Institute of Molecular Genetics

In contrast to humans, zebrafish have an outstanding ability to regenerate injured heart through a highly orchestrated process involving all cardiac structures. To replace the lost myocardium, resident cardiomyocytes (CMs) dedifferentiate and proliferate, invading the injured area. The response of the myocardium is preceded by the activation of the epicardium and endocardium, which form active scaffolds to provide mechanical and paracrine support to guide regeneration. New CMs use protrusions to migrate and invade fibrotic injured tissue, replacing it with functional myocardium. Here, we investigated the expression profile of the stress-responsive ankrd1a gene in different cardiac structures, at key time points during regeneration, aiming to gain insight into its precise roles during zebrafish heart regeneration. In the TgBAC(ankrd1a:EGFP) reporter line, transgene upregulation was restricted to the myocardium, initiated as early as 15h post-cryoinjury, and consistently marked CMs bordering the injury or scar area during regeneration. Transcriptome profiling and immunostaining revealed a potential role of ankrd1a in regulating CMs' dedifferentiation, as well as changes in the expression of genes associated with antigen presentation and extracellular matrix composition in the ankrd1a mutant. Our results indicate that ankrd1a is dispensable for ventricular regeneration after cryoinjury, while it may serve as a marker and fine-tuner in the healing process of injured cardiac muscle.

In course of investigating the endophytic and nematode-associated fungus Polydomus karssenii for the production of secondary metabolites, seven previously undescribed natural products were isolated from liquid and solid-state fermentations. 1D and 2D NMR spectroscopy, together with HR-ESI–MS data, enabled the elucidation of the planar structures of 3-decalinoyltetramic acids polydosetins A–E (1–5) and cyclodepsipeptides pullularins G and H (6 and 7). The relative configurations of the decalin moiety of 1–5 were determined based on ROESY correlations and 1H–1H coupling constants. The configuration of the side chains was established through a detailed J-resolved analysis (Murata’s method) in combination with chemical shift comparison to model compounds. Absolute stereochemistry of 1–5 was assigned based on ECD data, and confirmed by Mosher’s method utilizing 3. Finally, the absolute configuration of amino acid residues in 6 and 7 was determined through advanced Marfey’s method. Bioassays revealed that compounds 1, 3, 5, and 7 were active against Gram-positive bacteria, 3 and 5 exhibited antifungal activity, and 1 and 2 showed nematicidal effects. These results underscore the untapped chemical potential of P. karssenii and highlight the importance of exploring nematode-associated fungi as sources of new natural products with potential antimicrobial and nematicidal properties.Supplementary InformationThe online version contains supplementary material available at 10.1007/s13659-025-00579-8.

Expansion microscopy is a powerful technique, which increases the effective resolution of a fluorescence microscope by physically enlarging the specimen within a swellable polymer matrix. When combined with confocal microscopy, it enables affordable and easy-to-implement super-resolution imaging of protein localization in an entire cellular volume. Here, we describe in detail a protocol for the expansion of Euglenozoa, such as Trypanosoma brucei and Euglena gracilis, which achieves an average expansion factor of 4.6 in the case of T. brucei and 3.5 in the case of E. gracilis. This method is compatible with a broad range of available antibodies targeting endogenous proteins or small epitope tags. Additionally, we demonstrate the use of a fluorescent NHS ester for whole-proteome staining, BODIPY lipid stain, and the SYTOX nucleic acid stain for reproducible DNA labeling in expanded cells of these organisms. These reagents further increase the versatility of this simple yet robust super-resolution approach for studies of the cell biology of Euglenozoa.

Cystic fibrosis (CF) sputum represents a highly permissive niche for microbial colonization, yet the contribution of Candida albicans to disease progression remains insufficiently investigated despite its frequent detection in CF airways. We hypothesized that the heterogeneous nature of CF lung, reflected through the emergence of oxygen-depleted niches during disease progression, modulates C. albicans pathogenicity and antifungal susceptibility. Using complementary in vitro and in vivo approaches, we show that clinical CF isolates of C. albicans are virulent in CF-mimicking environments. Synthetic CF medium (SCFM2) supported robust filamentation, with oxygen-nutrient interplay critically shaping fungal growth and drug response. In a novel CF infection model using zebrafish morphants, we observed heightened susceptibility to C. albicans compared to wild-type embryos. Reporter strains showed elevated ECE1 expression, indicating increased candidalysin production and virulence in vivo. Our study provides compelling evidence that CF isolates of C. albicans have pathogenic potential, warranting consideration in future therapeutic strategies.

APX3330 is an oral agent targeting the redox signaling activity of APE1/Ref-1 (Ref-1), a key regulator of transcription factors involved in inflammation and tumorigenesis. APX3330 selectively inhibits Ref-1's redox function without affecting its DNA repair role. This Phase 1, multicenter, open-label, dose-escalation study in advanced solid tumors was aimed at determining the recommended Phase 2 dose (RP2D) while assessing safety, pharmacokinetics, and biomarker evidence of target engagement. Nineteen cancer patients were treated, with eight completing follow-ups. Subjects received APX3330 orally twice daily in 21-day cycles, starting at 240 mg/d and escalating in 120 mg/d increments. Adverse event (AE) monitoring followed a 1 pt/cohort approach until a >G2 toxicity event, after which a 3 + 3 design was implemented. Treatment continued until disease progression, consent withdrawal, or intolerable toxicity. Antitumor activity was assessed using RECIST 1.1, and pharmacodynamic markers included serum Ref-1 levels and circulating tumor cells. Six of nineteen subjects had stable disease, and no treatment-related SAEs were observed. One subject (720 mg cohort) withdrew due to Grade 3 maculopapular rash (dose-limiting toxicity). Laboratory assessments and ECGs showed no clinically significant abnormalities. APX3330 showed preliminary signals of disease control and on-target pharmacology in this first-in-human study. Based on safety and PD, the RP2D is 600 mg/d. Given the small sample size, efficacy conclusions are exploratory (ClinicalTrials.gov Identifier: NCT03375086).

A minority of individuals who consume excessive alcohol develop cirrhosis. Variants in the patatin-like phospholipase domain-containing protein 3 gene (PNPLA3) and the transmembrane 6 superfamily member 2 gene (TM6SF2) have been previously identified as associated with alcohol-related cirrhosis (ALC). This study aimed to examine the variants of PNPLA3andTM6SF2and to develop and assess a polygenic risk score (PRS) for ALC. We enrolled 118 patients diagnosed with ALC and 131 control subjects, who were either abstainers or low-level alcohol consumers without evidence of liver disease. Genotyping of risk variants was performed using PCR-RFLP methodology. PRS, based on independent allelic effect size estimates from genotyped genetic loci, were computed and compared across groups. The development of ALC was significantly associated with CG and GG genotypes of PNPLA3(CG: OR: 1.82; 95% CI: 1.05-3.17; p=0.033; GG: OR: 7.64; 95% CI: 3.06-19.07; p<0.001) and the CT genotype of TM6SF2(OR: 2.43; 95% CI: 1.27-4.63; p=0.007), controlling for age and sex. Patients with cirrhosis exhibited a significantly higher mean PRS compared to controls (0.32 vs. 0.167, p= 1.8e-07). The odds ratios (ORs) and 95% confidence intervals for the group with the highest PRS score compared to the reference group were 6.707; 95% CI: 3.313-13.581, p<0.001. In our ALC patient cohort, the PNPLA3rs738409 and TM6SF2rs58542926 variants were associated with an increased risk of ALC development. Moreover, the PRS derived from these two variants effectively identified the genetic components linked to cirrhosis within the study population.

In dynamic light microscopy applications, imaging specimens from multiple angles while maintaining controlled temperature conditions is crucial for comprehensive and accurate analysis. To address these challenges, we present iCAT, an open-source multifunctional accessory designed to enhance light microscopy. It enables specimen rotation along the axial plane, incorporates built-in modules for precise temperature control, features an integrated LED, and includes a camera for real-time specimen monitoring. It can be easily 3D-printed and assembled using readily available electrical components. Combined with any up-right microscope, this versatile device allows researchers to capture detailed images and videos of organoid cultures and live or fixed specimens, such as C. elegans, zebrafish, drosophila, or mouse embryos. The potential applications of iCAT in investigating dynamic cellular processes and complex developmental phenomena are vast, inspiring researchers to explore its possibilities and push the boundaries of biological research.