Computational drug prediction in hepatoblastoma by integrating pan-cancer transcriptomics with pharmacological response.

BACKGROUND AND AIMS: Hepatoblastoma (HB) is the predominant form of pediatric liver cancer, though it remains exceptionally rare. While treatment outcomes for children with HB have improved, patients with advanced tumors face limited therapeutic choices. Additionally, survivors often suffer from long-term adverse effects due to treatment, including ototoxicity, cardiotoxicity, delayed growth, and secondary tumors. Consequently, there is a pressing need to identify new and effective therapeutic strategies for patients with HB. Computational methods to predict drug sensitivity from a tumor's transcriptome have been successfully applied for some common adult malignancies, but specific efforts in pediatric cancers are lacking because of the paucity of data. APPROACH AND RESULTS: In this study, we used DrugSense to assess drug efficacy in patients with HB, particularly those with the aggressive C2 subtype associated with poor clinical outcomes. Our method relied on publicly available collections of pan-cancer transcriptional profiles and drug responses across 36 tumor types and 495 compounds. The drugs predicted to be most effective were experimentally validated using patient-derived xenograft models of HB grown in vitro and in vivo. We thus identified 2 cyclin-dependent kinase 9 inhibitors, alvocidib and dinaciclib as potent HB growth inhibitors for the high-risk C2 molecular subtype. We also found that in a cohort of 46 patients with HB, high cyclin-dependent kinase 9 tumor expression was significantly associated with poor prognosis. CONCLUSIONS: Our work proves the usefulness of computational methods trained on pan-cancer data sets to reposition drugs in rare pediatric cancers such as HB, and to help clinicians in choosing the best treatment options for their patients.

Finding a City Name in a Traffic Sign: Effects of Word Case and Visual Motion.

OBJECTIVES: To investigate the word recognition effects of the use of all-uppercase (e.g., VALENCIA) or titled-case (e.g., Valencia) for city names in traffic signs, controlling for word size, and comparing stationary and dynamic viewing situations. BACKGROUND: Prior studies provide mixed evidence regarding the effects of word case on the recognition of city names in traffic signs. Moreover, the evidence on the potential impact of visual motion on these effects is scarce. METHOD: We carried out an experimental study using simulated traffic signs. The task was to indicate, for each sign, whether it contained a given city name or not (word search task, 50% positive trials). Visual motion of signs was manipulated as a between-participants factor: stationary (the sign was still) versus dynamic (the sign expanded as if the participant was approaching to it). Word case was manipulated as a within-participants factor: all-uppercase versus two titled-case conditions varying in font size: width-matched titled-case and point size-matched titled-case. RESULTS: In both the stationary and dynamic conditions, all-uppercase resulted in more incorrect responses and slower latencies than width-matched titled-case. When compared to point size-matched titled-case, all-uppercase produced slower correct responses in the stationary condition, whereas faster in the dynamic condition. CONCLUSION: Other factors being equal, all-uppercase city names will be recognized worse than their titled-case versions in traffic signs, both in stationary and dynamic situations. APPLICATION: Results in the current experimental study would be of interest in the design of traffic signs and other circumstances in which text is presented in motion.

Partitioning resilience of a marine foundation species into resistance and recovery trajectories.

The resilience of an ecological unit encompasses resistance during adverse conditions and the capacity to recover. We adopted a 'resistance-recovery' framework to experimentally partition the resilience of a foundation species (the seagrass Cymodocea nodosa). The shoot abundances of nine seagrass meadows were followed before, during and after simulated light reduction conditions. We determined the significance of ecological, environmental and genetic drivers on seagrass resistance (% of shoots retained during the light deprivation treatments) and recovery (duration from the end of the perturbed state back to initial conditions). To identify whether seagrass recovery was linearly related to prior resistance, we then established the connection between trajectories of resistance and recovery. Finally, we assessed whether recovery patterns were affected by biological drivers (production of sexual products-seeds-and asexual propagation) at the meadow-scale. Resistance to shading significantly increased with the genetic diversity of the meadow and seagrass recovery was conditioned by initial resistance during shading. A threshold in resistance (here, at a ca. 70% of shoot abundances retained during the light deprivation treatments) denoted a critical point that considerably delays seagrass recovery if overpassed. Seed densities, but not rhizome elongation rates, were higher in meadows that exhibited large resistance and quick recovery, which correlated positively with meadow genetic diversity. Our results highlight the critical role of resistance to a disturbance for persistence of a marine foundation species. Estimation of critical trade-offs between seagrass resistance and recovery is a promising field of research to better manage impacts on seagrass meadows.

Epigenetic footprint enables molecular risk stratification of hepatoblastoma with clinical implications.

BACKGROUND & AIMS: Hepatoblastoma (HB) is a rare disease. Nevertheless, it is the predominant pediatric liver cancer, with limited therapeutic options for patients with aggressive tumors. Herein, we aimed to uncover the mechanisms of HB pathobiology and to identify new biomarkers and therapeutic targets in a move towards precision medicine for patients with advanced HB. METHODS: We performed a comprehensive genomic, transcriptomic and epigenomic characterization of 159 clinically annotated samples from 113 patients with HB, using high-throughput technologies. RESULTS: We discovered a widespread epigenetic footprint of HB that includes hyperediting of the tumor suppressor BLCAP concomitant with a genome-wide dysregulation of RNA editing and the overexpression of mainly non-coding genes of the oncogenic 14q32 DLK1-DIO3 locus. By unsupervised analysis, we identified 2 epigenomic clusters (Epi-CA, Epi-CB) with distinct degrees of DNA hypomethylation and CpG island hypermethylation that are associated with the C1/C2/C2B transcriptomic subtypes. Based on these findings, we defined the first molecular risk stratification of HB (MRS-HB), which encompasses 3 main prognostic categories and improves the current clinical risk stratification approach. The MRS-3 category (28%), defined by strong 14q32 locus expression and Epi-CB methylation features, was characterized by CTNNB1 and NFE2L2 mutations, a progenitor-like phenotype and clinical aggressiveness. Finally, we identified choline kinase alpha as a promising therapeutic target for intermediate and high-risk HBs, as its inhibition in HB cell lines and patient-derived xenografts strongly abrogated tumor growth. CONCLUSIONS: These findings provide a detailed insight into the molecular features of HB and could be used to improve current clinical stratification approaches and to develop treatments for patients with HB. LAY SUMMARY: Hepatoblastoma is a rare childhood liver cancer that has been understudied. We have used cutting-edge technologies to expand our molecular knowledge of this cancer. Our biological findings can be used to improve clinical management and pave the way for the development of novel therapies for this cancer.

Low-Dose radiation therapy for benign pathologies.

Radiotherapy (RT) has always been a mainstay for malignant tumors therapy, but it is also used for benign pathology. The application of low or intermediate doses of RT has been widely studied. This topic was presented and discussed in the last XX GOCO (Grup Oncològic Català-Occità) meeting. The aim of this article is to review the indications of low dose irradiation (LD-RT), total dose and different fractionations, the public to whom it can be directed, and to offer an analysis about secondary effects. We believe it can be useful not only for radiation oncologists, but for other physicians to consider this option for future patients.

Prognostic correlation of cell cycle progression score and Ki-67 as a predictor of aggressiveness, biochemical failure, and mortality in men with high-risk prostate cancer treated with external beam radiation therapy.

OBJECTIVES: Ki-67 is a proliferation marker in prostate cancer. A prognostic RNA signature was developed to characterize prostate cancer aggressiveness. The aim was to evaluate prognostic correlation of CCP and Ki-67 with biochemical failure (BF), and survival in high-risk prostate cancer patients (pts) treated with radiation therapy (RT). METHODS: CCP score and Ki-67 were derived retrospectively from pre-treatment paraffin-embedded prostate cancer tissue of 33 men diagnosed from 2002 to 2006. CCP score was calculated as an average expression of 31 CCP genes. Ki-67 was determined by IHC. Single pathologist evaluated all tissues. Factors associated to failure and survival were analyzed. RESULTS: Median CCP score was 0.9 (-0-1 - 2.6). CCP 0: 1 pt; CCP 1: 19 pts; CCP 2: 13 pts. Median Ki-67 was 8.9. Ki-67 cutpoint was 15.08%. BF and DSM were observed in 21% and 9%. Ki-67 ≥ 15% predicted BF (p = 0.043). With a median follow-up of 8.4 years, 10-year BF, OS, DM and DSM for CCP 1 vs. CCP 2 was 76-71% (p = 0.83), 83-73% (p = 0.86), 89-85% (p = 0.84), and 94-78% (p = 0.66). On univariate, high Ki-67 was correlated with BF (p = 0.013), OS (p = 0.023), DM (p = 0.007), and DSM (p = 0.01). On Cox MVA, high Ki-67 had a BF trend (p = 0.063). High CCP score was not correlated with DSM. CONCLUSIONS: High Ki-67 significantly predicted outcome and provided prognostic information. CCP score may improve accuracy stratification. We did not provide prognostic correlation of CCP and DSM. It should be validated in a larger cohort of pts.

Characterisation of Aberrant Metabolic Pathways in Hepatoblastoma Using Liquid Chromatography and Tandem Mass Spectrometry (LC-MS/MS).

Hepatoblastoma (HB) is a rare childhood tumour with an evolving molecular landscape. We present the first comprehensive metabolomic analysis using untargeted and targeted liquid chromatography coupled to high-resolution tandem mass spectrometry (LC-MS/MS) of paired tumour and non-tumour surgical samples in HB patients (n = 8 pairs). This study demonstrates that the metabolomic landscape of HB is distinct from that of non-tumour (NT) liver tissue, with 35 differentially abundant metabolites mapping onto pathways such as fatty acid transport, glycolysis, the tricarboxylic acid (TCA) cycle, branched-chain amino acid degradation and glutathione synthesis. Targeted metabolomics demonstrated reduced short-chain acylcarnitines and a relative accumulation of branched-chain amino acids. Medium- and long-chain acylcarnitines in HB were similar to those in NT. The metabolomic changes reported are consistent with previously reported transcriptomic data from tumour and non-tumour samples (49 out of 54 targets) as well as metabolomic data obtained using other techniques. Gene set enrichment analysis (GSEA) from RNAseq data (n = 32 paired HB and NT samples) demonstrated a downregulation of the carnitine metabolome and immunohistochemistry showed a reduction in CPT1a (n = 15 pairs), which transports fatty acids into the mitochondria, suggesting a lack of utilisation of long-chain fatty acids in HB. Thus, our findings suggest a reduced metabolic flux in HB which is corroborated at the gene expression and protein levels. Further work could yield novel insights and new therapeutic targets.

SARS-CoV-2 Serum Viral Load and Prognostic Markers Proposal for COVID-19 Pneumonia in Low-Dose Radiation Therapy Treated Patients.

Several studies have shown that the plasma RNA of SARS-CoV-2 seems to be associated with a worse prognosis of COVID-19. In the present study, we investigated plasma RNA in COVID-19 patients treated with low-dose radiotherapy to determine its prognostic value. Data were collected from the IPACOVID prospective clinical trial (NCT04380818). The study included 46 patients with COVID-19 pneumonia treated with a whole-lung dose of 0.5 Gy. Clinical follow-up, as well as laboratory variables, and SARS-CoV-2 serum viral load, were analyzed before LDRT, at 24 h, and one week after treatment. The mean age of the patients was 85 years, and none received any of the SARS-CoV-2 vaccine doses. The mortality ratio during the course of treatment was 33%. RT-qPCR showed amplification in 23 patients. Higher mortality rate was associated with detectable viremia. Additionally, C-reactive protein, lactate dehydrogenase, and aspartate aminotransferase were significant risk factors associated with COVID-19 mortality. Our present findings show that detectable SARS-CoV-2 plasma viremia 24 h before LDRT is significantly associated with increased mortality rates post-treatment, thus downsizing the treatment success.

Identification of IGF2 as Genomic Driver and Actionable Therapeutic Target in Hepatoblastoma.

Management of hepatoblastoma (HB), the most frequent pediatric liver cancer, is based on surgical resection and perioperative chemotherapy regimens. In this study, we aimed to identify actionable targets in HB and assess the efficacy of molecular therapies in preclinical models of HB. Paired tumor and adjacent tissues from 31 HBs and a validation set of 50 HBs were analyzed using RNA-seq, SNP, and methylation arrays. IGF2 overexpression was identified as the top targetable HB driver, present in 71% of HBs (22/31). IGF2high tumors displayed progenitor cell features and shorter recurrence-free survival. IGF2 overexpression was associated in 91% of cases with fetal promoter hypomethylation, ICR1 deregulation, 11p15.5 loss of heterozygosity or miR483-5p overexpression. The antitumor effect of xentuzumab (a monoclonal antibody targeting IGF1/2) alone or in combination with the conventional therapeutic agent cisplatin was assessed in HB cell lines, in PDX-derived HB organoids and in a xenograft HB murine model. The combination of xentuzumab with cisplatin showed strong synergistic antitumor effects in organoids and in IGF2high cell lines. In mice (n = 55), the combination induced a significant decrease in tumor volume and improved survival compared with cisplatin alone. These results suggest that IGF2 is an HB actionable driver and that, in preclinical models of HB, the combination of IGF1/2 inhibition with cisplatin induces superior antitumor effects than cisplatin monotherapy. Overall, our study provides a rationale for testing IGF2 inhibitors in combination with cisplatin in HB patients with IGF2 overexpression.

MacroH2As regulate enhancer-promoter contacts affecting enhancer activity and sensitivity to inflammatory cytokines.

MacroH2A histone variants have a function in gene regulation that is poorly understood at the molecular level. We report that macroH2A1.2 and macroH2A2 modulate the transcriptional ground state of cancer cells and how they respond to inflammatory cytokines. Removal of macroH2A1.2 and macroH2A2 in hepatoblastoma cells affects the contact frequency of promoters and distal enhancers coinciding with changes in enhancer activity or preceding them in response to the cytokine tumor necrosis factor alpha. Although macroH2As regulate genes in both directions, they globally facilitate the nuclear factor κB (NF-κB)-mediated response. In contrast, macroH2As suppress the response to the pro-inflammatory cytokine interferon gamma. MacroH2A2 has a stronger contribution to gene repression than macroH2A1.2. Taken together, our results suggest that macroH2As have a role in regulating the response of cancer cells to inflammatory signals on the level of chromatin structure. This is likely relevant for the interaction of cancer cells with immune cells of their microenvironment.

Effect of Low-Dose Radiotherapy on the Circulating Levels of Paraoxonase-1-Related Variables and Markers of Inflammation in Patients with COVID-19 Pneumonia.

The aim of our study was to investigate the changes produced by low-dose radiotherapy (LDRT) in the circulating levels of the antioxidant enzyme paraoxonase-1 (PON1) and inflammatory markers in patients with COVID-19 pneumonia treated with LDRT and their interactions with clinical and radiological changes. Data were collected from the IPACOVID prospective clinical trial (NCT04380818). The study included 30 patients treated with a whole-lung dose of 0.5 Gy. Clinical follow-up, as well as PON1-related variables, cytokines, and radiological parameters were analyzed before LDRT, at 24 h, and 1 week after treatment. Twenty-five patients (83.3%) survived 1 week after LDRT. Respiratory function and radiological images improved in survivors. Twenty-four hours after LDRT, PON1 concentration significantly decreased, while transforming growth factor beta 1 (TGF-ß1) increased with respect to baseline. One week after LDRT, patients had increased PON1 activities and lower PON1 and TGF-ß1 concentrations compared with 24 h after LDRT, PON1 specific activity increased, lactate dehydrogenase (LDH), and C-reactive protein (CRP) decreased, and CD4+ and CD8+ cells increased after one week. Our results highlight the benefit of LDRT in patients with COVID-19 pneumonia and it might be mediated, at least in part, by an increase in serum PON1 activity at one week and an increase in TGF-ß1 concentrations at 24 h.

Stratification and management of cardiovascular risk in cancer patients. A consensus document of the SEC, FEC, SEOM, SEOR, SEHH, SEMG, AEEMT, AEEC, and AECC.

Both cancer treatment and survival have significantly improved, but these advances have highlighted the deleterious effects of vascular complications associated with anticancer therapy. This consensus document aims to provide a coordinated, multidisciplinary and practical approach to the stratification, monitoring and treatment of cardiovascular risk in cancer patients. The document is promoted by the Working Group on Cardio Oncology of the Spanish Society of Cardiology (SEC) and was drafted in collaboration with experts from distinct areas of expertise of the SEC and the Spanish Society of Hematology and Hemotherapy (SEHH), the Spanish Society of Medical Oncology (SEOM), the Spanish Society of Radiation Oncology (SEOR), the Spanish Society of General and Family Physicians (SEMG), the Spanish Association of Specialists in Occupational Medicine (AEEMT), the Spanish Association of Cardiovascular Nursing (AEEC), the Spanish Heart Foundation (FEC), and the Spanish Cancer Association (AECC).

Seagrass Cymodocea nodosa across biogeographical regions and times: Differences in abundance, meadow structure and sexual reproduction.

Seagrasses are key habitat-forming species of coastal areas. While previous research has demonstrated considerable small-scale variation in seagrass abundance and structure, studies teasing apart local from large-scale variation are scarce. We determined how different biogeographic scenarios, under varying environmental and genetic variation, explained variation in the abundance and structure (morphology and biomass allocation), epiphytes and sexual reproduction intensity of the seagrass Cymodocea nodosa. Regional and local-scale variation, including their temporal variability, contributed to differentially explain variation in seagrass attributes. Structural, in particular morphological, attributes of the seagrass leaf canopy, most evidenced regional seasonal variation. Allocation to belowground tissues was, however, mainly driven by local-scale variation. High seed densities were observed in meadows of large genetic diversity, indicative of sexual success, which likely resulted from the different evolutionary histories undergone by the seagrass at each region. Our results highlight that phenotypic plasticity to local and regional environments need to be considered to better manage and preserve seagrass meadows.

Seasonal Influenza A H1N1pdm09 Virus and Severe Outcomes: A Reason for Broader Vaccination in Non-Elderly, At-Risk People.

BACKGROUND: Recent pandemics of influenza A H1N1pdm09 virus have caused severe illness, especially in young people. Very few studies on influenza A H1N1pdm09 in post-pandemic periods exist, and there is no information on the severity of both seasonal influenza A(H1N1) and A(H3N2) from the same season, adjusting for potential confounders, including vaccine. METHODS AND RESULTS: We performed a retrospective observational study of adults hospitalized during the 2014 season with influenza A(H1N1) or A(H3N2). All patients underwent the same diagnostic and therapeutic protocol in a single hospital, including early Oseltamivir therapy. We included 234 patients: 146 (62.4%) influenza A(H1N1) and 88 (37.6%) A(H3N2). A(H1N1) patients were younger (p<0.01), developed more pneumonia (p<0.01), respiratory complications (p = 0.015), ARDS (p = 0.047), and septic shock (p = 0.049), were more frequently admitted to the ICU (p = 0.022), required IMV (p = 0.049), and were less frequently vaccinated (p = 0.008). After adjusting for age, comorbidities, time from onset of illness, and vaccine status, influenza A(H1N1) (OR, 2.525), coinfection (OR, 2.821), and no vaccination (OR, 3.086) were independent risk factors for severe disease. CONCLUSIONS: Hospitalized patients with influenza A(H1N1) were more than twice as likely to have severe influenza. They were younger and most had not received the vaccine. Our findings suggest that seasonal influenza A(H1N1) maintains some features of pandemic viruses, and recommend wider use of vaccination in younger adult high-risk patients.