Van Andel Institute

Conditional genetics and single-embryo RNA-seq show that SETDB1 extinguishes the transient, retroelement-driven transcriptional programs of the totipotent two-cell state to facilitate the exit from totipotency and ensure preimplantation development.

DNA sliding clamps are essential for processive DNA synthesis in all domains of life and are loaded by ATP-dependent clamp loaders that recognize recessed 3′ ends. How clamp loaders function at nicks and small ssDNA gaps—common intermediates during DNA repair—remains incompletely understood. Here, we show that the bacterial Escherichia coli DnaX clamp loader employs a fundamentally different mechanism from its eukaryotic counterpart. Whereas eukaryotic RFC unwinds DNA at the recessed 3′ end and stabilizes the 5′-dsDNA at a dedicated shoulder site, the bacterial DnaX-complex neither unwinds DNA nor stably binds the 5′-dsDNA in vitro. Instead, cryo-EM structures reveal that the β-clamp itself contains a conserved external DNA-binding site that enables sharp bending of gapped DNA by ~150°, promoting insertion of the 3′-dsDNA into the clamp. This DNA-bending mechanism allows efficient β-clamp loading at nicks and small gaps and reveals a distinct bacterial strategy for clamp loading. Because small DNA gaps are frequently associated with DNA damage, clamps loaded at these sites are likely important for DNA repair.

Parkinson’s disease (PD) symptom onset is typically unilateral, which may be related to molecular differences underlying hemispheric vulnerability. Here we sampled prefrontal cortex bilaterally from people with PD and healthy controls and performed RNA-seq on neuronal nuclei to determine hemispheric and disease-related differences. Brain hemispheres were categorized based on whether they corresponded to the side of symptom onset (severe) or the opposite side (moderate) and compared for differences in gene expression. We employed two a priori approaches; first we identified genes differentially expressed between PD and controls and between PD brain hemispheres. Second, we examined the presence of, and correlates to, variations in the asymmetry for some differentially expressed genes. We found large variation among individuals with PD, and so PD stratification by gene expression signature was required for patterns of genetic asymmetry to emerge. For a subset of PD brains, hemispherical variation of CCT gene levels correlated with the side of PD symptom onset. In a mouse model of PD, neurons with α-synuclein inclusions had decreased Cct expression. These results suggest that CCT expression plays a protective role in PD.

TPS857 Background: While the most frequently mutated solid tumor oncogenes, RAS and RAF , function via aberrant RAF dimerization, approved BRAF inhibitors are only active against mutated BRAF monomers and approved KRAS G12C inhibitors are ineffective for patients with RAS non-G12C tumors. There is a high unmet clinical need for RAF inhibitors that target a broad spectrum of mutated RAF and RAS proteins in solid tumor malignancies. S241656 (previously BDTX-4933) is an oral, CNS-penetrant small-molecule inhibitor engineered to suppress oncogenic K/H/NRAS and class I/II/III BRAF signaling, while avoiding paradoxical MAPK activation, thus creating a broad therapeutic window. Pre-clinical studies demonstrated tumor regression in multiple xenograft models, supporting first-in-human evaluation. The objective of this trial is to evaluate the safety, PK and PD parameters, and antitumor efficacy of S241656. Methods: This phase 1/2 dose escalation (DE) (part 1) and dose optimization and expansion (part 2) study (NCT05786924) will enroll patients in several settings who are aged ≥18 years, ECOG 0/1 who meet the following cohort-related criteria. The BOIN method is used for DE. Gastrointestinal (GI) cancers: Patients with relapsed/refractory advanced GI cancers with selected RAS or RAF alterations who have received at least 1 prior line of standard of care therapy will be enrolled into a monotherapy DE cohort and combination DE cohorts with 2nd line gemcitabine/nab-paclitaxel (PDAC patients) and with 2nd line investigator choice 5FU doublet and anti-EGFR therapy (cetuximab or panitumumab) (CRC patients). After selection of a dose, monotherapy dose expansion cohorts will enroll patients with (a) PDAC; (b) CRC; and (c) biliary tract cancer. NSCLC: Patients with relapsed/refractory advanced NSCLC with RAS or RAF alterations who have received at least one prior line of standard of care therapy will be enrolled into monotherapy DE cohorts. After selection of a dose in DE and/or dose optimization, expansion arms will enroll patients with (a) KRAS non-G12C alterations; (b) BRAF alterations (all classes); (c) KRAS G12C alterations post-progression on G12C targeted therapy; and (d) active CNS metastasis. Other Solid Tumors: Patients with relapsed/refractory advanced other non-NSCLC or non-GI solid tumors with RAS or RAF alterations who have received at least 1 prior line of standard of care therapy will be enrolled into a monotherapy DE cohort. All patients will provide blood and FFPE tumor samples for correlative analyses. The primary objective is safety and tolerability. Secondary endpoints include anti-tumor efficacy, PK studies, and ctDNA analysis. As of September 2025, 23 patients are enrolled. Enrollment is ongoing and the trial is opening more sites in the US, Australia, EU, UK, China, and Japan. Clinical trial information: NCT05786924 .

Epigenetic mechanisms mediate interactions between aging, genetics, and environmental factors in sporadic Parkinson's disease (PD). While multiple studies have explored DNA modifications in PD, few focus on 5-hydroxymethylcytosine (5hmc), which is important in the central nervous system and sensitive to environmental exposures. Existing studies have not differentiated between 5-methylcytosine (5mc) and 5hmc or have analyzed them separately. In this study, we modeled 5mc and 5hmc data simultaneously. We identified 108 cytosines with significant PD-associated shifts between these marks in an enriched neuronal population from PD postmortem parietal cortex, within 83 genes and 34 enhancers associated with 67 genes. These data potentially link epigenetic regulation of genes related to LRRK2 and endolysosomal sorting (RAB32 and AGAP1), and genes involved in neuroinflammation, the inflammasome, and neurodevelopment with early changes in PD and suggest that there are significant shifts between 5mC and 5hmC associated with PD in genes not captured by standard methods.

Parkinson's disease is a common neurodegenerative disease related to both genetic and environmental insults. Epidemiological studies have linked Helicobacter pylori (H. pylori) infection to Parkinson's disease risk, but the underlying mechanisms of this association remain unclear. In this study, we investigated whether chronic infection with a pathogenic H. pylori strain could induce α-synuclein aggregation or neurodegeneration, and whether infection clearance mitigates these effects. We also assessed whether H. pylori infection exacerbates α-synuclein pathology and neuron loss when combined with seeding of α-synuclein pathology. We find that chronic H. pylori infection induces a sustained immune response in the gut and plasma that leads to mild brain inflammation and dopaminergic neuron loss, independent of α-synuclein pathology. These effects are attenuated by eradication of the infection. In mice with α-synuclein pathology induced by pre-formed fibrils, H. pylori does not further exacerbate the extent of pathology or neuronal death. Together, these results suggest that H. pylori infection can lead to neurodegeneration through inflammatory mechanisms independent of α-synuclein aggregation. Our findings offer mechanistic insights into how pathogens could influence the risk and progression of Parkinson's disease.

H/ACA small nucleolar ribonucleoproteins (H/ACA snoRNPs) facilitate essential cellular processes such as RNA modification, folding, and stability. Here, we present multiple cryo-EM structures of endogenous insect H/ACA snoRNPs containing two protomers assembled on a two-hairpin H/ACA snoRNA. By characterizing key protein-protein and protein-RNA interactions, we reveal the coordination of pseudouridylation activity across the two protomers which explains the predominance of two-hairpin structures in eukaryotic H/ACA snoRNAs. Moreover, we found that several mutations in H/ACA proteins associated with dyskeratosis congenita (DC) directly impair pseudouridine formation suggesting how these mutations disrupt RNA modification and ribosome biogenesis in this disease. Additionally, we uncover coordinated structural changes between Nop10, Nhp2, and the N-terminal extensions of Cbf5 in the 3' protomer that resemble active and inactive conformations and may regulate H/ACA snoRNP activity. In summary, this study provides detailed insight into the structure and function of RNA modification-competent H/ACA snoRNPs, which play pivotal roles in cellular processes including ribosome biogenesis, rRNA folding, (m)RNA modification, and telomere maintenance.