Biology subjects

Palmer, R.

Publications and source records attributed to Palmer, R..

14 recordsLinked to original sources

bioRxiv2026

Neurofibromin Regulates Sleep Consolidation via Cholinergic Neurons in a Drosophila Model of Neurofibromatosis 1

Neurofibromatosis type 1 (NF1) patients frequently present with fragmented, poor-quality sleep, but the neural circuits and molecular mechanisms underlying this deficit remain undefined. Using Drosophila, we show that loss of the NF1 ortholog dNf1 recapitulates the human phenotype: null mutants exhibit markedly reduced total sleep with blunted nighttime consolidation, reflected in fewer and shorter sleep bouts and elevated inter-bout activity, a recessive phenotype reproduced by independent null alleles and by pan-neuronal RNAi knockdown. Despite the broad expression of dNf1 across the adult CNS, including the mushroom bodies, ellipsoid body, dorsal fan-shaped body, and GABAergic neurons, cell-type-restricted knockdown showed the protein is dispensable for sleep regulation in each of these populations. Instead, dNf1 loss specifically in cholinergic neurons, the most abundant neuronal class in the fly brain, was sufficient to reproduce the deficient, fragmented sleep of null mutants, and restoring wild-type dNf1 to cholinergic neurons of null animals was both necessary and sufficient to rescue sleep. Mechanistically, cholinergic expression of the GAP-related domain (GRD) alone, which normalizes elevated Ras/MAPK signaling, fully restored sleep in nulls, whereas a catalytically dead GRD variant did not, establishing Ras/MAPK dysregulation in cholinergic neurons as the proximate cause. Two disease-associated missense mutations, dNf1C1045Y and dNf1R1861C, produced distinct, dose-graded sleep phenotypes. dNf1C1045Y showed severe deficits resembling the null and was resistant to pan-neuronal, but responded to cholinergic neuron-restricted rescue, consistent with a dominant-negative effect on dNf1 dimerization. In contrast, dNf1R1861C presented a milder phenotype that was largely reversible by wild-type dNf1 but only partially by the GRD domain, implicating an additional, GRD-independent mechanism. Collectively, these findings define cholinergic neurons as the key circuit through which Neurofibromin regulates sleep consolidation via Ras/MAPK signaling and reveal mutation-specific mechanisms that mirror the phenotypic heterogeneity seen in NF1 patients, with implications for genotype-informed understanding of sleep disturbance in this disorder.

neuroscience↗

bioRxiv2026

ALK R1275Q mutation drives expansion of SCP-like cells during sympathoadrenal commitment and primes neuroblastoma initiation.

Neuroblastoma (NB) is a pediatric malignancy developing in the sympathoadrenal lineage of the neural crest, characterized by clinical heterogeneity ranging from spontaneous regression to poor outcomes. Activating mutations in the receptor tyrosine kinase anaplastic lymphoma kinase (ALK) are frequently observed in both sporadic and familial NB, yet the functional role of ALK in tumor initiation is not fully understood. Using a patient-derived human induced pluripotent stem cell (iPSC) model of sympathoadrenal development, we show that upon sympathoadrenal lineage commitment, ALK R1275Q, the most common hotspot mutation found in familial NB, sustain a proliferative, immature Schwann cell precursor (SCP)-like cell state with elevated ALK signaling and increased susceptibility to MYCN-driven transformation. While ALK-mutant cells alone did not form tumors in vivo, they cooperated with MYCN to accelerate tumor initiation, suggesting that ALK R1275Q creates a permissive but insufficient state for transformation. These findings define an ALK-driven cell progenitor-like state that facilitates the initiation of NB during embryonal development.

cancer biology↗

bioRxiv2025

ALK/ATR combination therapy is effective in neuroblastoma mouse tumors driven by MYCN

Summary paragraphOne of the key features of high-risk neuroblastoma (NB) is MYCN-amplification. While MYCN is still regarded as therapeutically challenging despite intensive efforts to find targeting compounds, inhibitors against Anaplastic Lymphoma Kinase (ALK) are now being evaluated among ALK-driven NB patients with promising results. There is a pressing need to find alternative treatment regimens for ALK naive MYCN-amplified patients, as current regimes are accompanied by significant mortality and morbidity. Here we show that genetically removing Alk in the Th-MYCN-driven engineered NB mouse model (GEMM) resulted in decreased tumor penetrance, and survival of Th-MYCN homozygote GEMMs, suggesting that Alk activity contributes to aggressiv e neuroblastoma development in this model. Given the high levels of replication stress induced in Th-MYCN tumors, we employed inhibitors of Ataxia Telangiectasia Rad3 related (ATR), combining ATR and ALK inhibition in a 14-day treatment regime, and comparing with ATR inhibitor monotreatment. Th-MYCN tumor bearing mice that received ATRi/ALKi combination treatment exhibited significantly increased survival compared to ATRi alone, that was sustained over time. Together, our data highlight a potentially effective treatment option for the currently challenging category of MYCN-amplified NB patients lacking ALK mutations.

cancer biology↗

bioRxiv2024

Spatial transcriptomics exploration of the primary neuroblastoma microenvironment unveils novel paracrine interactions

High-risk neuroblastomas exhibit a high degree of intratumoral heterogeneity. Single-cell RNA sequencing has greatly improved our understanding of these tumors, but the method lacks cellular tissue context and spatial information about local signaling dynamics. To address this gap, we profiled untreated and chemotherapy-treated high-risk neuroblastomas from 2 patients using spatial transcriptomics. We confirmed the transcriptional and cellular heterogeneous nature of the neuroblastoma microenvironment and identified several unique spatial niches and patterns. In one of the treated tumors, a spatially constrained cluster of undifferentiated and 11p-gained cancer cells was identified, surrounded by a rim of macrophages. A signaling interaction between the chemokine CCL18 and its receptor PITPNM3 was predicted between these cells and we experimentally demonstrated that CCL18 increases neuroblastoma cell migration. In the other tumor, we identified a stromal cluster with high transcriptional similarity to the adrenal cortex. These adrenocortical-like cells expressed the ALK ligand ALKAL2 and were predicted to communicate with neighboring ALK expressing cancer cells. We demonstrated a unique developmental pattern of adrenal medulla-specific expression of ALK and adrenocortical-specific expression of ALKAL2, suggesting a role of these signaling interactions in neuroblastoma carcinogenesis.

cancer biology↗

bioRxiv2024

RUVBL1 and RUVBL2 are druggable MYCN regulators in neuroblastoma.

High-risk neuroblastoma is characterized by MYCN amplification and high MYCN or MYC gene expression. These patients have a poor prognosis and there is an urgent need for more effective drugs. While strategies to develop inhibitors that directly target the MYC proteins have remained largely unsuccessful, recent preclinical studies have identified ATR, a key protein of the DNA damage response, as a promising alternative therapeutic target. Here we identified a strong RUVBL1 and RUVBL2 signature in transcriptomics data derived from different MYCN-driven mice tumors treated with ATR inhibitors. The RUVBL proteins form a complex with ATPase activity that has broad cellular functions and we demonstrate that pharmacological inhibition of this protein complex results in a strong reduction of MYC signaling, cell cycle arrest, DNA damage and apoptosis. We confirmed the association with MYCN and identified the RUVBL genes as independent prognosticators in human primary neuroblastoma data.

cancer biology↗

bioRxiv2024

FGFR2 promotes resistance to ALK tyrosine kinase inhibitors and its inhibition acts synergistically with lorlatinib in the treatment of ALK-expressing neuroblastoma

Anaplastic Lymphoma Kinase inhibitors (ALK TKIs) are approved for the treatment of ALK-positive non-small cell lung cancer (NSCLC) and are in clinical trial for ALK-aberrant high-risk neuroblastoma (NB) patients, particularly loratinib. However, resistance to ALK inhibitors can occur in patients, via the activation of bypass-signalling pathways, and there is a need to identify these mechanisms as well as drugs that inhibit them to design therapeutic approaches that prevent resistance, and to treat ALK TKI relapsed/refractory disease. Using genome-wide CRISPR-Cas9 overexpression screens, we identified and validated FGFR2 as a desensitizer to lorlatinib in aberrant ALK-expressing high-risk NB. FGFR2 and FGFR2-associated pathways are up-regulated in lorlatinib-resistant NB cells. Moreover, high-throughput screens using a library of 1,430 FDA approved drugs identified kinase inhibitors including those targeting FGFR2 as efficacious in reducing the survival of lorlatinib resistant NB cells. Hence, the FGFR pathway was investigated as a therapeutic target applying the pan-FGFR inhibitor erdafitinib or the multi-kinase inhibitor ponatinib, resulting in reduced survival of lorlatinib-resitant cells in comparison to their lorlatinib-sensitive counterparts. Moreover, both FGFR inhibitors act synergistically with lorlatinib in vitro and in vivo, using patient-derived xenografts (PDXs) and genetically engineered models (GEMM) of ALK-expressing NB. FGFR2 mRNA expression also correlate with a poorer prognosis for NB patients, regardless of sub-type, suggesting that a broader range of patients may benefit from FGFR inhibitors. Overall, our data suggests that FGFR2 potentially plays roles in lorlatinib resistance in NB and that combined pharmacological inhibition of ALK and FGFR constitutes a therapeutic approach to treat high-risk NB.

cancer biology↗

bioRxiv2023

BHLHE40 drives protective polyfunctional CD4 T cell differentiation in the female reproductive tract against Chlamydia

The protein basic helix-loop-helix family member e40 (BHLHE40) is a transcription factor recently emerged as a key regulator of host immunity to infections, autoimmune diseases and cancer. In this study, we investigated the role of Bhlhe40 in protective T cell responses to the intracellular bacterium Chlamydia in the female reproductive tract (FRT). Mice deficient in Bhlhe40 exhibited severe defects in their ability to control Chlamydia muridarum shedding from the FRT. The heightened bacterial burdens in Bhlhe40-/-mice correlated with a marked increase in IL-10-producing T regulatory type 1 (Tr1) cells and decreased polyfunctional CD4 T cells co-producing IFN-{gamma}, IL-17A and GM-CSF. Genetic ablation of IL-10 or functional blockade of IL-10R increased CD4 T cell polyfunctionality and partially rescued the defects in bacterial control in Bhlhe40-/- mice. Using single-cell RNA sequencing coupled with TCR profiling, we detected a significant enrichment of stem-like T cell signatures in Bhlhe40-deficient CD4 T cells, whereas WT CD4 T cells were further down on the differentiation trajectory with distinct effector functions beyond IFN-{gamma} production by Th1 cells. Altogether, we identified Bhlhe40 as a key molecular driver of CD4 T cell differentiation and polyfunctional responses in the FRT against Chlamydia.

immunology↗

bioRxiv2023

Preclinical exploration of the DNA Damage Response pathway using the interactive neuroblastoma cell line explorer CLEAN.

Neuroblastoma (NB) is the most common cancer in infancy with an urgent need for more efficient targeted therapies. The development of novel (combinatorial) treatment strategies relies on extensive explorations of signaling perturbations in neuroblastoma cell lines, using RNA-Seq or other high throughput technologies (e.g., phosphoproteomics). This typically requires dedicated bioinformatics support, which is not always available. Additionally, while data from published studies are highly valuable and raw data (e.g., fastq files) are nowadays released in public repositories, data processing is time-consuming and again difficult without bioinformatics support. To facilitate NB research, more user-friendly and immediately accessible platforms are needed to explore newly generated as well as existing high throughput data. To make this possible, we developed an interactive data centralization and visualization web application, called CLEAN (the Cell Line Explorer web Application of Neuroblastoma data; https://ccgg.ugent.be/shiny/clean/). By focusing on the regulation of the DNA damage response, a therapeutic target of major interest in neuroblastoma, we demonstrate how CLEAN can be used to gain novel mechanistic insights and identify putative drug targets in neuroblastoma.

cancer biology↗

bioRxiv2023

The Alk receptor tyrosine kinase regulates Sparkly, a novel activity regulating neurosecretory protein in the Drosophila CNS.

Numerous roles for the Alk receptor tyrosine kinase have been described in Drosophila, including functions in the central nervous system (CNS), however the molecular details are poorly understood. To gain mechanistic insight, we employed Targeted DamID (TaDa) transcriptional profiling to identify targets of Alk signaling in the larval CNS. TaDa was employed in larval CNS tissues, while genetically manipulating Alk signaling output. The resulting TaDa data were analysed together with larval CNS scRNA-seq datasets performed under similar conditions, identifying a role for Alk in the transcriptional regulation of neuroendocrine gene expression. Further integration with bulk/scRNA-seq and protein datasets from larval brains in which Alk signaling was manipulated, identified a previously uncharacterized Drosophila neuropeptide precursor encoded by CG4577 as an Alk signaling transcriptional target. CG4577, which we named Sparkly (Spar), is expressed in a subset of Alk-positive neuroendocrine cells in the developing larval CNS, including circadian clock neurons. In agreement with our TaDa analysis, overexpression of the Drosophila Alk ligand Jeb resulted in increased levels of Spar protein in the larval CNS. We show that Spar protein is expressed in circadian (Clock) neurons, and flies lacking Spar exhibit defects in sleep and circadian activity control. In summary, we report a novel activity regulating neuropeptide precursor gene that is regulated by Alk signaling in the Drosophila CNS.

developmental biology↗

bioRxiv2021

The Relationship Between Soldier Height, Weight and Army Combat Fitness Scores

The United States Army recently implemented the Army Combat Fitness Test (ACFT) which was designed to more accurately measure functional-combat fitness constructs. The ACFT replaced the former Army Physical Fitness Test (APFT). The three advent APFT consisted of: two-minute push-ups (PU), two-minute sit-ups (SU), and a timed two-mile run (RUN). The ACFT consists of six events; 3 Rep Max Deadlift (MDL), Standing Power Throw (SPT), Hand Release Push-up (HRP), Sprint-Drag-Carry (SDC), Hanging Leg Tuck (LTK), and a timed two-mile run (2MR). This study investigated the relationship between Soldier height (1.79{+/-}0.07 m) and weight (body mass 86.8{+/-}14.2 kg, BMI 27.1{+/-}3.9) on ACFT scores (442.3{+/-}54.4) of 655 male U.S. Army National Guard Soldiers in a Field Artillery Brigade. For the purpose of the investigation body mass index (BMI) was calculated as the metric representing the Soldiers height and weight. The mean and standard deviation (sd) were calculated for the ACFT event and total scores. Pearson correlation coefficients (PCCs or r) were calculated between BMI and ACFT event and total scores. Likewise, PCCs were calculated between the ACFT event and total scores. The ACFT mean{+/-}sd scores were as follows: MDL=92.2{+/-}31.8 (3 maximum repetitions), SPT=9.5{+/-}2.2 (meters), HRP=24.6{+/-}13.1 (repetitions), SDC=119.8{+/-}21.7 (seconds), LTK=6.2{+/-}5.4 (repetitions), 2MR=1095.0{+/-}233.7 (seconds), ACFT total score=442.3{+/-}54.4 (points). Significant positive correlations were found between the ACFT total score: MDL (r=0.70), SPT (r=0.50), HRP (r=0.74), and LTK (r=0.76) events. Conversely, significant negative correlations were identified between ACFT total score: SDC (r=-0.68) and 2MR (r=-0.53) events. Within the parameters of this study, Soldier BMI demonstrated "no to weak" association with individual ACFT event or ACFT total scores. Further, the range of PCCs between the ACFT event scores were "no to moderately high". Military leaders may consider the results provided as combat and fitness tests continue to evolve.

physiology↗

bioRxiv2020

Pharmacological inhibition of the ALK axis elicits therapeutic potential in Consensus Molecular Subtype 1 colon cancer patients

In the last years, several efforts have been made to classify colorectal cancer (CRC) into well-defined molecular subgroups, representing the intrinsic inter-patient heterogeneity, known as Consensus Molecular Subtypes (CMSs). In this work, we performed a meta-analysis of 1700 CRC patients stratified into four CMSs. We identified a negative correlation between a high level of anaplastic lymphoma kinase (ALK) expression and relapse-free survival, exclusively in CMS1 subtype. Stemming from this observation, we tested several CMSs in vitro models with crizotinib (CZB) or alectinib (ALC), potent ALK inhibitors, already approved for clinical use. ALK interception strongly inhibits cell proliferation already at nanomolar doses, specifically in CMS1 cell lines, while no effect was found in CMS2/3/4 groups. Furthermore, in vivo imaging identified a role for ALK in the dynamic formation of 3D spheroids, which was impaired by the pharmacological inhibition of ALK. Consistently, CZB was responsible for the dampened activation of ALK along with the downstream AKT cascade. Mechanistically, we found a specific pro-apoptotic effect of ALK inhibition in CMS1 cell lines, both in 2D and 3D. Confocal analysis suggests that inhibition in CMS1 cells enhances cell-cell adhesion when growing in 3D. In agreement with our findings, an ALK signature encompassing 65 genes statistically associated with worse relapse-free survival in CMS1 subtype. Finally, the efficacy of ALK inhibition treatment was demonstrated in patient-derived organoids. Collectively, our findings suggest that ALK inhibition may represent an attractive therapy for CRC, and CMS classification may provide a useful tool to identify patients who could benefit from this treatment. These findings offer rationale and pharmacological strategies for the treatment of CMS1 CRC.

cancer biology↗

bioRxiv2019

nkx3.2 mutant zebrafish accommodate the jaw joint loss through a phenocopy of the head shapes of Paleozoic agnathans

The vertebrate jaw is a versatile feeding apparatus that facilitated explosive diversification. To function, it requires a joint between the upper and lower jaws, so jaw joint defects - such as osteoarthritis or even ankylosis - are often highly disruptive and difficult to study. To describe consequences of jaw-joint dysfunction, we engineered two independent null alleles of a single jaw-joint marker gene, nkx3.2, in zebrafish. These mutations caused zebrafish to become functionally jawless via fusion of the upper and lower jaw cartilages (ankylosis). Despite lacking jaw joints, nkx3.2 mutants survive to adulthood and accommodate this defect by: a) remodeling their skulls; and b) altering their behavior from suction feeding to ram feeding. As a result of remodeling, nkx3.2 mutants developed superficial similarities to the skull shapes observed in two lineages of ancient jawless vertebrates (anaspids and furcacaudiid thelodonts), including: a fixed open gape, reduced snout, and enlarged branchial region. However, no homology exists in individual skull elements between these taxa, and most of the modified elements in the mutant zebrafish occur outside known expression domains of nkx3.2. Therefore, we interpret the adult nkx3.2 phenotype not as a reversal to an ancestral state, but as convergence due to similar functional requirement of feeding without moveable jaws. This remarkable convergence strongly suggests that jaw movements themselves dramatically influence the development of jawed vertebrate skulls, which implies that functionally viable skull morphologies are finite, with or without functional jaws. Because nkx3.2 null zebrafish display prominent joint ankylosis, drastically modified skull shape, and altered feeding behaviors, these mutants provide a unique model with which to investigate mechanisms of skeletal remodeling and joint diseases.

evolutionary biology↗

bioRxiv2018

Characterization of Drosophila Nidogen/entactin reveals roles in basement membrane stability, barrier function and nervous system plasticity

Basement membranes (BMs) are specialized layers of extracellular matrix (ECM) mainly composed of Laminin, type IV Collagen, Perlecan and Nidogen/entactin (NDG). While the essential and evolutionary conserved functions of Laminin, Collagen and Perlecan are well documented in Drosophila and other species, the proposed role of NDG as the major ECM linker molecule has been challenged by several in vivo studies revealing that NDG is dispensable for viability and BM formation. Here, we report the characterization of the single Ndg gene in Drosophila. Embryonic Ndg expression differed from that of other BM components and was primarily observed in mesodermal tissues and the chordotonal organs, whereas NDG protein localized to all BMs. While loss of Laminin strongly affected BM-localization of NDG, Ndg null mutants exhibited no overt changes in the distribution of BM core components. However, loss of NDG led to ultrastructural BM defects compromising barrier function and stability in vivo. Although Ndg mutants were viable, loss of NDG led to decreased fecundity in flies as well as impaired crawling behavior and reduced response to vibrational stimuli in larvae. Further morphological analysis revealed accompanying defects in the larval peripheral nervous system especially in the chordotonal organs and the neuromuscular junction (NMJ), where Ndg genetically interacted with the Leukocyte-antigen-related-like (Lar) receptor gene to regulate NMJ extension and synaptic differentiation. Taken together, our analysis suggests that NDG is not essential for BM assembly but mediates BM stability and ECM-dependent neural plasticity during Drosophila development.\n\nSummary StatementIn this study we characterize Drosophila Nidogen/Entactin (Ndg) mutants revealing that loss of Ndg impairs basement membrane (BM) stability and permeability as well as proper function of the nervous system.

developmental biology↗

bioRxiv2017

Serum proteins can successfully predict self-reported ethnicity: Implications for precision-medicine

The effects of inter-individual variability on disease treatment and prevention are important to the goals of \"precision medicine\" 1. In biomedical research, consideration of racial or ethnic differences allows generation and exploration of hypotheses about interactions among genetic and environmental factors responsible for differential medical outcomes. The US National Institutes of Health, therefore recommends adequate participation of subjects from ethnic minority groups in research studies. Nevertheless, considerable debate has focused on validity of race or ethnicity as biological construct 2. Inconsistent definition of race/ethnicity and insignificant genetic variations between ethnic groups have invited disregard to this construct 3. On the contrary, differences in prevalence, expression and outcomes of various diseases among ethnic groups argue for continued and focused attention to ethnicity as important predicting variable. In context of Alzheimers disease (AD), we have previously reported that ethnicity does moderates the proteomic markers of dementia 4. Here, we attempted to classify and predict selfreported ethnicity (Hispanic or non-Hispanic white, [NHW]) using a limited serum profile of 107 proteins. Random Forest (RF) classification method was able to discriminate those two ethnicities with 95% accuracy and could successfully predict ethnicity in an independent test-set (Area under ROC curve: 0.97). Variable selection method led to a condensed set of six proteins which yielded comparable classification and prediction accuracy. Our results provide preliminary evidence for proteomic variability between ethnic groups, and biological validity of ethnicity construct. Moreover, they also offer an opportunity to exploit these differences towards the objectives of precision medicine.

bioinformatics↗