Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations.

Mutations in splicing factor 3B subunit 1 (SF3B1) frequently occur in patients with chronic lymphocytic leukemia (CLL) and myelodysplastic syndromes (MDS). These mutations have different effects on the disease prognosis with beneficial effect in MDS and worse prognosis in CLL patients. A full-length transcriptome approach can expand our knowledge on SF3B1 mutation effects on RNA splicing and its contribution to patient survival and treatment options. We applied long-read transcriptome sequencing (LRTS) to 44 MDS and CLL patients, as well as two pairs of isogenic cell lines with and without SF3B1 mutations, and found >60% of novel isoforms. Splicing alterations were largely shared between cancer types and specifically affected the usage of introns and 3' splice sites. Our data highlighted a constrained window at canonical 3' splice sites in which dynamic splice site switches occurred in SF3B1-mutated patients. Using transcriptome-wide RNA binding maps and molecular dynamics simulations, we showed multimodal SF3B1 binding at 3' splice sites and predicted reduced RNA binding at the second binding pocket of SF3B1K700E Our work presents the hitherto most complete LRTS study of the SF3B1 mutation in CLL and MDS and provides a resource to study aberrant splicing in cancer. Moreover, we showed that different disease prognosis most likely results from the different cell types expanded during carcinogenesis rather than different mechanisms of action of the mutated SF3B1 These results have important implications for understanding the role of SF3B1 mutations in hematological malignancies and other related diseases.

Association of Lesion Pattern and Dysphagia in Acute Intracerebral Hemorrhage.

Background and Purpose: Dysphagia is a common and severe symptom of acute stroke. Although intracerebral hemorrhages (ICHs) account for 10% to 15% of all strokes, the occurrence of dysphagia in this subtype of stroke has not been widely investigated. The aim of this study was to evaluate the overall frequency and associated lesion locations and clinical predictors of dysphagia in patients with acute ICH. Methods: Our analysis included 132 patients with acute ICH. Clinical swallowing assessment was performed within 48 hours after admission. All patients underwent computed tomography imaging. Voxel-based lesion-symptom mapping was performed to determine lesion sites associated with dysphagia. Results: Eighty-four patients (63.6%) were classified as dysphagic. Higher scores on the National Institutes of Health Stroke Scale, larger ICH volumes, and higher degree of disability were associated with dysphagia. Voxels showing a statistically significant association with dysphagia were mainly located in the right insular cortex, the right central operculum, as well as the basal ganglia, corona radiata, and the left thalamus and left internal capsule. In contrast to lobar regions, in subcortical deep brain areas also small lesion volumes (<10 mL) were associated with a substantial risk of dysphagia. Intraventricular ICH extension and midline shift as imaging findings indicating a space-occupying effect were not associated with dysphagia in multivariate analysis. Conclusions: Dysphagia is a frequent symptom in acute ICH. Distinct cortical and subcortical lesion sites are related to swallowing dysfunction and predictive for the development of dysphagia. Therefore, patients with ICH should be carefully evaluated for dysphagia independently from lesion size, in particular if deep brain regions are affected.

Predictors of malignant swelling in space-occupying cerebellar infarction.

BACKGROUND: Malignant swelling is a fatal complication that can occur abruptly in space-occupying cerebellar infarction. We aimed to establish markers that predict malignant swelling in cerebellar infarction. METHODS: We retrospectively analysed data of stroke patients who were treated in our hospital between 2014 and 2020. Malignant swelling was defined as a mass effect in the posterior cranial fossa, accompanied by a decrease in consciousness due to compression of the brainstem and/or the development of obstructive hydrocephalus. Statistical analyses were performed on multiple variables to identify predictors of malignant swelling. RESULTS: Among 7284 stroke patients, we identified 487 patients with an infarct in the cerebellum. 93 patients were suitable for analysis having space-occupying cerebellar infarction. 33 of 93 (35.5%) patients developed malignant swelling. Multivariable analysis revealed infarct volume as the main predictor being independently associated with the development of malignant swelling with a cut-off infarct volume of 38 cm3 being associated with a swelling rate of >50% (OR 32.0, p<0.001). Higher NIHSS (National Institutes of Health Stroke Scale) score on admission (median NIHSS 12 vs 4, OR 1.078; p=0.008) and the presence of additional brainstem infarction (51.5% vs 16.7%, OR 5.312; p=0.013) were associated with the development of malignant swelling in univariate analyses. 13 of 33 (39.4%) cases of malignant swellings occurred after more than 3 days. CONCLUSIONS: Infarct volume was the key significant predictor of malignant swelling in space-occupying cerebellar infarction. With many cases of malignant swelling occurring after more than 72 hours, we advocate prolonged neurological monitoring.

Pericentromeric Satellite III transcripts induce etoposide resistance.

Non-coding RNA from pericentromeric satellite repeats are involved in stress-dependent splicing processes, maintenance of heterochromatin, and are required to protect genome stability. Here we show that the long non-coding satellite III RNA (SatIII) generates resistance against the topoisomerase IIa (TOP2A) inhibitor etoposide in lung cancer. Because heat shock conditions (HS) protect cells against the toxicity of etoposide, and SatIII is significantly induced under HS, we hypothesized that the protective effect could be traced back to SatIII. Using genome methylation profiles of patient-derived xenograft mouse models we show that the epigenetic modification of the SatIII DNA locus and the resulting SatIII expression predict chemotherapy resistance. In response to stress, SatIII recruits TOP2A to nuclear stress bodies, which protects TOP2A from a complex formation with etoposide and results in decreased DNA damage after treatment. We show that BRD4 inhibitors reduce the expression of SatIII, restoring etoposide sensitivity.