Insights from multi-omic modeling of neurodegeneration in xeroderma pigmentosum using an induced pluripotent stem cell system.

Xeroderma pigmentosum (XP) is caused by defective nucleotide excision repair of DNA damage. This results in hypersensitivity to ultraviolet light and increased skin cancer risk, as sunlight-induced photoproducts remain unrepaired. However, many XP patients also display early-onset neurodegeneration, which leads to premature death. The mechanism of neurodegeneration is unknown. Here, we investigate XP neurodegeneration using pluripotent stem cells derived from XP patients and healthy relatives, performing functional multi-omics on samples during neuronal differentiation. We show substantially increased levels of 5',8-cyclopurine and 8-oxopurine in XP neuronal DNA secondary to marked oxidative stress. Furthermore, we find that the endoplasmic reticulum stress response is upregulated and reversal of the mutant genotype is associated with phenotypic rescue. Critically, XP neurons exhibit inappropriate downregulation of the protein clearance ubiquitin-proteasome system (UPS). Chemical enhancement of UPS activity in XP neuronal models improves phenotypes, albeit inadequately. Although more work is required, this study presents insights with intervention potential.

Refinement of paramagnetic bead-based digestion protocol for automatic sample preparation using an artificial neural network.

Despite technological advances in the proteomics field, sample preparation still represents the main bottleneck in mass spectrometry (MS) analysis. Bead-based protein aggregation techniques have recently emerged as an efficient, reproducible, and high-throughput alternative for protein extraction and digestion. Here, a refined paramagnetic bead-based digestion protocol is described for Opentrons® OT-2 platform (OT-2) as a versatile, reproducible, and affordable alternative for the automatic sample preparation for MS analysis. For this purpose, an artificial neural network (ANN) was applied to maximize the number of peptides without missed cleavages identified in HeLa extract by combining factors such as the quantity (µg) of trypsin/Lys-C and beads (MagReSyn® Amine), % (w/v) SDS, % (v/v) acetonitrile, and time of digestion (h). ANN model predicted the optimal conditions for the digestion of 50 µg of HeLa extract, pointing to the use of 2.5% (w/v) SDS and 300 µg of beads for sample preparation and long-term digestion (16h) with 0.15 µg Lys-C and 2.5 µg trypsin (≈1:17 ratio). Based on the results of the ANN model, the manual protocol was automated in OT-2. The performance of the automatic protocol was evaluated with different sample types, including human plasma, Arabidopsis thaliana leaves, Escherichia coli cells, and mouse tissue cortex, showing great reproducibility and low sample-to-sample variability in all cases. In addition, we tested the performance of this method in the preparation of a challenging biological fluid such as rat bile, a proximal fluid that is rich in bile salts, bilirubin, cholesterol, and fatty acids, among other MS interferents. Compared to other protocols described in the literature for the extraction and digestion of bile proteins, the method described here allowed identify 385 unique proteins, thus contributing to improving the coverage of the bile proteome.

An inverse agonist of orphan receptor GPR61 acts by a G protein-competitive allosteric mechanism.

GPR61 is an orphan GPCR related to biogenic amine receptors. Its association with phenotypes relating to appetite makes it of interest as a druggable target to treat disorders of metabolism and body weight, such as obesity and cachexia. To date, the lack of structural information or a known biological ligand or tool compound has hindered comprehensive efforts to study GPR61 structure and function. Here, we report a structural characterization of GPR61, in both its active-like complex with heterotrimeric G protein and in its inactive state. Moreover, we report the discovery of a potent and selective small-molecule inverse agonist against GPR61 and structural elucidation of its allosteric binding site and mode of action. These findings offer mechanistic insights into an orphan GPCR while providing both a structural framework and tool compound to support further studies of GPR61 function and modulation.

Modelling coastal upwelling off NW Iberian Peninsula: New insights on the fate of phytoplankton blooms.

The northwestern coast of the Iberian Peninsula is a region characterized by pronounced hydrologic and biogeochemical activity, resulting in important fish and shellfish resources whose exploitation has a strong local socioeconomic impact. This high biological diversity is strongly dependent on coastal upwelling induced by favourable winds, which presents seasonal variability. This motivates the present study, which aims to understand the relation between local circulation, hydrography and Chl-a concentration under summer upwelling events of different intensities and clarify their effects in the region. To achieve this purpose, a coupled physical-biological model was developed and validated for the northwestern coast of the Iberian Peninsula, based on the use of MOHID modelling system and the application of a nested domains methodology. Comparison of predictions with observations demonstrated the model's accuracy in reproducing the physical and biogeochemical properties of the study region, both at the surface and along the water column. The study of different summer upwelling events shows that the local phytoplankton patterns are dependent on the characteristics of the event. Results show that under high upwelling favourable winds, a surface southwestward flow and an equatorward flow through the water column develop near the coast, inducing offshore advection of nutrient and phytoplankton-rich waters. Otherwise, under light upwelling favourable winds, surface currents are weak, a poleward flow develops, and phytoplankton is retained near the coast.

Discovery of High-Affinity Small-Molecule Binders of the Epigenetic Reader YEATS4.

A series of small-molecule YEATS4 binders have been discovered as part of an ongoing research effort to generate high-quality probe molecules for emerging and/or challenging epigenetic targets. Analogues such as 4d and 4e demonstrate excellent potency and selectivity for YEATS4 binding versus YEATS1,2,3 and exhibit good physical properties and in vitro safety profiles. A new X-ray crystal structure confirms direct binding of this chemical series to YEATS4 at the lysine acetylation recognition site of the YEATS domain. Multiple analogues engage YEATS4 with nanomolar potency in a whole-cell nanoluciferase bioluminescent resonance energy transfer assay. Rodent pharmacokinetic studies demonstrate the competency of several analogues as in vivo-capable binders.

Characterisation and long-term follow-up of children with Brugada syndrome: experience from a tertiary paediatric referral centre.

AIMS: Brugada syndrome is an inherited condition, which typically presents in young adults. It can also be diagnosed in children, but data in this group remain scarce. This study aims to describe the clinical features, management, and follow-up of children with personal or family history of Brugada syndrome. METHODS: Retrospective study of consecutive patients with Brugada history followed up in a tertiary paediatric referral centre between 2009 and 2021. Patients were assessed according to the phenotype: positive (with variable genotype) or negative (with positive genotype). RESULTS: Thirty patients were included (mean age at diagnosis 7 ± 6 years, 53% male). Within the positive phenotype (n = 16), 81% were male, and 88% had spontaneous type 1 ECG pattern. A genetic test was performed in 88% and was positive in 57%. Fourteen patients had a negative phenotype-positive genotype, 79% female, all diagnosed during family screening; 43% mentioned family history of sudden cardiac death. Although most of the patients were asymptomatic, the prevalence of rhythm/conduction disturbances was not negligible, particularly if a positive phenotype. No clinically significant events were reported in the negative phenotype patients. Three patients were hospitalised due to an arrhythmic cause, all in patients with a positive phenotype. CONCLUSION: In our study, the documentation of rhythm and conduction disturbances was not infrequent, especially in patients with a positive phenotype. Despite the significant family history, phenotype negative patients had no relevant events during follow-up. Nevertheless, the management of these patients is not clear cut, and a personalised therapeutic strategy with close follow-up is essential.

Increased oyster aquaculture in the Sado Estuary (Portugal): How to ensure ecosystem sustainability?

Aquaculture is one of the fastest growing sectors in the world. However, this may come with a cost, as increasing aquatic production is likely to impose changes in the environment. To ensure ecosystem sustainability, it is essential to think on this larger scale. This study aims to use the Delft3D model suite to evaluate the ecological carrying capacity for bivalve production in the Sado Estuary (Portugal), under present and future conditions (2050). Scenarios for increased oyster production resulted in reductions of chlorophyll a associated with increased nutrient concentrations. In the most extreme production scenario, which considered an increase of 100 ha in production area, a predicted decrease of 90 % in phytoplankton biomass was observed. Climate change (CC) was incorporated as an increase in sea level and water temperature, as well as a reduction in river flow. Under present oyster production conditions, CC revealed contrasting patterns, i.e. an increase in chlorophyll a concentrations and a reduction in nutrients. These results suggest that CC has a positive effect in counteracting the impacts of increased oyster production, however further research is necessary. All scenarios point to reduced dissolved oxygen concentrations, highlighting the need to monitor this parameter. Given the difficulty in defining what are unacceptable impacts to the ecosystem it would be prudent to include a socio-ecological framework in the future, in order to integrate ecosystem services and the perception of local stakeholders.

Substitution mutational signatures in whole-genome-sequenced cancers in the UK population.

Whole-genome sequencing (WGS) permits comprehensive cancer genome analyses, revealing mutational signatures, imprints of DNA damage and repair processes that have arisen in each patient's cancer. We performed mutational signature analyses on 12,222 WGS tumor-normal matched pairs, from patients recruited via the UK National Health Service. We contrasted our results to two independent cancer WGS datasets, the International Cancer Genome Consortium (ICGC) and Hartwig Foundation, involving 18,640 WGS cancers in total. Our analyses add 40 single and 18 double substitution signatures to the current mutational signature tally. Critically, we show for each organ, that cancers have a limited number of 'common' signatures and a long tail of 'rare' signatures. We provide a practical solution for utilizing this concept of common versus rare signatures in future analyses.

Targeting the DNA Damage Response Pathways and Replication Stress in Colorectal Cancer.

PURPOSE: Genomic instability is a hallmark of cancer and targeting DNA damage response (DDR) is emerging as a promising therapeutic strategy in different solid tumors. The effectiveness of targeting DDR in colorectal cancer has not been extensively explored. EXPERIMENTAL DESIGN: We challenged 112 cell models recapitulating the genomic landscape of metastatic colorectal cancer with ATM, ATR, CHK1, WEE1, and DNA-PK inhibitors, in parallel with chemotherapeutic agents. We focused then on ATR inhibitors (ATRi) and, to identify putative biomarkers of response and resistance, we analyzed at multiple levels colorectal cancer models highly sensitive or resistant to these drugs. RESULTS: We found that around 30% of colorectal cancers, including those carrying KRAS and BRAF mutations and unresponsive to targeted agents, are sensitive to at least one DDR inhibitor. By investigating potential biomarkers of response to ATRi, we found that ATRi-sensitive cells displayed reduced phospho-RPA32 foci at basal level, while ATRi-resistant cells showed increased RAD51 foci formation in response to replication stress. Lack of ATM and RAD51C expression was associated with ATRi sensitivity. Analysis of mutational signatures and HRDetect score identified a subgroup of ATRi-sensitive models. Organoids derived from patients with metastatic colorectal cancer recapitulated findings obtained in cell lines. CONCLUSIONS: In conclusion, a subset of colorectal cancers refractory to current therapies could benefit from inhibitors of DDR pathways and replication stress. A composite biomarker involving phospho-RPA32 and RAD51 foci, lack of ATM and RAD51C expression, as well as analysis of mutational signatures could be used to identify colorectal cancers likely to respond to ATRi.

A Small-Molecule Oral Agonist of the Human Glucagon-like Peptide-1 Receptor.

Peptide agonists of the glucagon-like peptide-1 receptor (GLP-1R) have revolutionized diabetes therapy, but their use has been limited because they require injection. Herein, we describe the discovery of the orally bioavailable, small-molecule, GLP-1R agonist PF-06882961 (danuglipron). A sensitized high-throughput screen was used to identify 5-fluoropyrimidine-based GLP-1R agonists that were optimized to promote endogenous GLP-1R signaling with nanomolar potency. Incorporation of a carboxylic acid moiety provided considerable GLP-1R potency gains with improved off-target pharmacology and reduced metabolic clearance, ultimately resulting in the identification of danuglipron. Danuglipron increased insulin levels in primates but not rodents, which was explained by receptor mutagensis studies and a cryogenic electron microscope structure that revealed a binding pocket requiring a primate-specific tryptophan 33 residue. Oral administration of danuglipron to healthy humans produced dose-proportional increases in systemic exposure (NCT03309241). This opens an opportunity for oral small-molecule therapies that target the well-validated GLP-1R for metabolic health.

Preclinical In Vivo Validation of the RAD51 Test for Identification of Homologous Recombination-Deficient Tumors and Patient Stratification.

PARP inhibitors (PARPi) are approved drugs for platinum-sensitive, high-grade serous ovarian cancer (HGSOC) and for breast, prostate, and pancreatic cancers (PaC) harboring genetic alterations impairing homologous recombination repair (HRR). Detection of nuclear RAD51 foci in tumor cells is a marker of HRR functionality, and we previously established a test to detect RAD51 nuclear foci. Here, we aimed to validate the RAD51 score cut off and compare the performance of this test to other HRR deficiency (HRD) detection methods. Laboratory models from BRCA1/BRCA2-associated breast cancer, HGSOC, and PaC were developed and evaluated for their response to PARPi and cisplatin. HRD in these models and patient samples was evaluated by DNA sequencing of HRR genes, genomic HRD tests, and RAD51 foci detection. We established patient-derived xenograft models from breast cancer (n = 103), HGSOC (n = 4), and PaC (n = 2) that recapitulated patient HRD status and treatment response. The RAD51 test showed higher accuracy than HRR gene mutations and genomic HRD analysis for predicting PARPi response (95%, 67%, and 71%, respectively). RAD51 detection captured dynamic changes in HRR status upon acquisition of PARPi resistance. The accuracy of the RAD51 test was similar to HRR gene mutations for predicting platinum response. The predefined RAD51 score cut off was validated, and the high predictive value of the RAD51 test in preclinical models was confirmed. These results collectively support pursuing clinical assessment of the RAD51 test in patient samples from randomized trials testing PARPi or platinum-based therapies. SIGNIFICANCE: This work demonstrates the high accuracy of a histopathology-based test based on the detection of RAD51 nuclear foci in predicting response to PARPi and cisplatin.

Analysis of T cell receptor clonotypes in tumor microenvironment identifies shared cancer-type-specific signatures.

Despite the conventional view that a truly random V(D)J recombination process should generate a highly diverse immune repertoire, emerging reports suggest that there is a certain bias toward the generation of shared/public immune receptor chains. These studies were performed in viral diseases where public T cell receptors (TCR) appear to confer better protective responses. Selective pressures generating common TCR clonotypes are currently not well understood, but it is believed that they confer a growth advantage. As very little is known about public TCR clonotypes in cancer, here we set out to determine the extent of shared TCR clonotypes in the intra-tumor microenvironments of virus- and non-virus-driven head and neck cancers using TCR sequencing. We report that tumor-infiltrating T cell clonotypes were indeed shared across individuals with the same cancer type, where the majority of shared sequences were specific to the cancer type (i.e., viral versus non-viral). These shared clonotypes were not particularly enriched in EBV-associated nasopharynx cancer but, in both cancers, exhibited distinct characteristics, namely shorter CDR3 lengths, restricted V- and J-gene usages, and also demonstrated convergent V(D)J recombination. Many of these shared TCRs were expressed in patients with a shared HLA background. Pattern recognition of CDR3 amino acid sequences revealed strong convergence to specific pattern motifs, and these motifs were uniquely found to each cancer type. This suggests that they may be enriched for specificity to common antigens found in the tumor microenvironment of different cancers. The identification of shared TCRs in infiltrating tumor T cells not only adds to our understanding of the tumor-adaptive immune recognition but could also serve as disease-specific biomarkers and guide the development of future immunotherapies.

From structure to clinic: Design of a muscarinic M1 receptor agonist with potential to treatment of Alzheimer's disease.

Current therapies for Alzheimer's disease seek to correct for defective cholinergic transmission by preventing the breakdown of acetylcholine through inhibition of acetylcholinesterase, these however have limited clinical efficacy. An alternative approach is to directly activate cholinergic receptors responsible for learning and memory. The M1-muscarinic acetylcholine (M1) receptor is the target of choice but has been hampered by adverse effects. Here we aimed to design the drug properties needed for a well-tolerated M1-agonist with the potential to alleviate cognitive loss by taking a stepwise translational approach from atomic structure, cell/tissue-based assays, evaluation in preclinical species, clinical safety testing, and finally establishing activity in memory centers in humans. Through this approach, we rationally designed the optimal properties, including selectivity and partial agonism, into HTL9936-a potential candidate for the treatment of memory loss in Alzheimer's disease. More broadly, this demonstrates a strategy for targeting difficult GPCR targets from structure to clinic.

Applications of Cryo-EM in small molecule and biologics drug design.

Electron cryo-microscopy (cryo-EM) is a powerful technique for the structural characterization of biological macromolecules, enabling high-resolution analysis of targets once inaccessible to structural interrogation. In recent years, pharmaceutical companies have begun to utilize cryo-EM for structure-based drug design. Structural analysis of integral membrane proteins, which comprise a large proportion of druggable targets and pose particular challenges for X-ray crystallography, by cryo-EM has enabled insights into important drug target families such as G protein-coupled receptors (GPCRs), ion channels, and solute carrier (SLCs) proteins. Structural characterization of biologics, such as vaccines, viral vectors, and gene therapy agents, has also become significantly more tractable. As a result, cryo-EM has begun to make major impacts in bringing critical therapeutics to market. In this review, we discuss recent instructive examples of impacts from cryo-EM in therapeutics design, focusing largely on its implementation at Pfizer. We also discuss the opportunities afforded by emerging technological advances in cryo-EM, and the prospects for future development of the technique.

A habitat suitability model for aquaculture site selection: Ria de Aveiro and Rias Baixas.

Aquaculture is one of the fastest-growing activities worldwide. This strong and rapid development of the sector tends to be reflected in significant environmental impacts and new challenges in the management of the coastal areas. In this context, this work intends to contribute to the sustainability of the sector, by proposing an innovative method to identify preferred locations to ensure sustainable expansion of fish and mussels aquaculture, under optimal hydrodynamic and water quality conditions in Ria de Aveiro (Portugal) and Rias Baixas (Spain). A habitat model was developed, integrating hydrodynamic and water quality modelling results into a suitability index based on the definition of variable suitability functions. The results show that 22% of Ria de Aveiro is very good for fish production. In contrast, the production of pelagic fish in Rias Baixas is not recommended due to vertical gradients of water temperature and seasonal events of hypoxia. Concerning to mussels, the habitat model classifies 31% of Ria de Aveiro area as very good for production, while most of the Rias Baixas area presents this highest classification, confirming the high exploitation of the region. The definition of appropriate areas for aquaculture exploitation is highly related with the different geomorphological, hydrological and biogeochemical processes of Ria de Aveiro and Rias Baixas. Results for Ria de Aveiro indicate that the upstream areas are the most vulnerable from the water quality point of view, highlighting the importance of the advective processes in the lagoon's water quality, in opposition to Rias Baixas dynamics, where stratification is more relevant. In Rias Baixas, the strong vertical gradient of water temperature and dissolved oxygen prevents fish from having sustainable growth rates. Therefore, this work demonstrated the potential of the proposed method based on hydrodynamic and biogeochemical modelling to support the decision-making process in planning aquaculture expansion.

Economic Feasibility of Floating Offshore Wind Farms Considering Near Future Wind Resources: Case Study of Iberian Coast and Bay of Biscay.

Wind energy resources are subject to changes in climate, so the use of wind energy density projections in the near future is essential to determine the viability and profitability of wind farms at particular locations. Thus, a step forward in determining the economic assessment of floating offshore wind farms was taken by considering current and near-future wind energy resources in assessing the main parameters that determine the economic viability (net present value, internal rate of return, and levelized cost of energy) of wind farms. This study was carried out along the Atlantic coast from Brest to Cape St. Vincent. Results show that the future reduction in wind energy density (2%-6%) mainly affects the net present value (NPV) of the farm and has little influence on the levelized cost of energy (LCOE). This study provides a good estimate of the economic viability of OWFs (Offshore Wind Farms) by taking into account how wind resources can vary due to climate change over the lifetime of the farm.

Small-molecule inhibition of METTL3 as a strategy against myeloid leukaemia.

N6-methyladenosine (m6A) is an abundant internal RNA modification1,2 that is catalysed predominantly by the METTL3-METTL14 methyltransferase complex3,4. The m6A methyltransferase METTL3 has been linked to the initiation and maintenance of acute myeloid leukaemia (AML), but the potential of therapeutic applications targeting this enzyme remains unknown5-7. Here we present the identification and characterization of STM2457, a highly potent and selective first-in-class catalytic inhibitor of METTL3, and a crystal structure of STM2457 in complex with METTL3-METTL14. Treatment of tumours with STM2457 leads to reduced AML growth and an increase in differentiation and apoptosis. These cellular effects are accompanied by selective reduction of m6A levels on known leukaemogenic mRNAs and a decrease in their expression consistent with a translational defect. We demonstrate that pharmacological inhibition of METTL3 in vivo leads to impaired engraftment and prolonged survival in various mouse models of AML, specifically targeting key stem cell subpopulations of AML. Collectively, these results reveal the inhibition of METTL3 as a potential therapeutic strategy against AML, and provide proof of concept that the targeting of RNA-modifying enzymes represents a promising avenue for anticancer therapy.

Modelling the distribution of microplastics released by wastewater treatment plants in Ria de Vigo (NW Iberian Peninsula).

The accumulation of plastic waste in estuaries is growing due to the increase in their use in daily life and their inadequate treatment on wastewater plants (WWTPs). Hydrodynamic and particle-tracking models were validated and used to improve the knowledge about the distribution and concentration of microplastics released by WWTPs in the Ria de Vigo. Results showed that the Vigo WWTP is the main driver of microplastics to the Ria de Vigo. Besides, 21% of the released microplastics reach the adjacent ocean, 24% remain anchored around the Cies Islands, and a negligible percentage reaches the upper estuary when the emission occurs under ebb on spring tide conditions. A negligible number of released microplastics is exported to the nearby ocean when the emission occurs under neap tide conditions. This research can provide a useful tool to support the identification of monitoring processes and debris removal.

A practical framework and online tool for mutational signature analyses show inter-tissue variation and driver dependencies.

Mutational signatures are patterns of mutations that arise during tumorigenesis. We present an enhanced, practical framework for mutational signature analyses. Applying these methods on 3,107 whole genome sequenced (WGS) primary cancers of 21 organs reveals known signatures and nine previously undescribed rearrangement signatures. We highlight inter-organ variability of signatures and present a way of visualizing that diversity, reinforcing our findings in an independent analysis of 3,096 WGS metastatic cancers. Signatures with a high level of genomic instability are dependent on TP53 dysregulation. We illustrate how uncertainty in mutational signature identification and assignment to samples affects tumor classification, reinforcing that using multiple orthogonal mutational signature data is not only beneficial, it is essential for accurate tumor stratification. Finally, we present a reference web-based tool for cancer and experimentally-generated mutational signatures, called Signal (https://signal.mutationalsignatures.com), that also supports performing mutational signature analyses.