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Hypomethylating agents decitabine and azacytidine are regarded as interchangeable in the treatment of acute myeloid leukemia (AML). However, their mechanisms of action remain incompletely understood, and predictive biomarkers for HMA efficacy are lacking. Here, we show that the bioactive metabolite decitabine triphosphate, but not azacytidine triphosphate, functions as activator and substrate of the triphosphohydrolase SAMHD1 and is subject to SAMHD1-mediated inactivation. Retrospective immunohistochemical analysis of bone marrow specimens from AML patients at diagnosis revealed that SAMHD1 expression in leukemic cells inversely correlates with clinical response to decitabine, but not to azacytidine. SAMHD1 ablation increases the antileukemic activity of decitabine in AML cell lines, primary leukemic blasts, and xenograft models. AML cells acquire resistance to decitabine partly by SAMHD1 up-regulation. Together, our data suggest that SAMHD1 is a biomarker for the stratified use of hypomethylating agents in AML patients and a potential target for the treatment of decitabine-resistant leukemia.
Heißt es "er buk" oder "er backte", "staubgesaugt" oder "gestaubsaugt", "den Pilot" oder "den Piloten"? Derlei Zweifelsfragen bringen einen immer wieder ins Grübeln. Sie sind jedoch kein Beleg des Unwissens – im Gegenteil. Das Nachdenken darüber bringt Licht in die Natur von Sprache und Sprachwandel.
Comparative proteomics reveals a diagnostic signature for pulmonary head‐and‐neck cancer metastasis
(2018)
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.
The transcription factor Meis1 drives myeloid leukemogenesis in the context of Hox gene overexpression but is currently considered undruggable. We therefore investigated whether myeloid progenitor cells transformed by Hoxa9 and Meis1 become addicted to targetable signaling pathways. A comprehensive (phospho)proteomic analysis revealed that Meis1 increased Syk protein expression and activity. Syk upregulation occurs through a Meis1-dependent feedback loop. By dissecting this loop, we show that Syk is a direct target of miR-146a, whose expression is indirectly regulated by Meis1 through the transcription factor PU.1. In the context of Hoxa9 overexpression, Syk signaling induces Meis1, recapitulating several leukemogenic features of Hoxa9/Meis1-driven leukemia. Finally, Syk inhibition disrupts the identified regulatory loop, prolonging survival of mice with Hoxa9/Meis1-driven leukemia.
Purpose: Preoperative (neoadjuvant) chemoradiotherapy (CRT) and total mesorectal excision is the standard treatment for rectal cancer patients (UICC stage II/III). Up to one-third of patients treated with CRT achieve a pathological complete response (pCR). These patients could be spared from surgery and its associated morbidity and mortality, and assigned to a “watch and wait” strategy. However, reliably identifying pCR based on clinical or imaging parameters remains challenging.
Experimental design: We generated gene-expression profiles of 175 patients with locally advanced rectal cancer enrolled in the CAO/ARO/AIO-94 and -04 trials. One hundred and sixty-one samples were used for building, training and validating a predictor of pCR using a machine learning algorithm. The performance of the classifier was validated in three independent cohorts, comprising 76 patients from (i) the CAO/ARO/AIO-94 and -04 trials (n = 14), (ii) a publicly available dataset (n = 38) and (iii) in 24 prospectively collected samples from the TransValid A trial.
Results: A 21-transcript signature yielded the best classification of pCR in 161 patients (Sensitivity: 0.31; AUC: 0.81), when not allowing misclassification of non-complete-responders (False-positive rate = 0). The classifier remained robust when applied to three independent datasets (n = 76).
Conclusion: The classifier can identify >1/3 of rectal cancer patients with a pCR while never classifying patients with an incomplete response as having pCR. Importantly, we could validate this finding in three independent datasets, including a prospectively collected cohort. Therefore, this classifier could help select rectal cancer patients for a “watch and wait” strategy.
Translational relevance: Forgoing surgery with its associated side effects could be an option for rectal cancer patients if the prediction of a pathological complete response (pCR) after preoperative chemoradiotherapy would be possible. Based on gene-expression profiles of 161 patients a classifier was developed and validated in three independent datasets (n = 76), identifying over 1/3 of patients with pCR, while never misclassifying a non-complete-responder. Therefore, the classifier can identify patients suited for “watch and wait”.
In-depth analyses of cancer cell proteomes are needed to elucidate oncogenic pathomechanisms, as well as to identify potential drug targets and diagnostic biomarkers. However, methods for quantitative proteomic characterization of patient-derived tumors and in particular their cellular subpopulations are largely lacking. Here we describe an experimental set-up that allows quantitative analysis of proteomes of cancer cell subpopulations derived from either liquid or solid tumors. This is achieved by combining cellular enrichment strategies with quantitative Super-SILAC-based mass spectrometry followed by bioinformatic data analysis. To enrich specific cellular subsets, liquid tumors are first immunophenotyped by flow cytometry followed by FACS-sorting; for solid tumors, laser-capture microdissection is used to purify specific cellular subpopulations. In a second step, proteins are extracted from the purified cells and subsequently combined with a tumor-specific, SILAC-labeled spike-in standard that enables protein quantification. The resulting protein mixture is subjected to either gel electrophoresis or Filter Aided Sample Preparation (FASP) followed by tryptic digestion. Finally, tryptic peptides are analyzed using a hybrid quadrupole-orbitrap mass spectrometer, and the data obtained are processed with bioinformatic software suites including MaxQuant. By means of the workflow presented here, up to 8,000 proteins can be identified and quantified in patient-derived samples, and the resulting protein expression profiles can be compared among patients to identify diagnostic proteomic signatures or potential drug targets.
Sleep is regulated in a time-of-day dependent manner and profits working memory. However, the impact of the circadian timing system as well as contributions of specific sleep properties to this beneficial effect remains largely unexplored. Moreover, it is unclear to which extent inter-individual differences in sleep-wake regulation depend on circadian phase and modulate the association between sleep and working memory. Here, sleep electroencephalography (EEG) was recorded during a 40-h multiple nap protocol, and working memory performance was assessed by the n-back task 10 times before and after each scheduled nap sleep episode. Twenty-four participants were genotyped regarding a functional polymorphism in adenosine deaminase (rs73598374, 12 G/A-, 12 G/G-allele carriers), previously associated with differences in sleep-wake regulation. Our results indicate that genotype-driven differences in sleep depend on circadian phase: heterozygous participants were awake longer and slept less at the end of the biological day, while they exhibited longer non rapid eye movement (NREM) sleep and slow wave sleep concomitant with reduced power between 8–16 Hz at the end of the biological night. Slow wave sleep and NREM sleep delta EEG activity covaried positively with overall working memory performance, independent of circadian phase and genotype. Moreover, REM sleep duration benefitted working memory particularly when occurring in the early morning hours and specifically in heterozygous individuals. Even though based on a small sample size and thus requiring replication, our results suggest genotype-dependent differences in circadian sleep regulation. They further indicate that REM sleep, being under strong circadian control, boosts working memory performance according to genotype in a time-of-day dependent manner. Finally, our data provide first evidence that slow wave sleep and NREM sleep delta activity, majorly regulated by sleep homeostatic mechanisms, is linked to working memory independent of the timing of the sleep episode within the 24-h cycle.
Diese Untersuchung beschäftigt sich mit der Morphosyntax pronominaler Partitivanaphern im kontinentalwestgermanischen Dialektkontinuum im Allgemeinen und im deutschen (insbesondere hessischen) Sprachraum im Speziellen. Schwerpunkte sind dabei die sprachgeografische Verteilung, die morphosyntaktische Variation und die strukturelle Analyse pronominaler Ausdrucksmittel der unbestimmten Teilmenge. Es werden traditionell dialektologische Erkenntnisinteressen (Raumstruktur syntaktischer Variablen und Verlauf syntaktischer Isoglossen) mit Fragestellungen der (theoretisch orientierten) Syntaxforschung verbunden. Außerdem erfolgt erstmals eine wirklich sprachübergreifende Behandlung der verschiedenen Systeme pronominaler Partitivität, zum einen innerhalb der (West-)Germania, zum anderen durch den Einbezug (zentral-)romanischer Sprachen, um Unterschiede und Gemeinsamkeiten auf der Mikro- und Mesoebene herauszuarbeiten. Die gewählte Methode ist nicht nur kontrastiv, sondern auch geolinguistisch fundiert, insofern als morphologische Formen und syntaktische Variation im Raum abgebildet werden, wodurch nicht zuletzt auch interessante Korrelationen und Anti-Korrelationen in den Daten bestätigt bzw. entdeckt werden konnten.
Nach einer Gegenstandsbestimmung der morphosyntaktischen Variable und ihrer Varianten (Inventarisierung und Typisierung) sowie des Variationsrahmens (areal-horizontal, vertikal, morphosyntaktisch, historisch, idiolektal etc.) wird zunächst das DFG-Projekt „Syntax hessischer Dialekte“ (SyHD) vorgestellt, das die empirische Basis zur Untersuchung lieferte. Dabei werden generelle und spezifische Fragen der Datengewinnung (multivariate Methode mit indirekten und direkten Elementen) sowie der Datenanalyse und -interpretation (Instrument der Kartierung) diskutiert. Den Hauptteil der Arbeit bildet die diatopische, diachrone und distributionell-syntaktische Variation der Systeme pronominaler Partitivität. Als die vier Hauptstrategien zum Ausdruck partitiv-anaphorischer Referenz innerhalb des deutschsprachigen Gebiets finden sich das konservative System versteinerter Pronominalgenitive wie „(d)(e)r(e)“, „s(e)n“ und „es“ (vor allem in einem mitteldeutschen Streifen und randdialektal) - Relikte eines ehemals umfassenderen genitivbasierten Systems der Partitivität -, das sprachgeschichtlich junge und typologisch auffällige indefinit-partitive Pronomen „welch-“/„we(l)k-“ (im Nieder-/Norddeutschen und in der Standardsprache) sowie schließlich die innovativen Systeme der Null-Anapher (im Alemannischen bzw. Südwesten) und des generalisierten Indefinitpronomens „ein-“ (im Bairischen bzw. Südosten). Wenngleich sich diese areale Distribution im zentral gelegenen und daher unter dem Einfluss nahezu aller Strategien stehenden Hessen als Kleinraum bestätigt - mit Ausnahme der weitgehenden Abwesenheit des „ein“-Systems -, so zeigen sich doch einige überraschende Ergebnisse wie beispielsweise ein kategorialer Unterschied nach Numerus und zum Teil Genus bei der Vitalität der Genitivpartikeln. Sprachhistorisch können zwei Arten von Wandel beim Genitiv-System identifiziert werden: systeminterne Veränderungen (durch Merkmals- oder Formverlust) und systemexterne Verdrängungsprozesse (durch Ausbreitung der innovativen Ausdrucksformen, was in einem Dialekt bzw. intraindividuell zu konkurrierenden oder Mischsystemen führen kann). Darüber hinaus sind mit Blick auf die Art und Weise der Veränderungen für Sprachwandelprozesse allgemein typische zyklische Abfolgen von Abschwächung und Verstärkung erkennbar. In Bezug auf die syntaktische Distribution werden insbesondere die Genitivanaphern auf ihre Kompatibilität mit nominalen Modifikatoren wie Numeralien/(schwachen) Quantoren, „flektierten“ Zahlwörtern (Schwa), Adjektiven, verschiedenen Arten von Präpositionalphrasen sowie Relativ- vs. Komplementsätzen hin untersucht und - funktional wie formal - mit ihrem niederländischen partitiven/quantitativen Äquivalent „er“ sowie den romanischen, in ein partitives System integrierten Pronomina fr. „en“/it. „ne“ verglichen. Für die deutschen Partitivanaphern ergibt sich daraus Evidenz für zwei unterschiedliche Pronominalisierungsebenen. Abschließend wird das Phänomen in die allgemeine Diskussion um nominale Ellipsen eingebettet (Elision und Pronominalisierung). Aufgrund der Evaluation der in der Literatur diskutierten Lizenzierungsansätze anhand neuer dialektaler und typologischer Daten wird hier ein flexions-/kongruenzbasierter Ansatz favorisiert (Rolle von Adjektivmorphologie bzw. generell von unterschiedlichen Flexionssystemen, etwa im Deutschen vs. Englischen).
Malignant germ cell tumors (GCT) are the most common malignant tumors in young men between 18 and 40 years. The correct identification of histological subtypes, in difficult cases supported by immunohistochemistry, is essential for therapeutic management. Furthermore, biomarkers may help to understand pathophysiological processes in these tumor types. Two GCT cell lines, TCam-2 with seminoma-like characteristics, and NTERA-2, an embryonal carcinoma-like cell line, were compared by a quantitative proteomic approach using high-resolution mass spectrometry (MS) in combination with stable isotope labelling by amino acid in cell culture (SILAC). We were able to identify 4856 proteins and quantify the expression of 3936. 347 were significantly differentially expressed between the two cell lines. For further validation, CD81, CBX-3, PHF6, and ENSA were analyzed by western blot analysis. The results confirmed the MS results. Immunohistochemical analysis on 59 formalin-fixed and paraffin-embedded (FFPE) normal and GCT tissue samples (normal testis, GCNIS, seminomas, and embryonal carcinomas) of these proteins demonstrated the ability to distinguish different GCT subtypes, especially seminomas and embryonal carcinomas. In addition, siRNA-mediated knockdown of these proteins resulted in an antiproliferative effect in TCam-2, NTERA-2, and an additional embryonal carcinoma-like cell line, NCCIT. In summary, this study represents a proteomic resource for the discrimination of malignant germ cell tumor subtypes and the observed antiproliferative effect after knockdown of selected proteins paves the way for the identification of new potential drug targets.
Unquestionably (or: undoubtedly), every competent speaker has already come to doubt with respect to the question of which form is correct or appropriate and should be used (in the standard language) when faced with two or more almost identical competing variants of words, word forms or sentence and phrase structure (e.g. German "Pizzas/Pizzen/Pizze" 'pizzas', Dutch "de drie mooiste/mooiste drie stranden" 'the three most beautiful/most beautiful three beaches', Swedish "större än jag/mig" 'taller than I/me'). Such linguistic uncertainties or "cases of doubt" (cf. i.a. Klein 2003, 2009, 2018; Müller & Szczepaniak 2017; Schmitt, Szczepaniak & Vieregge 2019; Stark 2019 as well as the useful collections of data of Duden vol. 9, Taaladvies.net, Språkriktighetsboken etc.) systematically occur also in native speakers and they do not necessarily coincide with the difficulties of second language learners. In present-day German, most grammatical uncertainties occur in the domains of inflection (nominal plural formation, genitive singular allomorphy of strong masc./neut. nouns, inflectional variation of weak masc. nouns, strong/weak adjectival inflection and comparison forms, strong/weak verb forms, perfect auxiliary selection) and word-formation (linking elements in compounds, separability of complex verbs). As for syntax, there are often doubts in connection with case choice (pseudo-partitive constructions, prepositional case government) and agreement (especially due to coordination or appositional structures). This contribution aims to present a contrastive approach to morphological and syntactic uncertainties in contemporary Germanic languages (mostly German, Dutch, and Swedish) in order to obtain a broader and more fine-grained typology of grammatical instabilities and their causes. As will be discussed, most doubts of competent speakers - a problem also for general linguistic theory - can be attributed to processes of language change in progress, to language or variety contact, to gaps and rule conflicts in the grammar of every language or to psycholinguistic conditions of language processing. Our main concerns will be the issues of which (kinds of) common or different critical areas there are within Germanic (and, on the other hand, in which areas there are no doubts), which of the established (cross-linguistically valid) explanatory approaches apply to which phenomena and, ultimately, the question whether the new data reveals further lines of explanation for the empirically observable (standard) variation.