Machine learning predictions of MHC-II specificities reveal alternative binding mode of class II epitopes.

CD4+ T cells orchestrate the adaptive immune response against pathogens and cancer by recognizing epitopes presented on class II major histocompatibility complex (MHC-II) molecules. The high polymorphism of MHC-II genes represents an important hurdle toward accurate prediction and identification of CD4+ T cell epitopes. Here we collected and curated a dataset of 627,013 unique MHC-II ligands identified by mass spectrometry. This enabled us to precisely determine the binding motifs of 88 MHC-II alleles across humans, mice, cattle, and chickens. Analysis of these binding specificities combined with X-ray crystallography refined our understanding of the molecular determinants of MHC-II motifs and revealed a widespread reverse-binding mode in HLA-DP ligands. We then developed a machine-learning framework to accurately predict binding specificities and ligands of any MHC-II allele. This tool improves and expands predictions of CD4+ T cell epitopes and enables us to discover viral and bacterial epitopes following the aforementioned reverse-binding mode.

The dimorphic diaspore model Aethionema arabicum (Brassicaceae): Distinct molecular and morphological control of responses to parental and germination temperatures.

Plants in habitats with unpredictable conditions often have diversified bet-hedging strategies that ensure fitness over a wider range of variable environmental factors. A striking example is the diaspore (seed and fruit) heteromorphism that evolved to maximize species survival in Aethionema arabicum (Brassicaceae) in which external and endogenous triggers allow the production of two distinct diaspores on the same plant. Using this dimorphic diaspore model, we identified contrasting molecular, biophysical, and ecophysiological mechanisms in the germination responses to different temperatures of the mucilaginous seeds (M+ seed morphs), the dispersed indehiscent fruits (IND fruit morphs), and the bare non-mucilaginous M- seeds obtained by pericarp (fruit coat) removal from IND fruits. Large-scale comparative transcriptome and hormone analyses of M+ seeds, IND fruits, and M- seeds provided comprehensive datasets for their distinct thermal responses. Morph-specific differences in co-expressed gene modules in seeds, as well as in seed and pericarp hormone contents, identified a role of the IND pericarp in imposing coat dormancy by generating hypoxia affecting abscisic acid (ABA) sensitivity. This involved expression of morph-specific transcription factors, hypoxia response, and cell wall remodeling genes, as well as altered ABA metabolism, transport, and signaling. Parental temperature affected ABA contents and ABA-related gene expression and altered IND pericarp biomechanical properties. Elucidating the molecular framework underlying the diaspore heteromorphism can provide insight into developmental responses to globally changing temperatures.

Predictors of unsustained measurable residual disease negativity in transplant-eligible patients with multiple myeloma.

ABSTRACT: The role of measurable residual disease (MRD) negativity as a biomarker to stop treatment is being investigated in transplant-eligible patients with multiple myeloma (MM). Thus, it is important to identify risk factors of MRD resurgence and/or progressive disease (PD) among patients achieving undetectable MRD to avoid undertreating them. Here, we studied 267 newly diagnosed transplant-eligible patients with MM enrolled in the GEM2012MENOS65 and GEM2014MAIN clinical trials who achieved MRD negativity by next-generation flow cytometry. After a median follow-up of 73 months since the first MRD negative assessment, 111 of the 267 (42%) patients showed MRD resurgence and/or PD. The only prognostic factors at diagnosis that predicted MRD resurgence and/or PD were an International Staging System (ISS) 3 and the presence of ≥0.01% circulating tumor cells (CTCs). Failure to achieve MRD negativity after induction also predicted higher risk of MRD resurgence and/or PD. Patients having 0 vs 1 vs ≥2 risk factors (ISS 3, ≥0.01% CTCs, and late MRD negativity) showed 5-year rates of MRD resurgence and/or PD of 16%, 33%, and 57%, respectively (P < .001). Thus, these easily measurable risk factors could help refine the selection of patients for whom treatment cessation after MRD negativity is being investigated in clinical trials. This trial was registered at www.clinicaltrials.gov as NCT01916252 and NCT02406144.

SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina.

Drug discovery aims to identify potential therapeutic compounds capable of modulating the activity of specific biological targets. Molecular docking can efficiently support this process by predicting binding interactions between small molecules and macromolecular targets and potentially accelerating screening campaigns. SwissDock is a computational tool released in 2011 as part of the SwissDrugDesign project, providing a free web-based service for small-molecule docking after automatized preparation of ligands and targets. Here, we present the latest version of SwissDock, in which EADock DSS has been replaced by two state-of-the-art docking programs, i.e. Attracting Cavities and AutoDock Vina. AutoDock Vina provides faster docking predictions, while Attracting Cavities offers more accurate results. Ligands can be imported in various ways, including as files, SMILES notation or molecular sketches. Targets can be imported as PDB files or identified by their PDB ID. In addition, advanced search options are available both for ligands and targets, giving users automatized access to widely-used databases. The web interface has been completely redesigned for interactive submission and analysis of docking results. Moreover, we developed a user-friendly command-line access which, in addition to all options of the web site, also enables covalent ligand docking with Attracting Cavities. The new version of SwissDock is freely available at https://www.swissdock.ch/.

Largest comparison between onset and relapses of acquired thrombotic thrombocytopenic purpura reveals severe neurological involvement and worse analytic parameters at debut.

It has been proposed that the onset of Acquired Thrombotic Thrombocytopenic Purpura (iTTP) is more severe than subsequent relapses; however, existing studies have limitations. We conducted a retrospective observational study to compare analytical and clinical severity of onset and relapse aTTP cases between 2012 and 2023. A total of 370 episodes of aTTP were analyzed, comprising 272 at initial diagnosis and 98 relapses. At onset, analytical parameters indicative of severity (low hemoglobin, low platelet count, and increased LDH) were significantly worse; patients had severe neurological symptoms (p<0.001) and ≥ 3 points in the TMA mortality score (p<0.001). In conclusion, the onset of aTTP is associated with worse analytical parameters and severe neurological involvement.

Development of a Risk Prediction Nomogram for Carotid Restenosis in the One Year RECAST Registry.

OBJECTIVE: Long term benefit of carotid angioplasty and stenting (CAS) can be reduced by recurrent stroke related to in stent restenosis (ISR). An individualised predictive tool is needed to identify ISR events. A nomogram for individual risk assessment of ISR ≥ 70% after CAS is proposed. METHODS: A national observational, prospective, multicentre registry was conducted between January 2015 and December 2020. Cohorts of patients with symptomatic or asymptomatic severe carotid stenosis who underwent CAS were included with a follow up of at least 1 year after CAS. Duplex ultrasound was used to assess in stent restenosis. Pre-operative factors were compared between the non-ISR and ISR groups. Kaplan-Meier and Cox regression were used for variable selection. The nomogram was formulated and validated by concordance indices and calibration curves. An in stent restenosis risk table was generated for risk stratification. RESULTS: A total of 354 patients were included in the analysis. The ISR rate of ≥ 70% was 7.6% (n = 27). Peripheral arterial disease (hazard ratio [HR] 3.18, 95% confidence interval [CI] 1.23 - 8.24, p = .017), anterior communicating artery absence (HR 3.38, 95% CI 1.27 - 8.94, p = .016), diabetes mellitus (HR 3.34, 95% CI 1.21 - 9.26, p = .020), female sex (HR 2.99, 95% CI 1.04 - 8.60, p = .041), and pre-procedure pathologic ultrasound vasoreactivity (HR 3.87, 95% CI 1.43 -10.50, p = .008), as independent risk factors for ISR of ≥ 70%, were included in the nomogram. Concordance index at 12 and 24 months was 0.83. In low risk groups, ISR of ≥ 70% occurred in 4.8% of patients during follow up compared with 56.2% of patients in the high risk groups (p < .001). CONCLUSION: The nomogram and risk evaluation score have good predictive ability for ISR. They can be used as practical clinical tools for individualised risk assessment.

Transcriptomic analysis of turbot (Scophthalmus maximus) treated with zymosan a reveals that lncRNAs and inflammation-related genes mediate the protection conferred against Aeromonas salmonicida.

Aeromonas salmonicida is one of the most harmful pathogens in finfish aquaculture worldwide. Immunostimulants such as ß-glucans are used to enhance the immunity of cultured fish. However, their effects on fish physiology are not completely understood. In the present work, we evaluated the effect of a single intraperitoneal (ip) injection of zymosan A on fish survival against A. salmonicida infection. A single administration of this compound protected fish against A. salmonicida challenge and reduce the bacterial load in the head kidney one week after its administration. Transcriptome analyses of head kidney samples revealed several molecular mechanisms involved in the protection conferred by zymosan A and their regulation by long noncoding RNAs. The transcriptome profile of turbot exposed only to zymosan A was practically unaltered one week after ip injection. However, the administration of this immunostimulant induced significant transcriptomic changes once the fish were in contact with the bacteria and increased the survival of the infected turbot. Our results suggest that the restraint of the infection-induced inflammatory response, the management of apoptotic cell death, cell plasticity and cellular processes involving cytoskeleton dynamics support the protective effects of zymosan A. All this information provides insights on the cellular and molecular mechanisms involved in the protective effects of this widely used immunostimulant.

Mannheimia haemolytica-associated fibrinonecrotizing abomasitis in lambs.

Mannheimia haemolytica-associated abomasitis has been clinically described as a cause of sudden death in lambs, but it is poorly characterized. We describe the pathological features of a severe fibrinonecrotizing abomasitis in 3 lambs that died suddenly. All 3 abomasums had a thickened submucosa due to edema and necrotic areas delimited by bands of degenerate neutrophils with slender nuclei (oat cells) and angiocentric distributions. The overlying mucosa was congested. Myriads of gram-negative coccobacilli were observed within the oat cell bands. M. haemolytica was isolated from the abomasum in all 3 animals and was serotyped as A2 in one of them. Pericarditis and pleuritis were observed in 2 of the lambs. Clostridium spp. were isolated in 1 lamb and detected by immunohistochemistry in the 3 animals, suggesting clostridial co-infection. M. haemolytica should be considered among the differential diagnoses of necrotizing abomasitis in lambs.

A second S4 movement opens hyperpolarization-activated HCN channels.

Rhythmic activity in pacemaker cells, as in the sino-atrial node in the heart, depends on the activation of hyperpolarization-activated cyclic nucleotide-gated (HCN) channels. As in depolarization-activated K+ channels, the fourth transmembrane segment S4 functions as the voltage sensor in hyperpolarization-activated HCN channels. But how the inward movement of S4 in HCN channels at hyperpolarized voltages couples to channel opening is not understood. Using voltage clamp fluorometry, we found here that S4 in HCN channels moves in two steps in response to hyperpolarizations and that the second S4 step correlates with gate opening. We found a mutation in sea urchin HCN channels that separate the two S4 steps in voltage dependence. The E356A mutation in S4 shifts the main S4 movement to positive voltages, but channel opening remains at negative voltages. In addition, E356A reveals a second S4 movement at negative voltages that correlates with gate opening. Cysteine accessibility and molecular models suggest that the second S4 movement opens up an intracellular crevice between S4 and S5 that would allow radial movement of the intracellular ends of S5 and S6 to open HCN channels.

Risk Factors for Multiple Violations of Protective Orders in Intimate Partner Violence Against Women.

This study examined 1,134 cases of violence against women in intimate partner relationships with violations of protective orders in a monitoring period of up to 15 months. The dynamics of time and violence were analyzed in the cases of multiple violation versus one-time violation, with the objective of identifying and thus neutralizing the risk factors for this type of recidivism. The results showed that early violation, serious physical violence, death threats, as well as jealousy, harassment, and control are related to multiple violation. This article discusses the results in comparison with other research and proposes measures to avoid revictimizations.

Video Instruction for Pushing in the Second Stage: a randomized controlled trial.

BACKGROUND: The second stage of labor requires active patient engagement. Previous studies suggest that coaching can influence the second stage of labor duration. However, a standardized education tool has not been established, and patients face many barriers to accessing childbirth education before delivery. OBJECTIVE: This study aimed to investigate the effect of an intrapartum video pushing education tool on the second stage of labor duration. STUDY DESIGN: This was a randomized controlled trial of nulliparous patients with singleton pregnancies ≥37 weeks of gestation admitted for induction of labor or spontaneous labor with neuraxial anesthesia. Patients were consented on admission and block randomized in active labor to 1 of 2 arms in a 1:1 ratio. The study arm viewed a 4-minute video before the second stage of labor on what to anticipate in the second stage of labor and pushing techniques. The control arm received the standard of care: bedside coaching at 10 cm dilation from a nurse or physician. The primary outcome was second stage of labor duration. The secondary outcomes were birth satisfaction (using the Modified Mackey Childbirth Satisfaction Rating Scale), mode of delivery, postpartum hemorrhage, clinical chorioamnionitis, neonatal intensive care unit admission, and umbilical artery gases. Of note, 156 patients were needed to detect a 20% decrease in the second stage of labor duration with 80% power, 2-sided alpha level of .05, and 10% loss after randomization. Funding was provided by the Lucy Anarcha Betsy award from the division of clinical research at Washington University. RESULTS: Of 161 patients, 81 were randomized to standard of care, and 80 were randomized to intrapartum video education. Among these patients, 149 progressed to the second stage of labor and were included in the intention-to-treat analysis: 69 in the video group and 78 in the control group. Maternal demographics and labor characteristics were similar between groups. The second stage of labor duration was statistically similar between the video arm (61 minutes [interquartile range, 20-140]) and the control arm (49 minutes [interquartile range, 27-131]) (P=.77). There was no difference in mode of delivery, postpartum hemorrhage, clinical chorioamnionitis, neonatal intensive care unit admission, or umbilical artery gases between groups. Although the overall birth satisfaction score on the Modified Mackey Childbirth Satisfaction Rating Scale was similar between groups, patients in the video group rated their "level of comfort during birth" and "attitude of the doctors in birth" significantly higher or more positively than patients in the control group (P<.05 for both). CONCLUSION: Intrapartum video education was not associated with a shorter second stage of labor duration. However, patients who received video education reported a higher level of comfort and a more favorable perception of their physician, suggesting that video education may be a helpful tool to improve the birth experience.

SwissParam 2023: A Modern Web-Based Tool for Efficient Small Molecule Parametrization.

Most steps of drug discovery are now routinely supported and accelerated by computer-aided drug design tools. Among them, structure-based approaches use the three-dimensional structure of the targeted biomacromolecule as a major source of information. When it comes to calculating the interactions of small molecules with proteins using the equations of molecular mechanics, topologies, atom typing, and force field parameters are required. However, generating parameters for small molecules remains challenging due to the large number of existing chemical groups. The SwissParam web tool was first released in 2011 with the aim of generating parameters and topologies for small molecules based on the Merck molecular force field (MMFF) while being compatible with the CHARMM22/27 force field. Here, we present an updated version of SwissParam, providing various new features, including the possibility to setup covalent ligands. Molecules can now be imported from different file formats or via a molecular sketcher. The MMFF-based approach has been updated to provide parameters and topologies compatible with the CHARMM36 force field. An option was added to generate small molecule parametrizations following the CHARMM General Force Field via the multipurpose atom-typer for CHARMM (MATCH) approach. Additionally, SwissParam now generates information on probable alternative tautomers and protonation states of the query molecule so that the user can consider all microspecies relevant to its compound. The new version of SwissParam is freely available at www.swissparam.ch and can also be accessed through a newly implemented command-line interface.

Pharmacological Screening of Kv7.1 and Kv7.1/KCNE1 Activators as Potential Antiarrhythmic Drugs in the Zebrafish Heart.

Long QT syndrome (LQTS) can lead to ventricular arrhythmia and sudden cardiac death. The most common congenital cause of LQTS is mutations in the channel subunits generating the cardiac potassium current IKs. Zebrafish (Danio rerio) have been proposed as a powerful system to model human cardiac diseases due to the similar electrical properties of the zebrafish heart and the human heart. We used high-resolution all-optical electrophysiology on ex vivo zebrafish hearts to assess the effects of IKs analogues on the cardiac action potential. We found that chromanol 293B (an IKs inhibitor) prolonged the action potential duration (APD) in the presence of E4031 (an IKr inhibitor applied to drug-induced LQT2), and to a lesser extent, in the absence of E4031. Moreover, we showed that PUFA analogues slightly shortened the APD of the zebrafish heart. However, PUFA analogues failed to reverse the APD prolongation in drug-induced LQT2. However, a more potent IKs activator, ML-277, partially reversed the APD prolongation in drug-induced LQT2 zebrafish hearts. Our results suggest that IKs plays a limited role in ventricular repolarizations in the zebrafish heart under resting conditions, although it plays a more important role when the IKr is compromised, as if the IKs in zebrafish serves as a repolarization reserve as in human hearts. This study shows that potent IKs activators can restore the action potential duration in drug-induced LQT2 in the zebrafish heart.

Exploring the Contribution of the Transporter AGT1/rBAT in Cystinuria Progression: Insights from Mouse Models and a Retrospective Cohort Study.

More than 20 years have passed since the identification of SLC3A1 and SLC7A9 as causative genes for cystinuria. However, cystinuria patients exhibit significant variability in the age of lithiasis onset, recurrence, and response to treatment, suggesting the presence of modulatory factors influencing cystinuria severity. In 2016, a second renal cystine transporter, AGT1, encoded by the SLC7A13 gene, was discovered. Although it was discarded as a causative gene for cystinuria, its possible effect as a modulatory gene remains unexplored. Thus, we analyzed its function in mouse models of cystinuria, screened the SLC7A13 gene in 34 patients with different lithiasic phenotypes, and functionally characterized the identified variants. Mice results showed that AGT1/rBAT may have a protective role against cystine lithiasis. In addition, among the four missense variants detected in patients, two exhibited a 25% impairment in AGT1/rBAT transport. However, no correlation between SLC7A13 genotypes and lithiasis phenotypes was observed in patients, probably because these variants were found in heterozygous states. In conclusion, our results, consistent with a previous study, suggest that AGT1/rBAT does not have a relevant effect on cystinuria patients, although an impact in patients carrying homozygous pathogenic variants cannot be discarded.

Development and validation of the Male Post-coital Affect Scale for heterosexual men.

OBJECTIVE: The aim of this study was to examine the reliability and validity of the Male Post-coital Affect Scale (MPAS), which was developed to assess positive post-coital feelings in men. METHODS: After a pilot study, we validated our scale on a sample of American heterosexual men, who answered our questionnaire on the internet through Amazon Mechanical Turk. We tested the reliability using internal consistency. The validity was examined by assessing content, face and construct validity by testing the association between our scale, the Experience in Close Relationships Scale and other instruments. RESULTS: A total of 484 volunteers were included in the study. Cronbach's α for the scale was 0.83. Our scale was negatively correlated with attachment avoidance, r(482) = -0.36, p < 0.001) and Perceived Stress Scale, r(482) = -0.18, p < 0.001, and positively correlated with sexual satisfaction, r(482) = 0.18, p < 0.001. CONCLUSION: The MPAS is a reliable and valid tool to assess positive post-coital feelings in men.

Sequential repeated tibial tubercle osteotomy in a two-stage exchange strategy: a superior approach to treating a chronically infected knee arthroplasty?

PURPOSE: Surgical approach can impact the reliability of the debridement after a chronic total knee periprosthetic joint infection (PJI), a factor of utmost importance to eradicate the infection. The most adequate knee surgical approach in cases of PJI is a matter of debate. The purpose of this study was to determine the influence of performing a tibial tubercle osteotomy (TTO) in a two-stage exchange protocol for knee PJI treatment. METHODS: Retrospective cohort study examining patients managed with two-stage arthroplasty due to chronic knee PJI (2010-2019). Performance and timing of the TTO were collected. Primary end-point was infection control with a minimum FU of 12 months and according to internationally accepted criteria. Correlation between TTO timing and reinfection rate was reviewed. RESULTS: Fifty-two cases were finally included. Overall success (average follow-up: 46.2 months) was 90.4%. Treatment success was significantly higher among cases addressed using TTO during the second stage (97.1% vs. 76.5%, p value 0.03). Only 4.8% of the patients relapsed after performing a sequential repeated TTO, that is, during both first and second stages, compared to 23.1% cases in which TTO was not done (p value 0.28). No complications were observed among patients in the TTO group with a significant decrease in soft tissue necrosis (p: 0.052). CONCLUSION: Sequential repeated tibial tubercle osteotomy during a two-stage strategy is a reasonable option and offers high rates of infection control in complex cases of knee PJI with a low rate of complications.

Molecular mechanisms and hormonal regulation underpinning morphological dormancy: a case study using Apium graveolens (Apiaceae).

Underdeveloped (small) embryos embedded in abundant endosperm tissue, and thus having morphological dormancy (MD) or morphophysiological dormancy (MPD), are considered to be the ancestral state in seed dormancy evolution. This trait is retained in the Apiaceae family, which provides excellent model systems for investigating the underpinning mechanisms. We investigated Apium graveolens (celery) MD by combined innovative imaging and embryo growth assays with the quantification of hormone metabolism, as well as the analysis of hormone and cell-wall related gene expression. The integrated experimental results demonstrated that embryo growth occurred inside imbibed celery fruits in association with endosperm degradation, and that a critical embryo size was required for radicle emergence. The regulation of these processes depends on gene expression leading to gibberellin and indole-3-acetic acid (IAA) production by the embryo and on crosstalk between the fruit compartments. ABA degradation associated with distinct spatiotemporal patterns in ABA sensitivity control embryo growth, endosperm breakdown and radicle emergence. This complex interaction between gibberellins, IAA and ABA metabolism, and changes in the tissue-specific sensitivities to these hormones is distinct from non-MD seeds. We conclude that the embryo growth to reach the critical size and the associated endosperm breakdown inside MD fruits constitute a unique germination programme.

A tale of two morphs: developmental patterns and mechanisms of seed coat differentiation in the dimorphic diaspore model Aethionema arabicum (Brassicaceae).

The developmental transition from a fertilized ovule to a dispersed diaspore (seed or fruit) involves complex differentiation processes of the ovule's integuments leading to the diversity in mature seed coat structures in angiosperms. In this study, comparative imaging and transcriptome analysis were combined to investigate the morph-specific developmental differences during outer seed coat differentiation and mucilage production in Aethionema arabicum, the Brassicaceae model for diaspore dimorphism. One of the intriguing adaptations of this species is the production and dispersal of morphologically distinct, mucilaginous and non-mucilaginous diaspores from the same plant (dimorphism). The dehiscent fruit morph programme producing multiple mucilaginous seed diaspores was used as the default trait combination, similar to Arabidopsis thaliana, and was compared with the indehiscent fruit morph programme leading to non-mucilaginous diaspores. Synchrotron-based radiation X-ray tomographic microscopy revealed a co-ordinated framework of morph-specific early changes in internal anatomy of developing A. arabicum gynoecia including seed abortion in the indehiscent programme and mucilage production by the mucilaginous seed coat. The associated comparative analysis of the gene expression patterns revealed that the unique seed coat dimorphism of Ae. arabicum provides an excellent model system for comparative study of the control of epidermal cell differentiation and mucilage biosynthesis by the mucilage transcription factor cascade and their downstream cell wall and mucilage remodelling genes. Elucidating the underlying molecular framework of the dimorphic diaspore syndrome is key to understanding differential regulation of bet-hedging survival strategies in challenging environments, timely in the face of global climatic change.

Cold-induced secondary dormancy and its regulatory mechanisms in Beta vulgaris.

The dynamic behaviour of seeds in soil seed banks depends on their ability to act as sophisticated environmental sensors to adjust their sensitivity thresholds for germination by dormancy mechanisms. Here we show that prolonged incubation of sugar beet fruits at low temperature (chilling at 5°C, generally known to release seed dormancy of many species) can induce secondary nondeep physiological dormancy of an apparently nondormant crop species. The physiological and biophysical mechanisms underpinning this cold-induced secondary dormancy include the chilling-induced accumulation of abscisic acid in the seeds, a reduction in the embryo growth potential and a block in weakening of the endosperm covering the embryonic root. Transcriptome analysis revealed distinct gene expression patterns in the different temperature regimes and upon secondary dormancy induction and maintenance. The chilling caused reduced expression of cell wall remodelling protein genes required for embryo cell elongation growth and endosperm weakening, as well as increased expression of seed maturation genes, such as for late embryogenesis abundant proteins. A model integrating the hormonal signalling and master regulator expression with the temperature-control of seed dormancy and maturation programmes is proposed. The revealed mechanisms of the cold-induced secondary dormancy are important for climate-smart agriculture and food security.

First evidence of SOX2 mutations in Peters' anomaly: Lessons from molecular screening of 95 patients.

Peters' anomaly (PA) is a rare anterior segment dysgenesis characterized by central corneal opacity and irido-lenticulo-corneal adhesions. Several genes are involved in syndromic or isolated PA (B3GLCT, PAX6, PITX3, FOXE3, CYP1B1). Some copy number variations (CNVs) have also been occasionally reported. Despite this genetic heterogeneity, most of patients remain without genetic diagnosis. We retrieved a cohort of 95 individuals with PA and performed genotyping using a combination of comparative genomic hybridization, whole genome, exome and targeted sequencing of 119 genes associated with ocular development anomalies. Causative genetic defects involving 12 genes and CNVs were identified for 1/3 of patients. Unsurprisingly, B3GLCT and PAX6 were the most frequently implicated genes, respectively in syndromic and isolated PA. Unexpectedly, the third gene involved in our cohort was SOX2, the major gene of micro-anophthalmia. Four unrelated patients with PA (isolated or with microphthalmia) were carrying pathogenic variants in this gene that was never associated with PA before. Here we described the largest cohort of PA patients ever reported. The genetic bases of PA are still to be explored as genetic diagnosis was unavailable for 2/3 of patients. Nevertheless, we showed here for the first time the involvement of SOX2 in PA, offering new evidence for its role in corneal transparency and anterior segment development.