Genomics of Pulmonary Hypertension

Background - Pulmonary hypertension (PH), defined by mean pulmonary artery pressure >20 mmHg, is a common physiologic manifestation of many diseases. Pulmonary arterial hypertension (PAH) represents a smaller subgroup of patients who have PH, and PAH causes significant cardiorespiratory morbidity and premature mortality. PH can manifest across the lifespan, with similar incidence for both pediatric- and adult-onset disease. However, pediatric-onset disease is particularly challenging because it is frequently associated with a more severe clinical course and comorbidities including lung and heart developmental anomalies. For PH Group 1/pulmonary arterial hypertension, causal genetic variants can be identified in ~13% of adults and ~43% of children. Clinical implications – Education about the option for genetic testing is strongly recommended for all pediatric and adult HPAH/IPAH patients. Both gene panel and exome/genome sequencing tests can be useful in diagnosis, but exome/genome sequencing provides a comprehensive dataset for reanalysis over time for cases without an initial diagnosis. Knowledge of genetic diagnoses can immediately impact clinical management of PH, including multimodal medical treatment, surgical intervention, transplantation decisions, and screening for associated conditions. Conclusions - There is a need for large, diverse, international consortia with ever-improving analytical pipelines to confirm previously implicated genes, identify additional genes/variants, assess penetrance, and clinically characterize each genetic subtype for natural history, prognosis and response to therapies to inform more precise clinical management.

IOTG-01. Computational Neurosurgery in Brain Tumors: A paradigm shift on the use of Artificial Intelligence and Connectomics in pre- and intra-operative imaging

Computational Neurosurgery is a novel field where computational modeling and artificial intelligence (AI) are used to analyze diseases of neurosurgical interest. Our aim is to apply AI models to brain tumor (BT) images to a) automatically segment BTs on pre-operative MRI, b) predict the genetic subtype of glioma on intra- and post-operative histological specimens; and c) predict the extent of resection according to connectomics data. For the segmentation task, we used 510 BT images to train a deep learning (DL) model for automatic segmentation of the tumors’ edges and comparison of the AI-generated masks versus experts’ consensus (quantified by means of the dice score). For the histopathology task, we digitalized 266 hematoxylin/eosin slides of gliomas (including 130 IDH-wildtype and 136 IDH-mutant) and applied a DL architecture to predict the IDH genetic status, then validated by immunohistochemistry and genetic sequencing. The datasets were also augmented by generating synthetic glioma images by means of a Generative Adversarial Network methodology. The resection of 10 BTs was also customized according to connectomics data. In the segmentation experiment, we reached a dice score of ~0.9 (out of 1.0), while further demonstrating that only the T1, T1 after gadolinium, and FLAIR sequences are necessary for accurate automatic segmentation. In the histopathology task, we were able to predict the genetic status with accuracy between 76% and 95% using the DL model. The machine learning-based connectome analysis allowed us to perform safe supramaximal resection. We have shown the robustness of applying AI methodology or the automatic segmentation of BTs in MR imaging. Moreover, we have also shown that AI can be used to predict the genetic status, specifically, IDH, in histopathology images of gliomas. Our results support the use of AI in the clinical scenario for a fast and objective computerized characterization of patients affected by BTs.

Distinct clinical characteristics of DUX4 and PAX5 altered childhood B-lymphoblastic leukemia

In childhood B-ALL, among the recently described subtypes were DUX4 and PAX5 altered (PAX5alt). Using whole transcriptome RNA sequencing (RNA-Seq) in 377 B-ALL children from MaSpore ALL 2003/2010 (MS2003/MS2010) studies, we found that, after hyperdiploid and ETV6-RUNX1, the third and fourth most common subtypes were DUX4 (n= 51; 14%) and PAX5alt (n= 36; 10%). DUX4 also formed the largest genetic subtype among patients with poor Day 33 MRD (n=12/44). But despite the poor MRD, outcome of DUX4 B-ALL was excellent (5-year cumulative risk of relapse (CIR) 8.9% [95% CI, 2.8% to 19.5%], 5-year OS 97.8% [95% CI, 85.3% to 99.7%]). In MS2003, 21% DUX4 B-ALL had poor peripheral blood (PB) response to prednisolone at day 8, higher than other subtypes (8%; P=0.03). In MS2010, with vincristine at day 1, no day 8 poor PB response was observed in DUX4 subtype (P=0.03). PAX5alt group had an intermediate risk of relapse (5-year CIR 18.1%) but when IKZF1 was not deleted, outcome was excellent with no relapse among 23 patients. Compared to MS2003, outcome of PAX5alt B-ALL with IKZF1 co-deletion was improved by treatment intensification in MS2010 (5-year CIR 80.0% vs 0%; P=0.05). In conclusion, despite its poor initial response, DUX4 B-ALL had a favorable overall outcome, and the prognosis of PAX5alt was strongly dependent on IKZF1 co-deletion.

Novel class of ZNF384 aberrations in acute leukemia

Fusion of the ZNF384 gene as the 3' partner to several different 5' partner genes occurs recurrently in B-cell precursor acute lymphoblastic and mixed phenotype B/myeloid leukemia. These canonical fusions (ZNF384r) contain the complete ZNF384 coding sequence and are associated with a specific gene expression signature. Cases with this signature, but without canonical ZNF384 fusions (ZNF384r-like cases), have been described previously. Though some have been shown to harbor ZNF362 fusions, the primary aberrations remain unknown in a major proportion. We studied three patients with the ZNF384r signature and unknown primary genetic background and identified a previously unknown class of genetic aberration affecting the last exon of ZNF384 and resulting in disruption of the C-terminal portion of the ZNF384 protein. Importantly, in two cases, the ZNF384 aberration - indel - was missed during the bioinformatic analysis but revealed by the manual, targeted reanalysis. Two cases with the novel aberrations had a mixed (B/myeloid) immunophenotype commonly associated with canonical ZNF384 fusions. In conclusion, we present leukemia cases with a novel class of ZNF384 aberrations that phenocopy leukemia with ZNF384r. Therefore, we show that part of the so-called ZNF384r-like cases represent the same genetic subtype as leukemia with canonical ZNF384 fusions.

How to unmask unique vulnerabilities in leukaemia

How to unmask unique vulnerabilities in leukaemia Acute myeloid leukaemia (AML) is a group of haematologic malignancies that have been traditionally difficult to classify and treat. Nucleophosmin (NPM1) mutations are the most frequent genetic alteration (about 30 per cent) in AML and NPM1-mutated AML is a new entity in the WHO classification of myeloid neoplasms. However, mechanisms of leukemogenesis and a specific therapy for this leukaemia are missing. The ContraNPM1AML project aims to unravel the complex network of molecular interactions that take place in this distinct genetic subtype and find their vulnerabilities to identify new targets for therapy. The expected discoveries will lead to novel therapeutic approaches and make clinical trials available to patients.

Genetic Alterations in Childhood Acute Lymphoblastic Leukemia: Interactions with Clinical Features and Treatment Response

Acute lymphoblastic leukemia (ALL) is the most common cancer among children. This aggressive cancer comprises multiple molecular subtypes, each harboring a distinct constellation of somatic, and to a lesser extent, inherited genetic alterations. With recent advances in genomic analyses such as next-generation sequencing techniques, we can now clearly identify >20 different genetic subtypes in ALL. Clinically, identifying these genetic subtypes will better refine risk stratification and determine the optimal intensity of therapy for each patient. Underpinning each genetic subtype are unique clinical and therapeutic characteristics, such as age and presenting white blood cell (WBC) count. More importantly, within each genetic subtype, there is much less variability in treatment response and survival outcomes compared with current risk factors such as National Cancer Institute (NCI) criteria. We review how this new taxonomy of genetic subtypes in childhood ALL interacts with clinical risk factors used widely, i.e., age, presenting WBC, IKZF1del, treatment response, and outcomes.

Incidence of strabismus, strabismus surgeries, and other vision conditions in Prader-Willi syndrome: data from the Global Prader-Willi Syndrome Registry

Background There is a relative lack of information on the incidence and treatment of vision problems in Prader-Willi syndrome (PWS). Using data from the Global PWS Registry, we performed a cross-sectional study of vision problems in PWS. Methods Data, reported by caregivers who completed the Vision Survey in the Global PWS Registry between May of 2015 and March of 2020, were analyzed using descriptive statistics. Results There were 908 participants in this survey, with a mean age of 14.5 years (range 0–62 years). The prevalence of strabismus in this population was 40 %, with no statistically significant difference in prevalence by genetic subtype. Ninety-one percent of participants with strabismus were diagnosed before 5 years of age. Of those with strabismus, 42 % went on to have strabismus surgery, with 86 % of those having their first strabismus surgery before 5 years of age and 10.1 % having more than one strabismus surgery. Additional vision issues reported included myopia (41 %), hyperopia (25 %), astigmatism (25 %), and amblyopia (16 %). Conclusions The prevalence of strabismus, amblyopia, and hyperopia are considerably higher in the PWS population represented in the Global PWS Registry as compared to the general population. People with PWS should be screened early and regularly for vision problems.

The Genetics of Uveal Melanoma: Overview and Clinical Relevance

Over the last ten years, much has been learnt about the genetic characteristics and genetic evolution of uveal melanoma. It has been shown that uveal melanoma differs fundamentally from non-uveal melanoma and is an independent genetic subtype. Compared to other tumours, uveal melanoma has a low mutational burden. There are recurring chromosomal aberrations with losses of 1p, 6q, 8p and 16q, gains of 6p and 8q, and the presence of monosomy 3. GNAQ, GNA11, PLCB4, CYSLTR2, MAPKAPK5, as well as mutations in BAP1, SF3B1, SRSF2 and EIF1AX, the latter being linked to a higher risk of metastasis, have been identified as significantly mutated genes. In rare cases, a BAP1 germline mutation may also be present. In addition to higher risk of uveal melanoma, this variant is also linked with other tumours. In this case, additional work-up, genetic counselling and screening of family members should be offered. While the knowledge about the genetic characteristics of uveal melanoma is already routinely used for diagnostic and prognostic purposes, targeted genotype-dependent therapy of uveal melanoma is currently still missing.