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Biology subjects

Casanova, M.

Publications and source records attributed to Casanova, M..

9 recordsLinked to original sources

Stem-cell modeling of cerebellar dysfunction of Angelman syndrome

Angelman syndrome (AS) is a severe neurodevelopmental disorder caused by the loss of function of the maternal allele of the neuron-specific imprinted gene UBE3A. Although AS presents with developmental delay, ataxia, epilepsy, and speech impairment, the distinct roles of various brain regions in its pathology remain unclear, hindering the design of effective therapeutic strategies. Of all brain regions, the nature and impact of dysfunction of the cerebellum in AS remain elusive. To start addressing this, we leveraged our optimized stem cell-based model of regionally patterned human cerebellar organoids (hCerOs) capable of producing major cerebellar neuronal subtypes, including Purkinje and granule cells, further matured in a two-dimensional (2D) culture system. We modeled AS using induced pluripotent stem cell (iPSC) lines carrying the common class II deletion and unaffected controls previously validated in our system. hCerOs from both backgrounds recapitulate lineage commitment and neuron-specific UBE3A imprinting. AS hCerOs consistently show reduced size, impaired neuroepithelial expansion, and diminished expression of glutamatergic and GABAergic progenitor markers. Transcriptomic profiling and functional assays assessing neuronal activity during the maturation stage uncovered delayed maturation, abnormal firing and increased neuronal excitability in AS cultures. These results position our hCerO model as a robust platform for future mechanistic studies and therapeutic screening aimed at targeting cerebellar dysfunction in AS.

developmental biology↗

Harnessing CRISPR interference to re-sensitize laboratory strains and clinical isolates to last resort antibiotics

The global race against antimicrobial resistance requires novel antimicrobials that are not only effective in killing specific bacteria, but also minimize the emergence of new resistances. Recently, CRISPR/Cas-based antimicrobials were proposed to address killing specificity with encouraging results. However, the emergence of target sequence mutations triggered by Cas-cleavage was identified as an escape strategy, posing the risk of generating new antibiotic-resistance gene (ARG) variants. Here, we evaluated an antibiotic re-sensitization strategy based on CRISPR interference (CRISPRi), which inhibits gene expression without damaging target DNA. The resistance to four antibiotics, including last resort drugs, was significantly reduced by individual and multi-gene targeting of ARGs in low- to high-copy numbers in recombinant E. coli. Escaper analysis confirmed the absence of mutations in target sequence, corroborating the harmless role of CRISPRi in the selection of new resistances. E. coli clinical isolates carrying ARGs of severe clinical concern were then used to test the robustness of CRISPRi under different growth conditions. Meropenem, colistin and cefotaxime susceptibility was successfully increased in terms of MIC (up to >4-fold) and growth delay (up to 11-hours) in a medium-dependent fashion. To our knowledge, this is the first demonstration of CRISPRi-mediated re-sensitization to last-resort drugs in clinical isolates. This study laid the foundations for further leveraging CRISPRi as antimicrobial agent or research tool to selectively repress ARGs and investigate resistance mechanisms.

synthetic biology↗

Erosion of X-Chromosome Inactivation in female hiPSCs is heterogeneous and persists during differentiation

During culture, female human pluripotent stem cells (hPSCs), including human induced PSCs (hiPSCs) exhibit a propensity for erosion of X-chromosome inactivation (XCI). This phenomenon is characterized by the loss of XIST RNA expression and reactivation of a subset of X-linked genes from the inactive X chromosome (Xi). XCI erosion, despite its common occurrence, is often overlooked by the stem cell community, hindering a complete understanding of its impact on both fundamental and translational applications of hiPSCs. Investigating erosion dynamics in female hiPSCs, our study reveals that XCI erosion is a frequent yet heterogeneous phenomenon, resulting in the reactivation of several X-linked genes. The likelihood of a gene to erode increases for those located on the short arm of the X chromosome and within H3K27me3-enriched domains. Paradoxically, genes that typically escape XCI are hypersensitive to loss of XIST RNA and XCI erosion. This implies that XIST RNA normally restrains expression levels of these genes on the Xi. Importantly, increased X-linked gene expression upon erosion does not globally impact (hydroxy)methylation levels in hiPSCs or at imprinted regions. By exploring diverse differentiation paradigms, such as trilineage commitment and cardiac differentiation, our study reveals the persistence of abnormal XCI patterns throughout differentiation. This finding has significant implications for fundamental research, translational applications, and clinical use of stem cells. We underscore the importance of raising awareness within the stem cell community regarding XCI erosion and advocate for its inclusion in comprehensive hiPSC quality control.

molecular biology↗

XIST dampens X chromosome activity in a SPEN-dependent manner during early human development

XIST long non-coding RNA is responsible for X chromosome inactivation (XCI) in placental mammals, yet it accumulates on both X chromosomes in human female pre-implantation embryos without triggering X chromosome silencing. The long non-coding RNA XACT co-accumulates with XIST on active Xs and may antagonize XIST function. Here we used human ES cells in a naive state of pluripotency to assess the function of XIST and XACT in shaping the X chromosome chromatin and transcriptional landscapes during pre-implantation development. We show that XIST triggers the deposition of polycomb-mediated repressive histone modifications and attenuates transcription of most X-linked genes in a SPEN-dependent manner, while XACT deficiency does not significantly affect XIST activity or X-linked gene expression. Our study demonstrates that XIST is functional prior to XCI, confirms the existence of a transient process of X chromosome dosage compensation, and reveals that X chromosome inactivation and dampening rely on the same set of factors.

molecular biology↗

The importance of cellulolytic and xylanolytic activities of Bacillus subtilis on dairy cow feed digestibility

A large body of literature has accumulated on the beneficial impact of the administration of Bacilli to dairy cows, particularly on dry matter intake, lactation performances and milk composition. In this work we sought to establish whether the ability of B. subtilis to secrete cellulase and xylanase enzymes could be involved in the positive effect exerted by these bacteria. Several feed ingredients were treated with two B. subtilis strains only differing for the amount of secreted cellulosolytic and xylanolytic enzymes, and feed quality was assessed. We found that in vitro fibre digestibility correlated with the activity of those enzymes. Our results revealed that B. subtilis cellulases and xylanases can effectively improve forage quality, providing a scientific rationale on the use of Bacilli as forage supplements to improve animal productivity. Moreover, a particular care was taken in designing a sustainable and economically viable Bacillus-based additive preparation process.

microbiology↗

CRISPR interference as low burden logic inverters in synthetic circuits: characterization and tuning

The rational design of complex biological systems through the interconnection of single functional building blocks is hampered by many unpredictability sources; this is mainly due to the tangled context-dependency behavior of those parts once placed into an intrinsically complex living system. Among others, the finite amount of translational resources in prokaryotic cells leads to load effects in heterologous protein expression. As a result, hidden interactions among protein synthesis rates arise, leading to unexpected and counterintuitive behaviors. To face this issue in rational design of synthetic circuits in bacterial cells, CRISPR interference is here evaluated as genetic logic inverters with low translational resource usage, compared with traditional transcriptional regulators. This system has been studied and characterized in several circuit configurations. Each module composing the circuit architecture has been optimized in order to meet the desired specifications, and its reduced metabolic load has been eventually demonstrated via in-vivo assays.

synthetic biology↗

A primate-specific retroviral enhancer wires the XACT lncRNA into the core pluripotency network in human

Transposable elements (TEs) have been of paramount importance in shaping genomic and epigenomic landscapes of their hosts and in driving the expansion of gene regulatory networks during mammalian evolution. They are found in nearly all long non-coding RNAs (lncRNAs) and have promoted their evolution and function, often in a species- and tissue-specific manner. X-chromosome inactivation (XCI) is an essential process that relies on several TE-enriched lncRNAs. While XCI is conserved across species, one striking difference between human and mouse is the existence of XACT (X active coating transcript), a human-specific lncRNA that coats active X chromosomes in pluripotent cells and may oppose X chromosome silencing in this context. Here, we explore how different families of TEs have contributed to shaping the XACT locus and how they couple its expression to pluripotency in humans. Through a combination of sequence analysis across primates, transcriptional interference and genome editing in human embryonic stem cells (hESCs), we identify a critical enhancer for the transcriptional regulation of the XACT locus that evolved from an ancestral group (LTR48B/ERV1) of mammalian endogenous retroviruses (ERVs), prior to the emergence of XACT. Furthermore, we show that this ancient ERV was hijacked by evolutionarily younger hominoid-specific ERVs that gave rise to the promoter of XACT, thus wiring its expression to the pluripotency network. This work illustrates how retroviral-derived sequences may intervene in species-specific regulatory pathways.

molecular biology↗

Mechanistic diversification of XIST regulatory network in mammals

X chromosome inactivation (XCI) is a developmental regulatory process that initiates with remarkable diversity in various mammalian species. Here we addressed the contribution of XCI regulators, most of which are lncRNA genes characterized in the mouse, to this mechanistic diversity. By combining analysis of single-cell RNA-seq data from early human embryogenesis with various functional assays in naive and primed pluripotent stem cells and in differentiated cells, we demonstrate that JPX is a major regulator of XIST expression in human and in mouse. However, the underlying mechanisms differ radically between species and require Jpx RNA in the mouse and the act of transcription of JPX locus in the human. Moreover, biogenesis of XIST is affected at different regulatory steps between these species. This study illustrates how diversification of LRGs modes of action during evolution provide opportunities for innovations within constrained gene regulatory networks.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=164 SRC=\"FIGDIR/small/689430v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (25K):\norg.highwire.dtl.DTLVardef@18b8583org.highwire.dtl.DTLVardef@ea605aorg.highwire.dtl.DTLVardef@15bc8aborg.highwire.dtl.DTLVardef@d38689_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

Local Low Frequency fMRI Synchrony Is A Proxy For The Spatial Extent Of Functional Connectivity

Functional connectivity Magnetic Resonance Imaging (fcMRI) has assumed a central role in neuroimaging efforts to understand the changes underlying brain disorders. Current models of the spatial and temporal structure of fcMRI based connectivity contain strong a priori assumptions. We report that low temporal frequency fMRI signal synchrony within the local (3 mm radius) neighborhood of a location on the cortical surface strongly predicts the scale of its global functional connectivity. This relationship is tested vertex-wise across the cortex using Spearmans rank order correlation on an individual subject basis. Furthermore, this relationship is shown to be dynamically preserved across repeated within session scans. These results provide a model free data driven method to visualize and quantitatively analyze patterns of connectivity at the imaging voxel resolution across the entire cortex on an individual subject basis. The procedure thus provides a tool to check directly the validity of spatial and temporal prior assumptions incorporated in the analysis of fcMRI data.

neuroscience↗