Diverse Cellular Pathways Research Articles

THP as a sensor for the electrochemical detection of H2O2

Hydrogen peroxide (H2O2) detection is paramount in biological and clinical domains due to its pivotal role in various physiological and pathological processes. This molecule is a crucial metabolite and effector in cellular redox mechanisms, influencing diverse cellular signaling pathways and bolstering the body’s defense mechanisms against infection and oxidative stress. Organic molecule-based electrodes present unique advantages such as operational versatility and scalability, rendering them attractive candidates for sensor development across diverse fields encompassing food safety, healthcare, and environmental monitoring. This study explores the electrochemical properties of a tris(3-hydroxypyridin-4-one) THP, which has been unexplored in electrochemical sensing. Leveraging THP’s chelating properties, we aimed to develop an electrochemical probe for hydrogen peroxide detection. Our investigations reveal promising results, with the developed sensor exhibiting a low limit of detection (LOD) of 144 nM, underscoring its potential utility in sensitive and selective H2O2 detection applications. In addition, the new sensor was also tested on fetal bovine serum (FBS) to emphasize future applications on biological matrices. This research signifies a significant stride in advancing electrochemical sensor technologies for hydrogen peroxide detection with several novelties related to the usage of THP, such as high sensitivity and selectivity, performance in biological matrices, repeatability, stability, and reproducibility, economical and practical advantages. This research opens new avenues for enhanced biomedical diagnostics and therapeutic interventions.

Cell-type-specific consequences of mosaic structural variants in hematopoietic stem and progenitor cells

The functional impact and cellular context of mosaic structural variants (mSVs) in normal tissues is understudied. Utilizing Strand-seq, we sequenced 1,133 single-cell genomes from 19 human donors of increasing age, and discovered the heterogeneous mSV landscapes of hematopoietic stem and progenitor cells. While mSVs are continuously acquired throughout life, expanded subclones in our cohort are confined to individuals >60. Cells already harboring mSVs are more likely to acquire additional somatic structural variants, including megabase-scale segmental aneuploidies. Capitalizing on comprehensive single-cell micrococcal nuclease digestion with sequencing reference data, we conducted high-resolution cell-typing for eight hematopoietic stem and progenitor cells. Clonally expanded mSVs disrupt normal cellular function by dysregulating diverse cellular pathways, and enriching for myeloid progenitors. Our findings underscore the contribution of mSVs to the cellular and molecular phenotypes associated with the aging hematopoietic system, and establish a foundation for deciphering the molecular links between mSVs, aging and disease susceptibility in normal tissues.

Proteome Birthdating Reveals Age-Selectivity of Protein Ubiquitination

Within a cell, proteins have distinct and highly variable half-lives. As a result, the molecular ages of proteins can range from seconds to years. How the age of a protein influences its environmental interactions is a largely unexplored area of biology. To investigate the age-selectivity of cellular pathways, we developed a methodology termed “proteome birthdating” that barcodes proteins based on their time of synthesis. We demonstrate that this approach provides accurate measurements of protein turnover kinetics from a single biological sample encoding multiple labeling time-points. As a first application of the birthdated proteome, we investigated the age distribution of the human ubiquitinome. Our results indicate that the vast majority of ubiquitinated proteins in a cell consist of newly synthesized proteins and that these young proteins constitute the bulk of the degradative flux through the proteasome. Rapidly ubiquitinated nascent proteins are enriched in cytosolic subunits of large protein complexes. Conversely, proteins destined for the secretory pathway and vesicular transport have older ubiquitinated populations. Our data also identify a smaller subset of older ubiquitinated cellular proteins that do not appear to be targeted to the proteasome for rapid degradation. Together, our data provide an age census of the human ubiquitinome and establish proteome birthdating as a robust methodology for investigating the protein age-selectivity of diverse cellular pathways.

Exploring Southern Ecuador's Traditional Medicine: Biological Screening of Plant Extracts and Metabolites.

Ecuador stands as a nation inheriting a profound ancestral legacy in the utilization of medicinal plants, reflective of the rich biodiversity embraced by various ethnic groups. Despite this heritage, many of these therapeutic resources remain insufficiently explored concerning their toxicity and potential pharmacological effects. This study focused on a comprehensive evaluation of cytotoxicity and the potential subcellular targets within various extracts and nine isolated metabolites from carefully selected medicinal plants. Assessing their impact on the breast cancer cell line (MCF7), we subsequently examined the most active fractions for effects on the cell cycle, microtubule network, centrosome duplication, γH2AX foci, and E-cadherin. The investigated crude extracts and isolated compounds from Ecuadorian medicinal plants demonstrated cytotoxic effects, influencing diverse cellular pathways. These findings lend credence to the traditional uses of Ecuadorian medicinal plants, which have served diverse therapeutic purposes. Moreover, they beckon the exploration of the specific chemicals, whether in isolation or combination, responsible for these observed activities.

Biallelic loss-of-function variants of ZFTRAF1 cause neurodevelopmental disorder with microcephaly and hypotonia

PurposeNeurodevelopmental disorders exhibit clinical and genetic heterogeneity, ergo manifest dysfunction in components of diverse cellular pathways; the precise pathomechanism for the majority remains elusive. MethodsWe studied 5 affected individuals from 3 unrelated families manifesting global developmental delay, postnatal microcephaly, and hypotonia. We used exome sequencing and prioritized variants that were subsequently characterized using immunofluorescence, immunoblotting, pulldown assays, and RNA sequencing. ResultsWe identified biallelic variants in ZFTRAF1, encoding a protein of yet unknown function. Four affected individuals from 2 unrelated families segregated 2 homozygous frameshift variants in ZFTRAF1, whereas, in the third family, an intronic splice site variant was detected. We investigated ZFTRAF1 at the cellular level and signified it as a nucleocytoplasmic protein in different human cell lines. ZFTRAF1 was completely absent in the fibroblasts of 2 affected individuals. We also identified 110 interacting proteins enriched in mRNA processing and autophagy-related pathways. Based on profiling of autophagy markers, patient-derived fibroblasts show irregularities in the protein degradation process. ConclusionThus, our findings suggest that biallelic variants of ZFTRAF1 cause a severe neurodevelopmental disorder.

Bisubstrate Uridine‐Mimetic‐Peptide Conjugates as O‐GlcNAc Transferase (OGT) Inhibitors

AbstractO‐linked β‐N‐acetylglucosamine transferase (OGT) is the pivotal mammalian enzyme that serves as a nutrient sensor, linking metabolic status to diverse cellular signalling pathways by catalyzing N‐acetylglucosamine transfer to various proteins and detects fluctuations in UDP‐GlcNAc concentrations. Increased UDP‐GlcNAc levels induce O‐GlcNAcylation of proteins, influencing the stability and localization of biomolecules, including transcription factors, kinases, phosphatases, tumour suppressors, and histone‐modifying proteins. Dysregulation and excessive OGT expression can adversely impact cellular processes. The lack of potent and selective inhibitors for OGT has impeded the progress in understanding the enzyme and its molecular mechanisms. This research article details the successful development and synthesis of a series of bisubstrate analogue inhibitors, specifically focusing on inhibiting the O‐GlcNAc transferase (OGT) enzyme. Compound 29 emerged as a promising inhibitor, demonstrating an IC50 value of 134.40 μM in in‐vitro assays. The study emphasizes the crucial role of the acceptor substrate analogue in bisubstrate inhibitor design, highlighting its equal importance alongside the donor substrate analogue. While donor substrate mimetics alone exhibited limited inhibition, their conjugation with appropriate peptides significantly enhanced the overall potency of the final bisubstrate inhibitor. Particularly, peptide derivatives proved superior as acceptor substrate analogues compared to normal substrate peptides. Preliminary data suggest the potential of uridine‐mimetics, like Q6S and Q4 C, following scaffold structure refinement. In‐silico predictions propose that replacing pyrophosphate with a flexible linker substantially improves physicochemical properties relevant to cell permeation. This comprehensive investigation offers valuable insights into designing and optimizing bisubstrate analogue inhibitors for OGT, revealing potential avenues for further refinement and development.

Ubiquitin ligase and signalling hub MYCBP2 is required for efficient EPHB2 tyrosine kinase receptor function

Eph receptor tyrosine kinases participate in a variety of normal and pathogenic processes during development and throughout adulthood. This versatility is likely facilitated by the ability of Eph receptors to signal through diverse cellular signalling pathways: primarily by controlling cytoskeletal dynamics, but also by regulating cellular growth, proliferation, and survival. Despite many proteins linked to these signalling pathways interacting with Eph receptors, the specific mechanisms behind such links and their coordination remain to be elucidated. In a proteomics screen for novel EPHB2 multi-effector proteins, we identified human MYC binding protein 2 (MYCBP2 or PAM or Phr1). MYCBP2 is a large signalling hub involved in diverse processes such as neuronal connectivity, synaptic growth, cell division, neuronal survival, and protein ubiquitination. Our biochemical experiments demonstrate that the formation of a complex containing EPHB2 and MYCBP2 is facilitated by FBXO45, a protein known to select substrates for MYCBP2 ubiquitin ligase activity. Formation of the MYCBP2-EPHB2 complex does not require EPHB2 tyrosine kinase activity and is destabilised by binding of ephrin-B ligands, suggesting that the MYCBP2-EPHB2 association is a prelude to EPHB2 signalling. Paradoxically, the loss of MYCBP2 results in increased ubiquitination of EPHB2 and a decrease of its protein levels suggesting that MYCBP2 stabilises EPHB2. Commensurate with this effect, our cellular experiments reveal that MYCBP2 is essential for efficient EPHB2 signalling responses in cell lines and primary neurons. Finally, our genetic studies in Caenorhabditis elegans provide in vivo evidence that the ephrin receptor VAB-1 displays genetic interactions with known MYCBP2 binding proteins. Together, our results align with the similarity of neurodevelopmental phenotypes caused by MYCBP2 and EPHB2 loss of function, and couple EPHB2 to a signalling effector that controls diverse cellular functions.

Experimental measurement and computational prediction of bacterial Hanks-type Ser/Thr signaling system regulatory targets.

Bacteria possess diverse classes of signaling systems that they use to sense and respond to their environments and execute properly timed developmental transitions. One widespread and evolutionarily ancient class of signaling systems are the Hanks-type Ser/Thr kinases, also sometimes termed "eukaryotic-like" due to their homology with eukaryotic kinases. In diverse bacterial species, these signaling systems function as critical regulators of general cellular processes such as metabolism, growth and division, developmental transitions such as sporulation, biofilm formation, and virulence, as well as antibiotic tolerance. This multifaceted regulation is due to the ability of a single Hanks-type Ser/Thr kinase to post-translationally modify the activity of multiple proteins, resulting in the coordinated regulation of diverse cellular pathways. However, in part due to their deep integration with cellular physiology, to date, we have a relatively limited understanding of the timing, regulatory hierarchy, the complete list of targets of a given kinase, as well as the potential regulatory overlap between the often multiple kinases present in a single organism. In this review, we discuss experimental methods and curated datasets aimed at elucidating the targets of these signaling pathways and approaches for using these datasets to develop computational models for quantitative predictions of target motifs. We emphasize novel approaches and opportunities for collecting data suitable for the creation of new predictive computational models applicable to diverse species.

Exploring the origins of neurodevelopmental proteasomopathies associated with cardiac malformations: are neural crest cells central to certain pathological mechanisms?

Neurodevelopmental proteasomopathies constitute a recently defined class of rare Mendelian disorders, arising from genomic alterations in proteasome-related genes. These alterations result in the dysfunction of proteasomes, which are multi-subunit protein complexes essential for maintaining cellular protein homeostasis. The clinical phenotype of these diseases manifests as a syndromic association involving impaired neural development and multisystem abnormalities, notably craniofacial anomalies and malformations of the cardiac outflow tract (OFT). These observations suggest that proteasome loss-of-function variants primarily affect specific embryonic cell types which serve as origins for both craniofacial structures and the conotruncal portion of the heart. In this hypothesis article, we propose that neural crest cells (NCCs), a highly multipotent cell population, which generates craniofacial skeleton, mesenchyme as well as the OFT of the heart, in addition to many other derivatives, would exhibit a distinctive vulnerability to protein homeostasis perturbations. Herein, we introduce the diverse cellular compensatory pathways activated in response to protein homeostasis disruption and explore their potential implications for NCC physiology. Altogether, the paper advocates for investigating proteasome biology within NCCs and their early cranial and cardiac derivatives, offering a rationale for future exploration and laying the initial groundwork for therapeutic considerations.

Crystal structure of bacterial ubiquitin ADP-ribosyltransferase CteC reveals a substrate-recruiting insertion

ADP-ribosylation is a post-translational modification involved in regulation of diverse cellular pathways. Interestingly, many pathogens have been identified to utilize ADP-ribosylation as a way for host manipulation. A recent study found that CteC, an effector from the bacterial pathogen Chromobacterium violaceum, hinders host ubiquitin signaling pathways via installing mono-ADP-ribosylation on threonine 66 of ubiquitin. However, the molecular basis of substrate recognition by CteC is not well-understood. In this paper, we probed the substrate specificity of this effector at protein and residue levels. We also determined the crystal structure of CteC in complex with NAD+, which revealed a canonical mono-ADP-ribosyltransferase fold with an additional insertion domain. The AlphaFold predicted model differed significantly from the experimentally determined structure, even in regions not used in crystal packing. Biochemical and biophysical studies indicated unique features of the NAD+ binding pocket, while showing selectivity distinction between ubiquitin and structurally close ubiquitin-like modifiers and the role of the insertion domain in substrate recognition. Together, this study provides insights into the enzymatic specificities and the key structural features of a novel bacterial ADP-ribosyltransferase involved in host-pathogen interaction.

Ameliorating amyloid beta oligomer toxicity with NAC

AbstractBackgroundAlzheimer’s Disease (AD) has a complex neuropathology, involving diverse cellular pathways. Molecular mechanisms induced by beta‐amyloid oligomer (Aβo) toxicity are considered to be the major initiators of neuropathology. Therefore, Aβos are commonly used to mimic toxicity in AD. The primary effect of Abeta toxicity is increase in cellular oxidative stress. Likewise, recent AD drug research and preclinical trials has been focused on reducing ROS and/or increasing antioxidant capacity. N‐acetyl cysteine (NAC) is a well‐known mucolytic agent and a powerful antioxidant via increasing GSH levels. In this respect, we aimed to investigate the effect of NAC in reducing oxidative stress in Aβo‐induced cellular toxicity.MethodSH‐SY5Y cells were cultured in DMEM medium containing 10% FBS and 1% pen/strep. In order to establish Aβo toxicity, Aβ(1‐42) peptide was dissolved in NH4OH at various concentrations (5‐100 μM) and incubated at 4°C for 24h. Oligomer formation was verified with Bis‐ANS test and Aβo toxicity was analyzed using WST‐1. Changes in the oxidative stress levels of the cells due to Aβo toxicity and NAC was quantified using Total Oxidant/Antioxidant Capacity kits based on spectrophotometric absorbance.ResultBis‐ANS test showed a linear correlation between oligomer formation and Aβo concentration. According to the cell viability assay results, 10 μM Aβ42o for 24 hrs was used to establish Aβo toxicity in vitro. At 1 and 5mM concentrations, NAC was shown to increase the viability, GSH levels and antioxidant capacity of the SH‐SY5Y cells significantly. Likewise, 1,5, and 10mM NAC was shown to reduce Aβo‐induced toxicity significantly. Furthermore, although 20 and 40mM NAC decreases viability of healthy cells, they increase viability in Aβo‐treated cells.ConclusionAccording to our results, NAC can be regarded as a potent molecule in ameliorating Aβo‐induced toxicity.

Protein kinase Cdc7 supports viral replication by phosphorylating Avibirnavirus VP3 protein.

The Avibirnavirus infectious bursal disease virus is still an important agent which largely threatens global poultry farming industry economics. VP3 is a multifunctional scaffold structural protein that is involved in virus morphogenesis and the regulation of diverse cellular signaling pathways. However, little is known about the roles of VP3 phosphorylation during the IBDV life cycle. In this study, we determined that IBDV infection induced the upregulation of Cdc7 expression and phosphorylated the VP3 Ser13 site to promote viral replication. Moreover, we confirmed that the negative charge addition of phosphoserine on VP3 at the S13 site was essential for IBDV proliferation. This study provides novel insight into the molecular mechanisms of VP3 phosphorylation-mediated regulation of IBDV replication.

Conserved transcriptional programming across sex and species after peripheral nerve injury predicts treatments for neuropathic pain.

Chronic pain is a devastating problem affecting one in five individuals around the globe, with neuropathic pain the most debilitating and poorly treated type of chronic pain. Advances in transcriptomics have contributed to cataloguing diverse cellular pathways and transcriptomic alterations in response to peripheral nerve injury but have focused on phenomenology and classifying transcriptomic responses. To identifying new types of pain-relieving agents, we compared transcriptional reprogramming changes in the dorsal spinal cord after peripheral nerve injury cross-sex and cross-species, and imputed commonalities, as well as differences in cellular pathways and gene regulation. We identified 93 transcripts in the dorsal horn that were increased by peripheral nerve injury in male and female mice and rats. Following gene ontology and transcription factor analyses, we constructed a pain interactome for the proteins encoded by the differentially expressed genes, discovering new, conserved signalling nodes. We investigated the interactome with the Drug-Gene database to predict FDA-approved medications that may modulate key nodes within the network. The top hit from the analysis was fostamatinib, the molecular target of which is the non-receptor spleen associated tyrosine kinase (Syk), which our analysis had identified as a key node in the interactome. We found that intrathecally administrating the active metabolite of fostamatinib, R406 and another Syk inhibitor P505-15, significantly reversed pain hypersensitivity in both sexes. Thus, we have identified and shown the efficacy of an agent that could not have been previously predicted to have analgesic properties.

Polarized RPE Secretome Preserves Photoreceptors in Retinal Dystrophic RCS Rats.

Retinal degenerative diseases, including age-related macular degeneration (AMD) and retinitis pigmentosa, lack effective therapies. Conventional monotherapeutic approaches fail to target the multiple affected pathways in retinal degeneration. However, the retinal pigment epithelium (RPE) secretes several neurotrophic factors addressing diverse cellular pathways, potentially preserving photoreceptors. This study explored human embryonic stem cell-derived, polarized RPE soluble factors (PRPE-SF) as a combination treatment for retinal degeneration. PRPE-SF promoted retinal progenitor cell survival, reduced oxidative stress in ARPE-19 cells, and demonstrated critical antioxidant and anti-inflammatory effects for preventing retinal degeneration in the Royal College of Surgeons (RCS) rat model. Importantly, PRPE-SF treatment preserved retinal structure and scotopic b-wave amplitudes, suggesting therapeutic potential for delaying retinal degeneration. PRPE-SF is uniquely produced using biomimetic membranes for RPE polarization and maturation, promoting a protective RPE secretome phenotype. Additionally, PRPE-SF is produced without animal serum to avoid immunogenicity in future clinical development. Lastly, PRPE-SF is a combination of neurotrophic factors, potentially ameliorating multiple dysfunctions in retinal degenerations. In conclusion, PRPE-SF offers a promising therapeutic candidate for retinal degenerative diseases, advancing the development of effective therapeutic strategies for these debilitating conditions.

Biophysical Characterization of the Binding Mechanism between the MATH Domain of SPOP and Its Physiological Partners.

SPOP (Speckle-type POZ protein) is an E3 ubiquitin ligase adaptor protein that mediates the ubiquitination of several substrates. Furthermore, SPOP is responsible for the regulation of both degradable and nondegradable polyubiquitination of a number of substrates with diverse biological functions. The recognition of SPOP and its physiological partners is mediated by two protein-protein interaction domains. Among them, the MATH domain recognizes different substrates, and it is critical for orchestrating diverse cellular pathways, being mutated in several human diseases. Despite its importance, the mechanism by which the MATH domain recognizes its physiological partners has escaped a detailed experimental characterization. In this work, we present a characterization of the binding mechanism of the MATH domain of SPOP with three peptides mimicking the phosphatase Puc, the chromatin component MacroH2A, and the dual-specificity phosphatase PTEN. Furthermore, by taking advantage of site-directed mutagenesis, we address the role of some key residues of MATH in the binding process. Our findings are briefly discussed in the context of previously existing data on the MATH domain.

MDB-24. A DATA-DRIVEN APPROACH FOR THE IDENTIFICATION OF NEW SYNERGISTIC DRUG COMBINATIONS AGAINST NEURAL CANCERS

Abstract High-risk medulloblastomas are tumours with a poor survival prognosis (≤ 50%), which are currently treated with radiation therapy and DNA-damaging chemotherapy. The severe side effects of these treatments, including developmental problems and secondary tumours, underscore the need for new treatments with reduced toxicity. An attractive target for such therapy is the Myc-family proteins since high-risk medulloblastomas amplify either N-Myc (SHH-MB, G4-MB) or c-Myc (G3-MB). While the proteins from the Myc family themselves are often referred to as pharmacologically intractable, their levels and activity can be modulated by indirect targeting, e.g. inhibition of proteins located upstream or downstream of c-Myc/N-Myc. The diverse cellular processes and pathways that c-Myc and N-Myc are involved in, however, suggest that several Myc pathways must be interrupted simultaneously to achieve a lasting effect. To identify such multimodal interventions against Myc, we performed a principal component analysis of RNA sequencing data from patient-derived medulloblastoma cells (MB002, G3, MYC-amplified) and DAOY cells (SHH-group, no MYC amplification) that were treated with 120 small molecules. In the subsequent analysis, we focused on a selection of ~ 40 genes that represent common upstream regulators and downstream targets of either c-Myc or N-Myc. Applying a principal component analysis to these particular markers, we expect that the drugs that affect different pathways associated with c-Myc activity and are located at the opposite ends of the PC1 and PC2 axis should have a synergistic effect. Additionally, we expected that the drugs located closer to each other, which affect closely related pathways, would either have no effect or would be antagonistic. Our PCA distribution method can be used to select synergistic combinations in a manner that is easily extended to new compounds. This approach may allow fast screening of compounds for estimation of the treatment effect.

Isorhamnetin exerts anti-tumor activity in DEN + CCl4-induced HCC mice.

Hepatocellular carcinoma (HCC) is the most prevalent type of liver cancer and the main cause of cancer death globally. The use of medicinal herbs as chemotherapeutic agents in cancer treatment is receiving attention as they possess no or minimum side effects. Isorhamnetin (IRN), a flavonoid, has been under attention for its anti-inflammatory and anti-proliferative properties in a number of cancers, including colorectal, skin, and lung cancers. However, the in vivo mechanism of isorhamnetin to suppress liver cancer has yet to be explored. HCC was induced by N-diethylnitrosamine (DEN) and carbon tetrachloride (CCL4) in Swiss albino mice. Isorhamnetin (100mg/kg body weight) was given to examine its anti-tumor properties in HCC mice model. Histological analysis and liver function assays were performed to assess changes in liver anatomy. Probable molecular pathways were explored using immunoblot, qPCR, ELISA, and immunohistochemistry techniques. Isorhamnetin inhibited various pro-inflammatory cytokines to suppress cancer-inducing inflammation. Additionally, it regulated Akt and MAPKs to suppress Nrf2 signaling. Isorhamnetin activated PPAR-γ and autophagy while suppressing cell cycle progression in DEN + CCl4-administered mice. Additionally, isorhamnetin regulated various signaling pathways to suppress cell proliferation, metabolism, and epithelial-mesenchymal transition in HCC. Regulating diverse cellular signaling pathways makes isorhamnetin a better anti-cancer chemotherapeutic candidate in HCC. Importantly, the anti-TNF-α properties of isorhamnetin could prove it a valuable therapeutic agent in sorafenib-resistant HCC patients. Additionally, anti-TGF-β properties of isorhamnetin could be utilized to reduce the EMT-inducing side effects of doxorubicin.

Bioorthogonal Tethering Enhances Drug Fragment Affinity for G Protein-Coupled Receptors in Live Cells.

G protein-coupled receptors (GPCRs) modulate diverse cellular signaling pathways and are important drug targets. Despite the availability of high-resolution structures, the discovery of allosteric modulators remains challenging due to the dynamic nature of GPCRs in native membranes. We developed a strategy to covalently tether drug fragments adjacent to allosteric sites in GPCRs to enhance their potency and enable fragment-based drug screening in cell-based systems. We employed genetic code expansion to site-specifically introduce noncanonical amino acids with reactive groups in C-C chemokine receptor 5 (CCR5) near an allosteric binding site for the drug maraviroc. We then used molecular dynamics simulations to design heterobifunctional maraviroc analogues consisting of a drug fragment connected by a flexible linker to a reactive moiety capable of undergoing a bioorthogonal coupling reaction. We synthesized a library of these analogues and employed the bioorthogonal inverse electron demand Diels-Alder reaction to couple the analogues to the engineered CCR5 in live cells, which were then assayed using cell-based signaling assays. Tetherable low-affinity maraviroc fragments displayed an increase in potency for CCR5 engineered with reactive unnatural amino acids that were adjacent to the maraviroc binding site. The strategy we describe to tether novel drug fragments to GPCRs should prove useful to probe allosteric or cryptic binding site functionality in fragment-based GPCR-targeted drug discovery.

Transcriptomic profiling of the yeast Komagataella phaffii in response to environmental alkalinization

BackgroundAdaptation to alkalinization of the medium in fungi involves an extensive remodeling of gene expression. Komagataella phaffii is an ascomycetous yeast that has become an organism widely used for heterologous protein expression. We explore here the transcriptional impact of moderate alkalinization in this yeast, in search of suitable novel promoters able to drive transcription in response to the pH signal.ResultsIn spite of a minor effect on growth, shifting the cultures from pH 5.5 to 8.0 or 8.2 provokes significant changes in the mRNA levels of over 700 genes. Functional categories such as arginine and methionine biosynthesis, non-reductive iron uptake and phosphate metabolism are enriched in induced genes, whereas many genes encoding iron-sulfur proteins or members of the respirasome were repressed. We also show that alkalinization is accompanied by oxidative stress and we propose this circumstance as a common trigger of a subset of the observed changes. PHO89, encoding a Na+/Pi cotransporter, appears among the most potently induced genes by high pH. We demonstrate that this response is mainly based on two calcineurin-dependent response elements located in its promoter, thus indicating that alkalinization triggers a calcium-mediated signal in K. phaffii.ConclusionsThis work defines in K. phaffii a subset of genes and diverse cellular pathways that are altered in response to moderate alkalinization of the medium, thus setting the basis for developing novel pH-controlled systems for heterologous protein expression in this fungus.

Investigating the potential anti-depressive mechanisms of statins: a transcriptomic and Mendelian randomization analysis

Observational studies and randomized controlled trials presented inconsistent findings on the effects of cholesterol-lowering statins on depression. It therefore remains unclear whether statins have any beneficial effects on depression, and if so, what the underlying molecular mechanisms are. Here, we aimed to use genomic approaches to investigate this further. Using Connectivity Map (CMap), we first investigated whether statins and antidepressants shared pharmacological effects by interrogating gene expression responses to drug exposure in human cell lines. Second, using Mendelian randomization analysis, we investigated both on-target (through HMGCR inhibition) and potential off-target (through ITGAL and HDAC2 inhibition) causal effects of statins on depression risk and depressive symptoms, and traits related to the shared biological pathways identified from CMap analysis. Compounds inducing highly similar gene expression responses to statins in HA1E cells (indicated by an average connectivity score with statins > 90) were found to be enriched for antidepressants (12 out of 38 antidepressants; p = 9E-08). Genes perturbed in the same direction by both statins and antidepressants were significantly enriched for diverse cellular and metabolic pathways, and various immune activation, development and response processes. MR analysis did not identify any significant associations between statin exposure and depression risk or symptoms after multiple testing correction. However, genetically proxied HMGCR inhibition was strongly associated with alterations in platelets (a prominent serotonin reservoir) and monocyte percentage, which have previously been implicated in depression. Genetically proxied ITGAL inhibition was strongly associated with basophil, monocyte and neutrophil counts. We identified biological pathways that are commonly perturbed by both statins and antidepressants, and haematological biomarkers genetically associated with statin targets. Our findings warrant pre-clinical investigation of the causal role of these shared pathways in depression and potential as therapeutic targets, and investigation of whether blood biomarkers may be important considerations in clinical trials investigating effects of statins on depression.