Biology subjects

Friedlander, G.

Publications and source records attributed to Friedlander, G..

9 recordsLinked to original sources

bioRxiv2025

Temporal control of axonal floor plate crossing through a combination of incoherent feedforward and feedback loops of gene regulatory network regulating Robo3 expression

Spinal commissural neurons play a fundamental role in motor control and sensory perception. Robo3, a receptor expressed on pre-crossing commissural axons, is required for midline crossing. Its downregulation in post-crossing axons is essential for forming synapses with contralateral CNS targets. We demonstrate that, at the transcriptional level, the dynamic expression of Robo3 in pre-crossing neurons is controlled by incoherent feed-forward loops (iFFLs) and negative feedback loops (NFLs) that precisely regulate its transience and thereby determine midline crossing. Lhx2 and Lhx9 activate Robo3 while also inducing its repressor, Barhl2. Additionally, negative feedback loops fine-tune the transience of Robo3 expression by adjusting the relative strength of the activation and repression modules. Our genomic analysis reveals that this regulatory circuitry converges on an enhancer element of the Robo3 gene. These findings imply that diverse iFFLs, together with NFLs, are essential for regulating the extent of midline crossing across different spinal commissural subtypes.

developmental biology↗

bioRxiv2025

Dynamic Functional Pathway Development in Type 1 Spinal Interneurons: Stage-specific roles of retinoic acid activity

BackgrounddI1 spinal interneuron development requires precise coordination of proliferation, differentiation, and migration, yet the molecular and cellular properties underlying the temporal coupling of these processes remain unresolved. ResultsSingle-cell RNA sequencing of the E4 quail neural tube under control and retinoic acid (RA)-deprived conditions generated a high-resolution atlas spanning a continuous trajectory from dorsal progenitors to differentiated neurons. Pseudotime and RNA velocity analyses revealed transitions consistent with medial-to-lateral displacement in vivo. Early progenitors expressed cell cycle and BMP-associated programs, followed by induction of cytoskeletal and extracellular matrix remodelling genes and later activation of pan-neuronal and synaptic pathways. BMP signaling declined during differentiation through upregulation of BMP antagonists, whereas apoptosis-related genes were poised during specification without overt cell death. Autophagy-associated genes peaked during differentiation. Disruption of RA signaling by dominant-negative RAR403 uncovered stage-specific functions of RA. In progenitors, RA inhibition increased proliferation. In differentiating neurons, it upregulated BARHL1/2 and enhanced ion channel, synaptic, cytoskeletal, and extracellular matrix gene programs. RA inhibition also impaired ventral displacement of BarHL2-positive dI1 neurons, causing abnormal positioning. ConclusionsThese findings define a dI1-centered single-cell atlas of the progenitor-to-neuron transition and identify stage-specific roles for RA in dorsal hinterneuron maturation. Key findingsO_LIWe provide a high-resolution single-cell atlas of dI1 spinal interneuron development in the E4 quail neural tube, analysis of this single stage reveals a continuous trajectory from proliferative dorsal progenitors to differentiated neurons. C_LIO_LIDevelopment along this trajectory is tightly staged: early cells are dominated by cell-cycle and progenitor-maintenance programs, while later cells progressively activate cytoskeletal, extracellular matrix, axon-guidance, synaptic, and mature neuronal pathways. C_LIO_LIBMP signaling is strongest in early dI1 progenitors and is progressively attenuated during differentiation through the induction of BMP inhibitors, supporting a stage-specific role for BMP in early specification rather than late maturation. C_LIO_LIRetinoic acid acts in a stage-dependent manner: RA inhibition increases progenitor proliferation, alters differentiation-associated gene programs, and upregulates neuronal maturation, ion-channel, and synaptic genes in differentiating neurons. C_LIO_LIRepressing RA signaling causes BarHL2-positive dI1 neurons to fail their normal ventral migration. Instead, they accumulate near their dorsal origin and show ectopic localization, indicating that RA is required for proper migration. C_LI

developmental biology↗

bioRxiv2024

Retinoic acid, an essential component of the RP organizer, promotes the spatio-temporal segregation of dorsal neural fates

Dorsal neural tube-derived retinoic acid promotes the end of neural crest production and transition into a definitive roof plate. Here we analyze how this impacts the segregation of central and peripheral lineages, a process essential for tissue patterning and function. Localized in-ovo inhibition of retinoic acid activity followed by single cell transcriptomics unraveled a comprehensive list of differentially expressed genes relevant to these processes. Importantly, progenitors co-expressed neural crest, roof plate and dI1 interneuron markers indicating a failure in proper lineage segregation. Furthermore, we found that separation between roof plate and dI1 interneurons is mediated by Notch activity downstream of retinoic acid, highlighting their critical role in establishing the roof plate-dI1 boundary. Within the peripheral branch, where absence of retinoic acid resulted in neural crest production and emigration extending into the roof plate stage, sensory progenitors failed to separate from melanocytes leading to formation of a common glia-melanocyte cell with aberrant migratory patterns. Together, we uncover and characterize a molecular mechanism responsible for segregation of dorsal neural fates during development.

developmental biology↗

bioRxiv2023

Chemoresistome Mapping in Individual Breast Cancer Patients Unravels Diversity in Dynamic Transcriptional Adaptation

Emerging evidence reinforce the role of non-genetic adaptive resistance to chemotherapy, that involves rewiring of transcriptional programs in surviving tumors. We combined longitudinal transcriptomics with temporal pattern analysis to dissect patient-specific emergence of resistance in breast cancer. Matched triplets of tumor biopsies (pre-treatment, post-treatment and adjacent normal) were collected from breast cancer patients who received neo-adjuvant chemotherapy. Full transcriptome was analyzed by longitudinal pattern classification to follow patient-specific expression modulations. We found that dynamics of gene expression dictates resistance-related modulations. The results unraveled important principles in emergence of adaptive resistance: 1. Genes with resistance patterns are already dysregulated in the primary tumor, supporting a primed drug-tolerant state. 2. In each patient, multiple resistance-related genes are rewired but converge into few dysregulated modules. 3. Rewiring of diverse genes and pathway dysregulation vary among individuals who receive the same treatments. Patient-specific chemoresistome maps disclosed tumors acquired resistance and exposed their vulnerabilities. Mapping the complexity of dysregulated pathways in individual patients revealed important insights on adaptive resistance mechanisms. To survive the toxic drug effect, tumor cells either sustain a drug-tolerant state or intensify it, specifically bypassing the drugs interference. Depicting an individual road map to resistance can offer personalized therapeutic strategies.

cancer biology↗

bioRxiv2022

Redifferentiated cardiomyocytes retain residual dedifferentiation signatures and are protected against ischaemic injury

Cardiomyocyte renewal by dedifferentiation and proliferation has fueled the field of regenerative cardiology in recent years, while the reverse process of redifferentiation remains largely unexplored. Redifferentiation is characterised by the restoration of function that is lost during dedifferentiation and is key to the healing process following injury. Previously, we showed that ERBB2-mediated heart regeneration has these two distinct phases: dedifferentiation, followed by redifferentiation. Here, using temporal RNAseq and proteomics, we survey the landscape of the dedifferentiation-redifferentiation process in the adult mouse heart. We find well characterised dedifferentiation pathways, such as reduced oxphos, increased proliferation and increased EMT-like features, largely return to normal, though elements of residual dedifferentiation remain, even after contractile function is restored. These hearts appeared rejuvenated and showed robust resistance to ischaemic injury. We find that redifferentiation is driven by negative feedback signalling, notably through LATS1/2 Hippo pathway activity. Disabling LATS1/2 in dedifferentiated cardiomyocytes augments dedifferentiation in vitro and prevents redifferentiation in vivo. Taken together, our data reveal the non-trivial nature of redifferentiation, whereby elements of dedifferentiation linger in a surprisingly beneficial manner. This cycle of dedifferentiation-redifferentiation protects against future insult, in what could become a novel prophylactic treatment against ischemic heart disease for at-risk patients.

cell biology↗

bioRxiv2020

TENT4A poly(A) polymerase regulates translesion DNA synthesis and is mutated in endometrial cancer

TENT4A (PAPD7) is a non-canonical poly(A) polymerase, of which little is known. Here we focus on its multilayer regulation of translesion DNA synthesis (TLS), in which DNA lesions are bypassed by error-prone DNA polymerases. We show that TENT4A regulates mRNA stability and/or translation of DNA polymerase {eta} and RAD18 E3 ligase, which guides the polymerase to replication stalling sites, and monoubiquitinates PCNA, thereby enabling recruitment of error-prone DNA polymerases to damaged DNA sites. Remarkably, in addition to the effect on RAD18 mRNA stability via controlling its poly(A) tail, TENT4A indirectly regulates RAD18 via the tumor suppressor CYLD, and via the long non-coding antisense RNA PAXIP1-AS2, which had no known function. Knocking down the expression of TENT4A or CYLD, or overexpression of PAXIP1-AS2 led each to reduced amounts of the RAD18 protein and DNA polymerase {eta}, leading to reduced TLS, highlighting PAXIP1-AS2 as a new TLS regulator. Bioinformatics analysis revealed that TLS error-prone DNA polymerase genes and their TENT4A-related regulators are frequently mutated in endometrial cancer genomes, suggesting that TLS is dysregulated in this cancer.

molecular biology↗

bioRxiv2020

Epidermal stem cell compartment remains unaffected through aging in naked mole-rats.

Skin represents an informative and convenient organ for the analysis of the aging process. Naked mole-rats (NMR) are subterranean rodents remarkable for their longevity, with unexplained resistance to skin aging. In middle-aged NMR, extensive in situ analysis indicated that skin compartments and cell types remained similar to young animals. Using single-cell RNA-sequencing, we found three classical cellular states defining a unique keratinocyte differentiation trajectory that did not appear to be altered during aging after pseudotemporal reconstruction. Finally, NMR skin healing closure was strictly comparable between the two age groups. These results indicate that the content in stem cell populations as well as the differentiation process are preserved during aging in NMR and that such properties are related to the healing process.

cell biology↗

bioRxiv2020

Inhibition of the replication of SARS-CoV-2 in human cells by the FDA-approved drug chlorpromazine

Urgent action is needed to fight the ongoing COVID-19 pandemic by reducing the number of infected people along with the infection contagiousness and severity. Chlorpromazine (CPZ), the prototype of typical antipsychotics from the phenothiazine group, is known to inhibit clathrin-mediated endocytosis and acts as an antiviral, in particular against SARS-CoV-1 and MERS-CoV. In this study, we describe the in vitro testing of CPZ against a SARS-CoV-2 isolate in monkey and human cells. We evidenced an antiviral activity against SARS-CoV-2 with an IC50 of [~]10M. Because of its high biodistribution in lung, saliva and brain, such IC50 measured in vitro may translate to CPZ dosage used in clinical routine. This extrapolation is in line with our observations of a higher prevalence of symptomatic and severe forms of COVID-19 infections among health care professionals compared to patients in psychiatric wards. These preclinical findings support the repurposing of CPZ, a largely used drug with mild side effects, in COVID-19 treatment.

microbiology↗

bioRxiv2018

CSNAP, the smallest CSN subunit, modulates proteostasis through cullin-RING ubiquitin ligases

The cullin-RING ubiquitin E3 ligase (CRL) family consists of ~250 complexes that catalyze ubiquitylation of proteins to achieve cellular regulation. All CRLs are inhibited by the COP9 signalosome complex (CSN) through both enzymatic (deneddylation) and non-enzymatic (steric) mechanisms. The relative contribution of these two mechanisms is unclear. Here, we decouple the mechanisms using CSNAP, the recently discovered ninth subunit of the CSN. We find that CSNAP reduces the affinity of CSN toward CRL complexes. Removing CSNAP does not affect deneddylation, but leads to global effects on the CRL, causing altered reproductive capacity, suppressed DNA damage response, decreased viability, and delayed cell cycle progression. Thus, although CSNAP is only 2% of the CSN mass, it plays a critical role in the steric regulation of CRLs by the CSN.

biochemistry↗