Implementation of paediatric precision oncology into clinical practice: The Individualized Therapies for Children with cancer program ‘iTHER’

iTHER is a Dutch prospective national precision oncology program aiming to define tumour molecular profiles in children and adolescents with primary very high-risk, relapsed, or refractory paediatric tumours. Between April 2017 and April 2021, 302 samples from 253 patients were included. Comprehensive molecular profiling including low-coverage whole genome sequencing (lcWGS), whole exome sequencing (WES), RNA sequencing (RNA-seq), Affymetrix, and/or 850k methylation profiling was successfully performed for 226 samples with at least 20% tumour content. Germline pathogenic variants were identified in 16% of patients (35/219), of which 22 variants were judged causative for a cancer predisposition syndrome. At least one somatic alteration was detected in 204 (90.3%), and 185 (81.9%) were considered druggable, with clinical priority very high (6.1%), high (21.3%), moderate (26.0%), intermediate (36.1%), and borderline (10.5%) priority. iTHER led to revision or refinement of diagnosis in 8 patients (3.5%). Temporal heterogeneity was observed in paired samples of 15 patients, indicating the value of sequential analyses. Of 137 patients with follow-up beyond twelve months, 21 molecularly matched treatments were applied in 19 patients (13.9%), with clinical benefit in few. Most relevant barriers to not applying targeted therapies included poor performance status, as well as limited access to drugs within clinical trial. iTHER demonstrates the feasibility of comprehensive molecular profiling across all ages, tumour types and stages in paediatric cancers, informing of diagnostic, prognostic, and targetable alterations as well as reportable germline variants. Therefore, WES and RNA-seq is nowadays standard clinical care at the Princess Máxima Center for all children with cancer, including patients at primary diagnosis. Improved access to innovative treatments within biology-driven combination trials is required to ultimately improve survival

Implementation of paediatric precision oncology into clinical practice: The Individualized Therapies for Children with cancer program ‘iTHER’

iTHER is a Dutch prospective national precision oncology program aiming to define tumour molecular profiles in children and adolescents with primary very high-risk, relapsed, or refractory paediatric tumours. Between April 2017 and April 2021, 302 samples from 253 patients were included. Comprehensive molecular profiling including low-coverage whole genome sequencing (lcWGS), whole exome sequencing (WES), RNA sequencing (RNA-seq), Affymetrix, and/or 850k methylation profiling was successfully performed for 226 samples with at least 20% tumour content. Germline pathogenic variants were identified in 16% of patients (35/219), of which 22 variants were judged causative for a cancer predisposition syndrome. At least one somatic alteration was detected in 204 (90.3%), and 185 (81.9%) were considered druggable, with clinical priority very high (6.1%), high (21.3%), moderate (26.0%), intermediate (36.1%), and borderline (10.5%) priority. iTHER led to revision or refinement of diagnosis in 8 patients (3.5%). Temporal heterogeneity was observed in paired samples of 15 patients, indicating the value of sequential analyses. Of 137 patients with follow-up beyond twelve months, 21 molecularly matched treatments were applied in 19 patients (13.9%), with clinical benefit in few. Most relevant barriers to not applying targeted therapies included poor performance status, as well as limited access to drugs within clinical trial. iTHER demonstrates the feasibility of comprehensive molecular profiling across all ages, tumour types and stages in paediatric cancers, informing of diagnostic, prognostic, and targetable alterations as well as reportable germline variants. Therefore, WES and RNA-seq is nowadays standard clinical care at the Princess Máxima Center for all children with cancer, including patients at primary diagnosis. Improved access to innovative treatments within biology-driven combination trials is required to ultimately improve survival

Preserved reactive germinal centers in follicular lymphoma is a strong histopathologic indicator of limited disease stage

Follikuläre Lymphome (FL) zählen zu den Non-Hodgkin-Lymphomen und stellen die größte Untergruppe der B-Zell-Lymphome dar. Bedingt durch ihren meist indolenten Verlauf werden sie oft erst in einem fortgeschrittenen klinischen Stadium III/IV diagnostiziert und stellen dann eine systemische Erkrankung dar. Gelegentlich wird in der histopathologischen Untersuchung eines befallenen Lymphknotens eine nur partielle Infiltration beobachtet, die häufig auch in den angeschlossenen Stagingmaßnahmen mit einer nur lokalen Tumorausbreitung (klinisches Stadium I/II) assoziiert ist. Ein solches lokal begrenztes Stadium kann gemäß der Standard-Behandlungsprotokolle mit einer alleinigen Strahlentherapie ausreichend kontrolliert werden. Ziel der vorliegenden Arbeit war es zum einen, eine mögliche Assoziation einer nur partiellen Lymphknoteninfiltration beim FL mit einem lokal begrenzten klinischen Stadium zu untersuchen. Zum anderen sollte die Inzidenz einer nur partiellen Lymphknoten- Infiltration beim FL bestimmt werden. Der Vergleich der Studienkohorte mit einer nur partiellen Lymphknoteninfiltration, definiert als zumindest ein vollständig erhaltener Lymphfollikel, mit der Kontrollkohorte zeigte einen hochsignifikanten Unterschied: In der Studienkohorte befanden sich 38 von 40 Fälle (95%) in einem lokalen Stadium, wohingegen die Kontrollkohorte mit vollständiger Lymphknoteninfiltration nur bei 10 von 49 Patienten (20%) ein lokales Krankheitsstadium (p<0.001) aufwies. Um die erhaltenen Ergebnisse zu validieren, wurden alle FL Grad 1-3A aus dem exemplarischen Jahr 2001 untersucht. Hier zeigte sich in 34 Fällen (11 %) eine nur partielle Infiltration. In allen 18 Fällen mit mindestens einem vollständig erhaltenen reaktiven Keimzentrum lag in Übereinstimmung mit der initialen Studienkohorte ein lokales Krankheitsstadium I/II vor (p<0.001). Die erhaltenen Ergebnisse zeigen eindrücklich, dass follikuläre Lymphome mit einem nur partiellen Befall der Lymphknoten häufig mit einem (noch) lokalen klinischen Stadium assoziiert sind. In diesen Fällen käme eine alleinige Bestrahlung als Therapieoption in Betracht.Follicular lymphoma belongs to the non-Hodgkin lymphoma and represents the greatest subtype of B-cell-lymphomas. Due to their mostly indolent clinical course they are often diagnosed in clinical stages III/IV, i.e. as a systemic disease. We occasionally observed in cases with preserved reactive follicle structures (so called partial infiltration) an association with an only limited clinical stage I/II. According to standard protocolsthese cases can be controlled with radiotherapy alone. The purpose of this study was to analyze a possible association of a partial infiltration of follicular lymphoma with a limited stage I/II of disease and to determine the incidence of a partial infiltration in FL. Comparing the study group of 53 lymph node biopsies with a partial infiltration defined as at least one totally preserved follicle with the control group we found a highly significant difference: In the study group 38 of 40 cases (95%) showed a local clinical stage, while the control groupwith total infiltration of the lymph node only in 10 of 49 patients (20%) presented a local stage of disease (p<0.001). To validate these results all follicular lymphoma cases WHO grade1-3A in the exemplary year 2001 were examined. In 34 cases (11%) a partial lymph node infiltration was found. In all the 18 cases with at least one totally preserved reactive GC a local stage of disease I/II (p<0.001) was found according to the results of the initial study group. The results show impressively that follicular lymphoma with a partial infiltration of the lymph node are often associated with a (still) local clinical stage of disease. In these cases radiotherapy alone can be regarded as a treatment option

Interplay of PTEN subcellular localization and catalytic activities in vivo

This thesis describes the use of mammalian cells, S. cerevisiae and D. rerio to unravel the complex interplay of PTEN subcellular localization and catalytic activities. In Chapter 1 we provide a general introduction to the PI3K/Akt(PKB)/PTEN axis, PTEN phosphatase-dependent and –independent functions and regulation of those functions through changes in protein conformation and subcellular localization. Last, we give a short résumé on the role of PTEN in human health and disease. In Chapter 2, we give an overview of developmental and pathological processes that have been successfully studied in zebrafish pten models. Further, we introduce techniques that we and others have developed for modulation of Pten expression in vivo and for the establishment of zebrafish cell lines from tumors. In Chapter 3 we performed a comprehensive mutational and functional analysis of the PTEN N-terminus. To analyze the contribution of this region to PTEN tumor suppressor function in vivo, we studied a panel of tumor-related mutations, employing S.cerevisiae and mammalian cells. We found that most tumor-related N-terminal PTEN mutations that lead to a loss of PIP3-phosphatase activity also showed impaired nuclear localization. This suggests that PIP3 catalytic activity and nuclear localization of PTEN are coordinated by the PTEN N-terminus in an overlapping manner. Our results from soft agar colony formation assays further indicated that both the PTEN PIP3 phosphatase activity and the PTEN capacity to accumulate in the nucleus were important for the full tumor suppression capacity of PTEN. In Chapter 4 we focused on the classical protein import pathway as a possible major nuclear transport mechanism for PTEN and, by immunofluorescence and confocal microscopy performed in mammalian cells, we identified importin alpha3 as a factor involved in PTEN nuclear translocation. Further, we found that the PTEN N-terminal region (residues 1-32) could mediate nuclear accumulation of PTEN through interactions with nuclear transporters. Systematic introduction of point mutations in the importin alpha 3 substrate binding pockets allowed us to further narrow down the region of importin alpha 3 that is important for nuclear accumulation of PTEN to the minor binding pocket. Using the zebrafish as a model organism, in Chapter 5 we unveil a differential requirement of Pten lipid and protein phosphatase activity during embryonic development. To this end, we performed rescue assays. We propose that the role of Pten during angiogenesis mainly consists of suppressing PI3K signaling via its lipid phosphatase activity, whereas the complex process of embryonic development requires lipid and protein phosphatase activity of Pten. In Chapter 6 we characterize the subcellular localization and the functional consquences of the expression of open conformation PTEN. The functional hyperactivity of open conformation PTEN in comparison to PTEN wild type in our model seemed to result predominantly from its enhanced recruitment to the cytoplasmic membrane. In conclusion, we show that enhanced membrane localization of phosphatase active PTEN dramatically increased its biological function in suppression of angiogenic sprouting. The findings of this chapter demonstrate the requirement of tightly regulated and equilibrated Pten activity during zebrafish development and angiogenesis. Finally, Chapter 7 provides a summarizing discussion of the work presented in each previous chapter

Differential requirement for pten lipid and protein phosphatase activity during zebrafish embryonic development

The lipid- and protein phosphatase PTEN is one of the most frequently mutated tumor suppressor genes in human cancers and many mutations found in tumor samples directly affect PTEN phosphatase activity. In order to understand the functional consequences of these mutations in vivo, the aim of our study was to dissect the role of Pten phosphatase activities during zebrafish embryonic development. As in other model organisms, zebrafish mutants lacking functional Pten are embryonically lethal. Zebrafish have two pten genes and pten double homozygous zebrafish embryos develop a severe pleiotropic phenotype around 4 days post fertilization, which can be largely rescued by re-introduction of pten mRNA at the one-cell stage. We used this assay to characterize the rescue-capacity of Pten and variants with mutations that disrupt lipid, protein or both phosphatase activities. The pleiotropic phenotype at 4dpf could only be rescued by wild type Pten, indicating that both phosphatase activities are required for normal zebrafish embryonic development. An earlier aspect of the phenotype, hyperbranching of intersegmental vessels, however, was rescued by Pten that retained lipid phosphatase activity, independent of protein phosphatase activity. Lipid phosphatase activity was also required for moderating pAkt levels at 4 dpf. We propose that the role of Pten during angiogenesis mainly consists of suppressing PI3K signaling via its lipid phosphatase activity, whereas the complex process of embryonic development requires lipid and protein phosphatase of Pten

Pten function in zebrafish : Anything but a fish story

Zebrafish is an excellent model system for the analysis of gene function. We and others use zebrafish to investigate the function of the tumor suppressor, Pten, in tumorigenesis and embryonic development. Zebrafish have two pten genes, ptena and ptenb. The recently identified N-terminal extension of human PTEN that may facilitate cell membrane transfer, appears not to be conserved in zebrafish Ptena or Ptenb. Mutants that retain a single wild type pten allele develop tumors, predominantly hemangiosarcomas. Homozygous double mutants are embryonic lethal. Zebrafish embryos lacking functional Pten display enhanced proliferation of endothelial cells, resulting in hyperbranching of blood vessels. In addition, ptena-/-ptenb-/- mutant embryos display enhanced proliferation of hematopoietic stem and progenitor cells and concomitant arrest of differentiation, although Pten-deficient cells commit to all blood cell lineages. Zebrafish is an ideal model for intravital imaging and future work using ptena-/-ptenb-/- mutants will enhance our understanding of the function of Pten in vivo. (C) 2014 Elsevier Inc. All rights reserved

A functional dissection of PTEN N-terminus: implications in PTEN subcellular targeting and tumor suppressor activity.

Spatial regulation of the tumor suppressor PTEN is exerted through alternative plasma membrane, cytoplasmic, and nuclear subcellular locations. The N-terminal region of PTEN is important for the control of PTEN subcellular localization and function. It contains both an active nuclear localization signal (NLS) and an overlapping PIP2-binding motif (PBM) involved in plasma membrane targeting. We report a comprehensive mutational and functional analysis of the PTEN N-terminus, including a panel of tumor-related mutations at this region. Nuclear/cytoplasmic partitioning in mammalian cells and PIP3 phosphatase assays in reconstituted S. cerevisiae defined categories of PTEN N-terminal mutations with distinct PIP3 phosphatase and nuclear accumulation properties. Noticeably, most tumor-related mutations that lost PIP3 phosphatase activity also displayed impaired nuclear localization. Cell proliferation and soft-agar colony formation analysis in mammalian cells of mutations with distinctive nuclear accumulation and catalytic activity patterns suggested a contribution of both properties to PTEN tumor suppressor activity. Our functional dissection of the PTEN N-terminus provides the basis for a systematic analysis of tumor-related and experimentally engineered PTEN mutations

Fine-Tuning of Pten Localization and Phosphatase Activity Is Essential for Zebrafish Angiogenesis

The lipid- and protein phosphatase PTEN is an essential tumor suppressor that is highly conserved among all higher eukaryotes. As an antagonist of the PI3K/Akt cell survival and proliferation pathway, it exerts its most prominent function at the cell membrane, but (PIP3-independent) functions of nuclear PTEN have been discovered as well. PTEN subcellular localization is tightly controlled by its protein conformation. In the closed conformation, PTEN localizes predominantly to the cytoplasm. Opening up of the conformation of PTEN exposes N-terminal and C-terminal regions of the protein that are required for both interaction with the cell membrane and translocation to the nucleus. Lack of Pten leads to hyperbranching of the intersegmental vessels during zebrafish embryogenesis, which is rescued by expression of exogenous Pten. Here, we observed that expression of mutant PTEN with an open conformation rescued the hyperbranching phenotype in pten double homozygous embryos and suppressed the increased p-Akt levels that are characteristic for embryos lacking Pten. In addition, in pten mutant and wild type embryos alike, open conformation PTEN induced stalled intersegmental vessels, which fail to connect with the dorsal longitudinal anastomotic vessel. Functional hyperactivity of open conformation PTEN in comparison to wild type PTEN seems to result predominantly from its enhanced recruitment to the cell membrane. Enhanced recruitment of phosphatase inactive mutants to the membrane did not induce the stalled vessel phenotype nor did it rescue the hyperbranching phenotype in pten double homozygous embryos, indicating that PTEN phosphatase activity is indispensable for its regulatory function during angiogenesis. Taken together, our data suggest that PTEN phosphatase activity needs to be carefully fine-tuned for normal embryogenesis and that the control of its subcellular localization is a key mechanism in this process

Both Pten phosphatase activities are required to rescue the <i>ptena-/-ptenb-/-</i> pleiotropic phenotype.

<p>Zebrafish embryos from a <i>ptena+/- ptenb-/-</i> incross were injected with either wild type Ptenb-mCherry, Ptenb-mCherry C124S, Ptenb-mCherry G129E or Ptenb-mCherry Y138L encoding synthetic mRNA at the one-cell stage. <b>(A)</b> At 4 dpf the embryos were submitted to brightfield microscopy and analyzed for the pleiotropic phenotype. Pictures show representative, genotyped embryos. Non-injected control embryos (NIC) were included for reference. <b>(B)</b> Quantification of the embryos showing the typical <i>ptena</i>-/-<i>ptenb</i>-/- pleiptropic phenotype at 4dpf. In the non-injected control (NIC), approximately 25% of the embryos showed the characteristic phenotype (Mendelian segregation). Only wild type Ptenb-mCherry rescued the pleiotropic <i>ptena</i>-/-<i>ptenb</i>-/- phenotype significantly at 4dpf. The statistical significance of each of the conditions compared to the non-injected control was determined using two-tailed Fisher’s exact test and is indicated in the bar graph (ns = not significant, * = p-value < 0,05, ** = p-value < 0,01, *** = p-value < 0,001).</p

The hyperbranching vasculature phenotype, observed in Pten double homozygous zebrafish embryos at 3dpf, can be rescued by wild type Pten.

<p>Zebrafish embryos from a Tg(<i>kdrl</i>:<i>eGFP) ptena+/-ptenb-/-</i> incross were microinjected at the one-cell stage with 300 pg synthetic mRNA encoding Ptenb-mCherry. At 3dpf the embryos were analyzed for the hyperbranching vessel phenotype by confocal live imaging on a Leica TCS-SPE microscope (anterior to the left, 20x objective, 2μm z-stacks). Subsequently, the embryos were genotyped. Pictures show the trunk region distal from the urogenital opening of representative embryos; non-injected control embryos (control) were included for reference.</p