Nadina Ortiz-Brüchle

Background: Cholangiocarcinoma (CCA) are aggressive bile duct cancers with a poor prognosis for which there are only few established prognostic biomarkers and molecular targets available. The gene ITIH5, a known class II tumor suppressor gene (C2TSG), encodes a secreted protein of the extracellular matrix mediating tumor suppressive properties. Recently, it was surprisingly found that the ITIH5 protein is specifically upregulated in CCAs and that ITIH5 detection in blood could be an excellent liquid biopsy marker for indicating the presence of a CCA tumor in a patient. We therefore investigated whether patients with CCAs with abundant versus low ITIH5 protein expression also differ in their prognosis. Methods: To clarify this question, a large CCA cohort (n = 175) was examined using immunohistochemistry on a tissue microarray (TMA). Results: Abundant ITIH5 expression in CCA was associated with favorable survival, a low UICC stage and the absence of perineural invasion (PNI). Conclusions: ITIH5 has biomarker potential not only for the early detection of CCA from blood-based liquid biopsies but also as a prognostic tissue biomarker for risk stratification. Our results suggest that the upregulation of ITIH5 is particularly abundant in intrahepatic CCAs (iCCA). The mechanisms mediating the strong initial upregulation of ITIH5 during the oncogenic transformation of bile duct cells are still unclear.

In the 2016 WHO classification of genitourinary tumors Muellerian tumors of the urinary tract (MTUT) comprise clear cell adenocarcinomas and endometrioid carcinomas. Since these rare tumors remained understudied, we aimed to characterize their molecular background by performing DNA- and RNA-based targeted panel sequencing. All tumors (n = 11) presented single nucleotide alterations (SNVs), with ARID1A mutations being the most prevalent (5/11, 45%). Besides frequent ARID1A mutations, loss of ARID1A protein is not a suitable marker since protein expression is (partly) preserved also in mutated cases. Copy number alterations (CNVs) were found in 64% of cases (7/11), exclusively gene amplifications. Interestingly, a functionally relevant RSPO2 gene fusion/microdeletion was discovered in the endometrioid adenocarcinoma case. Comparing our findings with mutational profiles of other tumor entities, absence of TERT promoter mutations argues for a non-urothelial origin. No similarities were also found between MTUT and kidney cancers while parallels were observed for specific SNVs with endometrial carcinomas. In conclusion, immunohistochemical PAX8-positivity and lack of TERT promoter mutations could serve as key diagnostic features in difficult cases. Thus, understanding the molecular background of these tumors helps to refine treatment options and offers the possibility of targeted therapies in cases where needed.

Dysfunction of the SWI/SNF complex has been observed in various cancers including urothelial carcinomas. However, the clinical impact of the SWI/SNF complex in squamous-differentiated bladder cancers (sq-BLCA) remains unclear. Therefore, we aimed to analyze potential expression loss and genetic alterations of (putative) key components of the SWI/SNF complex considering the co-occurrence of genetic driver mutations and PD-L1 expression as indicators for therapeutic implications. Assessment of ARID1A, SMARCA2, SMARCA4, SMARCB1/INI1, SMARCC1, SMARCC2 and PBRM1 mutations in a TCGA data set of sq-BLCA (n = 45) revealed that ARID1A was the most frequently altered SWI/SNF gene (15%) while being associated with protein downregulation. Genetic alterations and loss of ARID1A were confirmed by Targeted Next Generation Sequencing (NGS) (3/6) and immunohistochemistry (6/116). Correlation with further mutational data and PD-L1 expression revealed co-occurrence of ARID1A loss and TP53 mutations, while positive correlations with other driver mutations such as PIK3CA were not observed. Finally, a rare number of sq-BLCA samples were characterized by both ARID1A protein loss and strong PD-L1 expression suggesting a putative benefit upon immune checkpoint inhibitor therapy. Hence, for the first time, our data revealed expression loss of SWI/SNF subunits in sq-BLCA, highlighting ARID1A as a putative target of a small subgroup of patients eligible for novel therapeutic strategies.

Molecular alterations in cancer can cause phenotypic changes in tumor cells and their microenvironment. Routine histopathology tissue slides, which are ubiquitously available, can reflect such morphological changes. Here, we show that deep learning can consistently infer a wide range of genetic mutations, molecular tumor subtypes, gene expression signatures and standard pathology biomarkers directly from routine histology. We developed, optimized, validated and publicly released a one-stop-shop workflow and applied it to tissue slides of more than 5,000 patients across multiple solid tumors. Our findings show that a single deep learning algorithm can be trained to predict a wide range of molecular alterations from routine, paraffin-embedded histology slides stained with hematoxylin and eosin. These predictions generalize to other populations and are spatially resolved. Our method can be implemented on mobile hardware, potentially enabling point-of-care diagnostics for personalized cancer treatment. More generally, this approach could elucidate and quantify genotype–phenotype links in cancer.

Ziliopathien stellen eine Gruppe von größtenteils syndromalen Erkrankungen dar, denen pathomechanistisch eine Funktionseinschränkung der primären Zilien bei den Patienten gemein ist. Veränderungen in einer Vielzahl von Genen wurden bereits beschrieben. Zystische Nierenveränderungen, Leberfibrose und Hirnanomalien sind häufige klinische Merkmale der Ziliopathien, zu denen beispielsweise das Bardet-Biedl-Syndrom, das Joubert-Syndrom und die Nephronophthise zählen. Aufgrund der ausgeprägten Heterogenie ist eine rationelle molekulargenetische Diagnostik oft schwierig. A priori ist bei blutsverwandten Familien von homozygoten Haplotypen für den krankheitsrelevanten Lokus auszugehen. In diesen Familien ist daher eine Homozygotie-Testung mittels SNP-Arrays zur Vorauswahl von potentiellen Kandidatengenen sinnvoll. Wir präsentieren hier unsere Erfahrungen mit dieser Methodik in etwa 20 blutsverwandten Familien. Dabei konnten zunächst bei acht Kontrollfamilien die von Mutationen betroffenen Gene klar als Kandidatengen bestätigt werden. In vier der im Vorfeld nicht aufgeklärten Familien wurden die mittels Array identifizierten Kandidatengene untersucht und homozygote Mutationen detektiert. In Familien mit zusätzlichen Ziliopathie-untypischen Symptomen wurde außerdem eine Auswertung bezüglich des molekularen Karyotyps durchgeführt. Dabei fand sich jedoch bisher bei keinem Patienten eine chromosomale Auffälligkeit. Es wurden ebenfalls keine größeren Deletionen in den Kandidatengenen identifiziert. Bei zwei Familien konnte die Diagnostik in Hinblick auf die für die jeweilige Verdachtsdiagnose bekannten Ziliopathie-Syndrom-Gene abgebrochen werden, da hier keine Homozygotie für die bekannten Gene identifiziert werden konnte. Die Analyse der weiteren Familien dauert derzeit noch an. Anhand der hier aufgeführten Daten werden wir die Vorteile und Limitationen der Homozygotie-Testung mittels SNP-Array bei Ziliopathie-Patienten in blutsverwandten Familien herausarbeiten.