22.12.2021 / RESEARCH

Epigenetic Priming in Chronic Liver Disease Impacts the Transcriptional and Genetic Landscapes of Hepatocellular Carcinoma

Epigenetic priming could influence disease outcome.

Hepatocellular carcinomas (HCCs) usually arise from chronic liver disease (CLD). Pre-cancerous cells in chronically inflamed environments may be 'epigenetically primed', sensitizing them to oncogenic transformation. The research group of Dr. Salvatore Piscuoglio investigated whether epigenetic priming in CLD may affect HCC outcomes by influencing the genomic and transcriptomic landscapes of HCC. In this study, Gallon and colleagues show that CLD and HCC samples from the same patient share broad transcriptional and epigenetic alterations which are compounded in HCC, highlighting how methylation changes in CLD may help not only to create a transcriptional landscape favorable for HCC emergence but that the influence of these changes may extend to consequences for disease outcomes. The study has been published in Molecular Oncology. For further information, please contact Dr. Salvatore Piscuoglio.

19.08.2021 / RESEARCH

Systematic Identification of Novel Cancer Genes Through Analysis of Deep shRNA Perturbation Screens

Overview of the APSiC algorithm

Systematic perturbation screens provide comprehensive resources for the elucidation of cancer driver genes. The perturbation of many genes in relatively few cell lines in such functional screens necessitates the development of specialized computational tools with sufficient statistical power. The research group of Dr. Salvatore Piscuoglio developed APSiC (Analysis of Perturbation Screens for identifying novel Cancer genes) to identify genetic drivers and effectors in perturbation screens even with few samples. Applying APSiC to the shRNA screen Project DRIVE (deep RNAi interrogation of viability effects in cancer), APSiC identified well-known and novel putative mutational and amplified cancer genes across all cancer types and in specific cancer types. Additionally, APSiC discovered tumor-promoting and tumor-suppressive effectors, respectively, for individual cancer types, including genes involved in cell cycle control, Wnt/β-catenin and hippo signalling pathways. In this study, they demonstrated that LRRC4B, a putative novel tumor-suppressive effector, suppresses proliferation by delaying cell cycle and modulates apoptosis in breast cancer. APSiC is a robust statistical framework for discovery of novel cancer genes through analysis of large-scale perturbation screens. The study has been published in Nucleic Acids Research. For further information, please contact Dr. Salvatore Piscuoglio. The analysis of DRIVE using APSiC is provided as a web portal at the following link:

08.06.2021 / RESEARCH

Pathology Basel Involved in Understanding the Mechanisms of Pancreatic Endocrine Dysfunction in COVID-19

SARS-CoV-2 spike mRNA expression (red dots) was detected within pancreatic β-cells (green). The nuclei were stained using DAPI (blue).

Clinical studies indicate that SARS-CoV-2 infection is associated with new-onset diabetes. The results, just published in the journal Cell Metabolism, contribute to a better understanding of the mechanisms of pancreatic endocrine dysfunction in COVID-19. This study was performed in a joint collaboration between the Institute of Pathology in Basel (lead contact: PD Dr. Matthias Matter) and the Stanford University School of Medicine.

In this study, autopsy material from patients in Basel was used to show that SARS-CoV-2 infects the insulin producing beta cells of the pancreas, primarily due to the higher expression of the viral receptor neuropilin-1 (NRP1), which is an alternative entry for SARS-CoV-2 besides ACE2. SARS-CoV-2 infection of beta-cells leads to a decrease in insulin production and induces apoptosis. Both can be counteracted by blocking NRP1 - the reduction in insulin production as well as beta-cell apoptosis. Phosphoproteomic pathway analysis of infected islets also indicated an apoptotic beta-cell signature similar to that observed in type 1 diabetes. The study was conducted with the support of the Botnar Research Centre for Child Health, Basel, Switzerland, among others. Please contact PD Dr. Matthias Matter for more information about this research.

06.05.2021 / HONORS AND AWARDS

Auszeichnung für die Hämatopathologie des Unispitals Basel

Prof. Stefan Dirnhofer (links) und Prof. Alexandar Tzankov

Prof. Stefan Dirnhofer und Prof. Alexandar Tzankov wurden in höchste Ämter am Kongress der europäischen Gesellschaft für Hämatopathologie (EAHP) gewählt.

Am diesjährigen Kongress der europäischen Gesellschaft für Hämatopathologie wurde Prof. Stefan Dirnhofer, Chefarzt Stellvertreter Pathologie USB und Leiter des Lymphom-Referenzzentrums der SAKK zum «President – elect» gewählt. Er ist damit Mitglied des Executive Boards und wird im September 2022 für zwei Jahre Präsident dieser - nach der amerikanischen Gesellschaft für Hämatopathologie - grössten hämatopathologischen Fachgesellschaft weltweit. In dieser Funktion wird er auch der erste Präsident aus der Schweiz seit deren Gründung Mitte der 80er Jahre sein. 

Gleichzeitig hat die europäische Arbeitsgruppe für Knochenmarkpathologie Prof. Alexandar Tzankov, Fachbereichsleiter Histopathologie und Autopsie, Pathologie USB zum «Chair – elect» gewählt. Er wird daher im September 2022 ebenfalls für zwei Jahre Vorsitzender dieser Arbeitsgruppe und damit ex-officio Mitglied des Executive Boards der EAHP.

Dies stellt eine grosse Auszeichnung und Wertschätzung der erfolgreichen Arbeit der Hämatopathologie am USB über die letzten Jahre dar und steigert weiter deren Visibilität und Reputation.

30.03.2021 / RESEARCH

ADSL is oncogenic in colorectal cancer by causing mitochondrial dysfunction and independent activation of NRF2 and mTOR-MYC-axis

Schematic representation of the putative oncogenic role of ADSL in colorectal carcinogenesis

Adenylosuccinate lyase (ADSL) is an essential enzyme for de novo purine biosynthesis and the purine nucleotide cycle. Given its crucial role in both cellular replication and metabolism, it is not surprising that ADSL has been found dysregulated in several malignancies, including breast and endometrial cancers as well as glioma. In our study we sought to investigate the putative role of ADSL in colorectal carcinoma (CRC) carcinogenesis and response to antimetabolites. Using data expression retrieved from The Cancer Genome Atlas (TCGA) dataset together with the data obtained by performing  immunohistochemistry analysis in a in-house TMA (tissue microarray) we found that ADSL expression was significantly increased in CRC tumors compared to non-tumor tissue. Moreover,  ADSL-high CRCs show upregulation of genes involved in DNA synthesis, DNA repair and cell cycle. Accordingly, ADSL overexpression accelerated progression through the cell cycle and significantly increased proliferation and migration in CRC cell lines. In line with the in vitro experiment and the role of ADSL, ADSL expression increased tumor growth in vivo and sensitized CRCs to 6-MP in vitro, ex vivo (PDOs) and in vivo (CAM model). Molecular experiments involving metabolomic and transcriptomic profile of ADSL overexpressing cells revealed that ADSL exerts its oncogenic function by affecting mitochondrial function via alteration of the TCA cycle and impairment of mitochondrial respiration. The KEAP1-NRF2 and mTORC1-cMyc axis were independently activated upon ADSL overexpression and may favor the survival and proliferation of ROS-accumulating cells, favoring DNA damage and tumorigenesis. Our results suggest that ADSL is a novel oncogene in CRC, modulating mitochondrial function, metabolism and oxidative stress, thus promoting cell cycle progression, proliferation and migration. Our results also suggest that ADSL is a predictive biomarker of response to 6-mercaptopurine in the pre-clinical setting. The study has been published in Theranostic. For further information, please contact Dr. Salvatore Piscuoglio.

30.03.2021 / HONORS AND AWARDS

Cloëtta Medical Research Position awarded to Dr. Salvatore Piscuoglio

Project Plan

Dr. Piscuoglio has been honored by the Cloëtta Foundation for a 5-year scholarship for his proposed project entitled: "Biomarker identification to guide surgical intervention after neoadjuvant chemoradiotherapy in rectal cancer". Patients with intermediate-stage rectal cancer are typically treated with chemoradiotherapy followed by surgical excision to remove any residual disease. Post-surgery histologic analysis reveals that ~25% of the patients achieve complete response to chemoradiotherapy, meaning that they would not have needed surgical intervention. For the remaining patients that do not achieve complete response to chemoradiotherapy, alternative therapeutic options are desirable. Thus the identification of robust biomarkers that will precisely predict which patients would likely achieve good response to chemoradiotherapy, thus sparing them the unnecessary surgery, are urgently needed. On the other hand, model systems that reflect the biological behavior of the tumors in individual patients to test alternative therapeutic options in an ex vivo manner are essential. This project will take several complementary approaches to address these outstanding challenges in precision oncology for rectal cancer patients. For further information, please contact Dr. Salvatore Piscuoglio

29.03.2021 / RESEARCH

TEAD4 exerts an oncogenic role in hepatocellular carcinoma by Hippo‐Independent regulation of HSP70 Family Members

TEAD4 impacts cell proliferation by directly binding HSP70 promoters and associated enhancers. See publication for detailed information.

Transcriptional enhancer factor domain family member 4 (TEAD4) is a downstream effector of the conserved Hippo signalling pathway, regulating the expression of genes involved in cell proliferation and differentiation. It is up‐regulated in several cancer types and is associated with metastasis and poor prognosis. However, its role in hepatocellular carcinoma (HCC) remains largely unexplored. In the study performed by our group, using data from The Cancer Genome Atlas, we found that TEAD4 was overexpressed in HCC and was associated with aggressive HCC features and worse outcome. Furthermore, the results obtained upon modulation of TEAD4 expression in in vitro and in vivo models, confirmed its association with pathways such as epithelial‐to‐mesenchymal transition, cell proliferation, and protein‐folding. We found that the TEAD4 role in cell proliferation was, in part, mediated by the expression of HSP70 family members in a Hippo‐independent mechanism. Importantly, TEAD4 was found to regulate HSP70 family members' expression by directly binding to their promoter and enhancer regions. Our study described a novel Hippo‐independent mechanism for TEAD4 promotes cell proliferation and tumor growth in HCC by directly regulating HSP70 family members. The study has been published in Hepatology Communications. For further information, please contact Dr. Salvatore Piscuoglio.

05.01.2021 / HONORS AND AWARDS

Verleihung des Roger Cotton-Preises der Zeitschrift Histopathology

Dr. Jasmin Dionne Haslbauer, Prof. Alexandar Tzankov und PD Dr. Thomas Menter (von rechts) sind stolze Preisträger des Roger Cotton-Preises 2020.

Die Zeitschrift Histopathology hat den Roger Cotton-Preis 2020 für die beste publizierte Originalarbeit für die Autopsie-Studie von COVID-19 Patienten aus dem Universitätsspital Basel vergeben. Die beiden Erstautoren Thomas Menter und Jasmin Haslbauer konnten unter Federführung von Alexandar Tzankov sowie dank der Mitarbeit zahlreicher KollegInnen des Universitätsspitals Basel und des Kantonsspitals Baselland die erste grössere umfassend charakterisierte Autopsieserie der Welt publizieren, welche die verschiedenartigen Befunde bei an COVID-19 verstorbenen Patienten aufzeigte (siehe Publikation). Neben einem äussert variablen Verlauf der pulmonalen Veränderungen (diskrete hyaline Membranen als Ausdruck eines diffusen Alveolarwandschadens bis hin zu schweren bilateralen suppurativen Bronchopneumonien), konnte auch eine unerwartete Störung der Mikrozirkulation in der Lunge und anderen Organen gezeigt werden. Viele Patienten hatten ein klassisches vaskuläres Risikoprofil (männlich, Alter >60 Jahre, Adipositas, arterielle Hypertonie, Diabetes mellitus, kardiovaskuläre Vorerkrankung), womit die Hypothese erhärtet werden konnte, dass die schwere COVID-19 Erkrankung ein angiozentrisches Syndrom darstellt und dadurch dieser Patientenkategorie besondere Aufmerksamkeit zuteilwerden konnte. Des Weiteren fand sich in überdurchschnittlich vielen Fällen der Basler Kohorte eine kardiale Amyloidose. Diese Arbeit wurde bis dato über dreihundertmal zitiert und die Ergebnisse ausnahmslos von anderen reproduziert. Basierend auf dieser Studie sind inzwischen weitere Publikationen der Arbeitsgruppe um Alexandar Tzankov erschienen, die dazu beigetragen haben, das pathogenetische Verständnis für COVID-19 zu verbessern und allfällige therapeutische Optionen aufzuzeigen (siehe Forschungsgruppe COVID-19). 

06.11.2020 / RESEARCH

ACE2 Localizes to the Respiratory Cilia and Is Not Increased by ACE Inhibitors or ARBs

Expression of ACE2 in lung tissue; note that only ciliated epithelia and some inflammatory cells express ACE2.

The angiotensin-converting enzyme 2 (ACE2) serves as receptor for SARS-CoV-2. ACE2 plays an important role in the renin-angiotensin-aldosterone system, which consists of a cascade of vasoactive substances and enzymes that maintain blood pressure. ACE inhibitors (ACEI) and angiotensin II receptor blockers (ARBs) are commonly used antihypertensive medications. In the context of COVID-19, concerns have been raised that these agents may increase expression of ACE2, and thereby elevate the risk of infection by SARS-CoV-2, providing a potential explanation for why hypertension is a common comorbidity in patients with COVID-19. In the current study, which included tissue samples from our Institute obtained during the first COVID-19 wave (see related publication in Histopathology), we found abundant ACE2 protein expression in multiciliated airway epithelial cells (Figure), spanning from the nasal cavity down to the lower bronchial tree. Furthermore, we observed robust localization of ACE2 in the motile cilia, suggesting them as initial entry and early subcellular site of SARS-CoV-2. Importantly, neither use of ACEI nor ARBs did enhance the expression of ACE2. Our findings are in line with the advice of several professional medical societies to maintain ACEI and ARBs as standard antihypertensive therapy during the ongoing SARS-CoV-2 outbreak. The study has been published in Nature Communications. For further information, please contact Prof. Dr. Alexandar Tzankov.   

13.10.2020 / RESEARCH

Molecular Profiling of Deceased COVID-19 Patients Reveals Two Distinct Patterns of Disease Reaction

A: COVID-19 case showing mild diffuse alveolar damage with hyaline membranes with only subtle inflammatory infiltrates B: COVID-19 case with extensive organizing diffuse alveolar damage, beginning remodeling of the lung parenchyma and increased inflammatory infiltrates.

In a collaborative effort of the departments of pathology of the University Hospital Basel, the Cantonal Hospital of Liestal as well as the University Hospitals of Zurich and Trento, Italy, and supported by Novartis, we could determine different patterns of immune reactions in deceased COVID-19 patients. We investigated lung parenchyma of our autopsy cohorts of COVID-19 patients (n=16) by combining results of conventional histology, quantitative computational image analysis and gene expression profiling. The findings of the study have been published in the current issue of Nature Communications.

We could decipher two distinct pathways of immunopathological reactions: one pathway was associated with high levels of cytokines, interferons and abundance of SARS-CoV-2 while the lung tissue was intact, the other group showed marked destruction of the lung parenchyma accompanied by cytotoxic T-cells and macrophages and local complement activation whereas the viral load and the interferon signature were low. It could also be seen that patients with prominent interferon signature died earlier in the course of the disease. Finding evidence for these two distinct patterns of COVID-19 which have also been postulated in primarily epidemiologic studies, we could contribute to a better understanding of the mechanisms of lethal COVID-19. Our findings may help to group COVID-19 patients into these two subgroups which also need different therapeutic approaches: targeting viral replication and the cytokine activation versus inhibiting activation of the complement system in the latter group. For additional information, please contact PD Dr. Thomas Menter.

08.10.2020 / RESEARCH

COVID-19: Hunting Coronavirus by Electron Microscopy

Infected Vero cell (derived from cell culture experiments) showing vesicles with assembled virions of SARS-CoV-2 (electron microscopy, magnification 110,000 x).

Are organ dysfunctions and associated morphological changes in COVID-19 patients due to direct infection with SARS-CoV-2, a result of the systemic immune response, or both? Electron microscopy is the only tool to visualize assembled virus in tissues, but the published “viral-like particles” in many tissues including kidney, liver, intestine, and placenta are highly contested. A current review published in Histopathology by Helmut Hopfer and colleagues puts the ultrastructural findings obtained in SARS-CoV-2-infected cell cultures into the context of viral replication and its associated changes in intracellular membrane systems. A number of pitfalls make electron microscopic identification of coronavirus much more challenging than anticipated. Despite some evidence suggesting viral replication outside the airways and the lungs, unassailable proof of direct viral infection is still missing. For additional information, please contact PD Dr. Helmut Hopfer.

09.09.2020 / RESEARCH

COVID-19 Neuropathology: (Too Much) Ado About Nothing?

Microglia activation in the pons (stained for HLA-DR) of COVID-19 patient (a) and a septic control patient (b).

With up to 80% of COVID-19 patients presenting with neurological symptoms, previous studies had reported conflicting observations on CNS involvement, ranging from pan-encephalitis and massive brain hemorrhage to no specific changes attributable to SARS-CoV-2 at all. In the current issue of Acta Neuropathologica, Nikolaus Deigendesch and colleagues report about neuropathological autopsy findings in a cohort of seven patients who died from COVID-19-associated complications. SARS-CoV-2 RNA was detected in four out of seven cases in the olfactory bulb but not in other brain regions investigated. Whereas in all COVID-19 cases pronounced microglial activation was found, similarly extensive reactive changes were present in brains of non-COVID-19 control patients who died of critical illness and/or sepsis. These data suggest that unspecific correlates of a critical illness-related encephalopathy, rather than specific COVID-19-related alterations, predominate COVID-19 brain neuropathology. For more information about this research topic, please contact Prof. Dr. Stephan Frank.

01.07.2020 / HONORS AND AWARDS

Two Swiss Cancer League Research Grants to Researchers from the Pathology

Dr. Clémentine Le Magnen and Dr. Salvatore Piscuoglio

We congratulate the two research group leaders Dr. Clémentine Le Magnen and Dr. Salvatore Piscuoglio, for their successful Swiss Cancer League grant applications. Out of the only five funded clinical research projects in Switzerland, their two applications were selected for a three year funding period. In the study, entitled Multidimensional imaging of patient-derived organoids: towards advancing models of urological cancers for personalized medicine,  Dr. Le Magnen’s team will use a combination of imaging technologies to dissect the phenotype of prostate and bladder cancer patient-derived organoids, with the ultimate goal of developing optimal models for personalized medicine. Dr. Piscuoglio will focus with his research project Augmenting precision medicine for colorectal cancer patients with ex-vivo drug screening on the use of next generation drug screening coupled with patient derived organoids to predict drug response in colorectal cancer patients. For more information about this research, please contact Dr. Le Magnen or Dr. Piscuoglio.

22.05.2020 / RESEARCH

Autopsy Study Reveals That Covid-19 Is an Angiocentric Clinical Syndrome

Upper row: Scanning electron micrographs of microvascular corrosion casts from the thin-walled alveolar plexus of an injured by COVID-19- (left) and a healthy lung (right). Lower row: (Sub)total occlusion of the arteries (red) in COVID-19-lungs (left), as compared to uninfected controls (right). (μCT 3D reconstruction) Modified from

Progressive respiratory failure is the primary cause of death in the COVID-19 pandemic. Despite widespread interest in COVID-19 pathophysiology, relatively little is known about the associated morphologic and molecular changes in the lungs of patients who die from SARS-CoV-2 infection. In the current issue of the New England Journal of Medicine (see also the editorial), Prof. Alexandar Tzankov and colleagues from different universities report about the comparison of COVID-19 autopsy lungs, obtained primarily from autopsies in Basel, to influenza A (H1N1) and age-matched uninfected control lungs. The COVID-19 lungs demonstrated rater unique and distinctive vascular features consisting of severe endothelial injury, associated with intracellular SARS-CoV-2, widespread thrombosis, microangiopathy and new vessel growth—predominantly by the mechanism of intussusceptive angiogenesis. This and previous data allow to conclude that COVID-19 is an angiocentric clinical syndrome. For more information about this study, please contact Prof. Dr. Alexandar Tzankov.

14.05.2020 / HONORS AND AWARDS

Pathology COVID-19 Research Study Selected by the BRCCH

Prof. Dr. Alexandar Tzankov

The research proposal of senior pathologist Prof. Dr. Alexandar Tzankov was selected by the Fast Track Call for Acute Global Health Challenges of the Botnar Research Centre for Child Health (BRCCH). This call is a unique emergency response to fight COVID-19 disease and its associated pandemic. The study proposed by Prof. Tzankov and his team receives funds for 1.3 Million CHF for the next three years and aims at disclosing the interactions of SARS-CoV-2 with tissues and organs from deceased patients. In a recently published autopsy study (see publication), Prof. Tzankov and colleagues already provided valuable insights into the different pathologies caused by COVID-19 and the potential risk factors. The novel interdisciplinary approach with researchers from pathology, immunology, internal medicine, intensive care and neurology, will further increase our knowledge of the pathogenesis of COVID-19 with the final goal to affect future more tailored medical interventions for this disease. For more information about this research, please contact Prof. Dr. Alexandar Tzankov.

05.05.2020 / RESEARCH

Autopsy Study Reveals New Insights Into Pathologies of Various Organs of COVID-19 Patients Suggesting Vascular Dysfunction and Presents Potential Risk Factors

A: Exudative diffuse alveolar damage; B: Syncytial cells of pneumocyte II origin C: Extensive capillary congestion; D: Microthrombi in alveolar capillaries (see publication: Menter et al.)

In a joint effort of the Institute of Medical Genetics and Pathology of the University Hospital Basel and the Institute of Pathology at the Cantonal Hospital Baselland, autopsy findings of 21 COVID-9 patients were published in Histopathology. The major finding was diffuse alveolar damage of various stages in the lung accompanied by massive capillary congestion and microthrombi. Bronchopneumonic superinfection was seen in half of the cases. Interestingly, a high rate of senile cardiac amyloidosis compared to the general population was found. All patients suffered from significant “cardio-vascular-centred” comorbidities such as hypertension, diabetes mellitus or obesity. This study gives the thus far largest comprehensive and detailed insight into pathologies to be encountered in COVID-19 patients. Accordingly, a special focus of attention should be set on preventing microcirculatory problems in COVID-19 patients as well as on dealing with comorbidities including amyloidosis. The study provides open-source scans of relevant histology findings of the patients freely accessible via the publication. For more information about this research area, please contact Prof. Dr. Alexandar Tzankov.

06.02.2020 / HONORS AND AWARDS

Fond’Action Contre le Cancer Young Investigator Award to Dr. Le Magnen

Dr. Clémentine Le Magnen (middle) receives the award from the chairman of the foundation Prof. Serge Leyvraz (left), and the chairman of the scientific committee Prof. Daniel Schorderet (right).

Dr. Clémentine Le Magnen was selected as the laureate of the Fond’Action Contre le Cancer Young Investigator Grant 2020. This prestigious prize is awarded every year to identify and support one promising young researcher in the field of Oncology in Switzerland. Dr. Le Magnen is a junior group leader in the Laboratory for Translational Genitourinary Cancer Research and received this award for her study entitled “Clinical and functional relevance of stemness in prostate cancer progression”. For more information about this research, please contact Dr. Clémentine Le Magnen.



31.01.2020 / RESEARCH

Identification of complex single-cell phenotypes by imaging mass cytometry might improve patient-specific breast cancer diagnosis

Schematic of imaging mass cytometry acquisition of multiplexed images from 281 breast cancer patients.

A team of researchers from the University of Zurich, led by Prof. Bernd Bodenmiller, has used a new method called imaging mass cytometry to investigate complex single-cell phenotypes and their spatial context in human breast cancer. In collaboration with PD Dr. S. Münst Soysal from our institute, 35 biomarkers were simultaneously quantified with imaging mass cytometry in breast cancer tissue from 352 patients, resulting in 720 high-dimensional pathology images. The analysis revealed multicellular features of the tumor microenvironment and novel subgroups of breast cancer that are associated with distinct clinical outcomes. This detailed characterization of intratumor phenotypic heterogeneity in a disease-relevant manner has the potential to improve patient-specific diagnosis and open new possibilities in the way of precision medicine. The results of this collaboration study were reported in the renowned journal Nature. For further details about this research topic, please contact PD Dr. Simone Münst Soysal.





16.12.2019 / HONORS AND AWARDS

Swiss Foundation against Liver Cancer Award to Dr. Salvatore Piscuoglio

Dr. Piscuoglio receives the award at the official ceremony in Lausanne.

Dr. Salvatore Piscuoglio received the prestigious award of the Swiss Foundation against Liver Cancer 2019 at the annual HCC day held in Lausanne. The prize for the best publication on hepatocellular carcinoma among the swiss institutions in 2019 was awarded for the publication entitled “Genetic profiling using plasma-derived cell-free DNA in therapy-naïve hepatocellular carcinoma patients: a pilot study”. This study showed for the first time the clinical utility of analyzing circulating tumor DNA in patients with advanced hepatocellular cancer. For more information about this research, please contact Dr. Salvatore Piscuoglio.

10.09.2019 / HONORS AND AWARDS

President’s Medal der International Skeletal Society geht an Prof. Daniel Baumhoer

Prof. Dr. Daniel Baumhoer mit der President’s Medal der International Skeletal Society.

Prof. Dr. med. Daniel Baumhoer hat anlässlich der Jahrestagung der International Skeletal Society in Vancouver, Kanada, die President’s Medal der Gesellschaft erhalten. Der Preis für herausragende wissenschaftliche Leistungen eines Mitglieds wurde dieses Jahr damit erstmals an einen Pathologen verliehen. Die International Skeletal Society ist eine interdisziplinäre Expertengruppe für muskuloskelettale Erkrankungen, die sich aus mehr als 600 Mitgliedern aus über 30 Ländern zusammensetzt. Bei den Jahrestagungen werden die neuesten wissenschaftlichen Erkenntnisse und exzeptionelle Fallbeispiele vorgestellt und diskutiert, es werden ausserdem Fortbildungsveranstaltungen ausgerichtet, an denen Radiologen, Pathologen, orthopädische Chirurgen und Radiotherapeuten aus der ganzen Welt teilnehmen. Prof. Baumhoer, der seit 2014 das Knochentumor-Referenzzentrum am USB leitet, ist seit 2015 Mitglied in der Gesellschaft und ebenfalls seit 2015 Inhaber einer Forschungsprofessur der Gertrude von Meissner Stiftung. Er wird für seine Arbeiten an knochenbildenden Tumoren, v.a. des Osteosarkoms, ausgezeichnet.

Zur Medienmitteilung des USB.

09.07.2019 / HONORS AND AWARDS

Rudolf-Virchow-Medaille 2019 für Herrn Prof. Dr. med. Michael Mihatsch

Prof. Michael Mihatsch anlässlich der Preisverleihung in Frankfurt am Main.

Anlässlich der Jahrestagung der Deutschen Gesellschaft für Pathologie (DGP) im Juni 2019 wurde dem ehemaligen Chefarzt des Instituts für Pathologie am Universitätsspital Basel, Herrn Prof. Dr. med. Michael Mihatsch, die Rudolf-Virchow-Medaille 2019 verliehen. Die DGP ehrt damit Herrn Prof. Mihatsch für sein Lebenswerk, das ein lebenslanges Engagement für das Fach Pathologie, vor allem auf seinem Spezialgebiet der Nierenpathologie umfasst. So hat er dazu beigetragen, dass die sogenannte „Phenacetin-Niere“ (eine spezielle Form der Analgetikanephropathie) der Vergangenheit angehört. Durch akribische histopathologische und elektronenmikroskopische Untersuchungen konnte Prof. Mihatsch einen Bezug zwischen Phenacetin-haltigen Schmerzmitteln und Nierenschädigungen nachweisen. Dies zu einer Zeit als die Analgetikanephropathie Ursache von bis zu 10% aller Fälle von chronischer Niereninsuffizienz in Europa ausmachte. Basierend auf seinen Studien erfolgte die „Ausrottung“ der Phenacetin-Niere durch das Verbot Phenacetin-haltiger Schmerzmittel. Herr Prof. Mihatsch wurde 1943 in Oberschlesien geboren und ist in Duisburg aufgewachsen. Er absolvierte sein Medizinstudium in Bonn und Freiburg und nahm 1970 seine Pathologieausbildung in Basel unter Herrn Prof. H.U. Zollinger auf. 1978 erhielt Herr Mihatsch eine Assistenzprofessur an der Universität Basel und von 1988 bis 2007 leitete er als Chefarzt das Institut für Pathologie am USB. 

09.07.2019 / HONORS AND AWARDS

International Lymphoma Study Group

Prof. Dr. Stephan Dirnhofer

Prof. Stefan Dirnhofer, Chefarzt-Stellvertreter Pathologie und Leiter des Referenzzentrums für Maligne Lymphome der SAKK am Institut für Medizinische Genetik und Pathologe wurde im Juni 2019 als neues Mitglied in die «International Lymphoma Study Group (ILSG)» gewählt. Die ILSG wurde 1991 von Peter Isaacson und Harald Stein gegründet, mit dem Ziel eine einheitliche und international akzeptierte Klassifikation von Lymphomen zu erstellen. Heute sind die Schwerpunkte der Gruppe die Entdeckung und Definition neuer Lymphom - Entitäten, die Entwicklung und Anwendung moderner molekularer Technologien zur Klassifikation und Diagnose von Lymphomen, die Weiterentwicklung und Aktualisierung der bestehenden WHO-Lymphomklassifikation und die wissenschaftliche Kollaboration zwischen den Mitgliedern. Die Mitglieder der ILSG sind durchwegs international anerkannte Experten, primär Pathologen aber auch andere Spezialisten mit komplementärer Expertise. Die Aufnahme von Prof. Dirnhofer in die ILSG stellt eine grosse Auszeichnung dar. Pro Jahr werden weltweit im Schnitt nur 2-3 neue Mitglieder aufgenommen, die Auswahl beruht ausschliesslich auf strikten wissenschaftlichen Kriterien und kann nur auf Einladung durch bestehende Mitglieder erfolgen.

02.07.2019 / RESEARCH

Genomic Characterization of Patients with Metastatic Breast Cancer

The authors analyzed the genomes of 617 patients with breast cancer.

Dr. Charlotte Ng and her colleagues Dr. Salvatore Piscuoglio and Dr. Maria De Filippo from the Institute of Medical Genetics and Pathology report in the renowned journal Nature their novel findings on the genomic characterization of metastatic breast cancers. In this study, they confirmed that metastatic breast cancer is the result of genomic evolution. Compared to early breast cancers, they found that metastatic breast cancers are more genomically complex and uncovered two evolutionary processes that drive the increased complexity: elevated mutation rate due to the activation of APOBEC proteins and the increased rate of deficiency in DNA repair. They further identified a number of genomic alterations that are associated with poor outcome, including some that may be targeted with existing drugs. These findings will allow earlier and better selection of patients who may benefit from therapy options that are still in clinical trials. This study was performed in collaboration with the Department of Medical Oncology (Gustav Roussy, Inserm). For more information, please access the publication or contact Dr. Charlotte Ng.

02.05.2019 / RESEARCH

20 Novel Gene Loci for Bipolar Disorder Identified

A recent study by a group of 207 institutions from 22 countries (Psychiatric Genomics Consortium – PGC) has identified 20 so far unknown genes that increase the risk of developing bipolar disorder, a common neuropsychiatric disorder affecting around 1% of the general population. The study compared the genetic variations in almost 30’000 patients with bipolar disorder and 160’000 control individuals. Prof. Sven Cichon from our institute and his research team (Dr. Andreas Forstner, Sascha Fischer, Stefan Herms, Dr. Per Hoffmann) had a leading role in this work, which has been published in Nature GeneticsSome of the genes found in this study represent ion channels that influence the communication between neurons. Moreover, there is now evidence for a possible involvement of insulin regulation and the endocannabinoid system in the disorder. The endocannbinoid system plays a role in pain regulation. The researcher also found differences in the genetic make-up between individuals with two clinically distinguishable subtpyes of the disorder, bipolar I and bipolar II disorder. Bipolar I disorder is characterized by more severe manic episodes than bipolar II disorder. Genetically, bipolar I disorder seems to be strongly genetically linked to schizophrenia, whereas bipolar II disorder is more strongly linked with major depressive disorder. The findings may be potential starting points for new therapies. A detailed understanding of the biological mechanisms relevant in these disorders will hopefully support the development of new medication and therapies. For further information, please contact Prof. Dr. Sven Cichon.

07.02.2019 / HONORS AND AWARDS

Pfizer Research Award to Researchers from Pathology Basel

PD Dr. Christian Ruiz, Dr. Cristina Quintavalle and Dr. Joël Federer-Gsponer receive the Pfizer Research Award from the chair Prof. Dr. Daniel Hayoz.

Three researchers from the Pathology Basel, Dr. Cristina Quintavalle, Dr. Joël Federer and PD Dr. Christian Ruiz, received the prestigious Pfizer Research Award in the category of urology. The researchers were awarded for their joint research study that was recently published: Delineation of human prostate cancer evolution identifies chromothripsis as a polyclonal event and FKBP4 as a potential driver of castration resistance. In this study, by application of genomic profiling technologies, the research group determined the different evolutionary patterns that lead to therapy resistance in patients with advanced prostate cancer. By further investigation of a larger cohort, they discovered increased expression of the gene FBKP4 as a potential mechanism for therapy resistance in these patients. This interdisciplinary research project was conducted in the Laboratory for Translational Uropathology Research, the joint research laboratory of the Department of Urology and the Institute for Pathology of the University Hospital Basel. For more information about this research, please contact PD Dr. Christian Ruiz.

19.12.2018 / DIAGNOSTICS

Referenzzentrum für Maligne Lymphome kommt in die Pathologie des USB

Prof. Dr. Stephan Dirnhofer

Die SAKK (Schweizerische Arbeitsgemeinschaft für Klinische Krebsforschung) unterhält ein Referenzzentrum zur histologischen Diagnostik von malignen Lymphomen (RZML). Seit 1998 war dieses am Institut für Pathologie des Kantonsspitals St. Gallen angesiedelt. Am 1. Januar 2019 wird das RZML nun nach Basel transferiert werden und unter der Leitung von Prof. Stephan Dirnhofer, Stv. Chefarzt am Institut für Medizinische Genetik und Pathologie des USB, stehen. Dieser Schritt soll sicherstellen, dass der immer wichtiger werdenden translationalen Forschung im Rahmen der klinischen Studien vonseiten der Pathologie besser entsprochen werden kann. Konkret bedeutet dies, dass für alle zukünftigen SAKK Lymphom-Studien der sogenannte «Central Pathology Review» (die zentrale Diagnoseüberprüfung) in der Pathologie des USB durch Prof. Dirnhofer durchgeführt wird, verbunden mit einem «biobanking» der Proben und – falls möglich – einem translationalen Forschungsprojekt. Neben dieser wichtigen Expertenfunktion in klinischen Studien wird das RZML auch eine nationale und internationale  Einrichtung zur konsiliarischen Beurteilung schwieriger hämatopathologischer Präparate sein. Dabei wird die ganze Bandbreite des Fachgebiets abgedeckt, das heisst neoplastische und nicht-neoplastische Erkrankungen des Knochenmarks, des Thymus, der Milz sowie nodale und extranodale Lymphoproliferationen.

22.11.2018 / HONORS AND AWARDS

SAKK/Astellas Award to Dr. David Müller

Dr. David Müller (middle) receives the prize from the chair Prof. Dr. Viviane Hess (left) and Dr. Oswaldo Mirantes (right) from Astellas.

We congratulate Dr. David Müller for receiving the SAKK/Astellas GU Oncology Award 2018. He received this prestigious award for his research in the field of urothelial cancer: Donor-derived, metastatic urothelial cancer after kidney transplantation associated with a potentially oncogenic BK polyomavirus. Here, for the first time, David Müller and colleagues link BK polyomavirus NCCR rearrangements with oncogenic transformation in urothelial cancer in an immunosuppressed patient. Dr. Müller performed this multidisciplinary work as a PhD student in the Laboratory for Translational Uropathology Research in collaboration with the Institute of Forensic Medicine and the Department of Biomedicine. The Laboratory for Translational Uropathology Research is the new joint research laboratory of the Department of Urology and the Institute for Pathology of the University Hospital Basel and focuses on advancing our understanding of urogenital diseases by combining basic, translational and clinical research. For more information about this research, please contact PD Dr. Cyrill Rentsch or Prof. Dr. Lukas Bubendorf.

08.08.2018 / RESEARCH

Neuronal Mitochondrial Dysfunction Activates the Integrated Stress Response to Induce Fibroblast Growth Factor 21

Graphical abstract. From Restelli L et al., Cell Reports, Volume 24, ISSUE 6, P1407-1414.

Normal functioning of the cells that make up our body requires the coordinated interplay between its various organelles. In many cases, an impaired interorganellar communication will activate a stress response to ensure the survival of affected cells. The molecular mechanisms underlying this stress response in brain neurons have now been characterized in detail by Lisa Restelli and Björn Oettinghaus, two postdoctoral researchers from Prof. Stephan Frank`s group at our institute. As the researchers write in Cell Reports, impairments on the level of mitochondria - organelles widely known as the „cell`s powerhouses“ for their capacity to generate ATP - impact the function of neighboring, interacting organelles such as the endoplasmic reticulum. This impaired interorganellar communication results in the induction and secretion of fibroblast growth factor 21 (FGF21) by affected nerve cells. Remarkably, as demonstrated by the researchers, this cytokine is also induced in various models of neurodegenerative disorders, where it can be detected prior to neuronal cell death.  As chronic cell stress is an important component in the pathogenic cascade leading to neurodegeneration, FGF21 might potentially lend itself as a biomarker for the pre-symptomatic detection of respective diseases, including e.g. Alzheimer`s dementia and Parkinson`s disease. However, as FGF21 can also be produced by other tissues and organs, such as adipose tissue and liver, further rigorous testing will be required. On the other hand, the availability of a robust biomarker would undoubtedly represent an important advance in the development of novel approaches targeting chronic cell stress to provide neuroprotection. The study was realized in collaboration with partners at the universities of Cambridge (UK) and Padua (IT). For more information, please contact Prof. Dr. Stephan Frank.

22.6.2018 / RESEARCH

Genetic Predisposition to Medulloblastomas

Proposed guidelines for medulloblastoma patient genetic counseling and testing. From Waszak SM et al., Lancet Oncology.

Recent advances in molecular neuropathology have changed our perception of medulloblastoma (MB), the most common malignant brain tumor of childhood. Once considered a single tumor entity, it has now become clear that „medulloblastoma“ in fact subsumes various biologically and molecularly different tumors. This concept has also been adopted by the WHO, which currently distinguishes four main MB subgroups, of which MBs arising from alterations of the SHH- and WNT-signaling pathways are best understood. A multicenter study with participation of our institute, published this month in Lancet Oncology, reports on the actual contribution of cancer predisposition syndromes to MB. In this context, besides the “usual suspects” in this case, APC (MB-WNT), PTCH1 & SUFU1 (MB-SHH), and TP53, the study also identified germline mutations in BRCA2 and PALB2, both so far only known in the context of Fanconi anemia. In contrast to MB patients with tumors of the so-called subgroups 3 and 4 where damaging germline mutations were only rarely identified, about one fifth of MB-SHH tumors developed in the context of genetic predisposition. The study thus highlights the need for dedicated genetic counseling and screening programs dependent on clinical and molecular MB characteristics. For more information, please contact Prof. Dr. Stephan Frank.

06.04.2018 / DEVELOPMENT

First Identification of Diagnostically Relevant BRAF Gene Mutations With Potential Therapeutic Impact in Nodal Marginal Zone Lymphomas

Immunohistochemical staining of a nodal MZL biopsy with positive BRAF status (left). The detected BRAF mutations were located in the protein tyrosine kinase domain (right).

Two postdoctoral researchers (Dr. Vincent Pillonel and Dr. Darius Juskevicius) from the hematopathology research group of Prof. Alexandar Tzankov have recently published the results of their study “High-throughput sequencing of nodal marginal zone lymphomas identifies recurrent BRAF mutations” in the renowned journal Leukemia.  By application of an especially devoted Next-Generation sequencing (NGS) pipeline consisting of exome sequencing and a customized lymphoma gene panel, followed by in-silico meta-analysis, they succeeded to comprehensively characterize defects in genes and pathways that are driving oncogenesis in nodal marginal zone lymphoma (MZL), which is an orphan disease mainly defined by negative findings. They also identified genetic alterations differentiating nodal MZL from other closely related entities, such as splenic and extranodal MZL, lymphoplasmacytic and follicular lymphomas. Of particular importance is the detection of the theranostic (and in a proportion of cases clonal) BRAF V600E mutation in multiple nodal MZL cases. Until recently this mutation, among B-cell neoplasms, was thought to occur only in hairy cell leukemia and was diagnostic (and of therapeutic importance) for this entity. Here, for the first time, diagnostically useful, and potentially therapeutically relevant BRAF mutations were detected in nodal MZL. For more information about this research area and/or its diagnostic application, please contact Prof. Alexandar Tzankov.

03.04.2018 / RESEARCH

Identification of a Novel Tumor Suppressor: the Protein Histidine Phosphatase LHPP

Lower expression of LHPP in hepatocellular carcinoma correlates with worse overall survival. From

A team of researchers, led by Prof. Michael N. Hall and Dr. Sravanth Hindupur from the Biozentrum, University of Basel, has discovered a new anti-cancer protein, called LHPP. In collaboration with several members of our institute (M. Matter, S. Piscuoglio, C. Ng, L. Quagliata and L. Terracciano) the function of this protein has been analyzed in detail. LHPP prevents the uncontrolled proliferation of liver cancer cells and is also suitable as a biomarker for the diagnosis and prognosis of liver cancer, as was reported in Nature.  Histidine phosphorylation is a poorly characterized post-translational modification of proteins. Analysis of murine and human liver cancer revealed that NME1 and NME2, the only known mammalian histidine kinases, were upregulated. Conversely, expression of the histidine phosphatase LHPP was downregulated in the tumor. Consistent with these observations, global histidine phosphorylation was significantly upregulated in the liver cancer and sustained hepatic expression of LHPP in a liver cancer mouse model reduced tumor burden. Furthermore, in patients with liver cancer, low expression of LHPP correlated with increased tumor severity and reduced overall survival. In conclusion, for the first time, a protein histidine phosphatase was described with a tumor suppressive function which may pave the way towards new strategies in the fight against cancer. For further details about this research topic, please contact Dr. Matthias Matter.


01.03.2018 / DIAGNOSTICS

Towards personalized medicine: Basel Institute of Pathology is the first Swiss institution to offer DNA methylation profiling for tumor diagnostics.

Capper et al.: DNA methylation-based classification of central nervous system tumours. From

Whereas epigenetic signatures have been recognized as important contributors to tumorigenesis a couple of years ago, this knowledge is currently being translated into routine molecular tumor diagnostics at an amazing speed. Today, the long-awaited DNA methylation-based brain tumor classifier finally saw the light of day as publication in Nature (Capper D et al.).  Using Illumina 850k chip technology, Stefan Pfister’s group at the DKFZ in Heidelberg spearheaded a comprehensive multi-center study, and the results have elevated brain tumor diagnostics to an unprecedented level of granularity. Having participated in the development of the DNA methylation brain tumor classifier, for which Basel was one of the five external validation centers, our neuropathologists, Dr. Jürgen Hench and Prof. Dr. Stephan Frank, started embracing this new technology almost one year ahead of the current publication. The overall experience gained from the analysis of more than 1100 brain tumors suggests that, in as many as 12% of the cases, methylation profiling leads to a more refined classification, and in some cases even to clinically relevant changes in diagnoses. With some 150 tumors analyzed with the help of medical geneticist Dr. Per Hofmann, Jürgen and Stephan are convinced of the transformative potential of this diagnostic approach, which has already started to find similar applications in the molecular workup of other tumor groups (carcinomas, sarcomas).  At present, Basel stands as the only center offering this approach for routine molecular tumor diagnostics in Switzerland. For more information about brain tumor diagnostics, please contact Prof. Dr. Stephan Frank.


01.08.2017 / HONORS AND AWARDS

Dr. Luca Quagliata Selected for New EORTC Leadership Program in Clinical Research

Dr. Luca Quagliata

Clinical research has become a complex science requiring multidisciplinary expertise not only in the field of medicine and oncology, but also in the intricate regulatory environment. New skills are required beyond the classical methodology of clinical research to allow the new generation of researchers to properly face the fast evolving economic and strategic challenges for health care. For these reasons, the European Organisation for Research and Treatment of Cancer (EORTC) has established a new program named: “Early Career Investigator Leadership Program”. The program will elapse over the next two years starting October 2017. It will be built and professionalized, specifically for the leadership training in partnership with McKinsey. The overall goal of the program is to support the development of selected individuals who will position at various levels within the EORTC organisation during the next years. EORTC groups have identified several promising individuals within their membership and 43 participants have been selected. Among those, Dr. Luca Quagliata has been chosen. This represents an important personal achievement for Dr. Quagliata as well as a recognition of the pivotal role of our Institute in the context of translational and clinical research.

01.05.2017 / DEVELOPMENT

Thermo Fisher Scientific establishes Institute of Pathology as a Center of Excellence Partner

Looking forward to a successful collaboration: Prof. Luigi Terracciano, Mark Stevenson (President of Life Sciences Solutions for Thermo Fisher Scientific), Prof. Markus Tolnay and Dr. Luca Quagliata (from left).

Thermo Fisher Scientific Inc. has signed a long-term collaborative agreement with the Institute of Pathology at University Hospital Basel to establish the leading institution as the first Center of Excellence under the Oncomine™ portfolio program, a new initiative designed to develop and refine next-generation sequencing (NGS)-based oncology research assays with the intent to eventually introduce them into the clinic as companion diagnostics. Thermo Fisher Scientific Inc. is the world leader in serving science, with revenues of $18 billion and more than 55,000 employees globally. As part of the agreement, both organizations will also collaborate to form global alliances and strategic partnerships with biopharma groups and others in an effort to accelerate oncology and immune-oncology trials. Additionally, the Institute of Pathology will serve as one of the Center of Excellence program’s global sites focused on conducting research and validation of Thermo Fisher’s Oncomine NGS portfolio of products.

21.02.2017 / HONORS AND AWARDS

SNF BioLink Grant to Pathology USB

The PathoLink Team at Pathology USB: Prof. Markus Tolnay, Dr. Serenella Eppenberger-Castori and Prof. Luigi Terracciano (from left).

The Swiss National Science Foundation launched the BioLink program for funding the networking of biobanks established for research purposes. BioLink is intended for investigators who wish to network their biobanks using IT systems. This harmonisation of the IT systems will result in the sharing of data so as to address well-defined, scientific questions. For the 2016 call, SNF supports three projects, one of which based at Pathology USB. In the project entitled "PathoLink: Connecting biobanks to determine mechanisms of metastasis formation" the five University based Institutes of Pathology are working in close collaboration together with the respective ICT units and the Swiss Institute of Bioinformatics. The project is aimed to foster translational cancer research within the framework of the Swiss Personalized Health Network.

01.02.2017 / DEVELOPMENT

New Custom Gene Panel for Molecular Diagnostics of Lymphoma

Four different ways of analyzing a lymphoma: By usage of A) immunohistochemistry; B) Fluorescence-In-Situ Hybridization; C) Sanger-Sequencing; D) Next-Generation-Sequencing (NGS) profiling.

The Research Unit of the Institute for Pathology is pleased that the laboratory department has integrated the lymphoma gene panel for next-generation sequencing (NGS) in its routine molecular diagnostic portfolio. This gene panel was developed by Dr. Darius Juskevicius as part of his PhD research project and was published last year in the journal Leukemia. It covers the 68 genes that are frequently mutated in B-cell lymphomas, such as MYD88, EZH2, PIM1, TP53, BCL2 or KMT2D. In 20 out of the 68 genes the targeted region covers all exons; in the remaining 48, specific exons or hotspots of the respective genes are selected. Detailed information about the genes and exons of this custom panel can be retrieved here. This new panel provides a useful tool for more accurate diagnosis of lymphoproliferative disorders and discloses potential genomic vulnerabilities that can be used for targeted personalized medicine approaches in patients with an advanced stage or relapsed disease. The rapid translation of the research findings to routine diagnostic application was possible due to the strong interaction of the research unit and the diagnostic laboratory department. Our research unit is composed of almost 30 researchers working in the two focal areas of translational cancer research and neurodegenerative diseases. We are dedicated towards developing novel diagnostic tools and assays based on the results of ours and other’s scientific investigations of underlying disease mechanisms. For more information about our research or diagnostic applications in lymphoma, please contact Prof. Dr. Alexander Tzankov (see article in UNI NOVA). For general inquiries about our research, PD Dr. Christian Ruiz.

26.09.2016 / HONORS AND AWARDS

First Poster Price of the SGU to Dr. David Müller

Dr. David Müller

We congratulate Dr. David Müller for winning the first poster prize of this year’s annual meeting of the Swiss Society of Urology (SGU). He received the award in the category of Basic Research for the work “Delineation of advanced prostate cancer evolution identifies chromothripsis as a polyclonal event selecting for FKBP4 as a driver of castration resistance”. Dr. Müller is a PhD student in the Uropathology research group of the Institute for Pathology and his research focuses on the genomic changes occurring due to androgen deprivation therapy in advanced prostate cancer. For more information about his research, please contact Dr. David Müller.

15.09.2016 / HONORS AND AWARDS

David Y Mason Award to Dr. Darius Juskevicius

Dr. Darius Juskevicius receives the David Y Mason Award glass sculpture from Prof. Dr. Stefan Dirnhofer.

The Research Unit of the Institute for Pathology is delighted that Dr. Darius Juskevicius, a postdoctoral fellow of the research group of Prof. Alexandar Tzankov, receives the David Y Mason Award. This prestigious prize is awarded every second year to support a promising research project of a young researcher in the field of hematopathology. Dr. Juskevicius receives this award for his research proposal entitled “Genetic profiling of Hodgkin- and Reed-Sternberg cells of classical Hodgkin lymphoma enriched from archival formalin-fixed and paraffin-embedded tissue”. The prize was awarded during the 18th Meeting of the European Association for Haematopathology [LINK:] in Basel. For more information about this research project, please contact Dr. Darius Juskevicius.

16.08.2016 / HONORS AND AWARDS

SNSF Ambizione Grant to Dr. Salvatore Piscuoglio

Dr. Piscuoglio Salvatore

Dr. Piscuoglio, a current postdoctoral fellow in the research unit of the Institute for Pathology has been awarded a Swiss National Science Foundation (SNSF) Ambizione grant. This highly competitive grant is provided by the SNSF to promote scientific independence of high potential investigators working at Swiss universities. This grant will allow Dr. Piscuoglio to pursue a new line of research and to establish his own research group within our institute. Dr. Piscuoglio’s research interests are to understand the genetic underpinnings of solid tumors and to identify genetic aberrations that can be exploited either as diagnostic markers and/or therapeutic targets using next generation sequencing (NGS) technologies. In particular, in the funded project, Dr. Piscuoglio will characterize the long-non coding RNA landscape of triple negative breast cancers. For more information please contact Dr. Salvatore Piscuoglio.

10.08.2016 / HONORS AND AWARDS

Dora Seif Award to Prof. Dr. Luigi Terracciano

Prof. Dr. Luigi Terracciano

We congratulate Prof. Dr. Luigi Terracciano for receiving the prestigious Dora Seif Award. Dr. Terracciano is professor for experimental pathology and head of the molecular pathology unit. His research group investigates the development of liver diseases, in particular the molecular and genomic structure of hepatocellular carcinoma. The Dora Seif prize is awarded every second year for the best research work leading to advances in early diagnostics and therapy treatment for patients with cancer. This year, Prof. Dr. Luigi Terracciano and Prof. Dr. Markus Heim receive this award in equal parts for their joint excellent work of investigating the development, classification and treatment of liver cancer. In particular, the award committee highlighted the successful and internationally esteemed collaboration of both awardees. For more information, please see the dedicated news of the University of Basel or contact Prof. Dr. Luigi Terracciano.

20.06.2016 / HONORS AND AWARDS

Maurice Goldblatt Award to Prof. Dr. Lukas Bubendorf

Award ceremony at International Congress of Cytology in Yokohama.

Prof. Dr. Lukas Bubendorf, professor for stem cell pathology and research group leader at the Institute for Pathology, was awarded with the prestigious Maurice Goldblatt Award of the International Academy of Cytology (IAC). He received this award and the associated gold medal at the opening ceremony of the 19th International Congress of Cytology in Yokohama (Japan). The award committee highlighted his merits “[…] for his innovative efforts to develop, test and introduce novel and modern techniques for the clinical practice in all aspects of cytology; and for his wide range of achievements in research […]”. Dr. Bubendorf is a senior consultant pathologist at the Institute for Pathology and head of the cytology unit. His research focuses on lung and urogenital cancers, in particular on the analysis of the molecular and genomic evolution. For more information, please visit the dedicated web site of the IAC.

01.06.2016 / RESEARCH

Genomic Analyses of DLBCLs Identify Clonally-Unrelated Relapses

Professor Alexandar Tzankov and his colleague Dr. Darius Juskevicius from the Institute for Pathology report in the current online issue of the journal Leukemia their novel findings on genomic analysis of relapsing diffuse large B-cell lymphomas (DLBCL). For this study they investigated a retrospective cohort of 20 paired relapsing and 20 non-relapsing DLBCL patients by array-comparative genomic hybridization and targeted deep sequencing. The researchers discovered that 15% of the patients who were affected by DLBCL recurrences suffered from novel clonally-unrelated tumors and not from clonally-related outgrowths of the primaries. This finding raises a question of immadiate clinical impact, i.e. whether a standard first-line treatment might be (again) effective for these patients, thus avoiding the side effects of a more aggressive chemotherapy that is usually applied to treat relapsed DLBCL. Additionally, they discovered that truly clonally-related DLBCL relapses can be genetically either closely or distantly related to the respective primary tumors. These differences potentially reflect different mechanisms through which primary tumors overcome therapy and recur. For the genomic analyses of this study, the researchers developed a custom lymphoma sequencing gene panel that is now being validated for use in diagnostic routine. For more information, please access the publication or contact Prof. Dr. Alexandar Tzankov.

18.05.2016 / HONORS AND AWARDS

Rudolf-Virchow-Preis 2016 Awarded to Prof. Dr. Daniel Baumhoer

The Research Unit of the Institute of Pathology congratulates Prof. Dr. Daniel Baumhoer for winning the prestigious Rudolf-Virchow-Preis. It is awarded by the German Society of Pathology to honor his outstanding scientific work on DNA repair deficiency in osteosarcomas (so-called BRCAness) recently published in Nature Communications. Dr. Baumhoer is a senior consultant pathologist at the Institute of Pathology and head of the Bone Tumor Reference Center in Basel. His research group focuses on the molecular evolution of bone tumours and especially of osteosarcomas. For more information, please see the official press release or contact Prof. Dr. Daniel Baumhoer.

01.05.2016 / HONORS AND AWARDS

Research Fund of the University of Basel to Dr. Lisa Restelli

The Research Unit of the Institute for Pathology is delighted that Dr. Lisa Restelli, a postdoctoral fellow of the research group of Prof. Stephan Frank, has been selected as recipient of the research fund of the career advancement center of Basel University. These grants are awarded in order to promote the academic careers of outstanding junior researchers at the local university. Lisa Restelli has obtained her PhD in Neurobiology from the University of Basel, studying the role of mitochondria shape regulators in brain physiology and metabolism. She will now further pursue this aspect by exploring the role of mitochondrial morphology in selected disease paradigms, e.g. Parkinson’s disease. For more information about our research in neurodegeneration, please visit our dedicated web site or contact Prof. Dr. Stephan Frank.

01.04.2016 / DEVELOPMENT

Start of Liquid Biopsy Diagnostics

Scanning electron microscopy (SEM) of human blood cells; © Dr. M. Oeggerli,

The research unit of the Institute for Pathology is pleased that the diagnostic department offers liquid biopsy genomics as diagnostic tests for cancer patients from 1st of April. Development and thorough validation of these tests was performed in the research unit of the Institute for Pathology in order to achieve highest accuracy, specificity and sensitivity. These assays are based on analysis of the circulating cell-free DNA (cfDNA) isolated from blood plasma by means of next-generation sequencing (NGS) and digital PCR. They specifically investigate the genomic profile of the patient’s tumor and presence of predictive mutations by using only a standard blood withdrawal. Our research unit continues on active developing of novel genomic assays for diagnostic routine, but does also apply these assays to samples from basic research as well as from clinical studies. For further information on cfDNA analysis in research, please contact Dr. Ivana Bratic Hench. For diagnostic cfDNA services, Dr. Luca Quagliata.

01.03.2016 / WELCOME!

Two Postdocs join the Institute for Pathology

The research unit of the Institute for Pathology is very pleased to welcome Dr. Charlotte Ng and Dr. Salvatore Piscuoglio as new research associates. Dr. Ng is a trained bioninformatician from the University of New South Wales (Australia) with a PhD from the University of Cambridge (UK). Dr. Piscuoglio graduated at the Federico II University in Naples (I) and obtained his PhD from the University of Basel. Both recently completed their postdoctoral fellowships at the Memorial Sloan Kettering Cancer Center in New York where they focused on the genomic analyses of solid tumor specimens and circulating cell-free tumor DNA (liquid biopsies) by next-generation sequencing. Their broad experience and know how in cancer genomics and data analysis complement the emphasis on genomics as the focal area of cancer research at our institute. The research unit of the Institute for Pathology now comprises 11 postdoctoral fellows and 10 PhD students. For more information about our research, please contact Dr. Christian Ruiz.

01.01.2016 / RESEARCH

Osteosarcoma Sequencing Project Identifies Novel BRCA Mutation Signatures

In the early December issue of Nature Communications, Prof. Dr. Daniel Baumhoer and his colleague Dr. Michal Kovac from the Institute for Pathology reported on their findings of exome sequenced osteosarcomas. These rare and aggressive tumours of bone are known to harbour complex karyotypes with abundant numerical and structural aberrations that differ significantly between individual tumours. They found osteosarcomas not only to represent polyclonal populations of tumour cells with up 16 distinct subclones per sample and identified 14 individual driver genes but importantly also detected a common genetic trait despite inter- and intratumoural heterogeneity. More than 80% of osteosarcomas exhibited a specific combination of single-base substitutions, LOH, or large-scale genome instability signatures characteristic of BRCA1/2-deficient tumours. Preliminary experiments involving osteosarcoma cell lines furthermore demonstrated a significant reduction of cell viability following PARP-inhibitor treatment indicating the genetic findings to be functionally relevant. These findings might serve as a molecular basis for more individualized and targeted treatment approaches in osteosarcoma which are urgently needed. For more information, please access the » publication or contact Prof. Dr. Daniel Baumhoer.

01.12.2015 / LABORATORY

Novel Research Laboratory inaugurated

Due to an increased demand, the research unit of the Institute for Pathology has continued enlarging its research capacities. The recent inauguration of the novel general research laboratory increases the number of laboratory and office spaces by 10 and 18, respectively. With this latest addition, the Institute for Pathology provides 296 m2 of laboratory area dedicated to research. In addition, 66 m2 area serve as research offices. The laboratory space is now composed of two general research laboratories as well as eight specialized research laboratories, such as immunohistochemistry and genomics. For further information, please visit our » research web or contact Dr. Christian Ruiz.