Regression Models for High-Dimensional, Biological Data

In this cumulative dissertation, statistical models for regression are discussed in light of high-dimensional, biological data. The dissertation includes three publications: RNA transcription and degradation of Alu retrotransposons depends on sequence features and evolutionary history examines Alu elements, RNA retrotransposons in the human genome. Their RNA metabolism is poorly understood, and the source of Alu transcripts is still unresolved. We have conducted a transcription shutoff experiment and metabolic RNA labelling to shed further light on the life cycle of Alu transcripts.We furthermore present a novel statistical test for detecting expression quantitative trait loci relying on k-mer sequence representation. Endoscopic hemostasis makes the difference: Angiographic treatment in patients with lower gastrointestinal bleeding uses retrospective study data from patients receiving either endoscopic or angiographic treatment for lower gastrointestinal bleeding. While a majority of patients can be treated successfully with the usually preferred endoscopic method, in some cases, angiography is required to achieve hemostasis. Using conditional inference trees, we construct a decision tree model predicting if a patient should receive angiographic treatment. Genetic instability and recurrent MYC amplification in ALK-translocated NSCLC: a central role of TP53 mutations investigates a molecular subtype of lung cancer exhibiting rearrangements of the ALK gene. This cancer type often resists treatments, and no reliable biomarker to identify patients at risk for relapse is known. Analysing biopsy and cell culture data, we find that mutations in the TP53 gene can lead to chromosomal instability and thus the amplification of known cancer genes. This, in turn, grants cancer cells a proliferative advantage compared to the wild-type, providing a new approach for diagnosis and treatment

Comparison of Resting Full-Cycle Ratio and Fractional Flow Reserve in a German Real-World Cohort

Objective: The aim of this study was to evaluate non-hyperemic resting pressure ratios (NHPRs), especially the novel resting full-cycle ratio (RFR; lowest pressure distal to the stenosis/aortic pressure during the entire cardiac cycle), compared to the gold standard fractional flow reserve (FFR) in a real-world setting.Methods: The study included patients undergoing coronary pressure wire studies at one German University Hospital. No patients were excluded based on any baseline or procedural characteristics, except for insufficient quality of traces. The diagnostic performance of four NHPRs vs. FFR 0.8 were LAD lesions, peripheral artery disease, age, female sex and non-focal stenoses. Predictors for discordance of RFR > 0.89/FFR <= 0.8 included non-LCX lesions, percent diameter stenosis and previous percutaneous coronary intervention in the target vessel. RFR and all other NHPRs were highly correlated with each other.Conclusion: All NHPRs have a similar correlation with the gold standard FFR and may facilitate the acceptance and implementation of physiological assessments of lesion severity. However, we found ~20% discordant results between NHPRs and FFR in our all-comers German cohort

Endoscopic hemostasis makes the difference: Angiographic treatment in patients with lower gastrointestinal bleeding

BACKGROUND The large majority of gastrointestinal bleedings subside on their own or after endoscopic treatment. However, a small number of these may pose a challenge in terms of therapy because the patients develop hemodynamic instability, and endoscopy does not achieve adequate hemostasis. Interventional radiology supplemented with catheter angiography (CA) and transarterial embolization have gained importance in recent times. AIM To evaluate clinical predictors for angiography in patients with lower gastro-intestinal bleeding (LGIB). METHODS We compared two groups of patients in a retrospective analysis. One group had been treated for more than 10 years with CA for LGIB (n = 41). The control group had undergone non-endoscopic or endoscopic treatment for two years and been registered in a bleeding registry (n = 92). The differences between the two groups were analyzed using decision trees with the goal of defining clear rules for optimal treatment. RESULTS Patients in the CA group had a higher shock index, a higher Glasgow-Blatchford bleeding score (GBS), lower serum hemoglobin levels, and more rarely achieved hemostasis in primary endoscopy. These patients needed more transfusions, had longer hospital stays, and had to undergo subsequent surgery more frequently (P < 0.001). CONCLUSION Endoscopic hemostasis proved to be the crucial difference between the two patient groups. Primary endoscopic hemostasis, along with GBS and the number of transfusions, would permit a stratification of risks. After prospective confirmation of the present findings, the use of decision trees would permit the identification of patients at risk for subsequent diagnosis and treatment based on interventional radiology

Unmasking lower gastrointestinal bleeding under administration of norepinephrine

BACKGROUNDBleeding in the gastrointestinal tract is common and transarterial embolization enables the clinician to control gastrointestinal bleeding. Contrast extravasation is a prerequisite for successful embolization. Provocative angiography is helpful in the detection of elusive bleeding.AIMWe performed a retrospective analysis of angiographic treatment in patients with lower gastrointestinal hemorrhage and initially negative angiographies, as well as the role of norepinephrine (NE) in unmasking bleeding. METHODSWe analyzed 41 patients with lower gastrointestinal bleeding after angiography who had undergone treatment over a period of 10 years. All patients had a positive shock index and needed intensive care.RESULTSIn three of four patients, angiography disclosed the site of bleeding when NE was used during the procedure for hemodynamic stabilization.CONCLUSIONWe suggest that angiography performed after the administration of NE in unstable patients with gastrointestinal bleeding and an initially negative angiography has the potential to unmask bleeding sites for successful embolization. However, this statement must be confirmed in prospective studies

RNA transcription and degradation of Alu retrotransposons depends on sequence features and evolutionary history

AbstractAlu elements are one of the most successful groups of RNA retrotransposons and make up 11% of the human genome with over 1 million individual loci. They are linked to genetic defects, increases in sequence diversity, and influence transcriptional activity. Still, their RNA metabolism is poorly understood yet. It is even unclear whether Alu elements are mostly transcribed by RNA Polymerase II or III. We have conducted a transcription shutoff experiment by α-amanitin and metabolic RNA labeling by 4-thiouridine combined with RNA fragmentation (TT-seq) and RNA-seq to shed further light on the origin and life cycle of Alu transcripts. We find that Alu RNAs are more stable than previously thought and seem to originate in part from RNA Polymerase II activity, as previous reports suggest. Their expression however seems to be independent of the transcriptional activity of adjacent genes. Furthermore, we have developed a novel statistical test for detecting the expression of quantitative trait loci in Alu elements that relies on the de Bruijn graph representation of all Alu sequences. It controls for both statistical significance and biological relevance using a tuned

Advance of theragnosis biomarkers in lung cancer: from clinical to molecular pathology and biology

One distinct molecular subtype of non-small cell lung cancer (NSCLC) is defined by rearrangement of the anaplastic lymphoma kinase (ALK). The increasing knowledge over the last years has enabled the continuous improvement of ALK inhibitors; however, resistance in these patients remains a major concern. In this review, we summarize recent findings in ALK+-adenocarcinoma of the lung, highlighting the role of TP53 mutations in this specific cancer type and suggest new diagnostic strategies for the future, in order to improve patient's outcome

Comparison of the genomic background of MET-altered carcinomas of the lung: biological differences and analogies

Although non-small-cell lung cancer is a leading cause of cancer-related deaths, the molecular characterization and classification of its genetic alterations has drastically changed treatment options and overall survival within the last few decades. In particular, tyrosine kinase inhibitors targeting specific molecular alterations, among other MET, have greatly improved the prognosis of non-small-cell lung cancer patients. Here, we compare the genomic background of a subset of non-small-cell lung cancer cases harboring either a MET high-level amplification (n = 24) or a MET exon 14 skipping mutation (n = 26), using next-generatison sequencing, fluorescence in situ hybridization, immunohistochemistry, and Nanostring nCounter (R) technology. We demonstrate that the MET-amplified cohort shows a higher genetic instability, compared with the mutant cohort (p < 0.001). Furthermore, MET mutations occur at high allele frequency and in the presence of co-occurring TP53 mutations (n = 7), as well as MDM2 (n = 7), CDK4 (n = 6), and HMGA2 (n = 5) co-amplifications. No other potential driver mutation has been detected. Conversely, in the MET-amplified group, we identify co-occurring pathogenic NRAS and KRAS mutations (n = 5) and a significantly higher number of TP53 mutations, compared with the MET-mutant cohort (p = 0.048). Of note, MET amplifications occur more frequently as subclonal events. Interestingly, despite the significantly (p = 0.00103) older age at diagnosis of stage IIIb/IV of MET-mutant patients (median 77 years), compared with MET high-level amplified patients (median 69 years), MET-mutant patients with advanced-stage tumors showed a significantly better prognosis at 12 months (p = 0.04). In conclusion, the two groups of MET genetic alterations differ, both clinically and genetically: our data strongly suggest that MET exon 14 skipping mutations represent an early driver mutation. In opposition, MET amplifications occur usually in the background of other strong genetic events and therefore MET amplifications should be interpreted in the context of each tumor's genetic background, rather than as an isolated driver event, especially when considering MET-specific treatment options

Genetic instability and recurrent MYC amplification in ALK-translocated NSCLC: a central role of TP53 mutations

The anaplastic lymphoma kinase (ALK) rearrangement defines a distinct molecular subtype of non-small cell lung cancer (NSCLC). Despite the excellent initial efficacy of ALK inhibitors in patients with ALK+ lung cancer, resistance occurs almost inevitably. To date, there is no reliable biomarker allowing the identification of patients at higher risk of relapse. Here, we analysed a subset of 53 ALK+ tumors with and without TP53 mutation and ALK+ NSCLC cell lines by NanoString nCounter technology. We found that the co-occurrence of early TP53 mutations in ALK+ NSCLC can lead to chromosomal instability: 24% of TP53-mutated patients showed amplifications of known cancer genes such as MYC (14%), CCND1 (10%), TERT (5%), BIRC2 (5%), ORAOV1 (5%), and YAP1 (5%). MYC-overexpressing ALK+ TP53-mutated cells had a proliferative advantage compared to wild-type cells. ChIP-Seq data revealed MYC-binding sites within the promoter region of EML4, and MYC overexpression in ALK+ TP53-mutated cells resulted in an upregulation of EML4-ALK, indicating a potential MYC-dependent resistance mechanism in patients with increased MYC copy number. Our study reveals that ALK+ NSCLC represents a more heterogeneous subgroup of tumors than initially thought, and that TP53 mutations in that particular cancer type define a subset of tumors that harbour chromosomal instability, leading to the co-occurrence of pathogenic aberrations. (c) 2018 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland

Prevalence and potential biological role of TERT amplifications in ALK translocated adenocarcinoma of the lung

Aims The advent of specific ALK-targeting drugs has radically changed the outcome of patients with ALK translocated non-small-cell lung cancer (NSCLC). However, emerging resistance to treatment with ALK inhibitors in these patients remains a major concern. In previous studies, we analysed two ALK+ patient cohorts (TP53 wild-type/TP53 mutated) in terms of copy number alterations. All patients belonging to the TP53 wild-type group had mainly genetically stable genomes, with one exception showing chromosomal instability and amplifications of several gene loci, including TERT. Here, we aimed to determine the prevalence of TERT amplifications in these ALK+ lung cancer patients by analysing an independent cohort of 109 ALK translocated cases. We further analysed the copy numbers of numerous cancer-relevant genes and other genetic aberrations. Methods and results The prevalence of TERT amplifications was determined by means of FISH analyses. Copy numbers of 87 cancer-relevant genes were determined by NanoString nCounter(R) technology, FoundationOne(R) and lung-specific NGS panels in some of these TERT-amplified samples, and clinical data on patients with TERT-amplified tumours were collected. Our data revealed that five (4.6%) of all 109 analysed ALK+ patients harboured amplification of TERT and that these patients had genetically unstable genomes. Conclusions Our preliminary study shows that ALK+ adenocarcinomas should be evaluated in the context of their genomic background in order to more clearly understand and predict patients' individual course of disease