@article{KunzWolfSchulzeetal.2016,
  author    = {Kunz, Meik and Wolf, Beat and Schulze, Harald and Atlan, David and Walles, Thorsten and Walles, Heike and Dandekar, Thomas},
  title     = {Non-Coding RNAs in Lung Cancer: Contribution of Bioinformatics Analysis to the Development of Non-Invasive Diagnostic Tools},
  series = {Genes},
  volume    = {8},
  journal   = {Genes},
  number    = {1},
  doi       = {10.3390/genes8010008},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147990},
  pages     = {8},
  year      = {2016},
  abstract  = {Lung cancer is currently the leading cause of cancer related mortality due to late diagnosis and limited treatment intervention. Non-coding RNAs are not translated into proteins and have emerged as fundamental regulators of gene expression. Recent studies reported that microRNAs and long non-coding RNAs are involved in lung cancer development and progression. Moreover, they appear as new promising non-invasive biomarkers for early lung cancer diagnosis. Here, we highlight their potential as biomarker in lung cancer and present how bioinformatics can contribute to the development of non-invasive diagnostic tools. For this, we discuss several bioinformatics algorithms and software tools for a comprehensive understanding and functional characterization of microRNAs and long non-coding RNAs.},
  language  = {en}
}
@phdthesis{Kotlyar2023,
  author    = {Kotlyar, Michael},
  title     = {Prognostische Rolle von microRNA-21, -126 und -221 im klarzelligen Nierenzellkarzinom mit Vena cava-Thrombus},
  doi       = {10.25972/OPUS-32181},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-321817},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Im Rahmen der Progression des klarzelligen Nierenzellkarzinoms kann es zur Invasion der Vena cava durch einen Tumorthrombus (ccRCC/TT) kommen. Allerdings besteht auch in diesem fortgeschrittenen Stadium eine deutliche Heterogenit{\"a}t bez{\"u}glich des klinischen Verlaufs. W{\"a}hrend sich mit bekannten Verfahren die Prognose bislang unzureichend vorhersagen ließ, gelang es in Vorarbeiten mittels im Tumorgewebe erfasster miRNA-Expressionen, ein {\"U}berlebensklassifikationsmodell auf Basis eines Kombinierten Risikoscores (miR-21, miR-126, miR-221) zu konzipieren. Hierdurch konnte das postoperative {\"U}berleben von ccRCC/TT Patienten des W{\"u}rzburger Universit{\"a}tsklinikums retrospektiv vorhergesagt werden. In der vorliegenden Arbeit war es m{\"o}glich, mit Hilfe molekularbiologischer und biostatistischer Methoden das vorbeschriebene Modell erfolgreich an einem unabh{\"a}ngigen, gr{\"o}ßeren Regensburger ccRCC/TT Patientenkollektiv zu validieren. Am Tumor verstorbene Patienten konnten erneut einer klinisch relevanten High-Risk-Gruppe bzw. einer prognostisch g{\"u}nstigeren Gruppe zugeordnet werden. MiR-21 und miR-126 waren erneut statistisch signifikant mit der Fernmetastasierung und dem tumorbedingten Versterben assoziiert. MiR-21 pr{\"a}sentierte sich sowohl in der am Tumor verstorbenen als auch in der fernmetastasierten Patientengruppe deutlich {\"u}berexprimiert, w{\"a}hrend die Expression von miR-126 stark vermindert war. Die neu untersuchte miR-205 zeigte sich in der fernmetastasierten sowie nodal positiven Patientengruppe hochreguliert, ein geringer Zusammengang mit dem tumorbedingten Versterben konnte hergestellt werden. Im zweiten Ansatz gelang es relevante miRNA-Expressionsunterschiede zwischen Seren W{\"u}rzburger ccRCC-Patienten mit und ohne Invasion des Gef{\"a}ßsystems sowie tumorfreien Kontrollen zu identifizieren. Die langfristige Herausforderung besteht darin, das validierte {\"U}berlebensklassifikationsmodell derart weiterzuentwickeln, dass es supportive klinische Anwendung in der Therapieplanung finden kann.},
  subject      = {Hypernephrom},
  language  = {de}
}
@article{FrankMarcudeOliveiraAlmeidaPetersenetal.2015,
  author    = {Frank, Benjamin and Marcu, Ana and de Oliveira Almeida Petersen, Antonio Luis and Weber, Heike and Stigloher, Christian and Mottram, Jeremy C. and Scholz, Claus J{\"u}rgen and Schurigt, Uta},
  title     = {Autophagic digestion of Leishmania major by host macrophages is associated with differential expression of BNIP3, CTSE, and the miRNAs miR-101c, miR-129, and miR-210},
  series = {Parasites \& Vectors},
  volume    = {8},
  journal   = {Parasites \& Vectors},
  number    = {404},
  doi       = {10.1186/s13071-015-0974-3},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-124997},
  year      = {2015},
  abstract  = {Background Autophagy participates in innate immunity by eliminating intracellular pathogens. Consequently, numerous microorganisms have developed strategies to impair the autophagic machinery in phagocytes. In the current study, interactions between Leishmania major (L. m.) and the autophagic machinery of bone marrow-derived macrophages (BMDM) were analyzed. Methods BMDM were generated from BALB/c mice, and the cells were infected with L. m. promastigotes. Transmission electron microscopy (TEM) and electron tomography were used to investigate the ultrastructure of BMDM and the intracellular parasites. Affymetrix® chip analyses were conducted to identify autophagy-related messenger RNAs (mRNAs) and microRNAs (miRNAs). The protein expression levels of autophagy related 5 (ATG5), BCL2/adenovirus E1B 19 kDa protein-interacting protein 3 (BNIP3), cathepsin E (CTSE), mechanistic target of rapamycin (MTOR), microtubule-associated proteins 1A/1B light chain 3B (LC3B), and ubiquitin (UB) were investigated through western blot analyses. BMDM were transfected with specific small interfering RNAs (siRNAs) against autophagy-related genes and with mimics or inhibitors of autophagy-associated miRNAs. The infection rates of BMDM were determined by light microscopy after a parasite-specific staining. Results The experiments demonstrated autophagy induction in BMDM after in vitro infection with L. m.. The results suggested a putative MTOR phosphorylation-dependent counteracting mechanism in the early infection phase and indicated that intracellular amastigotes were cleared by autophagy in BMDM in the late infection phase. Transcriptomic analyses and specific downregulation of protein expression with siRNAs suggested there is an association between the infection-specific over expression of BNIP3, as well as CTSE, and the autophagic activity of BMDM. Transfection with mimics of mmu-miR-101c and mmu-miR-129-5p, as well as with an inhibitor of mmu-miR-210-5p, demonstrated direct effects of the respective miRNAs on parasite clearance in L. m.-infected BMDM. Furthermore, Affymetrix® chip analyses revealed a complex autophagy-related RNA network consisting of differentially expressed mRNAs and miRNAs in BMDM, which indicates high glycolytic and inflammatory activity in the host macrophages. Conclusions Autophagy in L. m.-infected host macrophages is a highly regulated cellular process at both the RNA level and the protein level. Autophagy has the potential to clear parasites from the host. The results obtained from experiments with murine host macrophages could be translated in the future to develop innovative and therapeutic antileishmanial strategies for human patients.},
  language  = {en}
}
@article{AbuHalimaHaeuslerBackesetal.2017,
  author    = {Abu-Halima, Masood and H{\"a}usler, Sebastian and Backes, Christina and Fehlmann, Tobias and Staib, Claudia and Nestel, Sigrun and Nazarenko, Irina and Meese, Eckart and Keller, Andreas},
  title     = {Micro-ribonucleic acids and extracellular vesicles repertoire in the spent culture media is altered in women undergoing \(In\) \(Vitro\) Fertilization},
  series = {Scientific Reports},
  volume    = {7},
  journal   = {Scientific Reports},
  doi       = {10.1038/s41598-017-13683-8},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-173632},
  year      = {2017},
  abstract  = {MicroRNAs (miRNAs) are class of small RNA molecules with major impact on gene regulation. We analyzed the potential of miRNAs secreted from pre-implantation embryos into the embryonic culture media as biomarkers to predict successful pregnancy. Using microarray analysis, we profiled the miRNome of the 56 spent culture media (SCM) after embryos transfer and found a total of 621 miRNAs in the SCM. On average, we detected 163 miRNAs in SCM of samples with failed pregnancies, but only 149 SCM miRNAs of embryos leading to pregnancies. MiR-634 predicted an embryo transfer leading to a positive pregnancy with an accuracy of 71\% and a sensitivity of 85\%. Among the 621 miRNAs, 102 (16.4\%) showed a differential expression between positive and negative outcome of pregnancy with miR-29c-3p as the most significantly differentially expressed miRNA. The number of extracellular vehicles was lower in SCM with positive outcomes (3.8 × 10\(^9\)/mL EVs), as compared to a negative outcome (7.35 × 10\(^9\)/mL EVs) possibly explaining the reduced number of miRNAs in the SCM associated with failed pregnancies. The analysis of the miRNome in the SCM of couples undergoing fertility treatment lays the ground towards development of biomarkers to predict successful pregnancy and towards understanding the role of embryonic miRNAs found in the SCM.},
  language  = {en}
}