Advanced RPL19-TRAP-seq method reveals mechanism of action of bioactive compounds.

Natural products play a crucial role in new drug development, but their druggability is often limited by uncertain molecular targets and insufficient research on mechanisms of action. In this study, we developed a new RPL19-TRAP-seq method, combining CRISPR/Cas9 and TRAP technologies, to investigate these mechanisms. We identified and validated seven ribosomal large subunit surface proteins suitable for TRAP, selecting RPL19 for its high enrichment.

BCL-2 dependence is a favorable predictive marker of response to therapy for chronic lymphocytic leukemia.

Background: Established genetic biomarkers in chronic lymphocytic leukemia (CLL) have been useful in predicting response to chemoimmunotherapy but are less predictive of response to targeted therapies. With several such targeted therapies now approved for CLL, identifying novel, non-genetic predictive biomarkers of response may help to select the optimal therapy for individual patients.

Methods: We coupled data from a functional precision medicine technique called BH3-profiling, which assesses cellular cytochrome c loss levels as indicators for survival dependence on anti-apoptotic proteins, with multi-omics data consisting of targeted and whole-exome sequencing, genome-wide DNA methylation profiles, RNA-sequencing, protein and functional analyses, to identify biomarkers for treatment response in CLL patients.

The essential role of sphingolipids in TRPC5 ion channel localization and functionality within lipid rafts.

Sphingolipids are critical components of cellular membranes that play a pivotal role in modulating ion channel function by forming lipid rafts that stabilize and localize these channels. These lipids regulate membrane fluidity and protein-lipid interactions, directly influencing ion channel activity, trafficking, and signaling pathways essential for maintaining cellular homeostasis. Despite their fundamental role, the impact of sphingolipids on ion channel functionality, particularly within the nervous system, remains insufficiently understood.

IAP dependency of T-cell prolymphocytic leukemia identified by high-throughput drug screening.

T-cell prolymphocytic leukemia (T-PLL) is an aggressive lymphoid malignancy with limited treatment options. To discover new treatment targets for T-PLL, we performed high-throughput drug sensitivity screening on 30 primary patient samples ex-vivo. After screening over 2'800 unique compounds, we found T-PLL to be more resistant to most drug classes, including chemotherapeutics, compared to other blood cancers.

Dual Biological Role and Clinical Impact of De Novo Chromatin Activation in Chronic Lymphocytic Leukemia.

Previous studies have reported that chronic lymphocytic leukemia (CLL) shows a de novo chromatin activation pattern as compared to normal B cells. Here, we explored whether the level of chromatin activation is related to the clinical behavior of CLL. We identified that in some regulatory regions, increased de novo chromatin activation is linked to clinical progression whereas, in other regions, it is associated with an indolent course.

Detect influential points of feature rankings.

Background: Feature rankings are crucial in bioinformatics but can be distorted by influential points (IPs), which are often overlooked. This study aims to investigate the impact of IPs on feature rankings and propose IPs detection method METHOD: We use a leave-one-out approach to assess each case's influence on feature rankings by comparing rank changes after its removal. The rank changes are measured by a novel rank comparison method that involves using adaptive top-prioritized weights that are adjustable to the distribution of rank changes.

Aggressive Lymphoma after CD19 CAR T-Cell Therapy.

The development of a fatal, clonal, autonomously proliferating CD4-CD8- chimeric antigen receptor (CAR)+ peripheral T-cell lymphoma (PTCL) occurred 1 month after a patient received treatment with tisagenlecleucel for relapsed primary central nervous system lymphoma. The PTCL had a clonal T-cell receptor rearrangement, which was already detectable in the apheresis product for CAR T-cell manufacturing and 7 months earlier for autologous transplantation. Somatic and mutations in CD34+ stem cells and their progeny were detected in the PTCL, in the apheresis specimen that was obtained for CAR T-cell production, and in the autotransplant.

Construct prognostic models of multiple myeloma with pathway information incorporated.

Multiple myeloma (MM) is a hematological disease exhibiting aberrant clonal expansion of cancerous plasma cells in the bone marrow. The effects of treatments for MM vary between patients, highlighting the importance of developing prognostic models for informed therapeutic decision-making. Most previous models were constructed at the gene level, ignoring the fact that the dysfunction of the pathway is closely associated with disease development and progression.

Systemic aging fuels heart failure: Molecular mechanisms and therapeutic avenues.

Systemic aging influences various physiological processes and contributes to structural and functional decline in cardiac tissue. These alterations include an increased incidence of left ventricular hypertrophy, a decline in left ventricular diastolic function, left atrial dilation, atrial fibrillation, myocardial fibrosis and cardiac amyloidosis, elevating susceptibility to chronic heart failure (HF) in the elderly. Age-related cardiac dysfunction stems from prolonged exposure to genomic, epigenetic, oxidative, autophagic, inflammatory and regenerative stresses, along with the accumulation of senescent cells.

Urodynamic analysis of the effect of electroacupuncture at different acupoints on the bladder after spinal cord injury.

Objective: Guanyuan (CV4), Zhongji (CV3) and Sanyinjiao (SP6) are the most frequently used acupoints for treating neurogenic bladder after spinal cord injury (SCI). However, there has been no investigation to clarify the differences in effects of these acupoints in different types of neurogenic bladder.

Methods: The study was structured with a randomized, two-phase cross over design with a washout period.

Revisiting the diagnostic and prognostic significance of high-frequency QRS analysis in cardiovascular diseases: a comprehensive review.

Cardiovascular diseases (CVDs) present a significant global public health threat, contributing to a substantial number of cases involving morbidity and mortality. Therefore, the early and accurate detection of CVDs plays an indispensable role in enhancing patient outcomes. Decades of extensive research on electrocardiography at high frequencies have yielded a wealth of knowledge regarding alterations in the QRS complex during myocardial ischemia, as well as the methodologies to assess and quantify these changes.

Recovery of organic matters by activated sludge from municipal wastewater: Performance and characterization.

Municipal wastewater treatment processes consume a significant amount of energy and generate substantial carbon emissions. However, organic matters existing in municipal wastewater hold the potential as a valuable carbon source. Activated sludge has the potential to capture and recover the organic matters, thereby enriching carbon sources and facilitating subsequent sludge anaerobic digestion as well as in line with the concept of sustainable development.

Concurrent inhibition of ALK and SRC kinases disrupts the ALK lung tumor cell proteome.

Precision oncology has revolutionized the treatment of ALK-positive lung cancer with targeted therapies. However, an unmet clinical need still to address is the treatment of refractory tumors that contain drug-induced resistant mutations in the driver oncogene or exhibit resistance through the activation of diverse mechanisms. In this study, we established mouse tumor-derived cell models representing the two most prevalent EML4-ALK variants in human lung adenocarcinomas and characterized their proteomic profiles to gain insights into the underlying resistance mechanisms.

Mechanisms of transcranial direct current stimulation (tDCS) for pain in patients with fibromyalgia syndrome.

Fibromyalgia syndrome (FMS) is a recurrent pain condition that can be challenging to treat. Transcranial direct current stimulation (tDCS) has become a promising non-invasive therapeutic option in alleviating FMS pain, but the mechanisms underlying its effectiveness are not yet fully understood. In this article, we discuss the most current research investigating the analgesic effects of tDCS on FMS and discuss the potential mechanisms.

The changing career paths of PhDs and postdocs trained at EMBL.

Individuals with PhDs and postdoctoral experience in the life sciences can pursue a variety of career paths. Many PhD students and postdocs aspire to a permanent research position at a university or research institute, but competition for such positions has increased. Here, we report a time-resolved analysis of the career paths of 2284 researchers who completed a PhD or a postdoc at the European Molecular Biology Laboratory (EMBL) between 1997 and 2020.

PRMT1 Inhibition Activates the Interferon Pathway to Potentiate Antitumor Immunity and Enhance Checkpoint Blockade Efficacy in Melanoma.

Unlabelled: Despite the immense success of immune checkpoint blockade (ICB) in cancer treatment, many tumors, including melanoma, exhibit innate or adaptive resistance. Tumor-intrinsic T-cell deficiency and T-cell dysfunction have been identified as essential factors in the emergence of ICB resistance. Here, we found that protein arginine methyltransferase 1 (PRMT1) expression was inversely correlated with the number and activity of CD8+ T cells within melanoma specimen.

Negative feedback regulation of MAPK signaling is an important driver of chronic lymphocytic leukemia progression.

Despite available targeted treatments for the disease, drug-resistant chronic lymphocytic leukemia (CLL) poses a clinical challenge. The objective of this study is to examine whether the dual-specific phosphatases DUSP1 and DUSP6 are required to negatively regulate mitogen-activated protein kinases (MAPKs) and thus counterbalance excessive MAPK activity. We show that high expression of DUSP6 in CLL correlates with poor clinical prognosis.

Ex vivo drug response profiling for response and outcome prediction in hematologic malignancies: the prospective non-interventional SMARTrial.

Ex vivo drug response profiling is a powerful tool to study genotype-drug response associations and is being explored as a tool set for precision medicine in cancer. Here we conducted a prospective non-interventional trial to investigate feasibility of ex vivo drug response profiling for treatment guidance in hematologic malignancies (SMARTrial, NCT03488641 ). The primary endpoint to provide drug response profiling reports within 7 d was met in 91% of all study participants (N = 80).

Comparing the value of mono- vs coculture for high-throughput compound screening in hematological malignancies.

Large-scale compound screens are a powerful model system for understanding variability of treatment response and discovering druggable tumor vulnerabilities of hematological malignancies. However, as mostly performed in a monoculture of tumor cells, these assays disregard modulatory effects of the in vivo microenvironment. It is an open question whether and to what extent coculture with bone marrow stromal cells could improve the biological relevance of drug testing assays over monoculture.

Subgroup-specific gene expression profiles and mixed epistasis in chronic lymphocytic leukemia.

Understanding the molecular and phenotypic heterogeneity of cancer is a prerequisite for effective treatment. For chronic lymphocytic leukemia (CLL), recurrent genetic driver events have been extensively cataloged, but this does not suffice to explain the disease's diverse course. Here, we performed RNA sequencing on 184 CLL patient samples.