Biology subjects

Serra, E.

Publications and source records attributed to Serra, E..

At least 19 recordsLinked to original sources

bioRxiv2026

Ageing reshapes the resting-state network landscape of the human brain

Ageing alters brain rhythms and large-scale functional organisation, but whether these changes reflect isolated effects or a coordinated reconfiguration remains unclear. We applied Frequency-resolved Network Estimation via Source Separation (FREQ-NESS) to source-reconstructed resting-state MEG from 164 healthy younger and older adults across two independent datasets. FREQ-NESS revealed that ageing reshaped the frequency-resolved organisation of whole-brain networks. Older adults showed a slower alpha-network peak and a flatter decay of network prominence from alpha into beta frequencies, together with changes in entropy across the spectrum. These spectral changes were accompanied by shifts in the spatial expression of dominant networks along the lateral, posterior-anterior, and inferior-superior spatial axes. Rather than following a uniform anatomical shift, the direction of age differences varied across frequencies. Together, these findings show that healthy ageing is associated with a reshaped configuration of endogenous brain networks, characterised not simply by a uniform loss of network organisation, but by selective reconfiguration of the prominence and spatiotemporal expression of whole-brain activity across frequencies.

neuroscience↗

bioRxiv2026

Generalisable signatures of anaesthesia in the large-scale functional organisation of the marmoset brain

How the activity and connectivity of the brain support consciousness remains a central question in neuroscience. Recent progress driven by the use of functional MRI has seen growing recognition that large-scale distributed functional organisation of the human and non-human primate brain are systematically and consistently reshaped by anaesthetic-induced unconsciousness, across anaesthetics and across human and macaque. Here, we generalise these results to a different primate species that is gaining traction as model organism in neuroscience, the marmoset (Callithrix jacchus). We also generalise results to an additional anaesthetic, isoflurane, which we compare with propofol and sevoflurane. We report that under anaesthesia with propofol, sevoflurane, or isoflurane, distributed brain activity from functional MRI is increasingly constrained by the underlying structural connectivity across scales. Anaesthesia also induces a collapse of the principal gradient and intrinsic functional geometry of the marmoset brain, coinciding with a breakdown of hierarchical integration. Altogether, the present results indicate generalisable signatures of anaesthesia in the large-scale organisation of the primate brain.

neuroscience↗

bioRxiv2026

Efficient ageing: Simulated lesion of the structural connectome reveals optimised decline in the healthy ageing brain

Healthy ageing is associated with widespread white-matter change and altered connectome organisation, yet the link between local microstructural decline and whole-brain network communication remains unclear. Here we combined tract-based spatial statistics (TBSS) with probabilistic tractography and graph analysis to quantify the connectome-level consequences of age-sensitive white-matter hotspots. In two independent diffusion MRI datasets of healthy young and older adults (n = 144 total; Dataset 1: 77 participants; Dataset 2: 67 participants), we first identified age-sensitive fractional anisotropy clusters and then used them as constraints in a cross-dataset simulated-lesion framework. This allowed us to estimate how strongly each structural connection depended on age-sensitive tissue and to test the resulting network effects against matched-mass null lesions. Across both datasets, ageing hotspot lesioning reduced global efficiency, but consistently less than expected under the null model, indicating a less-than-random disruption of network integration. Age-sensitive tissue was disproportionately embedded in the brains integrative backbone: proportional degree loss was strongest in high-degree nodes, rich-club connections showed the greatest hotspot dependence, and nodewise losses were concentrated in frontal, cingulate and subcortical association systems, whereas posterior sensory and temporo-limbic regions were relatively spared. These findings suggest that healthy ageing reflects a selective and constrained reconfiguration of structural connectivity rather than simply pointing to uniform decline.

neuroscience↗

bioRxiv2026

PKA/CIP4 SIGNALING REGULATES CIP4 RELOCATION IN ACTIVATED NATURAL KILLER CELLS

Natural killer (NK) cells are cytotoxic lymphocytes of the innate immune system that eliminate virus-infected and transformed cells through the formation of a specialized immune synapse. Effective target cell killing requires coordinated plasma membrane remodeling and dynamic reorganization of the actin and microtubule cytoskeletons, enabling centrosome polarization and directed secretion of lytic granules. The scaffold protein CIP4 has emerged as an important regulator of cytoskeletal coordination in NK cells, yet how its subcellular localization is controlled during NK cell activation is unknown. CIP4 contains a unique protein kinase A (PKA) phosphorylation site (threonine 225, T225) within its F-BAR domain, a domain that mediates interactions with microtubules and the plasma membrane. We hypothesized that localized PKA signaling controls CIP4 redistribution during immune synapse assembly. To test this hypothesis, we analyzed CIP4 localization and phosphorylation in NK cells engaged with sensitive target cells using biochemical and imaging approaches. We show that NK-target cell interaction enhances PKA activity and promotes phosphorylation of CIP4, coinciding with its delocalization from microtubules and accumulation at the immune synapse. Importantly, this relocalization process requires the PKA-anchoring protein AKAP350, which positions PKA and CIP4 within the same protein complex, thereby facilitating CIP4 phosphorylation. Consistently, pharmacological inhibition of PKA prevented CIP4 delocalization from microtubules and reduced its accumulation at the immune synapse. The non-phosphorylatable CIP4 mutant T225A displayed increased association with microtubules compared with a phosphomimetic mutant, identifying phosphorylation at T225 as a key determinant of CIP4 spatial regulation. Together, these findings identify a signaling mechanism that links compartmentalized PKA activity to the spatial control of CIP4 during immune synapse formation, providing new insight into the molecular mechanisms governing immune synapse maturation.

immunology↗

bioRxiv2026

Identification of Malignant Peripheral Nerve Sheath Tumor subtypes with distinct genomic identities

Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive soft-tissue sarcomas arising sporadically or in people with neurofibromatosis type 1 (NF1). Their marked heterogeneity challenges diagnosis and has hampered an integrative view of MPNST molecular pathogenesis. Here, a thorough whole-genome and transcriptome analysis of MPNSTs and the re-analysis of a large independent cohort allowed us to identify three molecular subtypes of MPNSTs (G1-G3) with distinct genomic identities and clinicopathological features. Furthermore, it provided a simple and unifying model of MPNST development, defining a distinct progression path for each group. This work uncovers new genomic aspects of MPNSTs, including the identification of recurrent copy-neutral loss of heterozygosity regions, distinct copy-number profiles among G1-G3, and CDKN2A-inactivating translocations in pre-malignant lesions (ANNUBPs). Altogether, these analyses overcome the dominant influence of PRC2 status in MPNST classification and provide a framework for their differential diagnosis and potential precision oncology treatment. SIGNIFICANCEMPNST is a highly heterogeneous soft-tissue sarcoma with difficult clinical management and no effective systemic therapies. This work defines three molecular subtypes of MPNSTs with distinct development paths and histological and clinical characteristics with potential impact on translational studies and subtype-tailored treatments.

cancer biology↗

bioRxiv2026

Structural Insights into Bromodomain-Containing Complexes from Trypanosoma cruzi Revealed by Proximity Labeling and Stoichiometric Space Exploration

Trypanosoma cruzi is the causative agent of Chagas disease, a neglected illness with outdated treatments. Bromodomain factors (BDFs) are essential proteins that recognize acetylated lysines and have strong therapeutic potential. They form part of epigenetic complexes that regulate chromatin accessibility and, therefore, gene expression. However, little is known about their structure in trypanosomatids. Here, we used a combination of experimental and bioinformatic approaches to infer the stoichiometry and structure of T. cruzi bromodomain-containing complexes. By reconstructing the proximity networks of five BDFs using TurboID-directed proximity labeling, we identified highly interconnected components that assemble into the CRKT and NuA4 complexes. Using novel structure prediction strategies that systematically explore the stoichiometric space, we inferred that CRKT assembles into three distinct modules and NuA4 in two, with different degrees of interaction dynamics. The core module of CRKT contains two copies of each component, including BDF3, BDF5, and BDF8, arranged in a subcomplex with central symmetry. The catalytic module of CRKT has three subunits, including the histone acetyltransferase 2 (HAT2), while the BET (bromodomain and extra-terminal) module has one unit of both BDF4 and BDF1. The catalytic module of NuA4 closely resembles the yeast piccolo-NuA4 module and contains HAT1, while the TINTIN module associates with the catalytic module via the C-terminal domain of BDF6. These insights shed light on the structure and composition of epigenetic complexes in trypanosomatids, opening new avenues for rational drug design aimed at disrupting their function.

molecular biology↗

bioRxiv2025

NF2 lacking exon 11 isoform induced by antisense gene therapy is able to recover partially merlin deficiency on NF2-related Schwannomatosis iPSC-derived spheroid model

NF2-related Schwannomatosis (NF2-SWN) is an inherited autosomal dominant disorder resulting from loss-of-function mutations in the NF2 gene, for which no effective treatment is currently available. Furthermore, truncating variants in NF2 are associated with the severest phenotype compared to in-frame or missense variants. Previously, a shorter NF2 isoform with exon 11 skipped (merlin_e-11), induced through antisense morpholino oligomers (PMOs), was able to partially rescue the deleterious effect of nonsense variants located at that exon in patients primary fibroblast. To test the potential of this approach into Schwann cells, those responsible of NF2-SWN tumours, we developed an iPSC-based model carrying heterozygous and homozygous truncating variants on exon 11 of the NF2 gene and differentiated them to Schwann cells forming spheroids. After 3 days of treatment, merlin_e-11 expression was induced in NF2-deficient cell lines. Furthermore, key pathways associated with NF2-deficiency in schwannomas, such as PI3K/Akt/mTORC and YAP levels, were recovered without signs of toxicity. These results confirm that the PMO treatment induces effective skipping of exon 11 in Schwann cell spheroids, generating an hypomorphic merlin_e-11 that has the capacity to partially rescue merlin-deficiency in NF2-SWN spheroid cell model and it being a potential treatment of patients harbouring truncating variants located in exon 11.

genetics↗

bioRxiv2025

iPSC-derived NF1-CDKN2A-PRC2 deficient neural crest cells mimic glial-to-neuro-mesenchymal transition and form MPNST-like tumors in vivo

Neurofibromatosis Type 1 (NF1) predisposes to peripheral nerve tumor development. Commonly, the progression from a benign plexiform neurofibroma (PNF) towards a deadly malignant peripheral nerve sheath tumor (MPNST) involves a poorly understood glial-to-mesenchymal transition and the sequential loss of NF1, CDKN2A, and polycomb repressive complex 2 (PRC2). Using an iPSC-derived neural crest (NC) model, we reproduced this malignant transformation through gene editing. NF1-CDKN2A double-knockout (2KO) NCs retained glial differentiation capacity and formed neurofibroma-like tumors in vivo, requiring inactivation of p14ARF and p16INK4a. Additional PRC2 loss (3KO) disrupted pluripotency and induced mesenchymal stem cell-like features in iPSCs an NCs. 3KO NCs suffered a global chromatin reprograming that silenced SOX10 preventing gliogenesis and activated neuro-mesenchymal programs. Gene signatures characterizing this glial-to-neuro-mesenchymal transition were recapitulated in human PNF-ANNUBP-MPNST tumors. 3KO NC spheres formed MPNST-like tumors in vivo upon nerve engraftment, genuinely mimicking an early-stage MPNST. We used the developed 3D NC spheroid models for the discovery of drugs targeting MPNSTs by performing a high-throughput screening of an epigenetic compound library. We found that poly(ADP-ribose) polymerase inhibitors (PARPi) exhibit selective efficacy in PRC2-deficient NC spheroids. We confirmed that Olaparib-Selumetinib combination in a MPNST PDX mouse model was well tolerated and significantly suppressed tumor growth.

cancer biology↗

bioRxiv2025

TcBDF6 deficiency compromises intracellular amastigotes development and infectivity in Trypanosoma cruzi

Trypanosoma cruzi, the causative agent of Chagas disease, relies on complex gene regulatory mechanisms to adapt to its diverse host environments. In recent years, it has been established that epigenetics plays an essential role in these mechanisms via the regulation of chromatin structure. Bromodomain-containing factors (BDFs), known for recognizing acetylated lysines on histones, have emerged as key factors in chromatin remodeling complexes. Among the eight predicted BDFs in T. cruzi, BDF6 is part of a TINTIN-like complex with MRGx and MRGBP, homologous to components of the NuA4/TIP60 chromatin remodeling complex. We generated knockout (KO) parasites for bdf6 gene using CRISPR/Cas9 gene editing. BDF6-deficient epimastigotes exhibit normal morphology but decreased size and growth and the resulting metacyclic trypomastigotes displayed drastically reduced infectivity. Strikingly, once inside host cells, BDF6-deficient parasites differentiated into amastigotes but failed to replicate. This intracellular arrest was reversed by episomal complementation of BDF6. Consistently, BDF6-KO parasites also exhibited impaired infectivity in mice, a defect that was also rescued in the add back parasite strains. Our findings highlight BDF6 as a critical regulator of intracellular parasite development, operating in stages beyond epimastigotes where epigenetic plasticity is essential for host adaptation. This striking stage-specific phenotype of BDF6 KO underscores its functional importance and highlights the relevance of epigenetic regulators along T. cruzis life cycle.

microbiology↗

bioRxiv2025

FREQ-NESS reveals age-related differences in frequency-resolved brain networks during auditory recognition and resting state

Understanding how brain networks operate across different frequencies during cognitive tasks, and how these dynamics change with age, remains a central challenge in cognitive neuroscience. While previous studies have focused on resting-state activity and passive listening, less is known about frequency-specific brain dynamics during event-related tasks that require active memory engagement. In this study, we extend the recently developed FREQ-NESS analytical pipeline by adapting it to event-related task and resting state source-reconstructed magnetoencephalography (MEG) data from 70 healthy participants. This method quantified the variance explained by frequency-specific brain networks, their spatial organization, and associated time-resolved power estimates. We found significant effects of age, condition, and their interaction in the variance explained by leading components at 1.07 Hz, 2.86 Hz, and 10.00 Hz. Younger adults exhibited stronger peaks at 1.07 and 2.86 Hz during the task and a more pronounced 10.00 Hz peak at rest, whereas older adults showed the opposite pattern. Time-frequency analysis revealed age- and condition-dependent desynchronization in the alpha and beta bands (7.10-22.90 Hz). These findings demonstrate the effectiveness of the adapted FREQ-NESS pipeline for event-related tasks and highlight the importance of frequency-resolved network analysis for characterizing age-related changes in active auditory memory processing.

neuroscience↗

bioRxiv2025

Immortalization and Characterization of Schwann Cell Lines Derived from NF1 Associated Cutaneous Neurofibromas

Neurofibromatosis type 1 (NF1) is an autosomal dominant condition in which patients are heterozygous for a disruptive pathogenic variant in the NF1 gene. The most characteristic feature of the condition NF1 is the neurofibroma, a benign, multi-cellular tumor which initiates when a cell of the Schwann cell lineage gains a somatic pathogenic variant of the other NF1 allele. Neurofibromas developing at nerve termini in the skin are termed "cutaneous" neurofibromas (cNFs), while those developing within larger nerves are termed "plexiform." Most patients develop cNFs beginning in late childhood or early adulthood, continuing throughout life at variable rates. Some patients may develop only a few cNFs, while others suffer from thousands. There are no reliably effective physical or pharmaceutical therapies besides surgical removal. Although these are not life-threatening, they are disfiguring and can interfere with normal life functions. To provide a resource for research, we developed short-term cNF Schwann cell cultures from NF1 patients, from which we subsequently established the first semi-immortalized cNF cell lines through transduction with wild-type human telomerase reverse transcriptase (hTERT) and murine cyclin-dependent kinase 4 (mCdk4) genes. Here we present molecular, cellular, and functional characterization of these cell lines, which will be of utility for investigating and developing NF1 cNF therapies.

genomics↗

bioRxiv2024

Working memory predicts long-term recognition of auditory sequences: Dissociation between confirmed predictions and prediction errors

Memory is a crucial cognitive process involving several subsystems: sensory memory (SM), short-term memory (STM), working memory (WM), and long-term memory (LTM). While each has been extensively studied, the interaction between WM and LTM, particularly in relation to predicting temporal sequences, remains largely unexplored. This study investigates the relationship between WM and LTM, and how these relate to aging and musical training. Using three datasets with a total of 244 healthy volunteers across various age groups, we examined the impact of WM on LTM recognition of novel and previously memorized musical sequences. Our results show that WM abilities are significantly related to recognition of novel sequences, with a more pronounced effect in older compared to younger adults. In contrast, WM did not similarly impact the recognition of memorized sequences, which implies that different cognitive processes are involved in handling prediction errors compared to confirmatory predictions, and that WM contributes to these processes differently. Additionally, our findings confirm that musical training enhances memory performance. Future research should extend our investigation to populations with cognitive impairments and explore the underlying neural substrates.

neuroscience↗

bioRxiv2023

Neurophysiological correlates of short-term recognition of sounds: Insights from magnetoencephalography

Understanding the brains dynamic retrieval and updating of encoded information is a key focus in memory research. This study employed a same versus different auditory paradigm to investigate short-term auditory recognition within a predictive coding (PC) framework, concerning the perceptual interplay between experience-informed predictions and incoming sensory information. Using magnetoencephalography (MEG), we captured the neurophysiological correlates associated with a single-sound, short-term memory task. Twenty-six healthy participants were tasked with recognizing whether presented sounds were same or different compared to strings of standard stimuli. To prompt conscious memory retention, a white noise interlude separated these sounds from the standards. MEG sensor-level results revealed that recognition of same sounds elicited two significantly stronger negative components of the event-related field compared to different sounds. The first one was the N1, peaking 100ms post-sound onset, while the second one corresponded to a slower negative component arising between 300 and 600ms after sound onset. This effect was observed in several significant clusters of MEG sensors, especially temporal and parietal regions of the scalp. Conversely, different sounds produced scattered and smaller clusters of stronger activity than same sounds, peaking later than 600ms after sound onset. Source reconstruction using beamforming algorithms revealed the involvement of auditory cortices, hippocampus, and cingulate gyrus in both conditions. Overall, the results are coherent with PC principles and previous results on the brain mechanisms underlying auditory recognition, highlighting the relevance of early and later negative brain responses for successful prediction of previously listened sounds in the context of conscious short-term memory.

neuroscience↗

bioRxiv2022

Unbalancing cAMP and Ras/MAPK pathways as a therapeutic strategy for cutaneous neurofibromas

Cutaneous neurofibromas (cNFs) are benign Schwann cell (SC) tumors arising from subepidermal glia. Neurofibromatosis Type 1 (NF1) individuals may develop thousands of cNFs, greatly affecting their quality of life. cNF growth is governed by the proliferation of NF1(-/-) SCs, highly influenced by the interaction with a NF1(+/-) microenvironment, consisting of fibroblasts (FBs), immune cells, etc. To decompose crosstalk between SCs and the microenvironment we used single cultures and co-cultures of cNF-derived SCs and FBs and identified an expression signature specific to SC-FB interaction. This signature was enriched in genes involved in immune cell migration, that were functionally validated by secretion analysis of SC-FB co-cultures, suggesting a role of SC-FB crosstalk in immune cell recruitment. The signature also captured components of different developmental signaling pathways, among them, the cAMP elevator G protein-coupled receptor 68 (GPR68). Activation of Gpr68 by Ogerin reduced the viability and proliferation of cNF-derived SCs and SC-FB co-cultures. Moreover, Ogerin in combination with the MEKi Selumetinib induced loss of viability, SC differentiation, and death. These results were corroborated using an iPSC-derived 3D neurofibromasphere model. The unbalancing of the Ras and cAMP pathways by combining a MEKi and a cAMP elevator arises as a potential treatment for cNFs.

cancer biology↗

bioRxiv2022

Merlin-deficient iPSCs show altered pluripotency and constitute a potential in vitro model for NF2-related schwannomas

NF2-related schwannomatosis is an autosomal dominant syndrome that predisposes to the development of benign tumors of the nervous system. Schwannomas, particularly bilateral vestibular schwannomas (VS), are the most characteristic features of the disease. These tumors are caused by the bi-allelic inactivation of the NF2 gene in a cell of the Schwann cell lineage. Our current understanding of the molecular pathogenesis of the NF2 gene, as well as the development of new effective therapies is hampered by the absence of human non-perishable cell-based bearing distinct NF2 pathogenic variants. With this aim, we generated and characterized three isogenic paired induced pluripotent stem cell (iPSC) lines with single or bi-allelic inactivation of NF2 by combining the direct reprogramming of VS cells with the use of CRISPR/Cas9 editing. Our results show a critical function of NF2 for the maintenance of a stable pluripotent state. However, we were able to nudge them towards the Neural Crest-Schwann Cell (NC-SC) axis by applying a 3D Schwann cell differentiation protocol. NF2(+/-) and NF2(-/-) spheroids homogeneously expressed classical markers of the NC-SC lineage. In addition, NF2(-/-) SC-like spheroids showed dysregulation of multiple signaling pathways already described for merlin-deficient SC, and altered in human schwannomas. Therefore, NF2(+/-) and NF2(-/-) SC-like spheroids can represent a bona fide human in vitro cellular model to study the role of NF2 pathogenesis.

cell biology↗

bioRxiv2022

Predicting higher-order mutational effects in an RNA enzyme by machine learning of high-throughput experimental data

Ribozymes are RNA molecules that catalyze biochemical reactions. Self-cleaving ribozymes are a common naturally occurring class of ribozymes that catalyze site-specific cleavage of their own phosphodiester backbone. In addition to their natural functions, self-cleaving ribozymes have been used to engineer control of gene expression because they can be designed to alter RNA processing and stability. However, the rational design of ribozyme activity remains challenging, and many ribozyme-based systems are engineered or improved by random mutagenesis and selection (in vitro evolution). Improving a ribozyme-based system often requires several mutations to achieve the desired function, but extensive pairwise and higher-order epistasis prevent a simple prediction of the effect of multiple mutations that is needed for rational design. Recently, high-throughput sequencing-based approaches have produced data sets on the effects of numerous mutations in different ribozymes (RNA fitness landscapes). Here we used such high-throughput experimental data from variants of the CPEB3 self-cleaving ribozyme to train a predictive model through machine learning approaches. We trained models using either a random forest or long short-term memory (LSTM) recurrent neural network approach. We found that models trained on a comprehensive set of pairwise mutant data could predict active sequences at higher mutational distances, but the correlation between predicted and experimentally observed self-cleavage activity decreased with increasing mutational distance. Adding sequences with increasingly higher numbers of mutations to the training data improved the correlation at increasing mutational distances. Systematically reducing the size of the training data set suggests that a wide distribution of ribozyme activity may be the key to accurate predictions. Because the model predictions are based only on sequence and activity data, the results demonstrate that this machine learning approach allows readily obtainable experimental data to be used for RNA design efforts even for RNA molecules with unknown structures. The accurate prediction of RNA functions will enable a more comprehensive understanding of RNA fitness landscapes for studying evolution and for guiding RNA-based engineering efforts.

molecular biology↗

bioRxiv2022

A detailed landscape of genomic alterations in malignant peripheral nerve sheath tumor cell lines challenges the current MPNST diagnosis

BackgroundMalignant peripheral nerve sheath tumors (MPNSTs) are soft tissue sarcomas that arise from the peripheral nervous system. Half of the tumors develop in the context of the genetic disease Neurofibromatosis type 1 (NF1) and the rest are sporadic sarcomas. MPNSTs have a dismal prognosis due to their aggressiveness and tendency to metastasize, and new treatment options are needed. The diagnosis of MPNSTs can be challenging, especially outside of the NF1 context since specific histological criteria have not been completely established. Genomic analysis may both facilitate differential diagnoses and suggest precision medicine strategies. MethodsWe generated a complete genomic resource of a set of widely used human NF1-related and sporadic MPNST cell lines by applying ploidy analysis, whole genome and whole exome sequencing and SNP-array analysis, complemented by methylome-based classification and immunofluorescence of cell identity markers (SOX9, SOX10, S100B). ResultsNF1 MPNST cell lines faithfully recapitulated the genomic copy number profile of primary MPNSTs. Structural variants were key players in the complete inactivation of most recurrently altered tumor suppressor genes (TSGs) (NF1, CDKN2A, SUZ12/EED), while small variants played a minor role in the NF1 context, both concerning TSG inactivation and due to the absence of gain-of-function mutations. In clear contrast, the sporadic cell lines (STS-26T, HS-Sch-2, HS-PSS) did not recapitulate the copy number profile of primary MPNSTs. They carried different TSG inactivation and exhibited gain-of-function mutations by predicted kinase activation or generation of fusion genes. Mutational frequencies and signatures emerged as promising informative tools for aiding in MPNST differential diagnosis. Due to the multiple genomic differences exhibited, we complemented their characterization using a methylome-based classifier. All NF1-related cell lines were assigned within the MPNST group, while sporadic cell lines clustered either with melanomas or with an uncertain MPNST-like sarcoma group. The staining of cell identity markers reinforced the idea of a potential misdiagnose of the MPNSTs used to derive the sporadic cell lines analyzed. ConclusionsDeep genomic analysis, together with methylome-based sarcoma classification and cell identity marker analysis, challenged the MPNST identity of sporadic cell lines. Results presented here open an opportunity to revise MPNST differential diagnosis and classification.

genomics↗

bioRxiv2022

Antisense oligonucleotides targeting exon 11 are able to partially rescue the Neurofibromatosis Type 2 phenotype in vitro

Neurofibromatosis type 2 (NF2) is an autosomal dominant condition caused by loss of function variants in the NF2 gene, which codes for the protein Merlin, and characterized by the development of multiple tumours of the nervous system. The clinical presentation of the disease is variable and related to the type of the inherited germline variant. Here, we tested if PMOs could be used to correct the splice signalling caused by variants at +/-13 within the intron-exon boundary region. Here we show that the PMOs designed for these variants do not constitute a therapeutic approach. Furthermore, we evaluated the use of phosphorodiamidate morpholino oligomers (PMOs) to reduce the severity of the effects of NF2 truncating variants with the aim of generating milder hypomorphic isoforms in vitro through the induction of the in-frame deletion of the exon-carrying variant. We were able to specifically induce the skipping of exons 4, 8 and 11 maintaining the NF2 gene reading frame at cDNA level. Only the skipping of exon 11 produced a hypomorphic Merlin (Merlin-e11), able to partially rescue the observed phenotype in primary fibroblast cultures from NF2 patients, being encouraging for the treatment of patients harbouring truncating variants located in exon 11.

genetics↗