TY - JOUR A1 - Briese, Michael A1 - Saal, Lena A1 - Appenzeller, Silke A1 - Moradi, Mehri A1 - Baluapuri, Apoorva A1 - Sendtner, Michael T1 - Whole transcriptome profiling reveals the RNA content of motor axons JF - Nucleic Acids Research N2 - Most RNAs within polarized cells such as neurons are sorted subcellularly in a coordinated manner. Despite advances in the development of methods for profiling polyadenylated RNAs from small amounts of input RNA, techniques for profiling coding and non-coding RNAs simultaneously are not well established. Here, we optimized a transcriptome profiling method based on double-random priming and applied it to serially diluted total RNA down to 10 pg. Read counts of expressed genes were robustly correlated between replicates, indicating that the method is both reproducible and scalable. Our transcriptome profiling method detected both coding and long non-coding RNAs sized >300 bases. Compared to total RNAseq using a conventional approach our protocol detected 70% more genes due to reduced capture of ribosomal RNAs. We used our method to analyze the RNA composition of compartmentalized motoneurons. The somatodendritic compartment was enriched for transcripts with post-synaptic functions as well as for certain nuclear non-coding RNAs such as 7SK. In axons, transcripts related to translation were enriched including the cytoplasmic non-coding RNA 7SL. Our profiling method can be applied to a wide range of investigations including perturbations of subcellular transcriptomes in neurodegenerative diseases and investigations of microdissected tissue samples such as anatomically defined fiber tracts. KW - RNA KW - motor axons Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-126800 ER - TY - THES A1 - Baluapuri, Apoorva T1 - Molecular Mechanisms of MYC’s impact on Transcription Elongation T1 - Molekulare Mechanismen des Einflusses von MYC auf die Transkriptionselongation N2 - Expression of the MYC oncoprotein, which binds the DNA at promoters of most transcribed genes, is controlled by growth factors in non-tumor cells, thus stimulating cell growth and proliferation. Here in this thesis, it is shown that MYC interacts with SPT5, a subunit of the RNA polymerase II (Pol II) elongation factor DSIF. MYC recruits SPT5 to promoters of genes and is required for its association with Pol II. The transfer of SPT5 is mediated by CDK7 activity on TFIIE, which evicts it from Pol II and allows SPT5 to bind Pol II. MYC is required for fast and processive transcription elongation, consistent with known functions of SPT5 in yeast. In addition, MYC increases the directionality of promoters by stimulating sense transcription and by suppressing the synthesis of antisense transcripts. The results presented in this thesis suggest that MYC globally controls the productive assembly of Pol II with general elongation factors to form processive elongation complexes in response to growth-factor stimulation of non-tumour cells. However, MYC is found to be overexpressed in many tumours, and is required for their development and progression. In this thesis it was found that, unexpectedly, such overexpression of MYC does not further enhance transcription but rather brings about squelching of SPT5. This reduces the processivity of Pol II on selected set of genes that are known to be repressed by MYC, leading to a decrease in growth-suppressive gene transcription and uncontrolled tumour growth N2 - Die Expression des MYC-Onkoproteins, das die Promotoren der meisten exprimierten Gene bindet, wird in gesunden, nicht transformierten Zellen durch Wachstumsfaktoren reguliert und fördert das Zellwachstum und die Zellteilung. In dieser Arbeit wurde die Interaktion zwischen MYC und SPT5, einer Untereinheit des RNA-Polymerase (Pol II) Elongationsfaktors DSIF gezeigt. MYC ist für die Rekrutierung von SPT5 an Promotoren und die Assoziation mit Pol II notwendig. Der Transfer von SPT5 auf Pol II setzt die Aktivität der Proteinkinase CDK7 voraus, die TFIIE aus dem Pol II Komplex entfernt und es so SPT5 ermöglicht, an Pol II zu binden. MYC wird für eine schnelle und prozessive Transkriptionselongation benötigt, was mit bekannten Funktionen von SPT5 in Hefe übereinstimmt. Zusätzlich erhöht MYC die Direktionalität von Promotoren, indem es die Sense-Transkription stimuliert und die Synthese der Antisense-Transkripte unterdrückt. Die in dieser Arbeit vorgestellten Ergebnisse legen nahe, dass MYC in normalen, nicht-transformierten Zellen die produktive Assemblierung von Pol II mit allgemeinen Elongationsfaktoren global steigert, um prozessive Elongationskomplexe als Reaktion auf die Wachstumsfaktorstimulation zu bilden. Die meisten humanen Tumore exprimieren jedoch deutlich erhöhte Mengen des MYC Proteins, das für Tumorentstehung und Progression benötigt wird. In dieser Arbeit wurde festgestellt, dass eine solche Überexpression von MYC unerwarteterweise keine weitere Steigerung der Expression mit sich bringt, sondern zur Sequestrierung von SPT5 führt. Dies reduziert die Prozessivität von Pol II an ausgewählten Genen, welche durch MYC bekannterweise supprimiert werden, was zu einer Abnahme der wachstumsunterdrückenden Gentranskription und zu einem unkontrollierten Wachstum führt. KW - Transcription KW - MYC Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-243806 ER - TY - JOUR A1 - Jessen, Christina A1 - Kreß, Julia K. C. A1 - Baluapuri, Apoorva A1 - Hufnagel, Anita A1 - Schmitz, Werner A1 - Kneitz, Susanne A1 - Roth, Sabine A1 - Marquardt, André A1 - Appenzeller, Silke A1 - Ade, Casten P. A1 - Glutsch, Valerie A1 - Wobser, Marion A1 - Friedmann-Angeli, José Pedro A1 - Mosteo, Laura A1 - Goding, Colin R. A1 - Schilling, Bastian A1 - Geissinger, Eva A1 - Wolf, Elmar A1 - Meierjohann, Svenja T1 - The transcription factor NRF2 enhances melanoma malignancy by blocking differentiation and inducing COX2 expression JF - Oncogene N2 - The transcription factor NRF2 is the major mediator of oxidative stress responses and is closely connected to therapy resistance in tumors harboring activating mutations in the NRF2 pathway. In melanoma, such mutations are rare, and it is unclear to what extent melanomas rely on NRF2. Here we show that NRF2 suppresses the activity of the melanocyte lineage marker MITF in melanoma, thereby reducing the expression of pigmentation markers. Intriguingly, we furthermore identified NRF2 as key regulator of immune-modulating genes, linking oxidative stress with the induction of cyclooxygenase 2 (COX2) in an ATF4-dependent manner. COX2 is critical for the secretion of prostaglandin E2 and was strongly induced by H\(_2\)O\(_2\) or TNFα only in presence of NRF2. Induction of MITF and depletion of COX2 and PGE2 were also observed in NRF2-deleted melanoma cells in vivo. Furthermore, genes corresponding to the innate immune response such as RSAD2 and IFIH1 were strongly elevated in absence of NRF2 and coincided with immune evasion parameters in human melanoma datasets. Even in vitro, NRF2 activation or prostaglandin E2 supplementation blunted the induction of the innate immune response in melanoma cells. Transcriptome analyses from lung adenocarcinomas indicate that the observed link between NRF2 and the innate immune response is not restricted to melanoma. KW - NRF2 KW - melanoma malignancy KW - COX2 expression Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-235064 SN - 0950-9232 VL - 39 ER - TY - JOUR A1 - Otto, Christoph A1 - Kastner, Carolin A1 - Schmidt, Stefanie A1 - Uttinger, Konstantin A1 - Baluapuri, Apoorva A1 - Denk, Sarah A1 - Rosenfeldt, Mathias T. A1 - Rosenwald, Andreas A1 - Roehrig, Florian A1 - Ade, Carsten P. A1 - Schuelein-Voelk, Christina A1 - Diefenbacher, Markus E. A1 - Germer, Christoph-Thomas A1 - Wolf, Elmar A1 - Eilers, Martin A1 - Wiegering, Armin T1 - RNA polymerase I inhibition induces terminal differentiation, growth arrest, and vulnerability to senolytics in colorectal cancer cells JF - Molecular Oncology N2 - Ribosomal biogenesis and protein synthesis are deregulated in most cancers, suggesting that interfering with translation machinery may hold significant therapeutic potential. Here, we show that loss of the tumor suppressor adenomatous polyposis coli (APC), which constitutes the initiating event in the adenoma carcinoma sequence for colorectal cancer (CRC), induces the expression of RNA polymerase I (RNAPOL1) transcription machinery, and subsequently upregulates ribosomal DNA (rDNA) transcription. Targeting RNAPOL1 with a specific inhibitor, CX5461, disrupts nucleolar integrity, and induces a disbalance of ribosomal proteins. Surprisingly, CX5461-induced growth arrest is irreversible and exhibits features of senescence and terminal differentiation. Mechanistically, CX5461 promotes differentiation in an MYC-interacting zinc-finger protein 1 (MIZ1)- and retinoblastoma protein (Rb)-dependent manner. In addition, the inhibition of RNAPOL1 renders CRC cells vulnerable towards senolytic agents. We validated this therapeutic effect of CX5461 in murine- and patient-derived organoids, and in a xenograft mouse model. These results show that targeting ribosomal biogenesis together with targeting the consecutive, senescent phenotype using approved drugs is a new therapeutic approach, which can rapidly be transferred from bench to bedside. KW - CRC KW - CX5461 KW - MIZ1 KW - MYC KW - ribosome KW - RNAPOL1 Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-312806 VL - 16 IS - 15 ER - TY - JOUR A1 - Hartmann, Oliver A1 - Reissland, Michaela A1 - Maier, Carina R. A1 - Fischer, Thomas A1 - Prieto-Garcia, Cristian A1 - Baluapuri, Apoorva A1 - Schwarz, Jessica A1 - Schmitz, Werner A1 - Garrido-Rodriguez, Martin A1 - Pahor, Nikolett A1 - Davies, Clare C. A1 - Bassermann, Florian A1 - Orian, Amir A1 - Wolf, Elmar A1 - Schulze, Almut A1 - Calzado, Marco A. A1 - Rosenfeldt, Mathias T. A1 - Diefenbacher, Markus E. T1 - Implementation of CRISPR/Cas9 Genome Editing to Generate Murine Lung Cancer Models That Depict the Mutational Landscape of Human Disease JF - Frontiers in Cell and Developmental Biology N2 - Lung cancer is the most common cancer worldwide and the leading cause of cancer-related deaths in both men and women. Despite the development of novel therapeutic interventions, the 5-year survival rate for non-small cell lung cancer (NSCLC) patients remains low, demonstrating the necessity for novel treatments. One strategy to improve translational research is the development of surrogate models reflecting somatic mutations identified in lung cancer patients as these impact treatment responses. With the advent of CRISPR-mediated genome editing, gene deletion as well as site-directed integration of point mutations enabled us to model human malignancies in more detail than ever before. Here, we report that by using CRISPR/Cas9-mediated targeting of Trp53 and KRas, we recapitulated the classic murine NSCLC model Trp53fl/fl:lsl-KRasG12D/wt. Developing tumors were indistinguishable from Trp53fl/fl:lsl-KRasG12D/wt-derived tumors with regard to morphology, marker expression, and transcriptional profiles. We demonstrate the applicability of CRISPR for tumor modeling in vivo and ameliorating the need to use conventional genetically engineered mouse models. Furthermore, tumor onset was not only achieved in constitutive Cas9 expression but also in wild-type animals via infection of lung epithelial cells with two discrete AAVs encoding different parts of the CRISPR machinery. While conventional mouse models require extensive husbandry to integrate new genetic features allowing for gene targeting, basic molecular methods suffice to inflict the desired genetic alterations in vivo. Utilizing the CRISPR toolbox, in vivo cancer research and modeling is rapidly evolving and enables researchers to swiftly develop new, clinically relevant surrogate models for translational research. KW - non-small cell lung cancer KW - CRISPR-Cas9 KW - mouse model KW - lung cancer KW - MYC KW - JUN Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-230949 SN - 2296-634X VL - 9 ER - TY - JOUR A1 - Lorenzin, Francesca A1 - Benary, Uwe A1 - Baluapuri, Apoorva A1 - Walz, Susanne A1 - Jung, Lisa Anna A1 - von Eyss, Björn A1 - Kisker, Caroline A1 - Wolf, Jana A1 - Eilers, Martin A1 - Wolf, Elmar T1 - Different promoter affinities account for specificity in MYC-dependent gene regulation JF - eLife N2 - Enhanced expression of the MYC transcription factor is observed in the majority of tumors. Two seemingly conflicting models have been proposed for its function: one proposes that MYC enhances expression of all genes, while the other model suggests gene-specific regulation. Here, we have explored the hypothesis that specific gene expression profiles arise since promoters differ in affinity for MYC and high-affinity promoters are fully occupied by physiological levels of MYC. We determined cellular MYC levels and used RNA- and ChIP-sequencing to correlate promoter occupancy with gene expression at different concentrations of MYC. Mathematical modeling showed that binding affinities for interactions of MYC with DNA and with core promoter-bound factors, such as WDR5, are sufficient to explain promoter occupancies observed in vivo. Importantly, promoter affinity stratifies different biological processes that are regulated by MYC, explaining why tumor-specific MYC levels induce specific gene expression programs and alter defined biological properties of cells. KW - MYC KW - promoter affinity KW - human KW - mathematical modeling KW - mouse KW - ChIP-sequencing KW - MIZ1 KW - cancer biology KW - cell biology KW - WDR5 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-162913 VL - 5 ER - TY - JOUR A1 - Fischer, Thomas A1 - Hartmann, Oliver A1 - Reissland, Michaela A1 - Prieto-Garcia, Cristian A1 - Klann, Kevin A1 - Pahor, Nikolett A1 - Schülein-Völk, Christina A1 - Baluapuri, Apoorva A1 - Polat, Bülent A1 - Abazari, Arya A1 - Gerhard-Hartmann, Elena A1 - Kopp, Hans-Georg A1 - Essmann, Frank A1 - Rosenfeldt, Mathias A1 - Münch, Christian A1 - Flentje, Michael A1 - Diefenbacher, Markus E. T1 - PTEN mutant non-small cell lung cancer require ATM to suppress pro-apoptotic signalling and evade radiotherapy JF - Cell & Bioscience N2 - Background Despite advances in treatment of patients with non-small cell lung cancer, carriers of certain genetic alterations are prone to failure. One such factor frequently mutated, is the tumor suppressor PTEN. These tumors are supposed to be more resistant to radiation, chemo- and immunotherapy. Results We demonstrate that loss of PTEN led to altered expression of transcriptional programs which directly regulate therapy resistance, resulting in establishment of radiation resistance. While PTEN-deficient tumor cells were not dependent on DNA-PK for IR resistance nor activated ATR during IR, they showed a significant dependence for the DNA damage kinase ATM. Pharmacologic inhibition of ATM, via KU-60019 and AZD1390 at non-toxic doses, restored and even synergized with IR in PTEN-deficient human and murine NSCLC cells as well in a multicellular organotypic ex vivo tumor model. Conclusion PTEN tumors are addicted to ATM to detect and repair radiation induced DNA damage. This creates an exploitable bottleneck. At least in cellulo and ex vivo we show that low concentration of ATM inhibitor is able to synergise with IR to treat PTEN-deficient tumors in genetically well-defined IR resistant lung cancer models. KW - PTEN KW - ATM KW - IR KW - NSCLC KW - radiotherapy KW - cancer KW - DNA-PK KW - PI3K Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-299865 SN - 2045-3701 VL - 12 ER - TY - JOUR A1 - Pattschull, Grit A1 - Walz, Susanne A1 - Gründl, Marco A1 - Schwab, Melissa A1 - Rühl, Eva A1 - Baluapuri, Apoorva A1 - Cindric-Vranesic, Anita A1 - Kneitz, Susanne A1 - Wolf, Elmar A1 - Ade, Carsten P. A1 - Rosenwald, Andreas A1 - von Eyss, Björn A1 - Gaubatz, Stefan T1 - The Myb-MuvB complex is required for YAP-dependent transcription of mitotic genes JF - Cell Reports N2 - YAP and TAZ, downstream effectors of the Hippo pathway, are important regulators of proliferation. Here, we show that the ability of YAP to activate mitotic gene expression is dependent on the Myb-MuvB (MMB) complex, a master regulator of genes expressed in the G2/M phase of the cell cycle. By carrying out genome-wide expression and binding analyses, we found that YAP promotes binding of the MMB subunit B-MYB to the promoters of mitotic target genes. YAP binds to B-MYB and stimulates B-MYB chromatin association through distal enhancer elements that interact with MMB-regulated promoters through chromatin looping. The cooperation between YAP and B-MYB is critical for YAP-mediated entry into mitosis. Furthermore, the expression of genes coactivated by YAP and B-MYB is associated with poor survival of cancer patients. Our findings provide a molecular mechanism by which YAP and MMB regulate mitotic gene expression and suggest a link between two cancer-relevant signaling pathways. KW - YAP KW - B-MYB KW - Myb-MuvB KW - mitotic genes KW - enhancer KW - transcription Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-202039 VL - 27 IS - 12 ER - TY - JOUR A1 - Trifault, Barbara A1 - Mamontova, Victoria A1 - Cossa, Giacomo A1 - Ganskih, Sabina A1 - Wei, Yuanjie A1 - Hofstetter, Julia A1 - Bhandare, Pranjali A1 - Baluapuri, Apoorva A1 - Nieto, Blanca A1 - Solvie, Daniel A1 - Ade, Carsten P. A1 - Gallant, Peter A1 - Wolf, Elmar A1 - Larsen, Dorthe H. A1 - Munschauer, Mathias A1 - Burger, Kaspar T1 - Nucleolar detention of NONO shields DNA double-strand breaks from aberrant transcripts JF - Nucleic Acids Research N2 - RNA-binding proteins emerge as effectors of the DNA damage response (DDR). The multifunctional non-POU domain-containing octamer-binding protein NONO/p54\(^{nrb}\) marks nuclear paraspeckles in unperturbed cells, but also undergoes re-localization to the nucleolus upon induction of DNA double-strand breaks (DSBs). However, NONO nucleolar re-localization is poorly understood. Here we show that the topoisomerase II inhibitor etoposide stimulates the production of RNA polymerase II-dependent, DNA damage-inducible antisense intergenic non-coding RNA (asincRNA) in human cancer cells. Such transcripts originate from distinct nucleolar intergenic spacer regions and form DNA–RNA hybrids to tether NONO to the nucleolus in an RNA recognition motif 1 domain-dependent manner. NONO occupancy at protein-coding gene promoters is reduced by etoposide, which attenuates pre-mRNA synthesis, enhances NONO binding to pre-mRNA transcripts and is accompanied by nucleolar detention of a subset of such transcripts. The depletion or mutation of NONO interferes with detention and prolongs DSB signalling. Together, we describe a nucleolar DDR pathway that shields NONO and aberrant transcripts from DSBs to promote DNA repair. KW - genome integrity KW - repair and replication KW - NONO KW - DNA double-strand breaks KW - aberrant transcripts Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-350208 VL - 52 IS - 6 ER -