Minor intron splicing is critical for survival of lethal prostate cancer.

The evolutionarily conserved minor spliceosome (MiS) is required for protein expression of ∼714 minor intron-containing genes (MIGs) crucial for cell-cycle regulation, DNA repair, and MAP-kinase signaling. We explored the role of MIGs and MiS in cancer, taking prostate cancer (PCa) as an exemplar. Both androgen receptor signaling and elevated levels of U6atac, a MiS small nuclear RNA, regulate MiS activity, which is highest in advanced metastatic PCa. siU6atac-mediated MiS inhibition in PCa in vitro model systems resulted in aberrant minor intron splicing leading to cell-cycle G1 arrest. Small interfering RNA knocking down U6atac was ∼50% more efficient in lowering tumor burden in models of advanced therapy-resistant PCa compared with standard antiandrogen therapy. In lethal PCa, siU6atac disrupted the splicing of a crucial lineage dependency factor, the RE1-silencing factor (REST). Taken together, we have nominated MiS as a vulnerability for lethal PCa and potentially other cancers.

Single-cell atlas of the human brain vasculature across development, adulthood and disease.

A broad range of brain pathologies critically relies on the vasculature, and cerebrovascular disease is a leading cause of death worldwide. However, the cellular and molecular architecture of the human brain vasculature remains incompletely understood1. Here we performed single-cell RNA sequencing analysis of 606,380 freshly isolated endothelial cells, perivascular cells and other tissue-derived cells from 117 samples, from 68 human fetuses and adult patients to construct a molecular atlas of the developing fetal, adult control and diseased human brain vasculature. We identify extensive molecular heterogeneity of the vasculature of healthy fetal and adult human brains and across five vascular-dependent central nervous system (CNS) pathologies, including brain tumours and brain vascular malformations. We identify alteration of arteriovenous differentiation and reactivated fetal as well as conserved dysregulated genes and pathways in the diseased vasculature. Pathological endothelial cells display a loss of CNS-specific properties and reveal an upregulation of MHC class II molecules, indicating atypical features of CNS endothelial cells. Cell-cell interaction analyses predict substantial endothelial-to-perivascular cell ligand-receptor cross-talk, including immune-related and angiogenic pathways, thereby revealing a central role for the endothelium within brain neurovascular unit signalling networks. Our single-cell brain atlas provides insights into the molecular architecture and heterogeneity of the developing, adult/control and diseased human brain vasculature and serves as a powerful reference for future studies.

The expanding landscape of canonical and non-canonical protein phosphorylation.

Protein phosphorylation is a crucial regulatory mechanism in cell signaling, acting as a molecular switch that modulates protein function. Catalyzed by protein kinases and reversed by phosphoprotein phosphatases, it is essential in both normal physiological and pathological states. Recent advances have uncovered a vast and intricate landscape of protein phosphorylation that include histidine phosphorylation and more unconventional events, such as pyrophosphorylation and polyphosphorylation. Many questions remain about the true size of the phosphoproteome and, more importantly, its site-specific functional relevance. The involvement of unconventional actors such as pseudokinases and pseudophosphatases adds further complexity to be resolved. This review explores recent discoveries and ongoing challenges, highlighting the need for continued research to fully elucidate the roles and regulation of protein phosphorylation.

Shaping the brain vasculature in development and disease in the single-cell era.

The CNS critically relies on the formation and proper function of its vasculature during development, adult homeostasis and disease. Angiogenesis - the formation of new blood vessels - is highly active during brain development, enters almost complete quiescence in the healthy adult brain and is reactivated in vascular-dependent brain pathologies such as brain vascular malformations and brain tumours. Despite major advances in the understanding of the cellular and molecular mechanisms driving angiogenesis in peripheral tissues, developmental signalling pathways orchestrating angiogenic processes in the healthy and the diseased CNS remain incompletely understood. Molecular signalling pathways of the 'neurovascular link' defining common mechanisms of nerve and vessel wiring have emerged as crucial regulators of peripheral vascular growth, but their relevance for angiogenesis in brain development and disease remains largely unexplored. Here we review the current knowledge of general and CNS-specific mechanisms of angiogenesis during brain development and in brain vascular malformations and brain tumours, including how key molecular signalling pathways are reactivated in vascular-dependent diseases. We also discuss how these topics can be studied in the single-cell multi-omics era.

Identification of RSK substrates using an analog-sensitive kinase approach.

The p90 ribosomal S6 kinases (RSK) family of serine/threonine kinases comprises four isoforms (RSK1-4) that lie downstream of the ERK1/2 mitogen-activated protein kinase pathway. RSKs are implicated in fine tuning of cellular processes such as translation, transcription, proliferation, and motility. Previous work showed that pathogens such as Cardioviruses could hijack any of the four RSK isoforms to inhibit PKR activation or to disrupt cellular nucleocytoplasmic trafficking. In contrast, some reports suggest nonredundant functions for distinct RSK isoforms, whereas Coffin-Lowry syndrome has only been associated with mutations in the gene encoding RSK2. In this work, we used the analog-sensitive kinase strategy to ask whether the cellular substrates of distinct RSK isoforms differ. We compared the substrates of two of the most distant RSK isoforms: RSK1 and RSK4. We identified a series of potential substrates for both RSKs in cells and validated RanBP3, PDCD4, IRS2, and ZC3H11A as substrates of both RSK1 and RSK4, and SORBS2 as an RSK1 substrate. In addition, using mutagenesis and inhibitors, we confirmed analog-sensitive kinase data showing that endogenous RSKs phosphorylate TRIM33 at S1119. Our data thus identify a series of potential RSK substrates and suggest that the substrates of RSK1 and RSK4 largely overlap and that the specificity of the various RSK isoforms likely depends on their cell- or tissue-specific expression pattern.

Transmembrane receptor DCC associates with protein synthesis machinery and regulates translation.

Extracellular signals regulate protein translation in many cell functions. A key advantage of control at the translational level is the opportunity to regulate protein synthesis within specific cellular subregions. However, little is known about mechanisms that may link extracellular cues to translation with spatial precision. Here, we show that a transmembrane receptor, DCC, forms a binding complex containing multiple translation components, including eukaryotic initiation factors, ribosomal large and small subunits, and monosomes. In neuronal axons and dendrites DCC colocalizes in particles with translation machinery, and newly synthesized protein. The extracellular ligand netrin promoted DCC-mediated translation and disassociation of translation components. The functional and physical association of a cell surface receptor with the translation machinery leads to a generalizable model for localization and extracellular regulation of protein synthesis, based on a transmembrane translation regulation complex.

Focal Adhesion- and IGF1R-Dependent Survival and Migratory Pathways Mediate Tumor Resistance to mTORC1/2 Inhibition.

Aberrant signaling by the mammalian target of rapamycin (mTOR) contributes to the devastating features of cancer cells. Thus, mTOR is a critical therapeutic target and catalytic inhibitors are being investigated as anti-cancer drugs. Although mTOR inhibitors initially block cell proliferation, cell viability and migration in some cancer cells are quickly restored. Despite sustained inhibition of mTORC1/2 signaling, Akt, a kinase regulating cell survival and migration, regains phosphorylation at its regulatory sites. Mechanistically, mTORC1/2 inhibition promotes reorganization of integrin/focal adhesion kinase-mediated adhesomes, induction of IGFR/IR-dependent PI3K activation, and Akt phosphorylation via an integrin/FAK/IGFR-dependent process. This resistance mechanism contributes to xenograft tumor cell growth, which is prevented with mTOR plus IGFR inhibitors, supporting this combination as a therapeutic approach for cancers.

EMT and primary ciliogenesis: For better or worse in sickness and in health.

Epithelial-mesenchymal transition (EMT) and primary ciliogenesis are two cell-biological programs that are essential for development of multicellular organisms and whose abnormal regulation results in many diseases (i.e., developmental anomalies and cancers). Emerging studies suggest an intricate interplay between these two processes. Here, we discuss physiological and pathological contexts in which their interconnections promote normal development or disease progression. We describe underlying molecular mechanisms of the interplay and EMT/ciliary signaling axes that influence EMT-related processes (i.e., stemness, motility and invasion). Understanding the molecular and cellular mechanisms of the relationship between EMT and primary ciliogenesis may provide new insights in the etiology of diseases related to EMT and cilia dysfunction.

Circulating small extracellular vesicles mediate vascular hyperpermeability in diabetes.

AIMS/HYPOTHESIS: A hallmark chronic complication of type 2 diabetes mellitus is vascular hyperpermeability, which encompasses dysfunction of the cerebrovascular endothelium and the subsequent development of associated cognitive impairment. The present study tested the hypothesis that during type 2 diabetes circulating small extracellular vesicles (sEVs) exhibit phenotypic changes that facilitate pathogenic disruption of the vascular barrier. METHODS: sEVs isolated from the plasma of a mouse model of type 2 diabetes and from diabetic human individuals were characterised for their ability to disrupt the endothelial cell (EC) barrier. The contents of sEVs and their effect on recipient ECs were assessed by proteomics and identified pathways were functionally interrogated with small molecule inhibitors. RESULTS: Using intravital imaging, we found that diabetic mice (Leprdb/db) displayed hyperpermeability of the cerebrovasculature. Enhanced vascular leakiness was recapitulated following i.v. injection of sEVs from diabetic mice into non-diabetic recipient mice. Characterisation of circulating sEV populations from the plasma of diabetic mice and humans demonstrated increased quantity and size of sEVs compared with those isolated from non-diabetic counterparts. Functional experiments revealed that sEVs from diabetic mice or humans induced the rapid and sustained disruption of the EC barrier through enhanced paracellular and transcellular leak but did not induce inflammation. Subsequent sEV proteome and recipient EC phospho-proteome analysis suggested that extracellular vesicles (sEVs) from diabetic mice and humans modulate the MAPK/MAPK kinase (MEK) and Rho-associated protein kinase (ROCK) pathways, cell-cell junctions and actin dynamics. This was confirmed experimentally. Treatment of sEVs with proteinase K or pre-treatment of recipient cells with MEK or ROCK inhibitors reduced the hyperpermeability-inducing effects of circulating sEVs in the diabetic state. CONCLUSIONS/INTERPRETATION: Diabetes is associated with marked increases in the concentration and size of circulating sEVs. The modulation of sEV-associated proteins under diabetic conditions can induce vascular leak through activation of the MEK/ROCK pathway. These data identify a new paradigm by which diabetes can induce hyperpermeability and dysfunction of the cerebrovasculature and may implicate sEVs in the pathogenesis of cognitive decline during type 2 diabetes.

Proteomic analysis of the actin cortex in interphase and mitosis.

Many animal cell shape changes are driven by gradients in the contractile tension of the actomyosin cortex, a thin cytoskeletal network supporting the plasma membrane. Elucidating cortical tension control is thus essential for understanding cell morphogenesis. Increasing evidence shows that alongside myosin activity, actin network organisation and composition are key to cortex tension regulation. However, owing to a poor understanding of how cortex composition changes when tension changes, which cortical components are important remains unclear. In this article, we compared cortices from cells with low and high cortex tensions. We purified cortex-enriched fractions from cells in interphase and mitosis, as mitosis is characterised by high cortical tension. Mass spectrometry analysis identified 922 proteins consistently represented in both interphase and mitotic cortices. Focusing on actin-related proteins narrowed down the list to 238 candidate regulators of the mitotic cortical tension increase. Among these candidates, we found that there is a role for septins in mitotic cell rounding control. Overall, our study provides a comprehensive dataset of candidate cortex regulators, paving the way for systematic investigations of the regulation of cell surface mechanics. This article has an associated First Person interview with the first author of the paper.

Microbiota signature of oral chronic graft-versus-host disease 6+ years after transplantation.

Not available.

Impedance and Functional Outcomes in Robotic-Assisted or Manual Cochlear Implantation: A Comparative Study.

INTRODUCTION: Preservation of residual hearing, mainly the low frequencies, is the current main objective of cochlear implantation. New electrode arrays and the development of minimally invasive surgery have allowed electroacoustic stimulation. Over the past several years, robotic-assisted cochlear implant surgery aimed to improve the insertion process while respecting inner ear structures. However, the introduction of a foreign body inside the cochlea can lead to the development of fibrous tissue around the electrode array, or even induce osteogenesis. These histological changes disrupt the parameters of the cochlear implant, resulting in elevated impedance. In addition, long-term auditory performance can be affected, with a deterioration in word comprehension. We evaluated the potential impact of RobOtol® on impedance changes over time, leading to potentially positive functional outcomes. METHODS: Cochlear implant surgery with a round window approach was performed under general anesthesia. Fifteen Med-El Flex24 electrode arrays were inserted manually and 24 using RobOtol®. All subjects underwent pure-tone audiometry tests before the surgery and at regular intervals up to 1 year after the surgery. Based on the pure-tone average at the low frequencies from 250 to 1,000 Hz, we divided the patients according to the degree of auditory preservation (full preservation ≤15 dB, partial preservation 15 dB-30 dB, significant loss >30 dB). These different groups were compared in terms of impedance changes and auditory performance, specifically word recognition score. RESULTS: We found proportionally fewer patients who experienced significant low-frequency hearing loss after robotic insertion (53.33% in the manual group compared to 41.67% in the robot-assisted insertion group). Impedance changes at the apex of the electrode array, especially at the first electrode (p = 0.04), after robotic surgery, with less overall variability, a continuous decreasing trend without secondary elevation, and lower values in cases of complete residual hearing preservation (for the three first electrodes: p = 0.017, p = 0.04, p = 0.045). The speech intelligibility amelioration over time showed favorable evolution in patients with complete residual hearing preservation regardless of the insertion method. However, in the absence of auditory preservation, the positive evolution continued more than 6 months after robotic surgery but stagnated after manual insertion (difference at 1 year, p = 0.038; median auditory capacity index 83% vs. 57%). CONCLUSION: Atraumatic electrode array insertion with consistent, slow speed and the assistance of RobOtol® minimizes disturbances in the delicate neurosensory structures of the inner ear and leads to better auditory performance.

Factors Predictive of Binaural Hearing Restoration by Cochlear Implant in Single-Sided Deafness.

INTRODUCTION: Cochlear implants (CIs) can restore binaural hearing in cases of single-sided deafness (SSD). However, studies with a high level of evidence in support of this phenomenon are lacking. The aim of this study is to analyze the effectiveness of CIs using several spatialized speech-in-noise tests and to identify potential predictors of successful surgery. METHODS: Ten cases underwent standard CI surgery (MEDEL-Flex24). The speech-in-noise test was used in three different spatial configurations. The noise was presented from the front (N0), toward the CI (NCI), and toward the ear (Near), while the speech was always from the front (S0). For each test, the speech-to-noise ratio at 50% intelligibility (SNR50) was evaluated. Seven different effects were assessed (summation, head shadow [HS], speech released of masking [SRM], and squelch for the CI and for the ear). RESULTS: A significant summation effect of 1.5 dB was observed. Contralateral PTA was positively correlated with S0N0-B and S0NCI-B (CIon and unplugged ear). S0N0-B results were positively correlated with S0N0-CIoff (p < 0.0001) and with S0Near-CIoff results (p = 0.004). A significant positive correlation was found between delay post-activation and HS gain for the CI (p = 0.005). Finally, the HS was negatively correlated with the squelch effect for the ear. CONCLUSION: CI benefits patients with SSD in noise and can improve the threshold for detecting low-level noise. Contralateral PTA could predict good postoperative results. Simple tests performed preoperatively can predict the likelihood of surgical success in reversing SSD.

Cochlear Implant: Analysis of the Frequency-to-Place Mismatch with the Table-Based Software OTOPLAN® and Its Influence on Hearing Performance.

OBJECTIVE: The purpose of this study was to compare the originally applied frequency allocation of cochlear implant electrodes assigned by default at the time of activation with a more recent frequency allocation that is anatomy-based by a software called OTOPLAN®. Based on a computed tomography scan of the temporal bone, this software calculates the position of each electrode in the cochlea and its corresponding tonotopic frequency. We also evaluated whether patients with a significant mismatch between these two allocations present poorer speech intelligibility. MATERIALS AND METHODS: Patients who underwent cochlear implantation from 2016 to 2021 at the University Hospital of Liege were included in this retrospective study. We used OTOPLAN® to calculate the tonotopic frequency allocation of each electrode according to its exact position in the cochlear duct. This anatomical frequency mapping was compared with the default frequency mapping at the time of cochlear implant activation. Finally, we compared the mismatch with the patients' auditory performance, represented by the Auditory Capacity Index (ACI). RESULTS: Thirteen patients were included in the study. All patients had a mismatch between the two frequency maps, to a variable extent (200 Hz-1,100 Hz). Frequency shift was significantly inversely correlated with ACI and with the time needed to improve speech intelligibility. CONCLUSION: Our primary results show that patients with a larger mismatch between default frequency mapping and anatomically assigned frequency mapping experience poorer hearing performance and slower adaptation to a cochlear implant.

Sleep-disordered breathing diagnosis: a comprehensive audit of home sleep testing in real clinical settings.

PURPOSE: This study aimed to investigate the indications and outcomes of Home Sleep Testing (HST) for patients with suspected obstructive sleep apnea (OSA), aligning with guidelines set forth by the American Academy of Sleep Medicine and the European Sleep Research Society. Specifically, we aimed to audit whether validated type 3 polygraphy could effectively ensure patient care while optimizing resource utilization. METHODS: A retrospective analysis was conducted on data from patients undergoing type 3 polygraphy for suspected OSA in a tertiary referral hospital between January 2022 and December 2022. Demographic, clinical, and management data were collected. The efficacy of HST in guiding management plans was evaluated, with outcomes categorized as effective or ineffective based on subsequent need for in-laboratory polysomnography. RESULTS: While 85% of patients received a reliable diagnosis, 44.4% of them still required subsequent polysomnography, primarily due to adherence to funding regulations, rather than clinical need for further testing. Factors impacting the efficacy of HST included patient age, severity of apnea, and referral by a certified sleep specialist physician. CONCLUSION: Our study highlighted the potential of type 3 polygraphy, as a valuable tool for diagnosing OSA in an outpatient setting. However, having the result interpreted by a certified sleep specialist doctor was not enough. To streamline the care pathway, the referral for polygraphy had also to be made by a trained specialist. Challenges related to funding regulations, patient demographics and physician training stress the need for optimized diagnostic pathways to improve patient care and resource utilization.

RIOK2 phosphorylation by RSK promotes synthesis of the human small ribosomal subunit.

Ribosome biogenesis lies at the nexus of various signaling pathways coordinating protein synthesis with cell growth and proliferation. This process is regulated by well-described transcriptional mechanisms, but a growing body of evidence indicates that other levels of regulation exist. Here we show that the Ras/mitogen-activated protein kinase (MAPK) pathway stimulates post-transcriptional stages of human ribosome synthesis. We identify RIOK2, a pre-40S particle assembly factor, as a new target of the MAPK-activated kinase RSK. RIOK2 phosphorylation by RSK stimulates cytoplasmic maturation of late pre-40S particles, which is required for optimal protein synthesis and cell proliferation. RIOK2 phosphorylation facilitates its release from pre-40S particles and its nuclear re-import, prior to completion of small ribosomal subunits. Our results bring a detailed mechanistic link between the Ras/MAPK pathway and the maturation of human pre-40S particles, which opens a hitherto poorly explored area of ribosome biogenesis.

Are Redox-Active Centers Bridged by Saturated Flexible Linkers Systematically Electrochemically Independent?

The extent to which electrophores covalently bridged by a saturated linker are electrochemically independent was investigated considering the charge/spin duality of the electron and functionality of the electrophore as a spin carrier upon reduction. By combining computational modeling with electrochemical experiments, we investigated the mechanism by which tethered electrophores react together within 4,4'-oligo[n]methylene-bipyridinium assemblies (with n=2 to 5). We show that native dicationic electrophores (redox state Z=+2) are folded prior to electron injection into the system, allowing the emergence of supra-molecular orbitals (supra-MOs) likely to support the process of the reductive σ bond formation giving cyclomers. Indeed, for Z=+2, London Dispersion (LD) forces contribute to flatten the potential energy surface such that all-trans and folded conformers are approximately isoenergetic. Then, upon one-electron injection, for radical cations (Z=+1), LD forces significantly stabilize the folded conformers, except for the ethylene derivative deprived of supra-MOs. For radical cations equipped with supra-MOs, the unpaired electron is delocalized over both heterocycles through space. Cyclomer completion (Z=0) upon the second electron transfer occurs according to the inversion of redox potentials. This mechanism explains why intramolecular reactivity is favored and why pyridinium electrophores are not independent.

Parkinson's disease pathology is directly correlated to SIRT3 in human subjects and animal models: Implications for AAV.SIRT3-myc as a disease-modifying therapy.

In Parkinson's disease (PD), post-mortem studies in affected brain regions have demonstrated a decline in mitochondrial number and function. This combined with many studies in cell and animal models suggest that mitochondrial dysfunction is central to PD pathology. We and others have shown that the mitochondrial protein deacetylase, SIRT3, has neurorestorative effects in PD models. In this study, to determine whether there is a link between PD pathology and SIRT3, we analysed SIRT3 levels in human subjects with PD, and compared to age-matched controls. In the SNc of PD subjects, SIRT3 was reduced by 56.8 ± 15.5% compared to control, regardless of age (p < 0.05, R = 0.6539). Given that age is the primary risk factor for PD, this finding suggests that reduced SIRT3 may contribute to PD pathology. Next, we measured whether there was a correlation between α-synuclein and SIRT3. In a parallel study, we assessed the disease-modifying potential of SIRT3 over-expression in a seeding model of α-synuclein. In PFF rats, infusion of rAAV1.SIRT3-myc reduced abundance of α-synuclein inclusions by 30.1 ± 18.5%. This was not observed when deacetylation deficient SIRT3H248Y was transduced, demonstrating the importance of SIRT3 deacetylation in reducing α-synuclein aggregation. These studies confirm that there is a clear difference in SIRT3 levels in subjects with PD compared to age-matched controls, suggesting a link between SIRT3 and the progression of PD. We also demonstrate that over-expression of SIRT3 reduces α-synuclein aggregation, further validating AAV.SIRT3-myc as a potential disease-modifying solution for PD.

De Novo Variants in SPOP Cause Two Clinically Distinct Neurodevelopmental Disorders.

Recurrent somatic variants in SPOP are cancer specific; endometrial and prostate cancers result from gain-of-function and dominant-negative effects toward BET proteins, respectively. By using clinical exome sequencing, we identified six de novo pathogenic missense variants in SPOP in seven individuals with developmental delay and/or intellectual disability, facial dysmorphisms, and congenital anomalies. Two individuals shared craniofacial dysmorphisms, including congenital microcephaly, that were strikingly different from those of the other five individuals, who had (relative) macrocephaly and hypertelorism. We measured the effect of SPOP variants on BET protein amounts in human Ishikawa endometrial cancer cells and patient-derived cell lines because we hypothesized that variants would lead to functional divergent effects on BET proteins. The de novo variants c.362G>A (p.Arg121Gln) and c. 430G>A (p.Asp144Asn), identified in the first two individuals, resulted in a gain of function, and conversely, the c.73A>G (p.Thr25Ala), c.248A>G (p.Tyr83Cys), c.395G>T (p.Gly132Val), and c.412C>T (p.Arg138Cys) variants resulted in a dominant-negative effect. Our findings suggest that these opposite functional effects caused by the variants in SPOP result in two distinct and clinically recognizable syndromic forms of intellectual disability with contrasting craniofacial dysmorphisms.