » ... ng cancer (NSCLC) cell line H23. We show that di-acetylation at K5 and K8 of histone H4 (H4K5acK8ac) co-localizes with H3K27ac and BRD2 in the majority of active enhancers and promoters, where BRD2 has a stronger association with H4K5acK8ac than H3K27ac. Although BET inhibition by JQ1 led to complete reduction of BRD2 binding to chromatin, only local changes of H4K5acK8ac levels were observed, suggesting that recruitment of BRD2 does not influence global histone H4 hyperacetylation levels. This finding supports a model in which recruitment of BET proteins via histone H4 hyperacetylation is predominant over hyperacetylation of histone H4 by BET protein-associated acetyltransferases. In addition, we found that a remarkable number of BRD2-bound genes, including MYC and its downstream target genes, were transcriptionally upregulated upon JQ1 treatment. Using BRD2-enriched sites and transcriptional activity analysis, we identified candidate transcription factors potentially involved in the JQ1 response in BRD2-dependent and -independent manner. ARTICLE HISTORY
doi:10.1080/15592294.2018.1469891 pmid:30080437 fatcat:5fz5avn5srapboeb64tql7mqvm

Cancers of unknown primary origin (CUP) are characterized by chromosomal instability (CIN) compared to metastasis of know origin

Jonas Vikeså, Anne Kirstine H Møller, Bogumil Kaczkowski, Rehannah Borup, Ole Winther, Ricardo Henao, Anders Krogh, Katharina Perell, Flemming Jensen, Gedske Daugaard, Finn C Nielsen
2015 BMC Cancer  
Cancers of unknown primary (CUPs) constitute~5% of all cancers. The tumors have an aggressive biological and clinical behavior. The aim of the present study has been to uncover whether CUPs exhibit distinct molecular features compared to metastases of known origin. Methods: Employing genome wide transcriptome analysis, Linear Discriminant Analysis (LDA) and Quadratic Discriminant Analysis (QDA), we defined the putative origins of a large series of CUP and how closely related a particular CUP
more » ... to corresponding metastases of known origin. LDA predictions were subsequently used to define a universal CUP core set of differentially expressed genes, that by means of gene set enrichment analysis was exploited to depict molecular pathways characterizing CUP. Results: The analyses show that CUPs are distinct from metastases of known origin. CUPs exhibit inconsistent expression of conventional cancer biomarkers and QDA derived outlier scores show that CUPs are more distantly related to their primary tumor class than corresponding metastases of known origin. Gene set enrichment analysis showed that CUPs display increased expression of genes involved in DNA damage repair and mRNA signatures of chromosome instability (CIN), indicating that CUPs are chromosome unstable compared to metastases of known origin. Conclusions: CIN may account for the uncommon clinical presentation, chemoresistance and poor outcome in patients with CUP and warrant selective diagnostic strategies and treatment.
doi:10.1186/s12885-015-1128-x pmid:25885340 pmcid:PMC4404593 fatcat:ktosfcguvba45et6dgjyc73rmm

Integrative CAGE and DNA Methylation Profiling Identify Epigenetically Regulated Genes in NSCLC

Masafumi Horie, Bogumil Kaczkowski, Mitsuhiro Ohshima, Hirotaka Matsuzaki, Satoshi Noguchi, Yu Mikami, Marina Lizio, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Piero Carninci, Yoshihide Hayashizaki (+6 others)
2017 Molecular Cancer Research  
Lung cancer is the leading cause of cancer-related deaths worldwide. The majority of cancer driver mutations have been identified; however, relevant epigenetic regulation involved in tumorigenesis has only been fragmentarily analyzed. Epigenetically regulated genes have a great theranostic potential, especially in tumors with no apparent driver mutations. Here, epigenetically regulated genes were identified in lung cancer by an integrative analysis of promoter-level expression profiles from Cap
more » ... Analysis of Gene Expression (CAGE) of 16 nonsmall cell lung cancer (NSCLC) cell lines and 16 normal lung primary cell specimens with DNA methylation data of 69 NSCLC cell lines and 6 normal lung epithelial cells. A core set of 49 coding genes and 10 long noncoding RNAs (lncRNA), which are upregulated in NSCLC cell lines due to promoter hypomethylation, was uncovered. Twenty-two epigenetically regulated genes were validated (upregulated genes with hypomethylated promoters) in the adenocarcinoma and squamous cell cancer subtypes of lung cancer using The Cancer Genome Atlas data. Furthermore, it was demonstrated that multiple copies of the REP522 DNA repeat family are prominently upregulated due to hypomethylation in NSCLC cell lines, which leads to cancer-specific expression of lncRNAs, such as RP1-90G24.10, AL022344.4, and PCAT7. Finally, Myeloma Overexpressed (MYEOV) was identified as the most promising candidate. Functional studies demonstrated that MYEOV promotes cell proliferation, survival, and invasion. Moreover, high MYEOV expression levels were associated with poor prognosis. Implications: This report identifies a robust list of 22 candidate driver genes that are epigenetically regulated in lung cancer; such genes may complement the known mutational drivers. Development of methodology: M. Horie, M. Itoh, P. Carninci Acquisition of data (provided animals, acquired and managed patients, provided facilities, etc.): M. Horie, M. Itoh, T. Lassmann, Y. Yamaguchi Analysis and interpretation of data (e.g., statistical analysis, biostatistics, computational analysis):
doi:10.1158/1541-7786.mcr-17-0191 pmid:28698358 fatcat:6fr5osqxcnedtakbaptlsziiaa

Batf2/Irf1 Induces Inflammatory Responses in Classically Activated Macrophages, Lipopolysaccharides, and Mycobacterial Infection

Sugata Roy, Reto Guler, Suraj P. Parihar, Sebastian Schmeier, Bogumil Kaczkowski, Hajime Nishimura, Jay W. Shin, Yutaka Negishi, Mumin Ozturk, Ramona Hurdayal, Atsutaka Kubosaki, Yasumasa Kimura (+4 others)
2015 Journal of Immunology  
doi:10.4049/jimmunol.1402521 pmid:25957166 fatcat:icuhwhbrsffnrdvswreutwefyq

Down-Regulation of miR-129-5p and the let-7 Family in Neuroendocrine Tumors and Metastases Leads to Up-Regulation of Their Targets Egr1, G3bp1, Hmga2 and Bach1

Kristina Døssing, Tina Binderup, Bogumil Kaczkowski, Anders Jacobsen, Maria Rossing, Ole Winther, Birgitte Federspiel, Ulrich Knigge, Andreas Kjær, Lennart Friis-Hansen
2014 Genes  
doi:10.3390/genes6010001 pmid:25546138 pmcid:PMC4377830 fatcat:bqbcpakahrcrnnjzeepx4pr3km

CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors

Kosuke Hashimoto, Ana Maria Suzuki, Alexandre Dos Santos, Christophe Desterke, Agnese Collino, Serena Ghisletti, Emilie Braun, Alessandro Bonetti, Alexandre Fort, Xian-Yang Qin, Enrico Radaelli, Bogumil Kaczkowski (+7 others)
2015 Genome Research  
tumors widespread activation of retroviral LTR promoters in virus-induced CAGE profiling of ncRNAs in hepatocellular carcinoma reveals Material Supplemental http://genome.cshlp.org/content/suppl/2015/10/15/gr.191031.115.DC1
doi:10.1101/gr.191031.115 pmid:26510915 pmcid:PMC4665003 fatcat:a6p5tajqpffw7cl2qhvwdeyai4
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