Changes in environmental exposures over decades may influence the genetic architecture of severe spermatogenic failure

STUDY QUESTION

Do the genetic determinants of idiopathic severe spermatogenic failure (SPGF) differ between generations?

SUMMARY ANSWER

Our data support that the genetic component of idiopathic SPGF is impacted by dynamic changes in environmental exposures over decades.

WHAT IS KNOWN ALREADY

The idiopathic form of SPGF has a multifactorial etiology wherein an interaction between genetic, epigenetic, and environmental factors leads to the disease onset and progression. At the genetic level, genome-wide association studies (GWASs) allow the analysis of millions of genetic variants across the genome in a hypothesis-free manner, as a valuable tool for identifying susceptibility risk loci. However, little is known about the specific role of non-genetic factors and their influence on the genetic determinants in this type of conditions.

STUDY DESIGN, SIZE, DURATION

Case-control genetic association analyses were performed including a total of 912 SPGF cases and 1360 unaffected controls.

PARTICIPANTS/MATERIALS, SETTING, METHODS

All participants had European ancestry (Iberian and German). SPGF cases were diagnosed during the last decade either with idiopathic non-obstructive azoospermia (n = 547) or with idiopathic non-obstructive oligozoospermia (n = 365). Case-control genetic association analyses were performed by logistic regression models considering the generation as a covariate and by in silico functional characterization of the susceptibility genomic regions.

MAIN RESULTS AND THE ROLE OF CHANCE

This analysis revealed 13 novel genetic association signals with SPGF, with eight of them being independent. The observed associations were mostly explained by the interaction between each lead variant and the age-group. Additionally, we established links between these loci and diverse non-genetic factors, such as toxic or dietary habits, respiratory disorders, and autoimmune diseases, which might potentially influence the genetic architecture of idiopathic SPGF.

LARGE SCALE DATA

GWAS data are available from the authors upon reasonable request.

LIMITATIONS, REASONS FOR CAUTION

Additional independent studies involving large cohorts in ethnically diverse populations are warranted to confirm our findings.

WIDER IMPLICATIONS OF THE FINDINGS

Overall, this study proposes an innovative strategy to achieve a more precise understanding of conditions such as SPGF by considering the interactions between a variable exposome through different generations and genetic predisposition to complex diseases.

STUDY FUNDING/COMPETING INTEREST(S)

This work was supported by the "Plan Andaluz de Investigación, Desarrollo e Innovación (PAIDI 2020)" (ref. PY20_00212, P20_00583), the Spanish Ministry of Economy and Competitiveness through the Spanish National Plan for Scientific and Technical Research and Innovation (ref. PID2020-120157RB-I00 funded by MCIN/ AEI/10.13039/501100011033), and the 'Proyectos I+D+i del Programa Operativo FEDER 2020' (ref. B-CTS-584-UGR20). ToxOmics-Centre for Toxicogenomics and Human Health, Genetics, Oncology and Human Toxicology, is also partially supported by the Portuguese Foundation for Science and Technology (Projects: UIDB/00009/2020; UIDP/00009/2020). The authors declare no competing interests.

TRIAL REGISTRATION NUMBER

N/A.

The Role of 5-Hydroxymethylcytosine as a Potential Epigenetic Biomarker in a Large Series of Thyroid Neoplasms

Cytosine modifications at the 5-carbon position play a critical role in gene expression regulation and have been implicated in cancer development. 5-Hydroxymethylcytosine (5hmC), arising from 5-methylcytosine (5-mC) oxidation, has shown promise as a potential malignancy marker due to its depletion in various human cancers. However, its significance in thyroid tumors remains underexplored, primarily due to limited data. In our study, we evaluated 5hmC expression levels by immunohistochemistry in a cohort of 318 thyroid tumors. Our analysis revealed significant correlations between 5hmC staining extension scores and nodule size, vascular invasion, and oncocytic morphology. Nuclear 5hmC staining intensity demonstrated associations with focality, capsule status, extrathyroidal extension, vascular invasion, and oncocytic morphology. Follicular/oncocytic adenomas exhibited higher 5hmC expression than uncertain malignant potential (UMP) or noninvasive follicular thyroid neoplasms with papillary-like nuclear features (NIFTP), as well as malignant neoplasms, including papillary thyroid carcinomas (PTCs), oncocytic carcinomas (OCAs), follicular thyroid carcinomas (FTCs), and invasive encapsulated follicular variants of PTC (IEFV-PTC). TERT promoter mutation cases showed notably lower values for the 5hmC expression, while RAS (H, N, or K) mutations, particularly HRAS mutations, were associated with higher 5hmC expression. Additionally, we identified, for the first time, a significant link between 5hmC expression and oncocytic morphology. However, despite the merits of these discoveries, we acknowledge that 5hmC currently cannot segregate minimally invasive from widely invasive tumors, although 5hmC levels were lower in wi-FPTCs. Further research is needed to explore the potential clinical implications of 5hmC in thyroid tumors.

Surgical aortic valve replacement in octogenarians: Single-center perioperative outcomes and five-year survival

INTRODUCTION AND OBJECTIVES

Aortic stenosis is the most common valvular heart disease. The number of octogenarians proposed for intervention is growing due to increased lifespan. In this manuscript we aim to evaluate perioperative outcome and long-term survival after surgical aortic valve replacement (SAVR) in octogenarians, comparing patients with low surgical risk (EuroscoreII <4%) with intermediate-high risk (EuroscoreII ≥4%).

METHODS

A retrospective observational single-center cohort study with 195 patients aged ≥80 years old, who underwent SAVR between 2017 and 2021, was conducted. Patients were divided into two groups according to EuroscoreII: (1) Low risk (EuroscoreII <4%) with intermediate-high risk (EuroscoreII ≥4%). Continuous variables are presented in median (IQR), analyzed using Wilcoxon rank sum test; categorical variables in percentages, analyzed using chi-squared test; and survival was analyzed by Kaplan-Meier, open cohort, and the log-rank test was performed.

RESULTS

The overall median age was 82 (IQR 81-83), with 4.6% of the patients ≥85 years old. 23.6% of the patients presented EuroscoreII ≥4%. No complications were observed in 26.2%, with a significantly higher rate in intermediate-high risk patients. Postoperative need for hemodynamic support was the most frequent complication, followed by postoperative acute kidney injury and the use of blood products. Overall median ICU stay was three days (2-4) and hospital length of stay (LOS) six days (5-8). Patients with intermediate-high risk and those with complications had longer ICU LOS. At 12 months, overall survival was 96.4%, at three years 94.1% and 5 years 75.4%. Patients with low surgical risk had higher survival proportions up to 5 years.

CONCLUSION

SAVR in patients ≥80 years is associated with low in-hospital mortality, although a significant proportion of patients develop complications. Long-term follow-up up to five years after surgery is acceptable in octogenarians with low surgical risk.

Antiviral Action against SARS-CoV-2 of a Synthetic Peptide Based on a Novel Defensin Present in the Transcriptome of the Fire Salamander (Salamandra salamandra)

The potential emergence of zoonotic diseases has raised significant concerns, particularly in light of the recent pandemic, emphasizing the urgent need for scientific preparedness. The bioprospection and characterization of new molecules are strategically relevant to the research and development of innovative drugs for viral and bacterial treatment and disease management. Amphibian species possess a diverse array of compounds, including antimicrobial peptides. This study identified the first bioactive peptide from Salamandra salamandra in a transcriptome analysis. The synthetic peptide sequence, which belongs to the defensin family, was characterized through MALDI TOF/TOF mass spectrometry. Molecular docking assays hypothesized the interaction between the identified peptide and the active binding site of the spike WT RBD/hACE2 complex. Although additional studies are required, the preliminary evaluation of the antiviral potential of synthetic SS-I was conducted through an in vitro cell-based SARS-CoV-2 infection assay. Additionally, the cytotoxic and hemolytic effects of the synthesized peptide were assessed. These preliminary findings highlighted the potential of SS-I as a chemical scaffold for drug development against COVID-19, hindering viral infection. The peptide demonstrated hemolytic activity while not exhibiting cytotoxicity at the antiviral concentration.

Acute Hepatitis E-Associated Guillain-Barré Syndrome

Guillain-Barré syndrome (GBS) is a rare autoimmune disorder of the peripheral nervous system that causes progressive weakness and sensory disturbances, usually following an infection or immunization. It has been associated with multiple causes, including bacterial and viral infections. Hepatitis E virus (HEV) is a common cause of acute viral hepatitis that can rarely develop neurological complications. We report a case of a 72-year-old man who developed GBS secondary to an acute HEV infection. He presented with numbness and weakness of the lower limbs that rapidly evolved into respiratory failure requiring mechanical ventilation and intravenous immunoglobulin therapy (IVIg). This case adds to the literature on the association between HEV infection and GBS and the importance of early detection of this rapidly progressive condition.

Polyphenol Composition by HPLC-DAD-(ESI-)MS/MS and Bioactivities of Extracts from Grape Agri-Food Wastes

BACKGROUND

Grape agri-food wastes, such as skin, seeds, and other discarded by-products, contain phytochemical compounds that offer potential health benefits.

METHODS

This study aimed to investigate the polyphenol composition and bioactivities of different extracts obtained from grape marc and seeds, with the goal of exploring their potential for application as natural food additives.

RESULTS

Regardless of the extraction method used (dynamic maceration, ultrasound-assisted extraction (UAE), and microwave-assisted extraction (MAE)), all extracts exhibited relatively high concentrations of phenolic compounds. The chemical characterization of the extracts revealed the presence of specific compounds and chemical groups associated with each extraction methodology. Moreover, the extracts displayed satisfactory antioxidant activities, especially in inhibiting lipoperoxidation as assessed by the TBARS assay. Additionally, the extracts demonstrated effective inhibition against different strains of bacteria and fungi known as food contaminants. Taken together, these findings indicate that those extracts have the potential to be tested as natural antioxidants and preservatives with sustainable origins in food and beverage systems. Among the extraction methods evaluated, traditional maceration and UAE provided extracts with the highest antioxidant and antimicrobial activities.

CONCLUSIONS

Our results suggest the opportunity to explore grape marc and seeds discarded by the winery industry in Portugal as natural sources of bioactive compounds, which could be employed as functional food ingredients or technological additives. The valorization of grape biowastes offers a promising strategy to reduce waste and harness their potential health benefits.

Unveiling LoRa's Oceanic Reach: Assessing the Coverage of the Azores LoRaWAN Network from an Island

In maritime settings, effective communication between vessels and land infrastructure is crucial, but existing technologies often prove impractical for energy-sensitive IoT applications, like deploying sensors at sea. In this study, we explore the viability of a low-power, cost-effective wireless communication solution for maritime sensing data. Specifically, we conduct an experimental assessment of the Azorean Long Range Wide Area Network (LoRaWAN) coverage. Our tests involve positioning the gateway at the island's highest point and installing end nodes on medium-sized fishing vessels. Through measurements of received signal strength indicator (RSSI), signal-to-noise ratio (SNR), and lines of sight (LOS), we showcase the potential of LoRaWAN transmissions to achieve communication distances exceeding 130 km in a LOS-free scenario over the ocean. These findings highlight the promising capabilities of LoRaWAN for reliable and long-range maritime communication of sensing data.

Non-News Websites Expose People to More Political Content Than News Websites: Evidence from Browsing Data in Three Countries

Most scholars focus on the prevalence and democratic effects of (partisan) news exposure. This focus misses large parts of online activities of a majority of politically disinterested citizens. Although political content also appears outside of news outlets and may profoundly shape public opinion, its prevalence and effects are under-studied at scale. This project combines three-wave panel survey data from three countries (total N = 7,266) with online behavioral data from the same participants (over 106M visits). We create a multi-lingual classifier to identify political content both in news and outside (e.g. in shopping or entertainment sites). We find that news consumption is infrequent: just 3.4% of participants' online browsing comprised visits to news sites. Only between 14% (NL) and 36% (US) of these visits were to news about politics. The overwhelming majority of participants' visits were to non-news sites. Although only 1.6\% of those visits related to politics, in absolute terms, citizens encounter politics more frequently outside of news than within news. Out of every 10 visits to political content, 3.4 come from news and 6.6 from non-news sites. Furthermore, exposure to political content outside news domains had the same - and in some cases stronger - associations with key democratic attitudes and behaviors as news exposure. These findings offer a comprehensive analysis of the online political (not solely news) ecosystem and demonstrate the importance of assessing the prevalence and effects of political content in non-news sources.

Chemical and Bioactive Screening of Green Polyphenol-Rich Extracts from Chestnut By-Products: An Approach to Guide the Sustainable Production of High-Added Value Ingredients

Opportunities for the valorisation of agro-industrial residues of the chestnut (Castanea sativa Mill.) production chain have been fostered with the production of multifunctional polyphenol-rich extracts with the potential to be introduced as natural additives or active components in several products. Nonetheless, it is crucial to explore the feasibility of different extracts from the various by-products for these applications through the exhaustive study of their composition and bioactivities without losing sight of the sustainable character of the process. This work aimed at the screening of the phenolic compound composition and bioactivities of different green extracts of chestnut burs, shells and leaves, as the first step to establish their potential application as natural ingredients, primarily as food preservatives. To this end, maceration (MAC) as a conventional extraction method besides ultrasound and microwave-assisted extractions (UAE and MAE) was employed to obtain the extracts from chestnut by-products using water (W) and hydroethanolic solution (HE) as solvents. Phenolic compounds were analysed by HPLC-DAD-(ESI-)MS/MS; the antioxidant capacity was assessed by colourimetric assays, and the antimicrobial activity was evaluated against several strains of food-borne bacteria and fungi. The leaf extracts obtained by MAC-HE and UAE-HE presented the highest concentration of phenolic compounds (70.92 ± 2.72 and 53.97 ± 2.41 mg.g^-1 extract dw, respectively), whereas, for burs and shells, the highest recovery of total phenolic compounds was achieved by using UAE-HE and UAE-W (36.87 ± 1.09 and 23.03 ± 0.26 mg.g^-1 extract dw, respectively). Bis-HHDP-glucose isomers, chestanin and gallic acid were among the most abundant compounds. Bur extracts (MAC-HE and UAE-HE) generally presented the highest antioxidant capacity as measured by TBARS, while the best results in DPPH and reducing power assays were found for shell extracts (MAE-W and MAC-HE). Promising antibacterial activity was noticed for the aqueous extracts of burs, leaves and hydroethanolic extracts of shells, with emphasis on the MAE-W extract of burs that showed bactericidal activity against E. cloacae, P. aeruginosa and S. aureus (MBC 5 mg.mL^-1). Overall, it can be concluded that chestnut by-products, including burs, shells and leaves, are sources of polyphenolic compounds with significant antioxidant and antimicrobial activities. The choice of extraction method and solvent greatly influenced the composition and bioactivity of the extracts. These findings highlight the potential of chestnut by-products for the development of natural additives, particularly for food preservation, while also emphasizing the importance of sustainable utilization of agricultural waste materials. Further research is warranted to optimize extraction techniques and explore additional applications for these valuable bioactive compounds.

Congenital adrenal hyperplasia with a CYP21A2 deletion overlapping the tenascin-X gene: an atypical presentation

OBJECTIVES

Congenital Adrenal Hyperplasia (CAH) is a group of genetic diseases characterized by impaired cortisol biosynthesis. 95% of CAH cases result from mutation in the CYP21A2 gene encoding 21-hydroxilase. TNX-B gene partially overlaps CYP21A2 and encodes a matrix protein called Tenascin-X (TNX). Complete tenascin deficiency causes Enlers-Danlos syndrome (EDS). A mono allelic variant called CAH-X CH-1 was recently described, resulting from a CYP21A2 complete deletion that extends into the TNXB. This haploinsufficiency of TNX may be associated with a mild hypermobility form of EDS, as well as other connective tissue comorbidities such as hernia, cardiac defects and chronic arthralgia.

CASE PRESENTATION

We report four patients heterozygous for a CAH-X CH-1 allele that do not present clinical manifestations of the EDS.

CONCLUSIONS

All CAH patients, carriers of these TNXA/TNXB chimeras, should be evaluated for clinical manifestations related to connective tissue hypermobility, cardiac abnormalities and other EDS features, allowing for better clinical surveillance management.

Diverse monogenic subforms of human spermatogenic failure

Non-obstructive azoospermia (NOA) is the most severe form of male infertility and typically incurable. Defining the genetic basis of NOA has proven challenging, and the most advanced classification of NOA subforms is not based on genetics, but simple description of testis histology. In this study, we exome-sequenced over 1000 clinically diagnosed NOA cases and identified a plausible recessive Mendelian cause in 20%. We find further support for 21 genes in a 2-stage burden test with 2072 cases and 11,587 fertile controls. The disrupted genes are primarily on the autosomes, enriched for undescribed human "knockouts", and, for the most part, have yet to be linked to a Mendelian trait. Integration with single-cell RNA sequencing data shows that azoospermia genes can be grouped into molecular subforms with synchronized expression patterns, and analogs of these subforms exist in mice. This analysis framework identifies groups of genes with known roles in spermatogenesis but also reveals unrecognized subforms, such as a set of genes expressed across mitotic divisions of differentiating spermatogonia. Our findings highlight NOA as an understudied Mendelian disorder and provide a conceptual structure for organizing the complex genetics of male infertility, which may provide a rational basis for disease classification.

Contribution of TEX15 genetic variants to the risk of developing severe non-obstructive oligozoospermia

Background: Severe spermatogenic failure (SPGF) represents one of the most relevant causes of male infertility. This pathological condition can lead to extreme abnormalities in the seminal sperm count, such as severe oligozoospermia (SO) or non-obstructive azoospermia (NOA). Most cases of SPGF have an unknown aetiology, and it is known that this idiopathic form of male infertility represents a complex condition. In this study, we aimed to evaluate whether common genetic variation in TEX15, which encodes a key player in spermatogenesis, is involved in the susceptibility to idiopathic SPGF. Materials and Methods: We designed a genetic association study comprising a total of 727 SPGF cases (including 527 NOA and 200 SO) and 1,058 unaffected men from the Iberian Peninsula. Following a tagging strategy, three tag single-nucleotide polymorphisms (SNPs) of TEX15 (rs1362912, rs323342, and rs323346) were selected for genotyping using TaqMan probes. Case-control association tests were then performed by logistic regression models. In silico analyses were also carried out to shed light into the putative functional implications of the studied variants. Results: A significant increase in TEX15-rs1362912 minor allele frequency (MAF) was observed in the group of SO patients (MAF = 0.0842) compared to either the control cohort (MAF = 0.0468, OR = 1.90, p = 7.47E-03) or the NOA group (MAF = 0.0472, OR = 1.83, p = 1.23E-02). The genotype distribution of the SO population was also different from those of both control (p = 1.14E-02) and NOA groups (p = 4.33-02). The analysis of functional annotations of the human genome suggested that the effect of the SO-associated TEX15 variants is likely exerted by alteration of the binding affinity of crucial transcription factors for spermatogenesis. Conclusion: Our results suggest that common variation in TEX15 is involved in the genetic predisposition to SO, thus supporting the notion of idiopathic SPGF as a complex trait.

Sutureless bioprosthesis for aortic valve replacement: Surgical and clinical outcomes

BACKGROUND

Aortic valve stenosis is the most common adult valve disease in industrialized countries. The aging population and the increase in comorbidities urge the development of safer alternatives to the current surgical treatment. Sutureless bioprosthesis has shown promising results, especially in complex procedures and in patients requiring concomitant surgeries.

OBJECTIVES

Assess the clinical and hemodynamic performance, safety, and durability of the Perceval® prosthetic valve.

METHODS

This single-center retrospective longitudinal cohort study collected data from all adult patients with aortic valve disease who underwent aortic valve replacement with a Perceval® prosthetic valve between February 2015 and October 2020. Of the 196 patients included (mean age 77.20 ± 5.08 years; 45.4% female; mean EuroSCORE II 2.91 ± 2.20%), the majority had aortic stenosis.

RESULTS

Overall mean cross-clamp and cardiopulmonary bypass times were 33.31 ± 14.09 min and 45.55 ± 19.04 min, respectively. Mean intensive care unit and hospital stay were 3.32 ± 3.24 days and 7.70 ± 5.82 days, respectively. Procedural success was 98.99%, as two explants occurred. Four valves were reimplanted due to intraoperative misplacement. Mean transvalvular gradients were 7.82 ± 3.62 mmHg. Pacemaker implantation occurred in 12.8% of patients, new-onset atrial fibrillation in 21.9% and renal replacement support was necessary for 3.1%. Early mortality was 2.0%. We report no structural valve deterioration, strokes, or endocarditis, and one successfully treated valve thrombosis.

CONCLUSIONS

Our study confirms the excellent clinical and hemodynamic performance and safety of a truly sutureless aortic valve, up to a 5-year follow-up. These results were consistent in isolated and concomitant interventions, solidifying this device as a viable option for the treatment of isolated aortic valve disease.

Towards personalized antibody cancer therapy: development of a microfluidic cell culture device for antibody selection

Antibody therapy has been one of the most successful therapies for a wide range of diseases, including cancer. One way of expediting antibody therapy development is through phage display technology. Here, by screening thousands of randomly assembled peptide sequences, it is possible to identify potential therapeutic candidates. Conventional screening technologies do not accommodate perfusion through the system, as is the case of standard plate-based cultures. This leads to a poor translation of the experimental results obtained in vitro when moving to a more physiologically relevant setting, such as the case of preclinical animal models or clinical trials. Microfluidics is a technology that can improve screening efficacy by replicating more physiologically relevant conditions such as shear stress. In this work, a polydimethylsiloxane/polystyrene-based microfluidic system for a continuously perfused culture of cancer cells is reported. Human colorectal adenocarcinoma cells (HCT116) expressing CXCR4 were used as a cell target. Fluorescently labeled M13 phages anti-CXCR4 were used to study the efficiency of the microfluidic system as a tool to study the binding kinetics of the engineered bacteriophages. Using our microfluidic platform, we estimated a dissociation constant of 0.45 pM for the engineered phage. Additionally, a receptor internalization assay was developed using SDF-1α to verify phage specificity to the CXCR4 receptor. Upon receptor internalization there was a signal reduction, proving that the anti-CXCR4 fluorescently labelled M13 phages bound specifically to the CXCR4 receptor. The simplicity and ease of use of the microfluidic device design presented in this work can form the basis of a generic platform that facilitates the study and optimization of therapies based on interaction with biological entities such as mammalian cells.

Mycotic Pseudoaneurysm of the Aortic Arch

A 59 year-old male presents with fever and left parasternal pain. Past medical history included arterial hypertension, dyslipidemia, smoking, obesity. His clinical exam was unremarkable. Both C-reactive protein and leucocytes were elevated. Chest computed tomography (CT) demonstrated a 18mm saccular pseudoaneurysm of the aortic arch with extensive adjacent densification and adenopathy (Figure 1 and 2). Methicillin-sensible Staphylococcus aureus was isolated from blood cultures. A transesophageal echocardiogram excluded endocarditis. Control Angio-CT after seven days showed a contained rupture and increase in diameter of the pseudoaneurysm. He underwent emergent surgery with circulatory arrest and anterograde cerebral perfusion; extensive resection of the pseudoaneurysmal aorta was performed, with reconstruction of the aortic arch using autologous pericardium, without implantation of foreign or synthetic material (Figure 3 and 4). He completed 4 weeks of Flucloxacillin IV, having been discharged under oral antibiotics.

Imaging of intraspinal cystic lesions: A review

Several distinct conditions present as cystic or pseudocystic lesions within the spinal canal. Some of the most common spinal cystic lesions include spinal meningeal cysts, juxtafacet cysts, dermoid/epidermoid cysts, nerve sheath tumors, and syringohydromyelia. Clinical presentation is usually nonspecific and imaging characteristics are frequently overlapping, which may pose a challenging presurgical diagnosis. We provide a pictorial review of cystic intraspinal lesions and discuss the main imaging features that can aid the neuroradiologist in the differential diagnosis. First, we propose a categorization of the lesions according to their location as extradural, intradural extramedullary, and intramedullary. This is a crucial initial step in the diagnostic workup and surgical planning. Second, for each of these locations, we organize the lesions according to their etiology: congenital and developmental disorders, degenerative disorders, traumatic or postsurgical collections, infectious conditions, neoplastic lesions, and other miscellaneous disorders. Finally, we summarize the clinical highlights and MR features that provide important insights for the differential diagnosis. MR is the technique of choice in presurgical evaluation and postsurgery follow-up. It provides accurate lesion localization and characterization and, most of the times, it will allow a confident differential diagnosis. High-resolution three-dimensional T2-weighted sequences and diffusion-weighted imaging can provide important hints in specific cases. Signal correlation with T1-weighted and fat-saturated sequences allows to differentiate true cystic lesions from hemorrhage or fat tissue.

Decavanadate and metformin-decavanadate effects in human melanoma cells

Decavanadate is a polyoxometalate (POMs) that has shown extensive biological activities, including antidiabetic and anticancer activity. Importantly, vanadium-based compounds as well as antidiabetic biguanide drugs, such as metformin, have shown to exert therapeutic effects in melanoma. A combination of these agents, the metformin-decavanadate complex, was also recognized for its antidiabetic effects and recently described as a better treatment than the monotherapy with metformin enabling lower dosage in rodent models of diabetes. Herein, we compare the effects of decavanadate and metformin-decavanadate on Ca²⁺-ATPase activity in sarcoplasmic reticulum vesicles from rabbit skeletal muscles and on cell signaling events and viability in human melanoma cells. We show that unlike the decavanadate-mediated non-competitive mechanism, metformin-decavanadate inhibits Ca²⁺-ATPase by a mixed-type competitive-non-competitive inhibition with an IC₅₀ value about 6 times higher (87 μM) than the previously described for decavanadate (15 μM). We also found that both decavanadate and metformin-decavanadate exert antiproliferative effects on melanoma cells at 10 times lower concentrations than monomeric vanadate. Western blot analysis revealed that both, decavanadate and metformin-decavanadate increased phosphorylation of extracellular signal-regulated kinase (ERK) and serine/threonine protein kinase AKT signaling proteins upon 24 h drug exposure, suggesting that the anti-proliferative activities of these compounds act independent of growth-factor signaling pathways.

P-538 KATNAL1 polymorphisms confer susceptibility to severe phenotypes of male infertility in a large European cohort

Study question

What is the contribution of the common variation of KATNAL1 to the development of severe spermatogenic failure (SPGF) in a phenotypically well-characterized cohort?

Summary answer

An allelic combination of KATNAL1 single-nucleotide polymorphisms (SNPs) increases the risk to develop SPGF, likely by altering the expression and splicing pattern of the gene.

What is known already

Spermatogenesis is a process that requires an exhaustive control of gene expression, and subtle alterations of its molecular regulatory network can lead to male infertility. The aetiology of most SPGF cases remains unknown, and increasing evidence clearly suggests that the idiopathic form of SPGF represents a complex trait, in which genetic susceptibility is conferred by the accumulation of risk alleles in genetically predisposed men. In this regard, previous studies reported that rare genetic mutations and polymorphisms in the KATNAL1 locus lead to male infertility through the disruption of microtubule remodelling and premature germ cell exfoliation.

Study design, size, duration

We designed a case-control genetic association study including three SNPs (rs2077011, rs7338931, and rs2149971) in the 3' and 5' regulatory regions of KATNAL1, which tagged the common genetic variability in the region. The allele frequencies in the study population, composed of 715 infertile men diagnosed with idiopathic SPGF, were compared to those observed in a control group comprising 1058 fertile men from Spain and Portugal.

Participants/materials, setting, methods

The SPGF group comprised 210 men with severe oligospermia (SO) and 505 with non-obstructive azoospermia (NOA). The latter were phenotypically characterised according to the histological examination of testis biopsies and its outcome (Sertoli cell-only syndrome, SCO; maturation arrest, MA; hypospermatogenesis, HS; and testicular sperm extraction, TESE). After genotyping, case-control association analyses by logistic regression were conducted. In silico functional characterization of risk variants was also carried out using public multiomic databases and bioinformatic tools.

Main results and the role of chance

Significant genetic associations with different SPGF patterns and/or TESE outcome were observed even after correction for multiple testing when independent SNP models were tested. However, in all cases, the haplotype model including the three risk alleles (rs2077011*C | rs7338931*T | rs2149971*A) was the most informative. This haplotype was specifically over-represented in the SPGF group (P = 3.45E-02, OR = 2.33), which includes all infertile men, and in the NOA group (P = 8.22E-03, OR = 2.97). In addition, subtype-specific associations were observed with the most severe subgroups, namely MA (P = 2.44E-02, OR = 5.00), SCO (P = 4.03E-03, OR = 5.16), and unsuccessful TESE outcome (P = 2.22E-04, OR = 6.13), which indicates the relevant role of KATNAL1 in spermatogenesis development. We prioritized the most likely causal variant/s based on in silico analyses addressing the possible functional implication of the tagged variants. We observed that an alteration of the KATNAL1 splicing pattern, by favouring the overrepresentation of a short non-functional transcript isoform in the testis, might be the cause behind the observed genetic association. The analysis of the testis transcriptome at the single cell level showed that KATNAL1 transcripts were mostly presented in spermatocytes and early spermatids at puberty, which correlates with its effect of premature exfoliation and loss of the germ cells.

Limitations, reasons for caution

Although a previous low-powered study reported suggestive associations between KATNAL1 and SPGF, additional genetic association studies in independent populations should be conducted to confirm our findings. Moreover, the statistical power for the overall analysis was appropriate, but the subphenotype analyses were performed with reduced power due to smaller study groups.

Wider implications of the findings

Our results suggest a relevant role of the common genetic variation of KATNAL1 in the susceptibility to develop the most severe histological phenotypes of NOA (i.e., SCO and MA). Studies like the one presented here may definitively help to develop future non-invasive molecular markers of TESE success.

Trial registration number

Not Applicable

P-536 Common variation in the PIN1 locus increases the genetic risk to suffer from Sertoli Cell Only syndrome

Study question

Are the common genetic variants located in the PIN1 region associated with human male infertility due to severe spermatogenic failure (SPGF)?

Summary answer

PIN1 gene polymorphisms may play a relevant role in the development of Sertoli Cell Only syndrome (SCO), the most extreme form of SPGF.

What is known already

PIN1 is a relevant prolyl isomerase in humans, that catalyzes cis/trans isomerization of peptide bonds. It has a central role in cell cycle progression and cancer, and it has been linked to the immune system promoting inflammation and reactive-oxygen species. Pin1 gene is highly expressed in adult mice testes, particularly in spermatogonia and Sertoli cells, and it is required to control the proliferation of spermatogonial stem cells. Additionally, it controls the integrity of the blood-testis barrier, helping to maintain the immune privilege of the testis. Nevertheless, mutations in PIN1 have not yet been described in human male infertility cases.

Study design, size, duration

A genetic association study was performed including samples from 715 men diagnosed with SPGF and classified as suffering from non-obstructive azoospermia (NOA, n = 505) or severe oligospermia (SO, n = 210), and 1,058 matched unaffected male controls from the Iberian Peninsula (Spain and Portugal). Allelic association on SPGF susceptibility were evaluated by testing three PIN1 single nucleotide polymorphisms (SNPs; rs2287839, rs2233678, and rs62105751), which tagged most of the common genetic variation present in this locus.

Participants/materials, setting, methods

Participants signed an informed written consent approved by the ethical committees of each participating center. SO and NOA were clinically defined according to the guidelines of the World Health Organization. Genomic DNA from blood samples was genotyped using TaqMan assays and statistical analyses were carried out by the means of logistic regression models. An in silico functional prioritization of the associated variants and their linked polymorphisms was also performed.

Main results and the role of chance

A subtype-specific genetic association with the subset of NOA patients classified as suffering from SCO was identified for the three analyzed genetic variants under the additive model (rs2287839: P = 1.94E-02, rs2233678: P = 1.94E-02, rs62105751: P = 1.94E-02). The minor alleles showed strong risk effects for this subset (rs2287839: OR = 1.85 [1.17-2.93], rs2233678: OR = 1.62 [1.11-2.36], rs62105751: OR = 1.43 [1.06-1.93]). Dependence analysis showed that all associated variants tagged the same signal. The variants underlying the identified association signal were prioritized based on their functional impact on the PIN1 locus, being rs3810166 the most likely candidate for functionality. The minor allele of such variant (G) is in linkage disequilibrium with the observed rs2287839-G risk allele and it is predicted to affect both gene expression and isoform balance of PIN1. The rs3810166 SNP likely influences the binding affinity of both HDAC2 and NRSF transcription factors, which are involved in cell cycle progression and transcription, respectively. Moreover, the tagged variants rs28802413 and rs10425775 were also predicted to alter the binding of significant transcription factors of the spermatogenic process, such as SIN3A and NANOG.

Limitations, reasons for caution

Although the overall statistical power of the study cohort was appropriate to detect the expected effects, the sample sizes in the subtype analyses were considerably lower, which may influence the obtained results. Further analyses including a larger SCO cohort should be performed to confirm our findings.

Wider implications of the findings

The obtained results shed light into the genetic contribution of common variation to male infertility, which may contribute to design a future panel of genetic markers to predict the testicular sperm extraction outcome, avoiding surgical interventions in NOA cases in which the probability of spermatozoa finding is much reduced.

Trial registration number

Not applicable

Common genetic variation in KATNAL1 non-coding regions is involved in the susceptibility to severe phenotypes of male infertility

Background

Previous studies in animal models evidenced that genetic mutations of KATNAL1, resulting in dysfunction of its encoded protein, lead to male infertility through disruption of microtubule remodelling and premature germ cell exfoliation. Subsequent studies in humans also suggested a possible role of KATNAL1 single‐nucleotide polymorphisms in the development of male infertility as a consequence of severe spermatogenic failure.

Objectives

The main objective of the present study is to evaluate the effect of the common genetic variation of KATNAL1 in a large and phenotypically well‐characterised cohort of infertile men because of severe spermatogenic failure.

Materials and methods

A total of 715 infertile men because of severe spermatogenic failure, including 210 severe oligospermia and 505 non‐obstructive azoospermia patients, as well as 1058 unaffected controls were genotyped for three KATNAL1 single‐nucleotide polymorphism taggers (rs2077011, rs7338931 and rs2149971). Case–control association analyses by logistic regression assuming different models and in silico functional characterisation of risk variants were conducted.

Results

Genetic associations were observed between the three analysed taggers and different severe spermatogenic failure groups. However, in all cases, the haplotype model (rs2077011*C | rs7338931*T | rs2149971*A) better explained the observed associations than the three risk alleles independently. This haplotype was associated with non‐obstructive azoospermia (adjusted p = 4.96E‐02, odds ratio = 2.97), Sertoli‐cell only syndrome (adjusted p = 2.83E‐02, odds ratio = 5.16) and testicular sperm extraction unsuccessful outcomes (adjusted p = 8.99E‐04, odds ratio = 6.13). The in silico analyses indicated that the effect on severe spermatogenic failure predisposition could be because of an alteration of the KATNAL1 splicing pattern.

Conclusions

Specific allelic combinations of KATNAL1 genetic polymorphisms may confer a risk of developing severe male infertility phenotypes by favouring the overrepresentation of a short non‐functional transcript isoform in the testis.

Multiple Lines of Ecological Evidence Support Ancient Contact Between the African Wild Dog and the Dhole

Genomic tools have greatly enhanced our ability to uncover ancient interspecific gene flow, including cases involving allopatric lineages and/or lineages that have gone extinct. Recently, a genomic analysis revealed the unexpected gene flow between the African wild dog (Lycaon pictus) and the dhole (Cuon alpinus). The two species have currently highly disjunct and patchy distributions in Africa and Asia, respectively, which are remnants of a much wider past distribution. Yet, no reported evidence of their past contact has ever been documented. By hindcasting the past potential distribution of both species during the Last Glacial Maximum and the Last Interglacial, validating paleoclimatic reconstructions with fossil evidence, quantifying the intersection of their bioclimatic niches, and assessing interspecific compatibility, we investigate the location and favorable conditions for such contact and its ecological validity. We were able to identify the Levant region in Eastern Mediterranean during the Last Interglacial as the most suitable spatio-ecological context for the co-occurrence of the two canids, and to provide evidence of a highly significant overlap of the African wild dog niche with the wider niche of the dhole. These results, combined with ecologic traits, including key compatibility features such as cooperative breeding and hunting, provide consistent support for the potential co-occurrence of both canids. We suggest that the ranges of these canids came into contact multiple times during periods resembling the Last Interglacial, eventually facilitating gene flow between the African wild dog and the dhole in their post-divergence history. Our results are highly supportive of the key role of the Levant region in providing connectivity between African and Eurasian faunas and provide further impetus to combine different tools and approaches in advancing the understanding of species evolutionary histories.

Actionable secondary findings following exome sequencing of 836 non-obstructive azoospermia cases and their value in patient management

STUDY QUESTION

What is the load, distribution and added clinical value of secondary findings (SFs) identified in exome sequencing (ES) of patients with non-obstructive azoospermia (NOA)?

SUMMARY ANSWER

One in 28 NOA cases carried an identifiable, medically actionable SF.

WHAT IS KNOWN ALREADY

In addition to molecular diagnostics, ES allows assessment of clinically actionable disease-related gene variants that are not connected to the patient's primary diagnosis, but the knowledge of which may allow the prevention, delay or amelioration of late-onset monogenic conditions. Data on SFs in specific clinical patient groups, including reproductive failure, are currently limited.

STUDY DESIGN, SIZE, DURATION

The study group was a retrospective cohort of patients with NOA recruited in 10 clinics across six countries and formed in the framework of the international GEMINI (The GEnetics of Male INfertility Initiative) study.

PARTICIPANTS/MATERIALS, SETTING, METHODS

ES data of 836 patients with NOA were exploited to analyze SFs in 85 genes recommended by the American College of Medical Genetics and Genomics (ACMG), Geisinger's MyCode, and Clinical Genome Resource. The identified 6374 exonic variants were annotated with ANNOVAR and filtered for allele frequency, retaining 1381 rare or novel missense and loss-of-function variants. After automatic assessment of pathogenicity with ClinVar and InterVar, 87 variants were manually curated. The final list of confident disease-causing SFs was communicated to the corresponding GEMINI centers. When patient consent had been given, available family health history and non-andrological medical data were retrospectively assessed.

MAIN RESULTS AND THE ROLE OF CHANCE

We found a 3.6% total frequency of SFs, 3.3% from the 59 ACMG SF v2.0 genes. One in 70 patients carried SFs in genes linked to familial cancer syndromes, whereas 1 in 60 cases was predisposed to congenital heart disease or other cardiovascular conditions. Retrospective assessment confirmed clinico-molecular diagnoses in several cases. Notably, 37% (11/30) of patients with SFs carried variants in genes linked to male infertility in mice, suggesting that some SFs may have a co-contributing role in spermatogenic impairment. Further studies are needed to determine whether these observations represent chance findings or the profile of SFs in NOA patients is indeed different from the general population.

LIMITATIONS, REASONS FOR CAUTION

One limitation of our cohort was the low proportion of non-Caucasian ethnicities (9%). Additionally, as comprehensive clinical data were not available retrospectively for all men with SFs, we were not able to confirm a clinico-molecular diagnosis and assess the penetrance of the specific variants.

WIDER IMPLICATIONS OF THE FINDINGS

For the first time, this study analyzed medically actionable SFs in men with spermatogenic failure. With the evolving process to incorporate ES into routine andrology practice for molecular diagnostic purposes, additional assessment of SFs can inform about future significant health concerns for infertility patients. Timely detection of SFs and respective genetic counseling will broaden options for disease prevention and early treatment, as well as inform choices and opportunities regarding family planning. A notable fraction of SFs was detected in genes implicated in maintaining genome integrity, essential in both mitosis and meiosis. Thus, potential genetic pleiotropy may exist between certain adult-onset monogenic diseases and NOA.

STUDY FUNDING/COMPETING INTEREST(S)

This work was supported by the Estonian Research Council grants IUT34-12 and PRG1021 (M.L. and M.P.); National Institutes of Health of the United States of America grant R01HD078641 (D.F.C., K.I.A. and P.N.S.); National Institutes of Health of the United States of America grant P50HD096723 (D.F.C. and P.N.S.); National Health and Medical Research Council of Australia grant APP1120356 (M.K.O'B., D.F.C. and K.I.A.); Fundação para a Ciência e a Tecnologia (FCT)/Ministério da Ciência, Tecnologia e Inovação grant POCI-01-0145-FEDER-007274 (A.M.L., F.C. and J.G.) and FCT: IF/01262/2014 (A.M.L.). J.G. was partially funded by FCT/Ministério da Ciência, Tecnologia e Ensino Superior (MCTES), through the Centre for Toxicogenomics and Human Health-ToxOmics (grants UID/BIM/00009/2016 and UIDB/00009/2020). M.L.E. is a consultant for, and holds stock in, Roman, Sandstone, Dadi, Hannah, Underdog and has received funding from NIH/NICHD. Co-authors L.K., K.L., L.N., K.I.A., P.N.S., J.G., F.C., D.M.-M., K.A., K.A.J., M.K.O'B., A.M.L., D.F.C., M.P. and M.L. declare no conflict of interest.

TRIAL REGISTRATION NUMBER

N/A.

Accurate and rapid microfluidic ELISA to monitor Infliximab titers in patients with inflammatory bowel diseases

Inflammatory bowel disease (IBD) is a term used to describe disorders that involve chronic inflammation in the gastrointestinal tract, affecting more than 6.8 million people worldwide. Biological therapy is used in the most severe cases of IBD where anti-tumour necrosis factor-alpha (TNF-α) antibodies are the first choice for a biological treatment. When administrated to patients, these antibodies interact with TNF-α, usually overexpressed in these diseases, neutralizing its biological activity. Because of the chronic nature of these diseases, a recurring administration of the therapeutic antibodies is required, thus making therapy monitorization essential for the correct management of these diseases. The aim of this work is the development of an enzyme-linked immunosorbent assay (ELISA) microfluidic biosensor to quantify the therapeutic antibodies in IBD patient plasma samples, where the commercial monoclonal antibody Infliximab (IFX) is used as a model target. By providing a faster and more accurate measurement of IFX, the proposed method leads to improved therapy scheduling and a reduced risk of endogenous anti-drug antibodies (ADAs) reducing the efficacy of the treatment. The time needed between sample insertion and result output for the microfluidic ELISA (mELISA) is 24 minutes, drastically shorter than the time required by the conventional ELISA (cELISA). The mELISA presented in this work has a LoD of 0.026 μg mL^-1, while commercially available solutions provide a LoD of 0.15 μg mL^-1. Results acquired by the mELISA are highly correlated with the results obtained from the cELISA (r = 0.998; R² = 0.996; p < 0.0001), demonstrating the validity of the microfluidic approach for the quantification of IFX from patient plasma and its potential for use at the point-of-care (POC).

Transcriptome-Wide Off-Target Effects of Steric-Blocking Oligonucleotides

Steric-blocking oligonucleotides (SBOs) are short, single-stranded nucleic acids designed to modulate gene expression by binding to RNA transcripts and blocking access from cellular machinery such as splicing factors. SBOs have the potential to bind to near-complementary sites in the transcriptome, causing off-target effects. In this study, we used RNA-seq to evaluate the off-target differential splicing events of 81 SBOs and differential expression events of 46 SBOs. Our results suggest that differential splicing events are predominantly hybridization driven, whereas differential expression events are more common and driven by other mechanisms (including spurious experimental variation). We further evaluated the performance of in silico screens for off-target splicing events, and found an edit distance cutoff of three to result in a sensitivity of 14% and false discovery rate (FDR) of 99%. A machine learning model incorporating splicing predictions substantially improved the ability to prioritize low edit distance hits, increasing sensitivity from 4% to 26% at a fixed FDR of 90%. Despite these large improvements in performance, this approach does not detect the majority of events at an FDR <99%. Our results suggest that in silico methods are currently of limited use for predicting the off-target effects of SBOs, and experimental screening by RNA-seq should be the preferred approach.

APOBEC3B Potently Restricts HIV-2 but Not HIV-1 in a Vif-Dependent Manner

Vif is a lentiviral accessory protein that counteracts the antiviral activity of cellular APOBEC3 (A3) cytidine deaminases in infected cells. The exact contribution of each member of the A3 family for the restriction of HIV-2 is still unclear. Thus, the aim of this work was to identify the A3s with anti-HIV-2 activity and compare their restriction potential for HIV-2 and HIV-1. We found that A3G is a strong restriction factor of both types of viruses and A3C restricts neither HIV-1 nor HIV-2. Importantly, A3B exhibited potent antiviral activity against HIV-2, but its effect was negligible against HIV-1. Whereas A3B is packaged with similar efficiency into both viruses in the absence of Vif, HIV-2 and HIV-1 differ in their sensitivity to A3B. HIV-2 Vif targets A3B by reducing its cellular levels and inhibiting its packaging into virions, whereas HIV-1 Vif did not evolve to antagonize A3B. Our observations support the hypothesis that during wild-type HIV-1 and HIV-2 infections, both viruses are able to replicate in host cells expressing A3B but using different mechanisms, probably resulting from a Vif functional adaptation over evolutionary time. Our findings provide new insights into the differences between Vif protein and their cellular partners in the two human viruses. Of note, A3B is highly expressed in some cancer cells and may cause deamination-induced mutations in these cancers. Thus, A3B may represent an important therapeutic target. As such, the ability of HIV-2 Vif to induce A3B degradation could be an effective tool for cancer therapy. IMPORTANCE Primate lentiviruses encode a series of accessory genes that facilitate virus adaptation to its host. Among those, the vif-encoded protein functions primarily by targeting the APOBEC3 (A3) family of cytidine deaminases. All lentiviral Vif proteins have the ability to antagonize A3G; however, antagonizing other members of the A3 family is variable. Here, we report that HIV-2 Vif, unlike HIV-1 Vif, can induce degradation of A3B. Consequently, HIV-2 Vif but not HIV-1 Vif can inhibit the packaging of A3B. Interestingly, while A3B is packaged efficiently into the core of both HIV-1 and HIV-2 virions in the absence of Vif, it only affects the infectivity of HIV-2 particles. Thus, HIV-1 and HIV-2 have evolved two distinct mechanisms to antagonize the antiviral activity of A3B. Aside from its antiviral activity, A3B has been associated with mutations in some cancers. Degradation of A3B by HIV-2 Vif may be useful for cancer therapies.

Chirality and Magnetocaloricity in GdFeTeO6 as Compared to GdGaTeO6

GdFeTeO₆ and GdGaTeO₆ have been prepared and their structures refined by the Rietveld method. Both are superstructures of the rosiaite type (space group P3¯1c). Their thermodynamic properties have been investigated by means of magnetization M and specific heat C_p measurements, evidencing the formation of the long-range antiferromagnetic order at T_N = 2.4 K in the former compound and paramagnetic behavior down to 2 K in the latter compound. Large magnetocaloric effect allows considering GdFeTeO₆ for the magnetic refrigeration at liquid hydrogen stage. Density functional theory calculations produce estimations of leading Gd–Gd, Gd–Fe and Fe–Fe interactions suggesting unique chiral 120° magnetic structure of Fe³⁺ (S = 5/2) moments and Gd³⁺ (J = 7/2) moments rotating in opposite directions (clockwise/anticlockwise) within weakly coupled layers of the rosiaite type crystal structure.

SDM-CropProj - A model-assisted framework to forecast crop environmental suitability and fruit production

The effects of climate change (CC) will impact species ranges, and crops are no exception. Anticipating these changes through forecasting the environmentally suitable area of crops would help to reduce or mitigate the impact and adapt ecological and economic strategies. To forecast the CC effects on crops, we describe here a model-assisted framework (hereafter SDM-CropProj) that combines two modelling steps to be implemented in sequence: i) a multi-technique calibration process and ensemble-forecasting approach to predict the current and future environmental suitability of target crops; ii) a parsimonious univariate log-log linear model to relate the average total annual production to the current SDM-based suitable area. Different metrics for assessing the model's predictive performance showed that:•

Crop production is related to model-predicted suitable area, thus allowing to obtain future projections of total fruit production based on climate scenarios.

•

The SDM-CropProj framework can assess potential pathways and trends in annual production due to changes in the environmental suitability and the distribution of multiple crop varieties/types as a consequence of CC, offering insights to other areas and crop types.

O-118 New insight into the genetic contribution of common variants to the development of extreme phenotypes of unexplained male infertility: a multicenter genome-wide association study

Study question

What is the contribution of the common genetic variation to the development of unexplained male infertility due to severe spermatogenic failure (SPGF)?

Summary answer

Genetic polymorphisms of key immune and spermatogenesis loci are involved in the etiology of the most severe SPGF cases, defined by Sertoli cell-only (SCO) phenotype.

What is known already

Male infertility is a rising worldwide concern that affects millions of couples. Non-obstructive azoospermia (NOA) and severe oligospermia (SO) are two extreme manifestations characterized by SPGF. A genetic cause can be established in only around 20% of affected men, with the remaining cases being classified as otherwise unexplained. To date, the genome-wide association study (GWAS) strategy, although already successfully applied in several other complex traits and diseases, was less fruitful in studies that attempted to decipher the genetic component of unexplained SPGF, mainly due to both a lack of well-powered samples in different ancestries and limitations in study design.

Study design, size, duration

We designed a GWAS for unexplained male infertility due to SPGF including a total of 1,274 affected cases and 1,951 fertile controls from the Iberian Peninsula (Spain and Portugal) and Germany. Different biostatistics and bioinformatics approaches were used to evaluate the possible effect of single-nucleotide polymorphisms (SNPs) across the whole genome in the susceptibility to specific subtypes of unexplained SPGF.

Participants/materials, setting, methods

The case cohort comprised 502 SO and 772 NOA patients, who were subdivided according to histological phenotypes (SCO, maturation arrest, and hypospermatogenesis) and the outcome of testicular sperm extraction techniques (TESE) from testis biopsies. Genotyping was performed with the GSA platform (Illumina). After quality-control and genotype imputation, 6,539,982 SNPs remained for the analysis, which was performed by logistic regression models. The datasets went through a meta-analysis by the inverse variance weighted method under fixed effects.

Main results and the role of chance

Genetic associations with SCO at the genome-wide-level of significance were identified in the major histocompatibility (MHC) class II region (rs1136759, OR = 1.80, P = 1.32E-08) and in a regulatory region of chromosome 14 nearby the vaccinia-related kinase 1 (VRK1) gene (rs115054029, OR = 3.14, P = 4.37-08). VRK1 is a relevant proliferative factor for spermatogenesis that causes progressive loss of spermatogonia when disrupted in mouse models. The role of the MHC system in SCO susceptibility was comprehensively evaluated through a validated imputation method that infers classical MHC alleles and polymorphic amino acid positions. A serine at position 13 of the HLA-DRβ1 protein (defined by the risk allele of the lead variant rs1136759) explained most of the SCO association signals within the MHC class II region. This residue is located in the binding pocket of the HLA-DR molecule and interacts directly with the presented antigen. Interestingly, position 13 of HLA-DRβ1 is the most relevant risk amino acid position for a wide spectrum of immune-mediated disorders. The HLA-DRB1*13 haplotype (which includes the serine at position 13 and represents the strongest NOA-associated marker in Asians to date) was the strongest signal amongst the classical MHC alleles in our study cohort (OR = 1.93, P = 9.90E-07).

Limitations, reasons for caution

Although the statistical power for the overall analysis was appropriate, the subphenotype analyses performed had considerably lower counts, which may influence the identification of genetic variants conferring low to moderate risk effects. Independent studies in larger SCO study cohorts should be performed to confirm our findings.

Wider implications of the findings

The molecular mechanisms underlying unexplained SPGF are largely unknown. Our data suggest a relevant role of common genetic variation in the development of SCO, the most extreme histological phenotype of NOA. SCO is characterized by the loss of germ cells and, therefore, implies a considerably higher probability of unsuccessful TESE.

Trial registration number

N/A

Biosimilars in an era of rising oncology treatment options

New diagnostic technologies, including molecular profiling, have enabled advances in treatments of various cancers; this has significantly improved clinical outcomes, including overall survival. However, the high cost of biologic drugs may prevent patients from having access to optimal treatment. Introduction of lower priced biosimilar agents into the therapeutic armamentarium brings the potential to ease the burden on healthcare expenditure and facilitate better access to effective cancer treatments. Oncology biosimilars have shown comparable efficacy and safety based on clinical evidence and physicochemical quality data as well as in real-world settings. This paper aims to review changes in the management of oncology treatment and their implication with respect to biosimilars.

Effect and in silico characterization of genetic variants associated with severe spermatogenic disorders in a large Iberian cohort

BACKGROUND

Severe spermatogenic failure (SpF) represents the most extreme manifestation of male infertility, as it decreases drastically the semen quality leading to either severe oligospermia (SO, <5 million spermatozoa/mL semen) or non-obstructive azoospermia (NOA, complete lack of spermatozoa in the ejaculate without obstructive causes).

OBJECTIVES

The main objective of the present study is to analyze in the Iberian population the effect of 6 single-nucleotide polymorphisms (SNPs) previously associated with NOA in Han Chinese through genome-wide association studies (GWAS) and to establish their possible functional relevance in the development of specific SpF patterns.

MATERIALS AND METHODS

We genotyped 674 Iberian infertile men (including 480 NOA and 194 SO patients) and 1058 matched unaffected controls for the GWAS-associated variants PRMT6-rs12097821, PEX10-rs2477686, CDC42BPA-rs3000811, IL17A-rs13206743, ABLIM1-rs7099208, and SOX5-rs10842262. Their association with SpF, SO, NOA, and different NOA phenotypes was evaluated by logistic regression models, and their functional relevance was defined by comprehensive interrogation of public resources.

RESULTS

ABLIM1-rs7099208 was associated with SpF under both additive (OR = 0.86, p = 0.036) and dominant models (OR = 0.78, p = 0.026). The CDC42BPA-rs3000811 minor allele frequency was significantly increased in the subgroup of NOA patients showing maturation arrest (MA) of germ cells compared to the remaining NOA cases under the recessive model (OR = 4.45, p = 0.044). The PEX10-rs2477686 SNP was associated with a negative testicular sperm extraction (TESE) outcome under the additive model (OR = 1.32, p = 0.034). The analysis of functional annotations suggested that these variants affect the testis-specific expression of nearby genes and that lincRNA may play a role in SpF.

CONCLUSIONS

Our data support the association of three previously reported NOA risk variants in Asians (ABLIM1-rs7099208, CDC42BPA-rs3000811, and PEX10-rs2477686) with different manifestations of SpF in Iberians of European descent, likely by influencing gene expression and lincRNA deregulation.

CDKL kinase regulates the length of the ciliary proximal segment

Cilia are organelles found throughout most unicellular eukaryotes and different metazoan cell types. To accomplish their essential roles in cell motility, fluid flow, and signaling, cilia are divided into subcompartments with variable structures, compositions, and functions. How these specific subcompartments are built remains almost completely unexplored. Here, we show that C. elegans CDKL-1, related to the human CDKL kinase family (CDKL1/CDKL2/CDKL3/CDKL4/CDKL5), specifically controls the length of the proximal segment, a ciliary subdomain conserved in evolution from Tetrahymena motile cilia to C. elegans chemosensory, mammalian olfactory, and photoreceptor non-motile cilia. CDKL-1 associates with intraflagellar transport (IFT), influences the distribution of the IFT anterograde motors heterotrimeric kinesin-II and homodimeric OSM-3-kinesin/KIF17 in the proximal segment, and shifts the boundary between the proximal and distal segments (PS/DS boundary). CDKL-1 appears to function independently from several factors that influence cilium length, namely the kinases DYF-5 (mammalian CILK1/MAK) and NEKL-1 (NEK9), as well as the depolymerizing kinesins KLP-13 (KIF19) and KLP-7 (KIF2). However, a different kinase, DYF-18 (CCRK), is needed for the correct localization and function of CDKL-1 and similarly influences the length of the proximal segment. Loss of CDKL-1, which affects proximal segment length without impairing overall ciliary microtubule structural integrity, also impairs cilium-dependent processes, namely cGMP-signaling-dependent body length control and CO₂ avoidance. Collectively, our findings suggest that cilium length is regulated by various pathways and that the IFT-associated kinase CDKL-1 is essential for the construction of a specific ciliary compartment and contributes to development and sensory physiology.

Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals

BACKGROUND

In octocorals (Cnidaria Octocorallia), the functional relationship between host health and its symbiotic consortium has yet to be determined. Here, we employed comparative metagenomics to uncover the distinct functional and phylogenetic features of the microbiomes of healthy Eunicella gazella, Eunicella verrucosa, and Leptogorgia sarmentosa tissues, in contrast with the microbiomes found in seawater and sediments. We further explored how the octocoral microbiome shifts to a pathobiome state in E. gazella.

RESULTS

Multivariate analyses based on 16S rRNA genes, Clusters of Orthologous Groups of proteins (COGs), Protein families (Pfams), and secondary metabolite-biosynthetic gene clusters annotated from 20 Illumina-sequenced metagenomes each revealed separate clustering of the prokaryotic communities of healthy tissue samples of the three octocoral species from those of necrotic E. gazella tissue and surrounding environments. While the healthy octocoral microbiome was distinguished by so-far uncultivated Endozoicomonadaceae, Oceanospirillales, and Alteromonadales phylotypes in all host species, a pronounced increase of Flavobacteriaceae and Alphaproteobacteria, originating from seawater, was observed in necrotic E. gazella tissue. Increased abundances of eukaryotic-like proteins, exonucleases, restriction endonucleases, CRISPR/Cas proteins, and genes encoding for heat-shock proteins, inorganic ion transport, and iron storage distinguished the prokaryotic communities of healthy octocoral tissue regardless of the host species. An increase of arginase and nitric oxide reductase genes, observed in necrotic E. gazella tissues, suggests the existence of a mechanism for suppression of nitrite oxide production by which octocoral pathogens may overcome the host's immune system.

CONCLUSIONS

This is the first study to employ primer-less, shotgun metagenome sequencing to unveil the taxonomic, functional, and secondary metabolism features of prokaryotic communities in octocorals. Our analyses reveal that the octocoral microbiome is distinct from those of the environmental surroundings, is host genus (but not species) specific, and undergoes large, complex structural changes in the transition to the dysbiotic state. Host-symbiont recognition, abiotic-stress response, micronutrient acquisition, and an antiviral defense arsenal comprising multiple restriction endonucleases, CRISPR/Cas systems, and phage lysogenization regulators are signatures of prokaryotic communities in octocorals. We argue that these features collectively contribute to the stabilization of symbiosis in the octocoral holobiont and constitute beneficial traits that can guide future studies on coral reef conservation and microbiome therapy. Video Abstract.

LUZP1 and the tumor suppressor EPLIN modulate actin stability to restrict primary cilia formation

Cilia and flagella are microtubule-based cellular projections with important sensory and motility functions. Their absence or malfunction is associated with a growing number of human diseases collectively referred to as ciliopathies. However, the fundamental mechanisms underpinning cilia biogenesis and functions remain only partly understood. Here, we show that depleting LUZP1 or its interacting protein, EPLIN, increases the levels of MyosinVa at the centrosome and primary cilia formation. We further show that LUZP1 localizes to both actin filaments and the centrosome/basal body. Like EPLIN, LUZP1 is an actin-stabilizing protein that regulates actin dynamics, at least in part, by mobilizing ARP2 to the centrosomes. Both LUZP1 and EPLIN interact with known ciliogenesis and cilia-length regulators and as such represent novel players in actin-dependent centrosome to basal body conversion. Ciliogenesis deregulation caused by LUZP1 or EPLIN loss may thus contribute to the pathology of their associated disease states.

Challenges for Adoption of Integrated Pest Management (IPM): the Soybean Example

Soybean is considered one of today's most important crops. Planted on millions of hectares worldwide, the management of soybean pests usually requires large amounts of chemicals. However, a key component to meet the increasing demand for food due to the rapidly growing global population is protecting crops from pests while maintaining environmental quality through ecologically and economically sound integrated pest management (IPM) practices. Not only can IPM result in more profitable agriculture due to the reduction of pest control costs but also assures equitable, secure, sufficient, and stable flows of both food and ecosystem services. Despite those ecological and economic benefits, the vast areas of cultivated soybean as well as the convenience of spraying insecticides are encouraging the adoption of prophylactic pest control as a relatively inexpensive safeguard compared to IPM practices. Thus, in this forum, we discuss the reasons for soybean IPM not reaching its potential. We give examples of how we can revive this once successful pest management program with a focus on experiences in Brazil and the USA. We analyze IPM case studies to illustrate the need for growers to have easy and fast access to IPM information on its medium- and long-term benefits. Overall, this forum highlights the importance of IPM for agricultural sustainability including ecological and financial benefits.

Evaluation of Male Fertility-Associated Loci in a European Population of Patients with Severe Spermatogenic Impairment

Infertility is a growing concern in developed societies. Two extreme phenotypes of male infertility are non-obstructive azoospermia (NOA) and severe oligospermia (SO), which are characterized by severe spermatogenic failure (SpF). We designed a genetic association study comprising 725 Iberian infertile men as a consequence of SpF and 1058 unaffected controls to evaluate whether five single-nucleotide polymorphisms (SNPs), previously associated with reduced fertility in Hutterites, are also involved in the genetic susceptibility to idiopathic SpF and specific clinical entities. A significant difference in the allele frequencies of USP8-rs7174015 was observed under the recessive model between the NOA group and both the control group (p = 0.0226, OR = 1.33) and the SO group (p = 0.0048, OR = 1.78). Other genetic associations for EPSTI1-rs12870438 and PSAT1-rs7867029 with SO and between TUSC1-rs10966811 and testicular sperm extraction (TESE) success in the context of NOA were observed. In silico analysis of functional annotations demonstrated cis-eQTL effects of such SNPs likely due to the modification of binding motif sites for relevant transcription factors of the spermatogenic process. The findings reported here shed light on the molecular mechanisms leading to severe phenotypes of idiopathic male infertility, and may help to better understand the contribution of the common genetic variation to the development of these conditions.

Late Quaternary range shifts of marcescent oaks unveil the dynamics of a major biogeographic transition in southern Europe

Marcescent forests are ecotones distributed across southern Europe that host increased levels of biodiversity but their persistence is threatened by global change. Here we study the range dynamics of these forests in the Iberian Peninsula (IP) during the Late Quaternary, a period of profound climate and anthropic changes. We modeled and compared the distribution of eight oak taxa for the present and two paleoclimatic environments, the Last Glacial Maximum (LGM, ~ 21 kya) and the Mid-Holocene (MH, ~ 6 kya). Presence records were combined with bioclimatic and topographic data in an ensemble modelling framework to obtain spatial projections for present and past conditions across taxa. Substantial distribution shifts were projected between the three studied periods, that were explained by precipitation, winter cold and terrain ruggedness. Results were congruent with paleoclimatic records of the IP and showed that range shifts of these contact zones concurred with range dynamics of both Submediterranean and Temperate oaks. Notably, the distribution ranges of hybrid oaks and marcescent forests matched throughout the late Quaternary. This study contributes to unveil the complex Late-Quaternary biogeography of the ecotone belt occupied by marcescent forests and, more broadly, of Mediterranean oaks. Improved knowledge of species' responses to climate dynamics will allow us to anticipate and manage future range shifts driven by climate change.

Correction to: Biologic Drug Quality Assurance to Optimize HER2+ Breast Cancer Treatment: Insights from Development of the Trastuzumab Biosimilar SB3

The article Biologic Drug Quality Assurance to Optimize HER2+ Breast Cancer Treatment: Insights from Development of the Trastuzumab Biosimilar SB3.

Bi-allelic Mutations in M1AP Are a Frequent Cause of Meiotic Arrest and Severely Impaired Spermatogenesis Leading to Male Infertility

Male infertility affects ∼7% of men, but its causes remain poorly understood. The most severe form is non-obstructive azoospermia (NOA), which is, in part, caused by an arrest at meiosis. So far, only a few validated disease-associated genes have been reported. To address this gap, we performed whole-exome sequencing in 58 men with unexplained meiotic arrest and identified the same homozygous frameshift variant c.676dup (p.Trp226LeufsTer4) in M1AP, encoding meiosis 1 associated protein, in three unrelated men. This variant most likely results in a truncated protein as shown in vitro by heterologous expression of mutant M1AP. Next, we screened four large cohorts of infertile men and identified three additional individuals carrying homozygous c.676dup and three carrying combinations of this and other likely causal variants in M1AP. Moreover, a homozygous missense variant, c.1166C>T (p.Pro389Leu), segregated with infertility in five men from a consanguineous Turkish family. The common phenotype between all affected men was NOA, but occasionally spermatids and rarely a few spermatozoa in the semen were observed. A similar phenotype has been described for mice with disruption of M1ap. Collectively, these findings demonstrate that mutations in M1AP are a relatively frequent cause of autosomal recessive severe spermatogenic failure and male infertility with strong clinical validity.

The NEMP family supports metazoan fertility and nuclear envelope stiffness

Human genome-wide association studies have linked single-nucleotide polymorphisms (SNPs) in NEMP1 (nuclear envelope membrane protein 1) with early menopause; however, it is unclear whether NEMP1 has any role in fertility. We show that whole-animal loss of NEMP1 homologs in Drosophila, Caenorhabditis elegans, zebrafish, and mice leads to sterility or early loss of fertility. Loss of Nemp leads to nuclear shaping defects, most prominently in the germ line. Biochemical, biophysical, and genetic studies reveal that NEMP proteins support the mechanical stiffness of the germline nuclear envelope via formation of a NEMP-EMERIN complex. These data indicate that the germline nuclear envelope has specialized mechanical properties and that NEMP proteins play essential and conserved roles in fertility.

Intronic variation of the SOHLH2 gene confers risk to male reproductive impairment

OBJECTIVE

To evaluate whether SOHLH2 intronic variation contributes to the genetic predisposition to male infertility traits, including severe oligospermia (SO) and different nonobstructive azoospermia (NOA) clinical phenotypes.

DESIGN

Genetic association study.

SETTING

Not applicable.

PATIENT(S)

Five hundred five cases (455 infertile patients diagnosed with NOA and 50 with SO) and 1,050 healthy controls from Spain and Portugal.

INTERVENTION(S)

None.

MAIN OUTCOME MEASURE(S)

Genomic DNA extraction from peripheral blood mononuclear cells, genotyping of the SOHLH2 polymorphisms rs1328626 and rs6563386 using the TaqMan allelic discrimination technology, case-control association analyses using logistic regression models, and exploration of functional annotations in publicly available databases.

RESULT(S)

Evidence of association was observed for both rs6563386 with SO and rs1328626 with unsuccessful sperm retrieval after testicular sperm extraction (TESE-) in the context of NOA. A dominant effect of the minor alleles was suggested in both associations, either when the subset of patients with the manifestation were compared against the control group (rs6563386/SO: P=.021, odds ratio [OR] = 0.51; rs1328626/TESE-: P=.066, OR = 1.46) or against the group of patients without the manifestation (rs6563386/SO: P=.014, OR = 0.46; rs1328626/TESE-: P=.012, OR = 2.43). The haplotype tests suggested a combined effect of both polymorphisms. In silico analyses evidenced that this effect could be due to alteration of the isoform population.

CONCLUSION(S)

Our data suggest that intronic variation of SOHLH2 is associated with spermatogenic failure. The genetic effect is likely caused by different haplotypes of rs6563386 and rs1328626, which may predispose to SO or TESE- depending on the specific allelic combination.

IoT Sensing Platform as a Driver for Digital Farming in Rural Africa

Small-scale farming can benefit from the usage of information and communication technology (ICT) to improve crop and soil management and increase yield. However, in order to introduce digital farming in rural areas, related ICT solutions must be viable, seamless and easy to use, since most farmers are not acquainted with technology. With that in mind, this paper proposes an Internet of Things (IoT) sensing platform that provides information on the state of the soil and surrounding environment in terms of pH, moisture, texture, colour, air temperature, and light. This platform is coupled with computer vision to further analyze and understand soil characteristics. Moreover, the platform hardware is housed in a specifically designed robust casing to allow easy assembly, transport, and protection from the deployment environment. To achieve requirements of usability and reproducibility, the architecture of the IoT sensing platform is based on low-cost, off-the-shelf hardware and software modularity, following a do-it-yourself approach and supporting further extension. In-lab validations of the platform were carried out to finetune its components, showing the platform’s potential for application in rural areas by introducing digital farming to small-scale farmers, and help them delivering better produce and increasing income.