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Long non-coding RNAs (lncRNAs) play fundamental roles in cellular processes and pathologies, regulating gene expression at multiple levels. Despite being highly cell type-specific, their study at single-cell (sc) level is challenging due to their less accurate annotation and low expression compared to protein-coding genes. Here, we systematically benchmark different preprocessing methods and develop a computational framework, named ELATUS, based on the combination of the pseudoaligner Kallisto with selective functional filtering. ELATUS enhances the detection of functional lncRNAs from scRNA-seq data, detecting their expression with higher concordance than standard methods with the ATAC-seq profiles in single-cell multiome data. Interestingly, the better results of ELATUS are due to its advanced performance with an inaccurate reference annotation such as that of lncRNAs. We independently confirm the expression patterns of cell type-specific lncRNAs exclusively detected with ELATUS and unveil biologically important lncRNAs, such as AL121895.1 , a previously undocumented cis-repressor lncRNA, whose role in breast cancer progression is unnoticed by traditional methodologies. Our results emphasize the necessity for an alternative scRNA-seq workflow tailored to lncRNAs that sheds light on the multifaceted roles of lncRNAs. The inaccurate annotation of long noncoding RNAs (lncRNAs) hampers their detection by scRNA-seq. The computational workflow ELATUS, based on the pseudoaligner Kallisto, addresses this problem and uncovers functional lncRNAs, such as AL121895.1, that participates in breast cancer.

Cells must coordinate the activation of thousands of replication origins dispersed throughout their genome. Active transcription is known to favor the formation of mammalian origins, although the role that RNA plays in this process remains unclear. We show that the ORC1 subunit of the human Origin Recognition Complex interacts with RNAs transcribed from genes with origins in their transcription start sites (TSSs), displaying a positive correlation between RNA binding and origin activity. RNA depletion, or the use of ORC1 RNA-binding mutant, result in inefficient activation of proximal origins, linked to impaired ORC1 chromatin release. ORC1 RNA binding activity resides in its intrinsically disordered region, involved in intra- and inter-molecular interactions, regulation by phosphorylation, and phase-separation. We show that RNA binding favors ORC1 chromatin release, by regulating its phosphorylation and subsequent degradation. Our results unveil a non-coding function of RNA as a dynamic component of the chromatin, orchestrating the activation of replication origins. Here the authors describe that the human origin recognition complex subunit 1 (ORC1) binds to RNAs transcribed from genes with origins of replication at their TSS impacting origin activation.

Long non-coding RNAs (lncRNAs) play fundamental roles in cellular processes and pathologies, regulating gene expression at multiple levels. Despite being highly cell type-specific, their study at single-cell (sc) level has been challenging due to their less accurate annotation and low expression compared to protein-coding genes. To identify the important, albeit widely overlooked, specific lncRNAs from scRNA-seq data, here, we develop a computational framework, ELATUS, based on the pseudoaligner Kallisto that enhances the detection of functional lncRNAs previously undetected and exhibits higher concordance with the ATAC-seq profiles in single-cell multiome data. Importantly, we then independently confirmed the expression patterns of cell type-specific lncRNAs exclusively detected with ELATUS and unveiled biologically important lncRNAs, such as AL121895.1, a previously undocumented cis-repressor lncRNA, whose role in breast cancer progression was unnoticed by traditional methodologies. Our results emphasize the necessity for an alternative scRNA-seq workflow tailored to lncRNAs that sheds light on the multifaceted roles of lncRNAs.Competing Interest StatementThe authors have declared no competing interest.Footnotes* Section on ELATUS workflow updated to clarify the different steps.

The etiology of Alzheimer’s disease (AD) has been associated with impaired neurogenesis in the adult subventricular zone (SVZ), but the molecular mechanism leading to this impairment remains poorly understood. Neuronal dysfunction in the AD-affected brain might lead to reduced production of neuron-derived paracrine factors acting through receptors necessary for adult SVZ neurogenesis (ASN). To test this hypothesis, we focused on the TrkB receptor, which can transduce signals from the neurotrophins BDNF and NT4/5, since TrkB is known to regulate the ASN process and its function becomes altered in AD. Here we show that ASN is impaired in the SVZ of homozygous 5xFAD (h5xFAD) mice. This impairment is prevented by administering an AAV.PHP.eB vector that expresses in neurons the transcription factor E2F4 carrying the Thr249Ala/Th251Ala mutation (E2F4DN), a gene therapeutic approach previously demonstrated to exert multifactorial effects in this mouse model of AD. The use of culture media conditioned by primary cortical neurons expressing E2F4DN was able to recover the proliferative and differentiative capacity of neural stem cells (NSCs) isolated from h5xFAD mice. This effect was blocked by inhibiting the TrkB receptor. Accordingly, TrkB activation mimicked the effect of the E2F4DN-conditioned medium on the proliferative and differentiative capacity of h5xFAD NSCs, a finding consistent with the upregulation of NT4/5 expression in the E2F4DN-transduced neurons. We conclude that the activation of TrkB by neurotrophins released by E2F4DN-expressing neurons can recover the ASN phenotype in 5xFAD mice. Therefore, the multifactorial therapeutic capacity of E2F4DN includes the recovery of impaired ASN through the upregulation of TrkB signaling in NSCs.

Cells must coordinate the activation of thousands of replication origins dispersed throughout their genome. Active transcription is known to favor the formation of mammalian origins, although the role that RNA plays in this process remains unclear. We show that the ORC1 subunit of the human Origin Recognition Complex interacts with RNAs transcribed from genes with origins in their transcription start sites (TSSs), displaying a positive correlation between RNA binding and origin activity. RNA depletion, or the use of ORC1 RNA-binding mutant, result in inefficient activation of proximal origins, linked to impaired ORC1 chromatin release. ORC1 RNA binding activity resides in its intrinsically disordered region, involved in intra- and inter-molecular interactions, regulation by phosphorylation, and phase-separation. We show that RNA binding favors ORC1 chromatin release, by regulating its phosphorylation and subsequent degradation. We propose that fluctuating concentrations of RNA during the cell cycle may play a sequential role in controlling origins through interaction with this flexible region of ORC1. Our results unveil a novel non-coding function of RNA as a dynamic component of the chromatin, orchestrating the activation of replication origins.Competing Interest StatementThe authors have declared no competing interest.

Background Urogenital schistosomiasis is one of the most prevalent parasitic diseases in sub-Saharan Africa. It is a poverty-related disease conditioned by behavioural practices. Methods Our objective is to evaluate the awareness, mindset and habits about urogenital schistosomiasis in the community of Cubal (Angola), as well as its association with infection and urinary tract morbidity in pre-school age children. A cross-sectional study of knowledge, attitudes and practices at home was conducted between February and May 2022 with 250 participants. Results Overall, 93.6% of those surveyed had some prior knowledge about schistosomiasis and, among all the symptoms associated with this disease, blood in the urine was the best known (54.4%). Nevertheless, 57.6% obtained a medium knowledge score. Regarding attitude, the majority of respondents had a high attitude score (79.2%) with 96.0% willing to participate in mass drug administration campaigns. Laundry in the river was the most common risk practice (61.2%) and 55.2% out of the total were classified with a low practice score. Conclusion Low knowledge about symptoms and transmission by caregivers was the outstanding risk factor for infection in pre-school age children (OR = 16.93, 95%CI: 3.93-72.82), and lack of knowledge that avoiding entering the river prevents schistosomiasis was the main risk factor for morbidity in PSAC (OR = 8.14, 95%CI: 1.14-58.25).

Thrombotic microangiopathy (TMA) is an important complication associated with several diseases that are rare and life-threatening. TMA is common to thrombotic thrombocytopenic purpura (TTP) and hemolytic uremic syndrome (HUS). TTP is defined by a severe deficiency of ADAMTS13, and early treatment is associated with good prognosis. The diagnosis of HUS can be difficult due to the potential multiple etiologies, and the best treatment option in most cases is not well-established yet. The implementation of a multidisciplinary team (MDT) could decrease the time to diagnosis and treatment for HUS and may improve the outcomes of these patients. To determine the impact of MDT on morbidity and mortality [death or chronic renal replacement therapy (CRRT) requirements], incidence and response time [(RT) defined as the period between hospital admission and the first day of direct therapy administration], length of stay at an intensive care unit (ICU-LOS) and total hospitalization (T-LOS) were also assessed. We compared a pre-MDT implementation period (from January/2008 to May/2016) versus post-MDT period (from May/2016 to December/2016). The screening TMA diagnosis was made according the following criteria: hemolytic anemia, thrombocytopenia and acute renal damage and without ADAMTS13 deficiency. An online chat was implemented to provide instant medical information. Twenty-eight patients were included. The incidence changed from 2.3 cases/pre-MDT: (all cases: n = 18) to 10 cases/year post-MDT (all cases: n = 10). Two patients died in pre-MDT and post- MDT (11% versus 20%, P = 0.60). From pre-MDT, the number of patients who required CRRT by post-MDT decreased from 7 (39%) to 0, P = 0.03. Similarly, RT, ICU-LOS and T-LOS [median(p25-p75)] decreased from 10 (2-12) days to 0.5 (0-1.5) days, P = 0.04, from 16 (9-30) days to 10 (4-13) days, P = 0.01 and from 33 (22-53) days to 16 (12-32) days, P < 0.01, respectively. MDT implementation was associated with a greater number of patients who meet TMA criteria. A decrease in the RT and T-LOS periods were observed and associated with better outcomes in these patients.

E2F4 is a transcription factor involved in cellular homeostasis and a substrate of the stress-activated kinase p38MAPK, which phosphorylates a conserved Thr248/Thr250 motif. A non-phosphorylatable mutant, E2F4DN (Thr248Ala/Thr250Ala), has demonstrated preclinical efficacy in a murine model of Alzheimer's disease (AD), but its mechanism of action remains unknown. We hypothesized that cell stress-induced phosphorylation disrupts E2F4's homeostatic function, whereas exogenous E2F4DN restores it. To begin testing this hypothesis, we treated differentiated N2a neuroblastoma cells (N2a neuron-like cells) with camptothecin (CPT) to induce genotoxic stress. CPT activated p38MAPK within 8 h, leading to phosphorylation of E2F4 at Thr248/Thr250. We then overexpressed E2F4DN or a phosphomimetic variant, E2F4CA (Thr248Glu/Thr250Glu), and assessed apoptosis via procaspase-3 cleavage. The pro-apoptotic factor E2F1 strongly induced caspase-3 activation in this model system. This effect was partially mimicked by E2F4CA, while E2F4DN markedly suppressed it. Notably, E2F4DN, but not E2F4CA, upregulated the antiapoptotic factor Cited2, and knockdown experiments suggest it may contribute to E2F4DN's protective effect. Overall, these findings indicate that E2F4DN counteracts p38MAPK-driven neuronal apoptosis and helps preserve neuronal homeostasis, at least in part, through Cited2 upregulation. This provides mechanistic insight into the neuroprotective role of E2F4DN as a potential therapy for AD.E2F4 is a transcription factor involved in cellular homeostasis and a substrate of the stress-activated kinase p38MAPK, which phosphorylates a conserved Thr248/Thr250 motif. A non-phosphorylatable mutant, E2F4DN (Thr248Ala/Thr250Ala), has demonstrated preclinical efficacy in a murine model of Alzheimer's disease (AD), but its mechanism of action remains unknown. We hypothesized that cell stress-induced phosphorylation disrupts E2F4's homeostatic function, whereas exogenous E2F4DN restores it. To begin testing this hypothesis, we treated differentiated N2a neuroblastoma cells (N2a neuron-like cells) with camptothecin (CPT) to induce genotoxic stress. CPT activated p38MAPK within 8 h, leading to phosphorylation of E2F4 at Thr248/Thr250. We then overexpressed E2F4DN or a phosphomimetic variant, E2F4CA (Thr248Glu/Thr250Glu), and assessed apoptosis via procaspase-3 cleavage. The pro-apoptotic factor E2F1 strongly induced caspase-3 activation in this model system. This effect was partially mimicked by E2F4CA, while E2F4DN markedly suppressed it. Notably, E2F4DN, but not E2F4CA, upregulated the antiapoptotic factor Cited2, and knockdown experiments suggest it may contribute to E2F4DN's protective effect. Overall, these findings indicate that E2F4DN counteracts p38MAPK-driven neuronal apoptosis and helps preserve neuronal homeostasis, at least in part, through Cited2 upregulation. This provides mechanistic insight into the neuroprotective role of E2F4DN as a potential therapy for AD.