Publications by authors named "Tim Beissbarth"

179 Publications

Explaining decisions of graph convolutional neural networks: patient-specific molecular subnetworks responsible for metastasis prediction in breast cancer.

Genome Med 2021 Mar 11;13(1):42. Epub 2021 Mar 11.

Medical Bioinformatics, University Medical Center Göttingen, Göttingen, Germany.

Background: Contemporary deep learning approaches show cutting-edge performance in a variety of complex prediction tasks. Nonetheless, the application of deep learning in healthcare remains limited since deep learning methods are often considered as non-interpretable black-box models. However, the machine learning community made recent elaborations on interpretability methods explaining data point-specific decisions of deep learning techniques. We believe that such explanations can assist the need in personalized precision medicine decisions via explaining patient-specific predictions.

Methods: Layer-wise Relevance Propagation (LRP) is a technique to explain decisions of deep learning methods. It is widely used to interpret Convolutional Neural Networks (CNNs) applied on image data. Recently, CNNs started to extend towards non-Euclidean domains like graphs. Molecular networks are commonly represented as graphs detailing interactions between molecules. Gene expression data can be assigned to the vertices of these graphs. In other words, gene expression data can be structured by utilizing molecular network information as prior knowledge. Graph-CNNs can be applied to structured gene expression data, for example, to predict metastatic events in breast cancer. Therefore, there is a need for explanations showing which part of a molecular network is relevant for predicting an event, e.g., distant metastasis in cancer, for each individual patient.

Results: We extended the procedure of LRP to make it available for Graph-CNN and tested its applicability on a large breast cancer dataset. We present Graph Layer-wise Relevance Propagation (GLRP) as a new method to explain the decisions made by Graph-CNNs. We demonstrate a sanity check of the developed GLRP on a hand-written digits dataset and then apply the method on gene expression data. We show that GLRP provides patient-specific molecular subnetworks that largely agree with clinical knowledge and identify common as well as novel, and potentially druggable, drivers of tumor progression.

Conclusions: The developed method could be potentially highly useful on interpreting classification results in the context of different omics data and prior knowledge molecular networks on the individual patient level, as for example in precision medicine approaches or a molecular tumor board.
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http://dx.doi.org/10.1186/s13073-021-00845-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7953710PMC
March 2021

Effects of the Novel PFKFB3 Inhibitor KAN0438757 on Colorectal Cancer Cells and Its Systemic Toxicity Evaluation In Vivo.

Cancers (Basel) 2021 Feb 28;13(5). Epub 2021 Feb 28.

Clinic of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Robert-Koch-Straβe 40, 37075 Göttingen, Germany.

Background: Despite substantial progress made in the last decades in colorectal cancer (CRC) research, new treatment approaches are still needed to improve patients' long-term survival. To date, the promising strategy to target tumor angiogenesis metabolically together with a sensitization of CRC to chemo- and/or radiotherapy by PFKFB3 (6-phosphofructo-2-kinase/fructose-2,6-biphosphatase-3) inhibition has never been tested. Therefore, initial evaluation and validation of newly developed compounds such as KAN0438757 and their effects on CRC cells are crucial steps preceding to in vivo preclinical studies, which in turn may consolidate new therapeutic targets.

Materials And Methods: The efficiency of KAN0438757 to block PFKFB3 expression and translation in human CRC cells was evaluated by immunoblotting and real-time PCR. Functional in vitro assays assessed the effects of KAN0438757 on cell viability, proliferation, survival, adhesion, migration and invasion. Additionally, we evaluated the effects of KAN0438757 on matched patient-derived normal and tumor organoids and its systemic toxicity in vivo in C57BL6/N mice.

Results: High PFKFB3 expression is correlated with a worse survival in CRC patients. KAN0438757 reduces PFKFB3 protein expression without affecting its transcriptional regulation. Additionally, a concentration-dependent anti-proliferative effect was observed. The migration and invasion capacity of cancer cells were significantly reduced, independent of the anti-proliferative effect. When treating colonic patient-derived organoids with KAN0438757 an impressive effect on tumor organoids growth was apparent, surprisingly sparing normal colonic organoids. No high-grade toxicity was observed in vivo.

Conclusion: The PFKFB3 inhibitor KAN0438757 significantly reduced CRC cell migration, invasion and survival. Moreover, on patient-derived cancer organoids KAN0438757 showed significant effects on growth, without being overly toxic in normal colon organoids and healthy mice. Our findings strongly encourage further translational studies to evaluate KAN0438757 in CRC therapy.
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http://dx.doi.org/10.3390/cancers13051011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7957803PMC
February 2021

Prognostic value of the micronucleus assay for clinical endpoints in neoadjuvant radiochemotherapy for rectal cancer.

BMC Cancer 2021 Mar 4;21(1):219. Epub 2021 Mar 4.

University Medical Center Göttingen, Göttingen, Germany.

Background: The question whether lymphocyte radiosensitivity is representative of patients' response to radiotherapy (RT) remains unsolved. We analyzed lymphocyte cytogenetic damage in patients who were homogeneously treated with preoperative radiochemotherapy (RCT) for rectal cancer within clinical trials. We tested for interindividual variation and consistent radiosensitivity after in-vivo and in-vitro irradiation, analyzed the effect of patients' and RCT characteristics on cytogenetic damage, and tested for correlations with patients' outcome in terms of tumor response, survival and treatment-related toxicity.

Methods: The cytokinesis-block micronucleus cytome (CBMNcyt) assay was performed on the peripheral blood lymphocytes (PBLCs) of 134 patients obtained before, during, at the end of RCT, and during the 2-year follow-up. A subset of PBLCs obtained before RCT was irradiated in-vitro with 3 Gy. RCT included 50.4 Gy of pelvic RT with 5-fluorouracil (5-FU) alone (n = 78) or 5-FU plus oxaliplatin (n = 56). The analyzed variables included patients' age, gender, RT characteristics (planning target volume size [PTV size], RT technique), and chemotherapy characteristics (5-FU plasma levels, addition of oxaliplatin). Outcome was analyzed as tumor regression, patient survival, and acute and late toxicity.

Results: Cytogenetic damage increased significantly with the radiation dose and varied substantially between individuals. Women were more sensitive than men; no significant age-dependent differences were observed. There was a significant correlation between the cytogenetic damage after in-vitro irradiation and in-vivo RCT. We found a significant effect of the PTV size on the yields of cytogenetic damage after RCT, while the RT technique had no effect. Neither the addition of oxaliplatin nor the 5-FU levels influenced cytogenetic damage. We found no correlation between patient outcome and the cytogenetic damage.

Conclusions: We found consistent cytogenetic damage in lymphocytes after in-vivo RCT and in-vitro irradiation. Gender was confirmed as a well-known, and the PTV size was identified as a less well-known influencing variable on lymphocyte cytogenetic damage after partial-body irradiation. A consistent level of cytogenetic damage after in-vivo and in-vitro irradiation may indicate the importance of genetic factors for individual radiosensitivity. However, we found no evidence that in-vivo or in-vitro irradiation-induced cytogenetic damage is an adequate biomarker for the response to RCT in rectal cancer patients.
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http://dx.doi.org/10.1186/s12885-021-07914-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7931609PMC
March 2021

NOTCH Activation via gp130/STAT3 Signaling Confers Resistance to Chemoradiotherapy.

Cancers (Basel) 2021 Jan 26;13(3). Epub 2021 Jan 26.

Institute of Cellular and Molecular Immunology, University Medical Center Goettingen, 37073 Goettingen, Germany.

Resistance of tumor cells to chemoradiotherapy represents a fundamental problem in clinical oncology. The underlying mechanisms are actively debated. Here we show that blocking inflammatory cytokine receptor signaling via STAT3 re-sensitized treatment-refractory cancer cells and abolished tumor growth in a xenograft mouse model when applied together with chemoradiotherapy. STAT3 executed treatment resistance by triggering the expression of RBPJ, the key transcriptional regulator of the NOTCH pathway. The mandatory RBPJ interaction partner, NOTCH intracellular domain, was provided by tumor cell-intrinsic expression of NOTCH ligands that caused tonic NOTCH proteolysis. In fact, NOTCH inhibition phenocopied the effect of blocking STAT3 signaling. Moreover, genetic profiling of rectal cancer patients revealed the importance of the STAT3/NOTCH axis as NOTCH expression correlated with clinical outcome. Our data uncovered an unprecedented signal alliance between inflammation and cellular development that orchestrated resistance to chemoradiotherapy. Clinically, our findings allow for biomarker-driven patient stratification and offer novel treatment options.
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http://dx.doi.org/10.3390/cancers13030455DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7865718PMC
January 2021

A prediction-based method to estimate student learning outcome: Impact of response rate and gender differences on evaluation results.

Med Teach 2021 Jan 27:1-12. Epub 2021 Jan 27.

Department of Cardiology and Pneumology, University Medical Centre Göttingen, Göttingen, Germany.

Background: Low response rates threaten the reliability and validity of student evaluations of teaching. Previous research has shown that asking students to predict how satisfied their fellow students were with a course produces reliable results at lower response rates. The aim of this study was to investigate whether this prediction-based method can also be used to evaluate student learning outcome.

Methods: Before and after a cardiorespiratory module, 128 fourth-year medical students provided self-assessments and predictions of performance on 27 specific learning objectives and took formative tests on the respective contents. Pre-post performance gain was compared across all three modalities.

Results: Formative exam results indicated a performance gain of 63.0%. Self-assessed and prediction-based performance gains were identical (67.8%) but both slightly overestimated actual performance gain. Irrespective of the method used, a response rate of 20% was sufficient to produce reliable results. Compared to male students, females greatly overestimated their peers' performance which led to inflated performance gain values.

Conclusions: Student self-assessments and predictions are equally valid sources of learning outcome measures, and low response rates are sufficient to produce stable results. When using a prediction-based approach, a tendency to overestimate learning outcome in female students needs to be taken into account.
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http://dx.doi.org/10.1080/0142159X.2020.1867714DOI Listing
January 2021

TIM-3 Genetic Variants Are Associated with Altered Clinical Outcome and Susceptibility to Gram-Positive Infections in Patients with Sepsis.

Int J Mol Sci 2020 Nov 6;21(21). Epub 2020 Nov 6.

Department of Anesthesiology, University Medical Center, Georg August University, D-37075 Goettingen, Germany.

: Previous studies have reported the fundamental role of immunoregulatory proteins in the clinical phenotype and outcome of sepsis. This study investigated two functional single nucleotide polymorphisms (SNPs) of T cell immunoglobulin and mucin domain-containing protein 3 (TIM-3), which has a negative stimulatory function in the T cell immune response. : Patients with sepsis ( = 712) were prospectively enrolled from three intensive care units (ICUs) at the University Medical Center Goettingen since 2012. All patients were genotyped for the TIM-3 SNPs rs1036199 and rs10515746. The primary outcome was 28-day mortality. Disease severity and microbiological findings were secondary endpoints. : Kaplan-Meier survival analysis demonstrated a significantly lower 28-day mortality for TIM-3 rs1036199 AA homozygous patients compared to C-allele carriers (18% vs. 27%, = 0.0099) and TIM-3 rs10515746 CC homozygous patients compared to A-allele carriers (18% vs. 26%, = 0.0202). The TIM-3 rs1036199 AA genotype and rs10515746 CC genotype remained significant predictors for 28-day mortality in the multivariate Cox regression analysis after adjustment for relevant confounders (adjusted hazard ratios: 0.67 and 0.70). Additionally, patients carrying the rs1036199 AA genotype presented more Gram-positive and infections, and rs10515746 CC homozygotes presented more infections. : The studied TIM-3 genetic variants are associated with altered 28-day mortality and susceptibility to Gram-positive infections in sepsis.
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http://dx.doi.org/10.3390/ijms21218318DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7664272PMC
November 2020

Impact of pre-OP independence in patients with limited brain metastases on long-term survival.

BMC Cancer 2020 Oct 8;20(1):973. Epub 2020 Oct 8.

Clinic for Hematology/Medical Oncology, University Medical Center Göttingen, 37099, Göttingen, Germany.

Background: Brain metastasis represents a major complication with a significantly shorter overall survival of many oncological diseases, in particular of lung cancer, breast cancer and malignant melanoma patients. However, despite the poor prognosis, sometimes clinical decision-making, between on the one hand not to harm the patient and on the other hand not withholding a potential therapeutic option, is very challenging. Thus the aim of this retrospective study was to compare various scores, including scores for activities of daily living (ADL) before resection of brain metastases and to analyse their impact on survival.

Methods: Our single institution retrospective patient cohort (N = 100) with a median age of 63.6 years, which had all undergone resection of one or more brain metastases, was categorized using the original patient files. The cohort includes 52 patients with lung cancer, 27 patients with breast cancer, 8 patients with colorectal carcinoma and 13 patients with kidney cancer. To categorize, we used different score systems which were capable to evaluate the patient in relation to self-sufficiency, activity and self-determination as part of ADL. The retrospective analysis includes the ECOG-Status, Karnofsky-Index, Barthel-Index, ASA-Classification and Katz-Index. Pre-processing and the analysis of the data was implemented using KNIME, where we used the R-plugin nodes to perform the final statistical tests with R.

Results: Our analysis reveals that most of the ADL scores we tested are able to give a reliable prediction on overall survival after brain metastasis surgery. The survival rates decrease significantly with a lower score in all tested score systems, with the exception of the ASA-Risk score. In particular, the Katz Index < 6 was identified to have a significant correlation with a lower cancer specific survival (CSS) (HR 3.33, 95%-CI [2.17-5.00]; p-Value = 9.6*10), which is easy to use and has reproducible measurements.

Conclusions: Pre-operative independence assessment by indices of ADL represents a predictor for overall survival after resection of brain metastases. Especially the easily, objectively and rapidly applicable Katz-Score is a very helpful tool to assess the pre-operative status, which could be additionally included in clinical decision making in daily practice.
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http://dx.doi.org/10.1186/s12885-020-07459-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7545555PMC
October 2020

The long-term influence of hospital and surgeon volume on local control and survival in the randomized German Rectal Cancer Trial CAO/ARO/AIO-94.

Surg Oncol 2020 Dec 26;35:200-205. Epub 2020 Aug 26.

Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany.

Background: The association of treatment volume and oncological outcome of rectal cancer patients undergoing multidisciplinary treatment is subject of an ongoing debate. Prospective data on long-term local control and overall survival (OS) are not available so far. This study investigated the long-term influence of hospital and surgeon volume on local recurrence (LR) and OS in patients with locally advanced rectal cancers.

Methods: In a post-hoc analysis of the randomized phase III CAO/ARO/AIO-94 trial after a follow-up of more than 10 years, 799 patients with stage II/III rectal cancers were evaluated. LR-rates and OS were stratified by hospital recruitment volume (≤20 vs. 21-90 vs. >90 patients) and by surgeon volume (≤10 vs. 11-50 vs. >50 procedures).

Results: Patients treated in high-volume hospitals had a longer OS than those treated in hospitals with medium or low treatment volume (p = 0.03). The surgeon volume was adversely associated with LR (p = 0.01) but had no influence on overall survival. The positive effect of neoadjuvant chemoradiation (CRT) on local control was the strongest in patients being operated by medium-volume surgeons, less in patients being operated by high-volume surgeons and missing in those being operated by low-volume surgeons.

Conclusions: Patients with locally advanced rectal cancers might benefit from treatment in specialized high-volume hospitals. In particular, the surgeon volume had significant influence on long-term local tumour control. The effect of neoadjuvant CRT on local tumour control may likewise depend on the surgeon volume.
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http://dx.doi.org/10.1016/j.suronc.2020.08.021DOI Listing
December 2020

Discriminating malignant and benign clinical T1 renal masses on computed tomography: A pragmatic radiomics and machine learning approach.

Medicine (Baltimore) 2020 Apr;99(16):e19725

Department of Urology, University Medical Center Goettingen, Goettingen, Germany.

The aim of this study was to discriminate malignant and benign clinical T1 renal masses on routinely acquired computed tomography (CT) images using radiomics and machine learning techniques.Adult patients undergoing surgical resection and histopathological analysis of clinical T1 renal masses were included. Preoperative CT studies in venous phase from multiple referring centers were included, without restriction to specific CT scanners, slice thickness, or degrees of artifacts. Renal masses were segmented and 120 standardized radiomic features extracted. Machine learning algorithms were used to predict malignancy of renal masses using radiomics features and cross-validation. Diagnostic accuracy of machine learning models and assessment by independent blinded radiologists were compared based on the gold standard of histopathologic diagnosis.A total of 94 patients met inclusion criteria (benign renal masses: n = 18; malignant: n = 76). CT studies from 18 different scanners were assessed with median slice thickness of 2.5 mm and artifacts in 15 cases (15.9%).Area under the receiver-operating-characteristics curve (AUC) of random forest (random forest [RF], AUC = 0.83) was significantly higher compared to the radiologists (AUC = 0.68, P = .047). Sensitivity was significantly higher for RF versus radiologists (0.88 vs 0.80, P = .045), whereas specificity was numerically higher for RF (0.67 vs 0.50, P = .083).Although limited by an overall small sample size and few benign renal tumors, a radiomic features and machine learning approach suggests a high diagnostic accuracy for discrimination of malignant and benign clinical T1 renal masses on venous phase CT. The presented algorithm robustly outperforms human readers in a real-life scenario with nonstandardized imaging studies from various referring centers.
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http://dx.doi.org/10.1097/MD.0000000000019725DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7220487PMC
April 2020

Constructing temporal regulatory cascades in the context of development and cell differentiation.

PLoS One 2020 10;15(4):e0231326. Epub 2020 Apr 10.

Department of Medical Bioinformatics, University Medical Center Göttingen, Goettingen, Niedersachsen, Germany.

Cell differentiation is a complex process orchestrated by sets of regulators precisely appearing at certain time points, resulting in regulatory cascades that affect the expression of broader sets of genes, ending up in the formation of different tissues and organ parts. The identification of stage-specific master regulators and the mechanism by which they activate each other is a key to understanding and controlling differentiation, particularly in the fields of tissue regeneration and organoid engineering. Here we present a workflow that combines a comprehensive general regulatory network based on binding site predictions with user-provided temporal gene expression data, to generate a a temporally connected series of stage-specific regulatory networks, which we call a temporal regulatory cascade (TRC). A TRC identifies those regulators that are unique for each time point, resulting in a cascade that shows the emergence of these regulators and regulatory interactions across time. The model was implemented in the form of a user-friendly, visual web-tool, that requires no expert knowledge in programming or statistics, making it directly usable for life scientists. In addition to generating TRCs the tool links multiple interactive visual workflows, in which a user can track and investigate further different regulators, target genes, and interactions, directing the tool along the way into biologically sensible results based on the given dataset. We applied the TRC model on two different expression datasets, one based on experiments conducted on human induced pluripotent stem cells (hiPSCs) undergoing differentiation into mature cardiomyocytes and the other based on the differentiation of H1-derived human neuronal precursor cells. The model was successful in identifying previously known and new potential key regulators, in addition to the particular time points with which these regulators are associated, in cardiac and neural development.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0231326PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147753PMC
July 2020

Intensified Histopathological Work-Up after Pancreatic Head Resection Reveals Relevant Prognostic Markers.

Digestion 2021 21;102(2):265-273. Epub 2020 Jan 21.

Department of General, Visceral, and Pediatric Surgery, University Medical Center Goettingen, Goettingen, Germany,

Introduction: Local recurrence remains a major problem after pancreatic head resection. Intensified histopathological work-up of surgical specimens after pancreatic head resection has revealed an increased number of incomplete resections (R1) depending on tumor infiltration front at the resection margins (RMs). It remains unclear to which extent the increased R1 resection rate has a clinical relevance for the patients' prognosis.

Materials And Methods: Pancreatic head resections between 2006 and 2012 were histologically intensively worked-up by a previously described protocol. The distance between the tumor infiltration front and the resection planes or organ surfaces was documented. The impact of the size of the tumor and an additional portal vein resection was analyzed. The effect of a R1 resection status on development and type of recurrence was evaluated.

Results: A total of 203 pancreatic head resections were evaluated. Different definitions of R1 resection were applied. These led to significantly different prognosis for patients. A greater distance between the tumor infiltration front and the resection plane or organ surface was associated with a better outcome for the patients. For the ventral surface, the mesopancreas and the pancreatic body these differences were statistically significant comparing the different R1 definitions. For the dorsal surface, a significant difference in prognosis was found if the tumor was >2 mm away from the resection surface. A tumor size of 3 cm was identified to play a relevant role for the prognosis. Patients who had a portal vein resection without a histologically proven infiltration showed a statistically significant higher overall survival. Patients with R1 resection were at highest risk for developing local recurrence as well as distant metastasis.

Conclusion: Intensified histopathological work-up with an increased number of R1 resections has a clinical relevance for patients' prognosis. Tumors with a smaller size or with a greater distance to the organ surface or RM have a better outcome.
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http://dx.doi.org/10.1159/000504648DOI Listing
January 2020

Antibody signatures in patients with histopathologically defined multiple sclerosis patterns.

Acta Neuropathol 2020 03 16;139(3):547-564. Epub 2020 Jan 16.

Institute of Neuropathology, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075, Göttingen, Germany.

Early active multiple sclerosis (MS) lesions can be classified histologically into three main immunopathological patterns of demyelination (patterns I-III), which suggest pathogenic heterogeneity and may predict therapy response. Patterns I and II show signs of immune-mediated demyelination, but only pattern II is associated with antibody/complement deposition. In pattern III lesions, which include Baló's concentric sclerosis, primary oligodendrocyte damage was proposed. Serum antibody reactivities could reflect disease pathogenesis and thus distinguish histopathologically defined MS patterns. We established a customized microarray with more than 700 peptides that represent human and viral antigens potentially relevant for inflammatory demyelinating CNS diseases, and tested sera from 66 patients (pattern I n = 12; II n = 29; III n = 25, including 8 with Baló's), healthy controls, patients with Sjögren's syndrome and stroke patients. Cell-based assays were performed for aquaporin 1 (AQP1) and AQP4 antibody detection. No single peptide showed differential binding among study cohorts. Because antibodies can react with different peptides from one protein, we also analyzed groups of peptides. Patients with pattern II showed significantly higher reactivities to Nogo-A peptides as compared to patterns I (p = 0.02) and III (p = 0.02). Pattern III patients showed higher reactivities to AQP1 (compared to pattern I p = 0.002, pattern II p = 0.001) and varicella zoster virus (VZV, compared to pattern II p = 0.05). In patients with Baló's, AQP1 reactivity was also significantly higher compared to patients without Baló's (p = 0.04), and the former revealed distinct antibody signatures. Histologically, Baló's patients showed loss of AQP1 and AQP4 in demyelinating lesions, but no antibodies binding conformational AQP1 or AQP4 were detected. In summary, higher reactivities to Nogo-A peptides in pattern II patients could be relevant for enhanced axonal repair and remyelination. Higher reactivities to AQP1 peptides in pattern III patients and its subgroup of Baló's patients possibly reflect astrocytic damage. Finally, latent VZV infection may cause peripheral immune activation.
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http://dx.doi.org/10.1007/s00401-019-02120-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7035238PMC
March 2020

Favorable 90-Day Mortality in Obese Caucasian Patients with Septic Shock According to the Sepsis-3 Definition.

J Clin Med 2019 Dec 24;9(1). Epub 2019 Dec 24.

Department of Anesthesiology, University Medical Center, Georg August University, D-37075 Goettingen, Germany.

Septic shock is a frequent life-threatening condition and a leading cause of mortality in intensive care units (ICUs). Previous investigations have reported a potentially protective effect of obesity in septic shock patients. However, prior results have been inconsistent, focused on short-term in-hospital mortality and inadequately adjusted for confounders, and they have rarely applied the currently valid Sepsis-3 definition criteria for septic shock. This investigation examined the effect of obesity on 90-day mortality in patients with septic shock selected from a prospectively enrolled cohort of septic patients. A total of 352 patients who met the Sepsis-3 criteria for septic shock were enrolled in this study. Body-mass index (BMI) was used to divide the cohort into 24% obese (BMI ≥ 30 kg/m) and 76% non-obese (BMI < 30 kg/m) patients. Kaplan-Meier survival analysis revealed a significantly lower 90-day mortality (31% vs. 43%; = 0.0436) in obese patients compared to non-obese patients. Additional analyses of baseline characteristics, disease severity, and microbiological findings outlined further statistically significant differences among the groups. Multivariate Cox regression analysis estimated a significant protective effect of obesity on 90-day mortality after adjustment for confounders. An understanding of the underlying physiologic mechanisms may improve therapeutic strategies and patient prognosis.
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http://dx.doi.org/10.3390/jcm9010046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7019854PMC
December 2019

Clinical application of genomic high-throughput data: Infrastructural, ethical, legal and psychosocial aspects.

Eur Neuropsychopharmacol 2020 02 20;31:1-15. Epub 2019 Dec 20.

Department of Medical Informatics, University Medical Center Göttingen, Von-Siebold-Straße 3, 37075 Göttingen, Germany.

Genomic high-throughput technologies (GHTT) such as next-generation sequencing represent a fast and cost-effective tool toward a more comprehensive understanding of the molecular background of complex diseases. However, technological advances contrast with insufficient application in clinical practice. Thus, patients, physicians, and other professionals are faced with tough challenges that forestall the efficient and effective implementation. With the increasing application of genetic testing, it is of paramount importance that physicians and other professionals in healthcare recognize the restrictions and potential of GHTT, in order to understand and interpret the complex data in the context of health and disease. At the same time, the growing volume and complexity of data is forever increasing the need for sustainable infrastructure and state-of-the-art tools for efficient data management, including their analysis and integration. The large pool of sensitive information remains difficult to interpret and fundamental questions spanning from billing to legal, social, and ethical issues have still not been resolved. Here we summarize and discuss these obstacles in an interdisciplinary context and suggest ways to overcome them. Continuous discussion with clinicians, data managers, biostatisticians, systems medicine experts, ethicists, legal scholars, and patients illuminates the strengths, weakness, and current practices in the pipeline from biomaterial to sequencing and data management. This discussion also highlights the new, cross-disciplinary working collaborations to realize the wide-ranging challenges in clinical genomics including the exceptional demands placed on the staff preparing and presenting the data, as well as the question as to how to report the data and results to patients.
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http://dx.doi.org/10.1016/j.euroneuro.2019.09.008DOI Listing
February 2020

The prognostic capacities of CBP and p300 in locally advanced rectal cancer.

World J Surg Oncol 2019 Dec 19;17(1):224. Epub 2019 Dec 19.

Department of General, Visceral and Pediatric Surgery, University Medical Center, Robert-Koch-Str. 40, 37075, Göttingen, Germany.

Background: CREB-binding protein (CBP) and p300 represent histone acetyltransferases (HATs) and transcriptional coactivators that play essential roles in tumour initiation and progression. Both proteins are generally thought to function as tumour suppressors, although their distinct roles in colorectal cancer (CRC) remain inconsistent and ambiguous. Thus, we analysed the expression of these two HATs in human tissue samples from patients with locally advanced rectal cancer via immunohistochemistry and evaluated their potential impacts on future CRC diagnosis and treatment.

Methods: In our analysis, we included ninety-three (n = 93) patients diagnosed with adenocarcinoma in the upper third of the rectum. None of the patients received preoperative chemoradiotherapy, but the patients did undergo primary resection of the tumour within the phase II GAST-05 trial. By using H-scores, the expression of both proteins was visualised via immunohistochemistry in resected specimens from the patients. CBP and p300 expression were correlated with clinical and follow-up data.

Results: Our analysis showed that high expression of CBP was significantly associated with prolonged cancer-specific survival (CSS; p = 0.002). In univariate analysis, CBP was an independent prognostic parameter for CSS (p = 0.042). High nuclear CBP expression was observed in two-thirds of patients. In contrast, we could not find any significant correlation between the expression of p300 and cancer-specific survival in this cohort of patients (p = 0.09). We did not observe any cooperation between CBP and p300 in our analysis.

Conclusions: High expression of CBP was significantly associated with improved oncological outcomes. This finding could help to stratify patients in the future for CRC treatment. Histone deacetylase (HDAC) inhibitors are increasingly playing a role in oncological treatment and could additionally become therapeutic options in CRC. Our findings need to be further evaluated and verified in future clinical analyses.
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http://dx.doi.org/10.1186/s12957-019-1764-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6923994PMC
December 2019

Mapping Cellular Microenvironments: Proximity Labeling and Complexome Profiling (Seventh Symposium of the Göttingen Proteomics Forum).

Cells 2019 10 2;8(10). Epub 2019 Oct 2.

Institute of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany.

Mass spectrometry-based proteomics methods are finding increasing use in structural biology research. Beyond simple interaction networks, information about stable protein-protein complexes or spatially proximal proteins helps to elucidate the biological functions of proteins in a wider cellular context. To shed light on new developments in this field, the Göttingen Proteomics Forum organized a one-day symposium focused on complexome profiling and proximity labeling, two emerging technologies that are gaining significant attention in biomolecular research. The symposium was held in Göttingen, Germany on 23 May, 2019, as part of a series of regular symposia organized by the Göttingen Proteomics Forum.
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http://dx.doi.org/10.3390/cells8101192DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6830108PMC
October 2019

Combined targeting of HER-2 and HER-3 represents a promising therapeutic strategy in colorectal cancer.

BMC Cancer 2019 Sep 5;19(1):880. Epub 2019 Sep 5.

Department of General, Visceral and Pediatric Surgery, University Medical Center Goettingen, Robert-Koch-Str. 40, 37075, Goettingen, Germany.

Background: Abrogation of growth factor-dependent signaling represents an effective therapeutic strategy for patients with colorectal cancer (CRC). Here we evaluated the effectiveness of targeting the epidermal growth factor (EGF) receptors HER-2 and HER-3 in the three cell lines LS513, LS1034 and SW837.

Methods: Treatment with HER-2-specific antibodies trastuzumab and pertuzumab resulted in a mild reduction of cellular viability. In contrast, the antibody-drug conjugate T-DM1 mediated a strong and dose-dependent decrease of viability and Akt phosphorylation.

Results: The most striking effects were observed with the dual tyrosine kinase inhibitor lapatinib, and the Pan-ErbB inhibitor afatinib. Selectively, the effect of EGF receptor inhibition was augmented by a combination with 5-fluorouracil and oxaliplatin. Finally, high expression of HER-3 was detected in 121 of 172 locally advanced rectal cancers (70.3%). In conclusion, inhibition of EGF receptors effectively blocks downstream signaling and significantly impairs viability of CRC cells. However, the effectiveness of receptor inhibition highly depends on the inhibitors' mode of action, as targeting HER-2 alone is not sufficient.

Conclusion: Since HER-2 and HER-3 are expressed in a relevant number of patients, targeting both receptors may represent a promising therapeutic strategy for CRC.
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http://dx.doi.org/10.1186/s12885-019-6051-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6727342PMC
September 2019

Utilizing Molecular Network Information via Graph Convolutional Neural Networks to Predict Metastatic Event in Breast Cancer.

Stud Health Technol Inform 2019 Sep;267:181-186

Medical Bioinformatics, University Medical Center Göttingen.

Gene expression data is commonly available in cancer research and provides a snapshot of the molecular status of a specific tumor tissue. This high-dimensional data can be analyzed for diagnoses, prognoses, and to suggest treatment options. Machine learning based methods are widely used for such analysis. Recently, a set of deep learning techniques was successfully applied in different domains including bioinformatics. One of these prominent techniques are convolutional neural networks (CNN). Currently, CNNs are extending to non-Euclidean domains like graphs. Molecular networks are commonly represented as graphs detailing interactions between molecules. Gene expression data can be assigned to the vertices of these graphs, and the edges can depict interactions, regulations and signal flow. In other words, gene expression data can be structured by utilizing molecular network information as prior knowledge. Here, we applied graph CNN to gene expression data of breast cancer patients to predict the occurrence of metastatic events. To structure the data we utilized a protein-protein interaction network. We show that the graph CNN exploiting the prior knowledge is able to provide classification improvements for the prediction of metastatic events compared to existing methods.
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http://dx.doi.org/10.3233/SHTI190824DOI Listing
September 2019

Reconstruction of Different Modes of WNT Dependent Protein Networks from Time Series Protein Quantification.

Stud Health Technol Inform 2019 Sep;267:175-180

University Medical Center Göttingen, Hematology & Medical Oncology, 37099 Göttingen.

Protein signaling networks are crucial cornerstones in cellular responses. Deregulation causes various diseases, including cancer. One pathway that is frequently deregulated in cancer is the WNT signaling pathway. It has been shown that WNT signaling is highly context-dependent and the availability of receptors and ligands determines downstream signaling. In order to reveal which signaling pathways are activated by a specific receptor-ligand combination, we overexpressed the non-canonical WNT receptor ROR2 in the human breast cancer cell line MCF-7 and stimulated it with its putative ligand WNT11. Based on characterization of the cells by Reverse Phase Protein Array (RPPA), we integrated the proteomic data by network reconstruction analysis with prior knowledge from a pathway database. Using this approach, we were able to identify novel edges that differed upon ROR2 overexpression and WNT11 stimulation.
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http://dx.doi.org/10.3233/SHTI190823DOI Listing
September 2019

Leukocytosis and neutrophilia as independent prognostic immunological biomarkers for clinical outcome in the CAO/ARO/AIO-04 randomized phase 3 rectal cancer trial.

Int J Cancer 2019 10 2;145(8):2282-2291. Epub 2019 Apr 2.

Department of Radiotherapy and Oncology, University of Frankfurt, Frankfurt, Germany.

Peripheral blood leukocytosis and neutrophilia reflect cancer inflammation and have been proposed as prognostic immunological biomarkers in various malignancies. However, previous studies were limited by their retrospective nature and small patient numbers. Baseline peripheral blood leukocytes, neutrophils, hemoglobin, platelets, lactate dehydrogenase and carcinoembryonic antigen (CEA) were correlated with clinicopathologic characteristics, and clinical outcome in 1236 patients with rectal cancer treated with 5-FU-based preoperative chemoradiotherapy (CRT) alone or with oxaliplatin followed by surgery and adjuvant chemotherapy within the CAO/ARO/AIO-04 randomized phase 3 trial. Multivariable analyses were performed using Cox regression models. After a median follow-up of 50 months, baseline leukocytosis remained an independent adverse prognostic factor for disease-free survival (DFS; HR 1.457; 95% CI 1.163-1.825; p = 0.001), distant metastasis (HR 1.696; 95% CI 1.266-2.273; p < 0.001) and overall survival (OS; HR 1.716; 95% CI 1.264-2.329; p = 0.001) in multivariable analysis. Similar significant findings were observed for neutrophilia and high CEA levels. Conversely, treatment-induced leukopenia correlated with favorable DFS (p = 0.037), distant metastasis (p = 0.028) and OS (p = 0.012). Intriguingly, addition of oxaliplatin to 5-FU CRT resulted in a significant DFS improvement only in patients with neutrophilia and leukocytosis (p = 0.028 and p = 0.002). Our findings have important clinical implications and provide high-level evidence on the adverse prognostic role of leukocytes and neutrophils, and the impact of chemotherapy in the context of these biomarkers. These data could help guide patient stratification and should be further validated within prospective studies.
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http://dx.doi.org/10.1002/ijc.32274DOI Listing
October 2019

Lack of an Association between the Functional Polymorphism TREM-1 rs2234237 and the Clinical Course of Sepsis among Critically Ill Caucasian Patients-A Monocentric Prospective Genetic Association Study.

J Clin Med 2019 Mar 3;8(3). Epub 2019 Mar 3.

Department of Anesthesiology, University Medical Center, Georg August University, D-37075 Goettingen, Germany.

Sepsis is a life-threatening condition and a significant challenge for those working in intensive care, where it remains one of the leading causes of mortality. According to the sepsis-3 definition, sepsis is characterized by dysregulation of the host response to infection. The TREM-1 gene codes for the triggering receptor expressed on myeloid cells 1, which is part of the pro-inflammatory response of the immune system. This study aimed to determine whether the functional TREM-1 rs2234237 single nucleotide polymorphism was associated with mortality in a cohort of 649 Caucasian patients with sepsis. The 90-day mortality rate was the primary outcome, and disease severity and microbiological findings were analyzed as secondary endpoints. TREM-1 rs2234237 TT homozygous patients were compared to A-allele carriers for this purpose. Kaplan⁻Meier survival analysis revealed no association between the clinically relevant TREM-1 rs2234237 single nucleotide polymorphism and the 90-day or 28-day survival rate in this group of septic patients. In addition, the performed analyses of disease severity and the microbiological findings did not show significant differences between the TREM-1 rs2234237 genotypes. The TREM-1 rs2234237 genotype was not significantly associated with sepsis mortality and sepsis disease severity. Therefore, it was not a valuable prognostic marker for the survival of septic patients in the studied cohort.
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http://dx.doi.org/10.3390/jcm8030301DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6463065PMC
March 2019

CTLA-4 Genetic Variants Predict Survival in Patients with Sepsis.

J Clin Med 2019 Jan 10;8(1). Epub 2019 Jan 10.

Department of Anesthesiology, University Medical Center, Georg August University, D-37075 Goettingen, Germany.

Cytotoxic T lymphocyte-associated protein 4 (CTLA-4) is a coinhibitory checkpoint protein expressed on the surface of T cells. A recent study by our working group revealed that the rs231775 single nucleotide polymorphism (SNP) in the CTLA-4 gene was associated with the survival of patients with sepsis and served as an independent prognostic variable. To further investigate the impact of CTLA-4 genetic variants on sepsis survival, we examined the effect of two functional SNPs, CTLA-4 rs733618 and CTLA-4 rs3087243, and inferred haplotypes, on the survival of 644 prospectively enrolled septic patients. Kaplan⁻Meier survival analysis revealed significantly lower 90-day mortality for rs3087243 G allele carriers ( = 502) than for AA-homozygous ( = 142) patients (27.3% vs. 40.8%, = 0.0024). Likewise, lower 90-day mortality was observed for TAA haplotype-negative patients ( = 197; compound rs733618 T/rs231775 A/rs3087243 A) than for patients carrying the TAA haplotype ( = 447; 24.4% vs. 32.9%, = 0.0265). Carrying the rs3087243 G allele hazard ratio (HR): 0.667; 95% confidence interval (CI): 0.489⁻0.909; = 0.0103) or not carrying the TAA haplotype (HR: 0.685; 95% CI: 0.491⁻0.956; = 0.0262) remained significant covariates for 90-day survival in the multivariate Cox regression analysis and thus served as independent prognostic variables. In conclusion, our findings underscore the significance of CTLA-4 genetic variants as predictors of survival of patients with sepsis.
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http://dx.doi.org/10.3390/jcm8010070DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6352177PMC
January 2019

Anaemia requiring red blood cell transfusion is associated with unfavourable 90-day survival in surgical patients with sepsis.

BMC Res Notes 2018 Dec 11;11(1):879. Epub 2018 Dec 11.

Department of Anesthesiology, University Medical Center, Georg August University, Goettingen, Germany.

Objective: The mortality associated with sepsis remains unacceptably high, despite modern high-quality intensive care. Based on the results from previous studies, anaemia and its management in patients with sepsis appear to impact outcomes; however, the transfusion policy is still being debated, and the ideal approach may be extremely specific to the individual. This study aimed to investigate the long-term impact of anaemia requiring red blood cell (RBC) transfusion on mortality and disease severity in patients with sepsis. We studied a general surgical intensive care unit (ICU) population, excluding cardiac surgery patients. 435 patients were enrolled in this observational study between 2012 and 2016.

Results: Patients who received RBC transfusion between 28 days before and 28 days after the development of sepsis (n = 302) exhibited a significantly higher 90-day mortality rate (34.1% vs 19.6%; P = 0.004, Kaplan-Meier analysis). This association remained significant after adjusting for confounders in the multivariate Cox regression analysis (hazard ratio 1.68; 95% confidence interval 1.03-2.73; P = 0.035). Patients who received transfusions also showed significantly higher morbidity scores, such as SOFA scores, and ICU lengths of stay compared to patients without transfusions (n = 133). Our results indicate that anaemia and RBC transfusion are associated with unfavourable outcomes in patients with sepsis.
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http://dx.doi.org/10.1186/s13104-018-3988-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6290543PMC
December 2018

PI3K: A master regulator of brain metastasis-promoting macrophages/microglia.

Glia 2018 11 25;66(11):2438-2455. Epub 2018 Oct 25.

Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany.

Mutations and activation of the PI3K signaling pathway in breast cancer cells have been linked to brain metastases. However, here we describe that in some breast cancer brain metastases samples the protein expression of PI3K signaling components is restricted to the metastatic microenvironment. In contrast to the therapeutic effects of PI3K inhibition on the breast cancer cells, the reaction of the brain microenvironment is less understood. Therefore we aimed to quantify the PI3K pathway activity in breast cancer brain metastasis and investigate the effects of PI3K inhibition on the central nervous system (CNS) microenvironment. First, to systematically quantify the PI3K pathway activity in breast cancer brain metastases, we performed a prospective biomarker study using a reverse phase protein array (RPPA). The majority, namely 30 out of 48 (62.5%) brain metastatic tissues examined, revealed high PI3K signaling activity that was associated with a median overall survival (OS) of 9.41 months, while that of patients, whose brain metastases showed only moderate or low PI3K activity, amounted to only 1.93 and 6.71 months, respectively. Second, we identified PI3K as a master regulator of metastasis-promoting macrophages/microglia during CNS colonization; and treatment with buparlisib (BKM120), a pan-PI3K Class I inhibitor with a good blood-brain-barrier penetrance, reduced their metastasis-promoting features. In conclusion, PI3K signaling is active in the majority of breast cancer brain metastases. Since PI3K inhibition does not only affect the metastatic cells but also re-educates the metastasis-promoting macrophages/microglia, PI3K inhibition may hold considerable promise in the treatment of brain metastasis and the respective microenvironment.
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http://dx.doi.org/10.1002/glia.23485DOI Listing
November 2018

The CTLA-4 rs231775 GG genotype is associated with favorable 90-day survival in Caucasian patients with sepsis.

Sci Rep 2018 10 11;8(1):15140. Epub 2018 Oct 11.

Department of Anesthesiology, University Medical Center, Georg August University, Robert-Koch-Str. 40, D-37075, Goettingen, Germany.

Cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) is a surface protein on T cells, that has an inhibitory effect on the host immune reaction and prevents overreaction of the immune system. Because the functional single-nucleotide polymorphism (SNP) rs231775 of the CTLA-4 gene is associated with autoimmune diseases and because of the critical role of the immune reaction in sepsis, we intended to examine the effect of this polymorphism on survival in patients with sepsis. 644 septic adult Caucasian patients were prospectively enrolled in this study. Patients were followed up for 90 days. Mortality risk within this period was defined as primary outcome parameter. Kaplan-Meier survival analysis revealed a significantly lower 90-day mortality risk among GG homozygous patients (n = 101) than among A allele carriers (n = 543; 22% and 32%, respectively; p = 0.03565). Furthermore, the CTLA-4 rs231775 GG genotype remained a significant covariate for 90-day mortality risk after controlling for confounders in the multivariate Cox regression analysis (hazard ratio: 0.624; 95% CI: 0.399-0.975; p = 0.03858). In conclusion, our study provides the first evidence for CTLA-4 rs231775 as a prognostic variable for the survival of patients with sepsis and emphasizes the need for further research to reveal potential functional associations between CTLA-4 and the immune pathophysiology of sepsis.
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http://dx.doi.org/10.1038/s41598-018-33246-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6181961PMC
October 2018

FGFR3 mRNA overexpression defines a subset of oligometastatic colorectal cancers with worse prognosis.

Oncotarget 2018 Aug 14;9(63):32204-32218. Epub 2018 Aug 14.

Institute of Pathology, University Hospital Göttingen, Göttingen, Germany.

Objectives: Metastatic colorectal cancer (CRC) remains a leading cause of cancer related deaths. Patients with oligometastatic liver disease represent a clinical subgroup with heterogeneous course. Until now, biomarkers to characterize outcome and therapeutic options have not been fully established.

Methods: We investigated the prevalence of FGFR alterations in a total of 140 primary colorectal tumors and 63 liver metastases of 55 oligometastatic CRC patients. FGF receptors () and their ligands ( and ) were analyzed for gene amplifications and rearrangements as well as for RNA overexpression . Results were correlated with clinico-pathologic data and molecular subtypes.

Results: Primary tumors showed (6.3%) and (2.2%) amplifications as well as FGFR1 (10.1%), FGFR2 (5.5%) and FGFR3 (16.2%) overexpression. In metastases, we observed amplifications (4.8%) as well as FGFR1 (8.5%) and FGFR3 (14.9%) overexpression. Neither amplifications nor gene rearrangements were observed. FGFR3 overexpression was significantly associated with shorter overall survival in metastases (mOS 19.9 vs. 47.4 months, HR=3.14, p=0.0152), but not in primary CRC (HR=1.01, p=0.985). Although rare, also amplification was indicative of worse outcome (mOS 12.6 vs. 47.4 months, HR=8.83, p=0.00111).

Conclusions: We provide the so far most comprehensive analysis of FGFR alterations in primary and metastatic CRC. We describe FGFR3 overexpression in 15% of CRC patients with oligometastatic liver disease as a prognosticator for poor outcome. Recently FGFR3 overexpression has been shown to be a potential therapeutic target. Therefore, we suggest focusing on this subgroup in upcoming clinical trials with FGFR-targeted therapies.
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http://dx.doi.org/10.18632/oncotarget.25941DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6114946PMC
August 2018

Using RNA-Seq Data for the Detection of a Panel of Clinically Relevant Mutations.

Stud Health Technol Inform 2018 ;253:217-221

Department of Medical Statistics, University Medical Center Göttingen.

Somatic single nucleotide variants (SNVs) are genomic events with increasing implications in cancer treatment. The clinical standard for SNVs detection is whole genome/exome sequencing (WGS/WES) in matched tumor-normal samples. Yet, this is a very costly approach both economically and biologically and very often only tumor samples are sequenced. On the other hand, RNA sequencing (RNA-Seq) is the most popular technology to study gene expression, and has also the potential for a cost-effective identification of SNVs as an alternative to tumor-only WES. Here we present a method for the identification of SNVs in tumor-only RNA-Seq data putting a special focus on a small panel of clinically relevant SNVs. For evaluation purposeswe analyzed matched tumor-normal WEStumor-only RNA-Seq data from 14 cancer patients. We compared SNVs detected in i) RNA-Seq by our method, ii) WES tumor-only by Mutect2 and iii) WES matched tumor-normal by Mutect2. We did a detailed evaluation for a reduced panel of clinically relevant SNVs and reliably identified in RNA-Seq data a subset of mutations for which we had pathological annotation. Hence, RNA-Seq rises as a cost-effective option to detect in parallel gene expression as well as a small panel of clinically relevant SNVs in research.
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November 2018

Comparative proteomics reveals a diagnostic signature for pulmonary head-and-neck cancer metastasis.

EMBO Mol Med 2018 09;10(9)

Department of Medicine II, Hematology/Oncology, Goethe University, Frankfurt, Germany

Patients with head-and-neck cancer can develop both lung metastasis and primary lung cancer during the course of their disease. Despite the clinical importance of discrimination, reliable diagnostic biomarkers are still lacking. Here, we have characterised a cohort of squamous cell lung (SQCLC) and head-and-neck (HNSCC) carcinomas by quantitative proteomics. In a training cohort, we quantified 4,957 proteins in 44 SQCLC and 30 HNSCC tumours. A total of 518 proteins were found to be differentially expressed between SQCLC and HNSCC, and some of these were identified as genetic dependencies in either of the two tumour types. Using supervised machine learning, we inferred a proteomic signature for the classification of squamous cell carcinomas as either SQCLC or HNSCC, with diagnostic accuracies of 90.5% and 86.8% in cross- and independent validations, respectively. Furthermore, application of this signature to a cohort of pulmonary squamous cell carcinomas of unknown origin leads to a significant prognostic separation. This study not only provides a diagnostic proteomic signature for classification of secondary lung tumours in HNSCC patients, but also represents a proteomic resource for HNSCC and SQCLC.
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http://dx.doi.org/10.15252/emmm.201708428DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6127892PMC
September 2018

TGFβ1 regulates HGF-induced cell migration and hepatocyte growth factor receptor MET expression via C-ets-1 and miR-128-3p in basal-like breast cancer.

Mol Oncol 2018 09 30;12(9):1447-1463. Epub 2018 Jul 30.

Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany.

Breast cancer is the most common cancer in women worldwide. The tumor microenvironment contributes to tumor progression by inducing cell dissemination from the primary tumor and metastasis. TGFβ signaling is involved in breast cancer progression and is specifically elevated during metastatic transformation in aggressive breast cancer. In this study, we performed genomewide correlation analysis of TGFBR2 expression in a panel of 51 breast cancer cell lines and identified that MET is coregulated with TGFBR2. This correlation was confirmed at the protein level in breast cancer cell lines and human tumor tissues. Flow cytometric analysis of luminal and basal-like breast cancer cell lines and examination of 801 tumor specimens from a prospective cohort of breast cancer patients using reverse phase protein arrays revealed that expression of TGFBR2 and MET is increased in basal-like breast cancer cell lines, as well as in triple-negative breast cancer tumor tissues, compared to other subtypes. Using real-time cell analysis technology, we demonstrated that TGFβ1 triggered hepatocyte growth factor (HGF)-induced and MET-dependent migration in vitro. Bioinformatic analysis predicted that TGFβ1 induces expression of C-ets-1 as a candidate transcription factor regulating MET expression. Indeed, TGFβ1-induced expression of ETS1 and breast cancer cell migration was blocked by knockdown of ETS1. Further, we identified that MET is a direct target of miR-128-3p and that this miRNA is negatively regulated by TGFβ1. Overexpression of miR-128-3p reduced MET expression and abrogated HGF-induced cell migration of invasive breast cancer cells. In conclusion, we have identified that TGFβ1 regulates HGF-induced and MET-mediated cell migration, through positive regulation of C-ets-1 and negative regulation of miR-128-3p expression in basal-like breast cancer cell lines and in triple-negative breast cancer tissue.
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http://dx.doi.org/10.1002/1878-0261.12355DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6120235PMC
September 2018