bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antidepressant drugs and risk of developing glioma: a national registry-based case-control study and a meta-analysis
Authors: Malmberg Charlotte , Hellquist Barbro Numan , Sadanandan Sajna Anand , Sandström Maria , Wu Wendy Yi-Ying , Björkblom Benny , Melin Beatrice , Sjöberg Rickard L 
Published: May 2024

Abstract
Whether use of antidepressants is related to the risk of developing lower-grade (WHO grades 2-3) and higher-grade (WHO grade 4) glioma was investigated in this study. A registry-based case–control study was performed with 1283 glioma case patients and 6400 age-, sex-, and geographically matched control participants who were diagnosed in Sweden during 2009-2013. Conditional logistic regression was used to analyze whether selective serotonin reuptake inhibitors (SSRIs) or non-SSRIs were associated with the risk of developing lower- or higher-grade glioma in the study population. Our results show that use of antidepressant medication was not associated with the risk of developing glioma. We also performed a meta-analysis in which the data set from the present study was combined with results from 2 previous epidemiologic studies to answer the same questions. The meta-analysis showed a modest risk reduction of developing glioma in relation to antidepressant treatment (odds ratio = 0.90; 95% CI, 0.83-0.97) when all glioma subgroups and all forms of antidepressant medications were combined. In conclusion, it remains possible that antidepressants may have common monoaminergic mechanism(s) that reduce the risk of developing glioma.
Readon: a novel algorithm to identify read-through transcripts with long-read sequencing data
Authors: Chen Siang , Wang Hao , Zhang Dongdong , Chen Runsheng , Luo Jianjun 
Published: May 2024

Abstract

Motivation
There are many clustered transcriptionally active regions in the human genome, in which the transcription complex cannot immediately terminate transcription at the upstream gene termination site, but instead continues to transcribe intergenic regions and downstream genes, resulting in read-through transcripts. Several studies have demonstrated the regulatory roles of read-through transcripts in tumorigenesis and development. However, limited by the read length of next-generation sequencing, discovery of read-through transcripts has been slow. For long but also erroneous third-generation sequencing data, this study developed a novel minimizer sketch algorithm to accurately and quickly identify read-through transcripts.

Results
Readon initially splits the reference sequence into distinct active regions. It employs a sliding window approach within each region, calculates minimizers, and constructs the specialized structured arrays for query indexing. Following initial alignment anchor screening of candidate read-through transcripts, further confirmation steps are executed. Comparative assessments against existing software reveal Readon's superior performance on both simulated and validated real data. Additionally, two downstream tools are provided: one for predicting whether a read-through transcript is likely to undergo nonsense-mediated decay or encodes a protein, and another for visualizing splicing patterns.

Availability and implementation
Readon is freely available on GitHub (https://github.com/Bulabula45/Readon).
Characterization of senescence in human cardiac fibroblasts
Authors: Costa A , Ceresa D , Altieri P , Malatesta P , Ameri P 
Published: May 2024

Abstract

Funding Acknowledgements
None.

Background
Recent studies suggest that senescence of cardiac fibroblasts (cFib) plays a significant role in cardiac aging and disease. However, senescence of cultured cFib in response to classical pro-senescent stimuli has not been characterized yet.

Purpose
We thoroughly studied oncogene- and stress-induced senescence, as well as replicative senescence, in primary human cFib.

Methods
Human cFib were isolated from specimens of right atrial appendages, collected during cardiac surgery with extracorporeal circulation. These cells were subjected to oncogene-induced senescence by overexpression of HRasV12, were exposed to ionizing radiation (IR, 5 Gy) to recapitulate stress-induced senescence, and were passaged until replicative senescence was reached (P12-P14). Senescence was assessed by staining for senescence associated (SA) β-galactosidase and EdU and by RT-PCR for CDKN1A, CDKN2A, and LamB1.

Results
The main results are summarized in the graphical abstract. HRasV12 overexpression, IR, and prolonged culturing consistently caused senescence of cFib: in fact, all senescent models showed a significant increase in SA-β-gal activity and CDKN1A expression and a decrease in EdU uptake and LamB1 expression over control cells. Interestingly, cFib with HRasV12 overexpression exhibited a peculiar morphological phenotype with vacuoles and showed higher levels of the typical markers of senescence compared to control and to IR-treated or extensively passaged cFib. Moreover, only cFib with HRasV12 overexpression showed a strong downregulation of CDKN2A.

Conclusions
Cultured primary human cFib undergo senescence in response to established inducers of senescence. HRasV12 overexpression uniquely causes vacuolization of senescent cFib, which is currently being further characterized by transmission electron microscopy.
Exploiting spatial transcriptomics to investigate the molecular mechanisms involved in cardiac metastasis development
Authors: Lorizio D , Chiesa M , Pinamonti M , Bussani R , Ciucci G , Vuerich R , Zacchigna S 
Published: May 2024

Abstract

Funding Acknowledgements
Type of funding sources: Foundation. Main funding source(s): IEO-Monzino Foundation

Background
Cardiac metastasis is considered a relatively rare malignancy, although an increasing prevalence is expected in the future due to the increasing life expectancy. Several cases of cardiac metastases remain untreatable, given the anatomical location that often hampers both surgical eradication and bioptic collection for biological characterization. Here, we use spatial transcriptomics to provide an unbiased molecular characterization of cardiac metastases, and identify novel targets for their treatment.

Material and methods
We performed spatial transcriptomics on samples of primary tumor, cardiac, and extra-cardiac metastasis from three different patients. First, we checked RNA integrity by means of DV200 analysis. Spatial transcriptomic analysis was performed by using the GeoMX technology (Nanostring), which provides whole-transcriptome data along with spatial distribution information of the preselected samples from the candidate regions of interest (ROIs). ROIs were selected on the formalin-fixed paraffin-embedded sections by means of geometric shapes in combination with cell markers specific for tumor cells, cardiomyocytes and endothelial cells, respectively. Differential gene expression analysis and Gene Set Enrichment Analysis (GSEA) were performed on the entire transcriptome. Cell-cell interactions between cardiac cells and cancer cells were then evaluated by means of InterCellaR.

Results
Differential expression analysis between cardiac metastases and extra-cardiac tumors (primary tumors + extra-cardiac metastases) identified 92 differentially expressed genes (DEGs). Of these, 53 genes were significantly overexpressed in cardiac metastases, while 39 genes were overexpressed in the extra-cardiac samples, regardless of the site of origin of the tumor. Unsupervised hierarchical clustering of protein-coding genes clearly separated the samples according to their anatomical location, in particular cardiac metastasis from extra-cardiac tumors. GSEA identified several pathways enriched in cardiac metastases compared to the extra-cardiac tumors, including mechanotransduction (e.g. keratinization and cell-matrix interaction) and triglyceride metabolism, suggesting a potential role of these signaling pathways in the development of cardiac metastasis. Interactome analysis revealed a rich plethora of receptor-ligand interactions in cardiac metastasis, especially between tumor cells and cardiomyocytes.

Conclusions
These results start shedding light on the mechanisms that allow cancer cell growth in the heart and pave the way to the development of novel therapies to treat this malignancy.
The endocannabinoid ARA-S acts as an endogenous rescuing factor of Kv7.1/KCNE1 carrying Long QT syndrome mutations and paves the way for drug development strategies
Authors: Hiniesto Inigo I , Sridhar A , Lundholm S A , Liin S I 
Published: May 2024

Abstract
Funding Acknowledgements
Type of funding sources: Public grant(s) – EU funding. Main funding source(s): European Union’s Horizon 2020 research and innovation program
Long QT Syndrome (LQTS) is a cardiac arrhythmia characterized by delayed ventricular repolarization. LQTS occurs when there are loss-of-function mutations in genes encoding for voltage-gated channels and their beta subunits that contribute to the cardiac action potential. Among them, the most mutated channel is Kv7.1/KCNE1, which encodes for the slowly activating component of the delayed rectifier K+ current (IKs). Families with inherited mutations in the Kv7.1/KCNE1 exhibit inconsistent correlations between genotypes and phenotypes making the clinical management of LQTS challenging. A possible strategy to help guide clinical approaches involves exploring endogenous compounds capable of modulating the Kv7.1/KCNE1 channel function, acting as potential disease modifiers. Using the two-electrode voltage clamp technique, we previously found that the endogenous endocannabinoid-like compound ARA-S, which has an arachidonic acid tail and a serine head group, facilitates activation of the wild-type Kv7.1/KCNE1 channel expressed in Xenopus oocytes. This is seen as a left shift in the voltage dependence of channel opening and an increase in conductance. Moreover, we showed that ARA-S restores a physiological QT interval in isolated guinea pig hearts suffering from drug-induced LQTS. Hence, ARA-S is an interesting endogenous Kv7.1/KCNE1 channel modulator that may influence disease severity. However, it is uncertain whether ARA-S also activates the Kv7.1/KCNE1 when it carries LQTS-associated mutations. Therefore, the current study involves studying the effect of ARA-S on mutated Kv7.1/KCNE1 channels using two-electrode voltage clamp electrophysiology. We find that ARA-S facilitates the activation of all tested LQTS mutants. However, the magnitude of the effect varies among them, suggesting that the compound´s effect is dependent on the genetic background. To understand why ARA-S has different effects, we use computational simulation approaches to study how mutations in the putative ARA-S binding sites change ARA-S efficacy. This understanding aids in developing new substances that can activate different mutations, by, for example, modifying the ARA-S tail to enhance its efficacy. We also try to understand the concentration of ARA-S required to restore a wild-type-like function of each mutant, considering the mutant's intrinsic behavior and the apparent affinity of ARA-S for the specific mutant. Altogether, this work finds ARA-S to be an efficient activator of LQTS-associated mutant Kv7.1/KCNE1 channels and is a first step towards understanding how the genetic background determines the effect of this endogenous modulator.
Real-time (re)shaping of cardiac action potentials by an opto-electronic feedback control system in the multicellular setting
Authors: Ordog B , De Coster T , Bart C I , Zhang J , Boink G J J , Bax W , Deng S , Den Ouden B L , De Vries A A F , Pijnappels D A 
Published: May 2024

Abstract

Funding Acknowledgements
Type of funding sources: Public grant(s) – EU funding. Main funding source(s): European Research Council Starting Grant and Consolidator Grant to Daniël A Pijnappels

Background
The membrane potential (Vm) in cardiomyocytes fulfills essential regulatory roles in various biological functions, including not only action potential (AP) propagation and mechanical contraction, but also homeostatic regulation. In-depth studies into these roles have been severely hampered by the lack of research methods allowing full control over Vm, especially in multicellular cardiac preparations.

Purpose
We aimed to unlock new research possibilities by the development of an experimental system (APqr) capable of full Vm control, including instantaneous modulation of AP morphology on a multicellular levelin the multicellular setting.

Methods
Monolayers of immortalized human atrial myocytes (hiAMs, n=7) were genetically modified to express the blue light-activatable cation channel Cheriff and the red light-sensitive inward chloride pump Jaws for depolarizing and re- or hyperpolarizing effects, respectively. Real-time Vm readout was obtained by patch clamp electrophysiology. Deviations of Vm from reference values were calculated by a custom closed-coop controller. A 470-nm and a 617-nm LED were modulated by the controller in a Vm deviation-dependent manner, selectively activating Cheriff or Jaws. Electrical disturbances were introduced by application of 4-aminopyridien (4AP, 200 µM) or a preprogrammed blue-light pulse creating abnormal cation influx during the repolarization phase of the hiAM AP.

Results
Average AP durations at 90% repolarization (APD90) increased by 82.4 ms following 4AP application and by 362.5 ms in the presence of light-induced abnormal cation influx compared to control conditions. APqr reduced these APD90 differences to 1.9 ms and 4.6 ms on average, with Vm deviations less than 2.5 mV in 74.7% and 94.4% of the time, respectively. APqr could also be applied for the enforcement of arbitrary AP shapes. In these experiments, reference Vm values consisted of APs recorded from hiAM monolayers exposed to drugs with APD-prolonging (4AP) or shortening (carbachol) effects. APqr was able to enforce these reference APs on hiAM monolayers with high accuracy, with Vm deviations less than 2.5 mV in 95.8% and 94.4% of the time, respectively.

Conclusions
APqr preserves AP morphologies in the presence of electrical perturbations of different origin without any prior knowledge of the disturbance and enforces arbitrary AP morphologies with high accuracy in an immediate and self-regulatory manner. Collectively, these results set the stage for the refinement and application of opto-electronic control systems to enable in-depth investigation into the regulatory roles of the membrane potential in health and disease.
Modeling doxorubicin-induced cardiotoxicity with human myocardial tissue slices: insights on genetic susceptibility and cardioprotection
Authors: Van Der Geest J S A , Kelters I R , Van Der Kaaij N P , Dendorfer A , Doevendans P A F M , De Boer T P , Van Laake L W , Sluijter J P G , Sampaio Pinto V 
Published: May 2024

Abstract

Funding Acknowledgements
Type of funding sources: Public grant(s) – National budget only. Main funding source(s): PSIDER and HARVEY (ZonMW)

Introduction
Cardiotoxicity poses a significant challenge in drug development, often leading to the withdrawal of approved drugs. To address this issue, there is a critical need for improved models to predict cardiac adverse effects. In line with the imperative for animal-free preclinical testing, this study aimed to develop a novel model using human myocardial tissue slices to get a deeper understanding and potential prevention of doxorubicin-Induced cardiotoxicity.

Methods
Human myocardial tissue slices of 300 μm thick were derived from end-stage heart failure patients explanted hearts, including those harbouring likely or pathogenic cardiovascular mutations (class 4 and 5) (N=3) and non-genetic cardiovascular etiology (N=3). Myocardial tissue slices were cultured under physiological mechanical and electrical conditions. Slices were exposed to doxorubicin (1 µM) over a 10-day culture period, and their responses were compared to DMSO-vehicle controls, by recording contractile force and Ca2+ transients. Additionally, a subset of slices was treated with a cardioprotective agent, dexrazoxane (100 µM), 1 day prior to and during doxorubicin exposure to assess potential cardioprotection.

Results
Doxorubicin-exposed slices with a pathogenic mutation exhibited reduced mechanical force, increased threshold potential, and impaired ability to follow pacing at higher frequencies. Additionally, aberrations in calcium handling, manifested as arrhythmia-like disconnection of muscle fibers, were notably observed in these slices. Instead, slices from patients without pathogenic mutations showed minimal cardiotoxicity when exposed to doxorubicin. Encouragingly, pretreatment with dexrazoxane demonstrated a protective effect against doxorubicin-induced cardiotoxicity in the genetically susceptible group. Our functional findings corroborated our structural data, highlighting the breakdown of sarcomere structure and cell-cell connections and increased DNA damage, particularly in patients harbouring a genetic cardiovascular mutation.

Conclusion
In summary, human myocardial tissue slices faithfully recapitulate doxorubicin-induced cardiotoxicity. Importantly, our data suggests the utility of employing genetic testing for known cardiovascular mutations as a valuable step before initiating doxorubicin treatment. Additionally, we demonstrate for the first time the in vitro cardioprotective potential of dexrazoxane in a human tissue model. These findings pave the way for using ex vivo myocardial tissue slices to evaluate cardiotoxicity and their value as a powerful tool for evaluating the efficacy and delivery approaches.
Cardiovascular toxicity profile of doxorubicin: data mining of the FDA adverse event reporting system (FAERS)
Authors: Kattan L , Cerbito E , Dhulkifle H , Korashy H , Maayah Z 
Published: May 2024

Abstract

Funding Acknowledgements
None.

Background
Doxorubicin (DOX), an effective anticancer agent, is associated with dose-dependent cardiovascular toxicity. Understanding its mechanisms and risk factors will facilitate novel interventions to minimize DOX-induced cardiovascular toxicity.

Purpose
We aimed to perform a comprehensive analysis of the Food and Drug Administration Adverse Event Reporting System (FAERS) database to identify, describe, and quantify the latest cardiovascular DOX-associated adverse-events (AEs).

Methods
Data from 2004 Q1 – 2022 Q3, where DOX was the primary-suspect, were extracted from FAERS via OpenVigil 2.1. For data collection, preferred-terms (PTs) from Medical Dictionary for Regulatory Activities (MedDRA) were used, while ROR with 95% CIs for disproportionality analysis was performed.

Results
1987 reports were collected for significant PTs. The most prevalent DOX-associated AE was heart failure (77.6%, n=1542), followed by cardiac fibrosis and inflammation (7.75%, n=154) and vascular disorders (7.45%, n=148). Others include arrhythmias, systemic inflammation, and endothelial dysfunction. Most patients were females (51.1%, n=1016), 18-64 years-old (41%, n = 815), primarily from Europe (41.87%, n=832) and the United States (34.12%, n = 678). Six outcomes were associated with DOX-induced cardiotoxicities, mainly "Death", "Initial/prolonged hospitalization", and "Others".

Conclusion
This study provides valuable insights on DOX-induced cardiovascular toxicity using real-world data from FAERS.Total Case Count of all Adverse EventPatients' Demographics and outcomes
AAV-mediated gene delivery to the cardiac conduction system
Authors: Jonker T , Boender A R , Klerk M , Barnett P , De Vries A A F , Christoffels V M , Boink G J J 
Published: May 2024

Abstract

Funding Acknowledgements
Type of funding sources: Public grant(s) – National budget only. Main funding source(s): NWO open technology program Biopace #18485

Background
Gene therapy for cardiac arrhythmias has so far mostly focused on modifying the arrhythmogenic substrate in working myocardium or on creating biological pacemakers with viral vectors that did not selectively target the cardiac conduction system (CCS). As a result, CCS targeting by viral vectors is a relatively unexplored area.

Aim
In the current project, we explored the basic requirements for CCS targeting using adeno-associated virus (AAV) vectors.

Methods
Regular AAV9 and AAV-Myo4A capsid-pseudotyped AAV2 vectors (hereafter called AAV2/9 and AAV2/Myo4A vectors, respectively) expressing enhanced green fluorescent protein (eGFP) from a CMV or TNNT2 promoter, respectively, and an AAV2/9 vector expressing eGFP from a human GJA5 regulatory element were systemically injected in mice. After 4 weeks, hearts were harvested, fixed with paraformaldehyde and stained for TNNT2, eGFP, HCN4 and DNA to determine CCS transduction.

Results
Transduction of the sinoatrial and atrioventricular (AV) node using AAV2/9 vectors was very poor, while transduction was visible in the atrioventricular (i.e. His) bundle and working myocardium. In contrast, the transduction rate of the AV node and bundle using AAV2/Myo4A vectors were similar to that of the working myocardium.
The human GJA5 regulatory element was able to restrict eGFP expression by AAV2/9 vectors to the AV bundle in 2/3 animals but the transduction efficiency was low. A third animal showed no transduction of any tissue, either indicative of the low transduction efficiency or of a failed injection.

Conclusion
This study not only provides proof-of-principle for CCS-targeted gene therapy but also shows that CCS transduction can be improved through AAV capsid engineering and be restricted to (parts of) the CCS by using specific transcriptional control elements.