Search

Targeted protein degradation is a groundbreaking modality in drug discovery; however, the regulatory mechanisms are still not fully understood. Here, we identify cellular signaling pathways that modulate the targeted degradation of the anticancer target BRD4 and related neosubstrates BRD2/3 and CDK9 induced by CRL2 VHL - or CRL4 CRBN -based PROTACs. The chemicals identified as degradation enhancers include inhibitors of cellular signaling pathways such as poly-ADP ribosylation (PARG inhibitor PDD00017273), unfolded protein response (PERK inhibitor GSK2606414), and protein stabilization (HSP90 inhibitor luminespib). Mechanistically, PARG inhibition promotes TRIP12-mediated K29/K48-linked branched ubiquitylation of BRD4 by facilitating chromatin dissociation of BRD4 and formation of the BRD4-PROTAC-CRL2 VHL ternary complex; by contrast, HSP90 inhibition promotes BRD4 degradation after the ubiquitylation step. Consequently, these signal inhibitors sensitize cells to the PROTAC-induced apoptosis. These results suggest that various cell-intrinsic signaling pathways spontaneously counteract chemically induced target degradation at multiple steps, which could be liberated by specific inhibitors., (© 2024. The Author(s).)

Ubiquitin regulates various cellular functions by posttranslationally modifying substrates with diverse ubiquitin codes. Recent discoveries of new ubiquitin chain topologies, types of bonds, and non-protein substrates have substantially expanded the complexity of the ubiquitin code. Here, we describe the ubiquitin system covering the basic principles and recent discoveries related to mechanisms, technologies, and biological importance., (© 2024 Akizuki et al.)

Purpose: Accessory ossicles are caused by the failure of the fusion of secondary ossification centres and are more likely to occur due to heavy loading during the growth period or improper treatment after injury. This study aimed to investigate the incidence of foot and ankle accessory ossicles in male professional soccer players., Methods: This study included male professional soccer players who underwent medical checkups at our hospital between 2017 and 2023 as the soccer group. Medical checkups included radiographs of bilateral anteroposterior and oblique foot, as well as bilateral anteroposterior and lateral ankle. Male patients age-matched with the soccer group who visited our hospital undergoing anteroposterior and oblique foot or anteroposterior and lateral ankle radiography were included in the control group. The incidence of accessory ossicles was investigated and compared between the soccer and control groups., Results: In this study, 276 ankles and 276 feet, as well as 121 ankles and 79 feet, were included in the soccer and control groups, respectively. The incidence of accessory ossicles in the soccer and control groups was as follows: accessory navicular 35.9%, 24% (P = .049), os peroneum 8.0%, 2.5% (P = .09); os supranaviculare 7.6%, 1.3% (P = .039); os infranaviculare 1.4%, 1.3% (P = .090); os calcaneus secundarius 4.3%, 0% (P = .059); os vesalianum 0%, 0%; os subfiblare 12.7%, 2.5% (P < .001); os subtibiale 18.1%, 2.5% (P = .001); and os trigonum 89%, 24% (P < .001)., Conclusions: Male professional soccer players had a higher incidence of accessory navicular, os supranaviculare, os subfiblare, os subtibiale, and os trigonum., (© 2023. The Author(s) under exclusive licence to SICOT aisbl.)

Targeted protein degradation through chemical hijacking of E3 ubiquitin ligases is an emerging concept in precision medicine. The ubiquitin code is a critical determinant of the fate of substrates. Although two E3s, CRL2 VHL and CRL4 CRBN , frequently assemble with proteolysis-targeting chimeras (PROTACs) to attach lysine-48 (K48)-linked ubiquitin chains, the diversity of the ubiquitin code used for chemically induced degradation is largely unknown. Here we show that the efficacy of cIAP1-targeting degraders depends on the K63-specific E2 enzyme UBE2N. UBE2N promotes degradation of cIAP1 induced by cIAP1 ligands and subsequent cancer cell apoptosis. Mechanistically, UBE2N-catalyzed K63-linked ubiquitin chains facilitate assembly of highly complex K48/K63 and K11/K48 branched ubiquitin chains, thereby recruiting p97/VCP, UCH37 and the proteasome. Degradation of neo-substrates directed by cIAP1-recruiting PROTACs also depends on UBE2N. These results reveal an unexpected role for K63-linked ubiquitin chains and UBE2N in degrader-induced proteasomal degradation and demonstrate the diversity of the ubiquitin code used for chemical hijacking., (© 2022. The Author(s), under exclusive licence to Springer Nature America, Inc.)

Targeted protein degradation is an emerging therapeutic paradigm. Small-molecule degraders such as proteolysis-targeting chimeras (PROTACs) induce the degradation of neo-substrates by hijacking E3 ubiquitin ligases. Although ubiquitylation of endogenous substrates has been extensively studied, the mechanism underlying forced degradation of neo-substrates is less well understood. We found that the ubiquitin ligase TRIP12 promotes PROTAC-induced and CRL2 VHL -mediated degradation of BRD4 but is dispensable for the degradation of the endogenous CRL2 VHL substrate HIF-1α. TRIP12 associates with BRD4 via CRL2 VHL and specifically assembles K29-linked ubiquitin chains, facilitating the formation of K29/K48-branched ubiquitin chains and accelerating the assembly of K48 linkage by CRL2 VHL . Consequently, TRIP12 promotes the PROTAC-induced apoptotic response. TRIP12 also supports the efficiency of other degraders that target CRABP2 or TRIM24 or recruit CRBN. These observations define TRIP12 and K29/K48-branched ubiquitin chains as accelerators of PROTAC-directed targeted protein degradation, revealing a cooperative mechanism of branched ubiquitin chain assembly unique to the degradation of neo-substrates., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Watasenia scintillans, a sparkling enope squid, has bioluminescence organs to illuminate its body with its own luciferase activity. To clarify the molecular mechanism underlying its scintillation, we analysed high-throughput sequencing data acquired previously and obtained draft genome sequences accomplished with comparative genomic data among the cephalopods. The genome mapped by transcriptome data showed that (1) RNA editing contributed to transcriptome variation of lineage specific genes, such as W. scintillans luciferase, and (2) two types of luciferase enzymes were characterized with reasonable 3D models docked to a luciferin molecule. We report two different types of luciferase in one organism and possibly related to variety of colour types in the W. scintillans fluorescent organs.

Background: Diatoms play a great role in carbon fixation with about 20% of the whole fixation in the world. However, harmful algal bloom as known as red tide is a major problem in environment and fishery industry. Even though intensive studies have been conducted so far, the molecular mechanism behind harmful algal bloom was not fully understood. There are two major diatoms have been sequenced, but more diatoms should be examined at the whole genome level, and evolutionary genome studies were required to understand the landscape of molecular mechanism of the harmful algal bloom., Results: Here we sequenced the genome of Skeletonema costatum, which is the dominant diatom in Japan causing a harmful algal bloom, and also performed RNA-sequencing analysis for conditions where harmful algal blooms often occur. As results, we found that both evolutionary genomic and comparative transcriptomic studies revealed genes for oxidative stress response and response to cytokinin is a key for the proliferation of the diatom., Conclusions: Diatoms causing harmful algal blooms have gained multi-copy of genes related to oxidative stress response and response to cytokinin and obtained an ability to intensive gene expression at the blooms.

Of particular interest is a peculiar motion of guest atoms or ions confined to nanospace in cage compounds, called rattling. While rattling provides unexplored physical properties through the guest-host interactions, it has only been observed in a very limited class of materials. Herein, we introduce an A-site-ordered quadruple perovskite, CuCu3 V4 O12 , as a new family of cage compounds. This novel AA'3 B4 O12 -type perovskite has been obtained by a high-pressure synthesis technique and structurally characterized to have cubic Im$\bar 3$ symmetry with an ionic model of Cu(2+) Cu(2+) 3 V(4+) 4 O12 . The thermal displacement parameter of the A-site Cu(2+) ion is as large as Uiso ≈0.045 Å(2) at 300 K, indicating its large-amplitude thermal oscillations in the oversized icosahedral cages. Remarkably, the presence of localized phonon modes associated with rattling of the A-site Cu(2+) ion manifests itself in the low-temperature specific heat data. This work sheds new light on the structure-property relations in perovskites., (© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

A novel silver-containing perovskite, AgCu3V4O12, was synthesized under high-pressure and high-temperature conditions. It crystallizes in an A-site-ordered perovskite structure (space group Im3), in which silver ions occupy the 12-coordinated A sites forming regular icosahedra, and exhibits metallic behavior. Bond-valence-sum calculations and X-ray photoemission spectroscopy reveal that Ag ions are present in the mixed-valence state, most likely attributable to the coexistence of Ag(+) and Ag(3+), unlike the case of well-known perovskite-type AgNbO3 and AgTaO3 containing only Ag(+) ions. We discuss metallic conduction in relation to electronic structure calculations.

A novel cubic perovskite MnCu3V4O12 has been synthesized at a high pressure and high temperature of 12 GPa and 1373 K. This compound crystallizes in the A-site-ordered perovskite structure (space group Im3) with lattice constant a = 7.26684(10) Å at room temperature. The most notable feature of this compound lies in the fact that the Mn(2+) ion is surrounded by 12 equidistant oxide ions to form a regular icosahedron; the situation of Mn(2+) is unprecedented for the crystal chemistry of an oxide. An anomalously large atomic displacement parameter U(iso)= 0.0222(8) Å(2) is found for Mn(2+) at room temperature, indicating that the thermal oscillation of the small Mn(2+) ion in a large icosahedron is fairly active. Magnetic susceptibility and electric resistivity measurements reveal that 3d electrons of Mn(2+) ions are mainly localized, while 3d electrons in Cu(2+) and V(4+) ions are delocalized and contribute to the metallic conduction.

Object: Magnetoencephalography (MEG) has been typically used to localize epileptic activity by modeling interictal activity as equivalent current dipoles (ECDs). Synthetic aperture magnetometry (SAM) is a recently developed adaptive spatial filtering algorithm for MEG that provides some advantages over the ECD approach. The SAM-kurtosis algorithm (also known as SAM[g2]) additionally provides automated temporal detection of spike sources by using excess kurtosis value (steepness of epileptic spike on virtual sensors). To evaluate the efficacy of the SAM(g2) method, the authors applied it to readings obtained in children with intractable epilepsy secondary to tuberous sclerosis complex (TSC), and compared them to localizations obtained with ECDs., Methods: The authors studied 13 children with TSC (7 girls) whose ages ranged from 13 months to 16.3 years (mean 7.3 years). Video electroencephalography, MR imaging, and MEG studies were analyzed. A single ECD model was applied to localize ECD clusters. The SAM(g2) value was calculated at each SAM(g2) virtual voxel in the patient's MR imaging-defined brain volume. The authors defined the epileptic voxels of SAM(g2) (evSAM[g2]) as those with local peak kurtosis values higher than half of the maximum. A clustering of ECDs had to contain > or = 6 ECDs within 1 cm of each other, and a grouping of evSAM(g2)s had to contain > or = 3 evSAM(g2)s within 1 cm of each other. The authors then compared both ECD clusters and evSAM(g2) groups with the resection area and correlated these data with seizure outcome., Results: Seizures started when patients were between 6 weeks and 8 years of age (median 6 months), and became intractable secondary to multiple tubers in all cases. Ictal onset on scalp video electroencephalography was lateralized in 8 patients (62%). The MEG studies showed multiple ECD clusters in 7 patients (54%). The SAM(g2) method showed multiple groups of epileptic voxels in 8 patients (62%). Colocalization of grouped evSAM(g2) with ECD clusters ranged from 20 to 100%, with a mean of 82%. Eight patients underwent resection of single (1 patient) and multiple (7 patients) lobes, with 6 patients achieving freedom from seizures. Of 8 patients who underwent surgery, in 7 the resection area covered ECD clusters and grouped evSAM(g2)s. In the remaining patient the resection area partially included the ECD cluster and grouped evSAM(g2)s. Six of the 7 patients became seizure free., Conclusions: The combination of SAM(g2) and ECD analyses succeeded in localizing the complex epileptic zones in children with TSC who had intractable epilepsy secondary to multiple cortical tubers. For the subset of children with TSC who present with early-onset and nonlateralized seizures, MEG studies in which SAM(g2) and ECD are used might identify suitable candidates for resection to control seizures.

Purpose: To characterize the spatial and temporal course of ictal high-frequency oscillations (HFOs) recorded by subdural EEG in children with intractable neocortical epilepsy., Methods: We retrospectively studied nine children (four girls, five boys; 4-17 yr) who presented with intractable extrahippocampal localization-related epilepsy and who underwent extraoperative video subdural EEG (1000 Hz sampling rate) and cortical resection. We performed multiple band frequency analysis (MBFA) to evaluate the frequency, time course, and distribution of ictal HFOs. We compared ictal HFO changes before and after clinical onset and postsurgical seizure outcomes., Results: Seventy-eight of 79 seizures showed HFOs. We observed wide-band HFOs ( approximately 250 Hz, approximately 120 electrodes) in six patients either with partial seizures alone (three patients) or with epileptic spasms (three patients). Three patients with partial seizures that secondarily generalized had wide-band HFOs ( approximately 170 Hz) before clinical onset and sustained narrow-band HFOs (60-164 Hz) with electrodecremental events after clinical onset ( approximately 28 electrodes). In four postoperatively seizure-free patients, more electrodes recorded higher-frequency HFOs inside the resection area than outside before and after clinical seizure onset. In five patients with residual seizures, electrodes recorded more HFOs that were of higher or equal frequency outside the surgical area than inside after clinical onset., Conclusion: For partial seizures alone and epileptic spasms, more electrodes recorded only wide-band HFOs; for partial seizures that secondarily generalized, fewer electrodes recorded wide-band HFOs, but in these seizures electrodes also recorded subsequent sustained narrow-band ictal HFOs. Resection of those brain regions having electrodes with ictal, higher HFOs resulted in postsurgical seizure-free outcomes.